diff --git a/.buildinfo b/.buildinfo new file mode 100644 index 00000000..2daaaa02 --- /dev/null +++ b/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 036831cee2b1c6bd2152acf98e65bfc0 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 41cd17b2..00000000 --- a/.gitmodules +++ /dev/null @@ -1,3 +0,0 @@ -[submodule "sphinx/_themes/sphinx_rtd_theme"] - path = sphinx/_themes/sphinx_rtd_theme - url = https://github.com/cclib/sphinx_rtd_theme.git diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 7205d6f0..00000000 --- a/LICENSE +++ /dev/null @@ -1,504 +0,0 @@ -GNU LESSER GENERAL PUBLIC LICENSE - Version 2.1, February 1999 - - Copyright (C) 1991, 1999 Free Software Foundation, Inc. - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - -(This is the first released version of the Lesser GPL. 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The top level directory contains the website (including `index.html`), and the [reStructuredText](http://sphinx-doc.org/rest.html) sources are in the `sphinx` subdirectory. Some of the content is generated automatically from the cclib code using autodoc or custom Python scripts, and this should be handled by the Makefile. Therefore, it is normally quite straightforward for developers to add content or update the website: -```bash -$ git pull git@github.com:cclib/cclib.github.io.git -... some output ... -$ cd cclib.github.io/sphinx -$ vi changelog.rst -$ make -... lots of output ... -$ git status -... inspect changes ... -$ git commit -a -m "Update docs" -... -$ git push -``` - -For larger changes, it is also acceptable to fork this repository and submit a pull request. diff --git a/_sources/attributes.rst.txt b/_sources/attributes.rst.txt new file mode 100644 index 00000000..61acea2c --- /dev/null +++ b/_sources/attributes.rst.txt @@ -0,0 +1,151 @@ + ===================== ==================================================================== ================ ================================ + Name Description Units Data type + ===================== ==================================================================== ================ ================================ + `aonames`_ atomic orbital names list of strings + `aooverlaps`_ atomic orbital overlap matrix array of rank 2 + `atombasis`_ indices of atomic orbitals on each atom list of lists + `atomcharges`_ atomic partial charges dict of arrays of rank 1 + `atomcoords`_ atom coordinates angstroms array of rank 3 + `atommasses`_ atom masses daltons array of rank 1 + `atomnos`_ atomic numbers array of rank 1 + `atomspins`_ atomic spin densities dict of arrays of rank 1 + `ccenergies`_ molecular energies with Coupled-Cluster corrections eV array of rank 2 + `charge`_ net charge of the system integer + `coreelectrons`_ number of core electrons in atom pseudopotentials array of rank 1 + `dispersionenergies`_ dispersion energy corrections eV array of rank 1 + `enthalpy`_ sum of electronic and thermal enthalpies hartree/particle float + `entropy`_ entropy (float, hartree/ particle*kelvin + `etenergies`_ energies of electronic transitions 1/cm array of rank 1 + `etoscs`_ oscillator strengths of electronic transitions array of rank 1 + `etdips`_ electric transition dipoles of electronic transitions ebohr array of rank 2 + `etveldips`_ velocity-gauge electric transition dipoles of electronic transitions ebohr array of rank 2 + `etmagdips`_ magnetic transition dipoles of electronic transitions ebohr array of rank 2 + `etrotats`_ rotatory strengths of electronic transitions ?? array of rank 1 + `etsecs`_ singly-excited configurations for electronic transitions list of lists + `etsyms`_ symmetries of electronic transitions list of string + `freeenergy`_ sum of electronic and thermal free energies hartree/particle float + `fonames`_ fragment orbital names list of strings + `fooverlaps`_ fragment orbital overlap matrix array of rank 2 + `fragnames`_ names of fragments list of strings + `frags`_ indices of atoms in a fragment list of lists + `gbasis`_ coefficients and exponents of Gaussian basis functions PyQuante format + `geotargets`_ targets for convergence of geometry optimization array of rank 1 + `geovalues`_ current values for convergence of geometry optmization array of rank 1 + `grads`_ current values of forces (gradients) in geometry optimization array of rank 3 + `hessian`_ elements of the force constant matrix array of rank 1 + `homos`_ molecular orbital indices of HOMO(s) array of rank 1 + `metadata`_ various metadata about the package and computation dict + `mocoeffs`_ molecular orbital coefficients list of arrays of rank 2 + `moenergies`_ molecular orbital energies eV list of arrays of rank 1 + `moments`_ molecular multipole moments a.u. list of arrays[] + `mosyms`_ orbital symmetries list of lists + `mpenergies`_ molecular electronic energies with Møller-Plesset corrections eV array of rank 2 + `mult`_ multiplicity of the system integer + `natom`_ number of atoms integer + `nbasis`_ number of basis functions integer + `nmo`_ number of molecular orbitals integer + `nmrtensors`_ Nuclear magnetic resonance chemical shielding tensors dict of dicts of array of rank 2 + `nmrcouplingtensors`_ Nuclear magnetic resonance spin-spin coupling tensors dict of dicts of array of rank 2 + `nocoeffs`_ natural orbital coefficients array of rank 2 + `nooccnos`_ natural orbital occupation numbers array of rank 1 + `nsocoeffs`_ natural spin orbital coefficients list of array of rank 2 + `nsooccnos`_ natural spin orbital occupation numbers list of array of rank 1 + `optdone`_ flags whether an optimization has converged Boolean + `optstatus`_ optimization status for each set of atomic coordinates array of rank 1 + `polarizabilities`_ (dipole) polarizabilities, static or dynamic list of arrays of rank 2 + `pressure`_ pressure used for Thermochemistry atm float + `rotconsts`_ rotational constants GHz array of rank 2 + `scancoords`_ geometries of each scan step angstroms array of rank 3 + `scanenergies`_ energies of potential energy surface list + `scannames`_ names of variables scanned list of strings + `scanparm`_ values of parameters in potential energy surface list of tuples + `scfenergies`_ molecular electronic energies after SCF (Hartree-Fock, DFT) eV array of rank 1 + `scftargets`_ targets for convergence of the SCF array of rank 2 + `scfvalues`_ current values for convergence of the SCF list of arrays of rank 2 + `temperature`_ temperature used for Thermochemistry kelvin float + `time`_ time in molecular dynamics and other trajectories fs array of rank 1 + `transprop`_ all absorption and emission spectra (dictionary {name: etoscs etenergies + `vibanharms`_ vibrational anharmonicity constants 1/cm array of rank 2 + `vibdisps`_ cartesian displacement vectors delta angstrom array of rank 3 + `vibfreqs`_ vibrational frequencies 1/cm array of rank 1 + `vibfconsts`_ force constants of vibrations mDyne/angstrom array of rank 1 + `vibirs`_ IR intensities km/mol array of rank 1 + `vibramans`_ Raman activities A^4/Da array of rank 1 + `vibrmasses`_ reduced masses of vibrations daltons array of rank 1 + `vibsyms`_ symmetries of vibrations list of strings + `zpve`_ zero-point vibrational energy correction hartree/particle float + ===================== ==================================================================== ================ ================================ + +.. _`aonames`: data_notes.html#aonames +.. _`aooverlaps`: data_notes.html#aooverlaps +.. _`atombasis`: data_notes.html#atombasis +.. _`atomcharges`: data_notes.html#atomcharges +.. _`atomcoords`: data_notes.html#atomcoords +.. _`atommasses`: data_notes.html#atommasses +.. _`atomnos`: data_notes.html#atomnos +.. _`atomspins`: data_notes.html#atomspins +.. _`ccenergies`: data_notes.html#ccenergies +.. _`charge`: data_notes.html#charge +.. _`coreelectrons`: data_notes.html#coreelectrons +.. _`dispersionenergies`: data_notes.html#dispersionenergies +.. _`enthalpy`: data_notes.html#enthalpy +.. _`entropy`: data_notes.html#entropy +.. _`etenergies`: data_notes.html#etenergies +.. _`etoscs`: data_notes.html#etoscs +.. _`etdips`: data_notes.html#etdips +.. _`etveldips`: data_notes.html#etveldips +.. _`etmagdips`: data_notes.html#etmagdips +.. _`etrotats`: data_notes.html#etrotats +.. _`etsecs`: data_notes.html#etsecs +.. _`etsyms`: data_notes.html#etsyms +.. _`freeenergy`: data_notes.html#freeenergy +.. _`fonames`: data_notes.html#fonames +.. _`fooverlaps`: data_notes.html#fooverlaps +.. _`fragnames`: data_notes.html#fragnames +.. _`frags`: data_notes.html#frags +.. _`gbasis`: data_notes.html#gbasis +.. _`geotargets`: data_notes.html#geotargets +.. _`geovalues`: data_notes.html#geovalues +.. _`grads`: data_notes.html#grads +.. _`hessian`: data_notes.html#hessian +.. _`homos`: data_notes.html#homos +.. _`metadata`: data_notes.html#metadata +.. _`mocoeffs`: data_notes.html#mocoeffs +.. _`moenergies`: data_notes.html#moenergies +.. _`moments`: data_notes.html#moments +.. _`mosyms`: data_notes.html#mosyms +.. _`mpenergies`: data_notes.html#mpenergies +.. _`mult`: data_notes.html#mult +.. _`natom`: data_notes.html#natom +.. _`nbasis`: data_notes.html#nbasis +.. _`nmo`: data_notes.html#nmo +.. _`nmrtensors`: data_notes.html#nmrtensors +.. _`nmrcouplingtensors`: data_notes.html#nmrcouplingtensors +.. _`nocoeffs`: data_notes.html#nocoeffs +.. _`nooccnos`: data_notes.html#nooccnos +.. _`nsocoeffs`: data_notes.html#nsocoeffs +.. _`nsooccnos`: data_notes.html#nsooccnos +.. _`optdone`: data_notes.html#optdone +.. _`optstatus`: data_notes.html#optstatus +.. _`polarizabilities`: data_notes.html#polarizabilities +.. _`pressure`: data_notes.html#pressure +.. _`rotconsts`: data_notes.html#rotconsts +.. _`scancoords`: data_notes.html#scancoords +.. _`scanenergies`: data_notes.html#scanenergies +.. _`scannames`: data_notes.html#scannames +.. _`scanparm`: data_notes.html#scanparm +.. _`scfenergies`: data_notes.html#scfenergies +.. _`scftargets`: data_notes.html#scftargets +.. _`scfvalues`: data_notes.html#scfvalues +.. _`temperature`: data_notes.html#temperature +.. _`time`: data_notes.html#time +.. _`transprop`: data_notes.html#transprop +.. _`vibanharms`: data_notes.html#vibanharms +.. _`vibdisps`: data_notes.html#vibdisps +.. _`vibfreqs`: data_notes.html#vibfreqs +.. _`vibfconsts`: data_notes.html#vibfconsts +.. _`vibirs`: data_notes.html#vibirs +.. _`vibramans`: data_notes.html#vibramans +.. _`vibrmasses`: data_notes.html#vibrmasses +.. _`vibsyms`: data_notes.html#vibsyms +.. _`zpve`: data_notes.html#zpve diff --git a/_sources/attributes.txt b/_sources/attributes.txt deleted file mode 100644 index 38262d10..00000000 --- a/_sources/attributes.txt +++ /dev/null @@ -1,123 +0,0 @@ - =================== ================================================================ =========================== =============================== - Name Description Units Data type - =================== ================================================================ =========================== =============================== - `aonames`_ atomic orbital names list of strings - `aooverlaps`_ atomic orbital overlap matrix array of rank 2 - `atombasis`_ indices of atomic orbitals on each atom list of lists - `atomcharges`_ atomic partial charges dict of arrays of rank 1 - `atomcoords`_ atom coordinates angstroms array of rank 3 - `atommasses`_ atom masses daltons array of rank 1 - `atomnos`_ atomic numbers array of rank 1 - `atomspins`_ atomic spin densities dict of arrays of rank 1 - `charge`_ net charge of the system integer - `ccenergies`_ molecular energies with Coupled-Cluster corrections eV array of rank 2 - `coreelectrons`_ number of core electrons in atom pseudopotentials array of rank 1 - `enthalpy`_ sum of electronic and thermal enthalpies hartree/particle float - `entropy`_ entropy hartree/particle float - `etenergies`_ energies of electronic transitions 1/cm array of rank 1 - `etoscs`_ oscillator strengths of electronic transitions array of rank 1 - `etrotats`_ rotatory strengths of electronic transitions ?? array of rank 1 - `etsecs`_ singly-excited configurations for electronic transitions list of lists - `etsyms`_ symmetries of electronic transitions list of string - `freeenergy`_ sum of electronic and thermal free energies hartree/particle float - `fonames`_ fragment orbital names list of strings - `fooverlaps`_ fragment orbital overlap matrix array of rank 2 - `fragnames`_ names of fragments list of strings - `frags`_ indices of atoms in a fragment list of lists - `gbasis`_ coefficients and exponents of Gaussian basis functions PyQuante format - `geotargets`_ targets for convergence of geometry optimization array of rank 1 - `geovalues`_ current values for convergence of geometry optmization array of rank 1 - `grads`_ current values of forces (gradients) in geometry optimization array of rank 3 - `hessian`_ elements of the force constant matrix array of rank 1 - `homos`_ molecular orbital indices of HOMO(s) array of rank 1 - `metadata`_ various metadata about the package and computation dict - `mocoeffs`_ molecular orbital coefficients list of arrays of rank 2 - `moenergies`_ molecular orbital energies eV list of arrays of rank 1 - `moments`_ molecular multipole moments a.u. list of arrays[] - `mosyms`_ orbital symmetries list of lists - `mpenergies`_ molecular electronic energies with Møller-Plesset corrections eV array of rank 2 - `mult`_ multiplicity of the system integer - `natom`_ number of atoms integer - `nbasis`_ number of basis functions integer - `nmo`_ number of molecular orbitals integer - `nocoeffs`_ natural orbital coefficients array of rank 2 - `nooccnos`_ natural orbital occupation numbers array of rank 1 - `optdone`_ flags whether an optimization has converged Boolean - `optstatus`_ optimization status for each set of atomic coordinates array of rank 1 - `polarizabilities`_ (dipole) polarizabilities, static or dynamic list of arrays of rank 2 - `scancoords`_ geometries of each scan step angstroms array of rank 3 - `scanenergies`_ energies of potential energy surface list - `scannames`_ names of varaibles scanned list of strings - `scanparm`_ values of parameters in potential energy surface list of tuples - `scfenergies`_ molecular electronic energies after SCF (Hartree-Fock, DFT) eV array of rank 1 - `scftargets`_ targets for convergence of the SCF array of rank 2 - `scfvalues`_ current values for convergence of the SCF list of arrays of rank 2 - `temperature`_ temperature used for Thermochemistry kelvin float - `time`_ time in molecular dynamics and other trajectories fs array of rank 1 - `vibanharms`_ vibrational anharmonicity constants 1/cm array of rank 2 - `vibdisps`_ cartesian displacement vectors delta angstrom array of rank 3 - `vibfreqs`_ vibrational frequencies 1/cm array of rank 1 - `vibirs`_ IR intensities km/mol array of rank 1 - `vibramans`_ Raman intensities A^4/Da array of rank 1 - `vibsyms`_ symmetries of vibrations list of strings - =================== ================================================================ =========================== =============================== - -.. _`aonames`: data_notes.html#aonames -.. _`aooverlaps`: data_notes.html#aooverlaps -.. _`atombasis`: data_notes.html#atombasis -.. _`atomcharges`: data_notes.html#atomcharges -.. _`atomcoords`: data_notes.html#atomcoords -.. _`atommasses`: data_notes.html#atommasses -.. _`atomnos`: data_notes.html#atomnos -.. _`atomspins`: data_notes.html#atomspins -.. _`charge`: data_notes.html#charge -.. _`ccenergies`: data_notes.html#ccenergies -.. _`coreelectrons`: data_notes.html#coreelectrons -.. _`enthalpy`: data_notes.html#enthalpy -.. _`entropy`: data_notes.html#entropy -.. _`etenergies`: data_notes.html#etenergies -.. _`etoscs`: data_notes.html#etoscs -.. _`etrotats`: data_notes.html#etrotats -.. _`etsecs`: data_notes.html#etsecs -.. _`etsyms`: data_notes.html#etsyms -.. _`freeenergy`: data_notes.html#freeenergy -.. _`fonames`: data_notes.html#fonames -.. _`fooverlaps`: data_notes.html#fooverlaps -.. _`fragnames`: data_notes.html#fragnames -.. _`frags`: data_notes.html#frags -.. _`gbasis`: data_notes.html#gbasis -.. _`geotargets`: data_notes.html#geotargets -.. _`geovalues`: data_notes.html#geovalues -.. _`grads`: data_notes.html#grads -.. _`hessian`: data_notes.html#hessian -.. _`homos`: data_notes.html#homos -.. _`metadata`: data_notes.html#metadata -.. _`mocoeffs`: data_notes.html#mocoeffs -.. _`moenergies`: data_notes.html#moenergies -.. _`moments`: data_notes.html#moments -.. _`mosyms`: data_notes.html#mosyms -.. _`mpenergies`: data_notes.html#mpenergies -.. _`mult`: data_notes.html#mult -.. _`natom`: data_notes.html#natom -.. _`nbasis`: data_notes.html#nbasis -.. _`nmo`: data_notes.html#nmo -.. _`nocoeffs`: data_notes.html#nocoeffs -.. _`nooccnos`: data_notes.html#nooccnos -.. _`optdone`: data_notes.html#optdone -.. _`optstatus`: data_notes.html#optstatus -.. _`polarizabilities`: data_notes.html#polarizabilities -.. _`scancoords`: data_notes.html#scancoords -.. _`scanenergies`: data_notes.html#scanenergies -.. _`scannames`: data_notes.html#scannames -.. _`scanparm`: data_notes.html#scanparm -.. _`scfenergies`: data_notes.html#scfenergies -.. _`scftargets`: data_notes.html#scftargets -.. _`scfvalues`: data_notes.html#scfvalues -.. _`temperature`: data_notes.html#temperature -.. _`time`: data_notes.html#time -.. _`vibanharms`: data_notes.html#vibanharms -.. _`vibdisps`: data_notes.html#vibdisps -.. _`vibfreqs`: data_notes.html#vibfreqs -.. _`vibirs`: data_notes.html#vibirs -.. _`vibramans`: data_notes.html#vibramans -.. _`vibsyms`: data_notes.html#vibsyms diff --git a/_sources/attributes_dev.rst.txt b/_sources/attributes_dev.rst.txt new file mode 100644 index 00000000..b4ea1f62 --- /dev/null +++ b/_sources/attributes_dev.rst.txt @@ -0,0 +1,151 @@ + ===================== ==================================================================== ================ ================================ + Name Description Units Data type + ===================== ==================================================================== ================ ================================ + `aonames`_ atomic orbital names list of strings + `aooverlaps`_ atomic orbital overlap matrix array of rank 2 + `atombasis`_ indices of atomic orbitals on each atom list of lists + `atomcharges`_ atomic partial charges dict of arrays of rank 1 + `atomcoords`_ atom coordinates angstroms array of rank 3 + `atommasses`_ atom masses daltons array of rank 1 + `atomnos`_ atomic numbers array of rank 1 + `atomspins`_ atomic spin densities dict of arrays of rank 1 + `ccenergies`_ molecular energies with Coupled-Cluster corrections eV array of rank 2 + `charge`_ net charge of the system integer + `coreelectrons`_ number of core electrons in atom pseudopotentials array of rank 1 + `dispersionenergies`_ dispersion energy corrections eV array of rank 1 + `enthalpy`_ sum of electronic and thermal enthalpies hartree/particle float + `entropy`_ entropy (float, hartree/ particle*kelvin + `etenergies`_ energies of electronic transitions 1/cm array of rank 1 + `etoscs`_ oscillator strengths of electronic transitions array of rank 1 + `etdips`_ electric transition dipoles of electronic transitions ebohr array of rank 2 + `etveldips`_ velocity-gauge electric transition dipoles of electronic transitions ebohr array of rank 2 + `etmagdips`_ magnetic transition dipoles of electronic transitions ebohr array of rank 2 + `etrotats`_ rotatory strengths of electronic transitions ?? array of rank 1 + `etsecs`_ singly-excited configurations for electronic transitions list of lists + `etsyms`_ symmetries of electronic transitions list of string + `freeenergy`_ sum of electronic and thermal free energies hartree/particle float + `fonames`_ fragment orbital names list of strings + `fooverlaps`_ fragment orbital overlap matrix array of rank 2 + `fragnames`_ names of fragments list of strings + `frags`_ indices of atoms in a fragment list of lists + `gbasis`_ coefficients and exponents of Gaussian basis functions PyQuante format + `geotargets`_ targets for convergence of geometry optimization array of rank 1 + `geovalues`_ current values for convergence of geometry optimization array of rank 1 + `grads`_ current values of forces (gradients) in geometry optimization array of rank 3 + `hessian`_ elements of the force constant matrix array of rank 1 + `homos`_ molecular orbital indices of HOMO(s) array of rank 1 + `metadata`_ various metadata about the package and computation dict + `mocoeffs`_ molecular orbital coefficients list of arrays of rank 2 + `moenergies`_ molecular orbital energies eV list of arrays of rank 1 + `moments`_ molecular multipole moments a.u. list of arrays[] + `mosyms`_ orbital symmetries list of lists + `mpenergies`_ molecular electronic energies with Møller-Plesset corrections eV array of rank 2 + `mult`_ multiplicity of the system integer + `natom`_ number of atoms integer + `nbasis`_ number of basis functions integer + `nmo`_ number of molecular orbitals integer + `nmrtensors`_ Nuclear magnetic resonance chemical shielding tensors dict of dicts of array of rank 2 + `nmrcouplingtensors`_ Nuclear magnetic resonance spin-spin coupling tensors dict of dicts of array of rank 2 + `nocoeffs`_ natural orbital coefficients array of rank 2 + `nooccnos`_ natural orbital occupation numbers array of rank 1 + `nsocoeffs`_ natural spin orbital coefficients list of array of rank 2 + `nsooccnos`_ natural spin orbital occupation numbers list of array of rank 1 + `optdone`_ flags whether an optimization has converged bool or list of int + `optstatus`_ optimization status for each set of atomic coordinates array of rank 1 + `polarizabilities`_ (dipole) polarizabilities, static or dynamic list of arrays of rank 2 + `pressure`_ pressure used for Thermochemistry atm float + `rotconsts`_ rotational constants GHz array of rank 2 + `scancoords`_ geometries of each scan step angstroms array of rank 3 + `scanenergies`_ energies of potential energy surface list + `scannames`_ names of variables scanned list of strings + `scanparm`_ values of parameters in potential energy surface list of tuples + `scfenergies`_ molecular electronic energies after SCF (Hartree-Fock, DFT) eV array of rank 1 + `scftargets`_ targets for convergence of the SCF array of rank 2 + `scfvalues`_ current values for convergence of the SCF list of arrays of rank 2 + `temperature`_ temperature used for Thermochemistry kelvin float + `time`_ time in molecular dynamics and other trajectories fs array of rank 1 + `transprop`_ all absorption and emission spectra (dictionary {name: etoscs etenergies + `vibanharms`_ vibrational anharmonicity constants 1/cm array of rank 2 + `vibdisps`_ cartesian displacement vectors delta angstrom array of rank 3 + `vibfreqs`_ vibrational frequencies 1/cm array of rank 1 + `vibfconsts`_ force constants of vibrations mDyne/angstrom array of rank 1 + `vibirs`_ IR intensities km/mol array of rank 1 + `vibramans`_ Raman activities A^4/Da array of rank 1 + `vibrmasses`_ reduced masses of vibrations daltons array of rank 1 + `vibsyms`_ symmetries of vibrations list of strings + `zpve`_ zero-point vibrational energy correction hartree/particle float + ===================== ==================================================================== ================ ================================ + +.. _`aonames`: data_notes.html#aonames +.. _`aooverlaps`: data_notes.html#aooverlaps +.. _`atombasis`: data_notes.html#atombasis +.. _`atomcharges`: data_notes.html#atomcharges +.. _`atomcoords`: data_notes.html#atomcoords +.. _`atommasses`: data_notes.html#atommasses +.. _`atomnos`: data_notes.html#atomnos +.. _`atomspins`: data_notes.html#atomspins +.. _`ccenergies`: data_notes.html#ccenergies +.. _`charge`: data_notes.html#charge +.. _`coreelectrons`: data_notes.html#coreelectrons +.. _`dispersionenergies`: data_notes.html#dispersionenergies +.. _`enthalpy`: data_notes.html#enthalpy +.. _`entropy`: data_notes.html#entropy +.. _`etenergies`: data_notes.html#etenergies +.. _`etoscs`: data_notes.html#etoscs +.. _`etdips`: data_notes.html#etdips +.. _`etveldips`: data_notes.html#etveldips +.. _`etmagdips`: data_notes.html#etmagdips +.. _`etrotats`: data_notes.html#etrotats +.. _`etsecs`: data_notes.html#etsecs +.. _`etsyms`: data_notes.html#etsyms +.. _`freeenergy`: data_notes.html#freeenergy +.. _`fonames`: data_notes.html#fonames +.. _`fooverlaps`: data_notes.html#fooverlaps +.. _`fragnames`: data_notes.html#fragnames +.. _`frags`: data_notes.html#frags +.. _`gbasis`: data_notes.html#gbasis +.. _`geotargets`: data_notes.html#geotargets +.. _`geovalues`: data_notes.html#geovalues +.. _`grads`: data_notes.html#grads +.. _`hessian`: data_notes.html#hessian +.. _`homos`: data_notes.html#homos +.. _`metadata`: data_notes.html#metadata +.. _`mocoeffs`: data_notes.html#mocoeffs +.. _`moenergies`: data_notes.html#moenergies +.. _`moments`: data_notes.html#moments +.. _`mosyms`: data_notes.html#mosyms +.. _`mpenergies`: data_notes.html#mpenergies +.. _`mult`: data_notes.html#mult +.. _`natom`: data_notes.html#natom +.. _`nbasis`: data_notes.html#nbasis +.. _`nmo`: data_notes.html#nmo +.. _`nmrtensors`: data_notes.html#nmrtensors +.. _`nmrcouplingtensors`: data_notes.html#nmrcouplingtensors +.. _`nocoeffs`: data_notes.html#nocoeffs +.. _`nooccnos`: data_notes.html#nooccnos +.. _`nsocoeffs`: data_notes.html#nsocoeffs +.. _`nsooccnos`: data_notes.html#nsooccnos +.. _`optdone`: data_notes.html#optdone +.. _`optstatus`: data_notes.html#optstatus +.. _`polarizabilities`: data_notes.html#polarizabilities +.. _`pressure`: data_notes.html#pressure +.. _`rotconsts`: data_notes.html#rotconsts +.. _`scancoords`: data_notes.html#scancoords +.. _`scanenergies`: data_notes.html#scanenergies +.. _`scannames`: data_notes.html#scannames +.. _`scanparm`: data_notes.html#scanparm +.. _`scfenergies`: data_notes.html#scfenergies +.. _`scftargets`: data_notes.html#scftargets +.. _`scfvalues`: data_notes.html#scfvalues +.. _`temperature`: data_notes.html#temperature +.. _`time`: data_notes.html#time +.. _`transprop`: data_notes.html#transprop +.. _`vibanharms`: data_notes.html#vibanharms +.. _`vibdisps`: data_notes.html#vibdisps +.. _`vibfreqs`: data_notes.html#vibfreqs +.. _`vibfconsts`: data_notes.html#vibfconsts +.. _`vibirs`: data_notes.html#vibirs +.. _`vibramans`: data_notes.html#vibramans +.. _`vibrmasses`: data_notes.html#vibrmasses +.. _`vibsyms`: data_notes.html#vibsyms +.. _`zpve`: data_notes.html#zpve diff --git a/_sources/attributes_dev.txt b/_sources/attributes_dev.txt deleted file mode 100644 index 0dddb0f1..00000000 --- a/_sources/attributes_dev.txt +++ /dev/null @@ -1,125 +0,0 @@ - =================== ================================================================ =========================== =============================== - Name Description Units Data type - =================== ================================================================ =========================== =============================== - `aonames`_ atomic orbital names list of strings - `aooverlaps`_ atomic orbital overlap matrix array of rank 2 - `atombasis`_ indices of atomic orbitals on each atom list of lists - `atomcharges`_ atomic partial charges dict of arrays of rank 1 - `atomcoords`_ atom coordinates angstroms array of rank 3 - `atommasses`_ atom masses daltons array of rank 1 - `atomnos`_ atomic numbers array of rank 1 - `atomspins`_ atomic spin densities dict of arrays of rank 1 - `charge`_ net charge of the system integer - `ccenergies`_ molecular energies with Coupled-Cluster corrections eV array of rank 2 - `coreelectrons`_ number of core electrons in atom pseudopotentials array of rank 1 - `enthalpy`_ sum of electronic and thermal enthalpies hartree/particle float - `entropy`_ entropy hartree/particle float - `etenergies`_ energies of electronic transitions 1/cm array of rank 1 - `etoscs`_ oscillator strengths of electronic transitions array of rank 1 - `etrotats`_ rotatory strengths of electronic transitions ?? array of rank 1 - `etsecs`_ singly-excited configurations for electronic transitions list of lists - `etsyms`_ symmetries of electronic transitions list of string - `freeenergy`_ sum of electronic and thermal free energies hartree/particle float - `fonames`_ fragment orbital names list of strings - `fooverlaps`_ fragment orbital overlap matrix array of rank 2 - `fragnames`_ names of fragments list of strings - `frags`_ indices of atoms in a fragment list of lists - `gbasis`_ coefficients and exponents of Gaussian basis functions PyQuante format - `geotargets`_ targets for convergence of geometry optimization array of rank 1 - `geovalues`_ current values for convergence of geometry optmization array of rank 1 - `grads`_ current values of forces (gradients) in geometry optimization array of rank 3 - `hessian`_ elements of the force constant matrix array of rank 1 - `homos`_ molecular orbital indices of HOMO(s) array of rank 1 - `metadata`_ various metadata about the package and computation dict - `mocoeffs`_ molecular orbital coefficients list of arrays of rank 2 - `moenergies`_ molecular orbital energies eV list of arrays of rank 1 - `moments`_ molecular multipole moments a.u. list of arrays[] - `mosyms`_ orbital symmetries list of lists - `mpenergies`_ molecular electronic energies with Møller-Plesset corrections eV array of rank 2 - `mult`_ multiplicity of the system integer - `natom`_ number of atoms integer - `nbasis`_ number of basis functions integer - `nmo`_ number of molecular orbitals integer - `nocoeffs`_ natural orbital coefficients array of rank 2 - `nooccnos`_ natural orbital occupation numbers array of rank 1 - `optdone`_ flags whether an optimization has converged Boolean - `optstatus`_ optimization status for each set of atomic coordinates array of rank 1 - `polarizabilities`_ (dipole) polarizabilities, static or dynamic list of arrays of rank 2 - `pressure`_ temperature used for Thermochemistry atm float - `scancoords`_ geometries of each scan step angstroms array of rank 3 - `scanenergies`_ energies of potential energy surface list - `scannames`_ names of varaibles scanned list of strings - `scanparm`_ values of parameters in potential energy surface list of tuples - `scfenergies`_ molecular electronic energies after SCF (Hartree-Fock, DFT) eV array of rank 1 - `scftargets`_ targets for convergence of the SCF array of rank 2 - `scfvalues`_ current values for convergence of the SCF list of arrays of rank 2 - `temperature`_ temperature used for Thermochemistry kelvin float - `time`_ time in molecular dynamics and other trajectories fs array of rank 1 - `vibanharms`_ vibrational anharmonicity constants 1/cm array of rank 2 - `vibdisps`_ cartesian displacement vectors delta angstrom array of rank 3 - `vibfreqs`_ vibrational frequencies 1/cm array of rank 1 - `vibirs`_ IR intensities km/mol array of rank 1 - `vibramans`_ Raman intensities A^4/Da array of rank 1 - `vibsyms`_ symmetries of vibrations list of strings - =================== ================================================================ =========================== =============================== - -.. _`aonames`: data_notes.html#aonames -.. _`aooverlaps`: data_notes.html#aooverlaps -.. _`atombasis`: data_notes.html#atombasis -.. _`atomcharges`: data_notes.html#atomcharges -.. _`atomcoords`: data_notes.html#atomcoords -.. _`atommasses`: data_notes.html#atommasses -.. _`atomnos`: data_notes.html#atomnos -.. _`atomspins`: data_notes.html#atomspins -.. _`charge`: data_notes.html#charge -.. _`ccenergies`: data_notes.html#ccenergies -.. _`coreelectrons`: data_notes.html#coreelectrons -.. _`enthalpy`: data_notes.html#enthalpy -.. _`entropy`: data_notes.html#entropy -.. _`etenergies`: data_notes.html#etenergies -.. _`etoscs`: data_notes.html#etoscs -.. _`etrotats`: data_notes.html#etrotats -.. _`etsecs`: data_notes.html#etsecs -.. _`etsyms`: data_notes.html#etsyms -.. _`freeenergy`: data_notes.html#freeenergy -.. _`fonames`: data_notes.html#fonames -.. _`fooverlaps`: data_notes.html#fooverlaps -.. _`fragnames`: data_notes.html#fragnames -.. _`frags`: data_notes.html#frags -.. _`gbasis`: data_notes.html#gbasis -.. _`geotargets`: data_notes.html#geotargets -.. _`geovalues`: data_notes.html#geovalues -.. _`grads`: data_notes.html#grads -.. _`hessian`: data_notes.html#hessian -.. _`homos`: data_notes.html#homos -.. _`metadata`: data_notes.html#metadata -.. _`mocoeffs`: data_notes.html#mocoeffs -.. _`moenergies`: data_notes.html#moenergies -.. _`moments`: data_notes.html#moments -.. _`mosyms`: data_notes.html#mosyms -.. _`mpenergies`: data_notes.html#mpenergies -.. _`mult`: data_notes.html#mult -.. _`natom`: data_notes.html#natom -.. _`nbasis`: data_notes.html#nbasis -.. _`nmo`: data_notes.html#nmo -.. _`nocoeffs`: data_notes.html#nocoeffs -.. _`nooccnos`: data_notes.html#nooccnos -.. _`optdone`: data_notes.html#optdone -.. _`optstatus`: data_notes.html#optstatus -.. _`polarizabilities`: data_notes.html#polarizabilities -.. _`pressure`: data_notes.html#pressure -.. _`scancoords`: data_notes.html#scancoords -.. _`scanenergies`: data_notes.html#scanenergies -.. _`scannames`: data_notes.html#scannames -.. _`scanparm`: data_notes.html#scanparm -.. _`scfenergies`: data_notes.html#scfenergies -.. _`scftargets`: data_notes.html#scftargets -.. _`scfvalues`: data_notes.html#scfvalues -.. _`temperature`: data_notes.html#temperature -.. _`time`: data_notes.html#time -.. _`vibanharms`: data_notes.html#vibanharms -.. _`vibdisps`: data_notes.html#vibdisps -.. _`vibfreqs`: data_notes.html#vibfreqs -.. _`vibirs`: data_notes.html#vibirs -.. _`vibramans`: data_notes.html#vibramans -.. _`vibsyms`: data_notes.html#vibsyms diff --git a/_sources/bridge.rst.txt b/_sources/bridge.rst.txt new file mode 100644 index 00000000..820772c4 --- /dev/null +++ b/_sources/bridge.rst.txt @@ -0,0 +1,111 @@ +.. index:: + pair: module; bridge + +Bridges to other packages +========================= + +The following bridges in cclib allow using the parsed data to perform further analysis using other packages. + +.. index:: + single: bridge; horton + +horton +------ + +The horton bridge in cclib supports conversion of cclib's ccData object to horton's IOData object and vice versa. This bridge is useful in performing additional population analyses using the data parsed using cclib. +Before invoking the bridge function, ccData object should be prepared first by reading in previous calculations, following the procedures introduced in `how to parse`_ section. +Then, ``ccData`` object can be passed into the bridge function ``makehorton``. Following code block is an example that performs the conversion: + +.. _`how to parse`: how_to_parse.html + +.. code-block:: python + + from cclib.bridge.cclib2horton import makehorton + from cclib.parser import ccopen + + d = ccopen(sys.argv[1]).parse() + ht = makehorton(d) + +Converted IOData object can be used to run further analyses by referring to `horton documentation`_. + +.. _`horton documentation`: http://theochem.github.io/horton/2.1.1/ + +Becke Population Analysis +~~~~~~~~~~~~~~~~~~~~~~~~~ + +An example code below demonstrates how Becke charges can be calculated based on the script available on `Python interface`_ section in horton documentation. + +.. _`Python interface`: https://theochem.github.io/horton/2.1.0/user_postproc_aim.html#python-interface-to-the-partitioning-code + +.. code-block:: python + + from cclib.method.density import Density + from cclib.bridge.cclib2horton import makehorton + from cclib.parser import ccopen + + from horton import BeckeMolGrid, getgobasis, BeckeWPart + from horton.matrix.dense import DenseTwoIndex + + d = ccopen(sys.argv[1]).parse() + ht = makehorton(d) + + # Calculate density matrix using cclib + dens = Density(d) + dens.calculate() + den = DenseTwoIndex(len(ht.orb_alpha)) + den._array = dens.density[0] + dens.density[1] + + # Create integration grid for calculating Becke charges + grid = BeckeMolGrid(ht.coordinates, ht.numbers, ht.pseudo_numbers, mode='only') + + # Define Gaussian basis set + gob = get_gobasis(ht.coordinates, ht.numbers, default = 'STO-3G') + + # Partition charges + wpart = BeckeWPart(ht.coordinates, ht.numbers, ht.pseudo_numbers, grid, moldens, local=True) + wpart.do_charges() + print(wpart['charges']) + +Hirshfeld Population Analysis +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +An example code below demonstrates how Hirshfeld charges can be calculated based on the script available on `Python interface`_ section in horton documentation. +To calculate partial charges that require pro-atomic densities, follow the steps in `Building proatomic database`_ section in horton documentation. +Then read in the densities as below to calculate Hirshfeld or Hirshfeld-like charges: + +.. _`Building proatomic database`: https://theochem.github.io/horton/2.1.0/user_postproc_aim.html#horton-atomdb-py-build-a-pro-atom-database + +.. code-block:: python + + from cclib.method.density import Density + from cclib.bridge.cclib2horton import makehorton + from cclib.parser import ccopen + + from horton import BeckeMolGrid, getgobasis, HirshfeldWPart + from horton.matrix.dense import DenseTwoIndex + from horton.part.proatomdb import ProAtomDB + + d = ccopen(sys.argv[1]).parse() + ht = makehorton(d) + + # Calculate density matrix using cclib + dens = Density(d) + dens.calculate() + den = DenseTwoIndex(len(ht.orb_alpha)) + den._array = dens.density[0] + dens.density[1] + + # Create integration grid + grid = BeckeMolGrid(ht.coordinates, ht.numbers, ht.pseudo_numbers, mode='only') + + # Define Gaussian basis set + gob = get_gobasis(ht.coordinates, ht.numbers, default = 'STO-3G') + + # Read in pro-atomic density database + db = ProAtomDB.from_file('atoms.h5') + + # Partition charges + wpart = HirshfeldWPart(ht.coordinates, ht.numbers, ht.pseudo_numbers, grid, moldens, db) + wpart.do_charges() + print(wpart['charges']) + +.. diff --git a/_sources/changelog.rst.txt b/_sources/changelog.rst.txt new file mode 100644 index 00000000..3bd36614 --- /dev/null +++ b/_sources/changelog.rst.txt @@ -0,0 +1,678 @@ +.. index:: + single: development; changelog + +Changelog +========= + +Changes in cclib-1.8.1 +---------------------- + +**Features** + + * New parser: xTB (Andrew S. Rosen, Omri Abarbanel, #789, #1129, #1296) + * Support parsing number of CPUs and memory used for Gaussian, ORCA, and Turbomole (#1271, #1277) + * New attributes for the NBO parser (Weronika Zak, #1012, #1251) + * Remove obsolete Qt4Progress (#1285, #1315) + * Only keep the Sphinx version of the changelog (#1254, #1352) + * Stop using Read the Docs (#1267, #1312) + * Don't require specific versions of PySCF and Biopython optional dependencies (#1344) + +**Bugfixes** + + * Fix parsing aooverlaps from GAMESS (#1278) + * Fix ORCA excited states sometimes not being printed identically across sections (#1276) + * Make writing ASE objects more robust to missing cclib attributes (Andrew S. Rosen, #1299, #1300) + * Fix writing freeenergy to ASE objects (Andrew S. Rosen, #1319, #1320) + +**Developer facing changes** + + * Completely migrate from ``unittest`` to ``pytest`` (#648, #649, #766, #1309, #1346) + * Apply and enforce ruff for code formatting using pre-commit (Anselm Hahn, #536, #1122, #1303, #1306, #1307, #1310) + * Migrate to ``pyproject.toml`` from ``setup.py`` for package installation (#833, #1180, #1311, #1327, #1328, #1382) + * Handle nested dictionaries in setting attributes (Weronika Zak, #1257, #1258) + * Update developer guidelines (#1355) + * Drop 3.7 and add 3.11 to test suite (#1305) + * Automate versioning and pushing releases to PyPI (#1363, #1373, #1374) + * Add Dependabot for keeping GitHub Actions up to date (#1329, #1337) + * Update copyright years to 2024 with pre-commit enforcement (#1349) + * Remove obsolete UTF-8 pragmas in Python files (#1350) + * Fix warning about missing file for a Q-Chem regression test (#1338) + * Continuous integration fixes for pyquante2 (#997, #1263, #1301, #1304) + +Changes in cclib-1.8 +-------------------- + +**Features** + + * [GSoC 2023] New language bindings: Julia (Victor Hugo Cano Gil, #1053, https://github.com/cclib/Cclib.jl) + * [GSoC 2023] New parser: NBO (Weronika Zak, #1230, #1233, #1244) + * [GSoC 2023] New parser: GAMESS *.dat (Weronika Zak, #1208, #1214, #1229) + * New attribute: nmrcouplingtensors for NMR spin-spin couplings, initially from ORCA (#125, #1191) + * New attribute: rotconsts for rotational constants, initially from Gaussian (Mark Payne, #1054) + * New method: compute CM5 charges (Sai Murali Karthik Putcha, #676, #852, #1136) + * Support parsing atomcoords for more DALTON calculation types (#641, #1237) + * Be less restrictive in parsed data attributes required for Open Babel bridge (#641, #1236) + * Support parsing implicit solvation parameters from Gaussian, ORCA, QChem, and Turbomole (#1171, #1217, #1232) + * Support parsing excited state method from Gaussian, ORCA, and Turbomole (#1171, #1219) + * Support parsing post-HF excited states from ORCA (#1168) + * Support parsing Hessian from DALTON, GAMESS, NWChem, and Psi4 (#1199, #1200, #1201, #1202) + * Support parsing Psi4 1.7 (Dustin Wheeler, #1185, #1210) + * Support writing vibrational frequency attributes to MOLDEN (#1127, #1132) + * Support writing natural orbitals instead of canonical MOs to MOLDEN (#948) + * Support parsing Hirshfeld and CM5 charges from Gaussian, ORCA, and QChem (#1137) + * Support parsing CCSD(T) energies from ORCA and Psi4 (#1194, #1195) + * Support parsing NWChem 7.0 (#1131, #1133, #1188) + * Support parsing atommasses and vibdisps from NWChem (#1131, #1198) + * Support parsing Hartree-Fock and semiempirical excited states from ORCA (#1187, #1189) + * Support parsing etsyms from ORCA (#1166) + * Support parsing timing information from Gaussian, ORCA, and Turbomole (#1167) + * Support parsing methods and basis set from ORCA (#1170) + * Support parsing excited state using in geometry optimization from Gaussian (#1149, #1151) + * Support parsing etmagdips from Turbomole (#1139) + +**Bugfixes** + + * Fix edge case of XYZ files being interpreted as Turbomole outputs (#1207, #1238) + * Fix units for calculating nuclear repulsion energy (migatt, #1241, #1242, #1243) + * Fix infrastructure for reading CJSON (#1222, #1234) + * Fix edge cases when parsing certain Turbomole outputs (#1174, #1197, #1220, #1222) + * Fix precision in parsing Hirshfeld charges from ORCA (#1209, #1213) + * Fix parsing Hessian from formatted checkpoint files (#1204) + * Fix parsing etoscs for ORCA calculations with spin-orbit coupling (#1172) + * Fix parsing mocoeffs with non-standard population printing from Gaussian (#1162, #1169) + * Fix possible infinite loop in DDEC6 method (#1165) + * Improve checking of mpenergies in Gaussian (#1163, #1164) + * Fix sign of atomcharges in NWChem (#1156) + * Update core developers in documentation (#1144) + +**Developer facing changes** + + * Update copyright years to 2023 (#1245, #1246) + * Be more flexible in extend_attribute (Weronika Zak, #1224, #1228) + * Fix automatically updating both cclib.github.io and cclib.readthedocs.io and testing docs build (#709, #1154, #1158, #1203, #1216, #1223, #1227) + * Initial Black and isort configuration (#1211) + * Support development using Dev Containers (#1212) + * Use raw string in regular expression (#1206) + * More comprehensive testing of coupled cluster energies (#1196) + * Continue migration from unittest to pytest (#1181, #1182, #1183, #1184, #1186) + * Add type annotations to most functions and methods (#1179) + * More idiomatic checking of None (#991, #1178) + * Fix installation of pyquante2 in cclib environments (#1176) + * Test Python 3.9 and 3.10 (#1175) + * Increase minimum supported Python version to 3.7 (#1157, #1159, #1160, #1161) + * Modularize atomcharges testing (#1152) + * Update code coverage Action version (#1095) + +Changes in cclib-1.7.2 +---------------------- + +**Features** + + * Support vibfreqs, vibirs, etenergies, etsyms, etoscs and etsecs for NWChem (BenoitDemota) + * Support temperature, pressure, enthalpy, entropy, zpve and electronic_thermal_energy for NWChem (BenoitDamota) + * Better metadata support for point group detection + * Updated code and test file versions to QChem 5.4 and ORCA 5.0 + +**Bugfixes** + + * Fixed parsing mpenergies for optimization for Turbomole (Oliver Lee) + * Fixed ccenergies for Gaussian (Oliver Lee) + * Fixed oscillator strengths for ORCA (Felix Plasser) + * Fixed units of parsed MO energies for fchk + +Changes in cclib-1.7.1 +---------------------- + +**Features** + +* New parser: formatted checkpoint files +* New attribute: nmrtensors for nuclear magnetics resonance chemical shielding tensors (Jonathon Vandezande) +* Support atomcharges and atomspins for APT charges in Gaussian (Elliot Farrar) +* Support scannames and scanparms for ORCA logfiles +* Support geometry optimization output and metadata in Turbomole (Oliver Lee) +* Support moments, homos, mosyms, and moenergies in Turbomole (Oliver Lee) +* Support mpenergies and ccenergies in Turbomole (Oliver Lee) +* Support excited state attributes for TD-DFT, CC2 and ADC(2) methods in Turbomole (Oliver Lee) +* Support scfenergies, grad, hessian, atommasses, etenergies and etsyms for fchk output (Javier Cerezo) +* Support zpve for QChem, GAMESS, Psi4, Jaguar, ORCA, DALTON, ADF, GAMESSUK, Molcas and Molpro +* Support walltime and cpu time metadata for QChem output (Amanda Dumi) +* Support walltime and cpu time metadata for Gaussian output (Ellior Farrar) +* Support point group metadata in DALTON +* Plumbed through gbasis and mocoeffs to pyscf bridge (Amanda Dumi) +* Added MO symmetry to Molden writer (Amanda Dumi) + +**Bugfixes** + +* Improved parsing and testing enthalpy and freeenergy (Felipe S. S. Schneider) +* Fixed parsing ONIOM output for Gaussian (Elliot Farrar) +* Fixed parsing of GAMESS logfiles with more than 100 SCF iterations (simonaxelrod) +* Fixed parsing of very long (10K+) ORCA logfiles (Alex Maldonado) +* Fixed parsing of Turbomole outputs that don't compute SCF energies (Oliver Lee) +* Fixed parsing natural charges in Gaussian output +* Fixed parsing vibrational analysis (last, not first) in QChem +* Fixed indices for open shell systems in QChem (Hubert Weißmann) +* Cleaned up Turbomole unit test logfiles (froessler) +* Updated documentation for grads (Cyrille Lavigne) + +Changes in cclib-1.7 +-------------------- + +**Features** + +* Dropping support for Python 2 +* SciPy is now a hard dependency for cclib + +**Bugfixes** + +* Fixed parsing of Gaussian files missing scftargets (Hubert Weißmann) +* Fixed parsing TDA excited states from QChem (srtlg) +* Fixed parsing two character elements from Turbomole + +Changes in cclib-1.6.4 +---------------------- + +**Features** + +* [GSOC2020] New methods: Bader's QTAIM, Bickelhaupt, Stockholder, Hirshfeld, and DDEC6 partial charges (Minsik Cho) +* [GSOC2020] New bridge to Horton (Minsik Cho) +* [GSOC2020] Support reading cube files in volume method (Minsik Cho) +* New bridge to Atomic Simulation Environment (Felipe S. S. Schneider) +* New bridge to PySCF (Amanda Dumi) +* New attribute dispersionenergies for molecular dispersion energy corrections +* New attribute vibfconsts for vibrational force constants (Chikashi Shinagawa) +* New attribute vibrmasses for vibrational reduced masses (Chikashi Shinagawa) +* Support t1_diagnostic in metadata for most parsers + +**Bugfixes** + +* Fixed parsing of ORCA optimization with constraints (Jonathon Vandezande) +* Fixed parsing of too many excited states in Gaussian09 optimization (Oliver Lee) +* Fixed parsing Gaussian logfiles with NQMF / reduced number of atoms (Michael D'Addario) +* Fixed bug in QChem parser related to two letter chemical symbols (Amanda Dumi) +* Fixed Gaussian grads to align with standard orientation like other attributes (Chikashi Shinagawa) +* Fixed handling of open shell systems in modelwriter and wfxwriter (Dave Z.) + +Changes in cclib-1.6.3 +---------------------- + +**Features** + +* New bridge to Psi4 (Felipe S. S. Schneider) +* New attribute zpve for zero-point vibrational energy correction (kuriba) +* New attributes for electric transition dipoles of electronic transitions (mwykes) +* Support ccenergies in ORCA +* Support mpenergies in ORCA (Alex Maldonado) +* Support grads in MOLCAS (Daniele Padula) +* Support Mulliken atomspins in Gaussian (Peter St. John) +* Support temperature, pressure, enthalpy, entropy and freenergy attributes in GAMESS (Mark Perri) +* Support fuzzy matching of attribute in ccget script +* Updated test file versions to Psi4 1.3.1, and ORCA 4.2 + +**Bugfixes** + +* Fixed parsing of vibrational attribute for single atoms in ORCA (Felipe S. S. Schneider) +* Fixed parsing very long ORCA logfiles (Alex Maldonado) +* Fixed method code for principal moments of inertia, and mulliken charges in Gaussian (James E T Smith) +* Fixed scannames, scanparm and scanenergies in Gaussian (Dustin Wheeler) +* Fixed freeenergy in ORCA 4.2 (shijunang) +* Fixed name collisions in tests and use of periodic table in utilities (Waylon Peng) + +Changes in cclib-1.6.2 +---------------------- + +**Features** + +* Molden writer now supports ghost atoms (Shiv Upadhyay) +* Handle comments in XYZ files when reading and writing +* Updated regression testing framework (Amanda Dumi, Shiv Upadhyay) +* Updated test file versions to GAMESS-US 2018 (Shiv Upadhyay) + +**Bugfixes** + +* Fixed parsing ORCA output with user comments in coordinates (Felix Plasser) +* Fixed parsing ORCA output with embedding potentials +* Fixed parsing ORCA output with ROCIS in version 4.1 +* Fixed parsing etenergies and similar attribute in ORCA for excited states +* Fixed parsing of vibfreqs for ORCA for linear molecules +* Parsing geometry optimization in ORCA is mode robust wrt line endings + +Changes in cclib-1.6.1 +---------------------- + +**Features** + +* New attribute nsocoeffs for natural spin orbital coefficients (Shiv Upadhyay) +* New attribute nsooccnos for natural spin orbital occupation numbers (Shiv Upadhyay) +* New methods: alpha and beta electron counts (Jaime Rodríguez-Guerra) +* Support coreelectrons attribute in Molcas (Kunal Sharma) +* Support etoscs for response calculations in Dalton (Peter Reinholdt) +* Support etenergies for TDDFT in GAMESS +* Support etrotats attribute in ORCA +* Support functional name in metadata for Psi4 (Alessandro Genova) +* Updated testing framework (Jaime Rodríguez-Guerra, Maxim Stolyarchuk and others) +* Updated test file version to QChem 5.1 + +**Bugfixes** + +* Fixed parsing GAMESS output for EOM-CC output +* Fixed parsing Gaussian output for G3 jobs +* Fixed parsing ORCA output for certain invalid inputs (Felipe S. S. Schneider) +* Fixed parsing of mocoeffs in ORCA when they are glued together (Felipe S. S. Schneider) +* Fixed parsing of mocoeffs and vibfreqs in Psi4 (Alessandro Genova) +* Fixed parsing of mocoeffs in Molcas for some files (Shiv Upadhyay) +* Fixed parsing of etsecs in Dalton +* Fixed bond atom indices in CJSON output (Alessandro Genova) + +Changes in cclib-1.6 +-------------------- + +**Features** + +* New parser: cclib can now parse Molcas files (Kunal Sharma) +* New parser: cclib can now parse Turbomole files (Christopher Rowley, Kunal Sharma) +* New script: ccframe writes data table files from logfiles (Felipe S. S. Schneider) +* New method: stoichiometry builds the chemical formula of a system (Jaime Rodríguez-Guerra) +* Support package version in metadata for most parsers +* Support time attribute and BOMD output in Gaussian, NWChem, ORCA and QChem +* Support grads and metadata attributes in ORCA (Jonathon Vandezande) +* Experimental support for CASSCF output in ORCA (Jonathon Vandezande) +* Added entry in metadata for successful completion of jobs +* Updated test file versions to ORCA 4.0 +* Update minimum Python3 version to 3.4 + +**Bugfixes** + +* Fixed parsing ORCA output with linear molecules (Jonathon Vandezande) +* Fixed parsing NWChem output with incomplete SCF + +Changes in cclib-1.5.3 +---------------------- + +**Features** + +* New attribute transprop for electronic transitions (Jonathon Vandezande) +* Support grads attribute in Psi4 (Adam Abbott) +* Support grads attribute in Molpro (Oskar Weser) +* Support optstatus for IRCs and in Psi4 (Emmanuel LaTruelle) +* Updated test file versions to Gaussian16 (Andrew S. Rosen) +* Add ability to write XYZ coordinates for arbitrary indices + +**Bugfixes** + +* Fixed ccwrite script and added unit tests (Georgy Frolov) +* Fixed closed shell determination for Gaussian (Jaime Rodríguez-Guerra) +* Fixed parsing of natom for >9999 atoms in Gaussian (Jaime Rodríguez-Guerra) +* Fixed parsing of ADF jobs with no title +* Fixed parsing of charge and core electrons when using ECPs in QChem +* Fixed parsing of scfvalues for malformed output in Gaussian + +Changes in cclib-1.5.2 +---------------------- + +**Features** + +* Support for writing Molden and WFX files (Sagar Gaur) +* Support for thermochemistry attributes in ORCA (Jonathon Vandezande) +* Support for chelpg atomic charges in ORCA (Richard Gowers) +* Updated test file versions to GAMESS-US 2017 (Sagar Gaur) +* Added option to print full arrays with ccget (Sagar Gaur) + +**Bugfixes** + +* Fixed polarizability parsing bug in DALTON (Maxim Stolyarchuk) +* Fixed IRC parsing in Gaussian for large trajectories (Dénes Berta, LaTruelle) +* Fixed coordinate parsing for heavy elements in ORCA (Jonathon Vandezande) +* Fixed parsing of large mocoeffs in fixed width format for QChem (srtlg) +* Fixed parsing of large polarizabilities in fixed width format for DALTON (Maxim Stolyarchuk) +* Fixed parsing molecular orbitals when there are more than basis set functions in QChem + +Changes in cclib-1.5.1 +---------------------- + +**Features** + +* New attribute polarizabilities for static or dynamic dipole polarizability +* New attribute pressure for thermochemistry (renpj) +* Add property to detect closed shells in parsed data +* Handle RPA excited state calculation in ORCA, in addition to TDA +* Support for Python 3.6 + +**Bugfixes** + +* Restore alias cclib.parser.ccopen for backwards compatibility +* Fixed parsing thermochemistry for single atoms in QChem +* Fixed handling of URLs (Alexey Alnatanov) +* Fixed Atom object creation in Biopython bridge (Nitish Garg) +* Fixed ccopen when working with multiple files + +Changes in cclib-1.5 +-------------------- + +**Features** + +* Support for both reading and writing CJSON (Sanjeed Schamnad) +* New parser: cclib can now parse MOPAC files (Geoff Hutchison) +* New attribute time tracks coordinated for dynamics jobs (Ramon Crehuet) +* New attribute metadata holds miscellaneous information not in other attributes (bwang2453) +* Extract moments attribute for Gaussian (Geoff Hutchison) +* Extract atombasis for ADF in simple cases (Felix Plasser) +* License change to BSD 3-Clause License + +**Bugfixes** + +* Correct parsing of several attributes for ROHF calculations +* Fixed precision of scfvalues in ORCA +* Fixed MO parsing from older versions of Firefly (mkrompiec) + +Changes in cclib-1.4.1 +---------------------- + +**Features** + +* Preliminary support for writing CJSON (Sanjeed Schamnad) +* Tentative support for BOMD trajectories in Gaussian (Ramon Crehuet) +* Support for atombasis in ADF (Felix Plasser) +* Support for nocoeffs and nooccnos in Molpro + +**Bugfixes** + +* Fix for non-standard basis sets in DALTON +* Fix for non-standard MO coefficient printing in GAMESS + +Changes in cclib-1.4 +-------------------- + +**Features** + +* New parser: cclib can now parse DALTON files +* New parser: cclib can now parse ORCA files +* New attribute optstatus for status during geometry optimizations and scans +* Extract atommasses for GAMESS-US (Sagar Gaur) +* Extract atombasis, gbasis and mocoeffs for QChem +* Extract gbasis for ORCA (Felix Plasser) +* Handle multi-step jobs by parsing only the supersystem +* Improve parsing vibrational symmetries and displacements for Gaussian (mwykes) +* Improve support for compressed files (mwykes) +* Improve and update unit test and regression suites +* Support for Python 3.5 + +**Bugfixes** + +* Fix StopIteration crashes for most parsers +* Fix parsing basis section for Molpro job generated by Avogadro +* Fix parsing multi-job Gaussian output with different orbitals (Geoff Hutchinson) +* Fix parsing ORCA geometry optimization with improper internal coordinates (glideht) +* Fix units in atom coordinates parsed from GAMESS-UK files (mwykes) +* Fix test for vibrational frequencies in Turbomole (mwykes) +* Fix parsing vibration symmetries for Molpro (mwykes) +* Fix parsing eigenvectors in GAMESS-US (Alexis Otero-Calvis) +* Fix duplicate parsing of symmetry labels for Gaussian (Martin Peeks) + +Changes in cclib-1.3.2 +---------------------- + +**Features** + +* New attribute nooccnos for natural orbital occupation numbers +* Read data from XYZ files using Open Babel bridge +* Start basic tests for bridge functionality + +**Bugfixes** + +* Better handling of ONIOM logfiles in Gaussian (Clyde Fare) +* Fix IR intensity bug in Gaussian parser (Clyde Fare) +* Fix QChem parser for OpenMP output +* Fix parsing TDDFT/RPA transitions (Felix Plasser) +* Fix encoding issues for UTF-8 symbols in parsers and bridges + +Changes in cclib-1.3.1 +---------------------- + +**Features** + +* New attribute nooccnos for natural orbital occupation numbers +* Read data from XYZ files using Open Babel bridge +* Start basic tests for bridge functionality + +**Bugfixes** + +* Better handling of ONIOM logfiles in Gaussian (Clyde Fare) +* Fix IR intensity bug in Gaussian parser (Clyde Fare) +* Fix QChem parser for OpenMP output +* Fix parsing TDDFT/RPA transitions (Felix Plasser) +* Fix encoding issues for UTF-8 symbols in parsers and bridges + +Changes in cclib-1.3 +-------------------- + +**Features** + +* New parser: cclib can now parse NWChem files +* New parser: cclib can now parse Psi (versions 3 and 4) files +* New parser: cclib can now parse QChem files (by Eric Berquist) +* New method: Nuclear (currently calculates the repulsion energy) +* Handle Gaussian basis set output with GFPRINT keyword +* Attribute optdone reverted to single Boolean value by default +* Add --verbose and --future options to ccget and parsers +* Replaced PC-GAMESS test files with newer Firefly versions +* Updated test file versions to GAMESS-UK 8.0 + +**Bugfixes** + +* Handle GAMESS-US file with LZ value analysis (Martin Rahm) +* Handle Gaussian jobs with stars in output (Russell Johnson, NIST) +* Handle ORCA singlet-only TD calculations (May A.) +* Fix parsing of Gaussian jobs with fragments and ONIOM output +* Use UTF-8 encodings for files that need them (Matt Ernst) + +Changes in cclib-1.2 +-------------------- + +**Features** + +* Move project to GitHub +* Transition to Python 3 (Python 2.7 will still work) +* Add a multifile mode to ccget script +* Extract vibrational displacements for ORCA +* Extract natural atom charges for