Gaussian-PES

Interface for invoking PES from Gaussian

BasePES

BasePES is an abstract class that defines the protocol of a PES model. For some PES models with out analytical gradient, numerical gradient and force constant are also implemented.

GauDriver

GauDriver is an I/O driver for parsing Gaussian internal input file and writing the results calculated on PES into the internal output file. Therefore, One can use Gaussian as an optimizer and does geometrical tasks, e.g. optimization, transition state, IRC, scan, and etc.

Installation

Via pip

$ pip install git+https://github.com/CQPES/Gaussian-PES.git

From source

$ git clone https://github.com/CQPES/Gaussian-PES.git
$ cd Gaussian-PES
$ pip install .

Usage

Here is an example of defining a PES model and invoking it from Gaussian.

# h2o_pes.py
import numpy as np
from gau_pes import BasePES

_NUM_ATOMS = 3  # number of atoms of your system

class H2OPES(BasePES):
    def __init__(self) -> None:
        ...

    def calc_energy(
        self,
        coords: np.array,
    ) -> float
        """Calculate the potential energy of H2O system.

        Order of atoms: H H O
        """
        self._check_coords(_NUM_ATOMS, coords)

        # calculate energy
        energy = ...

        return energy


if __name__ == "__main__":
    from gau_pes import GauDriver

    driver = GauDriver.from_stdio()
    pes = H2OPES()

    driver.write(
        energy=pes.calc_energy(driver.coords),
        gradients=(pes.calc_gradients(driver.coords)
                   if driver.derivs in [1, 2] else None),
        force_constants=(pes.calc_force_constants(
            driver.coords) if driver.derivs == 2 else None),
    )

Then the input file be like

%nproc=1
%chk=H2O-opt-freq.chk
#p external="python3 -u /path/to/h2o_pes.py" opt=nomicro

H2O

0 1
 H     -0.00000002    0.00000000   -0.00000012
 H      0.92850569    0.00000000    1.19804603
 O     -0.00000008    0.00000000    0.95882669


--link1--
%nproc=1
%chk=H2O-opt-freq.chk
#p external="python3 -u /path/to/h2o_pes.py" freq geom=allcheck

Reference

(1) Gaussian, Inc. (n.d.). External. Gaussian.com. Retrieved March 16, 2024, from https://gaussian.com/external/