chi1chi2 0.7.0

set of scripts for calculating linear and nonlinear optical properties of organic crystals

chi1chi2 program

The aim of the program is to calculate linear (refractive indices) and nonlinear (chi(2) for second harmonic generation) optical properties of organic crystals.

[TOC]

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Installation

The easiest path with conda:

conda create --name chi1chi2 python=3.7 -y
conda activate chi1chi2
conda install -c tomeks86 chi1chi2

The easy path with docker image:

workdir=$(pwd) # or any other directory of your choice
docker run -v $(workdir):/chi1chi2 -it tomeks86/python-chi1chi2 bash

The hard path

Warning: manual installation and getting the program to its full functionality requires quite much of expertise even in linux (I do not give any warranty that it is possible to run it in any other OS) and can be a very daunting task.

Make sure you have installed:

• gfortran
• python 3.6
• open babel

Installation:

• pip install chi1chi2
• for the fortran programs a Makefile is provided with the repository: make command builds the programs in the build/ directory

Easier installation of openbabel using conda

• conda env create --file=chi1chi2.yaml
• for program usage activate the environment with: conda activate chi1chi2
• follow the installation of other dependencies with pip

#Description

The whole program constitutes a set of scripts that need to be executed in order.

There are four main steps:

1. Input preparation (optionally - geometry optimization)
2. Optical properties of molecular sub-units calculations
3. Calculations of bulk properties
4. Analysis of the results

The purpose of this file is to lead the user through all these steps.

Step 1 - Input preparation

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A) from Cif (easy path)

use chi.from_cif to get geometry for further optimization with e.g. crystal09/14/..

B) from fractional coordinates

use chi.from_fra script (see: examples/mna_cif.fra, examples/mna_cif2.fra to see the convention) (remember to adjust the symmetry operations!)

C) manually

see examples for the convention

Step 1a after geometry optimization

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D) use chi.from_crystal script to adjust the coordinates and charges after crystal geometry optimization

E) run chi.input_preparator script to get input files for:

• charge_generator program (example usage: charge_generator < chg1.inp)
• Lorentz tensor with lorentz program (example usage: lorentz < lorentz.inp > L.dat)

Step 2 - property calculation

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Use sets of charges, geometries and follow your favorite property calculation procedure. Additional shell scripts could be provided in later releases.

Step 3 - core calculations

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Use the script chi.main to get the chi(1) and chi(2) tensor components in the so called a'bc* reference frame.

Q-LFT calculations enabled! (since 0.1.1)

Step 4 - result analysis

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Use the script chi.analyze with output file generated in step 3

• Refractive indices analysis (since 0.1.3)
• Magnitude of the chi(2) tensor components in the direction of the optical indicatrix (since 0.1.3)

Helpers

Helper scripts are available to use around molecular calculations:

• read_g09.py for reading the molecular properties after the QC calculations
• scale_props.py for scaling the static properties with use of the reference calculations
• calc_pol.py for calculation of distributed polarizabilities using AIMALL output of finite field calculations

Note: the scripts minimize depencencies on the project library so that they could be used as standalone scripts on an external machine

Preparations for distributed polarizabilities calculations

Two variants are possible:

• with only one external field magnitude (0.003 a.u.)

The input files for AIMALL have to be preparated in the following convention:

1 /no field/; 2 /0.003, 0, 0/; 3 /0, 0.003, 0/; 4 /0, 0, 0.003/;

5 /-0.003, 0, 0/; 6 /0, -0.003, 0/; 7 /0, 0, -0.003/

• with two external field magnitudes (0.003 a.u. and 0.006 a.u.) (using Romberg numerical differentiation procedure)

The input files for AIMALL should follow the convention:

1 /no field/; 2 /0.003, 0, 0/; 3 /0, 0.003, 0/; 4 /0, 0, 0.003/;

5 /-0.003, 0, 0/; 6 /0, -0.003, 0/; 7 /0, 0, -0.003/

8 /0.006, 0, 0/; 9 /0, 0.006, 0/; 10 /0, 0, 0.006/;

11 /-0.006, 0, 0/; 12 /0, -0.006, 0/; 13 /0, 0, -0.006/

Examples

See the examples/examples.pdf to follow the steps used in the integration tests. The files used for the tests are located in the tests/integration directory:

• input as a starting point
• expected as a reference

Example gaussian09 input file for calculations could be found in examples/mna.com

Version history

• 0.1.0 - first release (31.01.2019)
• 0.1.1 - Q-LFT calculations support added (05.02.2019)
• 0.1.2 - a minor README fix on the PyPI (06.02.2019)
• 0.2.0 - analysis of the core calculations - reporting in tables (09.03.2019)
• 0.2.1 - property scaling helper (27.03.2019)
• 0.3.0 - atomic polarizability scaling approach change (03.03.2020)
• 0.4.0 - distributed polarizability calculation script & format change (10.03.2020)
• 0.4.1 - correction of molecules placement in the unit cell (23.03.2020)
• 0.5.0 - from_crystal old input backing up strategy change (04.04.2020)
• 0.5.1 - HYDROGEN_TOLERANCE environment variable could be used to modify default maximum hydrogen distance (1.15A)
• 0.6.1 - input preparation and main calculations allow for arbitrary redefinition of molecule-ionic composition of the unit cell (31.08.2020)
• 0.7.0 - fix for calculation of properties in non-orthogonal systems (15.02.2021)