StructurePrototypeAnalysisPackage

Structure Prototype Analysis Package can analyze symmetry and compare similarity of large amount of atomic structures.

Description:

The structure prototype analysis package (SPAP) can analyze symmetry and compare similarity of a large number of atomic structures. Typically, SPAP can analyze structures predicted by CALYPSO (www.calypso.cn). We use spglib to analyze symmetry. The coordination characterization function (CCF) is used to measure structural similarity. We developed a unique and advanced clustering method to automatically classify structures into groups. If you use this program and method in your research, please read and cite the publication: J. Phys. Condens. Matter 2017, 29, 165901.

Author:

Dr. Chuanxun Su
CAS Key Laboratory of Quantum Information, University of Science and Technology of China

Email:

sucx@ustc.edu.cn / suchuanxun@163.cn

Dependency:

This program uses numpy, spglib, and ase (https://wiki.fysik.dtu.dk/ase/). You could simply install them by one command: pip install numpy spglib ase

Installation:

Use command: pip install spap
Or download the source code and install: python3 setup.py install

Example Command:

You can run the program by the following commands:
spap -h (show help)
spap --nc (analyze symmetry and don't compare similarity)

spap -e 0.5 --cif --nd  
spap -a -t 0.01 --vasp --nc
spap
spap --vasp -d
spap -n 200 --cif --th 0.05 -r 7.0

Run by Script:

You can run SPAP by scripts. SPAP can run at many different modes.

To analyze CALYPSO structure prediction results, set i_mode=1. Run run_spap.py in results directory generated by CALYPSO. You can find this script in example directory.
To calculate symmetry and compare similarity of a set of structures, set i_mode=2. Put structure files in struc directory. The files should be named *.cif, *.vasp (VASP format), or any name and format ase can read automatically.
To read and analyze structures optimized by VASP, set i_mode=3. Define work_dir. It is the path where you put the optimized structures.
To calculate symmetry and compare similarity of a list of structures, set i_mode=4. Assign a list of Atoms objects to structure_list.

Output:

I try to organize the output files similar to those generated by cak.py (we actually don't need cak.py). So that it's easier for user to get familiar with SPAP. The Analysis_Output.dat lists the information about the analyzed structures. However we provide more information such as density (total number of atoms divided by volume), formula unit, and volume. The distance.dat stores the distances between structures and some other attributes. The analyzed_structures.db is in atomic simulation environment (ASE) database format for atoms. You can easily read and analyze these structures through ASE. You can also add and store properties you are interested in. This functionality is very useful for screening out good functional materials. SPAP can also write structures in cif and VASP format in dir_* directory. Technically speaking, SPAP can easily write any structure format supported by ASE.

Revision Log:

Project released on GitHub
August 19, 2019

Program released on the Python Package Index (PyPI)
December 8, 2019

chuanxun/StructurePrototypeAnalysisPackage