Gaussian (Fedor Zhuravlev) +* Updated test file versions to ADF2013.01, GAMESS-US 2012, Gaussian09, Molpro 2012 and ORCA 3.0.1 + +**Bugfixes** + +* Ignore Unicode errors in logfiles +* Handle Gaussian jobs with terse output (basis set count not reported) +* Handle Gaussian jobs using IndoGuess (Scott McKechnie) +* Handle Gaussian file with irregular ONIOM gradients (Tamilmani S) +* Handle ORCA file with SCF convergence issue (Melchor Sanchez) +* Handle Gaussian file with problematic IRC output (Clyde Fare) +* Handle ORCA file with AM1 output (Julien Idé) +* Handle GAMESS-US output with irregular frequency format (Andrew Warden) + +Changes in cclib-1.1 +-------------------- + +**Features** + +* Add progress info for all parsers +* Support ONIOM calculations in Gaussian (Karen Hemelsoet) +* New attribute atomcharges extracts Mulliken and Löwdin atomic charges if present +* New attribute atomspins extracts Mulliken and Löwdin atomic spin densities if present +* New thermodynamic attributes: freeenergy, temperature, enthalpy (Edward Holland) +* Extract PES information: scanenergies, scancoords, scanparm, scannames (Edward Holland) + +**Bugfixes** + +* Handle coupled cluster energies in Gaussian 09 (Björn Dahlgren) +* Vibrational displacement vectors missing for Gaussian 09 (Björn Dahlgren) +* Fix problem parsing vibrational frequencies in some GAMESS-US files +* Fix missing final scfenergy in ADF geometry optimisations +* Fix missing final scfenergy for ORCA where a specific number of SCF cycles has been specified +* ORCA scfenergies not parsed if COSMO solvent effects included +* Allow spin unrestricted calculations to use the fragment MO overlaps correctly for the MPA and CDA calculations +* Handle Gaussian MO energies that are printed as a row of asterisks (Jerome Kieffer) +* Add more explicit license notices, and allow LGPL versions after 2.1 +* Support Firefly calculations where nmo != nbasis (Pavel Solntsev) +* Fix problem parsing vibrational frequency information in recent GAMESS (US) files (Chengju Wang) +* Apply patch from Chengju Wang to handle GAMESS calculations with more than 99 atoms +* Handle Gaussian files with more than 99 atoms having pseudopotentials (Björn Baumeier) + +Changes in cclib-1.0.1 +---------------------- + +**Features** + +* New attribute atommasses - atomic masses in Dalton +* Added support for Gaussian geometry optimisations that change the number of linearly independent basis functions over the course of the calculation + +**Bugfixes** + +* Handle triplet PM3 calculations in Gaussian03 (Greg Magoon) +* Some Gaussian09 calculations were missing atomnos (Marius Retegan) +* Handle multiple pseudopotentials in Gaussian03 (Tiago Silva) +* Handle Gaussian calculations with >999 basis functions +* ADF versions > 2007 no longer print overlap info by default +* Handle parsing Firefly calculations that fail +* Fix parsing of ORCA calculation (Marius Retegan) + +Changes in cclib-1.0 +-------------------- + +**Features** + +* Handle PBC calculations from Gaussian +* Updates to handle Gaussian09 +* Support TDDFT calculations from ADF +* A number of improvements for GAMESS support +* ccopen now supports any file-like object with a read() method, so it can parse across HTTP + +**Bugfixes** + +* Many many additional files parsed thanks to bugs reported by users + +Changes in cclib-0.9 +-------------------- + +**Features** + +* New parser: cclib can now parse ORCA files +* Added option to use setuptools instead of distutils.core for installing +* Improved handling of CI and TD-DFT data: TD-DFT data extracted from GAMESS and etsecs standardised across all parsers +* Test suite changed to include output from only the newest program versions + +**Bugfixes** + +* A small number of parsing errors were fixed + +Changes in cclib-0.8 +-------------------- + +**Feaures** + +* New parser: cclib can now parse Molpro files +* Separation of parser and data objects: Parsed data is now returned is a ccData object that can be pickled, and converted to and from JSON +* Parsers: multiple files can be parsed with one parse command +* NumPy support: Dropped Numeric support in favour of NumPy +* API addition: 'charge' for molecular charge +* API addition: 'mult' for spin multiplicity +* API addition: 'atombasis' for indices of atom orbitals on each atom +* API addition: 'nocoeffs' for Natural Orbital (NO) coefficients +* GAMESS-US parser: added 'etoscs' (CIS calculations) +* Jaguar parser: added 'mpenergies' (LMP2 calculations) +* Jaguar parser: added 'etenergies' and 'etoscs' (CIS calculations) +* New method: Lowdin Population Analysis (LPA) +* Tests: unittests can be run from the Python interpreter, and for a single parser; the number of "passed" tests is also counted and shown + +**Bugfixes** + +* Several parsing errors were fixed +* Fixed some methods to work with different numbers of alpha and beta MO coefficients in mocoeffs (MPA, CSPA, OPA) + +Changes in cclib-0.7 +-------------------- + +**Feaures** + +* New parser: cclib can now parse Jaguar files +* ccopen: Can handle log files which have been compressed into .zip, .bz2 or .gz files. +* API addition: 'gbasis' holds the Gaussian basis set +* API addition: 'coreelectrons' contains the number of core electrons in each atom's pseudopotential +* API addition: 'mpenergies' holds the Moller-Plesset corrected molecular electronic energies +* API addition: 'vibdisps' holds the Cartesian displacement vectors +* API change: 'mocoeffs' is now a list of rank 2 arrays, rather than a rank 3 array +* API change: 'moenergies' is now a list of rank 1 arrays, rather than rank 2 array +* GAMESS-UK parser: added 'vibramans' +* New method: Charge Decomposition Analysis (CDA) for studying electron donation, back donation, and repulsion between fragments in a molecule +* New method: Fragment Analysis for studying bonding interactions between two or more fragments in a molecule +* New method: Ability to calculate the electron density or wavefunction + +**Bugfixes** + +* GAMESS parser: + - Failed to parse frequency calculation with imaginary frequencies + - Rotations and translations now not included in frequencies + - Failed to parse a DFT calculation +* GAMESS-UK parser: + - 'atomnos' not being extracted + - Rotations and translations now not included in frequencies +* bridge to Open Babel: No longer dependent on pyopenbabel + +Changes in cclib-0.6.1 +---------------------- + +**Bugfixes** + +* cclib: The "import cclib.parsers" statement failed due to references to Molpro and Jaguar parsers which are not present +* Gaussian parser: Failed to parse single point calculations where the input coords are a z-matrix, and symmetry is turned off. + +Changes in cclib-0.6.0 +---------------------- + +**Feaures** + +* ADF parser: If some MO eigenvalues are not present, the parser does not fail, but uses values of 99999 instead and A symmetry + +**Bugfixes** + +* ADF parser: The following bugs have been fixed P/D orbitals for single atoms not handled correctly Problem parsing homos in unrestricted calculations Problem skipping the Create sections in certain calculations +* Gaussian parser: The following bugs have been fixed Parser failed if standard orientation not found +* ccget: aooverlaps not included when using --list option + +Changes in cclib-0.6b +--------------------- + +**Feaures** + +* New parser: GAMESS-UK parser +* API addition: the .clean() method; the .clean() method of a parser clears all of the parsed attributes. This is useful if you need to reparse during the course of a calculation. +* Function rename: guesstype() has been renamed to ccopen() +* Speed up: Calculation of Overlap Density of States has been sped up by two orders of magnitude + +**Bugfixes** + +* ccopen: Minor problems fixed with identification of log files +* ccget: Passing multiple filenames now works on Windows too +* ADF parser: The following bugs have been fixed + - Problem with parsing SFOs in certain log files + - Handling of molecules with orbitals of E symmetry + - Couldn't find the HOMO in log files from new versions of ADF + - Parser used to miss attributes if SCF not converged + - For a symmetrical molecule, mocoeffs were in the wrong order and the homo was not identified correctly if degenerate +* Gaussian parser: The following bugs have been fixed + - SCF values was not extracting the dEnergy value + - Was extracting Depolar P instead of Raman activity + +Changes in cclib-0.5 +-------------------- + +**Features** + +* (src/scripts/ccget): Added handling of multiple filenames. It's now possible to use ccget as follows: ``ccget *.log``. This is a good way of checking out whether cclib is able to parse all of the files in a given directory. Also possible is: ``ccget homos *.log``. +* Change of license: Changed license from GPL to LGPL + +**Bugfixes** + +* src/cclib/parser/gamessparser.py: gamessparser was dying on GAMESS VERSION = 12 DEC 2003 gopts, as it was unable to parse the scftargets. +* src/cclib/parser/gamessparser.py: Remove assertion to catch instances where scftargets is unset. This occurs in the case of failed calculations (e.g. wrong multiplicity). +* src/cclib/parser/adfparser.py: Fixed one of the errors with the Mo5Obdt2-c2v-opt.adfout example, which had to do with the SFOs being made of more than two combinations of atoms (4, because of rotation in c2v point group). At least one error is still present with atomcoords. It looks like non-coordinate integers are being parsed as well, which makes some of the atomcoords list have more than the 3 values for x,y,z. +* src/cclib/parser/adfparser.py: Hopefully fixed the last error in Mo5Obdt2-c2v-opt. Problem was that it was adding line.split()[5:], but sometimes there was more than 3 fields left, so it was changed to [5:8]. Need to check actual parsed values to make sure it is parsed correctly. +* data/Gaussian, logfiledist, src/cclib/parser/gaussianparser.py, test/regression.py: Bug fix: Mo4OSibdt2-opt.log has no atomcoords despite being a geo-opt. This was due to the fact that the parser was extracting "Input orientation" and not "Standard orientation". It's now changed to "Standard orientation" which works for all of the files in the repository. diff --git a/_sources/changelog.txt b/_sources/changelog.txt deleted file mode 100644 index f62c076c..00000000 --- a/_sources/changelog.txt +++ /dev/null @@ -1,337 +0,0 @@ -.. index:: - single: development; changelog - -Changelog -========= - -Changes in cclib-1.5 --------------------- - -**Features** - -* Support for both reading and writing CJSON (Sanjeed Schamnad) -* New parser: cclib can now parse MOPAC files (Geoff Hutchison) -* New attribute time tracks coordinated for dynamics jobs (Ramon Crehuet) -* New attribute metadata holds miscellaneous information not in other attributes (bwang2453) -* Extract moments attribute for Gaussian (Geoff Hutchison) -* Extract atombasis for ADF in simple cases (Felix Plaser) -* License change to BSD 3-Clause License - -**Bugfixes** - -* Correct parsing of several attributes for ROHF calculations -* Fixed precision of scfvalues in ORCA -* Fixed MO parsing from older versions of Firefly (mkrompiec) - -Changes in cclib-1.4.1 ----------------------- - -**Features** - -* Preliminary support for writing CJSON (Sanjeed Schamnad) -* Tentative support for BOMD trajectories in Gaussian (Ramon Crehuet) -* Support for atombasis in ADF (Felix Plasser) -* Support for nocoeffs and nooccnos in Molpro - -**Bugfixes** - -* Fix for non-standard basis sets in DALTON -* Fix for non-standard MO coefficient printin in GAMESS - -Changes in cclib-1.4 --------------------- - -**Features** - -* New parser: cclib can now parse DALTON files -* New parser: cclib can now parse ORCA files -* New attribute optstatus for status during geometry optimizations and scans -* Extract atommasses for GAMESS-US (Sagar Gaur) -* Extract atombasis, gbasis and mocoeffs for QChem -* Extract gbasis for ORCA (Felix Plasser) -* Handle multi-step jobs by parsing only the supersystem -* Improve parsing vibrational symmetries and displacements for Gaussian (mwykes) -* Improve support for compressed files (mwykes) -* Improve and update unit test and regression suites -* Support for Python 3.5 - -**Bugfixes** - -* Fix StopIteration crashes for most parsers -* Fix parsing basis section for Molpro job generated by Avogadro -* Fix parsing multi-job Gaussian output with different orbitals (Geoff Hutchinson) -* Fix parsing ORCA geometry optimization with improper internal coordinates (glideht) -* Fix units in atom corodinates parsed from GAMESS-UK files (mwykes) -* Fix test for vibrational frequencies in Turbomole (mwykes) -* Fix parsing vibration symmetries for Molpro (mwykes) -* Fix parsing egenvectors in GAMESS-US (Alexis Otero-Calvis) -* Fix duplicate parsing of symmetry labels for Gaussian (Martin Peeks) - -Changes in cclib-1.3.2 ----------------------- - -**Features** - -* New attribute nooccnos for natural orbital occupation numbers -* Read data from XYZ files using OpenBabel bridge -* Start basic tests for bridge functionality - -**Bugfixes** - -* Better handling of ONIOM logfiles in Gaussian (Clyde Fare) -* Fix IR intensity bug in Gaussian parser (Clyde Fare) -* Fix QChem parser for OpenMP output -* Fix parsing TDDFT/RPA transitions (Felix Plasser) -* Fix encoding issues for UTF-8 symbols in parsers and bridges - -Changes in cclib-1.3.1 ----------------------- - -**Features** - -* New attribute nooccnos for natural orbital occupation numbers -* Read data from XYZ files using OpenBabel bridge -* Start basic tests for bridge functionality - -**Bugfixes** - -* Better handling of ONIOM logfiles in Gaussian (Clyde Fare) -* Fix IR intensity bug in Gaussian parser (Clyde Fare) -* Fix QChem parser for OpenMP output -* Fix parsing TDDFT/RPA transitions (Felix Plasser) -* Fix encoding issues for UTF-8 symbols in parsers and bridges - -Changes in cclib-1.3 --------------------- - -**Features** - -* New parser: cclib can now parse NWChem files -* New parser: cclib can now parse Psi (versions 3 and 4) files -* New parser: cclib can now parse QChem files (by Eric Berquist) -* New method: Nuclear (currently calculates the repulsion energy) -* Handle Gaussian basis set output with GFPRINT keyword -* Attribute optdone reverted to single Boolean value by default -* Add --verbose and --future options to ccget and parsers -* Replaced PC-GAMESS test files with newer Firefly versions -* Updated test file versions to GAMESS-UK 8.0 - -**Bugfixes** - -* Handle GAMESS-US file with LZ value analysis (Martin Rahm) -* Handle Gaussian jobs with stars in output (Russell Johnson, NIST) -* Handle ORCA singlet-only TD calculations (May A.) -* Fix parsing of Gaussian jobs with fragments and ONIOM output -* Use UTF-8 encodings for files that need them (Matt Ernst) - -Changes in cclib-1.2 --------------------- - -**Features** - -* Move project to github -* Transition to Python 3 (Python 2.7 will still work) -* Add a multifile mode to ccget script -* Extract vibrational displacements for ORCA -* Extract natural atom charges for Gaussian (Fedor Zhuravlev) -* Updated test file versions to ADF2013.01, GAMESS-US 2012, Gaussian09, Molpro 2012 and ORCA 3.0.1 - -**Bugfixes** - -* Ignore unicode errors in logfiles -* Handle Guassian jobs with terse output (basis set count not reported) -* Handle Gaussian jobs using IndoGuess (Scott McKechnie) -* Handle Gaussian file with irregular ONION gradients (Tamilmani S) -* Handle ORCA file with SCF convergence issue (Melchor Sanchez) -* Handle Gaussian file with problematic IRC output (Clyde Fare) -* Handle ORCA file with AM1 output (Julien Idé) -* Handle GAMESS-US output with irregular frequency format (Andrew Warden) - -Changes in cclib-1.1 --------------------- - -**Feaures** - -* Add progress info for all parsers -* Support ONIOM calculations in Gaussian (Karen Hemelsoet) -* New attribute atomcharges extracts Mulliken and Lowdin atomic charges if present -* New attribute atomspins extracts Mulliken and Lowdin atomic spin densities if present -* New thermodynamic attributes: freeenergy, temperature, enthalpy (Edward Holland) -* Extract PES information: scanenergies, scancoords, scanparm, scannames (Edward Holland) - -**Bugfixes** - -* Handle coupled cluster energies in Gaussian 09 (Björn Dahlgren) -* Vibrational displacement vectors missing for Gaussian 09 (Björn Dahlgren) -* Fix problem parsing vibrational frequencies in some GAMESS-US files -* Fix missing final scfenergy in ADF geometry optimisations -* Fix missing final scfenergy for ORCA where a specific number of SCF cycles has been specified -* ORCA scfenergies not parsed if COSMO solvent effects included -* Allow spin unrestricted calculations to use the fragment MO overlaps correctly for the MPA and CDA calculations -* Handle Gaussian MO energies that are printed as a row of asterisks (Jerome Kieffer) -* Add more explicit license notices, and allow LGPL versions after 2.1 -* Support Firefly calculations where nmo != nbasis (Pavel Solntsev) -* Fix problem parsing vibrational frequency information in recent GAMESS (US) files (Chengju Wang) -* Apply patch from Chengju Wang to handle GAMESS calculations with more than 99 atoms -* Handle Gaussian files with more than 99 atoms having pseudopotentials (Björn Baumeier) - -Changes in cclib-1.0.1 ----------------------- - -**Feaures** - -* New attribute atommasses - atomic masses in Dalton -* Added support for Gaussian geometry optimisations that change the number of linearly independent basis functions over the course of the calculation - -**Bugfixes** - -* Handle triplet PM3 calculations in Gaussian03 (Greg Magoon) -* Some Gaussian09 calculations were missing atomnos (Marius Retegan) -* Handle multiple pseudopotentials in Gaussian03 (Tiago Silva) -* Handle Gaussian calculations with >999 basis functions -* ADF versions > 2007 no longer print overlap info by default -* Handle parsing Firefly calculations that fail -* Fix parsing of ORCA calculation (Marius Retegan) - -Changes in cclib-1.0 --------------------- - -**Feaures** - -* Handle PBC calculations from Gaussian -* Updates to handle Gaussian09 -* Support TDDFT calculations from ADF -* A number of improvements for GAMESS support -* ccopen now supports any file-like object with a read() method, so it can parse across HTTP - -**Bugfixes** - -* Many many additional files parsed thanks to bugs reported by users - -Changes in cclib-0.9 --------------------- - -**Feaures** - -* New parser: cclib can now parse ORCA files -* Added option to use setuptools instead of distutils.core for installing -* Improved handling of CI and TD-DFT data: TD-DFT data extracted from GAMESS and etsecs standardised across all parsers -* Test suite changed to include output from only the newest program versions - -**Bugfixes** - -* A small number of parsing errors were fixed - -Changes in cclib-0.8 --------------------- - -**Feaures** - -* New parser: cclib can now parse Molpro files -* Separation of parser and data objects: Parsed data is now returned is a ccData object that can be pickled, and converted to and from JSON -* Parsers: multiple files can be parsed with one parse command -* NumPy support: Dropped Numeric support in favour of NumPy -* API addition: 'charge' for molecular charge -* API addition: 'mult' for spin multiplicity -* API addition: 'atombasis' for indices of atom orbitals on each atom -* API addition: 'nocoeffs' for Natural Orbital (NO) coefficients -* GAMESS-US parser: added 'etoscs' (CIS calculations) -* Jaguar parser: added 'mpenergies' (LMP2 calcualtions) -* Jaguar parser: added 'etenergies' and 'etoscs' (CIS calculations) -* New method: Lowdin Population Analysis (LPA) -* Tests: unittests can be run from the Python interpreter, and for a single parser; the number of "passed" tests is also counted and shown - -**Bugfixes** - -* Several parsing errors were fixed -* Fixed some methods to work with different numbers of alpha and beta MO coefficients in mocoeffs (MPA, CSPA, OPA) - -Changes in cclib-0.7 --------------------- - -**Feaures** - -* New parser: cclib can now parse Jaguar files -* ccopen: Can handle log files which have been compressed into .zip, .bz2 or .gz files. -* API addition: 'gbasis' holds the Gaussian basis set -* API addition: 'coreelectrons' contains the number of core electrons in each atom's pseudopotential -* API addition: 'mpenergies' holds the Moller-Plesset corrected molecular electronic energies -* API addition: 'vibdisps' holds the Cartesian displacement vectors -* API change: 'mocoeffs' is now a list of rank 2 arrays, rather than a rank 3 array -* API change: 'moenergies' is now a list of rank 1 arrays, rather than rank 2 array -* GAMESS-UK parser: added 'vibramans' -* New method: Charge Decomposition Analysis (CDA) for studying electron donation, back donation, and repulsion between fragments in a molecule -* New method: Fragment Analysis for studing bonding interactions between two or more fragments in a molecule -* New method: Ability to calculate the electron density or wavefunction - -**Bugfixes** - -* GAMESS parser: - - Failed to parse frequency calculation with imaginary frequencies - - Rotations and translations now not included in frequencies - - Failed to parse a DFT calculation -* GAMESS-UK parser: - - 'atomnos' not being extracted - - Rotations and translations now not included in frequencies -* bridge to OpenBabel: No longer dependent on pyopenbabel - -Changes in cclib-0.6.1 ----------------------- - -**Bugfixes** - -* cclib: The "import cclib.parsers" statement failed due to references to Molpro and Jaguar parsers which are not present -* Gaussian parser: Failed to parse single point calculations where the input coords are a z-matrix, and symmetry is turned off. - -Changes in cclib-0.6.0 ----------------------- - -**Feaures** - -* ADF parser: If some MO eigenvalues are not present, the parser does not fail, but uses values of 99999 instead and A symmetry - -**Bugfixes** - -* ADF parser: The following bugs have been fixed P/D orbitals for single atoms not handled correctly Problem parsing homos in unrestricted calculations Problem skipping the Create sections in certain calculations -* Gaussian parser: The following bugs have been fixed Parser failed if standard orientation not found -* ccget: aooverlaps not included when using --list option - -Changes in cclib-0.6b ---------------------- - -**Feaures** - -* New parser: GAMESS-UK parser -* API addition: the .clean() method; the .clean() method of a parser clears all of the parsed attributes. This is useful if you need to reparse during the course of a calculation. -* Function rename: guesstype() has been renamed to ccopen() -* Speed up: Calculation of Overlap Density of States has been sped up by two orders of magnitude - -**Bugfixes** - -* ccopen: Minor problems fixed with identification of log files -* ccget: Passing multiple filenames now works on Windows too -* ADF parser: The following bugs have been fixed - - Problem with parsing SFOs in certain log files - - Handling of molecules with orbitals of E symmetry - - Couldn't find the HOMO in log files from new versions of ADF - - Parser used to miss attributes if SCF not converged - - For a symmetrical molecule, mocoeffs were in the wrong order and the homo was not identified correctly if degenerate -* Gaussian parser: The following bugs have been fixed - - SCF values was not extracting the dEnergy value - - Was extracting Depolar P instead of Raman activity - -Changes in cclib-0.5 --------------------- - -**Features** - -* (src/scripts/ccget): Added handling of multiple filenames. It's now possible to use ccget as follows: ``ccget *.log``. This is a good way of checking out whether cclib is able to parse all of the files in a given directory. Also possible is: ``ccget homos *.log``. -* Change of license: Changed license from GPL to LGPL - -**Bugfixes** - -* src/cclib/parser/gamessparser.py: gamessparser was dying on GAMESS VERSION = 12 DEC 2003 gopts, as it was unable to parse the scftargets. -* src/cclib/parser/gamessparser.py: Remove assertion to catch instances where scftargets is unset. This occurs in the case of failed calculations (e.g. wrong multiplicity). -* src/cclib/parser/adfparser.py: Fixed one of the errors with the Mo5Obdt2-c2v-opt.adfout example, which had to do with the SFOs being made of more than two combinations of atoms (4, because of rotation in c2v point group). At least one error is still present with atomcoords. It looks like non-coordinate integers are being parsed as well, which makes some of the atomcoords list have more than the 3 values for x,y,z. -* src/cclib/parser/adfparser.py: Hopefully fixed the last error in Mo5Obdt2-c2v-opt. Problem was that it was adding line.split()[5:], but sometimes there was more than 3 fields left, so it was changed to [5:8]. Need to check actual parsed values to make sure it is parsed correctly. -* data/Gaussian, logfiledist, src/cclib/parser/gaussianparser.py, test/regression.py: Bug fix: Mo4OSibdt2-opt.log has no atomcoords despite being a geo-opt. This was due to the fact that the parser was extracting "Input orientation" and not "Standard orientation". It's now changed to "Standard orientation" which works for all of the files in the repository. diff --git a/_sources/contents.txt b/_sources/contents.rst.txt similarity index 96% rename from _sources/contents.txt rename to _sources/contents.rst.txt index a55d0bba..9339263c 100644 --- a/_sources/contents.txt +++ b/_sources/contents.rst.txt @@ -12,6 +12,7 @@ Table of Contents data data_notes methods + bridge development data_dev changelog diff --git a/_sources/coverage.rst.txt b/_sources/coverage.rst.txt new file mode 100644 index 00000000..b5ab38c3 --- /dev/null +++ b/_sources/coverage.rst.txt @@ -0,0 +1,151 @@ +===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== +attributes ADF DALTON FChk GAMESS GAMESSDAT GAMESSUK Gaussian Jaguar Molpro Molcas MOPAC NBO NWChem ORCA Psi4 QChem Turbomole XTB +===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== +`aonames`_ N/A T/D √ √ T/D √ √ √ √ √ T/D T/D √ √ T/D √ T/D T/D +`aooverlaps`_ √ T/D √ √ T/D √ √ √ √ T/D T/D T/D √ √ N/P N/P T/D T/D +`atombasis`_ √ √ √ √ √ √ √ √ √ T/D T/D T/D √ √ √ √ T/D T/D +`atomcharges`_ √ T/D √ √ T/D √ √ √ √ √ T/D √ √ √ √ √ T/D √ +`atomcoords`_ √ √ √ √ √ √ √ √ √ √ √ T/D √ √ √ √ √ √ +`atommasses`_ √ √ √ √ √ T/D √ T/D T/D T/D T/D T/D √ √ √ √ T/D T/D +`atomnos`_ √ √ √ √ √ √ √ √ √ √ √ T/D √ √ √ √ √ √ +`atomspins`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ T/D √ T/D T/D +`ccenergies`_ N/A √ T/D √ T/D T/D √ T/D √ √ T/D T/D √ √ √ √ √ T/D +`charge`_ √ √ √ √ T/D √ √ √ √ √ √ T/D √ √ √ √ √ √ +`coreelectrons`_ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ +`dispersionenergies`_ T/D √ T/D √ T/D T/D √ T/D T/D T/D T/D T/D √ √ √ √ T/D T/D +`enthalpy`_ T/D T/D T/D √ T/D T/D √ T/D T/D √ T/D T/D T/D √ T/D √ T/D √ +`entropy`_ √ T/D T/D √ T/D T/D √ T/D T/D √ T/D T/D √ √ T/D √ T/D T/D +`etdips`_ T/D T/D √ T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D √ T/D +`etenergies`_ √ √ √ √ T/D T/D √ √ T/D T/D T/D T/D √ √ T/D √ √ T/D +`etmagdips`_ T/D T/D √ T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D √ T/D +`etoscs`_ √ √ √ √ T/D T/D √ √ T/D T/D T/D T/D √ √ T/D √ √ T/D +`etrotats`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ T/D N/P √ T/D +`etsecs`_ √ √ T/D √ T/D T/D √ √ T/D T/D T/D T/D √ √ T/D √ √ T/D +`etsyms`_ √ √ √ √ T/D T/D √ √ T/D T/D T/D T/D √ √ T/D √ √ T/D +`etveldips`_ T/D T/D √ T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`fonames`_ √ N/A T/D N/A T/D N/A N/A N/A N/A T/D T/D T/D N/A N/A N/A N/A T/D T/D +`fooverlaps`_ √ N/A T/D N/A T/D N/A N/A N/A N/A T/D T/D T/D N/A N/A N/A N/A T/D T/D +`fragnames`_ √ N/A T/D N/A T/D N/A N/A N/A N/A T/D T/D T/D N/A N/A N/A N/A T/D T/D +`frags`_ √ N/A T/D N/A T/D N/A N/A N/A N/A T/D T/D T/D N/A N/A N/A N/A T/D T/D +`freeenergy`_ T/D T/D T/D √ T/D T/D √ T/D T/D √ T/D T/D T/D √ T/D √ T/D √ +`gbasis`_ T/D √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ T/D T/D +`geotargets`_ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`geovalues`_ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`grads`_ T/D T/D √ T/D T/D T/D √ T/D √ √ T/D T/D √ √ √ √ √ √ +`hessian`_ T/D √ √ √ T/D T/D T/D T/D √ T/D T/D T/D √ T/D T/D √ T/D T/D +`homos`_ √ √ √ √ √ √ √ √ √ √ T/D T/D √ √ √ √ √ √ +`metadata`_ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ +`mocoeffs`_ √ T/D √ √ √ √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`moenergies`_ √ √ √ √ T/D √ √ √ √ √ √ T/D √ √ √ √ √ √ +`moments`_ √ √ T/D √ √ √ √ T/D √ T/D T/D T/D √ √ √ √ √ T/D +`mosyms`_ √ √ T/D √ T/D √ √ √ T/D T/D T/D T/D √ √ √ √ √ T/D +`mpenergies`_ N/A √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`mult`_ √ √ √ √ T/D √ √ √ √ T/D √ T/D √ √ √ √ √ T/D +`natom`_ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ +`nbasis`_ √ √ √ √ √ √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`nmo`_ √ √ √ √ √ √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`nmrcouplingtensors`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D +`nmrtensors`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D +`nocoeffs`_ T/D T/D T/D √ T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`nooccnos`_ T/D T/D T/D √ T/D √ √ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`nsocoeffs`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`nsooccnos`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`optdone`_ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`optstatus`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D √ T/D √ T/D +`polarizabilities`_ T/D √ √ √ T/D T/D √ T/D √ T/D T/D T/D √ √ T/D √ T/D T/D +`pressure`_ √ T/D T/D √ T/D √ √ √ T/D √ T/D T/D √ √ T/D √ T/D T/D +`rotconsts`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`scancoords`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`scanenergies`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`scannames`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D +`scanparm`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D +`scfenergies`_ √ √ √ √ √ √ √ √ √ √ √ T/D √ √ √ √ √ √ +`scftargets`_ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`scfvalues`_ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`temperature`_ √ T/D T/D √ T/D √ √ T/D T/D √ T/D T/D √ √ T/D √ T/D √ +`time`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ T/D T/D √ T/D T/D +`transprop`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D +`vibanharms`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`vibdisps`_ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ T/D +`vibfconsts`_ T/D T/D √ T/D T/D T/D √ √ T/D T/D T/D T/D N/P T/D √ √ T/D T/D +`vibfreqs`_ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ √ +`vibirs`_ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ √ +`vibramans`_ T/D √ √ √ T/D √ √ T/D T/D T/D T/D T/D T/D √ T/D √ T/D T/D +`vibrmasses`_ T/D T/D √ √ T/D T/D √ √ T/D √ T/D T/D N/P T/D √ √ √ √ +`vibsyms`_ T/D √ T/D T/D T/D T/D √ √ √ T/D T/D T/D T/D T/D √ T/D √ T/D +`zpve`_ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ √ +===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== + +.. _`aonames`: data_notes.html#aonames +.. _`aooverlaps`: data_notes.html#aooverlaps +.. _`atombasis`: data_notes.html#atombasis +.. _`atomcharges`: data_notes.html#atomcharges +.. _`atomcoords`: data_notes.html#atomcoords +.. _`atommasses`: data_notes.html#atommasses +.. _`atomnos`: data_notes.html#atomnos +.. _`atomspins`: data_notes.html#atomspins +.. _`ccenergies`: data_notes.html#ccenergies +.. _`charge`: data_notes.html#charge +.. _`coreelectrons`: data_notes.html#coreelectrons +.. _`dispersionenergies`: data_notes.html#dispersionenergies +.. _`enthalpy`: data_notes.html#enthalpy +.. _`entropy`: data_notes.html#entropy +.. _`etdips`: data_notes.html#etdips +.. _`etenergies`: data_notes.html#etenergies +.. _`etmagdips`: data_notes.html#etmagdips +.. _`etoscs`: data_notes.html#etoscs +.. _`etrotats`: data_notes.html#etrotats +.. _`etsecs`: data_notes.html#etsecs +.. _`etsyms`: data_notes.html#etsyms +.. _`etveldips`: data_notes.html#etveldips +.. _`fonames`: data_notes.html#fonames +.. _`fooverlaps`: data_notes.html#fooverlaps +.. _`fragnames`: data_notes.html#fragnames +.. _`frags`: data_notes.html#frags +.. _`freeenergy`: data_notes.html#freeenergy +.. _`gbasis`: data_notes.html#gbasis +.. _`geotargets`: data_notes.html#geotargets +.. _`geovalues`: data_notes.html#geovalues +.. _`grads`: data_notes.html#grads +.. _`hessian`: data_notes.html#hessian +.. _`homos`: data_notes.html#homos +.. _`metadata`: data_notes.html#metadata +.. _`mocoeffs`: data_notes.html#mocoeffs +.. _`moenergies`: data_notes.html#moenergies +.. _`moments`: data_notes.html#moments +.. _`mosyms`: data_notes.html#mosyms +.. _`mpenergies`: data_notes.html#mpenergies +.. _`mult`: data_notes.html#mult +.. _`natom`: data_notes.html#natom +.. _`nbasis`: data_notes.html#nbasis +.. _`nmo`: data_notes.html#nmo +.. _`nmrcouplingtensors`: data_notes.html#nmrcouplingtensors +.. _`nmrtensors`: data_notes.html#nmrtensors +.. _`nocoeffs`: data_notes.html#nocoeffs +.. _`nooccnos`: data_notes.html#nooccnos +.. _`nsocoeffs`: data_notes.html#nsocoeffs +.. _`nsooccnos`: data_notes.html#nsooccnos +.. _`optdone`: data_notes.html#optdone +.. _`optstatus`: data_notes.html#optstatus +.. _`polarizabilities`: data_notes.html#polarizabilities +.. _`pressure`: data_notes.html#pressure +.. _`rotconsts`: data_notes.html#rotconsts +.. _`scancoords`: data_notes.html#scancoords +.. _`scanenergies`: data_notes.html#scanenergies +.. _`scannames`: data_notes.html#scannames +.. _`scanparm`: data_notes.html#scanparm +.. _`scfenergies`: data_notes.html#scfenergies +.. _`scftargets`: data_notes.html#scftargets +.. _`scfvalues`: data_notes.html#scfvalues +.. _`temperature`: data_notes.html#temperature +.. _`time`: data_notes.html#time +.. _`transprop`: data_notes.html#transprop +.. _`vibanharms`: data_notes.html#vibanharms +.. _`vibdisps`: data_notes.html#vibdisps +.. _`vibfconsts`: data_notes.html#vibfconsts +.. _`vibfreqs`: data_notes.html#vibfreqs +.. _`vibirs`: data_notes.html#vibirs +.. _`vibramans`: data_notes.html#vibramans +.. _`vibrmasses`: data_notes.html#vibrmasses +.. _`vibsyms`: data_notes.html#vibsyms +.. _`zpve`: data_notes.html#zpve diff --git a/_sources/coverage.txt b/_sources/coverage.txt deleted file mode 100644 index 9136d4a3..00000000 --- a/_sources/coverage.txt +++ /dev/null @@ -1,123 +0,0 @@ -=================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== -attributes ADF DALTON GAMESS GAMESSUK Gaussian Jaguar Molpro NWChem ORCA Psi QChem -=================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== -`aonames`_ N/A T/D √ √ √ √ √ √ √ T/D √ -`aooverlaps`_ √ T/D √ √ √ √ √ √ √ N/P N/P -`atombasis`_ √ √ √ √ √ √ √ √ √ √ √ -`atomcharges`_ √ T/D √ √ √ √ √ √ √ √ √ -`atomcoords`_ √ √ √ √ √ √ √ √ √ √ √ -`atommasses`_ √ √ √ T/D √ T/D T/D T/D T/D √ √ -`atomnos`_ √ √ √ √ √ √ √ √ √ √ √ -`atomspins`_ T/D T/D T/D T/D T/D T/D T/D T/D √ T/D √ -`ccenergies`_ N/A √ √ T/D √ T/D √ √ T/D √ √ -`charge`_ √ √ √ √ √ √ √ √ √ √ √ -`coreelectrons`_ √ √ √ √ √ √ √ √ √ √ √ -`enthalpy`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ -`entropy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ -`etenergies`_ √ √ √ T/D √ √ T/D T/D √ T/D √ -`etoscs`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ -`etrotats`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D -`etsecs`_ √ √ √ T/D √ √ T/D T/D √ T/D √ -`etsyms`_ √ √ √ T/D √ √ T/D T/D √ T/D √ -`fonames`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A -`fooverlaps`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A -`fragnames`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A -`frags`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A -`freeenergy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ -`gbasis`_ T/D √ √ √ √ √ √ √ √ √ √ -`geotargets`_ √ √ √ √ √ √ √ √ √ √ √ -`geovalues`_ √ √ √ √ √ √ √ √ √ √ √ -`grads`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ -`hessian`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D √ -`homos`_ √ √ √ √ √ √ √ √ √ √ √ -`metadata`_ T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D -`mocoeffs`_ √ T/D √ √ √ √ √ √ √ √ √ -`moenergies`_ √ √ √ √ √ √ √ √ √ √ √ -`moments`_ √ √ √ √ √ T/D √ √ √ √ √ -`mosyms`_ √ √ √ √ √ √ T/D √ T/D √ √ -`mpenergies`_ N/A √ √ √ √ √ √ √ T/D √ √ -`mult`_ √ √ √ √ √ √ √ √ √ √ √ -`natom`_ √ √ √ √ √ √ √ √ √ √ √ -`nbasis`_ √ √ √ √ √ √ √ √ √ √ √ -`nmo`_ √ √ √ √ √ √ √ √ √ √ √ -`nocoeffs`_ T/D T/D √ T/D √ T/D T/D T/D T/D T/D T/D -`nooccnos`_ T/D T/D √ √ √ T/D T/D T/D T/D T/D T/D -`optdone`_ √ √ √ √ √ √ √ √ √ √ √ -`optstatus`_ T/D T/D T/D T/D √ T/D T/D T/D T/D √ T/D -`polarizabilities`_ T/D √ √ T/D √ T/D √ √ √ T/D √ -`scancoords`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scanenergies`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scannames`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scanparm`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scfenergies`_ √ √ √ √ √ √ √ √ √ √ √ -`scftargets`_ √ √ √ √ √ √ √ √ √ √ √ -`scfvalues`_ √ √ √ √ √ √ √ √ √ √ √ -`temperature`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ -`time`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`vibanharms`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`vibdisps`_ √ √ √ √ √ √ √ T/D √ √ √ -`vibfreqs`_ √ √ √ √ √ √ √ T/D √ √ √ -`vibirs`_ √ √ √ √ √ √ √ T/D √ N/P √ -`vibramans`_ T/D √ √ √ √ T/D T/D T/D √ T/D √ -`vibsyms`_ T/D √ T/D T/D √ √ √ T/D T/D √ T/D -=================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== - -.. _`aonames`: data_notes.html#aonames -.. _`aooverlaps`: data_notes.html#aooverlaps -.. _`atombasis`: data_notes.html#atombasis -.. _`atomcharges`: data_notes.html#atomcharges -.. _`atomcoords`: data_notes.html#atomcoords -.. _`atommasses`: data_notes.html#atommasses -.. _`atomnos`: data_notes.html#atomnos -.. _`atomspins`: data_notes.html#atomspins -.. _`ccenergies`: data_notes.html#ccenergies -.. _`charge`: data_notes.html#charge -.. _`coreelectrons`: data_notes.html#coreelectrons -.. _`enthalpy`: data_notes.html#enthalpy -.. _`entropy`: data_notes.html#entropy -.. _`etenergies`: data_notes.html#etenergies -.. _`etoscs`: data_notes.html#etoscs -.. _`etrotats`: data_notes.html#etrotats -.. _`etsecs`: data_notes.html#etsecs -.. _`etsyms`: data_notes.html#etsyms -.. _`fonames`: data_notes.html#fonames -.. _`fooverlaps`: data_notes.html#fooverlaps -.. _`fragnames`: data_notes.html#fragnames -.. _`frags`: data_notes.html#frags -.. _`freeenergy`: data_notes.html#freeenergy -.. _`gbasis`: data_notes.html#gbasis -.. _`geotargets`: data_notes.html#geotargets -.. _`geovalues`: data_notes.html#geovalues -.. _`grads`: data_notes.html#grads -.. _`hessian`: data_notes.html#hessian -.. _`homos`: data_notes.html#homos -.. _`metadata`: data_notes.html#metadata -.. _`mocoeffs`: data_notes.html#mocoeffs -.. _`moenergies`: data_notes.html#moenergies -.. _`moments`: data_notes.html#moments -.. _`mosyms`: data_notes.html#mosyms -.. _`mpenergies`: data_notes.html#mpenergies -.. _`mult`: data_notes.html#mult -.. _`natom`: data_notes.html#natom -.. _`nbasis`: data_notes.html#nbasis -.. _`nmo`: data_notes.html#nmo -.. _`nocoeffs`: data_notes.html#nocoeffs -.. _`nooccnos`: data_notes.html#nooccnos -.. _`optdone`: data_notes.html#optdone -.. _`optstatus`: data_notes.html#optstatus -.. _`polarizabilities`: data_notes.html#polarizabilities -.. _`scancoords`: data_notes.html#scancoords -.. _`scanenergies`: data_notes.html#scanenergies -.. _`scannames`: data_notes.html#scannames -.. _`scanparm`: data_notes.html#scanparm -.. _`scfenergies`: data_notes.html#scfenergies -.. _`scftargets`: data_notes.html#scftargets -.. _`scfvalues`: data_notes.html#scfvalues -.. _`temperature`: data_notes.html#temperature -.. _`time`: data_notes.html#time -.. _`vibanharms`: data_notes.html#vibanharms -.. _`vibdisps`: data_notes.html#vibdisps -.. _`vibfreqs`: data_notes.html#vibfreqs -.. _`vibirs`: data_notes.html#vibirs -.. _`vibramans`: data_notes.html#vibramans -.. _`vibsyms`: data_notes.html#vibsyms diff --git a/_sources/coverage_dev.rst.txt b/_sources/coverage_dev.rst.txt new file mode 100644 index 00000000..8e8906c2 --- /dev/null +++ b/_sources/coverage_dev.rst.txt @@ -0,0 +1,151 @@ +===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== +attributes ADF CFOUR DALTON FChk GAMESS GAMESSDAT GAMESSUK Gaussian Jaguar Molpro Molcas MOPAC NBO NWChem ORCA Psi4 QChem Serenity Turbomole XTB +===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== +`aonames`_ N/A √ T/D √ √ T/D √ √ √ √ √ T/D T/D √ √ T/D √ T/D T/D T/D +`aooverlaps`_ √ T/D T/D √ √ T/D √ √ √ √ T/D T/D T/D √ √ N/P N/P T/D T/D T/D +`atombasis`_ √ √ √ √ √ √ √ √ √ √ T/D T/D T/D √ √ √ √ T/D T/D T/D +`atomcharges`_ √ T/D T/D √ √ T/D √ √ √ √ √ T/D √ √ √ √ √ √ T/D √ +`atomcoords`_ √ √ √ √ √ √ √ √ √ √ √ √ T/D √ √ √ √ √ √ √ +`atommasses`_ √ T/D √ √ √ √ T/D √ T/D T/D T/D T/D T/D √ √ √ √ T/D T/D T/D +`atomnos`_ √ √ √ √ √ √ √ √ √ √ √ √ T/D √ √ √ √ √ √ √ +`atomspins`_ T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ T/D √ T/D T/D T/D +`ccenergies`_ N/A √ √ T/D √ T/D T/D √ T/D √ √ T/D T/D √ √ √ √ √ √ T/D +`charge`_ √ √ √ √ √ T/D √ √ √ √ √ √ T/D √ √ √ √ √ √ √ +`coreelectrons`_ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ +`dispersionenergies`_ T/D T/D √ T/D √ T/D T/D √ T/D T/D T/D T/D T/D √ √ √ √ √ T/D T/D +`enthalpy`_ T/D T/D T/D T/D √ T/D T/D √ √ T/D √ T/D T/D √ √ √ √ T/D T/D √ +`entropy`_ √ T/D T/D T/D √ T/D T/D √ √ T/D √ T/D T/D √ √ √ √ T/D T/D √ +`etdips`_ T/D T/D T/D √ T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D √ √ T/D +`etenergies`_ √ √ √ √ √ T/D T/D √ √ T/D T/D T/D T/D √ √ T/D √ √ √ T/D +`etmagdips`_ T/D T/D T/D √ T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D √ √ T/D +`etoscs`_ √ √ √ √ √ T/D T/D √ √ T/D T/D T/D T/D √ √ T/D √ √ √ T/D +`etrotats`_ T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ T/D N/P √ √ T/D +`etsecs`_ √ √ √ T/D √ T/D T/D √ √ T/D T/D T/D T/D √ √ T/D √ √ √ T/D +`etsyms`_ √ √ √ √ √ T/D T/D √ √ T/D T/D T/D T/D √ √ T/D √ T/D √ T/D +`etveldips`_ T/D T/D T/D √ T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D √ T/D T/D +`fonames`_ √ T/D N/A T/D N/A T/D N/A N/A N/A N/A T/D T/D T/D N/A N/A N/A N/A T/D T/D T/D +`fooverlaps`_ √ T/D N/A T/D N/A T/D N/A N/A N/A N/A T/D T/D T/D N/A N/A N/A N/A T/D T/D T/D +`fragnames`_ √ T/D N/A T/D N/A T/D N/A N/A N/A N/A T/D T/D T/D N/A N/A N/A N/A T/D T/D T/D +`frags`_ √ T/D N/A T/D N/A T/D N/A N/A N/A N/A T/D T/D T/D N/A N/A N/A N/A T/D T/D T/D +`freeenergy`_ T/D T/D T/D T/D √ T/D T/D √ √ T/D √ T/D T/D √ √ √ √ T/D T/D √ +`gbasis`_ T/D √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ T/D T/D T/D +`geotargets`_ √ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ T/D √ T/D +`geovalues`_ √ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ √ T/D +`grads`_ T/D √ T/D √ T/D T/D T/D √ T/D √ √ T/D T/D √ √ √ √ √ √ √ +`hessian`_ T/D T/D √ √ √ T/D T/D T/D T/D √ T/D T/D T/D √ T/D T/D √ T/D T/D T/D +`homos`_ √ √ √ √ √ √ √ √ √ √ √ T/D T/D √ √ √ √ √ √ √ +`metadata`_ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ +`mocoeffs`_ √ √ T/D √ √ √ √ √ √ √ √ T/D T/D √ √ √ √ √ √ T/D +`moenergies`_ √ √ √ √ √ T/D √ √ √ √ √ √ T/D √ √ √ √ √ √ √ +`moments`_ √ T/D √ √ √ √ √ √ T/D √ T/D T/D T/D √ √ √ √ √ √ T/D +`mosyms`_ √ √ √ T/D √ T/D √ √ √ T/D T/D T/D T/D √ √ √ √ T/D √ T/D +`mpenergies`_ N/A √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ √ T/D +`mult`_ √ √ √ √ √ T/D √ √ √ √ T/D √ T/D √ √ √ √ √ √ T/D +`natom`_ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ √ +`nbasis`_ √ √ √ √ √ √ √ √ √ √ √ T/D T/D √ √ √ √ √ √ T/D +`nmo`_ √ √ √ √ √ √ √ √ √ √ √ T/D T/D √ √ √ √ √ √ T/D +`nmrcouplingtensors`_ T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D √ T/D +`nmrtensors`_ T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D √ T/D +`nocoeffs`_ T/D T/D T/D T/D √ T/D T/D √ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`nooccnos`_ T/D T/D T/D T/D √ T/D √ √ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`nsocoeffs`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`nsooccnos`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`optdone`_ √ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ √ T/D +`optstatus`_ T/D T/D T/D √ T/D T/D T/D √ √ T/D T/D T/D T/D T/D √ √ √ √ √ T/D +`polarizabilities`_ T/D T/D √ √ √ T/D T/D √ T/D √ T/D T/D T/D √ √ T/D √ T/D T/D T/D +`pressure`_ √ T/D T/D T/D √ T/D √ √ √ T/D √ T/D T/D √ √ T/D √ T/D T/D T/D +`rotconsts`_ T/D T/D √ T/D √ T/D T/D √ √ T/D √ T/D T/D T/D √ T/D T/D T/D T/D √ +`scancoords`_ T/D T/D T/D T/D T/D T/D T/D √ √ T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D +`scanenergies`_ T/D T/D T/D T/D T/D T/D T/D √ √ T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D +`scannames`_ T/D T/D T/D T/D T/D T/D T/D √ √ T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D +`scanparm`_ T/D T/D T/D T/D T/D T/D T/D √ √ T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D +`scfenergies`_ √ √ √ √ √ √ √ √ √ √ √ √ T/D √ √ √ √ √ √ √ +`scftargets`_ √ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ √ T/D +`scfvalues`_ √ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ √ √ T/D +`temperature`_ √ T/D T/D T/D √ T/D √ √ √ T/D √ T/D T/D √ √ √ √ T/D T/D √ +`time`_ T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ T/D T/D √ T/D T/D T/D +`transprop`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D T/D +`vibanharms`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`vibdisps`_ √ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ T/D √ T/D +`vibfconsts`_ T/D T/D T/D √ T/D T/D T/D √ √ T/D T/D T/D T/D N/P T/D √ √ T/D T/D T/D +`vibfreqs`_ √ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ T/D √ √ +`vibirs`_ √ √ √ √ √ T/D √ √ √ √ √ T/D T/D √ √ √ √ T/D √ √ +`vibramans`_ T/D T/D √ √ √ T/D √ √ T/D T/D T/D T/D T/D T/D √ T/D √ T/D T/D T/D +`vibrmasses`_ T/D T/D T/D √ √ T/D T/D √ √ T/D √ T/D T/D N/P T/D √ √ T/D √ √ +`vibsyms`_ T/D √ √ T/D T/D T/D T/D √ √ √ T/D T/D T/D T/D T/D √ T/D T/D √ T/D +`zpve`_ √ √ √ T/D √ T/D √ √ √ √ √ T/D T/D √ √ √ √ T/D √ √ +===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== ===================== + +.. _`aonames`: data_notes.html#aonames +.. _`aooverlaps`: data_notes.html#aooverlaps +.. _`atombasis`: data_notes.html#atombasis +.. _`atomcharges`: data_notes.html#atomcharges +.. _`atomcoords`: data_notes.html#atomcoords +.. _`atommasses`: data_notes.html#atommasses +.. _`atomnos`: data_notes.html#atomnos +.. _`atomspins`: data_notes.html#atomspins +.. _`ccenergies`: data_notes.html#ccenergies +.. _`charge`: data_notes.html#charge +.. _`coreelectrons`: data_notes.html#coreelectrons +.. _`dispersionenergies`: data_notes.html#dispersionenergies +.. _`enthalpy`: data_notes.html#enthalpy +.. _`entropy`: data_notes.html#entropy +.. _`etdips`: data_notes.html#etdips +.. _`etenergies`: data_notes.html#etenergies +.. _`etmagdips`: data_notes.html#etmagdips +.. _`etoscs`: data_notes.html#etoscs +.. _`etrotats`: data_notes.html#etrotats +.. _`etsecs`: data_notes.html#etsecs +.. _`etsyms`: data_notes.html#etsyms +.. _`etveldips`: data_notes.html#etveldips +.. _`fonames`: data_notes.html#fonames +.. _`fooverlaps`: data_notes.html#fooverlaps +.. _`fragnames`: data_notes.html#fragnames +.. _`frags`: data_notes.html#frags +.. _`freeenergy`: data_notes.html#freeenergy +.. _`gbasis`: data_notes.html#gbasis +.. _`geotargets`: data_notes.html#geotargets +.. _`geovalues`: data_notes.html#geovalues +.. _`grads`: data_notes.html#grads +.. _`hessian`: data_notes.html#hessian +.. _`homos`: data_notes.html#homos +.. _`metadata`: data_notes.html#metadata +.. _`mocoeffs`: data_notes.html#mocoeffs +.. _`moenergies`: data_notes.html#moenergies +.. _`moments`: data_notes.html#moments +.. _`mosyms`: data_notes.html#mosyms +.. _`mpenergies`: data_notes.html#mpenergies +.. _`mult`: data_notes.html#mult +.. _`natom`: data_notes.html#natom +.. _`nbasis`: data_notes.html#nbasis +.. _`nmo`: data_notes.html#nmo +.. _`nmrcouplingtensors`: data_notes.html#nmrcouplingtensors +.. _`nmrtensors`: data_notes.html#nmrtensors +.. _`nocoeffs`: data_notes.html#nocoeffs +.. _`nooccnos`: data_notes.html#nooccnos +.. _`nsocoeffs`: data_notes.html#nsocoeffs +.. _`nsooccnos`: data_notes.html#nsooccnos +.. _`optdone`: data_notes.html#optdone +.. _`optstatus`: data_notes.html#optstatus +.. _`polarizabilities`: data_notes.html#polarizabilities +.. _`pressure`: data_notes.html#pressure +.. _`rotconsts`: data_notes.html#rotconsts +.. _`scancoords`: data_notes.html#scancoords +.. _`scanenergies`: data_notes.html#scanenergies +.. _`scannames`: data_notes.html#scannames +.. _`scanparm`: data_notes.html#scanparm +.. _`scfenergies`: data_notes.html#scfenergies +.. _`scftargets`: data_notes.html#scftargets +.. _`scfvalues`: data_notes.html#scfvalues +.. _`temperature`: data_notes.html#temperature +.. _`time`: data_notes.html#time +.. _`transprop`: data_notes.html#transprop +.. _`vibanharms`: data_notes.html#vibanharms +.. _`vibdisps`: data_notes.html#vibdisps +.. _`vibfconsts`: data_notes.html#vibfconsts +.. _`vibfreqs`: data_notes.html#vibfreqs +.. _`vibirs`: data_notes.html#vibirs +.. _`vibramans`: data_notes.html#vibramans +.. _`vibrmasses`: data_notes.html#vibrmasses +.. _`vibsyms`: data_notes.html#vibsyms +.. _`zpve`: data_notes.html#zpve diff --git a/_sources/coverage_dev.txt b/_sources/coverage_dev.txt deleted file mode 100644 index 25b31262..00000000 --- a/_sources/coverage_dev.txt +++ /dev/null @@ -1,125 +0,0 @@ -=================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== -attributes ADF DALTON GAMESS GAMESSUK Gaussian Jaguar Molpro MOPAC NWChem ORCA Psi QChem -=================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== -`aonames`_ N/A T/D √ √ √ √ √ T/D √ √ T/D √ -`aooverlaps`_ √ T/D √ √ √ √ √ T/D √ √ N/P N/P -`atombasis`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`atomcharges`_ √ T/D √ √ √ √ √ T/D √ √ √ √ -`atomcoords`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`atommasses`_ √ √ √ T/D √ T/D T/D T/D T/D √ √ √ -`atomnos`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`atomspins`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D √ T/D √ -`ccenergies`_ N/A √ √ T/D √ T/D √ T/D √ T/D √ √ -`charge`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`coreelectrons`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`enthalpy`_ T/D T/D T/D T/D √ T/D T/D T/D T/D √ T/D √ -`entropy`_ T/D T/D T/D T/D √ T/D T/D T/D T/D √ T/D √ -`etenergies`_ √ √ √ T/D √ √ T/D T/D T/D √ T/D √ -`etoscs`_ √ T/D √ T/D √ √ T/D T/D T/D √ T/D √ -`etrotats`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D T/D -`etsecs`_ √ √ √ T/D √ √ T/D T/D T/D √ T/D √ -`etsyms`_ √ √ √ T/D √ √ T/D T/D T/D √ T/D √ -`fonames`_ √ N/A N/A N/A N/A N/A N/A T/D N/A N/A N/A N/A -`fooverlaps`_ √ N/A N/A N/A N/A N/A N/A T/D N/A N/A N/A N/A -`fragnames`_ √ N/A N/A N/A N/A N/A N/A T/D N/A N/A N/A N/A -`frags`_ √ N/A N/A N/A N/A N/A N/A T/D N/A N/A N/A N/A -`freeenergy`_ T/D T/D T/D T/D √ T/D T/D T/D T/D √ T/D √ -`gbasis`_ T/D √ √ √ √ √ √ T/D √ √ √ √ -`geotargets`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`geovalues`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`grads`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D √ -`hessian`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D T/D √ -`homos`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`metadata`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`mocoeffs`_ √ T/D √ √ √ √ √ T/D √ √ √ √ -`moenergies`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`moments`_ √ √ √ √ √ T/D √ T/D √ √ √ √ -`mosyms`_ √ √ √ √ √ √ T/D T/D √ T/D √ √ -`mpenergies`_ N/A √ √ √ √ √ √ T/D √ T/D √ √ -`mult`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`natom`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`nbasis`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`nmo`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`nocoeffs`_ T/D T/D √ T/D √ T/D T/D T/D T/D T/D T/D T/D -`nooccnos`_ T/D T/D √ √ √ T/D T/D T/D T/D T/D T/D T/D -`optdone`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`optstatus`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ T/D -`polarizabilities`_ T/D √ √ T/D √ T/D √ T/D √ √ T/D √ -`pressure`_ T/D T/D T/D T/D √ T/D T/D T/D T/D √ T/D √ -`scancoords`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scanenergies`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scannames`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scanparm`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scfenergies`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`scftargets`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`scfvalues`_ √ √ √ √ √ √ √ T/D √ √ √ √ -`temperature`_ T/D T/D T/D T/D √ T/D T/D T/D T/D √ T/D √ -`time`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`vibanharms`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`vibdisps`_ √ √ √ √ √ √ √ T/D T/D √ √ √ -`vibfreqs`_ √ √ √ √ √ √ √ T/D T/D √ √ √ -`vibirs`_ √ √ √ √ √ √ √ T/D T/D √ N/P √ -`vibramans`_ T/D √ √ √ √ T/D T/D T/D T/D √ T/D √ -`vibsyms`_ T/D √ T/D T/D √ √ √ T/D T/D T/D √ T/D -=================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== =================== - -.. _`aonames`: data_notes.html#aonames -.. _`aooverlaps`: data_notes.html#aooverlaps -.. _`atombasis`: data_notes.html#atombasis -.. _`atomcharges`: data_notes.html#atomcharges -.. _`atomcoords`: data_notes.html#atomcoords -.. _`atommasses`: data_notes.html#atommasses -.. _`atomnos`: data_notes.html#atomnos -.. _`atomspins`: data_notes.html#atomspins -.. _`ccenergies`: data_notes.html#ccenergies -.. _`charge`: data_notes.html#charge -.. _`coreelectrons`: data_notes.html#coreelectrons -.. _`enthalpy`: data_notes.html#enthalpy -.. _`entropy`: data_notes.html#entropy -.. _`etenergies`: data_notes.html#etenergies -.. _`etoscs`: data_notes.html#etoscs -.. _`etrotats`: data_notes.html#etrotats -.. _`etsecs`: data_notes.html#etsecs -.. _`etsyms`: data_notes.html#etsyms -.. _`fonames`: data_notes.html#fonames -.. _`fooverlaps`: data_notes.html#fooverlaps -.. _`fragnames`: data_notes.html#fragnames -.. _`frags`: data_notes.html#frags -.. _`freeenergy`: data_notes.html#freeenergy -.. _`gbasis`: data_notes.html#gbasis -.. _`geotargets`: data_notes.html#geotargets -.. _`geovalues`: data_notes.html#geovalues -.. _`grads`: data_notes.html#grads -.. _`hessian`: data_notes.html#hessian -.. _`homos`: data_notes.html#homos -.. _`metadata`: data_notes.html#metadata -.. _`mocoeffs`: data_notes.html#mocoeffs -.. _`moenergies`: data_notes.html#moenergies -.. _`moments`: data_notes.html#moments -.. _`mosyms`: data_notes.html#mosyms -.. _`mpenergies`: data_notes.html#mpenergies -.. _`mult`: data_notes.html#mult -.. _`natom`: data_notes.html#natom -.. _`nbasis`: data_notes.html#nbasis -.. _`nmo`: data_notes.html#nmo -.. _`nocoeffs`: data_notes.html#nocoeffs -.. _`nooccnos`: data_notes.html#nooccnos -.. _`optdone`: data_notes.html#optdone -.. _`optstatus`: data_notes.html#optstatus -.. _`polarizabilities`: data_notes.html#polarizabilities -.. _`pressure`: data_notes.html#pressure -.. _`scancoords`: data_notes.html#scancoords -.. _`scanenergies`: data_notes.html#scanenergies -.. _`scannames`: data_notes.html#scannames -.. _`scanparm`: data_notes.html#scanparm -.. _`scfenergies`: data_notes.html#scfenergies -.. _`scftargets`: data_notes.html#scftargets -.. _`scfvalues`: data_notes.html#scfvalues -.. _`temperature`: data_notes.html#temperature -.. _`time`: data_notes.html#time -.. _`vibanharms`: data_notes.html#vibanharms -.. _`vibdisps`: data_notes.html#vibdisps -.. _`vibfreqs`: data_notes.html#vibfreqs -.. _`vibirs`: data_notes.html#vibirs -.. _`vibramans`: data_notes.html#vibramans -.. _`vibsyms`: data_notes.html#vibsyms diff --git a/_sources/data.txt b/_sources/data.rst.txt similarity index 72% rename from _sources/data.txt rename to _sources/data.rst.txt index 9f53f18d..6b820b19 100644 --- a/_sources/data.txt +++ b/_sources/data.rst.txt @@ -16,7 +16,10 @@ Click the attribute name in the table below to go the notes and specifications f Details of current implementation --------------------------------- +The autogenerated table below details which attributes are supported by which parsers based on unit tests. Note that only actively maintained parsers are listed here, although legacy parsers are still testing with old data as regressions. To see the full list of parsers, see the `summary`_ page. + **N/A** = not applicable, **N/P** = applicable, but not possible, **T/D** = to do .. include:: coverage.rst +.. _`summary`: index.html#summary diff --git a/_sources/data_dev.txt b/_sources/data_dev.rst.txt similarity index 100% rename from _sources/data_dev.txt rename to _sources/data_dev.rst.txt diff --git a/_sources/data_notes.txt b/_sources/data_notes.rst.txt similarity index 54% rename from _sources/data_notes.txt rename to _sources/data_notes.rst.txt index 338e21fc..cfb298de 100644 --- a/_sources/data_notes.txt +++ b/_sources/data_notes.rst.txt @@ -1,12 +1,12 @@ .. index:: - module: data_notes + pair: module; data_notes Parsed data notes ================= -This is a list of descriptions and notes for all the data attributes currently parsed by cclib, either in the official release (|release|) or development branch. In particular, this page contains technical details about the interpretation of attributes, how to produce them in the various programs and examples in some cases. For a summary and details of the current implementation by the different parsers, please see the `extracted data`_ page and its `development`_ version. +This is a list of descriptions and notes for all the data attributes currently parsed by cclib, either in the official release (|release|) or development branch. In particular, this page contains technical details about the interpretation of attributes, how to produce them in the various programs and examples in some cases. For a summary and details of the current implementation by the different parsers, please see the `parsed data`_ page and its `development`_ version. -.. _`extracted data`: data.html +.. _`parsed data`: data.html .. _`development`: data_dev.html aonames @@ -14,13 +14,23 @@ aonames This attribute contains the atomic orbital names. These are not normalised as the following examples show, although a reasonable attempt is made to get them close to each other. Users will need to know what each orbital is by knowing the basis set inside out, rather than relying on this data. Such is life, as GAMESS does not provide enough information. -* Gaussian gives names of the form: ['C1_1S', 'C1_2S', 'C1_2PX', 'C1_2PY', 'C1_2PZ', 'C2_1S', 'C2_2S', 'C2_2PX', 'C2_2PY', 'C2_2PZ', 'C3_1S', 'C3_2S', 'C3_2PX', 'C3_2PY', 'C3_2PZ', 'C4_1S', 'C4_2S', 'C4_2PX', 'C4_2PY', 'C4_2PZ', 'C5_1S', 'C5_2S', 'C5_2PX', 'C5_2PY', 'C5_2PZ', 'H6_1S', 'H7_1S', 'H8_1S', 'C9_1S', 'C9_2S', 'C9_2PX', 'C9_2PY', 'C9_2PZ', 'C10_1S', 'C10_2S', 'C10_2PX', 'C10_2PY', 'C10_2PZ', 'H11_1S', 'H12_1S', 'H13_1S', 'C14_1S', 'C14_2S', 'C14_2PX', 'C14_2PY', 'C14_2PZ', 'H15_1S', 'C16_1S', 'C16_2S', 'C16_2PX', 'C16_2PY', 'C16_2PZ', 'H17_1S', 'H18_1S', 'C19_1S', 'C19_2S', 'C19_2PX', 'C19_2PY', 