Description:

chi1chi2 0.9.5

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]

Installation
Make sure you have installed:

gfortran
python 3.6

Installation:

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

#Description
The whole program constitutes a set of scripts that need to be executed in order.
There are four main steps:

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

The purpose of this file is to lead the user through all these steps.
Step 1 - Input preparation

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

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

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

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

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)
0.8.0 - added script for calculation of d_effective for selected solid angles (21.02.2021)
0.9.0 - openbabel dependency removed (30.12.2021)
0.9.5 - automatic release pipeline (7.01.2022)

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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