mstk.wrapper.Gauss

class mstk.wrapper.Gauss(gauss_bin, scrdir=None)

Wrapper for Gaussian for quantum calculations

Parameters:

  • gauss_bin (str) – Path of the Gaussian binary executable

  • scrdir (str, optional) – Path of the scratch dir for Gaussian calculations. If not provided, the ramdisk /dev/shm will be used.

Methods

__init__(gauss_bin[, scrdir])

generate_gjf_cv(name, py_mol[, method, ...])

Genrate GJF input file for calculating heat capacity with Gaussian

run_gjf(gjf[, nprocs, memMB, get_cmd, sh_out])

Process the GJF file so that it is ready for multi-core Gaussian calculation, and then return the commands for calculation.
generate_gjf_cv(name, py_mol, method='B3LYP', basis='6-31G*', scale=0.9613, T_list=None)

Genrate GJF input file for calculating heat capacity with Gaussian

The molecule is provided through a pybel.Molecule object. Therefore, openbabel should be installed. The pybel.Molecule object should contain information about positions of all atoms.

The hindered-rotor model is used to describing the low-frequency dihedral vibrations.

A list of temperature can be provided. Then the thermodynamic analysis will be performed at all the provided temperatures, so that the result at intermediate temperature can be interpolated.

Parameters:

  • name (str) –

  • py_mol (pybel.Molecule) –

  • method (str) –

  • basis (str) –

  • scale (float) –

  • T_list (list of float, optional) –

run_gjf(gjf, nprocs=1, memMB=1000, get_cmd=False, sh_out=None)

Process the GJF file so that it is ready for multi-core Gaussian calculation, and then return the commands for calculation.

The commands return can be feed into a Scheduler for running on a HPC.

Parameters:

  • gjf (str) – The GJF file to be processed

  • nprocs (str) – Number of cores to use

  • memMB (int) – Maxium size of memory to use in unit of MB

  • get_cmd (bool) – Whether or not return the commands for running Gaussian calculation

  • sh_out (str, optional) – If provided, the commmands for running Gaussian calculation will be written to this shell script

Returns:

commands – If get_cmd is True, the commands for running Gaussian will be returned

Return type:

list of str, or None