'C19_2PZ', 'H20_1S'] -* GAMESS gives names of the form: ['C1_1S', 'C1_2S', 'C1_3X', 'C1_3Y', 'C1_3Z', 'C2_1S', 'C2_2S', 'C2_3X', 'C2_3Y', 'C2_3Z', 'C3_1S', 'C3_2S', 'C3_3X', 'C3_3Y', 'C3_3Z', 'C4_1S', 'C4_2S', 'C4_3X', 'C4_3Y', 'C4_3Z', 'C5_1S', 'C5_2S', 'C5_3X', 'C5_3Y', 'C5_3Z', 'C6_1S', 'C6_2S', 'C6_3X', 'C6_3Y', 'C6_3Z', 'H7_1S', 'H8_1S', 'H9_1S', 'H10_1S', 'C11_1S', 'C11_2S', 'C11_3X', 'C11_3Y', 'C11_3Z', 'C12_1S', 'C12_2S', 'C12_3X', 'C12_3Y', 'C12_3Z', 'H13_1S', 'H14_1S', 'C15_1S', 'C15_2S', 'C15_3X', 'C15_3Y', 'C15_3Z', 'C16_1S', 'C16_2S', 'C16_3X', 'C16_3Y', 'C16_3Z', 'H17_1S', 'H18_1S', 'H19_1S', 'H20_1S'] +* Gaussian gives names of the form:: -And for a large basis set calculation on a single C atom...: + ['C1_1S', 'C1_2S', 'C1_2PX', 'C1_2PY', 'C1_2PZ', 'C2_1S', 'C2_2S', 'C2_2PX', 'C2_2PY', 'C2_2PZ', 'C3_1S', 'C3_2S', 'C3_2PX', 'C3_2PY', 'C3_2PZ', 'C4_1S', 'C4_2S', 'C4_2PX', 'C4_2PY', 'C4_2PZ', 'C5_1S', 'C5_2S', 'C5_2PX', 'C5_2PY', 'C5_2PZ', 'H6_1S', 'H7_1S', 'H8_1S', 'C9_1S', 'C9_2S', 'C9_2PX', 'C9_2PY', 'C9_2PZ', 'C10_1S', 'C10_2S', 'C10_2PX', 'C10_2PY', 'C10_2PZ', 'H11_1S', 'H12_1S', 'H13_1S', 'C14_1S', 'C14_2S', 'C14_2PX', 'C14_2PY', 'C14_2PZ', 'H15_1S', 'C16_1S', 'C16_2S', 'C16_2PX', 'C16_2PY', 'C16_2PZ', 'H17_1S', 'H18_1S', 'C19_1S', 'C19_2S', 'C19_2PX', 'C19_2PY', 'C19_2PZ', 'H20_1S'] -* Gaussian: ['C1_1S', 'C1_2S', 'C1_3S', 'C1_4S', 'C1_5S', 'C1_6PX', 'C1_6PY', 'C1_6PZ', 'C1_7PX', 'C1_7PY', 'C1_7PZ', 'C1_8PX', 'C1_8PY', 'C1_8PZ', 'C1_9PX', 'C1_9PY', 'C1_9PZ', 'C1_10D 0', 'C1_10D+1', 'C1_10D-1', 'C1_10D+2', 'C1_10D-2', 'C1_11D 0', 'C1_11D+1', 'C1_11D-1', 'C1_11D+2', 'C1_11D-2', 'C1_12D 0', 'C1_12D+1', 'C1_12D-1', 'C1_12D+2', 'C1_12D-2', 'C1_13F 0', 'C1_13F+1', 'C1_13F-1', 'C1_13F+2', 'C1_13F-2', 'C1_13F+3', 'C1_13F-3', 'C1_14F 0', 'C1_14F+1', 'C1_14F-1', 'C1_14F+2', 'C1_14F-2', 'C1_14F+3', 'C1_14F-3', 'C1_15G 0', 'C1_15G+1', 'C1_15G-1', 'C1_15G+2', 'C1_15G-2', 'C1_15G+3', 'C1_15G-3', 'C1_15G+4', 'C1_15G-4', 'C1_16S', 'C1_17PX', 'C1_17PY', 'C1_17PZ', 'C1_18D 0', 'C1_18D+1', 'C1_18D-1', 'C1_18D+2', 'C1_18D-2', 'C1_19F 0', 'C1_19F+1', 'C1_19F-1', 'C1_19F+2', 'C1_19F-2', 'C1_19F+3', 'C1_19F-3', 'C1_20G 0', 'C1_20G+1', 'C1_20G-1', 'C1_20G+2', 'C1_20G-2', 'C1_20G+3', 'C1_20G-3', 'C1_20G+4', 'C1_20G-4'] -* GAMESS: ['C1_1S', 'C1_2S', 'C1_3S', 'C1_4S', 'C1_5S', 'C1_6X', 'C1_6Y', 'C1_6Z', 'C1_7X', 'C1_7Y', 'C1_7Z', 'C1_8X', 'C1_8Y', 'C1_8Z', 'C1_9X', 'C1_9Y', 'C1_9Z', 'C1_10XX', 'C1_10YY', 'C1_10ZZ', 'C1_10XY', 'C1_10XZ', 'C1_10YZ', 'C1_11XX', 'C1_11YY', 'C1_11ZZ', 'C1_11XY', 'C1_11XZ', 'C1_11YZ', 'C1_12XX', 'C1_12YY', 'C1_12ZZ', 'C1_12XY', 'C1_12XZ', 'C1_12YZ', 'C1_13XXX', 'C1_13YYY', 'C1_13ZZZ', 'C1_13XXY','C1_13XXZ', 'C1_13YYX', 'C1_13YYZ', 'C1_13ZZX', 'C1_13ZZY', 'C1_13XYZ', 'C1_14XXX', 'C1_14YYY', 'C1_14ZZZ', 'C1_14XXY', 'C1_14XXZ', 'C1_14YYX', 'C1_14YYZ', 'C1_14ZZX', 'C1_14ZZY', 'C1_14XYZ', 'C1_15XXXX', 'C1_15YYYY', 'C1_15ZZZZ', 'C1_15XXXY', 'C1_15XXXZ', 'C1_15YYYX', 'C1_15YYYZ', 'C1_15ZZZX', 'C1_15ZZZY', 'C1_15XXYY', 'C1_15XXZZ', 'C1_15YYZZ', 'C1_15XXYZ', 'C1_15YYXZ', 'C1_15ZZXY', 'C1_16S', 'C1_17S', 'C1_18S', 'C1_19X', 'C1_19Y', 'C1_19Z', 'C1_20X', 'C1_20Y', 'C1_20Z', 'C1_21X', 'C1_21Y', 'C1_21Z', 'C1_22XX', 'C1_22YY', 'C1_22ZZ', 'C1_22XY', 'C1_22XZ', 'C1_22YZ', 'C1_23XX', 'C1_23YY', 'C1_23ZZ', 'C1_23XY', 'C1_23XZ', 'C1_23YZ', 'C1_24XXX', 'C1_24YYY', 'C1_24ZZZ', 'C1_24XXY', 'C1_24XXZ', 'C1_24YYX', 'C1_24YYZ', 'C1_24ZZX', 'C1_24ZZY', 'C1_24XYZ', 'C1_25S', 'C1_26X', 'C1_26Y', 'C1_26Z', 'C1_27XX', 'C1_27YY', 'C1_27ZZ', 'C1_27XY', 'C1_27XZ', 'C1_27YZ', 'C1_28XXX', 'C1_28YYY', 'C1_28ZZZ', 'C1_28XXY', 'C1_28XXZ', 'C1_28YYX', 'C1_28YYZ', 'C1_28ZZX', 'C1_28ZZY', 'C1_28XYZ', 'C1_29XXXX', 'C1_29YYYY', 'C1_29ZZZZ', 'C1_29XXXY', 'C1_29XXXZ', 'C1_29YYYX', 'C1_29YYYZ', 'C1_29ZZZX', 'C1_29ZZZY', 'C1_29XXYY', 'C1_29XXZZ', 'C1_29YYZZ', 'C1_29XXYZ', 'C1_29YYXZ', 'C1_29ZZXY'] +* GAMESS gives names of the form:: + + ['C1_1S', 'C1_2S', 'C1_3X', 'C1_3Y', 'C1_3Z', 'C2_1S', 'C2_2S', 'C2_3X', 'C2_3Y', 'C2_3Z', 'C3_1S', 'C3_2S', 'C3_3X', 'C3_3Y', 'C3_3Z', 'C4_1S', 'C4_2S', 'C4_3X', 'C4_3Y', 'C4_3Z', 'C5_1S', 'C5_2S', 'C5_3X', 'C5_3Y', 'C5_3Z', 'C6_1S', 'C6_2S', 'C6_3X', 'C6_3Y', 'C6_3Z', 'H7_1S', 'H8_1S', 'H9_1S', 'H10_1S', 'C11_1S', 'C11_2S', 'C11_3X', 'C11_3Y', 'C11_3Z', 'C12_1S', 'C12_2S', 'C12_3X', 'C12_3Y', 'C12_3Z', 'H13_1S', 'H14_1S', 'C15_1S', 'C15_2S', 'C15_3X', 'C15_3Y', 'C15_3Z', 'C16_1S', 'C16_2S', 'C16_3X', 'C16_3Y', 'C16_3Z', 'H17_1S', 'H18_1S', 'H19_1S', 'H20_1S'] + +And for a large basis set calculation on a single C atom: + +* Gaussian:: + + ['C1_1S', 'C1_2S', 'C1_3S', 'C1_4S', 'C1_5S', 'C1_6PX', 'C1_6PY', 'C1_6PZ', 'C1_7PX', 'C1_7PY', 'C1_7PZ', 'C1_8PX', 'C1_8PY', 'C1_8PZ', 'C1_9PX', 'C1_9PY', 'C1_9PZ', 'C1_10D 0', 'C1_10D+1', 'C1_10D-1', 'C1_10D+2', 'C1_10D-2', 'C1_11D 0', 'C1_11D+1', 'C1_11D-1', 'C1_11D+2', 'C1_11D-2', 'C1_12D 0', 'C1_12D+1', 'C1_12D-1', 'C1_12D+2', 'C1_12D-2', 'C1_13F 0', 'C1_13F+1', 'C1_13F-1', 'C1_13F+2', 'C1_13F-2', 'C1_13F+3', 'C1_13F-3', 'C1_14F 0', 'C1_14F+1', 'C1_14F-1', 'C1_14F+2', 'C1_14F-2', 'C1_14F+3', 'C1_14F-3', 'C1_15G 0', 'C1_15G+1', 'C1_15G-1', 'C1_15G+2', 'C1_15G-2', 'C1_15G+3', 'C1_15G-3', 'C1_15G+4', 'C1_15G-4', 'C1_16S', 'C1_17PX', 'C1_17PY', 'C1_17PZ', 'C1_18D 0', 'C1_18D+1', 'C1_18D-1', 'C1_18D+2', 'C1_18D-2', 'C1_19F 0', 'C1_19F+1', 'C1_19F-1', 'C1_19F+2', 'C1_19F-2', 'C1_19F+3', 'C1_19F-3', 'C1_20G 0', 'C1_20G+1', 'C1_20G-1', 'C1_20G+2', 'C1_20G-2', 'C1_20G+3', 'C1_20G-3', 'C1_20G+4', 'C1_20G-4'] + +* GAMESS:: + + ['C1_1S', 'C1_2S', 'C1_3S', 'C1_4S', 'C1_5S', 'C1_6X', 'C1_6Y', 'C1_6Z', 'C1_7X', 'C1_7Y', 'C1_7Z', 'C1_8X', 'C1_8Y', 'C1_8Z', 'C1_9X', 'C1_9Y', 'C1_9Z', 'C1_10XX', 'C1_10YY', 'C1_10ZZ', 'C1_10XY', 'C1_10XZ', 'C1_10YZ', 'C1_11XX', 'C1_11YY', 'C1_11ZZ', 'C1_11XY', 'C1_11XZ', 'C1_11YZ', 'C1_12XX', 'C1_12YY', 'C1_12ZZ', 'C1_12XY', 'C1_12XZ', 'C1_12YZ', 'C1_13XXX', 'C1_13YYY', 'C1_13ZZZ', 'C1_13XXY','C1_13XXZ', 'C1_13YYX', 'C1_13YYZ', 'C1_13ZZX', 'C1_13ZZY', 'C1_13XYZ', 'C1_14XXX', 'C1_14YYY', 'C1_14ZZZ', 'C1_14XXY', 'C1_14XXZ', 'C1_14YYX', 'C1_14YYZ', 'C1_14ZZX', 'C1_14ZZY', 'C1_14XYZ', 'C1_15XXXX', 'C1_15YYYY', 'C1_15ZZZZ', 'C1_15XXXY', 'C1_15XXXZ', 'C1_15YYYX', 'C1_15YYYZ', 'C1_15ZZZX', 'C1_15ZZZY', 'C1_15XXYY', 'C1_15XXZZ', 'C1_15YYZZ', 'C1_15XXYZ', 'C1_15YYXZ', 'C1_15ZZXY', 'C1_16S', 'C1_17S', 'C1_18S', 'C1_19X', 'C1_19Y', 'C1_19Z', 'C1_20X', 'C1_20Y', 'C1_20Z', 'C1_21X', 'C1_21Y', 'C1_21Z', 'C1_22XX', 'C1_22YY', 'C1_22ZZ', 'C1_22XY', 'C1_22XZ', 'C1_22YZ', 'C1_23XX', 'C1_23YY', 'C1_23ZZ', 'C1_23XY', 'C1_23XZ', 'C1_23YZ', 'C1_24XXX', 'C1_24YYY', 'C1_24ZZZ', 'C1_24XXY', 'C1_24XXZ', 'C1_24YYX', 'C1_24YYZ', 'C1_24ZZX', 'C1_24ZZY', 'C1_24XYZ', 'C1_25S', 'C1_26X', 'C1_26Y', 'C1_26Z', 'C1_27XX', 'C1_27YY', 'C1_27ZZ', 'C1_27XY', 'C1_27XZ', 'C1_27YZ', 'C1_28XXX', 'C1_28YYY', 'C1_28ZZZ', 'C1_28XXY', 'C1_28XXZ', 'C1_28YYX', 'C1_28YYZ', 'C1_28ZZX', 'C1_28ZZY', 'C1_28XYZ', 'C1_29XXXX', 'C1_29YYYY', 'C1_29ZZZZ', 'C1_29XXXY', 'C1_29XXXZ', 'C1_29YYYX', 'C1_29YYYZ', 'C1_29ZZZX', 'C1_29ZZZY', 'C1_29XXYY', 'C1_29XXZZ', 'C1_29YYZZ', 'C1_29XXYZ', 'C1_29YYXZ', 'C1_29ZZXY'] aooverlaps ---------- @@ -32,11 +42,11 @@ Some examples: * ``aooverlaps[0,3]`` is the overlap between the 1st and 4th basis function * ``aooverlaps[2,:]`` is a 1-dimensional array containing the overlap between every basis function and the 3rd basis function -**ADF**: not present by default, printed when `PRINT Smat` is in the input; do not mistake with `fooverlaps`_ +**ADF**: not present by default, printed when ``PRINT Smat`` is in the input; do not mistake with `fooverlaps`_. -**DALTON**: no option to print as of version 2013 +**DALTON**: no option to print as of version 2013. -**Gaussian**: iop(3/33=1) must be specified in the input file +**Gaussian**: ``iop(3/33=1)`` must be specified in the input file. .. _`Mulliken`: methods.html#mulliken-population-analysis-mpa .. _`C squared`: methods.html#c-squared-population-analysis-cspa @@ -48,23 +58,47 @@ atombasis The attribute ``atombasis`` is a list, each element being a list that contains the atomic orbital indices on the respective atom. For example, ``atombasis[1]`` will contain the indices of atomic orbitals on the second atom of the molecule. .. index:: - single: properties; atoimcharges (attribute) + single: properties; atomcharges (attribute) atomcharges ----------- The attribute ``atomcharges`` contains the atomic partial charges as taken from the output file. Since these charges are arbitrary and depend on the details of a population analysis, this attribute is dictionary containing any number of various atomic charges. The keys in this dictionary are strings naming the population analysis, and the values are arrays of rank 1 and contain the actual charges. -Currently, cclib parses Mulliken, Löwdin, NPA and CHELPG charges, whose respective dictionary keys are ``mulliken``, ``lowdin``, ``natural`` and ``chelpg``. +Currently, cclib parses several different charge types depending on the program: + + ============ ============================== + charge type name of key in ``atomcharges`` + ============ ============================== + Mulliken ``mulliken`` + Löwdin ``lowdin`` + NPA ``natural`` + `APT`_ ``apt`` + `CHELPG`_ ``chelpg`` + `Hirshfeld`_ ``hirshfeld`` + `CM5`_ ``cm5`` + `ESP`_ ``esp`` + `RESP`_ ``resp`` + ============ ============================== + +In practice, these may differ somewhat from the values cclib calculates in the various `calculation methods`_. -Note that in practice these may differ somewhat from the values cclib calculates in the various calculation methods. +**Gaussian**: additional sections are present where the partial charge on each hydrogen is added into the heavy atom it is connected to ("charges with hydrogens summed into heavy atoms"). For each charge schema (such as ``mulliken``), a corresponding key with ``_sum`` appended will be present (``mulliken_sum``) with these charges, and hydrogens will be present but set to zero. -**Molpro**: use the ``pop`` command (see http://www.molpro.net/info/2010.1/doc/manual/node450.html) +**Molpro**: use the ``pop`` command (see https://www.molpro.net/manual/doku.php?id=properties_and_expectation_values&s[]=population&s[]=analysis#calling_the_population_analysis_program_pop). + +.. _`calculation methods`: methods.html +.. _`APT`: https://doi.org/10.1016/j.theochem.2010.06.011 +.. _`CHELPG`: https://doi.org/10.1002/jcc.540110311 +.. _`Hirshfeld`: https://doi.org/10.1007/BF01113058 +.. _`CM5`: https://doi.org/10.1021/ct200866d +.. _`ESP`: https://doi.org/10.1002/jcc.540050204 +.. _`RESP`: https://doi.org/10.1021/j100142a004 atomcoords ---------- -The attribute ``atomcoords`` contains the atomic coordinates as taken from the output file. This is an array of rank 3, with a shape (n,m,3) where n is 1 for a single point calculation and >=1 for a geometry optimisation and m is the number of atoms. +The attribute ``atomcoords`` contains the atomic coordinates as taken from the output file. This is an array of rank 3, with a shape (n,m,3) where n is 1 for a single point calculation and >=1 for a geometry optimisation and m is the number of atoms. **Gaussian**: for geometry optimisations, the "Standard orientation" sections are extracted. @@ -105,40 +139,23 @@ coreelectrons The attribute ``coreelectrons`` contains the number of core electrons in each atom's pseudopotentials. It is an array of rank 1, with as many integer elements as there are atoms. -etenergies ----------- - -This is a rank 1 array that contains the energies of electronic transitions from a reference state to the excited states of the molecule, in ``cm-1``. There should be as many elements to this array as there are excited states calculated. Any type of excited state calculation should provide output that can be parsed into this attribute. +dispersionenergies +------------------ -Availability: +This is a rank 1 array that contains the isolated dispersion energy for each geometry. This will be populated for empirical models, such as those from Grimme that only depend on relative atomic positions. For self-consistently determined corrections that are incorporated during SCF iterations, there is no separable dispersion energy contribution, so this attribute will not be present. -* Configuration Interaction (CIS): Gaussian -* Time-dependent DFT (TD-DFT): Gaussian -* Time-dependent Hartree-Fock (TD-HF): Gaussian +However, in *all* cases the dispersion energy for a given geometry will also be a part of `scfenergies`_. -Availability (development version): +etenergies +---------- -* Configuration Interaction (CIS): Gaussian, GAMESS, Jaguar -* Time-dependent DFT (TD-DFT): Gaussian -* Time-dependent Hartree-Fock (TD-HF): Gaussian +This is a rank 1 array that contains the energies of electronic transitions from a reference state to the excited states of the molecule, in ``cm-1``. There should be as many elements to this array as there are excited states calculated. Any type of excited state calculation should provide output that can be parsed into this attribute. etoscs ------ The attribute ``etoscs`` is a rank 1 array that contains the oscillator strengths of transitions from the reference (ground) state to the excited electronic states of the of the molecule. As for `etenergies`_ and other attributes related to excited states, there should as many elements in this array as there are excited states in the calculation. -Availability: - -* Configuration Interaction (CIS): Gaussian -* Time-dependent DFT (TD-DFT): Gaussian -* Time-dependent Hartree-Fock (TD-HF): Gaussian - -Availability (development version): - -* Configuration Interaction (CIS): GAMESS, Gaussian, Jaguar -* Time-dependent DFT (TD-DFT): Gaussian -* Time-dependent Hartree-Fock (TD-HF): Gaussian - etsecs ------ @@ -152,18 +169,6 @@ In these tuples, the value of alpha/beta is 0 or 1, respectively. For a restrict The excitation coefficient is always converted to its unnormalized value by cclib - so the sum of the squared coefficients of all alpha and beta excitations should be unity. It is important to keep in mind, however, that only the square of the excitation coefficient has a physical meaning, and its sign depends on the numerical procedures used by each program. -Availability: - -* Configuration Interaction (CIS): Gaussian -* Time-dependent DFT (TD-DFT): Gaussian -* Time-dependent Hartree-Fock (TD-HF): Gaussian - -Availability (development version): - -* Configuration Interaction (CIS): GAMESS, Gaussian, Jaguar -* Time-dependent DFT (TD-DFT): GAMESS, Gaussian -* Time-dependent Hartree-Fock (TD-HF): Gaussian - etsyms ------ @@ -171,18 +176,6 @@ The attributes ``etsyms`` is a list containing the symmetries (strings) of the e Note that while the symmetry descriptions start with the string ``Singlet`` or ``Triplet``, the exact format differs between programs. -Availability: - -* Configuration Interaction (CIS): Gaussian -* Time-dependent DFT (TD-DFT): Gaussian -* Time-dependent Hartree-Fock (TD-HF): Gaussian - -Availability: - -* Configuration Interaction (CIS): GAMESS, Gaussian, Jaguar -* Time-dependent DFT (TD-DFT): Gaussian -* Time-dependent Hartree-Fock (TD-HF): Gaussian - fonames ------- @@ -219,9 +212,9 @@ The difficulty in handling the basis for a molecule with symmetry and the availa gbasis ------ -This attribute stores information about the Gaussian basis functions that were used in the calculation, per atom using the same conventions as [http://pyquante.sf.net PyQuante]. Specifically, ``gbasis`` is a list of lists iterating over atoms and Gaussian basis functions. The elements (basis functions) are tuples of length 2 consisting of orbital type (e.g. 'S', 'P' or 'D') and a list (per contracted GTO) of tuples of size 2 consisting of the exponent and coefficient. Confused? Well, here's ``gbasis`` for a molecule consisting of a single C atom with a STO-3G basis: +This attribute stores information about the Gaussian basis functions that were used in the calculation, per atom using the same conventions as `PyQuante `_. Specifically, ``gbasis`` is a list of lists iterating over atoms and Gaussian basis functions. The elements (basis functions) are tuples of length 2 consisting of orbital type (e.g. 'S', 'P' or 'D') and a list (per contracted GTO) of tuples of size 2 consisting of the exponent and coefficient. Confused? Well, here's ``gbasis`` for a molecule consisting of a single C atom with a STO-3G basis: -.. +.. code-block:: python [ # per atom [ @@ -245,19 +238,19 @@ This attribute stores information about the Gaussian basis functions that were u For D and F functions there is an important distinction between pure (5D, 7F) or Cartesian (6D, 10F) functions. PyQuante can only handle Cartesian functions, but we should extract this information in any case, and perhaps work to extend the PyQuante basis set format to include this. -**Gaussian**: the `GFINPUT`_ keyword should normally be used (`GFPRINT`_ gives equivalent information in a different format and is supported in cclib after v1.2). +**Gaussian**: the `GFINPUT`_ keyword should normally be used (`GFPRINT`_ gives equivalent information in a different format). **GAMESS/GAMESS-UK**: no special keywords are required, but the basis is only available for symmetry inequivalent atoms. There does not seem to be any way to get GAMESS to say which atoms are related through symmetry. As a result, if you want to get basis set info for every atom, you need to reduce the symmetry to C1. -**Jaguar**: for more information see manual (for example at http://yfaat.ch.huji.ac.il/jaguar-help/mand.html#114223) +**Jaguar**: for more information see manual (for example at https://web.archive.org/web/20141117001641/http://yfaat.ch.huji.ac.il/jaguar-help/mand.html) **ORCA**: include ``Print[ P_Basis ] 2`` in the ``output`` block -.. _`GFINPUT`: http://www.gaussian.com/g_tech/g_ur/k_gfinput.htm -.. _`GFPRINT`: http://www.gaussian.com/g_tech/g_ur/k_gfprint.htm +.. _`GFINPUT`: https://gaussian.com/gfinput/ +.. _`GFPRINT`: https://gaussian.com/gfprint/ .. index:: - single: geomtry optimisation; geotargets (attribute) + single: geometry optimisation; geotargets (attribute) geotargets ---------- @@ -273,7 +266,7 @@ In some special cases, the values in ``geotargets`` will be `numpy.inf`_. - maximum gradient below TOL * 1/4, - average gradient below TOL * 1/6. -.. _`GAMESS-UK manual section on controlling optimisation`:http://www.cfs.dl.ac.uk/docs/html/part4/node14.html +.. _`GAMESS-UK manual section on controlling optimisation`: https://web.archive.org/web/20190809095414/http://www.cfs.dl.ac.uk/docs/html/part4/node14.html **Jaguar** has several geometry convergence criteria, @@ -285,11 +278,11 @@ In some special cases, the values in ``geotargets`` will be `numpy.inf`_. Note that a value for gconv7 is not available until the second iteration, so it is set to zero in the first element of `geovalues`_. -**Molpro** has custom convergence criteria, as described in the `manual`_: +**Molpro** has custom convergence criteria, as described in the `manual `_: - The standard MOLPRO convergency criterion requires the maximum component of the gradient to be less then :math:`3 \cdot 10^{-4}` [a.u.] and the maximum energy change to be less than :math:`1 \cdot 10^{-6}` [H] or the maximum component of the gradient to be less then $ 3 \cdot 10^{-4}$ [a.u.] and the maximum component of the step to be less then :math:`3 \cdot 10^{-4}` [a.u.]. + The standard MOLPRO convergence criterion requires the maximum component of the gradient to be less than :math:`3 \cdot 10^{-4}` [a.u.] and the maximum energy change to be less than :math:`1 \cdot 10^{-6}` [H] or the maximum component of the gradient to be less than :math:`3 \cdot 10^{-4}` [a.u.] and the maximum component of the step to be less than :math:`3 \cdot 10^{-4}` [a.u.]. -.. _`manual`: https://www.molpro.net/info/2012.1/doc/manual/node592.html +.. _Molpro manual convergence: https://www.molpro.net/manual/doku.php?id=geometry_optimization_optg#options_to_modify_convergence_criteria **ORCA** tracks the change in energy as well as RMS and maximum gradients and displacements. As of version 3.0, an optimisation is considered converged when all the tolerances are met, and there are four exceptions: @@ -300,9 +293,9 @@ Note that a value for gconv7 is not available until the second iteration, so it **Psi** normally tracks five different values, as described `in the documentation`_, but their use various depending on the strategy employed. The default strategy (QCHEM) check whether the maximum force is converged and if the maximum energy change or displacement is converged. Additionally, to aid with flat potential energy surfaces, convergence is as assumed when the root mean square force converged to 0.01 of its default target. Note that Psi print values even for targets that are not being used -- in these cases the targets are parsed as `numpy.inf`_ so that they can still be used (any value will be converged). -.. _`in the documentation`: http://sirius.chem.vt.edu/psi4manual/latest/optking.html +.. _`in the documentation`: https://psicode.org/psi4manual/master/optking.html#convergence-criteria -.. _`numpy.inf`: http://docs.scipy.org/doc/numpy-1.8.1/user/misc.html#ieee-754-floating-point-special-values +.. _`numpy.inf`: https://numpy.org/doc/stable/user/misc.html#ieee-754-floating-point-special-values .. index:: single: geomtry optimisation; geovalues (attribute) @@ -312,16 +305,21 @@ geovalues These are the current values for the criteria used to determine whether a geometry has converged in the course of a geometry optimisation. It is an array of dimensions ``m x n``, where ``m`` is the number of geometry optimisation iterations and ``n`` the number of target criteria. -Note that many programs print atomic coordinates before and after a geomtry optimisation, which means that there will not necessarily be ``m`` elements in ``atomcoords``_. +Note that many programs print atomic coordinates before and after a geometry optimisation, which means that there will not necessarily be ``m`` elements in `atomcoords`_. If the optimisation has finished successfully, the values in the last row should be smaller than the values in geotargets_ (unless the convergence criteria require otherwise). + +grads +----- +The attribute ``grads`` contains the forces on the atoms, that is, the negative gradient of the energy with respect to atomic coordinates in atomic units (Hartree / Bohr). ``grads`` is an array of rank 3, with dimensions ``[n, m, 3]`` where ``n`` is 1 for a single point calculation and ``>=1`` for a geometry optimisation, ``m`` is the number of atoms and the last dimension contains the x, y and z components of the gradient. The orientation of ``grads`` corresponds to that of `atomcoords`_. + +**Gaussian**: In calculations that include point-group symmetry, ``grads`` is converted to standard orientation to match the orientation of ``atomcoords`` and other quantities. Because of this, the ``grads`` group will differ from that printed in the output file by Gaussian (which is always in the input orientation). Calculations without symmetry (that is, with the ``Symmetry=None`` keyword) yield everything in the input orientation and in those cases ``grads`` should match exactly what is printed in the output file. + hessian ------- -An array of rank 1 that contains the elements of [http://en.wikipedia.org/wiki/Hessian_matrix hessian] or the force constant matrix. Only the lower triangular part of the 3Nx3N matrix is stored (this may change in the future, maybe also only the force-constant , unwighted matrix will be parsed). - -* currently available only in ``Molpro`` +An array of rank 2 that contains the elements of the `hessian `_ or force constant matrix. The full symmetric ``[3N, 3N]`` matrix is stored. .. index:: single: molecular orbitals; homos (attribute) @@ -329,11 +327,47 @@ An array of rank 1 that contains the elements of [http://en.wikipedia.org/wiki/H homos ----- -A 1D array that holds the indexes of the highest occupied molecular orbitals (HOMOs), which contains one element for restricted and two elements for unrestricted calculations. These indexes can be applied to other attributes describing molecular orbitals, such as `moenergies`_ and `mocoeffs`_. +A 1D array that holds the indexes of the highest occupied molecular orbitals (HOMOs), with one element for restricted and two elements for unrestricted calculations. These indexes can be applied to other attributes describing molecular orbitals, such as `moenergies`_ and `mocoeffs`_. For example: + +.. code-block:: python + + data = cclib.io.ccread('water_mp2') + last_occupied_energy = data.moenergies[0][data.homos[0]] + +>> **Note:** All indexes in cclib start from zero, as per Python conventions. This applies to the contents of ``homos`` as well, which means ``homos[0]`` refers to the *index* of the HOMO when referencing other attributes and not the number of occupied orbitals. .. index:: single: molecular orbitals; mocoeffs (attribute) +metadata +-------- + +A dictionary containing metadata_ (data about data) for the calculation. Currently, it can contain the following possible attributes, not all of which are implemented for each parser. + +* ``basis_set``: A string with the name of the basis set, if it is printed anywhere as a standard name. +* ``comments``: A list of strings of the user-provided input file comment sections. There is one string per discovered job in the output. +* ``coord_type``: For the ``coords`` field, a string for the representation of stored coordinates. Currently, it is one of ``xyz``, ``int``/``internal``, or ``gzmat``. +* ``coords``: A list of lists with shape ``[natoms, 4]`` which contains the input coordinates (those found in the input file). The first column is the atomic symbol as a string, and the next three columns are floats. This is useful as many programs reorient coordinates for symmetry reasons. +* ``cpu_time``: A list of datetime.timedeltas containing the CPU time of each calculation in the output. +* ``functional``: A string with the name of the density functional used. +* ``info``: A list of strings, each of which is an information or log message produced during a calculation. +* ``input_file_contents``: A string containing the entire input file, if it is echoed back during the calculation. +* ``input_file_name``: A string containing the name of the input file, with file extension. It may not contain the entire path to the file. +* ``keywords``: A list of strings corresponding to the keywords used in the input file, in the loose format used by ORCA. For Gaussian there is one string per discovered job in the output. +* ``methods``: A list of strings containing each method used in order. Currently, the list may contain ``HF``, ``DFT``, ``LMP2``/``DF-MP2``/``MP2``, ``MP3``, ``MP4``, ``CCSD``, and/or ``CCSD(T)``/``CCSD-T``. +* ``package``: A string with the name of the quantum chemistry program used. +* ``package_version``: A string representation of the package version. It is formatted to allow comparison using relational operators. +* ``symmetry_detected``: A string representing the full or largest point group detected by the program. +* ``symmetry_used``: A string representing the point group used by the program for the calculation. This may be different from ``symmetry_detected`` if the full point group is non-abelian and the program can only take advantage of abelian groups. For example, when performing a calculation on benzene with symmetry turned on, ``symmetry_detected`` may be ``d6h``, but ``symmetry_used`` is most likely ``d2h``, since D2h is the largest abelian subgroup of D6h. +* ``success``: A boolean for whether or not the calculation completed properly. +* ``unrestricted``: A boolean for whether or not the calculation was performed with a unrestricted wavefunction. +* ``wall_time``: A list of datetime.timedeltas containing the wall time of each calculation in the output. +* ``warnings``: A list of strings, each of which is a warning produced during a calculation. + +The implementation and coverage of metadata is currently inconsistent. In the future, metadata may receive its own page similar to :doc:`extracted data `. + +.. _metadata: https://en.wikipedia.org/wiki/Metadata + mocoeffs -------- @@ -362,7 +396,7 @@ A list of rank 1 arrays containing the molecular orbital energies in eV. The lis **Jaguar**: the first ten virtual orbitals are printed by default. In order to print more, use the ``ipvirt`` keyword, with ``ipvirt=-1`` printing all virtual orbitals. -.. _`FORMAT HIGH`: http://www.cfs.dl.ac.uk/docs/html/part3/node8.html#SECTION00083000000000000000 +.. _`FORMAT HIGH`: https://web.archive.org/web/20190809100513/http://www.cfs.dl.ac.uk/docs/html/part3/node8.html .. index:: single: properties; moments (attribute) @@ -399,21 +433,22 @@ The symmetry labels are normalised and cclib reports standard symmetry names: A" AAA A' ' a" or a' ' A" App A1' AA1 A1' a1' A1' A1p A1" AAA1 A1" a1" A1" A1pp - sigma Sigma SG - pi Pi PI - phi Phi PHI (inferred) - delta Delta DLTA but DLTU/DLTG - sigma.g Sigma.g SGG + sigma Sigma SG + pi Pi PI + phi Phi PHI (inferred) + delta Delta DLTA but DLTU/DLTG + sigma.g Sigma.g SGG ======= ======= ======= ========== ================== ====== -* ADF - the full list can be found [http://www.scm.com/Doc/Doc2005.01/ADF/ADFUsersGuide/page339.html here]. -* GAMESS-UK - to get the list, 'grep "data yr" input.m' if you have access to the source. Note that for E, it's split into "e1+" and "e1-" for instance. -* Jaguar - to get the list, look at the examples in schrodinger/jaguar-whatever/samples if you have access to Jaguar. Note that for E, it's written as E1pp/Ap, for instance. -* NWChem - if molecular symmetry is turned off or set to C1, symmetry adaption for orbitals is also deactivated, and can be explicitely turned on with `adapt on` in the SCF block +* ADF - the full list can be found `here `_. +* GAMESS-UK - to get the list, ``grep "data yr" input.m`` if you have access to the source. Note that for E, it's split into "e1+" and "e1-" for instance. +* Jaguar - to get the list, look at the examples in ``schrodinger/jaguar-whatever/samples`` if you have access to Jaguar. Note that for E, it's written as E1pp/Ap, for instance. +* NWChem - if molecular symmetry is turned off or set to C1, symmetry adaption for orbitals is also deactivated, and can be explicitly turned on with ``adapt on`` in the SCF block Developers: -* The use of a function with doctests for each of these cases is recommended, to make sure that the conversion is robust. There is a prototype called normalisesym() in logfileparser.py which should be overwritten in the subclasses if necessary (there is a unittest to make sure that this has been done). -* The character tables [http://www.mpip-mainz.mpg.de/~gelessus/group.html here] may be useful in determining the correspondence between the labels used by the comp chem package and the commonly-used symbols. + +* The tests for these functions live in ``test/parser/testspecficparser.py``. +* `These `_ character tables may be useful in determining the correspondence between the labels used by the comp chem package and the commonly-used symbols. .. index:: single: energy; mpenergies (attribute) @@ -433,6 +468,8 @@ The attribute ``mpenergies`` holds the total molecule energies including Møller **Jaguar**: the LMP2 is available. +**ORCA**: MP2 and MP3 are available. The MP2 module can be called with the ``MP2`` keyword; while MP3 corrections are included in the matrix driven configuration interaction (MDCI) module through the ``MP3`` keyword. + mult ---- @@ -441,7 +478,7 @@ The attribute ``mult`` is an integer and represents the spin multiplicity of the natom ----- -``Natom`` is an integer, the number of atoms treated in the calculation. +An integer representing the number of atoms treated in the calculation. .. index:: single: basis sets; nbasis (attribute) @@ -463,7 +500,79 @@ Commands to get information on all orbitals: **GAMESS-UK**: only usually prints information on the 5 lowest virtual orbitals. "FORMAT HIGH" should make it do this for all of the orbitals, although GAMESS-UK 7.0 has a bug that means that this only works for restricted calculations. -**Jaguar**: the first ten virtual orbitals are printed by default; in order to print more of them, use the ``ipvirt`` keyword in the input file, with ``ipvirt=-1`` printing all virtual orbitals (see the [http://www.pdc.kth.se/doc/jaguar4.1/html/manual/mang.html#644675 manual] for more information). +**Jaguar**: the first ten virtual orbitals are printed by default; in order to print more of them, use the ``ipvirt`` keyword in the input file, with ``ipvirt=-1`` printing all virtual orbitals (see the `manual `_ for more information). + +.. _Jaguar manual nmo: http://www.pdc.kth.se/doc/jaguar4.1/html/manual/mang.html#644675 + +nmrtensors +---------- + +A dictionary where the keys zero-index the atomic center for which the chemical shielding tensor is calculated, and the values are themselves dictionaries containing the keys ``total`` and ``isotropic``, and optionally ``paramagnetic``, and ``diamagnetic``. ``total``, ``paramagnetic`` and ``diamagnetic`` correspond to the total chemical shielding tensor and its separation into paramagnetic and diamagnetic components, where :math:`\sigma_{K}^{\textrm{tot}} = \sigma_{K}^{\textrm{para}} + \sigma_{K}^{\textrm{dia}}` for a nucleus :math:`K`. Each tensor is represented as a 3-by-3 NumPy array. If no breakdown for paramagnetic and diamagnetic contributions to the chemical shielding is available, then ``paramagnetic`` and ``diamagnetic`` will be absent. ``isotropic`` contains the total isotropic shielding value for the atom, which corresponds to the mean of the eigenvalues of the ``total`` tensor. All values are in ppm. + +.. code-block:: python + + { + # Atomic index. + 0: { + 'diamagnetic': array([[267.113, -0.561, 0. ], + [ -0.693, 260.076, 0. ], + [ 0. , 0. , 244.893]] + ), + 'isotropic': 114.114, + 'paramagnetic': array([[-217.434, 5.104, 0. ], + [ 7.253, -179.952, 0. ], + [ 0. , -0. , -32.354]] + ), + 'total': array([[ 49.679, 4.542, 0. ], + [ 6.56 , 80.124, 0. ], + [ 0. , -0. , 212.538]] + ) + } + # ... + } + +nmrcouplingtensors +------------------ + +A dictionary of spin-spin coupling tensors. The keys of ``nmrcouplingtensors`` are each a pair of atomic indices, indicating the atoms between which the coupling is taking place, and the values are themselves dictionaries containing pairs of atomic isotopes as keys, where the ordering of the isotopes matches that of the atomic indices. The values of the isotope dictionaries are a third layer of dictionaries, where the keys represent different contributions to the coupling tensor, and the values are the tensors themselves as a 3-by-3 NumPy array. The available tensor types depends on what is available in the calculation, but may include ``fermi``, ``spin-dipolar-fermi``, ``diamagnetic``, ``paramagnetic``, and ``spin-dipolar``. The ``total`` spin tensor is always available. Additionally, the ``isotropic`` key contains the total isotropic coupling value for the atom pair. All values are in Hz, and include the atomic g-factors (the J matrix). + +.. code-block:: python + + { + # Atomic pair. + (1,0): { + # Istopes, here two C13 atoms. + (13,13): { + 'diamagnetic': array([[ 0.4902, -0.1273, -0. ], + [-0.1273, -0.2556, 0. ], + [ 0. , -0. , -0.1391]] + ), + 'fermi': array([[7.44, 0. , 0. ], + [0. , 7.44, 0. ], + [0. , 0. , 7.44]] + ), + 'isotropic': 9.485, + 'paramagnetic': array([[ 1.188 , -0.2805, 0. ], + [-0.2804, -0.5528, 0. ], + [-0. , 0. , -0.0408]] + ), + 'spin-dipolar': array([[ 0.7239, 0.0401, 0. ], + [ 0.0398, 1.1012, -0. ], + [-0. , 0. , 3.6195]] + ), + 'spin-dipolar-fermi': array([[ 1.9809, 0.0177, 0. ], + [ 0.0177, 2.2309, -0. ], + [ 0. , -0. , -4.2119]] + ), + 'total': array([[11.8229, -0.3499, 0. ], + [-0.3501, 9.9637, -0. ], + [-0. , 0. , 6.6676]] + ) + } + } + # ... + } + optdone ------- @@ -472,12 +581,12 @@ Flags whether a geometry optimisation has completed. Currently this attribute is .. code-block:: bash - $ ccget optdone data/Gaussian/basicGaussian09/dvb_gopt.out + $ ccget optdone data/Gaussian/basicGaussian09/dvb_gopt.out Attempting to parse data/Gaussian/basicGaussian09/dvb_gopt.out optdone: True - $ ccget --future optdone data/Gaussian/basicGaussian09/dvb_gopt.out + $ ccget --future optdone data/Gaussian/basicGaussian09/dvb_gopt.out Attempting to parse data/Gaussian/basicGaussian09/dvb_gopt.out optdone: [4] @@ -490,17 +599,53 @@ or by providing the corresponding argument to ``ccopen``, parser = ccopen("filename", optdone_as_list=True) # could also do future=True instead of optdone_as_list data = parser.parse() +optstatus +--------- + +A list of integers representing the status of each step in an optimisation. The possible optimisation statuses are defined in bit value notation to allow for coding for multiple states and are given by: + + * ``OPT_UNKNOWN = 0b000 = 0`` is the default and means optimisation is in progress. + * ``OPT_NEW = 0b001 = 1`` is set for every new optimisation (e.g. PES, IRCs, etc.) + * ``OPT_DONE = 0b010 = 2`` is set for the last step of an optimisation that converged. + * ``OPT_UNCONVERGED = 0b100 = 4`` is set for every unconverged step (e.g. should be mutually exclusive with ``OPT_DONE``) + +So, to robustly check if step ``i`` has converged, one should check ``data.optstatus[i] & OPT_DONE`` instead of ``data.optstatus[i] == OPT_DONE``. + +scancoords +---------- + +An array containing the geometries for each step of shape ``[number of scan steps, number of atoms, 3]``. In the case of an unrelaxed scan this is equivalent to `atomcoords`_, however this is not the case for a relaxed scan as a geometry optimization is performed at each scan step. + +scanenergies +------------ + +A list containing the energies at each point of the scan. As with `scancoords`_, ``scanenergies`` is only equivalent to ``{scf,mp,cc}energies`` in the case of an unrelaxed scan of the SCF, MP, and/or CC potential energy surface. + +scannames +--------- + +A list containing the names of each parameter scanned. + +scanparm +-------- + +A list of lists where each list contains the values scanned for each parameter in `scannames`_. + scfenergies ----------- An array containing the converged SCF energies of the calculation, in eV. For an optimisation log file, there will be as many elements in this array as there were optimisation steps. +If a dispersion correction of any form was used, it is part of the SCF energy and, in the event that it is separable, such as with D3 and similar empirical corrections, it is also available separately under `dispersionenergies`_. + +If any other corrections were present in calculating the SCF energy, in particular perturbative, empirical, or "single-shot" corrections, assume that they are *not* present in ``scfenergies``. Corrections included self-consistently, such as from implicit solvation models, should be present. Check the parsed result carefully and, when in doubt, ask on the issue tracker. + **Molpro**: typically prints output about geometry optimisation in a separate logfile. So, both that and the initial output need to be passed to the cclib parser. scftargets ---------- -Target thesholds for determining whether the current SCF run has converged, stored in a ``n x m`` array, where ``n`` is the number of geometry optimisation steps (1 for a single point calculation) and ``m`` is the number of criteria. The criteria vary between programs, and depending on the program they may be constant for the whole of a geometry optimisation or they may change between optimisation steps. A more complete description for each program follows. +Target thresholds for determining whether the current SCF run has converged, stored in a ``n x m`` array, where ``n`` is the number of geometry optimisation steps (1 for a single point calculation) and ``m`` is the number of criteria. The criteria vary between programs, and depending on the program they may be constant for the whole of a geometry optimisation or they may change between optimisation steps. A more detailed description for each program follows. **ADF**: There are two convergence criteria which are controlled by ``SCFcnv`` in the `CONVERGE subkey of the SCF block`_. @@ -515,13 +660,13 @@ For intermediate steps in a geometry optimisation the situation is more complica where ``old criteria`` is the initial value or from the previous geometry cycle, ``grdmax`` is the maximum gradient from the last geometry step and ``accint`` is the current integration accuracy. -.. _`CONVERGE subkey of the SCF block`: http://www.scm.com/Doc/Doc2014/ADF/ADFUsersGuide/page235.html#keyscheme%20INTEGRATION +.. _`CONVERGE subkey of the SCF block`: https://www.scm.com/doc/ADF/Input/SCF.html#main-options **GAMESS**: Two criteria are, the maximum and root-mean-square (RMS) density matrix change, are used with a default starting value of 5.0E-05. It seems these values can change over the course of a geometry optimisation. ROHF calculations use SQCDF instead of the standard RMS change. -**GAMESS-UK**: According to `the manual`_, convergence is determined by convergence of density matrix elements. The default value for SCF is 1E-5, but it appears to be 1E-7 for geoopts. +**GAMESS-UK**: According to `the manual `_, convergence is determined by convergence of density matrix elements. The default value for SCF is 1E-5, but it appears to be 1E-7 for geoopts. -.. _`the manual`: http://www.cfs.dl.ac.uk/docs/html/part4/node6.html +.. _`GAMESS-UK manual convergence`: https://web.archive.org/web/20190809100922/http://www.cfs.dl.ac.uk/docs/html/part4/node6.html **Gaussian**: normally three criteria are used. @@ -537,13 +682,23 @@ scfvalues The attribute ``scfvalues`` is a list of arrays of dimension ``n x m`` (one element for each step in a geometry optimisation), where ``n`` is the number of SCF cycles required for convergence and ``m`` is the number of SCF convergence target criteria. For some packages, you may need to include a directive to make sure that SCF convergence information is printed to the log file -**Gaussian**: requires the `route section`_ to start with #P +**Gaussian**: requires the `route section`_ to start with ``#P`` -.. _`route section`: http://www.gaussian.com/g_tech/g_ur/k_route.htm +.. _`route section`: https://gaussian.com/route/ **GAMESS-UK**: convergence information is printed only for the first optimisation step by default, but can be forced at all steps by adding ``IPRINT SCF`` to the input file. vibdisps -------- -The attribute ``vibdisps`` stores the Cartesian displacement vectors from the output of a vibrational frequency calculation. It is a rank 3 array having dimensions ``M x N x 3``, where ``M`` is the number of normal modes and ``N`` is the number of atoms. ``M`` is typically ``3N-6`` (``3N-5`` for linear molecules). +The attribute ``vibdisps`` stores the Cartesian displacement vectors from the output of a vibrational frequency calculation. It is a rank 3 array having dimensions ``[M, N, 3]``, where ``M`` is the number of normal modes and ``N`` is the number of atoms. ``M`` is typically ``3N-6`` (``3N-5`` for linear molecules). + +vibfconsts +---------- + +The attribute ``vibrmasses`` stores the force constants in :math:`\mathrm{Å^4/Da}` from vibrational frequency calculation. It is a rank 1 array having dimension ``M``, where ``M`` is the number of normal modes. + +vibrmasses +---------- + +The attribute ``vibrmasses`` stores the reduced masses in Daltons (Da) from vibrational frequency calculation. It is a rank 1 array having dimension ``M``, where ``M`` is the number of normal modes. diff --git a/_sources/development.rst.txt b/_sources/development.rst.txt new file mode 100644 index 00000000..7bac1ce8 --- /dev/null +++ b/_sources/development.rst.txt @@ -0,0 +1,298 @@ +=========== +Development +=========== + +Basic instructions +================== + +The default cclib files distributed with a release, as described in `How to install`_, do not include any unit tests and logfiles necessary to run those tests. This section covers how to download the full source along with all test data and scripts, and how to use these for development and testing. + +.. _`How to install`: how_to_install.html + +Cloning cclib from GitHub +~~~~~~~~~~~~~~~~~~~~~~~~~ + +cclib is hosted by the fantastic people at `GitHub`_ in a `git`_ repository. You can download a `zipped archive`_ of the current development version (called ``master``) for installation and testing or browse the available `releases`_. In order to contribute any changes, however, you will need to create a local copy of the repository: + +.. code-block:: bash + + git clone https://github.com/cclib/cclib.git + +If you would like to contribute fixes, it is more likely that you want to fork the repository (see guidelines below) and clone that. + +.. _`GitHub`: https://github.com +.. _`git`: https://git-scm.com +.. _`zipped archive`: https://github.com/cclib/cclib/archive/master.zip +.. _`releases`: https://github.com/cclib/cclib/releases + +Installation and running tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Once you have a copy of cclib, + +#. Create a virtual environment using a either `venv`_ or `conda`_ then activate it +#. Install cclib in development mode with all dependencies: ``cd /location/of/cclib; python -m pip install -e '.[dev]'`` +#. To run unit tests, ``python -m pytest`` +#. To run regression tests, ``python -m pytest test/regression.py`` (requires `cclib-data download`_) + +You may not be interested in running all tests because they take too much time (some calculation methods), require a dependency not immediately available (primarily Psi4), or simply aren't relevant for the code you'll touch. Call `pytest`_ with the ``-k`` flag to select a subset of tests. Using the ``--co`` flag will show the names of matching tests without actually running them. + +.. _`venv`: https://docs.python.org/3/library/venv.html +.. _`conda`: https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html#creating-environments +.. _`cclib-data download`: https://github.com/cclib/cclib/blob/07590622dbd571c31f8b874697ce024908345d9a/data/regression_download.sh +.. _`pytest`: https://docs.pytest.org/en/latest/how-to/usage.html + +Guidelines +~~~~~~~~~~ + +We follow a typical GitHub collaborative model, relying on `forks and pull requests`_. In short, the development process consists of: + +* `Creating your own fork`_ of cclib in order to develop +* `Creating a pull request`_ to contribute your changes +* Reviewing and merging open pull requests (PRs) into the main branch +* Using `issues`_ to plan and prioritize future work + +.. _`forks and pull requests`: https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests +.. _`creating your own fork`: https://docs.github.com/en/get-started/quickstart/fork-a-repo +.. _`creating a pull request`: https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request +.. _`issues`: https://github.com/cclib/cclib/issues + +Here are some general guidelines for developers who are contributing code: + +* All contributions should be reviewed by at least one core developer +* Contributions from a core developer need to be reviewed by another core developer +* Run and review the unit tests (see below) before submitting a pull request. +* There should normally not be more failed tests than before your changes. +* For larger changes or features that take some time to implement, `using branches`_ is recommended. + +.. _`using branches`: https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches + +Releasing a new version +~~~~~~~~~~~~~~~~~~~~~~~ + +The release cycle of cclib is irregular, with new versions being created as deemed necessary after significant changes or new features. We roughly follow semantic versioning with respect to the `parsed attributes`_. + +When creating a new release on GitHub, start by creating a new issue based on the following template that provides a high-level overview of the steps to take. + +.. code-block:: md + + This is to track the work to be done for release v1.8.1: + + - [ ] Migrate non-urgent issues/PRs to the 2.0 label ([2.0 list](https://github.com/cclib/cclib/issues?q=is%3Aopen+is%3Aissue+milestone%3Av2.0)) + - [ ] Close out remaining PRs and issues ([PRs](https://github.com/cclib/cclib/pulls?q=is%3Aopen+is%3Apr+milestone%3Av1.8.1), [issues](https://github.com/cclib/cclib/issues?q=is%3Aopen+is%3Aissue+milestone%3Av1.8.1)) + - [ ] Create `release-1.8.1` branch ([branch](https://github.com/cclib/cclib/tree/release-1.8.1)) + - [ ] Bump version, update changelog, docs and other files (TODO) + - [ ] Create a v1.8.1 tag for the release + - [ ] Update release tag to HEAD on release branch + - [ ] Create a draft release from the v1.8.1 tag + - [ ] Attach source tar and zip archives to release on GitHub + - [ ] When ready, publish the draft release (https://github.com/cclib/cclib/releases/tag/v1.8.1) + - [ ] Upload new version to PyPI (https://pypi.org/project/cclib/1.8.1/) + - [ ] Make sure conda picks up the change (https://github.com/conda-forge/cclib-feedstock/pull/TODO) + - [ ] Update Zenodo if a major or minor version (https://zenodo.org/record/TODO) + - [ ] Make sure Zenodo parts of documentation get updated (https://github.com/cclib/cclib/pull/TODO) + - [ ] Merge the `release-1.8.1` branch back into master (https://github.com/cclib/cclib/pull/TODO) + - [ ] Send email to MLs + +An example of a past finished release is `1.8`_. + +* Update the `CHANGELOG`_, `ANNOUNCE`_ and any other files that might change content with the new version +* Make sure that `setup.py`_ has the right version number, as well as __version__ in `__init__.py`_ and any other relevant files +* Update the download and install instructions in the documentation, if appropriate +* Create a branch for the release, so that development can continue +* Run all tests for a final time and fix any remaining issues +* Tag the release (make sure to use an annotated tag using ``git -a``) and upload it (``git push --tags``) +* Run `manifest.py`_ to update the MANIFEST file +* Create the source distributions (``python setup.py sdist --formats=gztar,zip``) and Windows binary installers (``python setup.py bdist_wininst``) +* Create a release on GitHub using the created tag (see `Creating releases`_) and upload the source distributions and Windows binaries +* Email the users and developers mailing list with the message in `ANNOUNCE`_ +* Update the `Python package index`_, normally done by ``python setup.py register`` +* For significant releases, if appropriate, send an email to the `CCL list`_ and any mailing lists for computational chemistry packages supported by cclib + +.. _`parsed attributes`: data.html + +.. _`1.8`: https://github.com/cclib/cclib/issues/1249 + +.. _`ANNOUNCE`: https://github.com/cclib/cclib/blob/master/ANNOUNCE +.. _`Python package index`: https://pypi.org/project/cclib/ +.. _`CHANGELOG`: https://github.com/cclib/cclib/blob/master/CHANGELOG +.. _`setup.py`: https://github.com/cclib/cclib/blob/master/setup.py +.. _`__init__.py`: https://github.com/cclib/cclib/blob/master/cclib/__init__.py +.. _`manifest.py`: https://github.com/cclib/cclib/blob/master/manifest.py + +.. _`Creating releases`: https://docs.github.com/en/github/administering-a-repository/releasing-projects-on-github/managing-releases-in-a-repository + +.. _`CCL list`: http://www.ccl.net + +Testing +======= + +.. index:: + single: testing; unit tests + +The `test directory`_, which is not included in the default download, contains the test scripts that keep cclib reliable, and keep the developers sane. With any new commit or pull request to cclib on GitHub the tests are triggered and run with `GitHub Actions`_. + +The input files for tests, which are logfiles from computational chemistry programs, are located in the `data directory`_. These are a central part of cclib, and any progress should always be supported by corresponding tests. When a user opens an issue or reports a bug, it is prudent to write a test that reproduces the bug as well as fixing it. This ensures it will remain fixed in the future. Likewise, extending the coverage of data attributes to more programs should proceed in parallel with the growth of unit tests. + +.. _`GitHub Actions`: https://github.com/cclib/cclib/actions + +.. _`data directory`: https://github.com/cclib/cclib/tree/master/data +.. _`test directory`: https://github.com/cclib/cclib/tree/master/test + +.. index:: + single: testing; unit tests + +Unit tests +~~~~~~~~~~ + +Unit tests check that the parsers work correctly for typical calculation types on small molecules, usually water or 1,4-divinylbenzene (dvb) with :math:`C_{\mathrm{2h}}` symmetry. The corresponding logfiles stored in folders like ``data/NWChem/basicNWChem6.0`` are intended to test logfiles for an approximate major version of a program, and are standardized for all supported programs to the extent possible. They are located alongside the code in the repository, but are not normally distributed with the source. Attributes are considered supported only if they are checked by at least one test, and the `table of attribute coverage`_ is generated automatically using this criterion. + +The job types currently included as unit tests: + +* restricted and unrestricted single point energies for dvb (RHF/STO-3G **and** B3LYP/STO-3G) +* geometry optimization and scan for dvb (RHF/STO-3G and/or B3LYP/STO-3G) +* frequency calculation with IR intensities and Raman activities for dvb (RHF/STO-3G or B3LYP/STO-3G) +* single point energy for carbon atom using a large basis set such as aug-cc-pCVQZ +* Møller–Plesset and coupled cluster energies for water (STO-3G basis set) +* static polarizabilities for tryptophan (RHF/STO-3G) + +In addition to the above unit tests for data, there are also unit tests for each bridge, calculation method, IO format, and helper utilities, all located inside the `tests `_ directory, with each category receiving its own subdirectory. + +.. _`table of attribute coverage`: data_dev.html#details-of-current-implementation + +Adding a new attribute +^^^^^^^^^^^^^^^^^^^^^^ + +Definitions of attributes (``mocoeffs``, ``natom``, etc.) are located inside the `ccdata `_ class. Use existing attributes for guidance. + +#. Add a line containing the attribute name, a short description of the attribute, the type and shape (if not a scalar quantity) of the attribute, and relevant units to the docstring. +#. Add an `entry `_ for the code representation of an attribute. +#. Some attributes require additional processing into certain container or data types; `available processing rules and their descriptions `_ are below the attribute entries. + +Without these modifications, saving the parsed attribute will appear to work inside the parser, but will be filtered out by ``ccData.setattributes`` before the ``ccData`` instance is returned. (This also means that arbitrary attributes can be set on and used from ``self`` inside a parser and they will be automatically cleaned up.) + +Once the above is complete, and the new attribute is parsed and saved inside at least one parser, a new unit test should be added. + +Adding a new unit test +^^^^^^^^^^^^^^^^^^^^^^ + +Navigate to the relevant subdirectory of the ``tests`` directory. All filenames containing unit tests must start with ``test``. Generally, each file containing an implementation in the cclib source has a matching test file. The exception is parsers, for which there are some program-specific tests, but most relevant are the ``data`` tests that are grouped by attribute. + +Examples of how unit tests are written are those for `population methods `_ or the `MOLDEN writer `_. + +* A class whose name ends in ``Test`` is used to hold test methods. Many test files only contain a single test class, but others contain multiple, usually specialized for a specific program or method. An example is having a basic ``PopulationTest`` but more specific ``GaussianBickelhauptTest`` and ``GaussianMPA`` classes for checking the results specific to Bickelhaupt and Mulliken population analyses. +* Each method in a test class is meant for testing a single logical piece of functionality. Common checks are for whether or not the dimensions of calculated quantities are consistent and for certain chemical or physical invariants to hold, such as the total charge from a population analysis summing to the total formal charge of a system. + +Adding a unit test for a new attribute or new methods on an existing data unit test class requires all of the above with the addition of: + +* An entry in the `testdata`_ file that matches the output for a program at a specific version with the test class the output should be used with. An output may be used with multiple tests and a test may be used for many different outputs: there are no restrictions. +* Each method should, after ``self``, take an argument called ``data`` that corresponds to a parsed ``ccData`` instance. + + * ``data`` is a pytest fixture; other test classes may have their own local fixtures defined. All cclib-specific but general fixtures are located in the `pytest runtime configuration`_. + +.. _`testdata`: https://github.com/cclib/cclib/blob/master/test/testdata +.. _`pytest runtime configuration`: https://github.com/cclib/cclib/blob/master/test/conftest.py + +Adding a new program version +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +There are a few conventions when adding a new supported program version to the unit tests: + +* Two different recent versions are typically used in the unit tests. If there already are two, move the older version(s) the regression suite (see below). +* When adding files for the new version: + + #. Make a commit that copies the corresponding files from the last version already in cclib to the new directory. + #. Make a commit that replaces these files with those for the actual new version. This procedure makes it easy to look at the differences introduced with the new version in git clients. + #. See https://github.com/cclib/cclib/pull/575/commits for an example. + +.. index:: + single: testing; regressions + +Regression tests +~~~~~~~~~~~~~~~~ + +Regression tests ensure that bugs, once fixed, stay fixed. These are real-life files that at some point broke a cclib parser and are stored in folders like ``data/regression/Jaguar/Jaguar6.4``. The files associated with regression tests are not stored together with the source code as they are often quite large. A separate repository on GitHub, `cclib-data`_, is used to track these files, and we do not distribute them with any releases. + +For every bug found in the parsers, there should be a corresponding regression test that tests if this bug stays fixed. The process is automated by `regression.py`_, which runs through all of our test data, both the basic data and regression files, opens them, tries to parse, and runs any relevant regression tests defined for that file. + +Using both the unit and regression tests, the