pyar

PyAR

PyAR stands for “Python program for aggregation and reaction”

Installation

Download the file pyar-master.zip. Unzip it. Go the the folder and sudo python3 setup.py install This will create python package in the path /usr/local/lib/python3.6/dist-packages/pyar/ and will create the command line interface pyar-cli in /usr/local/bin

or

Run the following command in the pyar folder sudo -H pip install .

Features:

• Automated prediction of unknown reactions between two reactants (A+B)
• Automated prediction of the geometries of aggregates, atomic clusters etc.
• Automated search for reaction for bond forming between two atoms in two different molecules.

Setting Up Environment

To set up your environment for the tasks, you can create and edit your .bashrc or .bash_profile file, depending on your system configuration. After that source ~/.bashrc to run those changes.

# Create an alias for "mndo2020"
alias mndobin="mndo2020"

# Add Gaussian 16 to your PATH
export PATH=$PATH:/home/apps/g16

# Create an alias for GAUSS_EXEDIR
alias GAUSS_EXEDIR="g16"

# Create an alias for MLatom.py
alias mlatom="MLatom.py"

# Install dftd4 executable in this way
conda config --add channels conda-forge
conda install dftd4
conda install -c conda-forge openbabel
alias dftd4bin="dftd4"

#DBCV is not directly accessable via scikit-learn
pip install hdbscan
pip install git+https://github.com/christopherjenness/DBCV.git

Requirements

• python >= 3.6
• numpy>=1.18.4
• pandas>=1.0.5
• scipy>=1.5.2
• scikit-learn>=0.23.2
• autograd>=1.3

Interfaced with electronic structure theory programmes

• mlatom_aiqm1
• aimnet2
• Mopac
• Turbomole
• Psi4
• Xtb
• Orca

Molecule generations

pyar-cli -a c.xyz h.xyz -N 8 -as 6 6 --software aiqm1_mlatom -m 1 2

Molecular clusters

XTB

pyar-cli -s water.xyz water.xyz --software xtb -ss 10 -N 16 -c 0 0 -m 1 1

AIMNet2

pyar-cli -s water.xyz water.xyz --software aimnet_2 -ss 10 -N 16 -c 0 0 -m 1 1

This will generate a molecules upto maximum 6 carbon and 6 hydrogens with mlatom_aiqm1 potential using 8 trial orientations. Here c.xyz and h.xyz are standard cartesian coordinate files.

1
carbon
C  0.0  0.0   0.0

1
hydrogen
H  0.0  0.0   0.0

Reaction

To study the reaction between two reactants A and B using ORCA software interface, with force from 100 to 1000 using N=8 trial orientation, the commandline line argument is,

pyar-cli -r A.xyz B.xyz -N 8 -gmin 100 -gmax 1000 --ssoftware orca

A.xyz and B.xyz are the cartesian coordinate files of the reactants

pyar-cli

The main program can be used as below:

pyar-cli options files

There are other scripts for a few automation tasks.

pyar-tabu

pyar-tabu can be used for

• for making different orientations of two molecules.
• Making a composite molecule containing a seed molecule and N number of monomer molecules.
• Orient two molecules such that i‘th atom of one molecule and j ‘th atom of second molecule have shortest distance between them

pyar-clustering

• for a clustering analysis of n input molecules to find unique molecules.

pyar-optimiser

• for the bulk optimisation of several molecules

References

1. “A Global Optimizer for Nanoclusters “, Maya Khatun, Rajat Shubhro Majumdar, Anakuthil Anoop Frontiers in Chemistry 2019, 644
2. “A tabu-search based strategy for modeling molecular aggregates and binary reactions” S Nandi, SR McAnanama-Brereton, MP Waller, A Anoop, Computational and Theoretical Chemistry 2017, 1111, 69-81

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