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Update docs manually after v1.7.1 release (with sphinx 3.5.4 and RTD theme 0.5.1) #40

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Merged
berquist merged 1 commit into from
Sep 24, 2021
Merged

Update docs manually after v1.7.1 release (with sphinx 3.5.4 and RTD theme 0.5.1) #40

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16 changes: 9 additions & 7 deletions _sources/attributes.rst.txt
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===================== ==================================================================== ================ ========================
Name Description Units Data type
===================== ==================================================================== ================ ========================
===================== ==================================================================== ================ ================================
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
Expand All @@ -14,7 +14,7 @@
`coreelectrons`_ number of core electrons in atom pseudopotentials array of rank 1
`dispersionenergies`_ a molecular dispersion energy corrections eV array of rank 1
`enthalpy`_ sum of electronic and thermal enthalpies hartree/particle float
`entropy`_ entropy 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
Expand Down Expand Up @@ -44,6 +44,7 @@
`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
`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
Expand All @@ -54,8 +55,8 @@
`pressure`_ pressure 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 lists
`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
Expand All @@ -71,7 +72,7 @@
`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
Expand Down Expand Up @@ -116,6 +117,7 @@
.. _`natom`: data_notes.html#natom
.. _`nbasis`: data_notes.html#nbasis
.. _`nmo`: data_notes.html#nmo
.. _`nmrtensors`: data_notes.html#nmrtensors
.. _`nocoeffs`: data_notes.html#nocoeffs
.. _`nooccnos`: data_notes.html#nooccnos
.. _`nsocoeffs`: data_notes.html#nsocoeffs
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16 changes: 9 additions & 7 deletions _sources/attributes_dev.rst.txt
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===================== ==================================================================== ================ ========================
Name Description Units Data type
===================== ==================================================================== ================ ========================
===================== ==================================================================== ================ ================================
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
Expand All @@ -14,7 +14,7 @@
`coreelectrons`_ number of core electrons in atom pseudopotentials array of rank 1
`dispersionenergies`_ a molecular dispersion energy corrections eV array of rank 1
`enthalpy`_ sum of electronic and thermal enthalpies hartree/particle float
`entropy`_ entropy 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
Expand Down Expand Up @@ -44,6 +44,7 @@
`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
`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
Expand All @@ -54,8 +55,8 @@
`pressure`_ pressure 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 lists
`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
Expand All @@ -71,7 +72,7 @@
`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
Expand Down Expand Up @@ -116,6 +117,7 @@
.. _`natom`: data_notes.html#natom
.. _`nbasis`: data_notes.html#nbasis
.. _`nmo`: data_notes.html#nmo
.. _`nmrtensors`: data_notes.html#nmrtensors
.. _`nocoeffs`: data_notes.html#nocoeffs
.. _`nooccnos`: data_notes.html#nooccnos
.. _`nsocoeffs`: data_notes.html#nsocoeffs
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35 changes: 34 additions & 1 deletion _sources/changelog.rst.txt
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Changelog
=========

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 Schneider)
* Fixed parsing ONION 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
* New parser: formatted checkpoint files (QChem only right now)

**Bugfixes**

Expand Down
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