line-by-line `test coverage`_ shows which parts of cclib are touched by at least one test. When adding new features and tests, the GitHub Actions `testing script`_ can be run locally to generate the HTML coverage pages and ensure that the tests exercise the feature code. + +.. _`cclib-data`: https://github.com/cclib/cclib-data +.. _`regression.py`: https://github.com/cclib/cclib/blob/master/test/regression.py + +.. _`test coverage`: coverage/index.html +.. _`testing script`: https://github.com/cclib/cclib/blob/master/.github/scripts/run_pytest.bash + +Adding a new regression test +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +A regression test consists of one or more output files and optionally a test function and/or multiple test classes. + +New regression tests are added by creating entries in `regressionfiles.yaml`_. There are three kinds of tests: + +* A regression may be parsed, but specific attributes on the regression are not checked: no test function or class is added. +* A regression may be parsed and also explicitly tested. +* A regression may be explicitly tested but not parsed (this is uncommon). + +More details, such as where to place regression data, how to control parsing, and what to name the optional tests are available in the `pytest config `_ and at the top of `regressionfiles.yaml`_. + +.. _`regressionfiles.yaml`: https://github.com/cclib/cclib-data/blob/master/regressionfiles.yaml + +Code conventions +================ + +* All aspects of code formatting are handled automatically by a combination of `isort `_ and `ruff `_. Formatting is enforced by running `pre-commit `_ on all PRs. We encourage contributors to also run pre-commit locally. + * Non-functional changes to code are ideally in separate PRs. This makes PRs quicker to review and merge. +* Print output is controlled via Python's standard logging library and levels. Any output that might be presentable to the user, from detecting that there may have been a problem with the calculation to general debug-type printing, should use the logger with an appropriate log level. Be generous with logging rather than erring on the side of caution. See `this issue `_ for historical information. +* Setting parsed attributes inside a parser's ``extract`` method is fundamentally identical to setting attributes on a basic Python object (``self.myattr = thing``). + +Documentation +~~~~~~~~~~~~~ + +All new functions should contain a docstring in `NumPy style `_. A docstring should focus on the user-facing interaction and purpose of a function rather than any implementation details. Additional code comments may also be necessary; `here `_ are some general guidelines for writing code comments. + +Larger features, such as adding a new parser, method, or bridge, may also warrant additional high-level documentation in these pages. Please reach out to us about this if you have questions, or we may ask for some as part of discussion on an issue or PR. + +Websites related to cclib +========================= + +* The official `cclib organization on github`_ +* The `cclib page for GitHub Actions`_ +* The `cclib entry on PyPI`_ +* The `cclib entry on libraries.io`_ +* The `cclib entry on Open Hub`_ + +.. _`cclib organization on github`: https://github.com/cclib +.. _`cclib page for GitHub Actions`: https://github.com/cclib/cclib/actions +.. _`cclib entry on PyPI`: https://pypi.org/project/cclib/ +.. _`cclib entry on libraries.io`: https://libraries.io/pypi/cclib +.. _`cclib entry on Open Hub`: https://www.openhub.net/p/cclib + +Developers +========== + +Besides input from a number of people `listed in the repository`_, the following are core developers (in alphabetical order): + +* `Eric Berquist`_ +* `Minsik Cho`_ +* `Amanda Dumi`_ +* `Geoff Hutchison`_ +* `Karol M. Langner`_ +* `Oliver Lee`_ +* `Noel O'Boyle`_ (retired) +* `Felipe S. S. Schneider`_ +* `Adam Tenderholt`_ (retired) +* `Shiv Upadhyay`_ + +.. _`listed in the repository`: https://github.com/cclib/cclib/blob/master/THANKS + +.. _`Eric Berquist`: https://github.com/berquist +.. _`Minsik Cho`: https://github.com/mscho527 +.. _`Amanda Dumi`: https://github.com/amandadumi +.. _`Geoff Hutchison`: https://github.com/ghutchis +.. _`Karol M. Langner`: https://github.com/langner +.. _`Oliver Lee`: https://github.com/oliver-s-lee +.. _`Noel O'Boyle`: https://github.com/baoilleach +.. _`Felipe S. S. Schneider`: https://github.com/schneiderfelipe +.. _`Adam Tenderholt`: https://github.com/ATenderholt +.. _`Shiv Upadhyay`: https://github.com/shivupa diff --git a/_sources/development.txt b/_sources/development.txt deleted file mode 100644 index 5297b3f0..00000000 --- a/_sources/development.txt +++ /dev/null @@ -1,190 +0,0 @@ -=========== -Development -=========== - -Basic instructions -=========================== - -The default cclib files distributed with a release, as described in `How to install`_, do not include any unit tests and logfiles necessary to run those tests. This section covers how to download the full source along with all test data and scripts, and how to use these for development and testing. - -.. _`How to install`: how_to_install.html - -Cloning cclib from GitHub -~~~~~~~~~~~~~~~~~~~~~~~~~ - -cclib is hosted by the fantastic people at `GitHub`_ (previously at `Sourceforge`_) in a `git`_ repository. You can download a `zipped archive`_ of the current development version (called `master`) for installation and testing or browse the available `releases`_. In order to contribute any changes, however, you will need to create a local copy of the repository: - -.. code-block:: bash - - git clone https://github.com/cclib/cclib.git cclib - -.. _`GitHub`: https://github.com -.. _`Sourceforge`: https://sourceforge.net -.. _`git`: http://git-scm.com -.. _`zipped archive`: https://github.com/cclib/cclib/archive/master.zip -.. _`releases`: https://github.com/cclib/cclib/releases - -Guidelines -~~~~~~~~~~~~~~~~ - -We follow a typical GitHub collaborative model, relying on `forks and pull requests`_. In short, the development process consists of: - -* `Creating your own fork`_ of cclib in order to develop -* `Creating a pull request`_ to contribute your changes -* Reviewing and merging open pull requests (by someone else) -* Using `issues`_ to plan and prioritize future work - -.. _`creating your own fork`: https://help.github.com/articles/fork-a-repo -.. _`creating a pull request`: https://help.github.com/articles/creating-a-pull-request -.. _`forks and pull requests`: https://help.github.com/articles/using-pull-requests -.. _`issues`: https://github.com/cclib/cclib/issues - -Here are some general guidelines for developers who are contributing code: - -* Run and review the unit tests (see below) before submitting a pull request -* There should normally not be more failed tests than before your changes -* For larger changes or features that take some time to implement, `using branches`_ is recommended - -.. _`using branches`: https://help.github.com/articles/branching-out - -Releasing a new version -~~~~~~~~~~~~~~~~~~~~~~~ - -The release cycle of cclib is irregular, with new versions being created as deemed necessary after significant changes or new features. We roughly follow semantic versioning with respect to the `parsed attributes`_. - -When creating a new release on GitHub, the typical procedure might include the following steps: - -* Update the `CHANGELOG`_, `ANNOUNCE`_ and any other files that might change content with the new version -* Make sure that `setup.py`_ has the right version number, as well as __version__ in `__init__.py`_ and any other relevant files -* Update the download and install instructions in the documentation, if appropriate -* Create a branch for the release, so that development can continue -* Run all tests for a final time and fix any remaining issues -* Tag the release (make sure to use an annotated tag using ``git -a``) and upload it (``git push --tags``) -* Run `manifest.py`_ to update the MANIFEST file -* Create the source distributions (``python setup.py sdist --formats=gztar,zip``) and Windows binary installers (``python setup.py bdist_wininst``) -* Create a release on Github using the created tag (see `Creating releases`_) and upload the source distribiuions and Windows binaries -* Email the users and developers mailing list with the message in `ANNOUNCE`_ -* Update the Python package index (https://pypi.python.org/pypi/cclib), normally done by ``python setup.py register`` -* For significant releases, if appropriate, send an email to the `CCL list`_ and any mailing lists for computational chemistry packages supported by cclib - -.. _`parsed attributes`: data.html - -.. _`ANNOUNCE`: https://github.com/cclib/cclib/blob/master/ANNOUNCE -.. _`CHANGELOG`: https://github.com/cclib/cclib/blob/master/CHANGELOG -.. _`setup.py`: https://github.com/cclib/cclib/blob/master/setup.py -.. _`__init__.py`: https://github.com/cclib/cclib/blob/master/src/cclib/__init__.py -.. _`manifest.py`: https://github.com/cclib/cclib/blob/master/manifest.py - -.. _`Creating releases`: https://help.github.com/articles/creating-releases - -.. _`CCL list`: http://www.ccl.net - -Testing -======= - -.. index:: - single: testing; unit tests - -The `test directory`_, which is not included in the default download, contains the test scripts that keep cclib reliable, and keep the developers sane. With any new commit or pull request to cclib on GitHub the tests are triggered and run with `Travis CI`_, for both the current production version |release| (|travis_prod|) as well as master (|travis_master|). - -The input files for tests, which are logfiles from computational chemistry programs, are located in the `data directory`_. These are a central part of cclib, and any progress should always be supported by corresponding tests. When a user opens an issue or reports a bug, it is prudent to write a test that reproduces the bug as well as fixing it. This ensures it will remain fixed in the future. Likewise, extending the coverage of data attributes to more programs should proceed in parallel with the growth of unit tests. - -.. _`Travis CI`: https://travis-ci.org/cclib/cclib - -.. |travis_prod| image:: https://travis-ci.org/cclib/cclib.svg?branch=v1.4 -.. |travis_master| image:: https://travis-ci.org/cclib/cclib.svg?branch=master - -.. _`data directory`: https://github.com/cclib/cclib/tree/master/test -.. _`test directory`: https://github.com/cclib/cclib/tree/master/test - -.. index:: - single: testing; unit tests - -Unit tests -~~~~~~~~~~ - -Unit tests check that the parsers work correctly for typical calculation types on small molecules, usually water or 1,4-divinylbenzene (dvb) with C2h symmetry. The corresponding logfiles stored in folders like ``data/NWChem/basicNWChem6.0`` are intended to test logfiles for an approximate major version of a program, and are standardized for all supported programs to the extent possible. They are located alongside the code in the repository, but are not normally distributed with the source. Two different recent versions are often used in the unit tests, with older versions being moved to the regression suite (see below). Attributes are considered supported only if they are checked by at least one test, and the `table of attribute coverage`_ is generated automatically using this criterion. - -The job types currently included as unit tests: - -* restricted and unrestricted single point energies for dvb (RHF/STO-3G **and** B3LYP/STO-3G) -* geometry optimization and scan for dvb (RHF/STO-3G and/or B3LYP/STO-3G) -* frequency calculation with IR and Raman intensities for dvb (RHF/STO-3G or B3LYP/STO-3G) -* single point energy for carbon atom using a large basis set such as aug-cc-pCVQZ -* Møller–Plesset and coupled cluster energies for water (STO-3G or 6-31G basis set) - -.. _`table of attribute coverage`: data_dev.html#details-of-current-implementation - -.. index:: - single: testing; regressions - -Regression tests -~~~~~~~~~~~~~~~~ - -Regression tests ensure that bugs, once fixed, stay fixed. These are real-life files that at some point broke a cclib parser, and are stored in folders like ``data/regression/Jaguar/Jaguar6.4``. The files associated with regression tests are not stored stored together with the source code as they are often quite large. A separate repository on github, `cclib-data`_, is used to track these files, and we do not distribute them with any releases. - -For every bug found in the parsers, there should be a corresponding regression test that tests this bug stays fixed. The process is automated by `run_regressions.py`_, which runs through all of our test data, both the basic data and regression files, opens them, tries to parse, and runs any relevant regression tests defined for that file. New regression tests are added by creating a function ``testMyFileName_out`` according to the examples at the start of `run_regressions.py`_. - -.. _`cclib-data`: https://github.com/cclib/cclib-data -.. _`run_regressions.py`: https://github.com/cclib/cclib/blob/master/test/run_regressions.py - -Doctests -~~~~~~~~~ - -Doctests are a useful Python feature for unit testing individual functions. To run the doctests in a particular file, you need to run the script. For example, ``python gaussianparser.py`` runs the doctests contained in `gaussianparser.py`_. To run all of the doctests at once, you need to install a testing tool such as `nose`_, and then use the following command (note that many errors may be due to missing libraries like `biopython`_): - -.. code-block:: bash - - $ nose cclib --with-doctest -e test* -v - ERROR - ERROR - Doctest: cclib.bridge.cclib2openbabel.makeopenbabel ... ok - ERROR - ERROR - Doctest: cclib.parser.adfparser.ADF.normalisesym ... ok - Doctest: cclib.parser.gamessparser.GAMESS.normalise_aonames ... ok - Doctest: cclib.parser.gamessparser.GAMESS.normalisesym ... ok - Doctest: cclib.parser.gamessukparser.GAMESSUK.normalisesym ... ok - Doctest: cclib.parser.gaussianparser.Gaussian.normalisesym ... ok - Doctest: cclib.parser.jaguarparser.Jaguar.normalisesym ... ok - Doctest: cclib.parser.logfileparser.Logfile.float ... ok - Doctest: cclib.parser.utils.PeriodicTable ... ok - Doctest: cclib.parser.utils.convertor ... ok - ERROR - ERROR - ...... - -.. _`gaussianparser.py`: https://github.com/cclib/cclib/blob/master/src/cclib/parser/gaussianparser.py -.. _`nose`: https://nose.readthedocs.org/en/latest/ -.. _`biopython`: http://biopython.org/wiki/Main_Page - -Websites related to cclib -========================= - -* The official `cclib organization on github`_ -* The `cclib project page on Sourceforge`_ (inactive now) -* The `cclib page for Travis CI`_ -* The `cclib entry on PyPI`_ -* The `cclib entry on Ohloh`_ - -.. _`cclib organization on github`: https://github.com/cclib -.. _`cclib project page on Sourceforge`: http://sourceforge.net/projects/cclib/ -.. _`cclib entry on PyPI`: http://www.python.org/pypi/cclib -.. _`cclib page for Travis CI`: https://travis-ci.org/cclib/cclib -.. _`cclib entry on Ohloh`: https://www.ohloh.net/p/cclib - -Developers -========== - -Besides input from a number of people `listed in the repository`_, the following developers have contributed code to cclib (in alphabetical order): - -* Eric Berquist -* `Karol M. Langner`_ -* `Noel O'Boyle`_ -* Christopher Rowley -* Adam Tenderholt - -.. _`listed in the repository`: https://github.com/cclib/cclib/blob/master/THANKS - -.. _`Karol M. Langner`: https://github.com/langner -.. _`Noel O'Boyle`: http://www.redbrick.dcu.ie/~noel diff --git a/_sources/how_to_install.rst.txt b/_sources/how_to_install.rst.txt new file mode 100644 index 00000000..df9e304f --- /dev/null +++ b/_sources/how_to_install.rst.txt @@ -0,0 +1,134 @@ +How to install +============== + +This page describes how to download, install and use the basic functionality of cclib. + +Requirements +------------ + +Before you install cclib, you need to make sure that you have the following: + * Python (at least version 3.7 is recommended) + * NumPy (at least version 1.15 is recommended) + +Python is an open-source programming language available from https://www.python.org. It is available for Windows as well as being included in most Linux distributions. In Debian/Ubuntu it is installed as follows (as root): + +.. code-block:: bash + + apt-get install python python-dev + +NumPy (Numerical Python) adds a fast array facility and linear algebra routines to Python. It is available from https://numpy.org/. Windows users should use the most recent NumPy installation for the Python version they have (e.g. numpy-1.0.3.1.win32-py2.4.exe for Python 2.4). Linux users are recommended to find a binary package for their distribution rather than compiling it themselves. In Debian/Ubuntu it is installed as follows (as root): + +.. code-block:: bash + + apt-get install python-numpy + +To test whether Python is on the ``PATH``, open a command prompt window and type: + +.. code-block:: bash + + python + +If Python is not on the ``PATH`` and you use Windows, add the full path to the directory containing it to the end of the ``PATH`` variable under Control Panel/System/Advanced Settings/Environment Variables. If you use Linux and Python is not on the ``PATH``, put/edit the appropriate line in your .bashrc or similar startup file. + +To test that NumPy is working, try importing it at the Python prompt. You should see something similar to the following:: + + $ python + Python 3.7.0 (default, Jul 15 2018, 10:44:58) + [GCC 8.1.1 20180531] on linux + Type "help", "copyright", "credits" or "license" for more information. + >>> import numpy as np + >>> np.__version__ + '1.15.0' + >>> + +(To exit, press CTRL+D in Linux or CTRL+Z,Enter in Windows) + +Installing using pip +-------------------- + +pip_ is a command-line tool that often comes pre-packaged with Python distributions which can download packages from the `Python Package Index`_ (PyPI). To see if it's installed, on Linux or macOS try:: + + $ which pip + +and on Windows:: + + cmd> where.exe pip + +The version of `cclib uploaded to PyPI`_ can then be installed globally using:: + + python -m pip install cclib + +or to your home directory using:: + + python -m pip install --user cclib + +.. _pip: https://pip.pypa.io/en/stable/ +.. _`Python Package Index`: https://pypi.org/ +.. _`cclib uploaded to PyPI`: https://pypi.org/project/cclib/ + +Installing using a system package manager +----------------------------------------- + +If you're using `Debian GNU/Linux`_, `Ubuntu`_, or a similar distribution, there are official `cclib packages`_ that you can install via your package manager: + +.. code-block:: bash + + apt install cclib + +There are in fact multiple packages, `python3-cclib`_ containing the Python module, and `cclib`_ which installs the user scripts and depends on the Python module. If you also need to also install the unittests and logfiles we distribute, you will need to install the `cclib-data`_ package from the non-free repositories (due to license issues). Because of distribution release cycles, package manager versions of cclib may be out of date compared to the PyPI version. + +.. _`Debian GNU/Linux`: https://www.debian.org +.. _`Ubuntu`: https://ubuntu.com/ +.. _`cclib packages`: https://packages.debian.org/search?searchon=sourcenames&keywords=cclib +.. _`python3-cclib`: https://packages.debian.org/bookworm/python3-cclib +.. _`cclib`: https://packages.debian.org/bookworm/cclib +.. _`cclib-data`: https://packages.debian.org/bookworm/cclib-data + +Manual download and install +--------------------------- + +The source code of the newest release of cclib (version |release|) is distributed as: + +* A .zip file: https://github.com/cclib/cclib/releases/download/v1.8.1/cclib-1.8.1.zip +* A .tar.gz file: https://github.com/cclib/cclib/releases/download/v1.8.1/cclib-1.8.1.tar.gz +* Windows binary installers (see the `newest release page`_) + +On Windows, if you choose to download the .exe files instead, you can install simply by double-clicking on the file. To uninstall, use the "Add and Remove Programs" menu in the Control Panel. + +None of these files include the tests and logfiles used for testing. In order to download all tests, we also provide source archives on the `newest release page`_. + +If you are using the .zip or .tar.gz files, extract the contents of the file at an appropriate location, which we will call INSTALLDIR. Open a command prompt and change directory to INSTALLDIR. Next, run the following commands to install cclib: + +.. code-block:: bash + + python setup.py build + python setup.py install # (as root) + +or, if pip_ is available:: + + python -m pip install . + +To test, trying importing '''cclib''' at the Python prompt. You should see something similar to the following:: + + $ python + Python 3.7.0 (default, Jul 15 2018, 10:44:58) + [GCC 8.1.1 20180531] on linux + Type "help", "copyright", "credits" or "license" for more information. + >>> import cclib + >>> cclib.__version__ + '1.6.2' + >>> + +.. _`newest release page`: https://github.com/cclib/cclib/releases/tag/v1.8.1 + +What next? +---------- + + * Read the list and specifications of the `parsed data`_ and related `data notes`_ + * Test the program using the test data files included in the full source distribution + * Run the unit and regression tests in the test directory (``testall.py`` and ``regression.py``) + * Send any questions to the cclib-users mailing list at https://groups.google.com/g/cclib. + * Write some computational chemistry algorithms using information parsed from cclib and donate the code to the project + +.. _`parsed data`: data.html +.. _`data notes`: data_notes.html diff --git a/_sources/how_to_install.txt b/_sources/how_to_install.txt deleted file mode 100644 index 90106825..00000000 --- a/_sources/how_to_install.txt +++ /dev/null @@ -1,110 +0,0 @@ -How to install -============== - -This page describes how to download, install and use the basic functionality of cclib. - -Requirements ------------- - -Before you install cclib, you need to make sure that you have the following: - * Python (at least version 3.0 is recommended, although 2.7 is still tested) - * NumPy (at least version 1.5 is recommended) - -Python is an open-source programming language available from http://www.python.org. It is available for Windows as well as being included in most Linux distributions. In Debian/Ubuntu it is installed as follows (as root): - -.. code-block:: bash - - apt-get install python python-dev - -NumPy (Numerical Python) adds a fast array facility and linear algebra routines to Python. It is available from http://www.numpy.org. Windows users should use the most recent NumPy installation for the Python version they have (e.g. numpy-1.0.3.1.win32-py2.4.exe for Python 2.4). Linux users are recommended to find a binary package for their distribution rather than compiling it themselves. In Debian/Ubuntu it is installed as follows (as root): - -.. code-block:: bash - - apt-get install python-numpy - -To test whether Python is on the PATH, open a command prompt window and type: - -.. code-block:: bash - - python - -If Python is not on the PATH and you use Windows, add the full path to the directory containing it to the end of the PATH variable under Control Panel/System/Advanced Settings/Environment Variables. If you use Linux and Python is not on the PATH, put/edit the appropriate line in your .bashrc or similar startup file. - -To test that Numpy is working, try importing it at the Python prompt. You should see something similar to the following: - -.. code-block:: bash - - $ python3 - Python 3.2.3 (default, Feb 27 2014, 21:31:18) - [GCC 4.6.3] on linux2 - Type "help", "copyright", "credits" or "license" for more information. - >>> import numpy - >>> numpy.__version__ - '1.6.1' - >>> - -(To exit, press CTRL+D in Linux or CTRL+Z,Enter in Windows) - -Debian GNU/Linux systems ------------------------- - -If you're using `Debian GNU/Linux`_, `Ubuntu`_ or a similar distribution, there are official `cclib packages`_ that you can install in any package manager (should as synaptic) or with one simple command: - -.. code-block:: bash - - aptitude install cclib - -There are in fact two packages, `python-cclib`_ containing the Python module, and `cclib`_ which installs just the user scripts. If you also need to also install the unittests and logfiles we distribute, you will need to install the `cclib-data`_ package from the non-free repositories (due to license issues). - -.. _`Debian GNU/Linux`: http://www.debian.org -.. _`Ubuntu`: http://www.ubuntu.com -.. _`cclib packages`: http://packages.debian.org/src:cclib -.. _`python-cclib`: http://packages.debian.org/wheezy/python-cclib -.. _`cclib`: http://packages.debian.org/wheezy/cclib -.. _`cclib-data`: http://packages.debian.org/wheezy/cclib-data - -Manual download and install ---------------------------- - -The source code of the newest release of cclib (version 1.5) is distributed as: - * A .zip file: https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.zip - * A .tar.gz file: https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz - * Windows binary installers (see the `newest release page`_) - -On Windows, if you choose to download the .exe files instead, you can install simply by doubleclicking on the file. To uninstall, use the "Add and Remove Programs" menu in the Control Panel. - -None of these files include the tests and logfiles used for testing. In order to download all tests, we also provide source archives on the `newest release page`_. - -If you are using the .zip or .tar.gz files, extract the contents of the file at an appropriate location, which we will call INSTALLDIR. Open a command prompt and change directory to INSTALLDIR. Next, run the following commands to install cclib: - -.. code-block:: bash - - python setup.py build - python setup.py install # (as root) - -To test, trying importing '''cclib''' at the Python prompt. You should see something similar to the following: - -.. code-block:: python - - $ python3 - Python 3.2.3 (default, Feb 27 2014, 21:31:18) - [GCC 4.6.3] on linux2 - Type "help", "copyright", "credits" or "license" for more information. - >>> import cclib - >>> cclib.__version__ - '1.1' - >>> - -.. _`newest release page`: https://github.com/cclib/cclib/releases/tag/v1.5 - -What next? ----------- - - * Read the list and specifications of the `parsed data`_ and related `data notes`_ - * Test the program using the test data files included in the full source distribution - * Run the unit and regression tests in the test directory (``testall.py`` and ``run_regressions.py``) - * Send any questions to the cclib-users mailing list at https://lists.sourceforge.net/lists/listinfo/cclib-users. - * Write some computational chemistry algorithms using information parsed from cclib and donate the code to the project - -.. _`parsed data`: data.html -.. _`data notes`: data_notes.html diff --git a/sphinx/how_to_parse.rst b/_sources/how_to_parse.rst.txt similarity index 50% rename from sphinx/how_to_parse.rst rename to _sources/how_to_parse.rst.txt index dcd2282c..c9d72afb 100644 --- a/sphinx/how_to_parse.rst +++ b/_sources/how_to_parse.rst.txt @@ -1,134 +1,151 @@ How to parse and write ====================== -This page outlines the various ways cclib can be used to parse and write logfiles and provides several examples to get you started. +This page outlines the various ways cclib can be used to parse and write logfiles, and provides several examples to get you started. From Python -+++++++++ ++++++++++++ Importing cclib and parsing a file is a few lines of Python code, making it simple to access data from the output file of any supported computational chemistry program. For example: .. code-block:: python - import cclib - - filename = "logfile.out" - parser = cclib.parser.ccopen(filename) - data = parser.parse() - print("There are %i atoms and %i MOs" % (data.natom, data.nmo)) + >>> import cclib + + >>> filename = "water.out" + >>> parser = cclib.io.ccopen(filename) + >>> data = parser.parse() + >>> print("There are %i atoms and %i MOs" % (data.natom, data.nmo)) + + There are 3 atoms and 7 MOs + +A newer command, ``ccread``, combines both the format detection and parsing steps: + +.. code-block:: python + + >>> import cclib + + >>> filename = "logfile.out" + >>> data = cclib.io.ccread(filename) + >>> print("There are %i atoms and %i MOs" % (data.natom, data.nmo)) + + There are 3 atoms and 7 MOs + +The ``data`` object above contains all the information cclib was able to to parse from the output file, available as attributes on the object: + +.. code-block:: python + + >>> dir(data) + + [(...), 'atomcoords', 'atommasses', 'atomnos', 'charge', (...), 'mult', 'natom, 'nbasis', ...] + +You can find a full list of these attribute on the `parsed data`_ page. + +.. _`parsed data`: data.html From command line +++++++++++++++++ -The cclib package provides three scripts to parse and write data i.e. ``ccget``, ``ccwrite``, and ``cda`` +The cclib package provides four scripts to parse and write data: ``ccget``, ``ccwrite``, ``cda``, and ``ccframe``. 1. **ccget** is used to parse attribute data from output files. 2. **ccwrite** has the ability to list out all valid attribute data that can be parsed from an output format. It has the added feature of writing the output file into four different formats i.e. ``json``, ``cjson``, ``cml``, ``xyz``. 3. **cda** is used for the chemical decomposition analysis of output files. +4. **ccframe** is used to write data tables from output files. -This page describes how to use the ccget and ccwrite scripts to obtain data from output files. +This page describes how to use the ccget, ccwrite and ccframe scripts to obtain data from output files. ccget ----- The data types that can be parsed from the output file depends on the type of computation being conducted. The name of the output file used to show example usage is ``Benzeneselenol.out``. -Data type can be parsed from the output file by following this format - -.. code-block:: bash +Data type can be parsed from the output file by following this format:: ccget [] [] -where attribute can be any one of the attribute names available `here`_ +where ``attribute`` can be any one of the attribute names available `here`_. .. _`here`: data_dev.html 1. Atomic Charges - The atomic charges are obtained by using the ``atomcharges`` attribute with ``ccget`` -.. code-block:: bash + The atomic charges are obtained by using the ``atomcharges`` attribute:: - $ ccget atomcharges Benzeneselenol.out - Attempting to read Benzeneselenol.out - atomcharges: - {'mulliken': array([-0.49915 , 0.056965, 0.172161, 0.349794, -0.153072, 0.094583, - 0.016487, 0.050249, 0.002149, 0.01161 , 0.053777, -0.173671, - 0.018118])} + $ ccget atomcharges Benzeneselenol.out + Attempting to read Benzeneselenol.out + atomcharges: + {'mulliken': array([-0.49915 , 0.056965, 0.172161, 0.349794, -0.153072, 0.094583, + 0.016487, 0.050249, 0.002149, 0.01161 , 0.053777, -0.173671, + 0.018118])} 2. Electronic Energies - The molecular electronic energies after SCF (DFT) optimization of the input molecule is obtained by using the ``scfenergies`` attribute with ``ccget`` -.. code-block:: bash + The molecular electronic energies after SCF (DFT) optimization of the input molecule are printed by using the ``scfenergies`` attribute:: - $ ccget scfenergies Benzeneselenol.out - Attempting to read Benzeneselenol.out - scfenergies: - [-71671.43702915 -71671.4524142 -71671.4534768 -71671.45447492 - -71671.4556548 -71671.45605671 -71671.43194906 -71671.45761021 - -71671.45850275 -71671.39630296 -71671.45915119 -71671.45935854 - -71671.4594614 -71671.45947338 -71671.45948807 -71671.4594946 - -71671.4594946 ] + $ ccget scfenergies Benzeneselenol.out + Attempting to read Benzeneselenol.out + scfenergies: + [-71671.43702915 -71671.4524142 -71671.4534768 -71671.45447492 + -71671.4556548 -71671.45605671 -71671.43194906 -71671.45761021 + -71671.45850275 -71671.39630296 -71671.45915119 -71671.45935854 + -71671.4594614 -71671.45947338 -71671.45948807 -71671.4594946 + -71671.4594946 ] 3. Geometry Targets - The targets for convergence of geometry optimization can be obtained by using the ``geotargets`` attribute with ``ccget`` -.. code-block:: bash + The targets for convergence of geometry optimization can be obtained by using the ``geotargets`` attribute:: - $ ccget geotargets Benzeneselenol.out - Attempting to read Benzeneselenol.out - geotargets: - [ 0.00045 0.0003 0.0018 0.0012 ] + $ ccget geotargets Benzeneselenol.out + Attempting to read Benzeneselenol.out + geotargets: + [ 0.00045 0.0003 0.0018 0.0012 ] -**Chaining of attributes** +Chaining of attributes +^^^^^^^^^^^^^^^^^^^^^^ ccget provides the user with the option to chain attributes to obtain more than one type of data with a command call. The attributes can be chained in any particular order. A few chained examples are provided below. 1. Molecular Orbitals and Multiplicity - The number of molecular orbitals and the number of basis functions used to optimize the molecule can be obtained by running the following command -.. code-block:: bash + The number of molecular orbitals and the number of basis functions used to optimize the molecule can be obtained by running the following command:: - $ ccget nmo nbasis Benzeneselenol.out - Attempting to read Benzeneselenol.out - nmo: - 405 - nbasis: - 407 + $ ccget nmo nbasis Benzeneselenol.out + Attempting to read Benzeneselenol.out + nmo: + 405 + nbasis: + 407 2. Enthalpy and Vibrational Frequency - The enthalpy and the vibrational frequencies of the optimized molecule is conducted is obtained below: - -.. code-block:: bash - - $ ccget enthalpy vibfreqs Benzeneselenol.out - Attempting to read Benzeneselenol.out - enthalpy: - -2633.77264 - vibfreqs: - [ 129.5512 170.6681 231.4278 304.8614 407.8299 472.5026 - 629.9087 679.9032 693.2509 746.7694 812.5113 850.2578 - 915.8742 987.1252 988.1785 1002.8922 1038.1073 1091.4005 - 1102.3417 1183.3857 1209.2727 1311.3497 1355.6441 1471.4447 - 1510.1919 1611.9088 1619.0156 2391.2487 3165.1596 3171.3909 - 3182.0753 3188.5786 3198.0359] + + The enthalpy and the vibrational frequencies of the optimized molecule is conducted is obtained below:: + + $ ccget enthalpy vibfreqs Benzeneselenol.out + Attempting to read Benzeneselenol.out + enthalpy: + -2633.77264 + vibfreqs: + [ 129.5512 170.6681 231.4278 304.8614 407.8299 472.5026 + 629.9087 679.9032 693.2509 746.7694 812.5113 850.2578 + 915.8742 987.1252 988.1785 1002.8922 1038.1073 1091.4005 + 1102.3417 1183.3857 1209.2727 1311.3497 1355.6441 1471.4447 + 1510.1919 1611.9088 1619.0156 2391.2487 3165.1596 3171.3909 + 3182.0753 3188.5786 3198.0359] ccwrite ------- The same Benzeneselenol.out file used in the previous examples will be used as the input file for ccwrite. When the ccwrite script is used with a valid input, it prints out the valid attributes that can be parsed from the file. -Command line format: - -.. code-block:: bash +Command line format:: ccwrite [] -The valid output file formats are ``json``, ``cjson``, ``cml``, ``xyz`` +The valid output file formats are ``cjson``, ``cml``, and ``xyz``. -1. CML - -.. code-block:: bash +1. `Chemical markup language`_ (CML):: $ ccwrite cml Benzeneselenol.out Attempting to parse Benzeneselenol.out @@ -159,9 +176,11 @@ The valid output file formats are ``json``, ``cjson``, ``cml``, ``xyz`` vibirs vibsyms -A *Benzeneselenol.cml* output file is generated in the same directory as the Benzeneselenol.out file. +.. _`chemical markup language`: http://www.xml-cml.org/ + +A ``Benzeneselenol.cml`` output file is generated in the same directory as the ``Benzeneselenol.out`` file: -.. code-block:: bash +.. code-block:: xml @@ -197,11 +216,9 @@ A *Benzeneselenol.cml* output file is generated in the same directory as the Ben -2. xyz +2. XYZ_ -Using ``xyz`` as the with Benzeneselenol.out, we obtain the following *Benzeneselenol.xyz* file - -.. code-block:: bash +Using ``xyz`` as the ```` with ``Benzeneselenol.out``, we obtain the following ``Benzeneselenol.xyz`` file:: 13 Benzeneselenol.out: Geometry 17 @@ -218,3 +235,22 @@ Using ``xyz`` as the with Benzeneselenol.out, we obtain the f H -2.7028960000 -2.1530750000 0.0036640000 Se 1.8210800000 -0.0433780000 -0.0038760000 H 2.0043580000 1.4100070000 0.1034490000 + +.. _XYZ: https://en.wikipedia.org/wiki/XYZ_file_format + +ccframe +------- + +This script creates complete tables of data from output files in some of the formats supported by pandas_. +Since the pandas library is not a dependency of cclib, `it must be installed `_ separately. + +.. _pandas: https://pandas.pydata.org/ + +A complete data table can be parsed from many output files by following this format:: + + ccframe [--force|-f] -O [...] + +The argument for ``-O`` indicates the data file to be written and its extension specifies the filetype (e.g. csv, h5/hdf/hdf5, json, pickle/pkl, xlsx). +An error will be thrown if ```` already exists, but you can force overwriting by using the ``--force`` (or ``-f``) flag. +Since higher-dimensional attributes (e.g. ``atomcoords``) are handled as plain text in some file formats (such as Excel XLSX or CSV), we recommend storing JSON or HDF5 files. +Observe that the output data file is overwritten if it exits already. diff --git a/_sources/how_to_parse.txt b/_sources/how_to_parse.txt deleted file mode 100644 index b5cda0d1..00000000 --- a/_sources/how_to_parse.txt +++ /dev/null @@ -1,201 +0,0 @@ -How to parse and write -====================== - -The cclib package provides three scripts to parse and write data i.e. ``ccget``, ``ccwrite``, and ``cda`` - -1. **ccget** is used to parse attribute data from output files. -2. **ccwrite** has the ability to list out all valid attribute data that can be parsed from an output format. It has the added feature of writing the output file into four different formats i.e. ``json``, ``cjson``, ``cml``, ``xyz``. -3. **cda** is used for the chemical decomposition analysis of output files. - -This page describes how to use the ccget and ccwrite scripts to obtain data from output files. - -ccget ------ - -The data types that can be parsed from the output file depends on the type of computation being conducted. The name of the output file used to show example usage is ``Benzeneselenol.out``. - -Data type can be parsed from the output file by following this format - -.. code-block:: bash - - ccget [] [] - -where attribute can be any one of the attribute names available `here`_ - -.. _`here`: data_dev.html - -1. Atomic Charges - The atomic charges are obtained by using the ``atomcharges`` attribute with ``ccget`` - -.. code-block:: bash - - $ ccget atomcharges Benzeneselenol.out - Attempting to read Benzeneselenol.out - atomcharges: - {'mulliken': array([-0.49915 , 0.056965, 0.172161, 0.349794, -0.153072, 0.094583, - 0.016487, 0.050249, 0.002149, 0.01161 , 0.053777, -0.173671, - 0.018118])} - -2. Electronic Energies - The molecular electronic energies after SCF (DFT) optimization of the input molecule is obtained by using the ``scfenergies`` attribute with ``ccget`` - -.. code-block:: bash - - $ ccget scfenergies Benzeneselenol.out - Attempting to read Benzeneselenol.out - scfenergies: - [-71671.43702915 -71671.4524142 -71671.4534768 -71671.45447492 - -71671.4556548 -71671.45605671 -71671.43194906 -71671.45761021 - -71671.45850275 -71671.39630296 -71671.45915119 -71671.45935854 - -71671.4594614 -71671.45947338 -71671.45948807 -71671.4594946 - -71671.4594946 ] - - -3. Geometry Targets - The targets for convergence of geometry optimization can be obtained by using the ``geotargets`` attribute with ``ccget`` - -.. code-block:: bash - - $ ccget geotargets Benzeneselenol.out - Attempting to read Benzeneselenol.out - geotargets: - [ 0.00045 0.0003 0.0018 0.0012 ] - -**Chaining of attributes** - -ccget provides the user with the option to chain attributes to obtain more than one type of data with a command call. The attributes can be chained in any particular order. A few chained examples are provided below. - -1. Molecular Orbitals and Multiplicity - The number of molecular orbitals and the number of basis functions used to optimize the molecule can be obtained by running the following command - -.. code-block:: bash - - $ ccget nmo nbasis Benzeneselenol.out - Attempting to read Benzeneselenol.out - nmo: - 405 - nbasis: - 407 - -2. Enthalpy and Vibrational Frequency - The enthalpy and the vibrational frequencies of the optimized molecule is conducted is obtained below: - -.. code-block:: bash - - $ ccget enthalpy vibfreqs Benzeneselenol.out - Attempting to read Benzeneselenol.out - enthalpy: - -2633.77264 - vibfreqs: - [ 129.5512 170.6681 231.4278 304.8614 407.8299 472.5026 - 629.9087 679.9032 693.2509 746.7694 812.5113 850.2578 - 915.8742 987.1252 988.1785 1002.8922 1038.1073 1091.4005 - 1102.3417 1183.3857 1209.2727 1311.3497 1355.6441 1471.4447 - 1510.1919 1611.9088 1619.0156 2391.2487 3165.1596 3171.3909 - 3182.0753 3188.5786 3198.0359] - -ccwrite -------- - -The same Benzeneselenol.out file used in the previous examples will be used as the input file for ccwrite. When the ccwrite script is used with a valid input, it prints out the valid attributes that can be parsed from the file. - -Command line format: - -.. code-block:: bash - - ccwrite [] - -The valid output file formats are ``json``, ``cjson``, ``cml``, ``xyz`` - -1. CML - -.. code-block:: bash - - $ ccwrite cml Benzeneselenol.out - Attempting to parse Benzeneselenol.out - cclib can parse the following attributes from Benzeneselenol.out: - atomcharges - atomcoords - atomnos - charge - coreelectrons - enthalpy - geotargets - geovalues - grads - homos - moenergies - mosyms - mult - natom - nbasis - nmo - optdone - optstatus - scfenergies - scftargets - temperature - vibdisps - vibfreqs - vibirs - vibsyms - -A *Benzeneselenol.cml* output file is generated in the same directory as the Benzeneselenol.out file. - -.. code-block:: bash - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2. xyz - -Using ``xyz`` as the with Benzeneselenol.out, we obtain the following *Benzeneselenol.xyz* file - -.. code-block:: bash - - 13 - Benzeneselenol.out: Geometry 17 - C -2.8947620000 -0.0136420000 -0.0015280000 - C -2.2062510000 1.1938510000 -0.0025210000 - C -0.8164260000 1.2153020000 -0.0022010000 - C -0.1033520000 0.0183920000 0.0031060000 - C -0.7906630000 -1.1943840000 0.0058500000 - C -2.1799570000 -1.2059710000 0.0017890000 - H -3.9758430000 -0.0253010000 -0.0029040000 - H -2.7502340000 2.1291370000 -0.0052760000 - H -0.2961840000 2.1630180000 -0.0073260000 - H -0.2474670000 -2.1302310000 0.0132260000 - H -2.7028960000 -2.1530750000 0.0036640000 - Se 1.8210800000 -0.0433780000 -0.0038760000 - H 2.0043580000 1.4100070000 0.1034490000 diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 00000000..6174309f --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,105 @@ +Overview +======== + +**cclib** is an `open source`_ library, written in Python_, for parsing and interpreting the results of computational chemistry packages. +The goals of cclib are centered around the reuse of data obtained from these programs and contained in output files, specifically: + +- extract (parse) data from the output files generated by multiple programs +- provide a consistent interface to the results of computational chemistry calculations, particularly those results that are useful for algorithms or visualization +- facilitate the implementation of algorithms that are not specific to a particular computational chemistry package +- to maximize interoperability with other open source computational chemistry and cheminformatic software libraries + +Summary +------- + +The current version is **cclib 1.8** (see the changelog_ for what's new). The following programs are supported and systematically tested at the versions given in parentheses: + +- ADF_ (versions 2007 and 2013) +- DALTON_ (versions 2013 and 2015) +- Firefly_, formerly known as PC GAMESS (version 8.0) +- `GAMESS (US)`_ (versions 2017 and 2018) +- `GAMESS-UK`_ (versions 7.0 and 8.0) +- Gaussian_ (versions 09 and 16) +- Jaguar_ (versions 7.0 and 8.3) +- Molcas_ (version 18.0) +- Molpro_ (versions 2006 and 2012) +- MOPAC_ (version 2016) +- NBO_ (version 7.0) +- NWChem_ (versions 6.0, 6.1, 6.5, 6.6, 6.8, and 7.0) +- ORCA_ (versions 4.1, 4.2, and 5.0) +- Psi4_ (versions 1.2.1, 1.3.1, and 1.7) +- `Q-Chem`_ (versions 5.1, 5.4, and 6.0) +- Turbomole_ (versions 5.9, 7.2, 7.4, and 7.5) + +Output files from other versions of the above programs may still work, and regression tests are always welcome. The following legacy parsers are still tested as regressions, but not actively maintained: + +- Psi3 (version 3.4) + +Many types of output data are parsed by cclib, including atom coordinates, orbital information, vibrational modes and TD-DFT calculations. See the page on `Extracted Data`_ for a complete list with coverage for the different programs. Several `calculation methods`_ are also provided for interpreting the electronic properties of molecules. + +How to use cclib +---------------- + +You can download the `source package for cclib 1.8`_ or the `current development version`_ (from the `GitHub repository`_). For information on packages available in various Linux distributions, installing the source code and requirements, as well as basic usage, the `How to install`_ is a good place to start. + +If you need further help, find a bug, need new features or have any question, please send email to the `mailing list`_ or submit an issue to the `tracker`_. + +About cclib +----------- + +The code behind cclib was started as a collaboration between Noel O'Boyle, Adam Tenderholt and Karol M. Langner (see page about Development_ for details) and is licensed under the `BSD 3-clause license`_. Other developers are encouraged to contribute to this open source project -- send an email to the `mailing list`_. Applications that use cclib include GaussSum_ and QMForge_. It has also been used in the literature_. + +If you use cclib in your scientific work, please support our work by adding a reference to the following article(s): + +For the most up-to-date cclib reference: + +| E\. Berquist, A\. Dumi, S\. Upadhyay, O.\ D.\ Abarbanel, M.\ Cho, S.\ Gaur, V.\ H.\ Cano Gil, G.\ R.\ Hutchison, O.\ S.\ Lee, A.\ S.\ Rosen, S.\ Schamnad, F.\ S.\ S.\ Schneider, C.\ Steinmann, M.\ Stolyarchuk, J.\ E.\ Vandezande, W.\ Zak, K.\ M.\ Langner, *cclib 2.0: An updated architecture for interoperable computational chemistry*, J. Chem. Phys. 161 (4), pp. 042501, **2024** (DOI2_). +| + +For the original cclib paper: + +| N\. M\. O'Boyle, A\. L\. Tenderholt, K\. M\. Langner, *cclib: a library for package-independent computational chemistry algorithms*, J. Comp. Chem. 29 (5), pp. 839-845, **2008** (DOI_). +| + +A record for the latest release is also available on Zenodo_. + +.. _`open source`: https://en.wikipedia.org/wiki/Open_source +.. _Python: https://www.python.org +.. _`BSD 3-clause license`: https://en.wikipedia.org/wiki/BSD_licenses#3-clause_license_(%22BSD_License_2.0%22,_%22Revised_BSD_License%22,_%22New_BSD_License%22,_or_%22Modified_BSD_License%22) + +.. _changelog: changelog.html +.. _`extracted data`: data.html +.. _`calculation methods`: methods.html +.. _`installation page`: installation.html +.. _`How to install`: how_to_install.html +.. _development: development.html + +.. _ADF: https://www.scm.com/product/adf/ +.. _DALTON: https://daltonprogram.org/ +.. _Firefly: http://classic.chem.msu.su/gran/gamess/ +.. _`GAMESS (US)`: https://www.msg.chem.iastate.edu/gamess/ +.. _`GAMESS-UK`: https://web.archive.org/web/20190613042645/http://www.cfs.dl.ac.uk/ +.. _`Gaussian`: https://gaussian.com/ +.. _Jaguar: https://www.schrodinger.com/products/jaguar +.. _Molcas: https://gitlab.com/Molcas/OpenMolcas +.. _Molpro: https://www.molpro.net/ +.. _MOPAC: http://openmopac.net/ +.. _NBO: https://nbo7.chem.wisc.edu/ +.. _NWChem: https://nwchemgit.github.io/ +.. _ORCA: https://orcaforum.kofo.mpg.de/app.php/portal +.. _Psi4: https://psicode.org/ +.. _`Q-Chem`: https://q-chem.com/ +.. _Turbomole: http://www.turbomole-gmbh.com/ + +.. _`source package for cclib 1.8`: https://github.com/cclib/cclib/releases/download/v1.8/cclib-1.8.zip +.. _`current development version`: https://github.com/cclib/cclib/archive/master.zip +.. _`GitHub repository`: https://github.com/cclib/cclib +.. _`mailing list`: https://groups.google.com/g/cclib +.. _`tracker`: https://github.com/cclib/cclib/issues + +.. _GaussSum: http://gausssum.sourceforge.net/ +.. _QMForge: https://qmforge.net/ +.. _literature: https://doi.org/10.1021/jacs.5b05600 +.. _DOI: https://doi.org/10.1002/jcc.20823 +.. _Zenodo: https://zenodo.org/record/8280878 +.. _DOI2: https://doi.org/10.1063/5.0216778 diff --git a/_sources/index.txt b/_sources/index.txt deleted file mode 100644 index f52e8b19..00000000 --- a/_sources/index.txt +++ /dev/null @@ -1,86 +0,0 @@ -Overview -======== - -**cclib** is an `open source`_ library, written in Python_, for parsing and interpreting the results of computational chemistry packages. -The goals of cclib are centered around the reuse of data obtained from these programs and contained in output files, specifically: - -- extract (parse) data from the output files generated by multiple programs -- provide a consistent interface to the results of computational chemistry calculations, particularly those results that are useful for algorithms or visualisation -- facilitate the implementation of algorithms that are not specific to a particular computational chemistry package -- to maximise interoperability with other open source computational chemistry and cheminformatic software libraries - -Summary -------- - -The current version is **cclib 1.5** (see the changelog_ for what's new) and parses output files from the following programs (version in parentheses are tested): - -- ADF_ (versions 2007 and 2013) -- DALTON_ (versions 2013 and 2015) -- Firefly_, formerly known as PC GAMESS (version 8.0) -- `GAMESS (US)`_ (version 2012) -- `GAMESS-UK`_ (version 7.0) -- Gaussian_ (versions 03 and 09) -- Jaguar_ (versions 7.0 and 8.3) -- Molpro_ (versions 2006 and 2012) -- NWChem_ (versions 6.0 and 6.5) -- ORCA_ (versions 2.9 and 3.0) -- Psi_ (versions 3.4 and 4.0) -- `Q-Chem`_ (version 4.2) - -Many types of output data are parsed by cclib, including atom coordinates, orbital information, vibrational modes and TD-DFT calculations. See the page on `Extracted Data`_ for a comlete list with coverage for the different programs. Several `calculation methods`_ are also provided for interpreting the electronic properties of molecules. - -How to use cclib ----------------- - -You can download the `source package for cclib 1.5`_ or the `current development version`_ (from the `GitHub repository`_). For information on packages available in various Linux distributions, installing the source code and requirements, as well as basic usage, the `How to install`_ is a good place to start. - -If you need further help, find a bug, need new features or have any question, please send email to the `mailing list`_ or submit an issue to the `tracker`_. - -About cclib ------------ - -The code behind cclib was started as a collaboration between Noel O'Boyle, Adam Tenderholt and Karol M. Langner (see page about Development_ for details) and is licensed under the LGPL_. Other developers are encouraged to contribute to this open source project -- send an email to the `developers mailing list`_. Applications that use cclib include GaussSum_ and QMForge_. It has also been used in the literature_. - -If you use cclib in your scientific work, please support our work by adding a reference to the following article: - -| N\. M\. O'Boyle, A\. L\. Tenderholt, K\. M\. Langner, *cclib: a library for package-independent computational chemistry algorithms*, J. Comp. Chem. 29 (5), pp. 839-845, **2008** (DOI_). -| - -A record for the latest release is also available on Zenodo_. - -.. _`open source`: http://en.wikipedia.org/wiki/Open_source -.. _Python: http://www.python.org -.. _LGPL: http://www.gnu.org/copyleft/lgpl.html - -.. _changelog: changelog.html -.. _`extracted data`: data.html -.. _`calculation methods`: methods.html -.. _`installation page`: installation.html -.. _`How to install`: how_to_install.html -.. _development: development.html - -.. _ADF: https://www.scm.com/product/adf/ -.. _DALTON: http://daltonprogram.org -.. _Firefly: http://classic.chem.msu.su/gran/gamess/ -.. _`GAMESS (US)`: http://www.msg.ameslab.gov/GAMESS/GAMESS.html -.. _`GAMESS-UK`: http://www.cfs.dl.ac.uk -.. _`Gaussian`: http://www.gaussian.com -.. _Jaguar: http://www.schrodinger.com/ProductDescription.php?mID=6&sID=9 -.. _Molpro: http://www.molpro.net/ -.. _NWChem: http://www.nwchem-sw.org/index.php/Main_Page -.. _ORCA: http://www.thch.uni-bonn.de/tc/orca/ -.. _Psi: http://psicode.org/ -.. _`Q-Chem`: http://q-chem.com/ - -.. _`source package for cclib 1.5`: https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.zip -.. _`current development version`: https://github.com/cclib/cclib/archive/master.zip -.. _`GitHub repository`: https://github.com/cclib/cclib -.. _`mailing list`: https://lists.sourceforge.net/lists/listinfo/cclib-users -.. _`developers mailing list`: https://lists.sourceforge.net/lists/listinfo/cclib-devel -.. _`tracker`: https://github.com/cclib/cclib/issues - -.. _GaussSum: http://gausssum.sourceforge.net/ -.. _QMForge: http://qmforge.sourceforge.net/ -.. _literature: http://pubs.acs.org/doi/abs/10.1021/jacs.5b05600 -.. _DOI: http://dx.doi.org/10.1002/jcc.20823 -.. _Zenodo: http://dx.doi.org/10.5281/zenodo.44552 diff --git a/_sources/methods.rst.txt b/_sources/methods.rst.txt new file mode 100644 index 00000000..e60870ce --- /dev/null +++ b/_sources/methods.rst.txt @@ -0,0 +1,481 @@ +.. index:: + pair: module; methods + +Calculation methods +=================== + +The following methods in cclib allow further analysis of calculation output. + +.. _`methods in the development version`: methods_dev.html + +.. index:: + single: methods; C squared population analysis (CSPA) + +C squared population analysis (CSPA) +------------------------------------ + +**CSPA** can be used to determine and interpret the electron density of a molecule. The contribution of the a-th atomic orbital to the i-th molecular orbital can be written in terms of the molecular orbital coefficients: + +.. math:: \Phi_{ai} = \frac{c^2_{ai}}{\sum_k c^2_{ki}} + +The CSPA class available from cclib.method performs C-squared population analysis and can be used as follows: + +.. code-block:: python + + from cclib.io import ccread + from cclib.method import CSPA + + data = ccread("mycalc.out") + + m = CSPA(data) + m.calculate() + +After the ``calculate()`` method is called, the following attributes are available: + +* ``aoresults`` is a NumPy array[3] with spin, molecular orbital, and atomic/fragment orbitals as the axes (``aoresults[0][45][0]`` gives the contribution of the 1st atomic/fragment orbital to the 46th alpha/restricted molecular orbital) +* ``fragresults`` is a NumPy array[3] with spin, molecular orbital, and atoms as the axes (``atomresults[1][23][4]`` gives the contribution of the 5th atomic/fragment orbital to the 24th beta molecular orbital) +* ``fragcharges`` is a NumPy array[1] with the number of (partial) electrons in each atom (``atomcharges[2]`` gives the number of electrons on the 3rd atom) + +Custom fragments +~~~~~~~~~~~~~~~~ + +Calling the calculate method without an argument treats each atom as a fragment in the population analysis. An optional argument can be passed - a list of lists - containing the atomic orbital numbers to be included in each fragment. Calling with this additional argument is useful if one is more interested in the contributions of certain orbitals, such as metal d, to the molecular orbitals. For example: + +.. code-block:: python + + from cclib.io import ccread + from cclib.method import CSPA + + data = ccread("mycalc.out") + + m = CSPA(data) + m.calculate([[0, 1, 2, 3, 4], [5, 6], [7, 8, 9]]) # fragment one is made from basis functions 0 - 4 + # fragment two is made from basis functions 5 & 6 + # fragment three is made from basis functions 7 - 9 + +Custom progress +~~~~~~~~~~~~~~~ + +The CSPA class also can take a progress class as an argument so that the progress of the calculation can be monitored: + +.. code-block:: python + + from cclib.method import CSPA + from cclib.parser import Gaussian + from cclib.progress import TextProgress + + import logging + + progress = TextProgress() + p = Gaussian("mycalc.out", logging.ERROR) + d = p.parse(progress) + + m = CSPA(d, progress, logging.ERROR) + m.calculate() + +.. index:: + single: methods; Mulliken population analysis (MPA) + +Mulliken population analysis (MPA) +---------------------------------- + +MPA can be used to determine and interpret the electron density of a molecule. The contribution of the a-th atomic orbital to the i-th molecular orbital in this method is written in terms of the molecular orbital coefficients, c, and the overlap matrix, S: + +.. math:: \Phi_{ai} = \sum_b c_{ai} c_{bi} S_{ab} + +The MPA class available from cclib.method performs Mulliken population analysis and can be used as follows: + +.. code-block:: python + + import sys + + from cclib.method import MPA + from cclib.parser import ccopen + + d = ccopen(sys.argv[1]).parse() + m = MPA(d) + m.calculate() + +After the calculate() method is called, the following attributes are available: + +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[0][45][0]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][23][4]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[2]`` gives the number of electrons in the 3rd fragment. + +Custom fragments +~~~~~~~~~~~~~~~~ + +The calculate method chooses atoms as the fragments by default, and optionally accepts a list of lists containing the atomic orbital numbers (e.g. ``[[0, 1, 2], [3, 4, 5, 6], ...]