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‎_sources/bridge.rst.txt‎

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@@ -43,13 +43,13 @@ An example code below demonstrates how Becke charges can be calculated based on
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from cclib.method.density import Density
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from cclib.bridge.cclib2horton import makehorton
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from cclib.parser import ccopen
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from horton import BeckeMolGrid, getgobasis, BeckeWPart
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from horton.matrix.dense import DenseTwoIndex
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d = ccopen(sys.argv[1]).parse()
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ht = makehorton(d)
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# Calculate density matrix using cclib
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dens = Density(d)
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dens.calculate()
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# Define Gaussian basis set
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gob = get_gobasis(ht.coordinates, ht.numbers, default = 'STO-3G')
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# Partition charges
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wpart = BeckeWPart(ht.coordinates, ht.numbers, ht.pseudo_numbers, grid, moldens, local=True)
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wpart.do_charges()
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from cclib.method.density import Density
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from cclib.bridge.cclib2horton import makehorton
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from cclib.parser import ccopen
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from horton import BeckeMolGrid, getgobasis, HirshfeldWPart
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from horton.matrix.dense import DenseTwoIndex
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from horton.part.proatomdb import ProAtomDB
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d = ccopen(sys.argv[1]).parse()
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ht = makehorton(d)
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# Calculate density matrix using cclib
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dens = Density(d)
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dens.calculate()
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# Define Gaussian basis set
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gob = get_gobasis(ht.coordinates, ht.numbers, default = 'STO-3G')
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# Read in pro-atomic density database
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db = ProAtomDB.from_file('atoms.h5')
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print(wpart['charges'])
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..
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‎_sources/data_notes.rst.txt‎

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@@ -347,7 +347,7 @@ A dictionary containing metadata_ (data about data) for the calculation. Current
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* ``basis_set``: A string with the name of the basis set, if it is printed anywhere as a standard name.
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* ``coord_type``: For the ``coords`` field, a string for the representation of stored coordinates. Currently, it is one of ``xyz``, ``int``/``internal``, or ``gzmat``.
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* ``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.
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* ``cpu_time``: A list of datetime.timedeltas containing the CPU time of each calculation in the output.
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* ``cpu_time``: A list of datetime.timedeltas containing the CPU time of each calculation in the output.
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* ``functional``: A string with the name of the density functional used.
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* ``info``: A list of strings, each of which is an information or log message produced during a calculation.
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* ``input_file_contents``: A string containing the entire input file, if it is echoed back during the calculation.
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* ``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.
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* ``success``: A boolean for whether or not the calculation completed properly.
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* ``unrestricted``: A boolean for whether or not the calculation was performed with a unrestricted wavefunction.
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* ``wall_time``: A list of datetime.timedeltas containing the wall time of each calculation in the output.
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* ``wall_time``: A list of datetime.timedeltas containing the wall time of each calculation in the output.
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* ``warnings``: A list of strings, each of which is a warning produced during a calculation.
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The implementation and coverage of metadata is currently inconsistent. In the future, metadata may receive its own page similar to :doc:`extracted data <data>`.
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scanparm
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--------
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A list of lists where each list contains the values scanned for each parameter in `scannames`.
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A list of lists where each list contains the values scanned for each parameter in `scannames`.
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scfenergies
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-----------
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----------
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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.
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‎_sources/methods.rst.txt‎

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.. index::
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single: methods; Bader's QTAIM
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Bader's QTAIM
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----------------
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from cclib.parser import ccopen
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from cclib.progress import TextProgress
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import logging
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progress = TextProgress()
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d = ccopen("mycalc.out", logging.ERROR).parse(progress)
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.. index::
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single: methods; DDEC6
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DDEC6
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----------------
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.. index::
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single: methods; Hirshfeld Population Analysis
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Hirshfeld Population Analysis
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-----------------------------
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nre = nuclear.repulsion_energy()
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print(nre)
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Accessing additional methods through bridge
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-------------------------------------------
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‎attributes.html‎

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‎attributes_dev.html‎

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‎bridge.html‎

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‎changelog.html‎

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‎contents.html‎

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