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Python tools for quantum chemists

Project description

qctools

Updates

Python tools for quantum chemists

Features

Define Event Handlers for straightforward parsing of Quantum Chemistry Output

Example:

Read natoms from Gaussian Output file:

1. Step: Define the Event

The number of atoms are written typically in the following way in the Gaussian output file:

.Gaussian Log File

...
NAtoms=    3 NActive=    3 NUniq=    2 SFac= 2.25D+00 NAtFMM=   50 NAOKFM=F Big=F
One-electron integrals computed using PRISM.
...

the event should do the following:

  1. It should loop over all lines of the file, till it findes the Keyword NAtoms=
  2. It should return that line and extract the 2. element of that line as a string

The corresponding event looks like:

>>> NAtoms = Event('NAtoms',
...                'grep', {'keyword': 'NAtoms=',
...                         'ilen': 1,
...                         'ishift': 0},
...                func='split',
...                func_kwargs={'idx': 1, 'typ': int}
...)

The first entry is the name of the event, and can be any name. The second entry is the type of the event, in this case just grep. The third entry gives the parameter to the corresponding event function: [we want to search for ‘NAtoms=’ and return a single line (ilen=1) not shifted (ishift=0) from the keyword.]

Afterwards the line is given to a postprocessing function (‘split’) which splits the line by spaces and returns the element[1] of the line as an integer. Remember, this is Python/C notation to element[1] is the second element in the list.

For the Forces the event should look the following:

-------------------------------------------------------------------
Center     Atomic                   Forces (Hartrees/Bohr)
Number     Number              X              Y              Z
-------------------------------------------------------------------
     1        8           0.000000000    0.000000000    0.005485119
     2        1           0.000000000    0.017353174   -0.002742559
     3        1           0.000000000   -0.017353174   -0.002742559
------------------------------------------------------------------
>>> forces = Event('forces',
...                'xgrep', {'keyword': 'Forces (Hartrees/Bohr)',
...                          'ilen': 'NAtoms',
...                          'ishift': 3},
...                func='split',
...                func_kwargs={'idx': [2, 3, 4], 'typ': [float, float, float]},
...                settings={'multi': False},
...)

2. Step: Add the new event to an existing Event Handler

>>> GaussianReader.add_event("NAtoms", NAtoms)
>>> GaussianReader.add_event("forces", forces)

3. Step: Use the Event Handler to parse an file

>>> gauout = GaussianReader("h2o.log", ["NAtoms", "forces"])
>>> gauout["NAtoms"]
3
>>> gauout["forces"]
[[0.0,0.0,0.005485119],[0.0,0.017353174,-0.002742559],[0.0,-0.017353174,-0.002742559]]

Credits

Development Lead

  • Maximilian Menger

Contributors

Why not be the first?

Thanks to:

  • Boris Maryasin
  • Gustavo Cardenas

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.1.0 (2019-04-12)

  • First release on PyPI.

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