``) of arbitrary fragments. Calling it in this way is useful if one is more interested in the contributions of groups of atoms or even certain orbitals or orbital groups, such as metal d, to the molecular orbitals. In this case, fragresults and fragcharges reflect the chosen groups of atomic orbitals instead of atoms. + +Custom progress +~~~~~~~~~~~~~~~ + +The Mulliken class also can take a progress class as an argument so that the progress of the calculation can be monitored: + +.. code-block:: python + + from cclib.method import MPA + from cclib.parser import ccopen + from cclib.progress import TextProgress + import logging + + progress = TextProgress() + d = ccopen("mycalc.out", logging.ERROR).parse(progress) + + m = MPA(d, progress, logging.ERROR) + m.calculate() + +.. index:: + single: methods; Löwdin Population Analysis + +Löwdin Population Analysis +-------------------------- + +The LPA class available from cclib.method performs Löwdin population analysis and can be used as follows: + +.. code-block:: python + + import sys + + from cclib.method import LPA + from cclib.parser import ccopen + + d = ccopen(sys.argv[1]).parse() + m = LPA(d) + m.calculate() + +.. index:: + single: methods; Bickelhaupt Population Analysis + +Bickelhaupt Population Analysis +------------------------------- + +The Bickelhaupt class available from cclib.method performs Bickelhaupt population analysis that has been proposed in *Organometallics* 1996, 15, 13, 2923–2931. `doi:10.1021/om950966x `_ + +The contribution of the a-th atomic orbital to the i-th molecular orbital in this method is written in terms of the molecular orbital coefficients, c, and the overlap matrix, S: + +.. math:: \Phi_{ai,\alpha} = \sum_b w_{ab,\alpha} c_{ai,\alpha} c_{bi,\alpha} S_{ab} + +where the weights :math:`w_{ab}` that are applied on the Mulliken atomic orbital contributions are defined as following when the coefficients of the molecular orbitals are substituted into equation 11 in the original article. + +.. math:: w_{ab,\alpha} = 2 \frac{\sum_k c_{ak,\alpha}^2}{\sum_i c_{ai,\alpha}^2 + \sum_j c_{bj,\alpha}^2} + +In case of unrestricted calculations, :math:`\alpha` charges and :math:`\beta` charges are each determined to obtain total charge. In restricted calculations, :math:`\alpha` subscript can be ignored since the coefficients are equivalent for both spin orbitals. + +The weights are introduced to replace the somewhat arbitrary partitioning of off-diagonal charges in the Mulliken population analysis, which divides the off-diagonal charges identically to both atoms. Bickelhaupt population analysis instead divides the off-diagonal elements based on the relative magnitude of diagonal elements. + +.. code-block:: python + + import sys + + from cclib.method import Bickelhaupt + from cclib.parser import ccopen + + d = ccopen(sys.argv[1]).parse() + m = Bickelhaupt(d) + m.calculate() + +After the calculate() method is called, the following attributes are available: + +* ``aoresults``: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that ``aoresults[0][45][0]`` gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, +* ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1][23][4]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) +* ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[2]`` gives the number of electrons in the 3rd fragment. + +Custom fragments +~~~~~~~~~~~~~~~~ + +The calculate method chooses atoms as the fragments by default, and optionally accepts a list of lists containing the atomic orbital numbers (e.g. ``[[0, 1, 2], [3, 4, 5, 6], ...]``) of arbitrary fragments. Calling it in this way is useful if one is more interested in the contributions of groups of atoms or even certain orbitals or orbital groups, such as metal d, to the molecular orbitals. In this case, fragresults and fragcharges reflect the chosen groups of atomic orbitals instead of atoms. + +Custom progress +~~~~~~~~~~~~~~~ + +The Bickelhaupt class also can take a progress class as an argument so that the progress of the calculation can be monitored: + +.. code-block:: python + + from cclib.method import Bickelhaupt + from cclib.parser import ccopen + from cclib.progress import TextProgress + import logging + + progress = TextProgress() + d = ccopen("mycalc.out", logging.ERROR).parse(progress) + + m = Bickelhaupt(d, progress, logging.ERROR) + m.calculate() + +.. + Overlap Population Analysis + --------------------------- + +Density Matrix calculation +-------------------------- + +The Density class from cclib.method can be used to calculate the density matrix: + +.. code-block:: python + + from cclib.parser import ccopen + from cclib.method import Density + + parser = ccopen("myfile.out") + data = parser.parse() + + d = Density(data) + d.calculate() + +After ``calculate()`` is called, the density attribute is available. It is simply a NumPy array with three axes. The first axis is for the spin contributions, and the second and third axes are for the density matrix, which follows the standard definition. + +Mayer's Bond Orders +------------------- + +This method calculates the Mayer's bond orders for a given molecule: + +.. code-block:: python + + import sys + + from cclib.parser import ccopen + from cclib.method import MBO + + parser = ccopen(sys.argv[1]) + data = parser.parse() + + d = MBO(data) + d.calculate() + +After ``calculate()`` is called, the fragresults attribute is available, which is a NumPy array of rank 3. The first axis is for contributions of each spin to the MBO, while the second and third correspond to the indices of the atoms. + +Charge Decomposition Analysis +----------------------------- + +The Charge Decomposition Analysis (CDA) as developed by Gernot Frenking et al. is used to study the donor-acceptor interactions of a molecule in terms of two user-specified fragments. + +The CDA class available from cclib.method performs this analysis: + +.. code-block:: python + + from cclib.io import ccopen + from cclib.method import CDA + + molecule = ccopen("molecule.log") + frag1 = ccopen("fragment1.log") + frag2 = ccopen("fragment2.log") + + # if using CDA from an interactive session, it's best + # to parse the files at the same time in case they aren't + # parsed immediately---go get a drink! + + m = molecule.parse() + f1 = frag1.parse() + f2 = frag2.parse() + + cda = CDA(m) + cda.calculate([f1, f2]) + +After ``calculate()`` finishes, there should be the donations, bdonations (back donation), and repulsions attributes to the cda instance. These attributes are simply lists of 1-dimensional NumPy arrays corresponding to the restricted or alpha/beta molecular orbitals of the entire molecule. Additionally, the CDA method involves transforming the atomic basis functions of the molecule into a basis using the molecular orbitals of the fragments so the attributes mocoeffs and fooverlaps are created and can be used in population analyses such as Mulliken or C-squared (see Fragment Analysis for more details). + +There is also a script provided by cclib that performs the CDA from a command-line:: + + $ cda molecule.log fragment1.log fragment2.log + Charge decomposition analysis of molecule.log + + MO# d b r + ----------------------------- + 1: -0.000 -0.000 -0.000 + 2: -0.000 0.002 0.000 + 3: -0.001 -0.000 0.000 + 4: -0.001 -0.026 -0.006 + 5: -0.006 0.082 0.230 + 6: -0.040 0.075 0.214 + 7: 0.001 -0.001 0.022 + 8: 0.001 -0.001 0.022 + 9: 0.054 0.342 -0.740 + 10: 0.087 -0.001 -0.039 + 11: 0.087 -0.001 -0.039 + ------ HOMO - LUMO gap ------ + 12: 0.000 0.000 0.000 + 13: 0.000 0.000 0.000 + ...... + +Notes +~~~~~ + +* Only molecular orbitals with non-zero occupancy will have a non-zero value. +* The absolute values of the calculated terms have no physical meaning and only the relative magnitudes, especially for the donation and back donation terms, are of any real value (Frenking, et al.) +* The atom coordinates in molecules and fragments must be the same, which is usually accomplished with an argument in the QM program (the NoSymm keyword in Gaussian, for instance). +* The current implementation has some subtle differences than the code from the Frenking group. The CDA class in cclib follows the formula outlined in one of Frenking's CDA papers, but contains an extra factor of 2 to give results that agree with those from the original CDA program. It also doesn't include negligible terms (on the order of 10^-6) that result from overlap between MOs on the same fragment that appears to be included in the Frenking code. Contact atenderholt (at) gmail (dot) com for discussion and more information. + +.. index:: + single: methods; Bader's QTAIM + +Bader's QTAIM +---------------- + +Bader's QTAIM charges define the border between the atoms in the molecule as a surface where each point on the surface has zero flux. In other words, the points on the surface of the Bader spaces satisfy the equation :math:`\nabla \rho (r) \cdot n(r) = 0`. In cclib, numerical calculation of QTAIM charges through the algorithm proposed in `[Henkelman2006] `_ is implemented. + +Calculating the Bader's QTAIM charges in cclib follow similar steps as other population analysis methods. The following code provides an example of how QTAIM charges can be obtained. + +.. code-block:: python + + from cclib.method import Bader + from cclib.method import Volume + from cclib.parser import ccopen + from cclib.progress import TextProgress + import logging + + progress = TextProgress() + d = ccopen("mycalc.out", logging.ERROR).parse(progress) + + # Inputs for Volume object below are origin, top corner, and spacing + # represented in Cartesian coordinates and in angstroms. + vol = Volume((-3, -3, -3), (3, 3, 3), (.1, .1, .1)) + + m = Bader(d, vol) + m.calculate() + +After the calculate() method is called, the following attributes are available: + +* ``fragresults``: a three dimensional array x, y, and z coordinates from the Volume object as the axes, so that ``fragresults[1][2][3]`` gives the Bader space (in integers starting from 1) that the grid space in (0, 1, 2) position belongs to. +* ``matches``: a vector with the Bader space (integers starting from 1) that an atom is matched with. +* ``fragcharges``: a vector with the number of (partial) electrons in each atom, so that ``fragcharges[2]`` gives the number of electrons in the 3rd atom. + +Since some computational chemistry packages support writing out charge densities as cube files during calculations, it is highly recommended to do so especially for larger systems. +To calculate Bader charges from a cube file, a ``Volume`` object should be prepared by reading in a cube file and should be passed into a Bader object as shown below: + +.. code-block:: python + + from cclib.method import volume + from cclib.method import Bader + from cclib.parser import ccopen + from cclib.progress import TextProgress + import logging + + progress = TextProgress() + d = ccopen("mycalc.out", logging.ERROR).parse(progress) + + # Read in from cube file + vol = volume.read_from_cube("mycalc.cube") + + m = Bader(d, vol) + m.calculate() + + +.. index:: + single: methods; DDEC6 + +DDEC6 +----- + +DDEC6 is a Stockholder-like charge partitioning method introduced in `[Manz2016] `_. Proatom densities should be provided for DDEC6 method. Proatom densities generated [#proatom]_ using `horton`_ can be passed on as an argument for the constructor of the DDEC6 object. The DDEC6 algorithm requires many numerical integrations so a fine grid is necessary to obtain accurate results. Calculating the electron density on a fine grid using a Volume object is slow, therefore we recommend that electron densities are imported from cube files. + +Because a lot of numerical integrations are present in DDEC6 algorithm, fine grid is necessary to obtain satisfying results. + +.. _`horton`: http://theochem.github.io/horton/2.1.1/ + +.. code-block:: python + + from cclib.method import DDEC6 + from cclib.method import Volume + from cclib.parser import ccopen + from cclib.progress import TextProgress + import logging + + progress = TextProgress() + d = ccopen("mycalc.out", logging.ERROR).parse(progress) + + # Inputs for Volume object below are origin, top corner, and spacing + # represented in Cartesian coordinates and in angstroms. + vol = Volume((-3, -3, -3), (3, 3, 3), (.1, .1, .1)) + + # Alternatively, read in from cube file + vol = volume.read_from_cube("mycalc.cube") + + m = DDEC6(d, vol, '/path/to/horton_proatom_density_directory') + m.calculate() + +Third argument to the constructor of DDEC6 object points to the directory proatom densities are stored. The proatom densities can be generated by using `horton`_ . Follow the steps described in horton `documentation`_ for its ``horton-atomdb.py`` command. + +.. _`documentation`: http://theochem.github.io/horton/2.1.1/user_postproc_aim.html#horton-atomdb-py-build-a-pro-atom-database + +After the calculate() method is called, the following attributes are available: + +* ``fragcharges``: a vector with the number of (partial) electrons in each atom, so that ``fragcharges[2]`` gives the number of electrons in the 3rd atom. +* ``refcharges``: a two dimensional array where the first index indicates whether the reference charges are from first step of DDEC6 algorithm or the second step. Second index refers to the atoms that the charges are assigned to and follows the same order as the order used by the input ``ccData`` object. + +.. index:: + single: methods; Hirshfeld Population Analysis + +Hirshfeld Population Analysis +----------------------------- + +Hirshfeld Population Analysis is the most basic charge partitioning method among stockholder-type methods and was introduced initially in `[Hirshfeld1977] `_. +In Hirshfeld method, proatom densities, which are charge densities of neutral atoms that comprise the given molecule, are used to calculate the weights that will be applied to partition charge densities on each grid point. +Proatom densities can be generated [#proatom]_ using `horton`_ and can be passed on as an argument for the constructor of the Hirshfeld object. For Hirshfeld calculations, it is recommended that electron densities are imported from cube files. + +.. code-block:: python + + from cclib.method import Hirshfeld + from cclib.method import Volume + from cclib.parser import ccopen + from cclib.progress import TextProgress + import logging + + progress = TextProgress() + d = ccopen("mycalc.out", logging.ERROR).parse(progress) + + # Inputs for Volume object below are origin, top corner, and spacing + # represented in Cartesian coordinates and in angstroms. + vol = Volume((-3, -3, -3), (3, 3, 3), (.1, .1, .1)) + + # Alternatively, read in from cube file + vol = volume.read_from_cube("mycalc.cube") + + m = Hirshfeld(d, vol, '/path/to/horton_proatom_density_directory') + m.calculate() + +Third argument to the constructor of Hirshfeld object points to the directory proatom densities are stored. The proatom densities can be generated by using `horton`_ . Follow the steps described in horton `documentation`_ for its ``horton-atomdb.py`` command. + +After the calculate() method is called, the following attributes are available: + +* ``fragcharges``: a vector with the number of (partial) electrons in each atom, so that ``fragcharges[2]`` gives the number of electrons in the 3rd atom. + +.. index:: + single: methods; Accessing additional methods through bridge + + +Nuclear Properties +------------------ + +This method calculates various properties of nuclei based on the parsed data. + +Calculate the nuclear repulsion energy using the snippet below: + +.. code-block:: python + + import cclib + from cclib.method import Nuclear + + parser = cclib.io.ccopen("test.log") + data = parser.parse() + nuclear = Nuclear(data) + + nre = nuclear.repulsion_energy() + print(nre) + + +Accessing additional methods through bridge +------------------------------------------- + +Some other population analyses methods including Hirshfeld partial charges and Iterative Stockholder charges can be calculated using bridge functions implemented in cclib. For more information, refer to `bridge`_ section of the documentation. + +.. _`bridge`: bridge.html + +.. + Electron Density Calculation + ---------------------------- + + +.. rubric:: Footnotes + +.. [#proatom] To generate proatom densities from horton using Psi4, after generating Psi4 input files, add ``mv *.molden atom.default.molden`` on line 25 of ``run_psi4.sh`` before executing the script. diff --git a/_sources/methods.txt b/_sources/methods.txt deleted file mode 100644 index ce820379..00000000 --- a/_sources/methods.txt +++ /dev/null @@ -1,253 +0,0 @@ -.. index:: - module: methods - -Calculation methods -=================== - -The following methods in cclib allow further analysis of calculation output. - -.. _`methods in the development version`: methods_dev.html - -.. index:: - single: methods; C squared population analysis (CSPA) - -C squared population analysis (CSPA) ------------------------------------- - -**CSPA** can be used to determine and interpret the electron density of a molecule. The contribution of the a-th atomic orbital to the i-th molecular orbital can be written in terms of the molecular orbital coefficients: - -.. math:: \Phi_{ai} = \frac{c^2_{ai}}{\sum_k c^2_{ki}} - -The CSPA class available from cclib.method performs C-squared population analysis and can be used as follows: - -.. code-block:: python - - from cclib.method import CSPA - from cclib.parser import Gaussian - - p = Gaussian("mycalc.out") - d = p.parse() - - m = CSPA(d) - m.calculate() - -After the calculate() method is called, the following attributes are available: - -* ``aoresults`` is a Numpy array[3] with spin, molecular orbital, and atomic/fragment orbitals as the axes (aoresults[0][45][0] gives the contribution of the 1st atomic/fragment orbital to the 46th alpha/restricted molecular orbital) -* ``fragresults`` is a Numpy array[3] with spin, molecular orbital, and atoms as the axes (atomresults[1][23][4] gives the contribution of the 5th atomic/fragment orbital to the 24th beta molecular orbital) -* ``fragcharges`` is a Numpy array[1] with the number of (partial) electrons in each atom (atomcharges[2] gives the number of electrons on the 3rd atom) - -Custom fragments -~~~~~~~~~~~~~~~~ - -Calling the calculate method without an argument treats each atom as a fragment in the population analysis. An optional argument can be passed - a list of lists - containing the atomic orbital numbers to be included in each fragment. Calling with this additional argument is useful if one is more interested in the contributions of certain orbitals, such as metal d, to the molecular orbitals. For example: - -.. code-block:: python - - from cclib.method import CSPA - from cclib.parser import Gaussian - - p = Gaussian("mycalc.out") - d = p.parse() - - m = CSPA(d) - m.calculate([[0,1,2,3,4],[5,6],[7,8,9]]) #fragment one is made from basis functions 0-4 - #fragment two is made from basis functions 5&6 - #fragment three is made from basis functions 7-9 - -Custom progress -~~~~~~~~~~~~~~~ - -The CSPA class also can take a progress class as an argument so that the progress of the calculation can be monitored: - -.. code-block:: python - - from cclib.method import CSPA - from cclib.parser import Gaussian - from cclib.progress import TextProgress - - import logging - - progress=TextProgress() - p = Gaussian(“mycalc.out”, logging.ERROR) - d = p.parse(progress) - - m = CSPA(d, progress, logging.ERROR) - m.calculate() - -.. index:: - single: methods; Mulliken population analysis (MPA) - -Mulliken population analysis (MPA) ----------------------------------- - -MPA can be used to determine and interpret the electron density of a molecule. The contribution of the a-th atomic orbital to the i-th molecular orbital in this method is written in terms of the molecular orbital coefficients, c, and the overlap matrix, S: - -.. math:: \Phi_{ai} = \sum_b c_{ai} c_{bi} S_{ab} - -The MPA class available from cclib.method performs Mulliken population analysis and can be used as follows: - -.. code-block:: python - - import sys - - from cclib.method import MPA - from cclib.parser import ccopen - - d = ccopen(sys.argv[1]).parse() - m = MPA(d) - m.calculate() - -After the calculate() method is called, the following attributes are available: - -* aoresults: a three dimensional array with spin, molecular orbital, and atomic orbitals as the axes, so that aoresults[0][45][0] gives the contribution of the 1st atomic orbital to the 46th alpha/restricted molecular orbital, -* fragresults: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that fragresults[1][23][4] gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital) -* fragcharges: a vector with the number of (partial) electrons in each fragment, so that fragcharges[2] gives the number of electrons in the 3rd fragment. - -Custom fragments -~~~~~~~~~~~~~~~~ - -The calculate method chooses atoms as the fragments by default, and optionally accepts a list of lists containing the atomic orbital numbers (e.g. [[0,1,2],[3,4,5,6],...]) of arbitrary fragments. Calling it in this way is useful if one is more interested in the contributions of groups of atoms or even certain orbitals or orbital groups, such as metal d, to the molecular orbitals. In this case, fragresults and fragcharges reflect the chosen groups of atomic orbitals instead of atoms. - -Custom progress -~~~~~~~~~~~~~~~ - -The Mulliken class also can take a progress class as an argument so that the progress of the calculation can be monitored: - -.. code-block:: python - - from cclib.method import MPA - from cclib.parser import ccopen - from cclib.progress import TextProgress - import logging - - progress = TextProgress() - d = ccopen(“mycalc.out", logging.ERROR).parse(progress) - - m = MPA(d, progress, logging.ERROR) - m.calculate() - -.. index:: - single: methods; Löwdin Population Analysis - -Löwdin Population Analysis --------------------------- - -The LPA class available from cclib.method performs Löwdin population analysis and can be used as follows: - -.. code-block:: python - - import sys - - from cclib.method import LPA - from cclib.parser import ccopen - - d = ccopen(sys.argv[1]).parse() - m = LPA(d) - m.calculate() - -Overlap Population Analysis ---------------------------- - -Density Matrix calculation --------------------------- - -The Density class from cclib.method can be used to calculate the density matrix: - -.. code-block:: python - - from cclib.parser import ccopen - from cclib.method import Density - - parser = ccopen("myfile.out") - data = parser.parse() - - d = Density(data) - d.calculate() - -After calculate() is called, the density attribute is available. It is simply a Numpy array with three axes. The first axis is for the spin contributions, and the second and third axes are for the density matrix, which follows the standard definition. - -Mayer's Bond Orders -------------------- - -This method calculates the Mayer's bond orders for a given molecule: - -.. code-block:: python - - import sys - - from cclib.parser import ccopen - from cclib.method import MBO - - parser = ccopen(sys.argv[1]) - data = parser.parse() - - d = MBO(data) - d.calculate() - -After calculate() is called, the fragresults attribute is available, which is a Numpy array of rank 3. The first axis is for contributions of each spin to the MBO, while the second and third correspond to the indices of the atoms. - -Charge Decomposition Analysis ------------------------------ - -The Charge Decomposition Analysis (CDA) as developed by Gernot Frenking et al. is used to study the donor-acceptor interactions of a molecule in terms of two user-specified fragments. - -The CDA class available from cclib.method performs this analysis: - -.. code-block:: python - - from cclib.parser import ccopen - from cclib.method import CDA - - molecule = ccopen("molecule.log") - frag1 = ccopen("fragment1.log") - frag2 = ccopen("fragment2.log") - - # if using CDA from an interactive session, it's best - # to parse the files at the same time in case they aren't - # parsed immediately---go get a drink! - - m = molecule.parse() - f1 = frag1.parse() - f2 = frag2.parse() - - cda = CDA(m) - cda.calculate([f1, f2]) - -After calculate() finishes, there should be the donations, bdonations (back donation), and repulsions attributes to the cda instance. These attributes are simply lists of 1-dimensional Numpy arrays corresponding to the restricted or alpha/beta molecular orbitals of the entire molecule. Additionally, the CDA method involves transforming the atomic basis functions of the molecule into a basis using the molecular orbitals of the fragments so the attributes mocoeffs and fooverlaps are created and can be used in population analyses such as Mulliken or C-squared (see Fragment Analysis for more details). - -There is also a script provided by cclib that performs the CDA from a command-line: - -.. code-block:: bash - - $ cda molecule.log fragment1.log fragment2.log - Charge decomposition analysis of molecule.log - - MO# d b r - ----------------------------- - 1: -0.000 -0.000 -0.000 - 2: -0.000 0.002 0.000 - 3: -0.001 -0.000 0.000 - 4: -0.001 -0.026 -0.006 - 5: -0.006 0.082 0.230 - 6: -0.040 0.075 0.214 - 7: 0.001 -0.001 0.022 - 8: 0.001 -0.001 0.022 - 9: 0.054 0.342 -0.740 - 10: 0.087 -0.001 -0.039 - 11: 0.087 -0.001 -0.039 - ------ HOMO - LUMO gap ------ - 12: 0.000 0.000 0.000 - 13: 0.000 0.000 0.000 - ...... - -Notes -~~~~~ - -* Only molecular orbitals with non-zero occupancy will have a non-zero value. -* The absolute values of the calculated terms have no physical meaning and only the relative magnitudes, especially for the donation and back donation terms, are of any real value (Frenking, et al.) -* The atom coordinates in molecules and fragments must be the same, which is usually accomplished with an argument in the QM program (the NoSymm keyword in Gaussian, for instance). -* The current implementation has some subtle differences than the code from the Frenking group. The CDA class in cclib follows the formula outlined in one of Frenking's CDA papers, but contains an extra factor of 2 to give results that agree with those from the original CDA program. It also doesn't include negligible terms (on the order of 10^-6) that result from overlap between MOs on the same fragment that appears to be included in the Frenking code. Contact atenderholt (at) gmail (dot) com for discussion and more information. - -Electron Density Calculation ----------------------------- diff --git a/_sources/old/development_sourceforge.txt b/_sources/old/development_sourceforge.txt deleted file mode 100644 index 1a05f07e..00000000 --- a/_sources/old/development_sourceforge.txt +++ /dev/null @@ -1,225 +0,0 @@ -========================= -Development (sourceforge) -========================= - -This page contains old development content, from when cclib was hosted at Sourceforge, and which has become obsolete for the current version of cclib (|release|). - -Websites related to cclib -========================= - -* The official `cclib repository on github`_ -* The `cclib project page on Sourceforge`_ (inactive now) -* The `cclib entry on Freecode`_ -* The `cclib entry on Ohloh`_ -* The `cclib entry on Cheeseshop`_ - -.. _`cclib repository on github`: https://github.com/cclib/cclib -.. _`cclib project page on Sourceforge`: http://sourceforge.net/projects/cclib/ -.. _`cclib entry on Freecode`: http://freecode.com/projects/cclib -.. _`cclib entry on Ohloh`: https://www.ohloh.net/p/cclib -.. _`cclib entry on Cheeseshop`: http://www.python.org/pypi/cclib - -Instructions for developers -=========================== - -Checking cclib out of subversion -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -cclib is hosted by the fantastic people at Sourceforge. The development version of cclib is stored in a Subversion (SVN) repository at Sourceforge (you can read some background material on this at [1]). The following command will download the current development version into a folder called cclib: - -.. code-block:: bash - - svn checkout https://cclib.svn.sourceforge.net/svnroot/cclib/trunk cclib - -To install, follow the guidelines described on the Install page. - -Releasing a version -~~~~~~~~~~~~~~~~~~~ - -* Update the CHANGELOG and ANNOUNCE -* Make sure that setup.py has the right version number, as well as __version__ in __init__.py. -* Run manifest.py to update the MANIFEST if necessary. -* Do a final merge of the trunk to release branch -* Create the source distributions - -.. code-block:: bash - - python setup.py sdist --formats=gztar,zip upload - python setup.py bdist_wininst # rename from cclib-0.x.win32.exe to cclib-0.x-py2.3.exe - python2.4 setup.py bdist_wininst # rename to cclib-0.x-py2.4.exe - -* Run the tests for a final time after removing cclib (rm -rf $PYTHONDIR/Lib/site-packages/cclib) and reinstalling from the source distribution. -* Tag the release. -* Use releaseforge to make a new release -* Update the download instructions on the wiki -* Wait 24 hours (for the sourceforge mirrors to get a copy) -* Email the users and developers mailing list with the ANNOUNCE -* Create a news item and copy and paste ANNOUNCE into it -* Update http://www.freshmeat.net (click "Add release" - summarise the changelog in changes, and give the link to the changelog in the appropriate box) -* Update the Python cheeseshop - -.. code-block:: bash - - python setup.py register - -* For a major release, if appropriate, send an email to the CCL list, the GAMESS users list and the ADF users list. - -Creating a logfile release -~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Although all of the regression log files are stored on the web server, for the convenience of users we make periodic releases of all of these as one large .tar file (no point in .gz as they are already zipped). To create a release: - -.. code-block:: bash - - cd data - tar -c -f logfiles.tar -T regressionfiles.txt - -* Create a new release in package logfiles called logfiles-rnnn, where nnn is the current SVN revision. -* You can use a variation of the following text in the release notes: "A release of test logfiles for use with rnnn of the cclib code." - -Copying a logfile to sourceforge -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Use scp or winscp to connect to "USERNAME,cclib@web.sf.net". The logfiles are in htdocs/data. For interactive shell access, you will need to first type "ssh -t USERNAME,cclib@shell.sf.net create". After about 10 seconds, your own private shell will be created at SourceFroge which you can then log into. - -Release branches -~~~~~~~~~~~~~~~~ - -Historically, branches were managed by hand. Now I've now started using svnmerge.py, which keeps track of what's already been merged, and what's already been marked as 'not to merge'. - -* Create a release branch for cclib-1.0.1 - -.. code-block:: bash - - svn copy https://cclib.svn.sourceforge.net/svnroot/cclib/trunk https://cclib.svn.sourceforge.net/svnroot/cclib/branches/cclib-1.0.1 - -* Check it out - -.. code-block:: bash - - svn checkout https://svn.sourceforge.net/svnroot/branches/cclib-1.0.1 branchcclib101 - -* Initialise merge tracking - -.. code-block:: bash - - cd branchcclib101 - python svnmerge.py init ../trunk - svn commit -F svnmerge-commit-message.txt - -* Merge some stuff - -.. code-block:: bash - - python ..\svnmerge.py avail -S /trunk # or add "--log" - python ..\svnmerge.py merge -S /trunk # Merge all changes - svn commit -F svnmerge-commit-message.txt - -Source code upload policy -~~~~~~~~~~~~~~~~~~~~~~~~~ - -As a sort of guide for developers who are commiting source code revisions to the SVN repository, we recommend the following: - -* Run the tests before commiting (at least testall.py) -* If tests that previously passed now no longer do (when we have a more complete and stable release, this will read "If any tests fail"), and you don't have time to fix things before commiting, commits your changes to a branch as follows: - -.. code-block:: bash - - svn copy https://svn.sourceforge.net/svnroot/cclib/trunk https://..../branches/brokenadfparser - -m "Informative log message about why you're branching" - # change directory into the 'top' of your working copy where setup.py is - svn switch https://svn.sourceforge.net/svnroot/cclib/branches/brokenadfparser - # (note that this preserves the local modifications, only now these modifications - are to the branch instead of the trunk) - svn commit # (commits the local modifications to the branch) - -* As soon as the tests that previously passed are passed again, merge the changes and remove the branch (this should be within a revision or two of the branch): - -.. code-block:: bash - - svn log --stop-on-copy # (to find the revision when the branching took place) - svn switch https://...../mytrunk - svn merge --dry-run -r123:HEAD https://..../mybranch - svn merge -r123:HEAD https://..../mybranch - svn commit -m "Merging 123:HEAD of mybranch into trunk" - svn remove https://..../mybranch - -Ensuring source code quality -~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -To ensure source code quality, or at least consistency, we use the following tools/metrics: - -* `Cheesecake index` - -Testing -======= - -.. index:: - single: testing; unit tests - -Unit tests -~~~~~~~~~~ - -In order to check whether our parsers extract information in the correct format, with the correct units, we have unit tests that parse a series of basic data files (see below) of the same calculation undertaken with different programs. Running testall.py in the test directory runs the whole test suite, but it is also possible to individually run the tests for GeoOpts (testGeoOpt.py), Single Point calculations, and so on. - -Note that no change should be commited to the repository if it increases the number of failed tests (unless you are adding new tests, of course). - -.. index:: - single: testing; regressions - -Regression tests -~~~~~~~~~~~~~~~~ - -Regression tests ensure that bugs, once fixed, stay fixed. That is, for every bug found in our parsers, we should add a regression test and then fix the bug. This process is simplified by regression.py in the test directory. - -regression.py runs through all of our test data, both the basic data and the real life log files, uses 'ccopen()' to guess its type (checks for mistakes) and open it, parses it (catches any errors), and runs any relevant regression tests (catches any failures). - -New regression tests are added by creating a function testMyFileName_out following the examples at the start of *regression.py*. - -Test data -~~~~~~~~~ - -.. index:: - single: testing; test data - -The test directory (not included in the release version at the moment) contains all of the tests that help keep cclib working, and keep us sane. In general we use two types of data files for testing: - -1. 'basic' data files are stored in folders like "basicJaguar6.4" and are b3lyp/sto-3g calculations on 1,4-divinylbenzene (dvb) with C2h symmetry. These jobs (a geometry optimisation, a single point calculation (one restricted and another unrestricted), frequency calculation, a TD-DFT calculation, and any variants of these which break the parser such as symmetry/nosymmetry) are run for each parser. These data files are stored in SVN and may be included in future releases. -2. real-life parser-breaking files are stored in folders like "Jaguar6.4". These data files are *not* stored in SVN as they are often massive but are stored on the web server and downloaded using a shell script (contained in the data directory). These files are also available as a download from the File Release page on Sourceforge (only updated every so often). - -Doc tests -~~~~~~~~~ - -Doc tests are a nice Python invention for unit testing individual functions. To run the doctests in a particular file, you need to run the script. For example, "python gaussianparser.py" runs the doctests contained in gaussianparser.py. To run all of the doctests at once, you need to install a testing tool like nose, and then use the following command (note that many errors may be due to missing libraries like BioPython): - -.. code-block: bash - - > "C:\Program Files\Python24\Scripts\nosetests.exe" cclib --with-doctest -e test* -v - ERROR - ERROR - Doctest: cclib.bridge.cclib2openbabel.makeopenbabel ... ok - ERROR - ERROR - Doctest: cclib.parser.adfparser.ADF.normalisesym ... ok - Doctest: cclib.parser.gamessparser.GAMESS.normalise_aonames ... ok - Doctest: cclib.parser.gamessparser.GAMESS.normalisesym ... ok - Doctest: cclib.parser.gamessukparser.GAMESSUK.normalisesym ... ok - Doctest: cclib.parser.gaussianparser.Gaussian.normalisesym ... ok - Doctest: cclib.parser.jaguarparser.Jaguar.normalisesym ... ok - Doctest: cclib.parser.logfileparser.Logfile.float ... ok - Doctest: cclib.parser.utils.PeriodicTable ... ok - Doctest: cclib.parser.utils.convertor ... ok - ERROR - ERROR - ...... - -Other useful pages -================== - -* The `methods in the development version`_ -* The `parsed data in the development version`_ -* The `progress page`_, which describes where we are and what we are trying to do - -.. _`methods in the development version`: methods_dev.html -.. _`parsed data in the development version`: data_dev.html -.. _`progress page`: progress.html diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/_static/ajax-loader.gif b/_static/ajax-loader.gif deleted file mode 100644 index 61faf8ca..00000000 Binary files a/_static/ajax-loader.gif and /dev/null differ diff --git a/_static/base-stemmer.js b/_static/base-stemmer.js new file mode 100644 index 00000000..e6fa0c49 --- /dev/null +++ b/_static/base-stemmer.js @@ -0,0 +1,476 @@ +// @ts-check + +/**@constructor*/ +BaseStemmer = function() { + /** @protected */ + this.current = ''; + this.cursor = 0; + this.limit = 0; + this.limit_backward = 0; + this.bra = 0; + this.ket = 0; + + /** + * @param {string} value + */ + this.setCurrent = function(value) { + this.current = value; + this.cursor = 0; + this.limit = this.current.length; + this.limit_backward = 0; + this.bra = this.cursor; + this.ket = this.limit; + }; + + /** + * @return {string} + */ + this.getCurrent = function() { + return this.current; + }; + + /** + * @param {BaseStemmer} other + */ + this.copy_from = function(other) { + /** @protected */ + this.current = other.current; + this.cursor = other.cursor; + this.limit = other.limit; + this.limit_backward = other.limit_backward; + this.bra = other.bra; + this.ket = other.ket; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.in_grouping = function(s, min, max) { + /** @protected */ + if (this.cursor >= this.limit) return false; + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) return false; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return false; + this.cursor++; + return true; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_in_grouping = function(s, min, max) { + /** @protected */ + while (this.cursor < this.limit) { + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) + return true; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) + return true; + this.cursor++; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.in_grouping_b = function(s, min, max) { + /** @protected */ + if (this.cursor <= this.limit_backward) return false; + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) return false; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return false; + this.cursor--; + return true; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_in_grouping_b = function(s, min, max) { + /** @protected */ + while (this.cursor > this.limit_backward) { + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) return true; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return true; + this.cursor--; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.out_grouping = function(s, min, max) { + /** @protected */ + if (this.cursor >= this.limit) return false; + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) { + this.cursor++; + return true; + } + ch -= min; + if ((s[ch >>> 3] & (0X1 << (ch & 0x7))) == 0) { + this.cursor++; + return true; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_out_grouping = function(s, min, max) { + /** @protected */ + while (this.cursor < this.limit) { + var ch = this.current.charCodeAt(this.cursor); + if (ch <= max && ch >= min) { + ch -= min; + if ((s[ch >>> 3] & (0X1 << (ch & 0x7))) != 0) { + return true; + } + } + this.cursor++; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.out_grouping_b = function(s, min, max) { + /** @protected */ + if (this.cursor <= this.limit_backward) return false; + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) { + this.cursor--; + return true; + } + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) { + this.cursor--; + return true; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_out_grouping_b = function(s, min, max) { + /** @protected */ + while (this.cursor > this.limit_backward) { + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch <= max && ch >= min) { + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) != 0) { + return true; + } + } + this.cursor--; + } + return false; + }; + + /** + * @param {string} s + * @return {boolean} + */ + this.eq_s = function(s) + { + /** @protected */ + if (this.limit - this.cursor < s.length) return false; + if (this.current.slice(this.cursor, this.cursor + s.length) != s) + { + return false; + } + this.cursor += s.length; + return true; + }; + + /** + * @param {string} s + * @return {boolean} + */ + this.eq_s_b = function(s) + { + /** @protected */ + if (this.cursor - this.limit_backward < s.length) return false; + if (this.current.slice(this.cursor - s.length, this.cursor) != s) + { + return false; + } + this.cursor -= s.length; + return true; + }; + + /** + * @param {Among[]} v + * @return {number} + */ + this.find_among = function(v) + { + /** @protected */ + var i = 0; + var j = v.length; + + var c = this.cursor; + var l = this.limit; + + var common_i = 0; + var common_j = 0; + + var first_key_inspected = false; + + while (true) + { + var k = i + ((j - i) >>> 1); + var diff = 0; + var common = common_i < common_j ? common_i : common_j; // smaller + // w[0]: string, w[1]: substring_i, w[2]: result, w[3]: function (optional) + var w = v[k]; + var i2; + for (i2 = common; i2 < w[0].length; i2++) + { + if (c + common == l) + { + diff = -1; + break; + } + diff = this.current.charCodeAt(c + common) - w[0].charCodeAt(i2); + if (diff != 0) break; + common++; + } + if (diff < 0) + { + j = k; + common_j = common; + } + else + { + i = k; + common_i = common; + } + if (j - i <= 1) + { + if (i > 0) break; // v->s has been inspected + if (j == i) break; // only one item in v + + // - but now we need to go round once more to get + // v->s inspected. This looks messy, but is actually + // the optimal approach. + + if (first_key_inspected) break; + first_key_inspected = true; + } + } + do { + var w = v[i]; + if (common_i >= w[0].length) + { + this.cursor = c + w[0].length; + if (w.length < 4) return w[2]; + var res = w[3](this); + this.cursor = c + w[0].length; + if (res) return w[2]; + } + i = w[1]; + } while (i >= 0); + return 0; + }; + + // find_among_b is for backwards processing. Same comments apply + /** + * @param {Among[]} v + * @return {number} + */ + this.find_among_b = function(v) + { + /** @protected */ + var i = 0; + var j = v.length + + var c = this.cursor; + var lb = this.limit_backward; + + var common_i = 0; + var common_j = 0; + + var first_key_inspected = false; + + while (true) + { + var k = i + ((j - i) >> 1); + var diff = 0; + var common = common_i < common_j ? common_i : common_j; + var w = v[k]; + var i2; + for (i2 = w[0].length - 1 - common; i2 >= 0; i2--) + { + if (c - common == lb) + { + diff = -1; + break; + } + diff = this.current.charCodeAt(c - 1 - common) - w[0].charCodeAt(i2); + if (diff != 0) break; + common++; + } + if (diff < 0) + { + j = k; + common_j = common; + } + else + { + i = k; + common_i = common; + } + if (j - i <= 1) + { + if (i > 0) break; + if (j == i) break; + if (first_key_inspected) break; + first_key_inspected = true; + } + } + do { + var w = v[i]; + if (common_i >= w[0].length) + { + this.cursor = c - w[0].length; + if (w.length < 4) return w[2]; + var res = w[3](this); + this.cursor = c - w[0].length; + if (res) return w[2]; + } + i = w[1]; + } while (i >= 0); + return 0; + }; + + /* to replace chars between c_bra and c_ket in this.current by the + * chars in s. + */ + /** + * @param {number} c_bra + * @param {number} c_ket + * @param {string} s + * @return {number} + */ + this.replace_s = function(c_bra, c_ket, s) + { + /** @protected */ + var adjustment = s.length - (c_ket - c_bra); + this.current = this.current.slice(0, c_bra) + s + this.current.slice(c_ket); + this.limit += adjustment; + if (this.cursor >= c_ket) this.cursor += adjustment; + else if (this.cursor > c_bra) this.cursor = c_bra; + return adjustment; + }; + + /** + * @return {boolean} + */ + this.slice_check = function() + { + /** @protected */ + if (this.bra < 0 || + this.bra > this.ket || + this.ket > this.limit || + this.limit > this.current.length) + { + return false; + } + return true; + }; + + /** + * @param {number} c_bra + * @return {boolean} + */ + this.slice_from = function(s) + { + /** @protected */ + var result = false; + if (this.slice_check()) + { + this.replace_s(this.bra, this.ket, s); + result = true; + } + return result; + }; + + /** + * @return {boolean} + */ + this.slice_del = function() + { + /** @protected */ + return this.slice_from(""); + }; + + /** + * @param {number} c_bra + * @param {number} c_ket + * @param {string} s + */ + this.insert = function(c_bra, c_ket, s) + { + /** @protected */ + var adjustment = this.replace_s(c_bra, c_ket, s); + if (c_bra <= this.bra) this.bra += adjustment; + if (c_bra <= this.ket) this.ket += adjustment; + }; + + /** + * @return {string} + */ + this.slice_to = function() + { + /** @protected */ + var result = ''; + if (this.slice_check()) + { + result = this.current.slice(this.bra, this.ket); + } + return result; + }; + + /** + * @return {string} + */ + this.assign_to = function() + { + /** @protected */ + return this.current.slice(0, this.limit); + }; +}; diff --git a/_static/basic.css b/_static/basic.css index 43e8bafa..4738b2ed 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -1,12 +1,5 @@ /* - * basic.css - * ~~~~~~~~~ - * * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ /* -- main layout ----------------------------------------------------------- */ @@ -15,6 +8,12 @@ div.clearer { clear: both; } +div.section::after { + display: block; + content: ''; + clear: left; +} + /* -- relbar ---------------------------------------------------------------- */ div.related { @@ -52,6 +51,8 @@ div.sphinxsidebar { width: 230px; margin-left: -100%; font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; } div.sphinxsidebar ul { @@ -79,37 +80,46 @@ div.sphinxsidebar input { font-size: 1em; } +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + div.sphinxsidebar #searchbox input[type="text"] { - width: 170px; + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; } div.sphinxsidebar #searchbox input[type="submit"] { - width: 30px; + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; } + img { border: 0; + max-width: 100%; } /* -- search page ----------------------------------------------------------- */ ul.search { - margin: 10px 0 0 20px; - padding: 0; + margin-top: 10px; } ul.search li { - padding: 5px 0 5px 20px; - background-image: url(file.png); - background-repeat: no-repeat; - background-position: 0 7px; + padding: 5px 0; } ul.search li a { font-weight: bold; } -ul.search li div.context { +ul.search li p.context { color: #888; margin: 2px 0 0 30px; text-align: left; @@ -123,6 +133,8 @@ ul.keywordmatches li.goodmatch a { table.contentstable { width: 90%; + margin-left: auto; + margin-right: auto; } table.contentstable p.biglink { @@ -150,9 +162,14 @@ table.indextable td { vertical-align: top; } -table.indextable dl, table.indextable dd { +table.indextable ul { margin-top: 0; margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; } table.indextable tr.pcap { @@ -184,19 +201,45 @@ div.genindex-jumpbox { padding: 0.4em; } +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + /* -- general body styles --------------------------------------------------- */ +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + a.headerlink { visibility: hidden; } +a:visited { + color: #551A8B; +} + h1:hover > a.headerlink, h2:hover > a.headerlink, h3:hover > a.headerlink, h4:hover > a.headerlink, h5:hover > a.headerlink, h6:hover > a.headerlink, -dt:hover > a.headerlink { +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { visibility: visible; } @@ -208,10 +251,6 @@ div.body td { text-align: left; } -.field-list ul { - padding-left: 1em; -} - .first { margin-top: 0 !important; } @@ -221,19 +260,25 @@ p.rubric { font-weight: bold; } -img.align-left, .figure.align-left, object.align-left { +img.align-left, figure.align-left, .figure.align-left, object.align-left { clear: left; float: left; margin-right: 1em; } -img.align-right, .figure.align-right, object.align-right { +img.align-right, figure.align-right, .figure.align-right, object.align-right { clear: right; float: right; margin-left: 1em; } -img.align-center, .figure.align-center, object.align-center { +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { display: block; margin-left: auto; margin-right: auto; @@ -247,30 +292,45 @@ img.align-center, .figure.align-center, object.align-center { text-align: center; } +.align-default { + text-align: center; +} + .align-right { text-align: right; } /* -- sidebars -------------------------------------------------------------- */ -div.sidebar { +div.sidebar, +aside.sidebar { margin: 0 0 0.5em 1em; border: 1px solid #ddb; - padding: 7px 7px 0 7px; + padding: 7px; background-color: #ffe; width: 40%; float: right; + clear: right; + overflow-x: auto; } p.sidebar-title { font-weight: bold; } +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + /* -- topics ---------------------------------------------------------------- */ +nav.contents, +aside.topic, div.topic { border: 1px solid #ccc; - padding: 7px 7px 0 7px; + padding: 7px; margin: 10px 0 10px 0; } @@ -292,10 +352,6 @@ div.admonition dt { font-weight: bold; } -div.admonition dl { - margin-bottom: 0; -} - p.admonition-title { margin: 0px 10px 5px 0px; font-weight: bold; @@ -306,13 +362,55 @@ div.body p.centered { margin-top: 25px; } +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + /* -- tables ---------------------------------------------------------------- */ table.docutils { + margin-top: 10px; + margin-bottom: 10px; border: 0; border-collapse: collapse; } +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + table.docutils td, table.docutils th { padding: 1px 8px 1px 5px; border-top: 0; @@ -321,14 +419,6 @@ table.docutils td, table.docutils th { border-bottom: 1px solid #aaa; } -table.field-list td, table.field-list th { - border: 0 !important; -} - -table.footnote td, table.footnote th { - border: 0 !important; -} - th { text-align: left; padding-right: 5px; @@ -343,6 +433,126 @@ table.citation td { border-bottom: none; } +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + /* -- other body styles ----------------------------------------------------- */ ol.arabic { @@ -365,11 +575,81 @@ ol.upperroman { list-style: upper-roman; } +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + dl { margin-bottom: 15px; } -dd p { +dd > :first-child { margin-top: 0px; } @@ -383,30 +663,32 @@ dd { margin-left: 30px; } -dt:target, .highlighted { - background-color: #fbe54e; +.sig dd { + margin-top: 0px; + margin-bottom: 0px; } -dl.glossary dt { - font-weight: bold; - font-size: 1.1em; +.sig dl { + margin-top: 0px; + margin-bottom: 0px; } -.field-list ul { - margin: 0; - padding-left: 1em; +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; } -.field-list p { - margin: 0; +dt:target, span.highlighted { + background-color: #fbe54e; } -.refcount { - color: #060; +rect.highlighted { + fill: #fbe54e; } -.optional { - font-size: 1.3em; +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; } .versionmodified { @@ -447,6 +729,13 @@ dl.glossary dt { font-style: oblique; } +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + abbr, acronym { border-bottom: dotted 1px; cursor: help; @@ -459,37 +748,105 @@ pre { overflow-y: hidden; /* fixes display issues on Chrome browsers */ } +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + td.linenos pre { - padding: 5px 0px; border: 0; background-color: transparent; color: #aaa; } table.highlighttable { - margin-left: 0.5em; + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; } table.highlighttable td { - padding: 0 0.5em 0 0.5em; + margin: 0; + padding: 0; } -tt.descname { - background-color: transparent; - font-weight: bold; - font-size: 1.2em; +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; } -tt.descclassname { +div.code-block-caption code { background-color: 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#efc2c2; -} - -.note tt { - background: #d6d6d6; -} - -.viewcode-back { - font-family: sans-serif; -} - -div.viewcode-block:target { - background-color: #f4debf; - border-top: 1px solid #ac9; - border-bottom: 1px solid #ac9; -} \ No newline at end of file diff --git a/_static/doctools.js b/_static/doctools.js index d4619fdf..807cdb17 100644 --- a/_static/doctools.js +++ b/_static/doctools.js @@ -1,247 +1,150 @@ /* - * doctools.js - * ~~~~~~~~~~~ - * - * Sphinx JavaScript utilities for all documentation. - * - * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * + * Base JavaScript utilities for all Sphinx HTML documentation. */ - -/** - * select a different prefix for underscore - */ -$u = _.noConflict(); - -/** - * make the code below compatible with browsers without - * an installed firebug like debugger -if (!window.console || !console.firebug) { - var names = ["log", "debug", "info", "warn", "error", "assert", "dir", - "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace", - "profile", "profileEnd"]; - window.console = {}; - for (var i = 0; i < names.length; ++i) - window.console[names[i]] = function() {}; -} - */ - -/** - * small helper function to urldecode strings - */ -jQuery.urldecode = function(x) { - return decodeURIComponent(x).replace(/\+/g, ' '); -} - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. Multiple values per key are supported, - * it will always return arrays of strings for the value parts. - */ -jQuery.getQueryParameters = function(s) { - if (typeof s == 'undefined') - s = document.location.search; - var parts = s.substr(s.indexOf('?') + 1).split('&'); - var result = {}; - for (var i = 0; i < parts.length; i++) { - var tmp = parts[i].split('=', 2); - var key = jQuery.urldecode(tmp[0]); - var value = jQuery.urldecode(tmp[1]); - if (key in result) - result[key].push(value); - else - result[key] = [value]; - } - return result; -}; - -/** - * small function to check if an array contains - * a given item. - */ -jQuery.contains = function(arr, item) { - for (var i = 0; i < arr.length; i++) { - if (arr[i] == item) - return true; - } - return false; -}; - -/** - * highlight a given string on a jquery object by wrapping it in - * span elements with the given class name. - */ -jQuery.fn.highlightText = function(text, className) { - function highlight(node) { - if (node.nodeType == 3) { - var val = node.nodeValue; - var pos = val.toLowerCase().indexOf(text); - if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) { - var span = document.createElement("span"); - span.className = className; - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - } - } - else if (!jQuery(node).is("button, select, textarea")) { - jQuery.each(node.childNodes, function() { - highlight(this); - }); - } +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); } - return this.each(function() { - highlight(this); - }); }; /** * Small JavaScript module for the documentation. */ -var Documentation = { - - init : function() { - this.fixFirefoxAnchorBug(); - this.highlightSearchWords(); - this.initIndexTable(); +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); }, /** * i18n support */ - TRANSLATIONS : {}, - PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; }, - LOCALE : 'unknown', + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", // gettext and ngettext don't access this so that the functions // can safely bound to a different name (_ = Documentation.gettext) - gettext : function(string) { - var translated = Documentation.TRANSLATIONS[string]; - if (typeof translated == 'undefined') - return string; - return (typeof translated == 'string') ? translated : translated[0]; - }, - - ngettext : function(singular, plural, n) { - var translated = Documentation.TRANSLATIONS[singular]; - if (typeof translated == 'undefined') - return (n == 1) ? singular : plural; - return translated[Documentation.PLURALEXPR(n)]; - }, - - addTranslations : function(catalog) { - for (var key in catalog.messages) - this.TRANSLATIONS[key] = catalog.messages[key]; - this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')'); - this.LOCALE = catalog.locale; - }, - - /** - * add context elements like header anchor links - */ - addContextElements : function() { - $('div[id] > :header:first').each(function() { - $('\u00B6'). - attr('href', '#' + this.id). - attr('title', _('Permalink to this headline')). - appendTo(this); - }); - $('dt[id]').each(function() { - $('\u00B6'). - attr('href', '#' + this.id). - attr('title', _('Permalink to this definition')). - appendTo(this); - }); + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } }, - /** - * workaround a firefox stupidity - */ - fixFirefoxAnchorBug : function() { - if (document.location.hash && $.browser.mozilla) - window.setTimeout(function() { - document.location.href += ''; - }, 10); + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; }, - /** - * highlight the search words provided in the url in the text - */ - highlightSearchWords : function() { - var params = $.getQueryParameters(); - var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : []; - if (terms.length) { - var body = $('div.body'); - window.setTimeout(function() { - $.each(terms, function() { - body.highlightText(this.toLowerCase(), 'highlighted'); - }); - }, 10); - $('

' + _('Hide Search Matches') + '

