See cclib/cclib@6a6c66c from refs/heads/master

Author: cclib

_sources/attributes_dev.rst.txt

@@ -9,13 +9,13 @@
     `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                  hartree          array of rank 2
+    `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                                        hartree          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                                   hartree          array of rank 1
+    `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
@@ -36,10 +36,10 @@
     `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                                           hartree          list of arrays of rank 1
+    `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        hartree          array of rank 2
+    `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
@@ -50,7 +50,7 @@
     `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                                           list of int
+    `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
@@ -59,7 +59,7 @@
     `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)          hartree          array of rank 1
+    `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

_sources/data_notes.rst.txt

@@ -149,7 +149,7 @@ However, in *all* cases the dispersion energy for a given geometry will also be
 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 hartree. 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.
+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<sup>-1</sup>``. 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
 ------
@@ -389,7 +389,7 @@ Note: For restricted calculation, ``mocoeffs`` is still a list, but it only cont
 moenergies
 ----------
 
-A list of rank 1 arrays containing the molecular orbital energies in hartree. The list is of length 1 for restricted calculations, but length 2 for unrestricted calculations.
+A list of rank 1 arrays containing the molecular orbital energies in eV. The list is of length 1 for restricted calculations, but length 2 for unrestricted calculations.
 
 **GAMESS-UK**: similar to `mocoeffs`_, the directive `FORMAT HIGH`_ needs to be used if you want all of the eigenvalues printed.
 
@@ -511,7 +511,27 @@ A dictionary where the keys zero-index the atomic center for which the chemical
 optdone
 -------
 
-A list that indexes which elements of `atomcoords`_ represent converged geometries.
+Flags whether a geometry optimisation has completed. Currently this attribute is a single Boolean value, which is set to True when the final `atomcoords`_ represent a converged geometry optimisation. In the future, ``optdone`` will be a list that indexes which elements of `atomcoords`_ represent converged geometries. This functionality can be used starting from version 1.3, from the command line by passing the ``--future`` option to ``ccget``,
+
+.. code-block:: bash
+
+    $ 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
+    Attempting to parse data/Gaussian/basicGaussian09/dvb_gopt.out
+    optdone:
+    [4]
+
+or by providing the corresponding argument to ``ccopen``,
+
+.. code-block:: python
+
+    from cclib.parser import ccopen
+    parser = ccopen("filename", optdone_as_list=True) # could also do future=True instead of optdone_as_list
+    data = parser.parse()
 
 optstatus
 ---------
@@ -548,7 +568,7 @@ A list of lists where each list contains the values scanned for each parameter i
 scfenergies
 -----------
 
-An array containing the converged SCF energies of the calculation, in hartree. For an optimisation log file, there will be as many elements in this array as there were optimisation steps.
+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`_.
 

attributes_dev.html

@@ -135,7 +135,7 @@
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#ccenergies">ccenergies</a></p></td>
 <td><p>molecular energies with Coupled-Cluster corrections</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>array of rank 2</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#charge">charge</a></p></td>
@@ -150,7 +150,7 @@
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#dispersionenergies">dispersionenergies</a></p></td>
 <td><p>dispersion energy corrections</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>array of rank 1</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#enthalpy">enthalpy</a></p></td>
@@ -165,7 +165,7 @@
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#etenergies">etenergies</a></p></td>
 <td><p>energies of electronic transitions</p></td>
-<td><p>hartree</p></td>
+<td><p>1/cm</p></td>
 <td><p>array of rank 1</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#etoscs">etoscs</a></p></td>
@@ -270,7 +270,7 @@
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#moenergies">moenergies</a></p></td>
 <td><p>molecular orbital energies</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>list of arrays of rank 1</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#moments">moments</a></p></td>
@@ -285,7 +285,7 @@
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#mpenergies">mpenergies</a></p></td>
 <td><p>molecular electronic energies with Møller-Plesset corrections</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>array of rank 2</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#mult">mult</a></p></td>
@@ -341,7 +341,7 @@
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#optdone">optdone</a></p></td>
 <td><p>flags whether an optimization has converged</p></td>
 <td></td>
-<td><p>list of int</p></td>
+<td><p>bool or list of int</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#optstatus">optstatus</a></p></td>
 <td><p>optimization status for each set of atomic coordinates</p></td>
@@ -385,7 +385,7 @@
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#scfenergies">scfenergies</a></p></td>
 <td><p>molecular electronic energies after SCF (Hartree-Fock, DFT)</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>array of rank 1</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#scftargets">scftargets</a></p></td>

data_dev.html

@@ -147,7 +147,7 @@ <h2>Description of parsed data<a class="headerlink" href="#description-of-parsed
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#ccenergies">ccenergies</a></p></td>
 <td><p>molecular energies with Coupled-Cluster corrections</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>array of rank 2</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#charge">charge</a></p></td>
@@ -162,7 +162,7 @@ <h2>Description of parsed data<a class="headerlink" href="#description-of-parsed
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#dispersionenergies">dispersionenergies</a></p></td>
 <td><p>dispersion energy corrections</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>array of rank 1</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#enthalpy">enthalpy</a></p></td>
@@ -177,7 +177,7 @@ <h2>Description of parsed data<a class="headerlink" href="#description-of-parsed
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#etenergies">etenergies</a></p></td>
 <td><p>energies of electronic transitions</p></td>
-<td><p>hartree</p></td>
+<td><p>1/cm</p></td>
 <td><p>array of rank 1</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#etoscs">etoscs</a></p></td>
@@ -282,7 +282,7 @@ <h2>Description of parsed data<a class="headerlink" href="#description-of-parsed
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#moenergies">moenergies</a></p></td>
 <td><p>molecular orbital energies</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>list of arrays of rank 1</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#moments">moments</a></p></td>
@@ -297,7 +297,7 @@ <h2>Description of parsed data<a class="headerlink" href="#description-of-parsed
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#mpenergies">mpenergies</a></p></td>
 <td><p>molecular electronic energies with Møller-Plesset corrections</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>array of rank 2</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#mult">mult</a></p></td>
@@ -353,7 +353,7 @@ <h2>Description of parsed data<a class="headerlink" href="#description-of-parsed
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#optdone">optdone</a></p></td>
 <td><p>flags whether an optimization has converged</p></td>
 <td></td>
-<td><p>list of int</p></td>
+<td><p>bool or list of int</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#optstatus">optstatus</a></p></td>
 <td><p>optimization status for each set of atomic coordinates</p></td>
@@ -397,7 +397,7 @@ <h2>Description of parsed data<a class="headerlink" href="#description-of-parsed
 </tr>
 <tr class="row-even"><td><p><a class="reference external" href="data_notes.html#scfenergies">scfenergies</a></p></td>
 <td><p>molecular electronic energies after SCF (Hartree-Fock, DFT)</p></td>
-<td><p>hartree</p></td>
+<td><p>eV</p></td>
 <td><p>array of rank 1</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference external" href="data_notes.html#scftargets">scftargets</a></p></td>