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FerroDispCalc

Calculator of polarization displacements and polarization of ferroelectrics in molecular dynamics simulations.

This code is designed for:

  • build neighbor list for ferrorelectrics (ABO3 perovskite)
  • calculate the polarization and displacement from a LAMMPS dump file.

For better performence, the main part of code is written in C++.

Code Structure

.
├── example  //example of how to use code, in todo list
├── ferrodispcalc // python library
│   ├── build_neighbor_list.py  //Build neighbor list for ABO3 perovskite
│   ├── PolarPolter.py
│   └── type_map.py  //store the common type map
├── install.sh //installation script
├── LICENSE
├── README.md
├── src  //c++ source code
│   ├── basic.hpp //This file contains basic functions to read lammps dump files.
│   ├── get_averaged_structure.cpp //Calculate the average structure from LAMMPS dump file
│   ├── get_polarization.cpp //Calculate the polarization of each perovskite unit call using LAMMPS dump file
│   └── get_polarization_displacement.cpp //Calculate the polarization displacement from LAMMPS dump file
└── test //files related to testing
    ├── BaTiO3
    ├── compare.py
    ├── com_sys.py
    ├── PIN-PMN-PT
    ├── PIN-PMN-PT_multi_domain
    ├── PSZO
    ├── PZO
    ├── README.md
    └── run_test.sh

Installation

  1. Get source code:
git clone https://github.com/MoseyQAQ/FerroDispCalc.git

  1. Prerequisites:

    • C++ compiler
    • Eigen (For matrix operation)
    • numpy, pymatgen (can be easily installed through: pip3 install pymatgen)

  2. Edit the following variables in install.sh:

####### general seeting #######
EIGEN=/home/liulab/eigen-3.4.0  # path to your eigen header
CXX=g++                         # your c++ compiler
CXXFLAGS="-O3" # or "-O3 -march=native" for example
INSTALL_DIR=$(pwd)
###############################
  1. Run the install.sh:
chmod +x install.sh
./install.sh make    # compile the source code
./install.sh clean   # clean the compiled code
./install.sh test    # test the executable
./install.sh install # installation

Usage

  1. get_averaged_structure / get_a : calculate averaged structure from a LAMMPS dump file.
    Options:

    • input_file: LAMMPS dump file
    • output_file: output file in .xsf format
    • type_map_file: a file containing the atom types.
    • ratio: If < 1, the last "ratio"% of frame will be read. If >= 1, the last "ratio" frames will be read.

  2. get_polarization_displacement / get_d : calculate displacement from: LAMMPS dump / .xsf file.
    Options:

    • traj_file: LAMMPS dump or .xsf file
    • output_file: output file, each line contains the original coordinates and displacements of a cation.
    • nl_file: neighbor list file, it can be generated using build_neighbor_list.py
    • ratio/last_frame: If < 1, the last "ratio"% of frame will be read. If >= 1, the last "ratio" frames will be read. (only work when reading LAMMPS dump)

  3. get_polarization / get_p : calculate polarization from: LAMMPS dump / .xsf file.
    Options:

    • traj_file: LAMMPS dump or .xsf file
    • output_file: output file, each line contains the original coordinates and displacements of a cation.
    • a_nl_file: neighbor list file for A site cations
    • x_nl_file: neighbor list file for X site anions
    • type_map_file: file contains the type map of atom types
    • bec_file: file contains the Born effective charge of each atom type
    • ratio/last_frame: If < 1, the last "ratio"% of frame will be read. If >= 1, the last "ratio" frames will be read. (only work when reading LAMMPS dump)

Example

The example is still under developed. You can find examples in "test" folder.

Todo list

imporved IO, doc