') - .appendTo($('#searchbox')); - } + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})`, + ); + Documentation.LOCALE = catalog.locale; }, /** - * init the domain index toggle buttons + * helper function to focus on search bar */ - initIndexTable : function() { - var togglers = $('img.toggler').click(function() { - var src = $(this).attr('src'); - var idnum = $(this).attr('id').substr(7); - $('tr.cg-' + idnum).toggle(); - if (src.substr(-9) == 'minus.png') - $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); - else - $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); - }).css('display', ''); - if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { - togglers.click(); - } + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); }, /** - * helper function to hide the search marks again + * Initialise the domain index toggle buttons */ - hideSearchWords : function() { - $('#searchbox .highlight-link').fadeOut(300); - $('span.highlighted').removeClass('highlighted'); + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)), + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); }, - /** - * make the url absolute - */ - makeURL : function(relativeURL) { - return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; - }, + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS + && !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) + return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } - /** - * get the current relative url - */ - getCurrentURL : function() { - var path = document.location.pathname; - var parts = path.split(/\//); - $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { - if (this == '..') - parts.pop(); + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } }); - var url = parts.join('/'); - return path.substring(url.lastIndexOf('/') + 1, path.length - 1); - } + }, }; // quick alias for translations -_ = Documentation.gettext; +const _ = Documentation.gettext; -$(document).ready(function() { - Documentation.init(); -}); +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 00000000..a2422f1e --- /dev/null +++ b/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '1.8.1', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/_static/down-pressed.png b/_static/down-pressed.png deleted file mode 100644 index 6f7ad782..00000000 Binary files a/_static/down-pressed.png and /dev/null differ diff --git a/_static/down.png b/_static/down.png deleted file mode 100644 index 3003a887..00000000 Binary files a/_static/down.png and /dev/null differ diff --git a/_static/english-stemmer.js b/_static/english-stemmer.js new file mode 100644 index 00000000..056760ee --- /dev/null +++ b/_static/english-stemmer.js @@ -0,0 +1,1066 @@ +// Generated from english.sbl by Snowball 3.0.1 - https://snowballstem.org/ + +/**@constructor*/ +var EnglishStemmer = function() { + var base = new BaseStemmer(); + + /** @const */ var a_0 = [ + ["arsen", -1, -1], + ["commun", -1, -1], + ["emerg", -1, -1], + ["gener", -1, -1], + ["later", -1, -1], + ["organ", -1, -1], + ["past", -1, -1], + ["univers", -1, -1] + ]; + + /** @const */ var a_1 = [ + ["'", -1, 1], + ["'s'", 0, 1], + ["'s", -1, 1] + ]; + + /** @const */ var a_2 = [ + ["ied", -1, 2], + ["s", -1, 3], + ["ies", 1, 2], + ["sses", 1, 1], + ["ss", 1, -1], + ["us", 1, -1] + ]; + + /** @const */ var a_3 = [ + ["succ", -1, 1], + ["proc", -1, 1], + ["exc", -1, 1] + ]; + + /** @const */ var a_4 = [ + ["even", -1, 2], + ["cann", -1, 2], + ["inn", -1, 2], + ["earr", -1, 2], + ["herr", -1, 2], + ["out", -1, 2], + ["y", -1, 1] + ]; + + /** @const */ var a_5 = [ + ["", -1, -1], + ["ed", 0, 2], + ["eed", 1, 1], + ["ing", 0, 3], + ["edly", 0, 2], + ["eedly", 4, 1], + ["ingly", 0, 2] + ]; + + /** @const */ var a_6 = [ + ["", -1, 3], + ["bb", 0, 2], + ["dd", 0, 2], + ["ff", 0, 2], + ["gg", 0, 2], + ["bl", 0, 1], + ["mm", 0, 2], + ["nn", 0, 2], + ["pp", 0, 2], + ["rr", 0, 2], + ["at", 0, 1], + ["tt", 0, 2], + ["iz", 0, 1] + ]; + + /** @const */ var a_7 = [ + ["anci", -1, 3], + ["enci", -1, 2], + ["ogi", -1, 14], + ["li", -1, 16], + ["bli", 3, 12], + ["abli", 4, 4], + ["alli", 3, 8], + ["fulli", 3, 9], + ["lessli", 3, 15], + ["ousli", 3, 10], + ["entli", 3, 5], + ["aliti", -1, 8], + ["biliti", -1, 12], + ["iviti", -1, 11], + ["tional", -1, 1], + ["ational", 14, 7], + ["alism", -1, 8], + ["ation", -1, 7], + ["ization", 17, 6], + ["izer", -1, 6], + ["ator", -1, 7], + ["iveness", -1, 11], + ["fulness", -1, 9], + ["ousness", -1, 10], + ["ogist", -1, 13] + ]; + + /** @const */ var a_8 = [ + ["icate", -1, 4], + ["ative", -1, 6], + ["alize", -1, 3], + ["iciti", -1, 4], + ["ical", -1, 4], + ["tional", -1, 1], + ["ational", 5, 2], + ["ful", -1, 5], + ["ness", -1, 5] + ]; + + /** @const */ var a_9 = [ + ["ic", -1, 1], + ["ance", -1, 1], + ["ence", -1, 1], + ["able", -1, 1], + ["ible", -1, 1], + ["ate", -1, 1], + ["ive", -1, 1], + ["ize", -1, 1], + ["iti", -1, 1], + ["al", -1, 1], + ["ism", -1, 1], + ["ion", -1, 2], + ["er", -1, 1], + ["ous", -1, 1], + ["ant", -1, 1], + ["ent", -1, 1], + ["ment", 15, 1], + ["ement", 16, 1] + ]; + + /** @const */ var a_10 = [ + ["e", -1, 1], + ["l", -1, 2] + ]; + + /** @const */ var a_11 = [ + ["andes", -1, -1], + ["atlas", -1, -1], + ["bias", -1, -1], + ["cosmos", -1, -1], + ["early", -1, 5], + ["gently", -1, 3], + ["howe", -1, -1], + ["idly", -1, 2], + ["news", -1, -1], + ["only", -1, 6], + ["singly", -1, 7], + ["skies", -1, 1], + ["sky", -1, -1], + ["ugly", -1, 4] + ]; + + /** @const */ var /** Array */ g_aeo = [17, 64]; + + /** @const */ var /** Array */ g_v = [17, 65, 16, 1]; + + /** @const */ var /** Array */ g_v_WXY = [1, 17, 65, 208, 1]; + + /** @const */ var /** Array */ g_valid_LI = [55, 141, 2]; + + var /** boolean */ B_Y_found = false; + var /** number */ I_p2 = 0; + var /** number */ I_p1 = 0; + + + /** @return {boolean} */ + function r_prelude() { + B_Y_found = false; + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + base.bra = base.cursor; + if (!(base.eq_s("'"))) + { + break lab0; + } + base.ket = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + base.cursor = v_1; + /** @const */ var /** number */ v_2 = base.cursor; + lab1: { + base.bra = base.cursor; + if (!(base.eq_s("y"))) + { + break lab1; + } + base.ket = base.cursor; + if (!base.slice_from("Y")) + { + return false; + } + B_Y_found = true; + } + base.cursor = v_2; + /** @const */ var /** number */ v_3 = base.cursor; + lab2: { + while(true) + { + /** @const */ var /** number */ v_4 = base.cursor; + lab3: { + golab4: while(true) + { + /** @const */ var /** number */ v_5 = base.cursor; + lab5: { + if (!(base.in_grouping(g_v, 97, 121))) + { + break lab5; + } + base.bra = base.cursor; + if (!(base.eq_s("y"))) + { + break lab5; + } + base.ket = base.cursor; + base.cursor = v_5; + break golab4; + } + base.cursor = v_5; + if (base.cursor >= base.limit) + { + break lab3; + } + base.cursor++; + } + if (!base.slice_from("Y")) + { + return false; + } + B_Y_found = true; + continue; + } + base.cursor = v_4; + break; + } + } + base.cursor = v_3; + return true; + }; + + /** @return {boolean} */ + function r_mark_regions() { + I_p1 = base.limit; + I_p2 = base.limit; + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + lab1: { + /** @const */ var /** number */ v_2 = base.cursor; + lab2: { + if (base.find_among(a_0) == 0) + { + break lab2; + } + break lab1; + } + base.cursor = v_2; + if (!base.go_out_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + if (!base.go_in_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + } + I_p1 = base.cursor; + if (!base.go_out_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + if (!base.go_in_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + I_p2 = base.cursor; + } + base.cursor = v_1; + return true; + }; + + /** @return {boolean} */ + function r_shortv() { + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.out_grouping_b(g_v_WXY, 89, 121))) + { + break lab1; + } + if (!(base.in_grouping_b(g_v, 97, 121))) + { + break lab1; + } + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + lab2: { + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab2; + } + if (!(base.in_grouping_b(g_v, 97, 121))) + { + break lab2; + } + if (base.cursor > base.limit_backward) + { + break lab2; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("past"))) + { + return false; + } + } + return true; + }; + + /** @return {boolean} */ + function r_R1() { + return I_p1 <= base.cursor; + }; + + /** @return {boolean} */ + function r_R2() { + return I_p2 <= base.cursor; + }; + + /** @return {boolean} */ + function r_Step_1a() { + var /** number */ among_var; + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab0: { + base.ket = base.cursor; + if (base.find_among_b(a_1) == 0) + { + base.cursor = base.limit - v_1; + break lab0; + } + base.bra = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + base.ket = base.cursor; + among_var = base.find_among_b(a_2); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + switch (among_var) { + case 1: + if (!base.slice_from("ss")) + { + return false; + } + break; + case 2: + lab1: { + /** @const */ var /** number */ v_2 = base.limit - base.cursor; + lab2: { + { + /** @const */ var /** number */ c1 = base.cursor - 2; + if (c1 < base.limit_backward) + { + break lab2; + } + base.cursor = c1; + } + if (!base.slice_from("i")) + { + return false; + } + break lab1; + } + base.cursor = base.limit - v_2; + if (!base.slice_from("ie")) + { + return false; + } + } + break; + case 3: + if (base.cursor <= base.limit_backward) + { + return false; + } + base.cursor--; + if (!base.go_out_grouping_b(g_v, 97, 121)) + { + return false; + } + base.cursor--; + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_1b() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_5); + base.bra = base.cursor; + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + switch (among_var) { + case 1: + /** @const */ var /** number */ v_2 = base.limit - base.cursor; + lab2: { + lab3: { + /** @const */ var /** number */ v_3 = base.limit - base.cursor; + lab4: { + if (base.find_among_b(a_3) == 0) + { + break lab4; + } + if (base.cursor > base.limit_backward) + { + break lab4; + } + break lab3; + } + base.cursor = base.limit - v_3; + if (!r_R1()) + { + break lab2; + } + if (!base.slice_from("ee")) + { + return false; + } + } + } + base.cursor = base.limit - v_2; + break; + case 2: + break lab1; + case 3: + among_var = base.find_among_b(a_4); + if (among_var == 0) + { + break lab1; + } + switch (among_var) { + case 1: + /** @const */ var /** number */ v_4 = base.limit - base.cursor; + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab1; + } + if (base.cursor > base.limit_backward) + { + break lab1; + } + base.cursor = base.limit - v_4; + base.bra = base.cursor; + if (!base.slice_from("ie")) + { + return false; + } + break; + case 2: + if (base.cursor > base.limit_backward) + { + break lab1; + } + break; + } + break; + } + break lab0; + } + base.cursor = base.limit - v_1; + /** @const */ var /** number */ v_5 = base.limit - base.cursor; + if (!base.go_out_grouping_b(g_v, 97, 121)) + { + return false; + } + base.cursor--; + base.cursor = base.limit - v_5; + if (!base.slice_del()) + { + return false; + } + base.ket = base.cursor; + base.bra = base.cursor; + /** @const */ var /** number */ v_6 = base.limit - base.cursor; + among_var = base.find_among_b(a_6); + switch (among_var) { + case 1: + if (!base.slice_from("e")) + { + return false; + } + return false; + case 2: + { + /** @const */ var /** number */ v_7 = base.limit - base.cursor; + lab5: { + if (!(base.in_grouping_b(g_aeo, 97, 111))) + { + break lab5; + } + if (base.cursor > base.limit_backward) + { + break lab5; + } + return false; + } + base.cursor = base.limit - v_7; + } + break; + case 3: + if (base.cursor != I_p1) + { + return false; + } + /** @const */ var /** number */ v_8 = base.limit - base.cursor; + if (!r_shortv()) + { + return false; + } + base.cursor = base.limit - v_8; + if (!base.slice_from("e")) + { + return false; + } + return false; + } + base.cursor = base.limit - v_6; + base.ket = base.cursor; + if (base.cursor <= base.limit_backward) + { + return false; + } + base.cursor--; + base.bra = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + return true; + }; + + /** @return {boolean} */ + function r_Step_1c() { + base.ket = base.cursor; + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.eq_s_b("y"))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("Y"))) + { + return false; + } + } + base.bra = base.cursor; + if (!(base.out_grouping_b(g_v, 97, 121))) + { + return false; + } + lab2: { + if (base.cursor > base.limit_backward) + { + break lab2; + } + return false; + } + if (!base.slice_from("i")) + { + return false; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_2() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_7); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R1()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("tion")) + { + return false; + } + break; + case 2: + if (!base.slice_from("ence")) + { + return false; + } + break; + case 3: + if (!base.slice_from("ance")) + { + return false; + } + break; + case 4: + if (!base.slice_from("able")) + { + return false; + } + break; + case 5: + if (!base.slice_from("ent")) + { + return false; + } + break; + case 6: + if (!base.slice_from("ize")) + { + return false; + } + break; + case 7: + if (!base.slice_from("ate")) + { + return false; + } + break; + case 8: + if (!base.slice_from("al")) + { + return false; + } + break; + case 9: + if (!base.slice_from("ful")) + { + return false; + } + break; + case 10: + if (!base.slice_from("ous")) + { + return false; + } + break; + case 11: + if (!base.slice_from("ive")) + { + return false; + } + break; + case 12: + if (!base.slice_from("ble")) + { + return false; + } + break; + case 13: + if (!base.slice_from("og")) + { + return false; + } + break; + case 14: + if (!(base.eq_s_b("l"))) + { + return false; + } + if (!base.slice_from("og")) + { + return false; + } + break; + case 15: + if (!base.slice_from("less")) + { + return false; + } + break; + case 16: + if (!(base.in_grouping_b(g_valid_LI, 99, 116))) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_3() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_8); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R1()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("tion")) + { + return false; + } + break; + case 2: + if (!base.slice_from("ate")) + { + return false; + } + break; + case 3: + if (!base.slice_from("al")) + { + return false; + } + break; + case 4: + if (!base.slice_from("ic")) + { + return false; + } + break; + case 5: + if (!base.slice_del()) + { + return false; + } + break; + case 6: + if (!r_R2()) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_4() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_9); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R2()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_del()) + { + return false; + } + break; + case 2: + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.eq_s_b("s"))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("t"))) + { + return false; + } + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_5() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_10); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + switch (among_var) { + case 1: + lab0: { + lab1: { + if (!r_R2()) + { + break lab1; + } + break lab0; + } + if (!r_R1()) + { + return false; + } + { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab2: { + if (!r_shortv()) + { + break lab2; + } + return false; + } + base.cursor = base.limit - v_1; + } + } + if (!base.slice_del()) + { + return false; + } + break; + case 2: + if (!r_R2()) + { + return false; + } + if (!(base.eq_s_b("l"))) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_exception1() { + var /** number */ among_var; + base.bra = base.cursor; + among_var = base.find_among(a_11); + if (among_var == 0) + { + return false; + } + base.ket = base.cursor; + if (base.cursor < base.limit) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("sky")) + { + return false; + } + break; + case 2: + if (!base.slice_from("idl")) + { + return false; + } + break; + case 3: + if (!base.slice_from("gentl")) + { + return false; + } + break; + case 4: + if (!base.slice_from("ugli")) + { + return false; + } + break; + case 5: + if (!base.slice_from("earli")) + { + return false; + } + break; + case 6: + if (!base.slice_from("onli")) + { + return false; + } + break; + case 7: + if (!base.slice_from("singl")) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_postlude() { + if (!B_Y_found) + { + return false; + } + while(true) + { + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + golab1: while(true) + { + /** @const */ var /** number */ v_2 = base.cursor; + lab2: { + base.bra = base.cursor; + if (!(base.eq_s("Y"))) + { + break lab2; + } + base.ket = base.cursor; + base.cursor = v_2; + break golab1; + } + base.cursor = v_2; + if (base.cursor >= base.limit) + { + break lab0; + } + base.cursor++; + } + if (!base.slice_from("y")) + { + return false; + } + continue; + } + base.cursor = v_1; + break; + } + return true; + }; + + this.stem = /** @return {boolean} */ function() { + lab0: { + /** @const */ var /** number */ v_1 = base.cursor; + lab1: { + if (!r_exception1()) + { + break lab1; + } + break lab0; + } + base.cursor = v_1; + lab2: { + { + /** @const */ var /** number */ v_2 = base.cursor; + lab3: { + { + /** @const */ var /** number */ c1 = base.cursor + 3; + if (c1 > base.limit) + { + break lab3; + } + base.cursor = c1; + } + break lab2; + } + base.cursor = v_2; + } + break lab0; + } + base.cursor = v_1; + r_prelude(); + r_mark_regions(); + base.limit_backward = base.cursor; base.cursor = base.limit; + /** @const */ var /** number */ v_3 = base.limit - base.cursor; + r_Step_1a(); + base.cursor = base.limit - v_3; + /** @const */ var /** number */ v_4 = base.limit - base.cursor; + r_Step_1b(); + base.cursor = base.limit - v_4; + /** @const */ var /** number */ v_5 = base.limit - base.cursor; + r_Step_1c(); + base.cursor = base.limit - v_5; + /** @const */ var /** number */ v_6 = base.limit - base.cursor; + r_Step_2(); + base.cursor = base.limit - v_6; + /** @const */ var /** number */ v_7 = base.limit - base.cursor; + r_Step_3(); + base.cursor = base.limit - v_7; + /** @const */ var /** number */ v_8 = base.limit - base.cursor; + r_Step_4(); + base.cursor = base.limit - v_8; + /** @const */ var /** number */ v_9 = base.limit - base.cursor; + r_Step_5(); + base.cursor = base.limit - v_9; + base.cursor = base.limit_backward; + /** @const */ var /** number */ v_10 = base.cursor; + r_postlude(); + base.cursor = v_10; + } + return true; + }; + + /**@return{string}*/ + this['stemWord'] = function(/**string*/word) { + base.setCurrent(word); + this.stem(); + return base.getCurrent(); + }; +}; diff --git a/_static/file.png b/_static/file.png index d18082e3..a858a410 100644 Binary files a/_static/file.png and b/_static/file.png differ diff --git a/_static/fonts/FontAwesome.otf b/_static/fonts/FontAwesome.otf deleted file mode 100644 index 8b0f54e4..00000000 Binary files a/_static/fonts/FontAwesome.otf and /dev/null differ diff --git a/_static/fonts/Inconsolata-Bold.ttf 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- - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/_static/fonts/fontawesome-webfont.ttf b/_static/fonts/fontawesome-webfont.ttf deleted file mode 100644 index e89738de..00000000 Binary files a/_static/fonts/fontawesome-webfont.ttf and /dev/null differ diff --git a/_static/fonts/fontawesome-webfont.woff b/_static/fonts/fontawesome-webfont.woff deleted file mode 100644 index 8c1748aa..00000000 Binary files a/_static/fonts/fontawesome-webfont.woff and /dev/null differ diff --git a/_static/increase_max_width.css b/_static/increase_max_width.css new file mode 100644 index 00000000..b07bdb1b --- /dev/null +++ b/_static/increase_max_width.css @@ -0,0 +1,3 @@ +.wy-nav-content { + max-width: none; +} diff --git a/_static/jquery-1.11.1.js b/_static/jquery-1.11.1.js deleted file mode 100644 index d4b67f7e..00000000 --- a/_static/jquery-1.11.1.js +++ /dev/null @@ -1,10308 +0,0 @@ -/*! - * jQuery JavaScript Library v1.11.1 - * http://jquery.com/ - * - * Includes Sizzle.js - * http://sizzlejs.com/ - * - * Copyright 2005, 2014 jQuery Foundation, Inc. and other contributors - * Released under the MIT license - * http://jquery.org/license - * - * Date: 2014-05-01T17:42Z - */ - -(function( global, factory ) { - - if ( typeof module === "object" && typeof module.exports === "object" ) { - // For CommonJS and CommonJS-like environments where a proper window is present, - // execute the factory and get jQuery - // For environments that do not inherently posses a window with a document - // (such as Node.js), expose a jQuery-making factory as module.exports - // This accentuates the need for the creation of a real window - // e.g. var jQuery = require("jquery")(window); - // See ticket #14549 for more info - module.exports = global.document ? - factory( global, true ) : - function( w ) { - if ( !w.document ) { - throw new Error( "jQuery requires a window with a document" ); - } - return factory( w ); - }; - } else { - factory( global ); - } - -// Pass this if window is not defined yet -}(typeof window !== "undefined" ? window : this, function( window, noGlobal ) { - -// Can't do this because several apps including ASP.NET trace -// the stack via arguments.caller.callee and Firefox dies if -// you try to trace through "use strict" call chains. (#13335) -// Support: Firefox 18+ -// - -var deletedIds = []; - -var slice = deletedIds.slice; - -var concat = deletedIds.concat; - -var push = deletedIds.push; - -var indexOf = deletedIds.indexOf; - -var class2type = {}; - -var toString = class2type.toString; - -var hasOwn = class2type.hasOwnProperty; - -var support = {}; - - - -var - version = "1.11.1", - - // Define a local copy of jQuery - jQuery = function( selector, context ) { - // The jQuery object is actually just the init constructor 'enhanced' - // Need init if jQuery is called (just allow error to be thrown if not included) - return new jQuery.fn.init( selector, context ); - }, - - // Support: Android<4.1, IE<9 - // Make sure we trim BOM and NBSP - rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g, - - // Matches dashed string for camelizing - rmsPrefix = /^-ms-/, - rdashAlpha = /-([\da-z])/gi, - - // Used by jQuery.camelCase as callback to replace() - fcamelCase = function( all, letter ) { - return letter.toUpperCase(); - }; - -jQuery.fn = jQuery.prototype = { - // The current version of jQuery being used - jquery: version, - - constructor: jQuery, - - // Start with an empty selector - selector: "", - - // The default length of a jQuery object is 0 - length: 0, - - toArray: function() { - return slice.call( this ); - }, - - // Get the Nth element in the matched element set OR - // Get the whole matched element set as a clean array - get: function( num ) { - return num != null ? - - // Return just the one element from the set - ( num < 0 ? this[ num + this.length ] : this[ num ] ) : - - // Return all the elements in a clean array - slice.call( this ); - }, - - // Take an array of elements and push it onto the stack - // (returning the new matched element set) - pushStack: function( elems ) { - - // Build a new jQuery matched element set - var ret = jQuery.merge( this.constructor(), elems ); - - // Add the old object onto the stack (as a reference) - ret.prevObject = this; - ret.context = this.context; - - // Return the newly-formed element set - return ret; - }, - - // Execute a callback for every element in the matched set. - // (You can seed the arguments with an array of args, but this is - // only used internally.) - each: function( callback, args ) { - return jQuery.each( this, callback, args ); - }, - - map: function( callback ) { - return this.pushStack( jQuery.map(this, function( elem, i ) { - return callback.call( elem, i, elem ); - })); - }, - - slice: function() { - return this.pushStack( slice.apply( this, arguments ) ); - }, - - first: function() { - return this.eq( 0 ); - }, - - last: function() { - return this.eq( -1 ); - }, - - eq: function( i ) { - var len = this.length, - j = +i + ( i < 0 ? len : 0 ); - return this.pushStack( j >= 0 && j < len ? [ this[j] ] : [] ); - }, - - end: function() { - return this.prevObject || this.constructor(null); - }, - - // For internal use only. - // Behaves like an Array's method, not like a jQuery method. - push: push, - sort: deletedIds.sort, - splice: deletedIds.splice -}; - -jQuery.extend = jQuery.fn.extend = function() { - var src, copyIsArray, copy, name, options, clone, - target = arguments[0] || {}, - i = 1, - length = arguments.length, - deep = false; - - // Handle a deep copy situation - if ( typeof target === "boolean" ) { - deep = target; - - // skip the boolean and the target - target = arguments[ i ] || {}; - i++; - } - - // Handle case when target is a string or something (possible in deep copy) - if ( typeof target !== "object" && !jQuery.isFunction(target) ) { - target = {}; - } - - // extend jQuery itself if only one argument is passed - if ( i === length ) { - target = this; - i--; - } - - for ( ; i < length; i++ ) { - // Only deal with non-null/undefined values - if ( (options = arguments[ i ]) != null ) { - // Extend the base object - for ( name in options ) { - src = target[ name ]; - copy = options[ name ]; - - // Prevent never-ending loop - if ( target === copy ) { - continue; - } - - // Recurse if we're merging plain objects or arrays - if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) { - if ( copyIsArray ) { - copyIsArray = false; - clone = src && jQuery.isArray(src) ? src : []; - - } else { - clone = src && jQuery.isPlainObject(src) ? src : {}; - } - - // Never move original objects, clone them - target[ name ] = jQuery.extend( deep, clone, copy ); - - // Don't bring in undefined values - } else if ( copy !== undefined ) { - target[ name ] = copy; - } - } - } - } - - // Return the modified object - return target; -}; - -jQuery.extend({ - // Unique for each copy of jQuery on the page - expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), - - // Assume jQuery is ready without the ready module - isReady: true, - - error: function( msg ) { - throw new Error( msg ); - }, - - noop: function() {}, - - // See test/unit/core.js for details concerning isFunction. - // Since version 1.3, DOM methods and functions like alert - // aren't supported. They return false on IE (#2968). - isFunction: function( obj ) { - return jQuery.type(obj) === "function"; - }, - - isArray: Array.isArray || function( obj ) { - return jQuery.type(obj) === "array"; - }, - - isWindow: function( obj ) { - /* jshint eqeqeq: false */ - return obj != null && obj == obj.window; - }, - - isNumeric: function( obj ) { - // parseFloat NaNs numeric-cast false positives (null|true|false|"") - // ...but misinterprets leading-number strings, particularly hex literals ("0x...") - // subtraction forces infinities to NaN - return !jQuery.isArray( obj ) && obj - parseFloat( obj ) >= 0; - }, - - isEmptyObject: function( obj ) { - var name; - for ( name in obj ) { - return false; - } - return true; - }, - - isPlainObject: function( obj ) { - var key; - - // Must be an Object. - // Because of IE, we also have to check the presence of the constructor property. - // Make sure that DOM nodes and window objects don't pass through, as well - if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) { - return false; - } - - try { - // Not own constructor property must be Object - if ( obj.constructor && - !hasOwn.call(obj, "constructor") && - !hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) { - return false; - } - } catch ( e ) { - // IE8,9 Will throw exceptions on certain host objects #9897 - return false; - } - - // Support: IE<9 - // Handle iteration over inherited properties before own properties. - if ( support.ownLast ) { - for ( key in obj ) { - return hasOwn.call( obj, key ); - } - } - - // Own properties are enumerated firstly, so to speed up, - // if last one is own, then all properties are own. - for ( key in obj ) {} - - return key === undefined || hasOwn.call( obj, key ); - }, - - type: function( obj ) { - if ( obj == null ) { - return obj + ""; - } - return typeof obj === "object" || typeof obj === "function" ? - class2type[ toString.call(obj) ] || "object" : - typeof obj; - }, - - // Evaluates a script in a global context - // Workarounds based on findings by Jim Driscoll - // http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context - globalEval: function( data ) { - if ( data && jQuery.trim( data ) ) { - // We use execScript on Internet Explorer - // We use an anonymous function so that context is window - // rather than jQuery in Firefox - ( window.execScript || function( data ) { - window[ "eval" ].call( window, data ); - } )( data ); - } - }, - - // Convert dashed to camelCase; used by the css and data modules - // Microsoft forgot to hump their vendor prefix (#9572) - camelCase: function( string ) { - return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); - }, - - nodeName: function( elem, name ) { - return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); - }, - - // args is for internal usage only - each: function( obj, callback, args ) { - var value, - i = 0, - length = obj.length, - isArray = isArraylike( obj ); - - if ( args ) { - if ( isArray ) { - for ( ; i < length; i++ ) { - value = callback.apply( obj[ i ], args ); - - if ( value === false ) { - break; - } - } - } else { - for ( i in obj ) { - value = callback.apply( obj[ i ], args ); - - if ( value === false ) { - break; - } - } - } - - // A special, fast, case for the most common use of each - } else { - if ( isArray ) { - for ( ; i < length; i++ ) { - value = callback.call( obj[ i ], i, obj[ i ] ); - - if ( value === false ) { - break; - } - } - } else { - for ( i in obj ) { - value = callback.call( obj[ i ], i, obj[ i ] ); - - if ( value === false ) { - break; - } - } - } - } - - return obj; - }, - - // Support: Android<4.1, IE<9 - trim: function( text ) { - return text == null ? - "" : - ( text + "" ).replace( rtrim, "" ); - }, - - // results is for internal usage only - makeArray: function( arr, results ) { - var ret = results || []; - - if ( arr != null ) { - if ( isArraylike( Object(arr) ) ) { - jQuery.merge( ret, - typeof arr === "string" ? - [ arr ] : arr - ); - } else { - push.call( ret, arr ); - } - } - - return ret; - }, - - inArray: function( elem, arr, i ) { - var len; - - if ( arr ) { - if ( indexOf ) { - return indexOf.call( arr, elem, i ); - } - - len = arr.length; - i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0; - - for ( ; i < len; i++ ) { - // Skip accessing in sparse arrays - if ( i in arr && arr[ i ] === elem ) { - return i; - } - } - } - - return -1; - }, - - merge: function( first, second ) { - var len = +second.length, - j = 0, - i = first.length; - - while ( j < len ) { - first[ i++ ] = second[ j++ ]; - } - - // Support: IE<9 - // Workaround casting of .length to NaN on otherwise arraylike objects (e.g., NodeLists) - if ( len !== len ) { - while ( second[j] !== undefined ) { - first[ i++ ] = second[ j++ ]; - } - } - - first.length = i; - - return first; - }, - - grep: function( elems, callback, invert ) { - var callbackInverse, - matches = [], - i = 0, - length = elems.length, - callbackExpect = !invert; - - // Go through the array, only saving the items - // that pass the validator function - for ( ; i < length; i++ ) { - callbackInverse = !callback( elems[ i ], i ); - if ( callbackInverse !== callbackExpect ) { - matches.push( elems[ i ] ); - } - } - - return matches; - }, - - // arg is for internal usage only - map: function( elems, callback, arg ) { - var value, - i = 0, - length = elems.length, - isArray = isArraylike( elems ), - ret = []; - - // Go through the array, translating each of the items to their new values - if ( isArray ) { - for ( ; i < length; i++ ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - - // Go through every key on the object, - } else { - for ( i in elems ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - } - - // Flatten any nested arrays - return concat.apply( [], ret ); - }, - - // A global GUID counter for objects - guid: 1, - - // Bind a function to a context, optionally partially applying any - // arguments. - proxy: function( fn, context ) { - var args, proxy, tmp; - - if ( typeof context === "string" ) { - tmp = fn[ context ]; - context = fn; - fn = tmp; - } - - // Quick check to determine if target is callable, in the spec - // this throws a TypeError, but we will just return undefined. - if ( !jQuery.isFunction( fn ) ) { - return undefined; - } - - // Simulated bind - args = slice.call( arguments, 2 ); - proxy = function() { - return fn.apply( context || this, args.concat( slice.call( arguments ) ) ); - }; - - // Set the guid of unique handler to the same of original handler, so it can be removed - proxy.guid = fn.guid = fn.guid || jQuery.guid++; - - return proxy; - }, - - now: function() { - return +( new Date() ); - }, - - // jQuery.support is not used in Core but other projects attach their - // properties to it so it needs to exist. - support: support -}); - -// Populate the class2type map -jQuery.each("Boolean Number String Function Array Date RegExp Object Error".split(" "), function(i, name) { - class2type[ "[object " + name + "]" ] = name.toLowerCase(); -}); - -function isArraylike( obj ) { - var length = obj.length, - type = jQuery.type( obj ); - - if ( type === "function" || jQuery.isWindow( obj ) ) { - return false; - } - - if ( obj.nodeType === 1 && length ) { - return true; - } - - return type === "array" || length === 0 || - typeof length === "number" && length > 0 && ( length - 1 ) in obj; -} -var Sizzle = -/*! - * Sizzle CSS Selector Engine v1.10.19 - * http://sizzlejs.com/ - * - * Copyright 2013 jQuery Foundation, Inc. and other contributors - * Released under the MIT license - * http://jquery.org/license - * - * Date: 2014-04-18 - */ -(function( window ) { - -var i, - support, - Expr, - getText, - isXML, - tokenize, - compile, - select, - outermostContext, - sortInput, - hasDuplicate, - - // Local document vars - setDocument, - document, - docElem, - documentIsHTML, - rbuggyQSA, - rbuggyMatches, - matches, - contains, - - // Instance-specific data - expando = "sizzle" + -(new Date()), - preferredDoc = window.document, - dirruns = 0, - done = 0, - classCache = createCache(), - tokenCache = createCache(), - compilerCache = createCache(), - sortOrder = function( a, b ) { - if ( a === b ) { - hasDuplicate = true; - } - return 0; - }, - - // General-purpose constants - strundefined = typeof undefined, - MAX_NEGATIVE = 1 << 31, - - // Instance methods - hasOwn = ({}).hasOwnProperty, - arr = [], - pop = arr.pop, - push_native = arr.push, - push = arr.push, - slice = arr.slice, - // Use a stripped-down indexOf if we can't use a native one - indexOf = arr.indexOf || function( elem ) { - var i = 0, - len = this.length; - for ( ; i < len; i++ ) { - if ( this[i] === elem ) { - return i; - } - } - return -1; - }, - - booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped", - - // Regular expressions - - // Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace - whitespace = "[\\x20\\t\\r\\n\\f]", - // http://www.w3.org/TR/css3-syntax/#characters - characterEncoding = "(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+", - - // Loosely modeled on CSS identifier characters - // An unquoted value should be a CSS identifier http://www.w3.org/TR/css3-selectors/#attribute-selectors - // Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier - identifier = characterEncoding.replace( "w", "w#" ), - - // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors - attributes = "\\[" + whitespace + "*(" + characterEncoding + ")(?:" + whitespace + - // Operator (capture 2) - "*([*^$|!~]?=)" + whitespace + - // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]" - "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace + - "*\\]", - - pseudos = ":(" + characterEncoding + ")(?:\\((" + - // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: - // 1. quoted (capture 3; capture 4 or capture 5) - "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + - // 2. simple (capture 6) - "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + - // 3. anything else (capture 2) - ".*" + - ")\\)|)", - - // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter - rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), - - rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), - rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ), - - rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ), - - rpseudo = new RegExp( pseudos ), - ridentifier = new RegExp( "^" + identifier + "$" ), - - matchExpr = { - "ID": new RegExp( "^#(" + characterEncoding + ")" ), - "CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ), - "TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ), - "ATTR": new RegExp( "^" + attributes ), - "PSEUDO": new RegExp( "^" + pseudos ), - "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace + - "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace + - "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), - "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), - // For use in libraries implementing .is() - // We use this for POS matching in `select` - "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + - whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) - }, - - rinputs = /^(?:input|select|textarea|button)$/i, - rheader = /^h\d$/i, - - rnative = /^[^{]+\{\s*\[native \w/, - - // Easily-parseable/retrievable ID or TAG or CLASS selectors - rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, - - rsibling = /[+~]/, - rescape = /'|\\/g, - - // CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters - runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ), - funescape = function( _, escaped, escapedWhitespace ) { - var high = "0x" + escaped - 0x10000; - // NaN means non-codepoint - // Support: Firefox<24 - // Workaround erroneous numeric interpretation of +"0x" - return high !== high || escapedWhitespace ? - escaped : - high < 0 ? - // BMP codepoint - String.fromCharCode( high + 0x10000 ) : - // Supplemental Plane codepoint (surrogate pair) - String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); - }; - -// Optimize for push.apply( _, NodeList ) -try { - push.apply( - (arr = slice.call( preferredDoc.childNodes )), - preferredDoc.childNodes - ); - // Support: Android<4.0 - // Detect silently failing push.apply - arr[ preferredDoc.childNodes.length ].nodeType; -} catch ( e ) { - push = { apply: arr.length ? - - // Leverage slice if possible - function( target, els ) { - push_native.apply( target, slice.call(els) ); - } : - - // Support: IE<9 - // Otherwise append directly - function( target, els ) { - var j = target.length, - i = 0; - // Can't trust NodeList.length - while ( (target[j++] = els[i++]) ) {} - target.length = j - 1; - } - }; -} - -function Sizzle( selector, context, results, seed ) { - var match, elem, m, nodeType, - // QSA vars - i, groups, old, nid, newContext, newSelector; - - if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) { - setDocument( context ); - } - - context = context || document; - results = results || []; - - if ( !selector || typeof selector !== "string" ) { - return results; - } - - if ( (nodeType = context.nodeType) !== 1 && nodeType !== 9 ) { - return []; - } - - if ( documentIsHTML && !seed ) { - - // Shortcuts - if ( (match = rquickExpr.exec( selector )) ) { - // Speed-up: Sizzle("#ID") - if ( (m = match[1]) ) { - if ( nodeType === 9 ) { - elem = context.getElementById( m ); - // Check parentNode to catch when Blackberry 4.6 returns - // nodes that are no longer in the document (jQuery #6963) - if ( elem && elem.parentNode ) { - // Handle the case where IE, Opera, and Webkit return items - // by name instead of ID - if ( elem.id === m ) { - results.push( elem ); - return results; - } - } else { - return results; - } - } else { - // Context is not a document - if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) && - contains( context, elem ) && elem.id === m ) { - results.push( elem ); - return results; - } - } - - // Speed-up: Sizzle("TAG") - } else if ( match[2] ) { - push.apply( results, context.getElementsByTagName( selector ) ); - return results; - - // Speed-up: Sizzle(".CLASS") - } else if ( (m = match[3]) && support.getElementsByClassName && context.getElementsByClassName ) { - push.apply( results, context.getElementsByClassName( m ) ); - return results; - } - } - - // QSA path - if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { - nid = old = expando; - newContext = context; - newSelector = nodeType === 9 && selector; - - // qSA works strangely on Element-rooted queries - // We can work around this by specifying an extra ID on the root - // and working up from there (Thanks to Andrew Dupont for the technique) - // IE 8 doesn't work on object elements - if ( nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) { - groups = tokenize( selector ); - - if ( (old = context.getAttribute("id")) ) { - nid = old.replace( rescape, "\\$&" ); - } else { - context.setAttribute( "id", nid ); - } - nid = "[id='" + nid + "'] "; - - i = groups.length; - while ( i-- ) { - groups[i] = nid + toSelector( groups[i] ); - } - newContext = rsibling.test( selector ) && testContext( context.parentNode ) || context; - newSelector = groups.join(","); - } - - if ( newSelector ) { - try { - push.apply( results, - newContext.querySelectorAll( newSelector ) - ); - return results; - } catch(qsaError) { - } finally { - if ( !old ) { - context.removeAttribute("id"); - } - } - } - } - } - - // All others - return select( selector.replace( rtrim, "$1" ), context, results, seed ); -} - -/** - * Create key-value caches of limited size - * @returns {Function(string, Object)} Returns the Object data after storing it on itself with - * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) - * deleting the oldest entry - */ -function createCache() { - var keys = []; - - function cache( key, value ) { - // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) - if ( keys.push( key + " " ) > Expr.cacheLength ) { - // Only keep the most recent entries - delete cache[ keys.shift() ]; - } - return (cache[ key + " " ] = value); - } - return cache; -} - -/** - * Mark a function for special use by Sizzle - * @param {Function} fn The function to mark - */ -function markFunction( fn ) { - fn[ expando ] = true; - return fn; -} - -/** - * Support testing using an element - * @param {Function} fn Passed the created div and expects a boolean result - */ -function assert( fn ) { - var div = document.createElement("div"); - - try { - return !!fn( div ); - } catch (e) { - return false; - } finally { - // Remove from its parent by default - if ( div.parentNode ) { - div.parentNode.removeChild( div ); - } - // release memory in IE - div = null; - } -} - -/** - * Adds the same handler for all of the specified attrs - * @param {String} attrs Pipe-separated list of attributes - * @param {Function} handler The method that will be applied - */ -function addHandle( attrs, handler ) { - var arr = attrs.split("|"), - i = attrs.length; - - while ( i-- ) { - Expr.attrHandle[ arr[i] ] = handler; - } -} - -/** - * Checks document order of two siblings - * @param {Element} a - * @param {Element} b - * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b - */ -function siblingCheck( a, b ) { - var cur = b && a, - diff = cur && a.nodeType === 1 && b.nodeType === 1 && - ( ~b.sourceIndex || MAX_NEGATIVE ) - - ( ~a.sourceIndex || MAX_NEGATIVE ); - - // Use IE sourceIndex if available on both nodes - if ( diff ) { - return diff; - } - - // Check if b follows a - if ( cur ) { - while ( (cur = cur.nextSibling) ) { - if ( cur === b ) { - return -1; - } - } - } - - return a ? 1 : -1; -} - -/** - * Returns a function to use in pseudos for input types - * @param {String} type - */ -function createInputPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return name === "input" && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for buttons - * @param {String} type - */ -function createButtonPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return (name === "input" || name === "button") && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for positionals - * @param {Function} fn - */ -function createPositionalPseudo( fn ) { - return markFunction(function( argument ) { - argument = +argument; - return markFunction(function( seed, matches ) { - var j, - matchIndexes = fn( [], seed.length, argument ), - i = matchIndexes.length; - - // Match elements found at the specified indexes - while ( i-- ) { - if ( seed[ (j = matchIndexes[i]) ] ) { - seed[j] = !(matches[j] = seed[j]); - } - } - }); - }); -} - -/** - * Checks a node for validity as a Sizzle context - * @param {Element|Object=} context - * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value - */ -function testContext( context ) { - return context && typeof context.getElementsByTagName !== strundefined && context; -} - -// Expose support vars for convenience -support = Sizzle.support = {}; - -/** - * Detects XML nodes - * @param {Element|Object} elem An element or a document - * @returns {Boolean} True iff elem is a non-HTML XML node - */ -isXML = Sizzle.isXML = function( elem ) { - // documentElement is verified for cases where it doesn't yet exist - // (such as loading iframes in IE - #4833) - var documentElement = elem && (elem.ownerDocument || elem).documentElement; - return documentElement ? documentElement.nodeName !== "HTML" : false; -}; - -/** - * Sets document-related variables once based on the current document - * @param {Element|Object} [doc] An element or document object to use to set the document - * @returns {Object} Returns the current document - */ -setDocument = Sizzle.setDocument = function( node ) { - var hasCompare, - doc = node ? node.ownerDocument || node : preferredDoc, - parent = doc.defaultView; - - // If no document and documentElement is available, return - if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) { - return document; - } - - // Set our document - document = doc; - docElem = doc.documentElement; - - // Support tests - documentIsHTML = !isXML( doc ); - - // Support: IE>8 - // If iframe document is assigned to "document" variable and if iframe has been reloaded, - // IE will throw "permission denied" error when accessing "document" variable, see jQuery #13936 - // IE6-8 do not support the defaultView property so parent will be undefined - if ( parent && parent !== parent.top ) { - // IE11 does not have attachEvent, so all must suffer - if ( parent.addEventListener ) { - parent.addEventListener( "unload", function() { - setDocument(); - }, false ); - } else if ( parent.attachEvent ) { - parent.attachEvent( "onunload", function() { - setDocument(); - }); - } - } - - /* Attributes - ---------------------------------------------------------------------- */ - - // Support: IE<8 - // Verify that getAttribute really returns attributes and not properties (excepting IE8 booleans) - support.attributes = assert(function( div ) { - div.className = "i"; - return !div.getAttribute("className"); - }); - - /* getElement(s)By* - ---------------------------------------------------------------------- */ - - // Check if getElementsByTagName("*") returns only elements - support.getElementsByTagName = assert(function( div ) { - div.appendChild( doc.createComment("") ); - return !div.getElementsByTagName("*").length; - }); - - // Check if getElementsByClassName can be trusted - support.getElementsByClassName = rnative.test( doc.getElementsByClassName ) && assert(function( div ) { - div.innerHTML = "
"; - - // Support: Safari<4 - // Catch class over-caching - div.firstChild.className = "i"; - // Support: Opera<10 - // Catch gEBCN failure to find non-leading classes - return div.getElementsByClassName("i").length === 2; - }); - - // Support: IE<10 - // Check if getElementById returns elements by name - // The broken getElementById methods don't pick up programatically-set names, - // so use a roundabout getElementsByName test - support.getById = assert(function( div ) { - docElem.appendChild( div ).id = expando; - return !doc.getElementsByName || !doc.getElementsByName( expando ).length; - }); - - // ID find and filter - if ( support.getById ) { - Expr.find["ID"] = function( id, context ) { - if ( typeof context.getElementById !== strundefined && documentIsHTML ) { - var m = context.getElementById( id ); - // Check parentNode to catch when Blackberry 4.6 returns - // nodes that are no longer in the document #6963 - return m && m.parentNode ? [ m ] : []; - } - }; - Expr.filter["ID"] = function( id ) { - var attrId = id.replace( runescape, funescape ); - return function( elem ) { - return elem.getAttribute("id") === attrId; - }; - }; - } else { - // Support: IE6/7 - // getElementById is not reliable as a find shortcut - delete Expr.find["ID"]; - - Expr.filter["ID"] = function( id ) { - var attrId = id.replace( runescape, funescape ); - return function( elem ) { - var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id"); - return node && node.value === attrId; - }; - }; - } - - // Tag - Expr.find["TAG"] = support.getElementsByTagName ? - function( tag, context ) { - if ( typeof context.getElementsByTagName !== strundefined ) { - return context.getElementsByTagName( tag ); - } - } : - function( tag, context ) { - var elem, - tmp = [], - i = 0, - results = context.getElementsByTagName( tag ); - - // Filter out possible comments - if ( tag === "*" ) { - while ( (elem = results[i++]) ) { - if ( elem.nodeType === 1 ) { - tmp.push( elem ); - } - } - - return tmp; - } - return results; - }; - - // Class - Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) { - if ( typeof context.getElementsByClassName !== strundefined && documentIsHTML ) { - return context.getElementsByClassName( className ); - } - }; - - /* QSA/matchesSelector - ---------------------------------------------------------------------- */ - - // QSA and matchesSelector support - - // matchesSelector(:active) reports false when true (IE9/Opera 11.5) - rbuggyMatches = []; - - // qSa(:focus) reports false when true (Chrome 21) - // We allow this because of a bug in IE8/9 that throws an error - // whenever `document.activeElement` is accessed on an iframe - // So, we allow :focus to pass through QSA all the time to avoid the IE error - // See http://bugs.jquery.com/ticket/13378 - rbuggyQSA = []; - - if ( (support.qsa = rnative.test( doc.querySelectorAll )) ) { - // Build QSA regex - // Regex strategy adopted from Diego Perini - assert(function( div ) { - // Select is set to empty string on purpose - // This is to test IE's treatment of not explicitly - // setting a boolean content attribute, - // since its presence should be enough - // http://bugs.jquery.com/ticket/12359 - div.innerHTML = ""; - - // Support: IE8, Opera 11-12.16 - // Nothing should be selected when empty strings follow ^= or $= or *= - // The test attribute must be unknown in Opera but "safe" for WinRT - // http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section - if ( div.querySelectorAll("[msallowclip^='']").length ) { - rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); - } - - // Support: IE8 - // Boolean attributes and "value" are not treated correctly - if ( !div.querySelectorAll("[selected]").length ) { - rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); - } - - // Webkit/Opera - :checked should return selected option elements - // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked - // IE8 throws error here and will not see later tests - if ( !div.querySelectorAll(":checked").length ) { - rbuggyQSA.push(":checked"); - } - }); - - assert(function( div ) { - // Support: Windows 8 Native Apps - // The type and name attributes are restricted during .innerHTML assignment - var input = doc.createElement("input"); - input.setAttribute( "type", "hidden" ); - div.appendChild( input ).setAttribute( "name", "D" ); - - // Support: IE8 - // Enforce case-sensitivity of name attribute - if ( div.querySelectorAll("[name=d]").length ) { - rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); - } - - // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) - // IE8 throws error here and will not see later tests - if ( !div.querySelectorAll(":enabled").length ) { - rbuggyQSA.push( ":enabled", ":disabled" ); - } - - // Opera 10-11 does not throw on post-comma invalid pseudos - div.querySelectorAll("*,:x"); - rbuggyQSA.push(",.*:"); - }); - } - - if ( (support.matchesSelector = rnative.test( (matches = docElem.matches || - docElem.webkitMatchesSelector || - docElem.mozMatchesSelector || - docElem.oMatchesSelector || - docElem.msMatchesSelector) )) ) { - - assert(function( div ) { - // Check to see if it's possible to do matchesSelector - // on a disconnected node (IE 9) - support.disconnectedMatch = matches.call( div, "div" ); - - // This should fail with an exception - // Gecko does not error, returns false instead - matches.call( div, "[s!='']:x" ); - rbuggyMatches.push( "!=", pseudos ); - }); - } - - rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") ); - rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") ); - - /* Contains - ---------------------------------------------------------------------- */ - hasCompare = rnative.test( docElem.compareDocumentPosition ); - - // Element contains another - // Purposefully does not implement inclusive descendent - // As in, an element does not contain itself - contains = hasCompare || rnative.test( docElem.contains ) ? - function( a, b ) { - var adown = a.nodeType === 9 ? a.documentElement : a, - bup = b && b.parentNode; - return a === bup || !!( bup && bup.nodeType === 1 && ( - adown.contains ? - adown.contains( bup ) : - a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 - )); - } : - function( a, b ) { - if ( b ) { - while ( (b = b.parentNode) ) { - if ( b === a ) { - return true; - } - } - } - return false; - }; - - /* Sorting - ---------------------------------------------------------------------- */ - - // Document order sorting - sortOrder = hasCompare ? - function( a, b ) { - - // Flag for duplicate removal - if ( a === b ) { - hasDuplicate = true; - return 0; - } - - // Sort on method existence if only one input has compareDocumentPosition - var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; - if ( compare ) { - return compare; - } - - // Calculate position if both inputs belong to the same document - compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ? - a.compareDocumentPosition( b ) : - - // Otherwise we know they are disconnected - 1; - - // Disconnected nodes - if ( compare & 1 || - (!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) { - - // Choose the first element that is related to our preferred document - if ( a === doc || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) { - return -1; - } - if ( b === doc || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) { - return 1; - } - - // Maintain original order - return sortInput ? - ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) : - 0; - } - - return compare & 4 ? -1 : 1; - } : - function( a, b ) { - // Exit early if the nodes are identical - if ( a === b ) { - hasDuplicate = true; - return 0; - } - - var cur, - i = 0, - aup = a.parentNode, - bup = b.parentNode, - ap = [ a ], - bp = [ b ]; - - // Parentless nodes are either documents or disconnected - if ( !aup || !bup ) { - return a === doc ? -1 : - b === doc ? 1 : - aup ? -1 : - bup ? 1 : - sortInput ? - ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) : - 0; - - // If the nodes are siblings, we can do a quick check - } else if ( aup === bup ) { - return siblingCheck( a, b ); - } - - // Otherwise we need full lists of their ancestors for comparison - cur = a; - while ( (cur = cur.parentNode) ) { - ap.unshift( cur ); - } - cur = b; - while ( (cur = cur.parentNode) ) { - bp.unshift( cur ); - } - - // Walk down the tree looking for a discrepancy - while ( ap[i] === bp[i] ) { - i++; - } - - return i ? - // Do a sibling check if the nodes have a common ancestor - siblingCheck( ap[i], bp[i] ) : - - // Otherwise nodes in our document sort first - ap[i] === preferredDoc ? -1 : - bp[i] === preferredDoc ? 1 : - 0; - }; - - return doc; -}; - -Sizzle.matches = function( expr, elements ) { - return Sizzle( expr, null, null, elements ); -}; - -Sizzle.matchesSelector = function( elem, expr ) { - // Set document vars if needed - if ( ( elem.ownerDocument || elem ) !== document ) { - setDocument( elem ); - } - - // Make sure that attribute selectors are quoted - expr = expr.replace( rattributeQuotes, "='$1']" ); - - if ( support.matchesSelector && documentIsHTML && - ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && - ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { - - try { - var ret = matches.call( elem, expr ); - - // IE 9's matchesSelector returns false on disconnected nodes - if ( ret || support.disconnectedMatch || - // As well, disconnected nodes are said to be in a document - // fragment in IE 9 - elem.document && elem.document.nodeType !== 11 ) { - return ret; - } - } catch(e) {} - } - - return Sizzle( expr, document, null, [ elem ] ).length > 0; -}; - -Sizzle.contains = function( context, elem ) { - // Set document vars if needed - if ( ( context.ownerDocument || context ) !== document ) { - setDocument( context ); - } - return contains( context, elem ); -}; - -Sizzle.attr = function( elem, name ) { - // Set document vars if needed - if ( ( elem.ownerDocument || elem ) !== document ) { - setDocument( elem ); - } - - var fn = Expr.attrHandle[ name.toLowerCase() ], - // Don't get fooled by Object.prototype properties (jQuery #13807) - val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? - fn( elem, name, !documentIsHTML ) : - undefined; - - return val !== undefined ? - val : - support.attributes || !documentIsHTML ? - elem.getAttribute( name ) : - (val = elem.getAttributeNode(name)) && val.specified ? - val.value : - null; -}; - -Sizzle.error = function( msg ) { - throw new Error( "Syntax error, unrecognized expression: " + msg ); -}; - -/** - * Document sorting and removing duplicates - * @param {ArrayLike} results - */ -Sizzle.uniqueSort = function( results ) { - var elem, - duplicates = [], - j = 0, - i = 0; - - // Unless we *know* we can detect duplicates, assume their presence - hasDuplicate = !support.detectDuplicates; - sortInput = !support.sortStable && results.slice( 0 ); - results.sort( sortOrder ); - - if ( hasDuplicate ) { - while ( (elem = results[i++]) ) { - if ( elem === results[ i ] ) { - j = duplicates.push( i ); - } - } - while ( j-- ) { - results.splice( duplicates[ j ], 1 ); - } - } - - // Clear input after sorting to release objects - // See https://github.com/jquery/sizzle/pull/225 - sortInput = null; - - return results; -}; - -/** - * Utility function for retrieving the text value of an array of DOM nodes - * @param {Array|Element} elem - */ -getText = Sizzle.getText = function( elem ) { - var node, - ret = "", - i = 0, - nodeType = elem.nodeType; - - if ( !nodeType ) { - // If no nodeType, this is expected to be an array - while ( (node = elem[i++]) ) { - // Do not traverse comment nodes - ret += getText( node ); - } - } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { - // Use textContent for elements - // innerText usage removed for consistency of new lines (jQuery #11153) - if ( typeof elem.textContent === "string" ) { - return elem.textContent; - } else { - // Traverse its children - for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { - ret += getText( elem ); - } - } - } else if ( nodeType === 3 || nodeType === 4 ) { - return elem.nodeValue; - } - // Do not include comment or processing instruction nodes - - return ret; -}; - -Expr = Sizzle.selectors = { - - // Can be adjusted by the user - cacheLength: 50, - - createPseudo: markFunction, - - match: matchExpr, - - attrHandle: {}, - - find: {}, - - relative: { - ">": { dir: "parentNode", first: true }, - " ": { dir: "parentNode" }, - "+": { dir: "previousSibling", first: true }, - "~": { dir: "previousSibling" } - }, - - preFilter: { - "ATTR": function( match ) { - match[1] = match[1].replace( runescape, funescape ); - - // Move the given value to match[3] whether quoted or unquoted - match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape ); - - if ( match[2] === "~=" ) { - match[3] = " " + match[3] + " "; - } - - return match.slice( 0, 4 ); - }, - - "CHILD": function( match ) { - /* matches from matchExpr["CHILD"] - 1 type (only|nth|...) - 2 what (child|of-type) - 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) - 4 xn-component of xn+y argument ([+-]?