Automated calculation of crystal lattice energies with the many-body expansion.

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Overview

CrystaLattE is a software that automates the computation of crystal lattice energies using the many-body cluster expansion. The required computations on dimers, trimers, etc., within the crystal are independent of each other, leading to a naturally parallel approach. The algorithm exploits the long-range three-dimensional periodic order of crystals to automatically detect and avoid redundant or unnecessary computations.

General Information

CrystaLattE has an interface with the quantum chemistry package Psi4. To run, the code requires a crystallographic information file containing structural information of the crystal and an input file specifying execution details. Work continues in the creation of a CrystaLattE pip package. So, for the moment, the instructions to download and install CrystaLattE and to create a conda environment that includes Psi4 are presented below.

Installation

Minimal set of commands to install CrystaLattE on Linux, MacOS, or Windows (with the Windows Subsystem for Linux). Last tested on 4 October 2019:

1. Install Miniconda:

If you have an installation of Conda in your system, please skip to step 2. Otherwise, Miniconda is required and the installer is available from the the Anaconda website. To download the installer from the terminal (in Linux or the Windows Subsystem for Linux):

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

(Note) If you use MacOS, replace Linux by MacOSX on the previous command.

Run the installer following the on-screen instructions:

bash Miniconda3-latest-Linux-x86_64.sh

After the installation is complete, close the terminal and start a new shell.

(Optional) Disable automatic activation of the base conda environment:

conda config --set auto_activate_base false

2. Create a Conda Environment for CrystaLattE

CrystaLattE requires Psi4 and PyCIFRW. Conda offers the possibility of creating an environment that contains all the dependencies required by CrystaLattE. To download and install PSI4 and other related software tools in a new cle environment execute the command below and follow the on-screen instructions:

conda create -n cle python psi4 pycifrw -c conda-forge

3. Activate the cle environment

To use the recently created cle environment, activate it:

conda activate cle

4. Clone CrystaLattE from its GitHub repository:

In you file system navigate to the location where you would like to place the root directory of CrystaLattE and clone it from its corresponding GitHub repository:

git clone https://github.com/carlosborca/CrystaLattE.git

5. Test CrystaLattE

Go to the root directory of the CrystaLatte repository in the file system and run the test suite:

pytest

(Note) It is known that the v2rdm_casscf plugin of PSI4 may cause execution errors when trying to import PSI4 from CrystaLattE. If such error is encountered during testing, remove it.

conda remove v2rdm_casscf

How to run CrystaLattE

CrystaLattE requires a crystallographic information file (.cif) and an options input file (.cle). CIF files can be obtained from multiple sources. For example, from the Cambridge Crystallographic Data Centre (CCDC) website. The options file must be generated by the user. A template is presented below:

Preparing the options input

Example of an options input file for CrystaLattE.

# This is a typical CrystaLattE input template: input.cle

# Blank lines and lines starting with the hash character are omitted.
# Padding blank spaces are also ignored.

# The format is:
# Keywords  equal  Value

cif_input       =  ../MyCrystals/OneCrystal.cif
cif_output      =  ../MyCrystals/SuperCell.xyz
bfs_thresh      =  1.2
uniq_filter     =  ChSEV
nmers_up_to     =  3
r_cut_com       =  12.0
r_cut_monomer   =  15.0
r_cut_dimer     =  9.0
r_cut_trimer    =  12.0
r_cut_tetramer  =  6.0
r_cut_pentamer  =  4.0
cle_run_type    =  psi4api + quiet
psi4_method     =  MP2/aug-cc-pV[TQ]Z + D:FNO-CCSD(T)/aug-cc-pVDZ
psi4_bsse       =  cp
psi4_memory     =  8 GB
verbose         =  2

Keywords

Description of keywords and their acceptable values.

Keyword	Acceptable Values	Default	Example	Notes
cif_input	<RelativePath>/<FileName>.cif	No default	Benzene.cif	Must be a .cif
cif_output	<RelativePath>/<FileName>.xyz	sc.xyz	Benzene.xyz	Must be a .xyz
cif_a	Odd positive integer	5	9
cif_b	Odd positive integer	5	7
cif_c	Odd positive integer	5	11
bfs_thresh	Positive float	1.2	1.3	vdW radii multiplier
uniq_filter	ChSEV, Dreamaligner	ChSEV	Dreamaligner
nmers_up_to	2, 3, 4, 5	2	3	Dimers, Trimers...
r_cut_com	Positive float	10.0	12.0	Angstroms
r_cut_monomer	Positive float	12.0	15.0	Angstroms
r_cut_dimer	Positive float	10.0	8.0	Angstroms
r_cut_trimer	Positive float	8.0	10.0	Angstroms
r_cut_tetramer	Positive float	6.0	5.0	Angstroms
r_cut_pentamer	Positive float	4.0	3.0	Angstroms
cle_run_type	psi4api, psithon, makefp, test, quiet, timings	psi4api	test + quiet	Separate with +
psi4_method	String	HF/STO-3G	HF-3c	See PSI4 manual
psi4_bsse	vmfc, cp, nocp	cp	nocp
psi4_memory	String	500 MB	2 GB
verbose	0, 1, 2	1	2

Running CrystaLattE

Finally, to execute the code:

./crystalatte.py input.cle

Known Issues

Precision issues may arise when computing a large number of structures at default energy and density convergence criteria if using Psi4 1.3.2 and newer versions. Although the default energy and density convergence criteria for Psi4 calculations has been increased in CrystaLattE, the user should be careful.

Copyright

Copyright (c) 2020, Carlos H. Borca

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.0.