Space Group Restricted Crystal Structure Prediction

Provisionally accepted by Journal of Physics: Condensed Matter for final checks

Space Group Restricted Crystal Structure Prediction

Space Group Restricted Crystal Structure Prediction (SGRCSP) is a specialized tool designed for predicting crystal structures based on a given chemical composition. This tool is particularly suited for structures featuring rigid bodies or molecules. One of the major differences between SGRCSP and other popular Crystal Structure Prediction (CSP) packages, such as USPEX or CALYPSO, is the ability of SGRCSP to restrict atoms (or rigid bodies) to designated Wyckoff positions. This restriction ensures that symmetry is preserved throughout the simulation.

Prerequisites

Python Version

Python 3.9+

Required Packages

pymatgen
ase
pyxtal
chgnet

The pyxtal package will automatically install ASE version 3.18.0 and Pymatgen 2024.3.1 when you run:

pip install pyxtal

However, since the ASE package on PyPI has not been updated for two years, you need to install the latest ASE version from their GitLab repository to ensure compatibility with chgnet. You can do this by running:

pip install git+https://gitlab.com/ase/ase

PyXtal modification

SGRCSP uses PyXtal to generate symmetry-restricted structures. However, some modifications and bug fixes are required for the PyXtal package to support our desired functionality. Please copy the Python scripts from the pyxtal_modify folder to the corresponding PyXtal package directory.

Bond configuration

To generate molecular crystal structures, you need to set the bond lengths between atoms within the molecules. This configuration should be defined in the bonds.json file located in the database folder of the PyXtal package. Only approximate bond lengths are necessary.

Usage

Documentation is under development.

Input files

input.txt
Molecule files: MOL_1.xyz, MOL_2.xyz
First-principles calculation inputs

Please refer to the format of input files in the examples/Input folder. Currently, only VASP is supported as the first-principles calculation package.

Combinations of Molecules/Atoms in a Space Group

Given the chemical composition of a structure in a space group, you can see how many possible compositions are available.

Example input.txt:

# Molecules in the structures are MOL_1.xyz and MOL_2.xyz
MolFiles = MOL_1.xyz MOL_2.xyz
# Ratio between these two molecules is 1:3
MolNumber = 1 3
# Maximum number of molecules can be 3:9
RatioMaxMultiplier = 3
# Space groups to search for possible combinations
SpaceGroup = 1 4 7 28-31

Example Python Script:

from readconfig import ReadConfig
from combination import WyckoffCombinations

config = ReadConfig()
sg = config.space_group()
mol_list = config.mol_list()
mol_number = config.mol_number()
z = config.max_multiplier()

comb = WyckoffCombinations(mol_list)
for i in sg:
    comb_number = comb.mol_ratio_comb_list_sg(mol_number, i, z)

Example Output:

P1 (1), Z = 1, checking: 1/1, valid: 1, sites: [['1a'], ['1a', '1a', '1a']]                      
P1 (1), Z = 2, checking: 1/1, valid: 1, sites: [['1a', '1a'], ['1a', '1a', '1a', '1a', '1a', '1a']]                      
P1 (1), Z = 3, checking: 1/1, valid: 1, sites: [['1a', '1a', '1a'], ['1a', '1a', '1a', '1a', '1a', '1a', '1a', '1a', '1a']]                      
P21 (4), Z = 2, checking: 1/1, valid: 1, sites: [['2a'], ['2a', '2a', '2a']]                      
Pc (7), Z = 2, checking: 1/1, valid: 1, sites: [['2a'], ['2a', '2a', '2a']]                      
Pma2 (28), Z = 2, checking: 39/39, valid: 39, sites: [['2c'], ['4d', '2c']]                            
Pnc2 (30), Z = 2, checking: 12/12, valid: 12, sites: [['2b'], ['4c', '2b']]                            
Pmn21 (31), Z = 2, checking: 2/2, valid: 2, sites: [['2a'], ['4b', '2a']]