\d*n|) - 5 sign of xn-component - 6 x of xn-component - 7 sign of y-component - 8 y of y-component - */ - match[1] = match[1].toLowerCase(); - - if ( match[1].slice( 0, 3 ) === "nth" ) { - // nth-* requires argument - if ( !match[3] ) { - Sizzle.error( match[0] ); - } - - // numeric x and y parameters for Expr.filter.CHILD - // remember that false/true cast respectively to 0/1 - match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) ); - match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" ); - - // other types prohibit arguments - } else if ( match[3] ) { - Sizzle.error( match[0] ); - } - - return match; - }, - - "PSEUDO": function( match ) { - var excess, - unquoted = !match[6] && match[2]; - - if ( matchExpr["CHILD"].test( match[0] ) ) { - return null; - } - - // Accept quoted arguments as-is - if ( match[3] ) { - match[2] = match[4] || match[5] || ""; - - // Strip excess characters from unquoted arguments - } else if ( unquoted && rpseudo.test( unquoted ) && - // Get excess from tokenize (recursively) - (excess = tokenize( unquoted, true )) && - // advance to the next closing parenthesis - (excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) { - - // excess is a negative index - match[0] = match[0].slice( 0, excess ); - match[2] = unquoted.slice( 0, excess ); - } - - // Return only captures needed by the pseudo filter method (type and argument) - return match.slice( 0, 3 ); - } - }, - - filter: { - - "TAG": function( nodeNameSelector ) { - var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); - return nodeNameSelector === "*" ? - function() { return true; } : - function( elem ) { - return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; - }; - }, - - "CLASS": function( className ) { - var pattern = classCache[ className + " " ]; - - return pattern || - (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) && - classCache( className, function( elem ) { - return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== strundefined && elem.getAttribute("class") || "" ); - }); - }, - - "ATTR": function( name, operator, check ) { - return function( elem ) { - var result = Sizzle.attr( elem, name ); - - if ( result == null ) { - return operator === "!="; - } - if ( !operator ) { - return true; - } - - result += ""; - - return operator === "=" ? result === check : - operator === "!=" ? result !== check : - operator === "^=" ? check && result.indexOf( check ) === 0 : - operator === "*=" ? check && result.indexOf( check ) > -1 : - operator === "$=" ? check && result.slice( -check.length ) === check : - operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 : - operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : - false; - }; - }, - - "CHILD": function( type, what, argument, first, last ) { - var simple = type.slice( 0, 3 ) !== "nth", - forward = type.slice( -4 ) !== "last", - ofType = what === "of-type"; - - return first === 1 && last === 0 ? - - // Shortcut for :nth-*(n) - function( elem ) { - return !!elem.parentNode; - } : - - function( elem, context, xml ) { - var cache, outerCache, node, diff, nodeIndex, start, - dir = simple !== forward ? "nextSibling" : "previousSibling", - parent = elem.parentNode, - name = ofType && elem.nodeName.toLowerCase(), - useCache = !xml && !ofType; - - if ( parent ) { - - // :(first|last|only)-(child|of-type) - if ( simple ) { - while ( dir ) { - node = elem; - while ( (node = node[ dir ]) ) { - if ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) { - return false; - } - } - // Reverse direction for :only-* (if we haven't yet done so) - start = dir = type === "only" && !start && "nextSibling"; - } - return true; - } - - start = [ forward ? parent.firstChild : parent.lastChild ]; - - // non-xml :nth-child(...) stores cache data on `parent` - if ( forward && useCache ) { - // Seek `elem` from a previously-cached index - outerCache = parent[ expando ] || (parent[ expando ] = {}); - cache = outerCache[ type ] || []; - nodeIndex = cache[0] === dirruns && cache[1]; - diff = cache[0] === dirruns && cache[2]; - node = nodeIndex && parent.childNodes[ nodeIndex ]; - - while ( (node = ++nodeIndex && node && node[ dir ] || - - // Fallback to seeking `elem` from the start - (diff = nodeIndex = 0) || start.pop()) ) { - - // When found, cache indexes on `parent` and break - if ( node.nodeType === 1 && ++diff && node === elem ) { - outerCache[ type ] = [ dirruns, nodeIndex, diff ]; - break; - } - } - - // Use previously-cached element index if available - } else if ( useCache && (cache = (elem[ expando ] || (elem[ expando ] = {}))[ type ]) && cache[0] === dirruns ) { - diff = cache[1]; - - // xml :nth-child(...) or :nth-last-child(...) or :nth(-last)?-of-type(...) - } else { - // Use the same loop as above to seek `elem` from the start - while ( (node = ++nodeIndex && node && node[ dir ] || - (diff = nodeIndex = 0) || start.pop()) ) { - - if ( ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) && ++diff ) { - // Cache the index of each encountered element - if ( useCache ) { - (node[ expando ] || (node[ expando ] = {}))[ type ] = [ dirruns, diff ]; - } - - if ( node === elem ) { - break; - } - } - } - } - - // Incorporate the offset, then check against cycle size - diff -= last; - return diff === first || ( diff % first === 0 && diff / first >= 0 ); - } - }; - }, - - "PSEUDO": function( pseudo, argument ) { - // pseudo-class names are case-insensitive - // http://www.w3.org/TR/selectors/#pseudo-classes - // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters - // Remember that setFilters inherits from pseudos - var args, - fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || - Sizzle.error( "unsupported pseudo: " + pseudo ); - - // The user may use createPseudo to indicate that - // arguments are needed to create the filter function - // just as Sizzle does - if ( fn[ expando ] ) { - return fn( argument ); - } - - // But maintain support for old signatures - if ( fn.length > 1 ) { - args = [ pseudo, pseudo, "", argument ]; - return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? - markFunction(function( seed, matches ) { - var idx, - matched = fn( seed, argument ), - i = matched.length; - while ( i-- ) { - idx = indexOf.call( seed, matched[i] ); - seed[ idx ] = !( matches[ idx ] = matched[i] ); - } - }) : - function( elem ) { - return fn( elem, 0, args ); - }; - } - - return fn; - } - }, - - pseudos: { - // Potentially complex pseudos - "not": markFunction(function( selector ) { - // Trim the selector passed to compile - // to avoid treating leading and trailing - // spaces as combinators - var input = [], - results = [], - matcher = compile( selector.replace( rtrim, "$1" ) ); - - return matcher[ expando ] ? - markFunction(function( seed, matches, context, xml ) { - var elem, - unmatched = matcher( seed, null, xml, [] ), - i = seed.length; - - // Match elements unmatched by `matcher` - while ( i-- ) { - if ( (elem = unmatched[i]) ) { - seed[i] = !(matches[i] = elem); - } - } - }) : - function( elem, context, xml ) { - input[0] = elem; - matcher( input, null, xml, results ); - return !results.pop(); - }; - }), - - "has": markFunction(function( selector ) { - return function( elem ) { - return Sizzle( selector, elem ).length > 0; - }; - }), - - "contains": markFunction(function( text ) { - return function( elem ) { - return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1; - }; - }), - - // "Whether an element is represented by a :lang() selector - // is based solely on the element's language value - // being equal to the identifier C, - // or beginning with the identifier C immediately followed by "-". - // The matching of C against the element's language value is performed case-insensitively. - // The identifier C does not have to be a valid language name." - // http://www.w3.org/TR/selectors/#lang-pseudo - "lang": markFunction( function( lang ) { - // lang value must be a valid identifier - if ( !ridentifier.test(lang || "") ) { - Sizzle.error( "unsupported lang: " + lang ); - } - lang = lang.replace( runescape, funescape ).toLowerCase(); - return function( elem ) { - var elemLang; - do { - if ( (elemLang = documentIsHTML ? - elem.lang : - elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) { - - elemLang = elemLang.toLowerCase(); - return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; - } - } while ( (elem = elem.parentNode) && elem.nodeType === 1 ); - return false; - }; - }), - - // Miscellaneous - "target": function( elem ) { - var hash = window.location && window.location.hash; - return hash && hash.slice( 1 ) === elem.id; - }, - - "root": function( elem ) { - return elem === docElem; - }, - - "focus": function( elem ) { - return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex); - }, - - // Boolean properties - "enabled": function( elem ) { - return elem.disabled === false; - }, - - "disabled": function( elem ) { - return elem.disabled === true; - }, - - "checked": function( elem ) { - // In CSS3, :checked should return both checked and selected elements - // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked - var nodeName = elem.nodeName.toLowerCase(); - return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected); - }, - - "selected": function( elem ) { - // Accessing this property makes selected-by-default - // options in Safari work properly - if ( elem.parentNode ) { - elem.parentNode.selectedIndex; - } - - return elem.selected === true; - }, - - // Contents - "empty": function( elem ) { - // http://www.w3.org/TR/selectors/#empty-pseudo - // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), - // but not by others (comment: 8; processing instruction: 7; etc.) - // nodeType < 6 works because attributes (2) do not appear as children - for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { - if ( elem.nodeType < 6 ) { - return false; - } - } - return true; - }, - - "parent": function( elem ) { - return !Expr.pseudos["empty"]( elem ); - }, - - // Element/input types - "header": function( elem ) { - return rheader.test( elem.nodeName ); - }, - - "input": function( elem ) { - return rinputs.test( elem.nodeName ); - }, - - "button": function( elem ) { - var name = elem.nodeName.toLowerCase(); - return name === "input" && elem.type === "button" || name === "button"; - }, - - "text": function( elem ) { - var attr; - return elem.nodeName.toLowerCase() === "input" && - elem.type === "text" && - - // Support: IE<8 - // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" - ( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" ); - }, - - // Position-in-collection - "first": createPositionalPseudo(function() { - return [ 0 ]; - }), - - "last": createPositionalPseudo(function( matchIndexes, length ) { - return [ length - 1 ]; - }), - - "eq": createPositionalPseudo(function( matchIndexes, length, argument ) { - return [ argument < 0 ? argument + length : argument ]; - }), - - "even": createPositionalPseudo(function( matchIndexes, length ) { - var i = 0; - for ( ; i < length; i += 2 ) { - matchIndexes.push( i ); - } - return matchIndexes; - }), - - "odd": createPositionalPseudo(function( matchIndexes, length ) { - var i = 1; - for ( ; i < length; i += 2 ) { - matchIndexes.push( i ); - } - return matchIndexes; - }), - - "lt": createPositionalPseudo(function( matchIndexes, length, argument ) { - var i = argument < 0 ? argument + length : argument; - for ( ; --i >= 0; ) { - matchIndexes.push( i ); - } - return matchIndexes; - }), - - "gt": createPositionalPseudo(function( matchIndexes, length, argument ) { - var i = argument < 0 ? argument + length : argument; - for ( ; ++i < length; ) { - matchIndexes.push( i ); - } - return matchIndexes; - }) - } -}; - -Expr.pseudos["nth"] = Expr.pseudos["eq"]; - -// Add button/input type pseudos -for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { - Expr.pseudos[ i ] = createInputPseudo( i ); -} -for ( i in { submit: true, reset: true } ) { - Expr.pseudos[ i ] = createButtonPseudo( i ); -} - -// Easy API for creating new setFilters -function setFilters() {} -setFilters.prototype = Expr.filters = Expr.pseudos; -Expr.setFilters = new setFilters(); - -tokenize = Sizzle.tokenize = function( selector, parseOnly ) { - var matched, match, tokens, type, - soFar, groups, preFilters, - cached = tokenCache[ selector + " " ]; - - if ( cached ) { - return parseOnly ? 0 : cached.slice( 0 ); - } - - soFar = selector; - groups = []; - preFilters = Expr.preFilter; - - while ( soFar ) { - - // Comma and first run - if ( !matched || (match = rcomma.exec( soFar )) ) { - if ( match ) { - // Don't consume trailing commas as valid - soFar = soFar.slice( match[0].length ) || soFar; - } - groups.push( (tokens = []) ); - } - - matched = false; - - // Combinators - if ( (match = rcombinators.exec( soFar )) ) { - matched = match.shift(); - tokens.push({ - value: matched, - // Cast descendant combinators to space - type: match[0].replace( rtrim, " " ) - }); - soFar = soFar.slice( matched.length ); - } - - // Filters - for ( type in Expr.filter ) { - if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] || - (match = preFilters[ type ]( match ))) ) { - matched = match.shift(); - tokens.push({ - value: matched, - type: type, - matches: match - }); - soFar = soFar.slice( matched.length ); - } - } - - if ( !matched ) { - break; - } - } - - // Return the length of the invalid excess - // if we're just parsing - // Otherwise, throw an error or return tokens - return parseOnly ? - soFar.length : - soFar ? - Sizzle.error( selector ) : - // Cache the tokens - tokenCache( selector, groups ).slice( 0 ); -}; - -function toSelector( tokens ) { - var i = 0, - len = tokens.length, - selector = ""; - for ( ; i < len; i++ ) { - selector += tokens[i].value; - } - return selector; -} - -function addCombinator( matcher, combinator, base ) { - var dir = combinator.dir, - checkNonElements = base && dir === "parentNode", - doneName = done++; - - return combinator.first ? - // Check against closest ancestor/preceding element - function( elem, context, xml ) { - while ( (elem = elem[ dir ]) ) { - if ( elem.nodeType === 1 || checkNonElements ) { - return matcher( elem, context, xml ); - } - } - } : - - // Check against all ancestor/preceding elements - function( elem, context, xml ) { - var oldCache, outerCache, - newCache = [ dirruns, doneName ]; - - // We can't set arbitrary data on XML nodes, so they don't benefit from dir caching - if ( xml ) { - while ( (elem = elem[ dir ]) ) { - if ( elem.nodeType === 1 || checkNonElements ) { - if ( matcher( elem, context, xml ) ) { - return true; - } - } - } - } else { - while ( (elem = elem[ dir ]) ) { - if ( elem.nodeType === 1 || checkNonElements ) { - outerCache = elem[ expando ] || (elem[ expando ] = {}); - if ( (oldCache = outerCache[ dir ]) && - oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { - - // Assign to newCache so results back-propagate to previous elements - return (newCache[ 2 ] = oldCache[ 2 ]); - } else { - // Reuse newcache so results back-propagate to previous elements - outerCache[ dir ] = newCache; - - // A match means we're done; a fail means we have to keep checking - if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) { - return true; - } - } - } - } - } - }; -} - -function elementMatcher( matchers ) { - return matchers.length > 1 ? - function( elem, context, xml ) { - var i = matchers.length; - while ( i-- ) { - if ( !matchers[i]( elem, context, xml ) ) { - return false; - } - } - return true; - } : - matchers[0]; -} - -function multipleContexts( selector, contexts, results ) { - var i = 0, - len = contexts.length; - for ( ; i < len; i++ ) { - Sizzle( selector, contexts[i], results ); - } - return results; -} - -function condense( unmatched, map, filter, context, xml ) { - var elem, - newUnmatched = [], - i = 0, - len = unmatched.length, - mapped = map != null; - - for ( ; i < len; i++ ) { - if ( (elem = unmatched[i]) ) { - if ( !filter || filter( elem, context, xml ) ) { - newUnmatched.push( elem ); - if ( mapped ) { - map.push( i ); - } - } - } - } - - return newUnmatched; -} - -function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { - if ( postFilter && !postFilter[ expando ] ) { - postFilter = setMatcher( postFilter ); - } - if ( postFinder && !postFinder[ expando ] ) { - postFinder = setMatcher( postFinder, postSelector ); - } - return markFunction(function( seed, results, context, xml ) { - var temp, i, elem, - preMap = [], - postMap = [], - preexisting = results.length, - - // Get initial elements from seed or context - elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ), - - // Prefilter to get matcher input, preserving a map for seed-results synchronization - matcherIn = preFilter && ( seed || !selector ) ? - condense( elems, preMap, preFilter, context, xml ) : - elems, - - matcherOut = matcher ? - // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, - postFinder || ( seed ? preFilter : preexisting || postFilter ) ? - - // ...intermediate processing is necessary - [] : - - // ...otherwise use results directly - results : - matcherIn; - - // Find primary matches - if ( matcher ) { - matcher( matcherIn, matcherOut, context, xml ); - } - - // Apply postFilter - if ( postFilter ) { - temp = condense( matcherOut, postMap ); - postFilter( temp, [], context, xml ); - - // Un-match failing elements by moving them back to matcherIn - i = temp.length; - while ( i-- ) { - if ( (elem = temp[i]) ) { - matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem); - } - } - } - - if ( seed ) { - if ( postFinder || preFilter ) { - if ( postFinder ) { - // Get the final matcherOut by condensing this intermediate into postFinder contexts - temp = []; - i = matcherOut.length; - while ( i-- ) { - if ( (elem = matcherOut[i]) ) { - // Restore matcherIn since elem is not yet a final match - temp.push( (matcherIn[i] = elem) ); - } - } - postFinder( null, (matcherOut = []), temp, xml ); - } - - // Move matched elements from seed to results to keep them synchronized - i = matcherOut.length; - while ( i-- ) { - if ( (elem = matcherOut[i]) && - (temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) { - - seed[temp] = !(results[temp] = elem); - } - } - } - - // Add elements to results, through postFinder if defined - } else { - matcherOut = condense( - matcherOut === results ? - matcherOut.splice( preexisting, matcherOut.length ) : - matcherOut - ); - if ( postFinder ) { - postFinder( null, results, matcherOut, xml ); - } else { - push.apply( results, matcherOut ); - } - } - }); -} - -function matcherFromTokens( tokens ) { - var checkContext, matcher, j, - len = tokens.length, - leadingRelative = Expr.relative[ tokens[0].type ], - implicitRelative = leadingRelative || Expr.relative[" "], - i = leadingRelative ? 1 : 0, - - // The foundational matcher ensures that elements are reachable from top-level context(s) - matchContext = addCombinator( function( elem ) { - return elem === checkContext; - }, implicitRelative, true ), - matchAnyContext = addCombinator( function( elem ) { - return indexOf.call( checkContext, elem ) > -1; - }, implicitRelative, true ), - matchers = [ function( elem, context, xml ) { - return ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( - (checkContext = context).nodeType ? - matchContext( elem, context, xml ) : - matchAnyContext( elem, context, xml ) ); - } ]; - - for ( ; i < len; i++ ) { - if ( (matcher = Expr.relative[ tokens[i].type ]) ) { - matchers = [ addCombinator(elementMatcher( matchers ), matcher) ]; - } else { - matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches ); - - // Return special upon seeing a positional matcher - if ( matcher[ expando ] ) { - // Find the next relative operator (if any) for proper handling - j = ++i; - for ( ; j < len; j++ ) { - if ( Expr.relative[ tokens[j].type ] ) { - break; - } - } - return setMatcher( - i > 1 && elementMatcher( matchers ), - i > 1 && toSelector( - // If the preceding token was a descendant combinator, insert an implicit any-element `*` - tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" }) - ).replace( rtrim, "$1" ), - matcher, - i < j && matcherFromTokens( tokens.slice( i, j ) ), - j < len && matcherFromTokens( (tokens = tokens.slice( j )) ), - j < len && toSelector( tokens ) - ); - } - matchers.push( matcher ); - } - } - - return elementMatcher( matchers ); -} - -function matcherFromGroupMatchers( elementMatchers, setMatchers ) { - var bySet = setMatchers.length > 0, - byElement = elementMatchers.length > 0, - superMatcher = function( seed, context, xml, results, outermost ) { - var elem, j, matcher, - matchedCount = 0, - i = "0", - unmatched = seed && [], - setMatched = [], - contextBackup = outermostContext, - // We must always have either seed elements or outermost context - elems = seed || byElement && Expr.find["TAG"]( "*", outermost ), - // Use integer dirruns iff this is the outermost matcher - dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1), - len = elems.length; - - if ( outermost ) { - outermostContext = context !== document && context; - } - - // Add elements passing elementMatchers directly to results - // Keep `i` a string if there are no elements so `matchedCount` will be "00" below - // Support: IE<9, Safari - // Tolerate NodeList properties (IE: "length"; Safari: ) matching elements by id - for ( ; i !== len && (elem = elems[i]) != null; i++ ) { - if ( byElement && elem ) { - j = 0; - while ( (matcher = elementMatchers[j++]) ) { - if ( matcher( elem, context, xml ) ) { - results.push( elem ); - break; - } - } - if ( outermost ) { - dirruns = dirrunsUnique; - } - } - - // Track unmatched elements for set filters - if ( bySet ) { - // They will have gone through all possible matchers - if ( (elem = !matcher && elem) ) { - matchedCount--; - } - - // Lengthen the array for every element, matched or not - if ( seed ) { - unmatched.push( elem ); - } - } - } - - // Apply set filters to unmatched elements - matchedCount += i; - if ( bySet && i !== matchedCount ) { - j = 0; - while ( (matcher = setMatchers[j++]) ) { - matcher( unmatched, setMatched, context, xml ); - } - - if ( seed ) { - // Reintegrate element matches to eliminate the need for sorting - if ( matchedCount > 0 ) { - while ( i-- ) { - if ( !(unmatched[i] || setMatched[i]) ) { - setMatched[i] = pop.call( results ); - } - } - } - - // Discard index placeholder values to get only actual matches - setMatched = condense( setMatched ); - } - - // Add matches to results - push.apply( results, setMatched ); - - // Seedless set matches succeeding multiple successful matchers stipulate sorting - if ( outermost && !seed && setMatched.length > 0 && - ( matchedCount + setMatchers.length ) > 1 ) { - - Sizzle.uniqueSort( results ); - } - } - - // Override manipulation of globals by nested matchers - if ( outermost ) { - dirruns = dirrunsUnique; - outermostContext = contextBackup; - } - - return unmatched; - }; - - return bySet ? - markFunction( superMatcher ) : - superMatcher; -} - -compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { - var i, - setMatchers = [], - elementMatchers = [], - cached = compilerCache[ selector + " " ]; - - if ( !cached ) { - // Generate a function of recursive functions that can be used to check each element - if ( !match ) { - match = tokenize( selector ); - } - i = match.length; - while ( i-- ) { - cached = matcherFromTokens( match[i] ); - if ( cached[ expando ] ) { - setMatchers.push( cached ); - } else { - elementMatchers.push( cached ); - } - } - - // Cache the compiled function - cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) ); - - // Save selector and tokenization - cached.selector = selector; - } - return cached; -}; - -/** - * A low-level selection function that works with Sizzle's compiled - * selector functions - * @param {String|Function} selector A selector or a pre-compiled - * selector function built with Sizzle.compile - * @param {Element} context - * @param {Array} [results] - * @param {Array} [seed] A set of elements to match against - */ -select = Sizzle.select = function( selector, context, results, seed ) { - var i, tokens, token, type, find, - compiled = typeof selector === "function" && selector, - match = !seed && tokenize( (selector = compiled.selector || selector) ); - - results = results || []; - - // Try to minimize operations if there is no seed and only one group - if ( match.length === 1 ) { - - // Take a shortcut and set the context if the root selector is an ID - tokens = match[0] = match[0].slice( 0 ); - if ( tokens.length > 2 && (token = tokens[0]).type === "ID" && - support.getById && context.nodeType === 9 && documentIsHTML && - Expr.relative[ tokens[1].type ] ) { - - context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0]; - if ( !context ) { - return results; - - // Precompiled matchers will still verify ancestry, so step up a level - } else if ( compiled ) { - context = context.parentNode; - } - - selector = selector.slice( tokens.shift().value.length ); - } - - // Fetch a seed set for right-to-left matching - i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length; - while ( i-- ) { - token = tokens[i]; - - // Abort if we hit a combinator - if ( Expr.relative[ (type = token.type) ] ) { - break; - } - if ( (find = Expr.find[ type ]) ) { - // Search, expanding context for leading sibling combinators - if ( (seed = find( - token.matches[0].replace( runescape, funescape ), - rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context - )) ) { - - // If seed is empty or no tokens remain, we can return early - tokens.splice( i, 1 ); - selector = seed.length && toSelector( tokens ); - if ( !selector ) { - push.apply( results, seed ); - return results; - } - - break; - } - } - } - } - - // Compile and execute a filtering function if one is not provided - // Provide `match` to avoid retokenization if we modified the selector above - ( compiled || compile( selector, match ) )( - seed, - context, - !documentIsHTML, - results, - rsibling.test( selector ) && testContext( context.parentNode ) || context - ); - return results; -}; - -// One-time assignments - -// Sort stability -support.sortStable = expando.split("").sort( sortOrder ).join("") === expando; - -// Support: Chrome<14 -// Always assume duplicates if they aren't passed to the comparison function -support.detectDuplicates = !!hasDuplicate; - -// Initialize against the default document -setDocument(); - -// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) -// Detached nodes confoundingly follow *each other* -support.sortDetached = assert(function( div1 ) { - // Should return 1, but returns 4 (following) - return div1.compareDocumentPosition( document.createElement("div") ) & 1; -}); - -// Support: IE<8 -// Prevent attribute/property "interpolation" -// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx -if ( !assert(function( div ) { - div.innerHTML = ""; - return div.firstChild.getAttribute("href") === "#" ; -}) ) { - addHandle( "type|href|height|width", function( elem, name, isXML ) { - if ( !isXML ) { - return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); - } - }); -} - -// Support: IE<9 -// Use defaultValue in place of getAttribute("value") -if ( !support.attributes || !assert(function( div ) { - div.innerHTML = ""; - div.firstChild.setAttribute( "value", "" ); - return div.firstChild.getAttribute( "value" ) === ""; -}) ) { - addHandle( "value", function( elem, name, isXML ) { - if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { - return elem.defaultValue; - } - }); -} - -// Support: IE<9 -// Use getAttributeNode to fetch booleans when getAttribute lies -if ( !assert(function( div ) { - return div.getAttribute("disabled") == null; -}) ) { - addHandle( booleans, function( elem, name, isXML ) { - var val; - if ( !isXML ) { - return elem[ name ] === true ? name.toLowerCase() : - (val = elem.getAttributeNode( name )) && val.specified ? - val.value : - null; - } - }); -} - -return Sizzle; - -})( window ); - - - -jQuery.find = Sizzle; -jQuery.expr = Sizzle.selectors; -jQuery.expr[":"] = jQuery.expr.pseudos; -jQuery.unique = Sizzle.uniqueSort; -jQuery.text = Sizzle.getText; -jQuery.isXMLDoc = Sizzle.isXML; -jQuery.contains = Sizzle.contains; - - - -var rneedsContext = jQuery.expr.match.needsContext; - -var rsingleTag = (/^<(\w+)\s*\/?>(?:<\/\1>|)$/); - - - -var risSimple = /^.[^:#\[\.,]*$/; - -// Implement the identical functionality for filter and not -function winnow( elements, qualifier, not ) { - if ( jQuery.isFunction( qualifier ) ) { - return jQuery.grep( elements, function( elem, i ) { - /* jshint -W018 */ - return !!qualifier.call( elem, i, elem ) !== not; - }); - - } - - if ( qualifier.nodeType ) { - return jQuery.grep( elements, function( elem ) { - return ( elem === qualifier ) !== not; - }); - - } - - if ( typeof qualifier === "string" ) { - if ( risSimple.test( qualifier ) ) { - return jQuery.filter( qualifier, elements, not ); - } - - qualifier = jQuery.filter( qualifier, elements ); - } - - return jQuery.grep( elements, function( elem ) { - return ( jQuery.inArray( elem, qualifier ) >= 0 ) !== not; - }); -} - -jQuery.filter = function( expr, elems, not ) { - var elem = elems[ 0 ]; - - if ( not ) { - expr = ":not(" + expr + ")"; - } - - return elems.length === 1 && elem.nodeType === 1 ? - jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [] : - jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { - return elem.nodeType === 1; - })); -}; - -jQuery.fn.extend({ - find: function( selector ) { - var i, - ret = [], - self = this, - len = self.length; - - if ( typeof selector !== "string" ) { - return this.pushStack( jQuery( selector ).filter(function() { - for ( i = 0; i < len; i++ ) { - if ( jQuery.contains( self[ i ], this ) ) { - return true; - } - } - }) ); - } - - for ( i = 0; i < len; i++ ) { - jQuery.find( selector, self[ i ], ret ); - } - - // Needed because $( selector, context ) becomes $( context ).find( selector ) - ret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret ); - ret.selector = this.selector ? this.selector + " " + selector : selector; - return ret; - }, - filter: function( selector ) { - return this.pushStack( winnow(this, selector || [], false) ); - }, - not: function( selector ) { - return this.pushStack( winnow(this, selector || [], true) ); - }, - is: function( selector ) { - return !!winnow( - this, - - // If this is a positional/relative selector, check membership in the returned set - // so $("p:first").is("p:last") won't return true for a doc with two "p". - typeof selector === "string" && rneedsContext.test( selector ) ? - jQuery( selector ) : - selector || [], - false - ).length; - } -}); - - -// Initialize a jQuery object - - -// A central reference to the root jQuery(document) -var rootjQuery, - - // Use the correct document accordingly with window argument (sandbox) - document = window.document, - - // A simple way to check for HTML strings - // Prioritize #id over to avoid XSS via location.hash (#9521) - // Strict HTML recognition (#11290: must start with <) - rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/, - - init = jQuery.fn.init = function( selector, context ) { - var match, elem; - - // HANDLE: $(""), $(null), $(undefined), $(false) - if ( !selector ) { - return this; - } - - // Handle HTML strings - if ( typeof selector === "string" ) { - if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) { - // Assume that strings that start and end with <> are HTML and skip the regex check - match = [ null, selector, null ]; - - } else { - match = rquickExpr.exec( selector ); - } - - // Match html or make sure no context is specified for #id - if ( match && (match[1] || !context) ) { - - // HANDLE: $(html) -> $(array) - if ( match[1] ) { - context = context instanceof jQuery ? context[0] : context; - - // scripts is true for back-compat - // Intentionally let the error be thrown if parseHTML is not present - jQuery.merge( this, jQuery.parseHTML( - match[1], - context && context.nodeType ? context.ownerDocument || context : document, - true - ) ); - - // HANDLE: $(html, props) - if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) { - for ( match in context ) { - // Properties of context are called as methods if possible - if ( jQuery.isFunction( this[ match ] ) ) { - this[ match ]( context[ match ] ); - - // ...and otherwise set as attributes - } else { - this.attr( match, context[ match ] ); - } - } - } - - return this; - - // HANDLE: $(#id) - } else { - elem = document.getElementById( match[2] ); - - // Check parentNode to catch when Blackberry 4.6 returns - // nodes that are no longer in the document #6963 - if ( elem && elem.parentNode ) { - // Handle the case where IE and Opera return items - // by name instead of ID - if ( elem.id !== match[2] ) { - return rootjQuery.find( selector ); - } - - // Otherwise, we inject the element directly into the jQuery object - this.length = 1; - this[0] = elem; - } - - this.context = document; - this.selector = selector; - return this; - } - - // HANDLE: $(expr, $(...)) - } else if ( !context || context.jquery ) { - return ( context || rootjQuery ).find( selector ); - - // HANDLE: $(expr, context) - // (which is just equivalent to: $(context).find(expr) - } else { - return this.constructor( context ).find( selector ); - } - - // HANDLE: $(DOMElement) - } else if ( selector.nodeType ) { - this.context = this[0] = selector; - this.length = 1; - return this; - - // HANDLE: $(function) - // Shortcut for document ready - } else if ( jQuery.isFunction( selector ) ) { - return typeof rootjQuery.ready !== "undefined" ? - rootjQuery.ready( selector ) : - // Execute immediately if ready is not present - selector( jQuery ); - } - - if ( selector.selector !== undefined ) { - this.selector = selector.selector; - this.context = selector.context; - } - - return jQuery.makeArray( selector, this ); - }; - -// Give the init function the jQuery prototype for later instantiation -init.prototype = jQuery.fn; - -// Initialize central reference -rootjQuery = jQuery( document ); - - -var rparentsprev = /^(?:parents|prev(?:Until|All))/, - // methods guaranteed to produce a unique set when starting from a unique set - guaranteedUnique = { - children: true, - contents: true, - next: true, - prev: true - }; - -jQuery.extend({ - dir: function( elem, dir, until ) { - var matched = [], - cur = elem[ dir ]; - - while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) { - if ( cur.nodeType === 1 ) { - matched.push( cur ); - } - cur = cur[dir]; - } - return matched; - }, - - sibling: function( n, elem ) { - var r = []; - - for ( ; n; n = n.nextSibling ) { - if ( n.nodeType === 1 && n !== elem ) { - r.push( n ); - } - } - - return r; - } -}); - -jQuery.fn.extend({ - has: function( target ) { - var i, - targets = jQuery( target, this ), - len = targets.length; - - return this.filter(function() { - for ( i = 0; i < len; i++ ) { - if ( jQuery.contains( this, targets[i] ) ) { - return true; - } - } - }); - }, - - closest: function( selectors, context ) { - var cur, - i = 0, - l = this.length, - matched = [], - pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ? - jQuery( selectors, context || this.context ) : - 0; - - for ( ; i < l; i++ ) { - for ( cur = this[i]; cur && cur !== context; cur = cur.parentNode ) { - // Always skip document fragments - if ( cur.nodeType < 11 && (pos ? - pos.index(cur) > -1 : - - // Don't pass non-elements to Sizzle - cur.nodeType === 1 && - jQuery.find.matchesSelector(cur, selectors)) ) { - - matched.push( cur ); - break; - } - } - } - - return this.pushStack( matched.length > 1 ? jQuery.unique( matched ) : matched ); - }, - - // Determine the position of an element within - // the matched set of elements - index: function( elem ) { - - // No argument, return index in parent - if ( !elem ) { - return ( this[0] && this[0].parentNode ) ? this.first().prevAll().length : -1; - } - - // index in selector - if ( typeof elem === "string" ) { - return jQuery.inArray( this[0], jQuery( elem ) ); - } - - // Locate the position of the desired element - return jQuery.inArray( - // If it receives a jQuery object, the first element is used - elem.jquery ? elem[0] : elem, this ); - }, - - add: function( selector, context ) { - return this.pushStack( - jQuery.unique( - jQuery.merge( this.get(), jQuery( selector, context ) ) - ) - ); - }, - - addBack: function( selector ) { - return this.add( selector == null ? - this.prevObject : this.prevObject.filter(selector) - ); - } -}); - -function sibling( cur, dir ) { - do { - cur = cur[ dir ]; - } while ( cur && cur.nodeType !== 1 ); - - return cur; -} - -jQuery.each({ - parent: function( elem ) { - var parent = elem.parentNode; - return parent && parent.nodeType !== 11 ? parent : null; - }, - parents: function( elem ) { - return jQuery.dir( elem, "parentNode" ); - }, - parentsUntil: function( elem, i, until ) { - return jQuery.dir( elem, "parentNode", until ); - }, - next: function( elem ) { - return sibling( elem, "nextSibling" ); - }, - prev: function( elem ) { - return sibling( elem, "previousSibling" ); - }, - nextAll: function( elem ) { - return jQuery.dir( elem, "nextSibling" ); - }, - prevAll: function( elem ) { - return jQuery.dir( elem, "previousSibling" ); - }, - nextUntil: function( elem, i, until ) { - return jQuery.dir( elem, "nextSibling", until ); - }, - prevUntil: function( elem, i, until ) { - return jQuery.dir( elem, "previousSibling", until ); - }, - siblings: function( elem ) { - return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem ); - }, - children: function( elem ) { - return jQuery.sibling( elem.firstChild ); - }, - contents: function( elem ) { - return jQuery.nodeName( elem, "iframe" ) ? - elem.contentDocument || elem.contentWindow.document : - jQuery.merge( [], elem.childNodes ); - } -}, function( name, fn ) { - jQuery.fn[ name ] = function( until, selector ) { - var ret = jQuery.map( this, fn, until ); - - if ( name.slice( -5 ) !== "Until" ) { - selector = until; - } - - if ( selector && typeof selector === "string" ) { - ret = jQuery.filter( selector, ret ); - } - - if ( this.length > 1 ) { - // Remove duplicates - if ( !guaranteedUnique[ name ] ) { - ret = jQuery.unique( ret ); - } - - // Reverse order for parents* and prev-derivatives - if ( rparentsprev.test( name ) ) { - ret = ret.reverse(); - } - } - - return this.pushStack( ret ); - }; -}); -var rnotwhite = (/\S+/g); - - - -// String to Object options format cache -var optionsCache = {}; - -// Convert String-formatted options into Object-formatted ones and store in cache -function createOptions( options ) { - var object = optionsCache[ options ] = {}; - jQuery.each( options.match( rnotwhite ) || [], function( _, flag ) { - object[ flag ] = true; - }); - return object; -} - -/* - * Create a callback list using the following parameters: - * - * options: an optional list of space-separated options that will change how - * the callback list behaves or a more traditional option object - * - * By default a callback list will act like an event callback list and can be - * "fired" multiple times. - * - * Possible options: - * - * once: will ensure the callback list can only be fired once (like a Deferred) - * - * memory: will keep track of previous values and will call any callback added - * after the list has been fired right away with the latest "memorized" - * values (like a Deferred) - * - * unique: will ensure a callback can only be added once (no duplicate in the list) - * - * stopOnFalse: interrupt callings when a callback returns false - * - */ -jQuery.Callbacks = function( options ) { - - // Convert options from String-formatted to Object-formatted if needed - // (we check in cache first) - options = typeof options === "string" ? - ( optionsCache[ options ] || createOptions( options ) ) : - jQuery.extend( {}, options ); - - var // Flag to know if list is currently firing - firing, - // Last fire value (for non-forgettable lists) - memory, - // Flag to know if list was already fired - fired, - // End of the loop when firing - firingLength, - // Index of currently firing callback (modified by remove if needed) - firingIndex, - // First callback to fire (used internally by add and fireWith) - firingStart, - // Actual callback list - list = [], - // Stack of fire calls for repeatable lists - stack = !options.once && [], - // Fire callbacks - fire = function( data ) { - memory = options.memory && data; - fired = true; - firingIndex = firingStart || 0; - firingStart = 0; - firingLength = list.length; - firing = true; - for ( ; list && firingIndex < firingLength; firingIndex++ ) { - if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) { - memory = false; // To prevent further calls using add - break; - } - } - firing = false; - if ( list ) { - if ( stack ) { - if ( stack.length ) { - fire( stack.shift() ); - } - } else if ( memory ) { - list = []; - } else { - self.disable(); - } - } - }, - // Actual Callbacks object - self = { - // Add a callback or a collection of callbacks to the list - add: function() { - if ( list ) { - // First, we save the current length - var start = list.length; - (function add( args ) { - jQuery.each( args, function( _, arg ) { - var type = jQuery.type( arg ); - if ( type === "function" ) { - if ( !options.unique || !self.has( arg ) ) { - list.push( arg ); - } - } else if ( arg && arg.length && type !== "string" ) { - // Inspect recursively - add( arg ); - } - }); - })( arguments ); - // Do we need to add the callbacks to the - // current firing batch? - if ( firing ) { - firingLength = list.length; - // With memory, if we're not firing then - // we should call right away - } else if ( memory ) { - firingStart = start; - fire( memory ); - } - } - return this; - }, - // Remove a callback from the list - remove: function() { - if ( list ) { - jQuery.each( arguments, function( _, arg ) { - var index; - while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { - list.splice( index, 1 ); - // Handle firing indexes - if ( firing ) { - if ( index <= firingLength ) { - firingLength--; - } - if ( index <= firingIndex ) { - firingIndex--; - } - } - } - }); - } - return this; - }, - // Check if a given callback is in the list. - // If no argument is given, return whether or not list has callbacks attached. - has: function( fn ) { - return fn ? jQuery.inArray( fn, list ) > -1 : !!( list && list.length ); - }, - // Remove all callbacks from the list - empty: function() { - list = []; - firingLength = 0; - return this; - }, - // Have the list do nothing anymore - disable: function() { - list = stack = memory = undefined; - return this; - }, - // Is it disabled? - disabled: function() { - return !list; - }, - // Lock the list in its current state - lock: function() { - stack = undefined; - if ( !memory ) { - self.disable(); - } - return this; - }, - // Is it locked? - locked: function() { - return !stack; - }, - // Call all callbacks with the given context and arguments - fireWith: function( context, args ) { - if ( list && ( !fired || stack ) ) { - args = args || []; - args = [ context, args.slice ? args.slice() : args ]; - if ( firing ) { - stack.push( args ); - } else { - fire( args ); - } - } - return this; - }, - // Call all the callbacks with the given arguments - fire: function() { - self.fireWith( this, arguments ); - return this; - }, - // To know if the callbacks have already been called at least once - fired: function() { - return !!fired; - } - }; - - return self; -}; - - -jQuery.extend({ - - Deferred: function( func ) { - var tuples = [ - // action, add listener, listener list, final state - [ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ], - [ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ], - [ "notify", "progress", jQuery.Callbacks("memory") ] - ], - state = "pending", - promise = { - state: function() { - return state; - }, - always: function() { - deferred.done( arguments ).fail( arguments ); - return this; - }, - then: function( /* fnDone, fnFail, fnProgress */ ) { - var fns = arguments; - return jQuery.Deferred(function( newDefer ) { - jQuery.each( tuples, function( i, tuple ) { - var fn = jQuery.isFunction( fns[ i ] ) && fns[ i ]; - // deferred[ done | fail | progress ] for forwarding actions to newDefer - deferred[ tuple[1] ](function() { - var returned = fn && fn.apply( this, arguments ); - if ( returned && jQuery.isFunction( returned.promise ) ) { - returned.promise() - .done( newDefer.resolve ) - .fail( newDefer.reject ) - .progress( newDefer.notify ); - } else { - newDefer[ tuple[ 0 ] + "With" ]( this === promise ? newDefer.promise() : this, fn ? [ returned ] : arguments ); - } - }); - }); - fns = null; - }).promise(); - }, - // Get a promise for this deferred - // If obj is provided, the promise aspect is added to the object - promise: function( obj ) { - return obj != null ? jQuery.extend( obj, promise ) : promise; - } - }, - deferred = {}; - - // Keep pipe for back-compat - promise.pipe = promise.then; - - // Add list-specific methods - jQuery.each( tuples, function( i, tuple ) { - var list = tuple[ 2 ], - stateString = tuple[ 3 ]; - - // promise[ done | fail | progress ] = list.add - promise[ tuple[1] ] = list.add; - - // Handle state - if ( stateString ) { - list.add(function() { - // state = [ resolved | rejected ] - state = stateString; - - // [ reject_list | resolve_list ].disable; progress_list.lock - }, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock ); - } - - // deferred[ resolve | reject | notify ] - deferred[ tuple[0] ] = function() { - deferred[ tuple[0] + "With" ]( this === deferred ? promise : this, arguments ); - return this; - }; - deferred[ tuple[0] + "With" ] = list.fireWith; - }); - - // Make the deferred a promise - promise.promise( deferred ); - - // Call given func if any - if ( func ) { - func.call( deferred, deferred ); - } - - // All done! - return deferred; - }, - - // Deferred helper - when: function( subordinate /* , ..., subordinateN */ ) { - var i = 0, - resolveValues = slice.call( arguments ), - length = resolveValues.length, - - // the count of uncompleted subordinates - remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0, - - // the master Deferred. If resolveValues consist of only a single Deferred, just use that. - deferred = remaining === 1 ? subordinate : jQuery.Deferred(), - - // Update function for both resolve and progress values - updateFunc = function( i, contexts, values ) { - return function( value ) { - contexts[ i ] = this; - values[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; - if ( values === progressValues ) { - deferred.notifyWith( contexts, values ); - - } else if ( !(--remaining) ) { - deferred.resolveWith( contexts, values ); - } - }; - }, - - progressValues, progressContexts, resolveContexts; - - // add listeners to Deferred subordinates; treat others as resolved - if ( length > 1 ) { - progressValues = new Array( length ); - progressContexts = new Array( length ); - resolveContexts = new Array( length ); - for ( ; i < length; i++ ) { - if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) { - resolveValues[ i ].promise() - .done( updateFunc( i, resolveContexts, resolveValues ) ) - .fail( deferred.reject ) - .progress( updateFunc( i, progressContexts, progressValues ) ); - } else { - --remaining; - } - } - } - - // if we're not waiting on anything, resolve the master - if ( !remaining ) { - deferred.resolveWith( resolveContexts, resolveValues ); - } - - return deferred.promise(); - } -}); - - -// The deferred used on DOM ready -var readyList; - -jQuery.fn.ready = function( fn ) { - // Add the callback - jQuery.ready.promise().done( fn ); - - return this; -}; - -jQuery.extend({ - // Is the DOM ready to be used? Set to true once it occurs. - isReady: false, - - // A counter to track how many items to wait for before - // the ready event fires. See #6781 - readyWait: 1, - - // Hold (or release) the ready event - holdReady: function( hold ) { - if ( hold ) { - jQuery.readyWait++; - } else { - jQuery.ready( true ); - } - }, - - // Handle when the DOM is ready - ready: function( wait ) { - - // Abort if there are pending holds or we're already ready - if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { - return; - } - - // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). - if ( !document.body ) { - return setTimeout( jQuery.ready ); - } - - // Remember that the DOM is ready - jQuery.isReady = true; - - // If a normal DOM Ready event fired, decrement, and wait if need be - if ( wait !== true && --jQuery.readyWait > 0 ) { - return; - } - - // If there are functions bound, to execute - readyList.resolveWith( document, [ jQuery ] ); - - // Trigger any bound ready events - if ( jQuery.fn.triggerHandler ) { - jQuery( document ).triggerHandler( "ready" ); - jQuery( document ).off( "ready" ); - } - } -}); - -/** - * Clean-up method for dom ready events - */ -function detach() { - if ( document.addEventListener ) { - document.removeEventListener( "DOMContentLoaded", completed, false ); - window.removeEventListener( "load", completed, false ); - - } else { - document.detachEvent( "onreadystatechange", completed ); - window.detachEvent( "onload", completed ); - } -} - -/** - * The ready event handler and self cleanup method - */ -function completed() { - // readyState === "complete" is good enough for us to call the dom ready in oldIE - if ( document.addEventListener || event.type === "load" || document.readyState === "complete" ) { - detach(); - jQuery.ready(); - } -} - -jQuery.ready.promise = function( obj ) { - if ( !readyList ) { - - readyList = jQuery.Deferred(); - - // Catch cases where $(document).ready() is called after the browser event has already occurred. - // we once tried to use readyState "interactive" here, but it caused issues like the one - // discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15 - if ( document.readyState === "complete" ) { - // Handle it asynchronously to allow scripts the opportunity to delay ready - setTimeout( jQuery.ready ); - - // Standards-based browsers support DOMContentLoaded - } else if ( document.addEventListener ) { - // Use the handy event callback - document.addEventListener( "DOMContentLoaded", completed, false ); - - // A fallback to window.onload, that will always work - window.addEventListener( "load", completed, false ); - - // If IE event model is used - } else { - // Ensure firing before onload, maybe late but safe also for iframes - document.attachEvent( "onreadystatechange", completed ); - - // A fallback to window.onload, that will always work - window.attachEvent( "onload", completed ); - - // If IE and not a frame - // continually check to see if the document is ready - var top = false; - - try { - top = window.frameElement == null && document.documentElement; - } catch(e) {} - - if ( top && top.doScroll ) { - (function doScrollCheck() { - if ( !jQuery.isReady ) { - - try { - // Use the trick by Diego Perini - // http://javascript.nwbox.com/IEContentLoaded/ - top.doScroll("left"); - } catch(e) { - return setTimeout( doScrollCheck, 50 ); - } - - // detach all dom ready events - detach(); - - // and execute any waiting functions - jQuery.ready(); - } - })(); - } - } - } - return readyList.promise( obj ); -}; - - -var strundefined = typeof undefined; - - - -// Support: IE<9 -// Iteration over object's inherited properties before its own -var i; -for ( i in jQuery( support ) ) { - break; -} -support.ownLast = i !== "0"; - -// Note: most support tests are defined in their respective modules. -// false until the test is run -support.inlineBlockNeedsLayout = false; - -// Execute ASAP in case we need to set body.style.zoom -jQuery(function() { - // Minified: var a,b,c,d - var val, div, body, container; - - body = document.getElementsByTagName( "body" )[ 0 ]; - if ( !body || !body.style ) { - // Return for frameset docs that don't have a body - return; - } - - // Setup - div = document.createElement( "div" ); - container = document.createElement( "div" ); - container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px"; - body.appendChild( container ).appendChild( div ); - - if ( typeof div.style.zoom !== strundefined ) { - // Support: IE<8 - // Check if natively block-level elements act like inline-block - // elements when setting their display to 'inline' and giving - // them layout - div.style.cssText = "display:inline;margin:0;border:0;padding:1px;width:1px;zoom:1"; - - support.inlineBlockNeedsLayout = val = div.offsetWidth === 3; - if ( val ) { - // Prevent IE 6 from affecting layout for positioned elements #11048 - // Prevent IE from shrinking the body in IE 7 mode #12869 - // Support: IE<8 - body.style.zoom = 1; - } - } - - body.removeChild( container ); -}); - - - - -(function() { - var div = document.createElement( "div" ); - - // Execute the test only if not already executed in another module. - if (support.deleteExpando == null) { - // Support: IE<9 - support.deleteExpando = true; - try { - delete div.test; - } catch( e ) { - support.deleteExpando = false; - } - } - - // Null elements to avoid leaks in IE. - div = null; -})(); - - -/** - * Determines whether an object can have data - */ -jQuery.acceptData = function( elem ) { - var noData = jQuery.noData[ (elem.nodeName + " ").toLowerCase() ], - nodeType = +elem.nodeType || 1; - - // Do not set data on non-element DOM nodes because it will not be cleared (#8335). - return nodeType !== 1 && nodeType !== 9 ? - false : - - // Nodes accept data unless otherwise specified; rejection can be conditional - !noData || noData !== true && elem.getAttribute("classid") === noData; -}; - - -var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, - rmultiDash = /([A-Z])/g; - -function dataAttr( elem, key, data ) { - // If nothing was found internally, try to fetch any - // data from the HTML5 data-* attribute - if ( data === undefined && elem.nodeType === 1 ) { - - var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase(); - - data = elem.getAttribute( name ); - - if ( typeof data === "string" ) { - try { - data = data === "true" ? true : - data === "false" ? false : - data === "null" ? null : - // Only convert to a number if it doesn't change the string - +data + "" === data ? +data : - rbrace.test( data ) ? jQuery.parseJSON( data ) : - data; - } catch( e ) {} - - // Make sure we set the data so it isn't changed later - jQuery.data( elem, key, data ); - - } else { - data = undefined; - } - } - - return data; -} - -// checks a cache object for emptiness -function isEmptyDataObject( obj ) { - var name; - for ( name in obj ) { - - // if the public data object is empty, the private is still empty - if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) { - continue; - } - if ( name !== "toJSON" ) { - return false; - } - } - - return true; -} - -function internalData( elem, name, data, pvt /* Internal Use Only */ ) { - if ( !jQuery.acceptData( elem ) ) { - return; - } - - var ret, thisCache, - internalKey = jQuery.expando, - - // We have to handle DOM nodes and JS objects differently because IE6-7 - // can't GC object references properly across the DOM-JS boundary - isNode = elem.nodeType, - - // Only DOM nodes need the global jQuery cache; JS object data is - // attached directly to the object so GC can occur automatically - cache = isNode ? jQuery.cache : elem, - - // Only defining an ID for JS objects if its cache already exists allows - // the code to shortcut on the same path as a DOM node with no cache - id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey; - - // Avoid doing any more work than we need to when trying to get data on an - // object that has no data at all - if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && data === undefined && typeof name === "string" ) { - return; - } - - if ( !id ) { - // Only DOM nodes need a new unique ID for each element since their data - // ends up in the global cache - if ( isNode ) { - id = elem[ internalKey ] = deletedIds.pop() || jQuery.guid++; - } else { - id = internalKey; - } - } - - if ( !cache[ id ] ) { - // Avoid exposing jQuery metadata on plain JS objects when the object - // is serialized using JSON.stringify - cache[ id ] = isNode ? {} : { toJSON: jQuery.noop }; - } - - // An object can be passed to jQuery.data instead of a key/value pair; this gets - // shallow copied over onto the existing cache - if ( typeof name === "object" || typeof name === "function" ) { - if ( pvt ) { - cache[ id ] = jQuery.extend( cache[ id ], name ); - } else { - cache[ id ].data = jQuery.extend( cache[ id ].data, name ); - } - } - - thisCache = cache[ id ]; - - // jQuery data() is stored in a separate object inside the object's internal data - // cache in order to avoid key collisions between internal data and user-defined - // data. - if ( !pvt ) { - if ( !thisCache.data ) { - thisCache.data = {}; - } - - thisCache = thisCache.data; - } - - if ( data !== undefined ) { - thisCache[ jQuery.camelCase( name ) ] = data; - } - - // Check for both converted-to-camel and non-converted data property names - // If a data property was specified - if ( typeof name === "string" ) { - - // First Try to find as-is property data - ret = thisCache[ name ]; - - // Test for null|undefined property data - if ( ret == null ) { - - // Try to find the camelCased property - ret = thisCache[ jQuery.camelCase( name ) ]; - } - } else { - ret = thisCache; - } - - return ret; -} - -function internalRemoveData( elem, name, pvt ) { - if ( !jQuery.acceptData( elem ) ) { - return; - } - - var thisCache, i, - isNode = elem.nodeType, - - // See jQuery.data for more information - cache = isNode ? jQuery.cache : elem, - id = isNode ? elem[ jQuery.expando ] : jQuery.expando; - - // If there is already no cache entry for this object, there is no - // purpose in continuing - if ( !cache[ id ] ) { - return; - } - - if ( name ) { - - thisCache = pvt ? cache[ id ] : cache[ id ].data; - - if ( thisCache ) { - - // Support array or space separated string names for data keys - if ( !jQuery.isArray( name ) ) { - - // try the string as a key before any manipulation - if ( name in thisCache ) { - name = [ name ]; - } else { - - // split the camel cased version by spaces unless a key with the spaces exists - name = jQuery.camelCase( name ); - if ( name in thisCache ) { - name = [ name ]; - } else { - name = name.split(" "); - } - } - } else { - // If "name" is an array of keys... - // When data is initially created, via ("key", "val") signature, - // keys will be converted to camelCase. - // Since there is no way to tell _how_ a key was added, remove - // both plain key and camelCase key. #12786 - // This will only penalize the array argument path. - name = name.concat( jQuery.map( name, jQuery.camelCase ) ); - } - - i = name.length; - while ( i-- ) { - delete thisCache[ name[i] ]; - } - - // If there is no data left in the cache, we want to continue - // and let the cache object itself get destroyed - if ( pvt ? !isEmptyDataObject(thisCache) : !jQuery.isEmptyObject(thisCache) ) { - return; - } - } - } - - // See jQuery.data for more information - if ( !pvt ) { - delete cache[ id ].data; - - // Don't destroy the parent cache unless the internal data object - // had been the only thing left in it - if ( !isEmptyDataObject( cache[ id ] ) ) { - return; - } - } - - // Destroy the cache - if ( isNode ) { - jQuery.cleanData( [ elem ], true ); - - // Use delete when supported for expandos or `cache` is not a window per isWindow (#10080) - /* jshint eqeqeq: false */ - } else if ( support.deleteExpando || cache != cache.window ) { - /* jshint eqeqeq: true */ - delete cache[ id ]; - - // When all else fails, null - } else { - cache[ id ] = null; - } -} - -jQuery.extend({ - cache: {}, - - // The following elements (space-suffixed to avoid Object.prototype collisions) - // throw uncatchable exceptions if you attempt to set expando properties - noData: { - "applet ": true, - "embed ": true, - // ...but Flash objects (which have this classid) *can* handle expandos - "object ": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" - }, - - hasData: function( elem ) { - elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ]; - return !!elem && !isEmptyDataObject( elem ); - }, - - data: function( elem, name, data ) { - return internalData( elem, name, data ); - }, - - removeData: function( elem, name ) { - return internalRemoveData( elem, name ); - }, - - // For internal use only. - _data: function( elem, name, data ) { - return internalData( elem, name, data, true ); - }, - - _removeData: function( elem, name ) { - return internalRemoveData( elem, name, true ); - } -}); - -jQuery.fn.extend({ - data: function( key, value ) { - var i, name, data, - elem = this[0], - attrs = elem && elem.attributes; - - // Special expections of .data basically thwart jQuery.access, - // so implement the relevant behavior ourselves - - // Gets all values - if ( key === undefined ) { - if ( this.length ) { - data = jQuery.data( elem ); - - if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) { - i = attrs.length; - while ( i-- ) { - - // Support: IE11+ - // The attrs elements can be null (#14894) - if ( attrs[ i ] ) { - name = attrs[ i ].name; - if ( name.indexOf( "data-" ) === 0 ) { - name = jQuery.camelCase( name.slice(5) ); - dataAttr( elem, name, data[ name ] ); - } - } - } - jQuery._data( elem, "parsedAttrs", true ); - } - } - - return data; - } - - // Sets multiple values - if ( typeof key === "object" ) { - return this.each(function() { - jQuery.data( this, key ); - }); - } - - return arguments.length > 1 ? - - // Sets one value - this.each(function() { - jQuery.data( this, key, value ); - }) : - - // Gets one value - // Try to fetch any internally stored data first - elem ? dataAttr( elem, key, jQuery.data( elem, key ) ) : undefined; - }, - - removeData: function( key ) { - return this.each(function() { - jQuery.removeData( this, key ); - }); - } -}); - - -jQuery.extend({ - queue: function( elem, type, data ) { - var queue; - - if ( elem ) { - type = ( type || "fx" ) + "queue"; - queue = jQuery._data( elem, type ); - - // Speed up dequeue by getting out quickly if this is just a lookup - if ( data ) { - if ( !queue || jQuery.isArray(data) ) { - queue = jQuery._data( elem, type, jQuery.makeArray(data) ); - } else { - queue.push( data ); - } - } - return queue || []; - } - }, - - dequeue: function( elem, type ) { - type = type || "fx"; - - var queue = jQuery.queue( elem, type ), - startLength = queue.length, - fn = queue.shift(), - hooks = jQuery._queueHooks( elem, type ), - next = function() { - jQuery.dequeue( elem, type ); - }; - - // If the fx queue is dequeued, always remove the progress sentinel - if ( fn === "inprogress" ) { - fn = queue.shift(); - startLength--; - } - - if ( fn ) { - - // Add a progress sentinel to prevent the fx queue from being - // automatically dequeued - if ( type === "fx" ) { - queue.unshift( "inprogress" ); - } - - // clear up the last queue stop function - delete hooks.stop; - fn.call( elem, next, hooks ); - } - - if ( !startLength && hooks ) { - hooks.empty.fire(); - } - }, - - // not intended for public consumption - generates a queueHooks object, or returns the current one - _queueHooks: function( elem, type ) { - var key = type + "queueHooks"; - return jQuery._data( elem, key ) || jQuery._data( elem, key, { - empty: jQuery.Callbacks("once memory").add(function() { - jQuery._removeData( elem, type + "queue" ); - jQuery._removeData( elem, key ); - }) - }); - } -}); - -jQuery.fn.extend({ - queue: function( type, data ) { - var setter = 2; - - if ( typeof type !== "string" ) { - data = type; - type = "fx"; - setter--; - } - - if ( arguments.length < setter ) { - return jQuery.queue( this[0], type ); - } - - return data === undefined ? - this : - this.each(function() { - var queue = jQuery.queue( this, type, data ); - - // ensure a hooks for this queue - jQuery._queueHooks( this, type ); - - if ( type === "fx" && queue[0] !== "inprogress" ) { - jQuery.dequeue( this, type ); - } - }); - }, - dequeue: function( type ) { - return this.each(function() { - jQuery.dequeue( this, type ); - }); - }, - clearQueue: function( type ) { - return this.queue( type || "fx", [] ); - }, - // Get a promise resolved when queues of a certain type - // are emptied (fx is the type by default) - promise: function( type, obj ) { - var tmp, - count = 1, - defer = jQuery.Deferred(), - elements = this, - i = this.length, - resolve = function() { - if ( !( --count ) ) { - defer.resolveWith( elements, [ elements ] ); - } - }; - - if ( typeof type !== "string" ) { - obj = type; - type = undefined; - } - type = type || "fx"; - - while ( i-- ) { - tmp = jQuery._data( elements[ i ], type + "queueHooks" ); - if ( tmp && tmp.empty ) { - count++; - tmp.empty.add( resolve ); - } - } - resolve(); - return defer.promise( obj ); - } -}); -var pnum = (/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/).source; - -var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; - -var isHidden = function( elem, el ) { - // isHidden might be called from jQuery#filter function; - // in that case, element will be second argument - elem = el || elem; - return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem ); - }; - - - -// Multifunctional method to get and set values of a collection -// The value/s can optionally be executed if it's a function -var access = jQuery.access = function( elems, fn, key, value, chainable, emptyGet, raw ) { - var i = 0, - length = elems.length, - bulk = key == null; - - // Sets many values - if ( jQuery.type( key ) === "object" ) { - chainable = true; - for ( i in key ) { - jQuery.access( elems, fn, i, key[i], true, emptyGet, raw ); - } - - // Sets one value - } else if ( value !== undefined ) { - chainable = true; - - if ( !jQuery.isFunction( value ) ) { - raw = true; - } - - if ( bulk ) { - // Bulk operations run against the entire set - if ( raw ) { - fn.call( elems, value ); - fn = null; - - // ...except when executing function values - } else { - bulk = fn; - fn = function( elem, key, value ) { - return bulk.call( jQuery( elem ), value ); - }; - } - } - - if ( fn ) { - for ( ; i < length; i++ ) { - fn( elems[i], key, raw ? value : value.call( elems[i], i, fn( elems[i], key ) ) ); - } - } - } - - return chainable ? - elems : - - // Gets - bulk ? - fn.call( elems ) : - length ? fn( elems[0], key ) : emptyGet; -}; -var rcheckableType = (/^(?:checkbox|radio)$/i); - - - -(function() { - // Minified: var a,b,c - var input = document.createElement( "input" ), - div = document.createElement( "div" ), - fragment = document.createDocumentFragment(); - - // Setup - div.innerHTML = "
