crystmatch 1.1.2

Enumerating and analyzing crystal-structure matches for solid-solid phase transitions.

Crystmatch

If you use this code in your research, please cite the following paper:

[1] FC Wang, QJ Ye, YC Zhu, and XZ Li, Physical Review Letters 132, 086101 (2024)

You are also welcome to contact me at [e-mail] for any questions or comments.

Introduction

A solid-solid phase transition establishes an atom-to-atom correspondence between the initial and final crystal structures $\mathcal A$ and $\mathcal B$. Such correspondence is called a crystal-structure match (CSM) [1]. A CSM can be described by a pair of POSCAR files, which specifies how the lattice deforms from $\mathcal A$ to $\mathcal B$ and the correspondence between atoms in a supercell of $\mathcal A$ and those in $\mathcal B$.

The main goals of crystmatch are as follows:

• Enumeration:

  • Provide a complete list of representative [1] CSMs between two given crystal structures, with user-specified upper bounds on the multiplicity [1] and root-mean-square strain (RMSS).
  • (In progress) Provide a complete list of CSMs with user-specified upper bounds on the multiplicity, RMSS, and root-mean-square displacement (RMSD).

• Analysis:

  • Read a CSM from a pair of POSCAR files, and save CSMs in the same format.
  • Score CSMs by RMSS and RMSD.
  • Benchmark a CSM by its deviation angle from an orientation relationship (OR).

Congruent CSMs (those differ only by a space-group transformation) are identified and excluded from the enumeration using the spglib library by Atsushi Togo et al.

Installation

Make sure you have Python 3.9 or later installed. You can check it by running:

python3 --version

Clone this repository by:

git clone https://github.com/fangcheng-wang/crystmatch.git

Navigate to the directory where setup.py is located, run:

pip3 install .

Check whether crystmatch is successfully installed:

crystmatch --version

Usage

To run crystmatch, one of the following modes must be selected:

1. Enumeration mode: Generate a list of CSMs, save them to a CSM_LIST.npz file, and perform preliminary analysis. The initial and final crystal structures must be specified in the form of POSCAR files.
2. Read mode: Read CSMs from a CSM_LIST.npz file. You can export specific CSMs to POSCARs, perform OR analysis, generate CSV tables of CSM properties, and visualize the RMSD-RMSS-multiplicity distribution in a 2D scatter plot.
3. Single-CSM mode: Directly determine a single CSM by two POSCAR files (must have the same number and species of atoms) and perform detailed analysis.

We strongly recommend starting with the examples provided below. If you are still confused, run crystmatch directly in the command line without any arguments for an interactive calculation. To see all available options, run:

crystmatch --help

Examples

Enumerating CSMs

To generate a list of representative [1] CSMs between two crystal structures stored in ./fcc and ./bcc, with multiplicity upper bound MAX_MU = 4 and RMSS upper bound MAX_RMSS = 0.4, run:

crystmatch --initial fcc --final bcc --enumeration 4 0.4

The following files will be created in the current directory:

./
├── CSM_LIST-m4s0.40.npz       # stores the enumerated CSMs and metadata.
├── PLOT-m4s0.40.pdf           # shows the RMSD-RMSS distribution of the CSMs.
└── TABLE-m4s0.40.csv          # shows the multiplicity, RMSS, and RMSD of each CSM.

We recommend you to try MAX_MU <= 4 and MAX_RMSS = 0.4 first, and then gradually adjust these upper bounds (usually by increasing MAX_MU and decreasing MAX_RMSS) to obtain desired results. Otherwise, the enumeration may take a very long time, or find no CSMs at all.

Exporting CSMs from an NPZ file

After enumeration, you can see the properties of CSMs in the CSV file, which also contains their indices in the NPZ file. If you want to export the CSMs with indices 7 and 10 in CSM_LIST-foo.npz, run:

crystmatch --read CSM_LIST-foo.npz --export 7 10

Two folders will be created in the current directory, each containing a pair of POSCAR files representing the CSM. The current directory will look like this:

./
├── CSM_7/
│   ├── POSCAR_I
│   └── POSCAR_F
└── CSM_10/
    ├── POSCAR_I
    └── POSCAR_F

Orientation relationship analysis

To benchmark CSMs in CSM_LIST-foo.npz by their deviation angles from the OR $(111)_A\parallel(110)_B$, $[1\overline{1}0]_A\parallel[001]_B$, run:

crystmatch --read CSM_LIST-foo.npz --orientation 1 1 1 1 1 0 1 -1 0 0 0 1

Note that the arguments after --orientation must be Cartesian coordinates.

The ORs are determined via the rotation-free manner by default, and you can also use --uspfix to determine ORs via the USF-fixed manner; see Ref. [1] for their definitions.

Single-CSM analysis

To analyze a single CSM defined by two POSCAR files, run:

crystmatch --initial POSCAR1 --final POSCAR2 --single

crystmatch will also save the rigid-transformation optimized (with rotation-free orientation and RMSD-minimized overall position) CSM in the current directory like this:

./
└── CSM_single/
    ├── POSCAR1
    └── POSCAR2-optimized

Python API

You can also use crystmatch as a Python module in your own scripts. See the documentation for details.