plank.py

A fully parallel HF code to calculate orbital energies for a molecule. plank is written in Python using MPI4Py for parallel constructs and Cython. The code avoids the usage of recursive routines for the calculation of overlap, kinetic integrals and electron-nuclear interaction integrals, with iterative routines adapted from refrences [1] and [2] used instead. Electron-electron repulsion integrals are implemented using a recursive MD scheme. Currently plank only supports calculations on closed-shell singlet molecules.

Dependencies

1. Python 3.5+
2. mpi4py (for efficient parallelization)
3. numpy
4. math
5. yaml (for writing log files and reading Periodic Table)
6. Cython (for static compilation of libraries)

Installation

Follow the steps given below for installation

1. conda create -n plankhf && conda activate plankhf
2. conda install numpy cython mpi4py setuptools pyyaml
3. run python setup.py build_ext install --user

Since plank is written to be run in parallel mode, It is expected that openmpi exectubales (mpiexec or mpirun) is available on the machine. plank can be spawned as mpiexec -np [number of processors] python planksrc.py [input file]. Logfiles are generated automatically if a verbose option is provided in the input file.

mpiexec -np <procs> python plankmain.py <inputfile>

Users must obtain the required basis sets from Basis Set Exhange. Please ensure that the format of the downloaded basis set is Gaussian (.gbs extension).

Sample input file

Format for the input file is as follows:

[calculation type] [basis set]
[charge] [multiplicity]
[number of atoms]
[atom name] [coordinates]
[max number of SCF iterations] [DIIS] (set T for DIIS and F for Not using DIIS)

The user can choose to leave the last line blank, which would result in max number of SCF iterations = 100 and verbose = 0, meaning no log file would be generated.

Sample input calculates the energy of a water molecule at sto-3g level of theory.

energy	sto-3g
0	1
3
H                     0.866811829        0.601435779   0.000000
H                    -0.866811829        0.601435779   0.000000
O                     0.000000000       -0.075791844   0.000000

Running this input must generate four files overlap.[identifier].txt, kinetic.[identifier].txt, nuclear.[identifier].txt and electronic.[identifier].txt. The contents of the overlap, kinetic and nuclear files must resemble the ones that have been copied below.

overlap.txt

     1.000     0.182     0.038     0.386     0.268     0.210     0.000
     0.182     1.000     0.038     0.386    -0.268     0.210     0.000
     0.038     0.038     1.000     0.237     0.000    -0.000     0.000
     0.386     0.386     0.237     1.000     0.000     0.000     0.000
     0.268    -0.268     0.000     0.000     1.000     0.000     0.000
     0.210     0.210    -0.000     0.000     0.000     1.000     0.000
     0.000     0.000     0.000     0.000     0.000     0.000     1.000

kinetic.txt

     0.760    -0.004    -0.008     0.071     0.147     0.115     0.000
    -0.004     0.760    -0.008     0.071    -0.147     0.115     0.000
    -0.008    -0.008    29.003    -0.168     0.000     0.000     0.000
     0.071     0.071    -0.168     0.808     0.000     0.000     0.000
     0.147    -0.147     0.000     0.000     2.529     0.000     0.000
     0.115     0.115     0.000     0.000     0.000     2.529     0.000
     0.000     0.000     0.000     0.000     0.000     0.000     2.529

nuclear.txt

    -5.300    -1.067    -1.232    -2.977    -1.822    -1.472     0.000
    -1.067    -5.300    -1.232    -2.977     1.822    -1.472     0.000
    -1.232    -1.232   -61.581    -7.411     0.000    -0.014     0.000
    -2.977    -2.977    -7.411   -10.009     0.000    -0.177     0.000
    -1.822     1.822     0.000     0.000    -9.988     0.000     0.000
    -1.472    -1.472    -0.014    -0.177     0.000    -9.944     0.000
     0.000     0.000     0.000     0.000     0.000     0.000    -9.876

References

1. https://www.mathematica-journal.com/2012/02/16/evaluation-of-gaussian-molecular-integrals/
2. Cook, David B. Handbook of computational quantum chemistry. Courier Corporation, 2005.
3. https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.540030314
4. https://joshuagoings.com/2017/04/28/integrals/