a"; - - // IE strips leading whitespace when .innerHTML is used - support.leadingWhitespace = div.firstChild.nodeType === 3; - - // Make sure that tbody elements aren't automatically inserted - // IE will insert them into empty tables - support.tbody = !div.getElementsByTagName( "tbody" ).length; - - // Make sure that link elements get serialized correctly by innerHTML - // This requires a wrapper element in IE - support.htmlSerialize = !!div.getElementsByTagName( "link" ).length; - - // Makes sure cloning an html5 element does not cause problems - // Where outerHTML is undefined, this still works - support.html5Clone = - document.createElement( "nav" ).cloneNode( true ).outerHTML !== "<:nav>"; - - // Check if a disconnected checkbox will retain its checked - // value of true after appended to the DOM (IE6/7) - input.type = "checkbox"; - input.checked = true; - fragment.appendChild( input ); - support.appendChecked = input.checked; - - // Make sure textarea (and checkbox) defaultValue is properly cloned - // Support: IE6-IE11+ - div.innerHTML = ""; - support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; - - // #11217 - WebKit loses check when the name is after the checked attribute - fragment.appendChild( div ); - div.innerHTML = ""; - - // Support: Safari 5.1, iOS 5.1, Android 4.x, Android 2.3 - // old WebKit doesn't clone checked state correctly in fragments - support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; - - // Support: IE<9 - // Opera does not clone events (and typeof div.attachEvent === undefined). - // IE9-10 clones events bound via attachEvent, but they don't trigger with .click() - support.noCloneEvent = true; - if ( div.attachEvent ) { - div.attachEvent( "onclick", function() { - support.noCloneEvent = false; - }); - - div.cloneNode( true ).click(); - } - - // Execute the test only if not already executed in another module. - if (support.deleteExpando == null) { - // Support: IE<9 - support.deleteExpando = true; - try { - delete div.test; - } catch( e ) { - support.deleteExpando = false; - } - } -})(); - - -(function() { - var i, eventName, - div = document.createElement( "div" ); - - // Support: IE<9 (lack submit/change bubble), Firefox 23+ (lack focusin event) - for ( i in { submit: true, change: true, focusin: true }) { - eventName = "on" + i; - - if ( !(support[ i + "Bubbles" ] = eventName in window) ) { - // Beware of CSP restrictions (https://developer.mozilla.org/en/Security/CSP) - div.setAttribute( eventName, "t" ); - support[ i + "Bubbles" ] = div.attributes[ eventName ].expando === false; - } - } - - // Null elements to avoid leaks in IE. - div = null; -})(); - - -var rformElems = /^(?:input|select|textarea)$/i, - rkeyEvent = /^key/, - rmouseEvent = /^(?:mouse|pointer|contextmenu)|click/, - rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, - rtypenamespace = /^([^.]*)(?:\.(.+)|)$/; - -function returnTrue() { - return true; -} - -function returnFalse() { - return false; -} - -function safeActiveElement() { - try { - return document.activeElement; - } catch ( err ) { } -} - -/* - * Helper functions for managing events -- not part of the public interface. - * Props to Dean Edwards' addEvent library for many of the ideas. - */ -jQuery.event = { - - global: {}, - - add: function( elem, types, handler, data, selector ) { - var tmp, events, t, handleObjIn, - special, eventHandle, handleObj, - handlers, type, namespaces, origType, - elemData = jQuery._data( elem ); - - // Don't attach events to noData or text/comment nodes (but allow plain objects) - if ( !elemData ) { - return; - } - - // Caller can pass in an object of custom data in lieu of the handler - if ( handler.handler ) { - handleObjIn = handler; - handler = handleObjIn.handler; - selector = handleObjIn.selector; - } - - // Make sure that the handler has a unique ID, used to find/remove it later - if ( !handler.guid ) { - handler.guid = jQuery.guid++; - } - - // Init the element's event structure and main handler, if this is the first - if ( !(events = elemData.events) ) { - events = elemData.events = {}; - } - if ( !(eventHandle = elemData.handle) ) { - eventHandle = elemData.handle = function( e ) { - // Discard the second event of a jQuery.event.trigger() and - // when an event is called after a page has unloaded - return typeof jQuery !== strundefined && (!e || jQuery.event.triggered !== e.type) ? - jQuery.event.dispatch.apply( eventHandle.elem, arguments ) : - undefined; - }; - // Add elem as a property of the handle fn to prevent a memory leak with IE non-native events - eventHandle.elem = elem; - } - - // Handle multiple events separated by a space - types = ( types || "" ).match( rnotwhite ) || [ "" ]; - t = types.length; - while ( t-- ) { - tmp = rtypenamespace.exec( types[t] ) || []; - type = origType = tmp[1]; - namespaces = ( tmp[2] || "" ).split( "." ).sort(); - - // There *must* be a type, no attaching namespace-only handlers - if ( !type ) { - continue; - } - - // If event changes its type, use the special event handlers for the changed type - special = jQuery.event.special[ type ] || {}; - - // If selector defined, determine special event api type, otherwise given type - type = ( selector ? special.delegateType : special.bindType ) || type; - - // Update special based on newly reset type - special = jQuery.event.special[ type ] || {}; - - // handleObj is passed to all event handlers - handleObj = jQuery.extend({ - type: type, - origType: origType, - data: data, - handler: handler, - guid: handler.guid, - selector: selector, - needsContext: selector && jQuery.expr.match.needsContext.test( selector ), - namespace: namespaces.join(".") - }, handleObjIn ); - - // Init the event handler queue if we're the first - if ( !(handlers = events[ type ]) ) { - handlers = events[ type ] = []; - handlers.delegateCount = 0; - - // Only use addEventListener/attachEvent if the special events handler returns false - if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) { - // Bind the global event handler to the element - if ( elem.addEventListener ) { - elem.addEventListener( type, eventHandle, false ); - - } else if ( elem.attachEvent ) { - elem.attachEvent( "on" + type, eventHandle ); - } - } - } - - if ( special.add ) { - special.add.call( elem, handleObj ); - - if ( !handleObj.handler.guid ) { - handleObj.handler.guid = handler.guid; - } - } - - // Add to the element's handler list, delegates in front - if ( selector ) { - handlers.splice( handlers.delegateCount++, 0, handleObj ); - } else { - handlers.push( handleObj ); - } - - // Keep track of which events have ever been used, for event optimization - jQuery.event.global[ type ] = true; - } - - // Nullify elem to prevent memory leaks in IE - elem = null; - }, - - // Detach an event or set of events from an element - remove: function( elem, types, handler, selector, mappedTypes ) { - var j, handleObj, tmp, - origCount, t, events, - special, handlers, type, - namespaces, origType, - elemData = jQuery.hasData( elem ) && jQuery._data( elem ); - - if ( !elemData || !(events = elemData.events) ) { - return; - } - - // Once for each type.namespace in types; type may be omitted - types = ( types || "" ).match( rnotwhite ) || [ "" ]; - t = types.length; - while ( t-- ) { - tmp = rtypenamespace.exec( types[t] ) || []; - type = origType = tmp[1]; - namespaces = ( tmp[2] || "" ).split( "." ).sort(); - - // Unbind all events (on this namespace, if provided) for the element - if ( !type ) { - for ( type in events ) { - jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); - } - continue; - } - - special = jQuery.event.special[ type ] || {}; - type = ( selector ? special.delegateType : special.bindType ) || type; - handlers = events[ type ] || []; - tmp = tmp[2] && new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ); - - // Remove matching events - origCount = j = handlers.length; - while ( j-- ) { - handleObj = handlers[ j ]; - - if ( ( mappedTypes || origType === handleObj.origType ) && - ( !handler || handler.guid === handleObj.guid ) && - ( !tmp || tmp.test( handleObj.namespace ) ) && - ( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) { - handlers.splice( j, 1 ); - - if ( handleObj.selector ) { - handlers.delegateCount--; - } - if ( special.remove ) { - special.remove.call( elem, handleObj ); - } - } - } - - // Remove generic event handler if we removed something and no more handlers exist - // (avoids potential for endless recursion during removal of special event handlers) - if ( origCount && !handlers.length ) { - if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) { - jQuery.removeEvent( elem, type, elemData.handle ); - } - - delete events[ type ]; - } - } - - // Remove the expando if it's no longer used - if ( jQuery.isEmptyObject( events ) ) { - delete elemData.handle; - - // removeData also checks for emptiness and clears the expando if empty - // so use it instead of delete - jQuery._removeData( elem, "events" ); - } - }, - - trigger: function( event, data, elem, onlyHandlers ) { - var handle, ontype, cur, - bubbleType, special, tmp, i, - eventPath = [ elem || document ], - type = hasOwn.call( event, "type" ) ? event.type : event, - namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split(".") : []; - - cur = tmp = elem = elem || document; - - // Don't do events on text and comment nodes - if ( elem.nodeType === 3 || elem.nodeType === 8 ) { - return; - } - - // focus/blur morphs to focusin/out; ensure we're not firing them right now - if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { - return; - } - - if ( type.indexOf(".") >= 0 ) { - // Namespaced trigger; create a regexp to match event type in handle() - namespaces = type.split("."); - type = namespaces.shift(); - namespaces.sort(); - } - ontype = type.indexOf(":") < 0 && "on" + type; - - // Caller can pass in a jQuery.Event object, Object, or just an event type string - event = event[ jQuery.expando ] ? - event : - new jQuery.Event( type, typeof event === "object" && event ); - - // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) - event.isTrigger = onlyHandlers ? 2 : 3; - event.namespace = namespaces.join("."); - event.namespace_re = event.namespace ? - new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ) : - null; - - // Clean up the event in case it is being reused - event.result = undefined; - if ( !event.target ) { - event.target = elem; - } - - // Clone any incoming data and prepend the event, creating the handler arg list - data = data == null ? - [ event ] : - jQuery.makeArray( data, [ event ] ); - - // Allow special events to draw outside the lines - special = jQuery.event.special[ type ] || {}; - if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { - return; - } - - // Determine event propagation path in advance, per W3C events spec (#9951) - // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) - if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) { - - bubbleType = special.delegateType || type; - if ( !rfocusMorph.test( bubbleType + type ) ) { - cur = cur.parentNode; - } - for ( ; cur; cur = cur.parentNode ) { - eventPath.push( cur ); - tmp = cur; - } - - // Only add window if we got to document (e.g., not plain obj or detached DOM) - if ( tmp === (elem.ownerDocument || document) ) { - eventPath.push( tmp.defaultView || tmp.parentWindow || window ); - } - } - - // Fire handlers on the event path - i = 0; - while ( (cur = eventPath[i++]) && !event.isPropagationStopped() ) { - - event.type = i > 1 ? - bubbleType : - special.bindType || type; - - // jQuery handler - handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" ); - if ( handle ) { - handle.apply( cur, data ); - } - - // Native handler - handle = ontype && cur[ ontype ]; - if ( handle && handle.apply && jQuery.acceptData( cur ) ) { - event.result = handle.apply( cur, data ); - if ( event.result === false ) { - event.preventDefault(); - } - } - } - event.type = type; - - // If nobody prevented the default action, do it now - if ( !onlyHandlers && !event.isDefaultPrevented() ) { - - if ( (!special._default || special._default.apply( eventPath.pop(), data ) === false) && - jQuery.acceptData( elem ) ) { - - // Call a native DOM method on the target with the same name name as the event. - // Can't use an .isFunction() check here because IE6/7 fails that test. - // Don't do default actions on window, that's where global variables be (#6170) - if ( ontype && elem[ type ] && !jQuery.isWindow( elem ) ) { - - // Don't re-trigger an onFOO event when we call its FOO() method - tmp = elem[ ontype ]; - - if ( tmp ) { - elem[ ontype ] = null; - } - - // Prevent re-triggering of the same event, since we already bubbled it above - jQuery.event.triggered = type; - try { - elem[ type ](); - } catch ( e ) { - // IE<9 dies on focus/blur to hidden element (#1486,#12518) - // only reproducible on winXP IE8 native, not IE9 in IE8 mode - } - jQuery.event.triggered = undefined; - - if ( tmp ) { - elem[ ontype ] = tmp; - } - } - } - } - - return event.result; - }, - - dispatch: function( event ) { - - // Make a writable jQuery.Event from the native event object - event = jQuery.event.fix( event ); - - var i, ret, handleObj, matched, j, - handlerQueue = [], - args = slice.call( arguments ), - handlers = ( jQuery._data( this, "events" ) || {} )[ event.type ] || [], - special = jQuery.event.special[ event.type ] || {}; - - // Use the fix-ed jQuery.Event rather than the (read-only) native event - args[0] = event; - event.delegateTarget = this; - - // Call the preDispatch hook for the mapped type, and let it bail if desired - if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { - return; - } - - // Determine handlers - handlerQueue = jQuery.event.handlers.call( this, event, handlers ); - - // Run delegates first; they may want to stop propagation beneath us - i = 0; - while ( (matched = handlerQueue[ i++ ]) && !event.isPropagationStopped() ) { - event.currentTarget = matched.elem; - - j = 0; - while ( (handleObj = matched.handlers[ j++ ]) && !event.isImmediatePropagationStopped() ) { - - // Triggered event must either 1) have no namespace, or - // 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace). - if ( !event.namespace_re || event.namespace_re.test( handleObj.namespace ) ) { - - event.handleObj = handleObj; - event.data = handleObj.data; - - ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler ) - .apply( matched.elem, args ); - - if ( ret !== undefined ) { - if ( (event.result = ret) === false ) { - event.preventDefault(); - event.stopPropagation(); - } - } - } - } - } - - // Call the postDispatch hook for the mapped type - if ( special.postDispatch ) { - special.postDispatch.call( this, event ); - } - - return event.result; - }, - - handlers: function( event, handlers ) { - var sel, handleObj, matches, i, - handlerQueue = [], - delegateCount = handlers.delegateCount, - cur = event.target; - - // Find delegate handlers - // Black-hole SVG instance trees (#13180) - // Avoid non-left-click bubbling in Firefox (#3861) - if ( delegateCount && cur.nodeType && (!event.button || event.type !== "click") ) { - - /* jshint eqeqeq: false */ - for ( ; cur != this; cur = cur.parentNode || this ) { - /* jshint eqeqeq: true */ - - // Don't check non-elements (#13208) - // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) - if ( cur.nodeType === 1 && (cur.disabled !== true || event.type !== "click") ) { - matches = []; - for ( i = 0; i < delegateCount; i++ ) { - handleObj = handlers[ i ]; - - // Don't conflict with Object.prototype properties (#13203) - sel = handleObj.selector + " "; - - if ( matches[ sel ] === undefined ) { - matches[ sel ] = handleObj.needsContext ? - jQuery( sel, this ).index( cur ) >= 0 : - jQuery.find( sel, this, null, [ cur ] ).length; - } - if ( matches[ sel ] ) { - matches.push( handleObj ); - } - } - if ( matches.length ) { - handlerQueue.push({ elem: cur, handlers: matches }); - } - } - } - } - - // Add the remaining (directly-bound) handlers - if ( delegateCount < handlers.length ) { - handlerQueue.push({ elem: this, handlers: handlers.slice( delegateCount ) }); - } - - return handlerQueue; - }, - - fix: function( event ) { - if ( event[ jQuery.expando ] ) { - return event; - } - - // Create a writable copy of the event object and normalize some properties - var i, prop, copy, - type = event.type, - originalEvent = event, - fixHook = this.fixHooks[ type ]; - - if ( !fixHook ) { - this.fixHooks[ type ] = fixHook = - rmouseEvent.test( type ) ? this.mouseHooks : - rkeyEvent.test( type ) ? this.keyHooks : - {}; - } - copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props; - - event = new jQuery.Event( originalEvent ); - - i = copy.length; - while ( i-- ) { - prop = copy[ i ]; - event[ prop ] = originalEvent[ prop ]; - } - - // Support: IE<9 - // Fix target property (#1925) - if ( !event.target ) { - event.target = originalEvent.srcElement || document; - } - - // Support: Chrome 23+, Safari? - // Target should not be a text node (#504, #13143) - if ( event.target.nodeType === 3 ) { - event.target = event.target.parentNode; - } - - // Support: IE<9 - // For mouse/key events, metaKey==false if it's undefined (#3368, #11328) - event.metaKey = !!event.metaKey; - - return fixHook.filter ? fixHook.filter( event, originalEvent ) : event; - }, - - // Includes some event props shared by KeyEvent and MouseEvent - props: "altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "), - - fixHooks: {}, - - keyHooks: { - props: "char charCode key keyCode".split(" "), - filter: function( event, original ) { - - // Add which for key events - if ( event.which == null ) { - event.which = original.charCode != null ? original.charCode : original.keyCode; - } - - return event; - } - }, - - mouseHooks: { - props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "), - filter: function( event, original ) { - var body, eventDoc, doc, - button = original.button, - fromElement = original.fromElement; - - // Calculate pageX/Y if missing and clientX/Y available - if ( event.pageX == null && original.clientX != null ) { - eventDoc = event.target.ownerDocument || document; - doc = eventDoc.documentElement; - body = eventDoc.body; - - event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 ); - event.pageY = original.clientY + ( doc && doc.scrollTop || body && body.scrollTop || 0 ) - ( doc && doc.clientTop || body && body.clientTop || 0 ); - } - - // Add relatedTarget, if necessary - if ( !event.relatedTarget && fromElement ) { - event.relatedTarget = fromElement === event.target ? original.toElement : fromElement; - } - - // Add which for click: 1 === left; 2 === middle; 3 === right - // Note: button is not normalized, so don't use it - if ( !event.which && button !== undefined ) { - event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) ); - } - - return event; - } - }, - - special: { - load: { - // Prevent triggered image.load events from bubbling to window.load - noBubble: true - }, - focus: { - // Fire native event if possible so blur/focus sequence is correct - trigger: function() { - if ( this !== safeActiveElement() && this.focus ) { - try { - this.focus(); - return false; - } catch ( e ) { - // Support: IE<9 - // If we error on focus to hidden element (#1486, #12518), - // let .trigger() run the handlers - } - } - }, - delegateType: "focusin" - }, - blur: { - trigger: function() { - if ( this === safeActiveElement() && this.blur ) { - this.blur(); - return false; - } - }, - delegateType: "focusout" - }, - click: { - // For checkbox, fire native event so checked state will be right - trigger: function() { - if ( jQuery.nodeName( this, "input" ) && this.type === "checkbox" && this.click ) { - this.click(); - return false; - } - }, - - // For cross-browser consistency, don't fire native .click() on links - _default: function( event ) { - return jQuery.nodeName( event.target, "a" ); - } - }, - - beforeunload: { - postDispatch: function( event ) { - - // Support: Firefox 20+ - // Firefox doesn't alert if the returnValue field is not set. - if ( event.result !== undefined && event.originalEvent ) { - event.originalEvent.returnValue = event.result; - } - } - } - }, - - simulate: function( type, elem, event, bubble ) { - // Piggyback on a donor event to simulate a different one. - // Fake originalEvent to avoid donor's stopPropagation, but if the - // simulated event prevents default then we do the same on the donor. - var e = jQuery.extend( - new jQuery.Event(), - event, - { - type: type, - isSimulated: true, - originalEvent: {} - } - ); - if ( bubble ) { - jQuery.event.trigger( e, null, elem ); - } else { - jQuery.event.dispatch.call( elem, e ); - } - if ( e.isDefaultPrevented() ) { - event.preventDefault(); - } - } -}; - -jQuery.removeEvent = document.removeEventListener ? - function( elem, type, handle ) { - if ( elem.removeEventListener ) { - elem.removeEventListener( type, handle, false ); - } - } : - function( elem, type, handle ) { - var name = "on" + type; - - if ( elem.detachEvent ) { - - // #8545, #7054, preventing memory leaks for custom events in IE6-8 - // detachEvent needed property on element, by name of that event, to properly expose it to GC - if ( typeof elem[ name ] === strundefined ) { - elem[ name ] = null; - } - - elem.detachEvent( name, handle ); - } - }; - -jQuery.Event = function( src, props ) { - // Allow instantiation without the 'new' keyword - if ( !(this instanceof jQuery.Event) ) { - return new jQuery.Event( src, props ); - } - - // Event object - if ( src && src.type ) { - this.originalEvent = src; - this.type = src.type; - - // Events bubbling up the document may have been marked as prevented - // by a handler lower down the tree; reflect the correct value. - this.isDefaultPrevented = src.defaultPrevented || - src.defaultPrevented === undefined && - // Support: IE < 9, Android < 4.0 - src.returnValue === false ? - returnTrue : - returnFalse; - - // Event type - } else { - this.type = src; - } - - // Put explicitly provided properties onto the event object - if ( props ) { - jQuery.extend( this, props ); - } - - // Create a timestamp if incoming event doesn't have one - this.timeStamp = src && src.timeStamp || jQuery.now(); - - // Mark it as fixed - this[ jQuery.expando ] = true; -}; - -// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding -// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html -jQuery.Event.prototype = { - isDefaultPrevented: returnFalse, - isPropagationStopped: returnFalse, - isImmediatePropagationStopped: returnFalse, - - preventDefault: function() { - var e = this.originalEvent; - - this.isDefaultPrevented = returnTrue; - if ( !e ) { - return; - } - - // If preventDefault exists, run it on the original event - if ( e.preventDefault ) { - e.preventDefault(); - - // Support: IE - // Otherwise set the returnValue property of the original event to false - } else { - e.returnValue = false; - } - }, - stopPropagation: function() { - var e = this.originalEvent; - - this.isPropagationStopped = returnTrue; - if ( !e ) { - return; - } - // If stopPropagation exists, run it on the original event - if ( e.stopPropagation ) { - e.stopPropagation(); - } - - // Support: IE - // Set the cancelBubble property of the original event to true - e.cancelBubble = true; - }, - stopImmediatePropagation: function() { - var e = this.originalEvent; - - this.isImmediatePropagationStopped = returnTrue; - - if ( e && e.stopImmediatePropagation ) { - e.stopImmediatePropagation(); - } - - this.stopPropagation(); - } -}; - -// Create mouseenter/leave events using mouseover/out and event-time checks -jQuery.each({ - mouseenter: "mouseover", - mouseleave: "mouseout", - pointerenter: "pointerover", - pointerleave: "pointerout" -}, function( orig, fix ) { - jQuery.event.special[ orig ] = { - delegateType: fix, - bindType: fix, - - handle: function( event ) { - var ret, - target = this, - related = event.relatedTarget, - handleObj = event.handleObj; - - // For mousenter/leave call the handler if related is outside the target. - // NB: No relatedTarget if the mouse left/entered the browser window - if ( !related || (related !== target && !jQuery.contains( target, related )) ) { - event.type = handleObj.origType; - ret = handleObj.handler.apply( this, arguments ); - event.type = fix; - } - return ret; - } - }; -}); - -// IE submit delegation -if ( !support.submitBubbles ) { - - jQuery.event.special.submit = { - setup: function() { - // Only need this for delegated form submit events - if ( jQuery.nodeName( this, "form" ) ) { - return false; - } - - // Lazy-add a submit handler when a descendant form may potentially be submitted - jQuery.event.add( this, "click._submit keypress._submit", function( e ) { - // Node name check avoids a VML-related crash in IE (#9807) - var elem = e.target, - form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined; - if ( form && !jQuery._data( form, "submitBubbles" ) ) { - jQuery.event.add( form, "submit._submit", function( event ) { - event._submit_bubble = true; - }); - jQuery._data( form, "submitBubbles", true ); - } - }); - // return undefined since we don't need an event listener - }, - - postDispatch: function( event ) { - // If form was submitted by the user, bubble the event up the tree - if ( event._submit_bubble ) { - delete event._submit_bubble; - if ( this.parentNode && !event.isTrigger ) { - jQuery.event.simulate( "submit", this.parentNode, event, true ); - } - } - }, - - teardown: function() { - // Only need this for delegated form submit events - if ( jQuery.nodeName( this, "form" ) ) { - return false; - } - - // Remove delegated handlers; cleanData eventually reaps submit handlers attached above - jQuery.event.remove( this, "._submit" ); - } - }; -} - -// IE change delegation and checkbox/radio fix -if ( !support.changeBubbles ) { - - jQuery.event.special.change = { - - setup: function() { - - if ( rformElems.test( this.nodeName ) ) { - // IE doesn't fire change on a check/radio until blur; trigger it on click - // after a propertychange. Eat the blur-change in special.change.handle. - // This still fires onchange a second time for check/radio after blur. - if ( this.type === "checkbox" || this.type === "radio" ) { - jQuery.event.add( this, "propertychange._change", function( event ) { - if ( event.originalEvent.propertyName === "checked" ) { - this._just_changed = true; - } - }); - jQuery.event.add( this, "click._change", function( event ) { - if ( this._just_changed && !event.isTrigger ) { - this._just_changed = false; - } - // Allow triggered, simulated change events (#11500) - jQuery.event.simulate( "change", this, event, true ); - }); - } - return false; - } - // Delegated event; lazy-add a change handler on descendant inputs - jQuery.event.add( this, "beforeactivate._change", function( e ) { - var elem = e.target; - - if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "changeBubbles" ) ) { - jQuery.event.add( elem, "change._change", function( event ) { - if ( this.parentNode && !event.isSimulated && !event.isTrigger ) { - jQuery.event.simulate( "change", this.parentNode, event, true ); - } - }); - jQuery._data( elem, "changeBubbles", true ); - } - }); - }, - - handle: function( event ) { - var elem = event.target; - - // Swallow native change events from checkbox/radio, we already triggered them above - if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) { - return event.handleObj.handler.apply( this, arguments ); - } - }, - - teardown: function() { - jQuery.event.remove( this, "._change" ); - - return !rformElems.test( this.nodeName ); - } - }; -} - -// Create "bubbling" focus and blur events -if ( !support.focusinBubbles ) { - jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) { - - // Attach a single capturing handler on the document while someone wants focusin/focusout - var handler = function( event ) { - jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true ); - }; - - jQuery.event.special[ fix ] = { - setup: function() { - var doc = this.ownerDocument || this, - attaches = jQuery._data( doc, fix ); - - if ( !attaches ) { - doc.addEventListener( orig, handler, true ); - } - jQuery._data( doc, fix, ( attaches || 0 ) + 1 ); - }, - teardown: function() { - var doc = this.ownerDocument || this, - attaches = jQuery._data( doc, fix ) - 1; - - if ( !attaches ) { - doc.removeEventListener( orig, handler, true ); - jQuery._removeData( doc, fix ); - } else { - jQuery._data( doc, fix, attaches ); - } - } - }; - }); -} - -jQuery.fn.extend({ - - on: function( types, selector, data, fn, /*INTERNAL*/ one ) { - var type, origFn; - - // Types can be a map of types/handlers - if ( typeof types === "object" ) { - // ( types-Object, selector, data ) - if ( typeof selector !== "string" ) { - // ( types-Object, data ) - data = data || selector; - selector = undefined; - } - for ( type in types ) { - this.on( type, selector, data, types[ type ], one ); - } - return this; - } - - if ( data == null && fn == null ) { - // ( types, fn ) - fn = selector; - data = selector = undefined; - } else if ( fn == null ) { - if ( typeof selector === "string" ) { - // ( types, selector, fn ) - fn = data; - data = undefined; - } else { - // ( types, data, fn ) - fn = data; - data = selector; - selector = undefined; - } - } - if ( fn === false ) { - fn = returnFalse; - } else if ( !fn ) { - return this; - } - - if ( one === 1 ) { - origFn = fn; - fn = function( event ) { - // Can use an empty set, since event contains the info - jQuery().off( event ); - return origFn.apply( this, arguments ); - }; - // Use same guid so caller can remove using origFn - fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); - } - return this.each( function() { - jQuery.event.add( this, types, fn, data, selector ); - }); - }, - one: function( types, selector, data, fn ) { - return this.on( types, selector, data, fn, 1 ); - }, - off: function( types, selector, fn ) { - var handleObj, type; - if ( types && types.preventDefault && types.handleObj ) { - // ( event ) dispatched jQuery.Event - handleObj = types.handleObj; - jQuery( types.delegateTarget ).off( - handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType, - handleObj.selector, - handleObj.handler - ); - return this; - } - if ( typeof types === "object" ) { - // ( types-object [, selector] ) - for ( type in types ) { - this.off( type, selector, types[ type ] ); - } - return this; - } - if ( selector === false || typeof selector === "function" ) { - // ( types [, fn] ) - fn = selector; - selector = undefined; - } - if ( fn === false ) { - fn = returnFalse; - } - return this.each(function() { - jQuery.event.remove( this, types, fn, selector ); - }); - }, - - trigger: function( type, data ) { - return this.each(function() { - jQuery.event.trigger( type, data, this ); - }); - }, - triggerHandler: function( type, data ) { - var elem = this[0]; - if ( elem ) { - return jQuery.event.trigger( type, data, elem, true ); - } - } -}); - - -function createSafeFragment( document ) { - var list = nodeNames.split( "|" ), - safeFrag = document.createDocumentFragment(); - - if ( safeFrag.createElement ) { - while ( list.length ) { - safeFrag.createElement( - list.pop() - ); - } - } - return safeFrag; -} - -var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" + - "header|hgroup|mark|meter|nav|output|progress|section|summary|time|video", - rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g, - rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"), - rleadingWhitespace = /^\s+/, - rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi, - rtagName = /<([\w:]+)/, - rtbody = /\s*$/g, - - // We have to close these tags to support XHTML (#13200) - wrapMap = { - option: [ 1, "" ], - legend: [ 1, "
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" ], - - // IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags, - // unless wrapped in a div with non-breaking characters in front of it. - _default: support.htmlSerialize ? [ 0, "", "" ] : [ 1, "X
", "
" ] - }, - safeFragment = createSafeFragment( document ), - fragmentDiv = safeFragment.appendChild( document.createElement("div") ); - -wrapMap.optgroup = wrapMap.option; -wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; -wrapMap.th = wrapMap.td; - -function getAll( context, tag ) { - var elems, elem, - i = 0, - found = typeof context.getElementsByTagName !== strundefined ? context.getElementsByTagName( tag || "*" ) : - typeof context.querySelectorAll !== strundefined ? context.querySelectorAll( tag || "*" ) : - undefined; - - if ( !found ) { - for ( found = [], elems = context.childNodes || context; (elem = elems[i]) != null; i++ ) { - if ( !tag || jQuery.nodeName( elem, tag ) ) { - found.push( elem ); - } else { - jQuery.merge( found, getAll( elem, tag ) ); - } - } - } - - return tag === undefined || tag && jQuery.nodeName( context, tag ) ? - jQuery.merge( [ context ], found ) : - found; -} - -// Used in buildFragment, fixes the defaultChecked property -function fixDefaultChecked( elem ) { - if ( rcheckableType.test( elem.type ) ) { - elem.defaultChecked = elem.checked; - } -} - -// Support: IE<8 -// Manipulating tables requires a tbody -function manipulationTarget( elem, content ) { - return jQuery.nodeName( elem, "table" ) && - jQuery.nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ? - - elem.getElementsByTagName("tbody")[0] || - elem.appendChild( elem.ownerDocument.createElement("tbody") ) : - elem; -} - -// Replace/restore the type attribute of script elements for safe DOM manipulation -function disableScript( elem ) { - elem.type = (jQuery.find.attr( elem, "type" ) !== null) + "/" + elem.type; - return elem; -} -function restoreScript( elem ) { - var match = rscriptTypeMasked.exec( elem.type ); - if ( match ) { - elem.type = match[1]; - } else { - elem.removeAttribute("type"); - } - return elem; -} - -// Mark scripts as having already been evaluated -function setGlobalEval( elems, refElements ) { - var elem, - i = 0; - for ( ; (elem = elems[i]) != null; i++ ) { - jQuery._data( elem, "globalEval", !refElements || jQuery._data( refElements[i], "globalEval" ) ); - } -} - -function cloneCopyEvent( src, dest ) { - - if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) { - return; - } - - var type, i, l, - oldData = jQuery._data( src ), - curData = jQuery._data( dest, oldData ), - events = oldData.events; - - if ( events ) { - delete curData.handle; - curData.events = {}; - - for ( type in events ) { - for ( i = 0, l = events[ type ].length; i < l; i++ ) { - jQuery.event.add( dest, type, events[ type ][ i ] ); - } - } - } - - // make the cloned public data object a copy from the original - if ( curData.data ) { - curData.data = jQuery.extend( {}, curData.data ); - } -} - -function fixCloneNodeIssues( src, dest ) { - var nodeName, e, data; - - // We do not need to do anything for non-Elements - if ( dest.nodeType !== 1 ) { - return; - } - - nodeName = dest.nodeName.toLowerCase(); - - // IE6-8 copies events bound via attachEvent when using cloneNode. - if ( !support.noCloneEvent && dest[ jQuery.expando ] ) { - data = jQuery._data( dest ); - - for ( e in data.events ) { - jQuery.removeEvent( dest, e, data.handle ); - } - - // Event data gets referenced instead of copied if the expando gets copied too - dest.removeAttribute( jQuery.expando ); - } - - // IE blanks contents when cloning scripts, and tries to evaluate newly-set text - if ( nodeName === "script" && dest.text !== src.text ) { - disableScript( dest ).text = src.text; - restoreScript( dest ); - - // IE6-10 improperly clones children of object elements using classid. - // IE10 throws NoModificationAllowedError if parent is null, #12132. - } else if ( nodeName === "object" ) { - if ( dest.parentNode ) { - dest.outerHTML = src.outerHTML; - } - - // This path appears unavoidable for IE9. When cloning an object - // element in IE9, the outerHTML strategy above is not sufficient. - // If the src has innerHTML and the destination does not, - // copy the src.innerHTML into the dest.innerHTML. #10324 - if ( support.html5Clone && ( src.innerHTML && !jQuery.trim(dest.innerHTML) ) ) { - dest.innerHTML = src.innerHTML; - } - - } else if ( nodeName === "input" && rcheckableType.test( src.type ) ) { - // IE6-8 fails to persist the checked state of a cloned checkbox - // or radio button. Worse, IE6-7 fail to give the cloned element - // a checked appearance if the defaultChecked value isn't also set - - dest.defaultChecked = dest.checked = src.checked; - - // IE6-7 get confused and end up setting the value of a cloned - // checkbox/radio button to an empty string instead of "on" - if ( dest.value !== src.value ) { - dest.value = src.value; - } - - // IE6-8 fails to return the selected option to the default selected - // state when cloning options - } else if ( nodeName === "option" ) { - dest.defaultSelected = dest.selected = src.defaultSelected; - - // IE6-8 fails to set the defaultValue to the correct value when - // cloning other types of input fields - } else if ( nodeName === "input" || nodeName === "textarea" ) { - dest.defaultValue = src.defaultValue; - } -} - -jQuery.extend({ - clone: function( elem, dataAndEvents, deepDataAndEvents ) { - var destElements, node, clone, i, srcElements, - inPage = jQuery.contains( elem.ownerDocument, elem ); - - if ( support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) { - clone = elem.cloneNode( true ); - - // IE<=8 does not properly clone detached, unknown element nodes - } else { - fragmentDiv.innerHTML = elem.outerHTML; - fragmentDiv.removeChild( clone = fragmentDiv.firstChild ); - } - - if ( (!support.noCloneEvent || !support.noCloneChecked) && - (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) { - - // We eschew Sizzle here for performance reasons: http://jsperf.com/getall-vs-sizzle/2 - destElements = getAll( clone ); - srcElements = getAll( elem ); - - // Fix all IE cloning issues - for ( i = 0; (node = srcElements[i]) != null; ++i ) { - // Ensure that the destination node is not null; Fixes #9587 - if ( destElements[i] ) { - fixCloneNodeIssues( node, destElements[i] ); - } - } - } - - // Copy the events from the original to the clone - if ( dataAndEvents ) { - if ( deepDataAndEvents ) { - srcElements = srcElements || getAll( elem ); - destElements = destElements || getAll( clone ); - - for ( i = 0; (node = srcElements[i]) != null; i++ ) { - cloneCopyEvent( node, destElements[i] ); - } - } else { - cloneCopyEvent( elem, clone ); - } - } - - // Preserve script evaluation history - destElements = getAll( clone, "script" ); - if ( destElements.length > 0 ) { - setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); - } - - destElements = srcElements = node = null; - - // Return the cloned set - return clone; - }, - - buildFragment: function( elems, context, scripts, selection ) { - var j, elem, contains, - tmp, tag, tbody, wrap, - l = elems.length, - - // Ensure a safe fragment - safe = createSafeFragment( context ), - - nodes = [], - i = 0; - - for ( ; i < l; i++ ) { - elem = elems[ i ]; - - if ( elem || elem === 0 ) { - - // Add nodes directly - if ( jQuery.type( elem ) === "object" ) { - jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); - - // Convert non-html into a text node - } else if ( !rhtml.test( elem ) ) { - nodes.push( context.createTextNode( elem ) ); - - // Convert html into DOM nodes - } else { - tmp = tmp || safe.appendChild( context.createElement("div") ); - - // Deserialize a standard representation - tag = (rtagName.exec( elem ) || [ "", "" ])[ 1 ].toLowerCase(); - wrap = wrapMap[ tag ] || wrapMap._default; - - tmp.innerHTML = wrap[1] + elem.replace( rxhtmlTag, "<$1>" ) + wrap[2]; - - // Descend through wrappers to the right content - j = wrap[0]; - while ( j-- ) { - tmp = tmp.lastChild; - } - - // Manually add leading whitespace removed by IE - if ( !support.leadingWhitespace && rleadingWhitespace.test( elem ) ) { - nodes.push( context.createTextNode( rleadingWhitespace.exec( elem )[0] ) ); - } - - // Remove IE's autoinserted from table fragments - if ( !support.tbody ) { - - // String was a , *may* have spurious - elem = tag === "table" && !rtbody.test( elem ) ? - tmp.firstChild : - - // String was a bare or - wrap[1] === "
" && !rtbody.test( elem ) ? - tmp : - 0; - - j = elem && elem.childNodes.length; - while ( j-- ) { - if ( jQuery.nodeName( (tbody = elem.childNodes[j]), "tbody" ) && !tbody.childNodes.length ) { - elem.removeChild( tbody ); - } - } - } - - jQuery.merge( nodes, tmp.childNodes ); - - // Fix #12392 for WebKit and IE > 9 - tmp.textContent = ""; - - // Fix #12392 for oldIE - while ( tmp.firstChild ) { - tmp.removeChild( tmp.firstChild ); - } - - // Remember the top-level container for proper cleanup - tmp = safe.lastChild; - } - } - } - - // Fix #11356: Clear elements from fragment - if ( tmp ) { - safe.removeChild( tmp ); - } - - // Reset defaultChecked for any radios and checkboxes - // about to be appended to the DOM in IE 6/7 (#8060) - if ( !support.appendChecked ) { - jQuery.grep( getAll( nodes, "input" ), fixDefaultChecked ); - } - - i = 0; - while ( (elem = nodes[ i++ ]) ) { - - // #4087 - If origin and destination elements are the same, and this is - // that element, do not do anything - if ( selection && jQuery.inArray( elem, selection ) !== -1 ) { - continue; - } - - contains = jQuery.contains( elem.ownerDocument, elem ); - - // Append to fragment - tmp = getAll( safe.appendChild( elem ), "script" ); - - // Preserve script evaluation history - if ( contains ) { - setGlobalEval( tmp ); - } - - // Capture executables - if ( scripts ) { - j = 0; - while ( (elem = tmp[ j++ ]) ) { - if ( rscriptType.test( elem.type || "" ) ) { - scripts.push( elem ); - } - } - } - } - - tmp = null; - - return safe; - }, - - cleanData: function( elems, /* internal */ acceptData ) { - var elem, type, id, data, - i = 0, - internalKey = jQuery.expando, - cache = jQuery.cache, - deleteExpando = support.deleteExpando, - special = jQuery.event.special; - - for ( ; (elem = elems[i]) != null; i++ ) { - if ( acceptData || jQuery.acceptData( elem ) ) { - - id = elem[ internalKey ]; - data = id && cache[ id ]; - - if ( data ) { - if ( data.events ) { - for ( type in data.events ) { - if ( special[ type ] ) { - jQuery.event.remove( elem, type ); - - // This is a shortcut to avoid jQuery.event.remove's overhead - } else { - jQuery.removeEvent( elem, type, data.handle ); - } - } - } - - // Remove cache only if it was not already removed by jQuery.event.remove - if ( cache[ id ] ) { - - delete cache[ id ]; - - // IE does not allow us to delete expando properties from nodes, - // nor does it have a removeAttribute function on Document nodes; - // we must handle all of these cases - if ( deleteExpando ) { - delete elem[ internalKey ]; - - } else if ( typeof elem.removeAttribute !== strundefined ) { - elem.removeAttribute( internalKey ); - - } else { - elem[ internalKey ] = null; - } - - deletedIds.push( id ); - } - } - } - } - } -}); - -jQuery.fn.extend({ - text: function( value ) { - return access( this, function( value ) { - return value === undefined ? - jQuery.text( this ) : - this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) ); - }, null, value, arguments.length ); - }, - - append: function() { - return this.domManip( arguments, function( elem ) { - if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { - var target = manipulationTarget( this, elem ); - target.appendChild( elem ); - } - }); - }, - - prepend: function() { - return this.domManip( arguments, function( elem ) { - if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { - var target = manipulationTarget( this, elem ); - target.insertBefore( elem, target.firstChild ); - } - }); - }, - - before: function() { - return this.domManip( arguments, function( elem ) { - if ( this.parentNode ) { - this.parentNode.insertBefore( elem, this ); - } - }); - }, - - after: function() { - return this.domManip( arguments, function( elem ) { - if ( this.parentNode ) { - this.parentNode.insertBefore( elem, this.nextSibling ); - } - }); - }, - - remove: function( selector, keepData /* Internal Use Only */ ) { - var elem, - elems = selector ? jQuery.filter( selector, this ) : this, - i = 0; - - for ( ; (elem = elems[i]) != null; i++ ) { - - if ( !keepData && elem.nodeType === 1 ) { - jQuery.cleanData( getAll( elem ) ); - } - - if ( elem.parentNode ) { - if ( keepData && jQuery.contains( elem.ownerDocument, elem ) ) { - setGlobalEval( getAll( elem, "script" ) ); - } - elem.parentNode.removeChild( elem ); - } - } - - return this; - }, - - empty: function() { - var elem, - i = 0; - - for ( ; (elem = this[i]) != null; i++ ) { - // Remove element nodes and prevent memory leaks - if ( elem.nodeType === 1 ) { - jQuery.cleanData( getAll( elem, false ) ); - } - - // Remove any remaining nodes - while ( elem.firstChild ) { - elem.removeChild( elem.firstChild ); - } - - // If this is a select, ensure that it displays empty (#12336) - // Support: IE<9 - if ( elem.options && jQuery.nodeName( elem, "select" ) ) { - elem.options.length = 0; - } - } - - return this; - }, - - clone: function( dataAndEvents, deepDataAndEvents ) { - dataAndEvents = dataAndEvents == null ? false : dataAndEvents; - deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; - - return this.map(function() { - return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); - }); - }, - - html: function( value ) { - return access( this, function( value ) { - var elem = this[ 0 ] || {}, - i = 0, - l = this.length; - - if ( value === undefined ) { - return elem.nodeType === 1 ? - elem.innerHTML.replace( rinlinejQuery, "" ) : - undefined; - } - - // See if we can take a shortcut and just use innerHTML - if ( typeof value === "string" && !rnoInnerhtml.test( value ) && - ( support.htmlSerialize || !rnoshimcache.test( value ) ) && - ( support.leadingWhitespace || !rleadingWhitespace.test( value ) ) && - !wrapMap[ (rtagName.exec( value ) || [ "", "" ])[ 1 ].toLowerCase() ] ) { - - value = value.replace( rxhtmlTag, "<$1>" ); - - try { - for (; i < l; i++ ) { - // Remove element nodes and prevent memory leaks - elem = this[i] || {}; - if ( elem.nodeType === 1 ) { - jQuery.cleanData( getAll( elem, false ) ); - elem.innerHTML = value; - } - } - - elem = 0; - - // If using innerHTML throws an exception, use the fallback method - } catch(e) {} - } - - if ( elem ) { - this.empty().append( value ); - } - }, null, value, arguments.length ); - }, - - replaceWith: function() { - var arg = arguments[ 0 ]; - - // Make the changes, replacing each context element with the new content - this.domManip( arguments, function( elem ) { - arg = this.parentNode; - - jQuery.cleanData( getAll( this ) ); - - if ( arg ) { - arg.replaceChild( elem, this ); - } - }); - - // Force removal if there was no new content (e.g., from empty arguments) - return arg && (arg.length || arg.nodeType) ? this : this.remove(); - }, - - detach: function( selector ) { - return this.remove( selector, true ); - }, - - domManip: function( args, callback ) { - - // Flatten any nested arrays - args = concat.apply( [], args ); - - var first, node, hasScripts, - scripts, doc, fragment, - i = 0, - l = this.length, - set = this, - iNoClone = l - 1, - value = args[0], - isFunction = jQuery.isFunction( value ); - - // We can't cloneNode fragments that contain checked, in WebKit - if ( isFunction || - ( l > 1 && typeof value === "string" && - !support.checkClone && rchecked.test( value ) ) ) { - return this.each(function( index ) { - var self = set.eq( index ); - if ( isFunction ) { - args[0] = value.call( this, index, self.html() ); - } - self.domManip( args, callback ); - }); - } - - if ( l ) { - fragment = jQuery.buildFragment( args, this[ 0 ].ownerDocument, false, this ); - first = fragment.firstChild; - - if ( fragment.childNodes.length === 1 ) { - fragment = first; - } - - if ( first ) { - scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); - hasScripts = scripts.length; - - // Use the original fragment for the last item instead of the first because it can end up - // being emptied incorrectly in certain situations (#8070). - for ( ; i < l; i++ ) { - node = fragment; - - if ( i !== iNoClone ) { - node = jQuery.clone( node, true, true ); - - // Keep references to cloned scripts for later restoration - if ( hasScripts ) { - jQuery.merge( scripts, getAll( node, "script" ) ); - } - } - - callback.call( this[i], node, i ); - } - - if ( hasScripts ) { - doc = scripts[ scripts.length - 1 ].ownerDocument; - - // Reenable scripts - jQuery.map( scripts, restoreScript ); - - // Evaluate executable scripts on first document insertion - for ( i = 0; i < hasScripts; i++ ) { - node = scripts[ i ]; - if ( rscriptType.test( node.type || "" ) && - !jQuery._data( node, "globalEval" ) && jQuery.contains( doc, node ) ) { - - if ( node.src ) { - // Optional AJAX dependency, but won't run scripts if not present - if ( jQuery._evalUrl ) { - jQuery._evalUrl( node.src ); - } - } else { - jQuery.globalEval( ( node.text || node.textContent || node.innerHTML || "" ).replace( rcleanScript, "" ) ); - } - } - } - } - - // Fix #11809: Avoid leaking memory - fragment = first = null; - } - } - - return this; - } -}); - -jQuery.each({ - appendTo: "append", - prependTo: "prepend", - insertBefore: "before", - insertAfter: "after", - replaceAll: "replaceWith" -}, function( name, original ) { - jQuery.fn[ name ] = function( selector ) { - var elems, - i = 0, - ret = [], - insert = jQuery( selector ), - last = insert.length - 1; - - for ( ; i <= last; i++ ) { - elems = i === last ? this : this.clone(true); - jQuery( insert[i] )[ original ]( elems ); - - // Modern browsers can apply jQuery collections as arrays, but oldIE needs a .get() - push.apply( ret, elems.get() ); - } - - return this.pushStack( ret ); - }; -}); - - -var iframe, - elemdisplay = {}; - -/** - * Retrieve the actual display of a element - * @param {String} name nodeName of the element - * @param {Object} doc Document object - */ -// Called only from within defaultDisplay -function actualDisplay( name, doc ) { - var style, - elem = jQuery( doc.createElement( name ) ).appendTo( doc.body ), - - // getDefaultComputedStyle might be reliably used only on attached element - display = window.getDefaultComputedStyle && ( style = window.getDefaultComputedStyle( elem[ 0 ] ) ) ? - - // Use of this method is a temporary fix (more like optmization) until something better comes along, - // since it was removed from specification and supported only in FF - style.display : jQuery.css( elem[ 0 ], "display" ); - - // We don't have any data stored on the element, - // so use "detach" method as fast way to get rid of the element - elem.detach(); - - return display; -} - -/** - * Try to determine the default display value of an element - * @param {String} nodeName - */ -function defaultDisplay( nodeName ) { - var doc = document, - display = elemdisplay[ nodeName ]; - - if ( !display ) { - display = actualDisplay( nodeName, doc ); - - // If the simple way fails, read from inside an iframe - if ( display === "none" || !display ) { - - // Use the already-created iframe if possible - iframe = (iframe || jQuery( "