matsdp

The materials simulation and data processing toolkit.

Basic information

MATSDP--The materials simulation and data processing toolkit.

Requirements

• numpy
• scipy
• matplotlib
• scikit-learn

Functions

Vienna ab-initio simulation package (VASP) analyzing and postprocessing tools

• Build model by the following methods: atom substitution, atom selection, exfoliation (2D), make supercell, transformation (rotation + translation), reorientation, adding vacuum layer etc.
• Read and write VASP inputs/outputs.
• Visualization of model and results: Plot model based on the POSCAR/CONTCAR file, also support color mapping of atom properties); Plot DOS (PDOS, LDOS, TDOS); Plot band structure (including fat band).
• Analyzing tools: Calculate the nearest neighbor information, perform simple common neighbor analysis, calculate structural energy, overlap peak analyzer of DOS, get band gap.
• VASP tools: Check VASP errors/warnings and give solutions; Check the job status of multiple jobs; Check lattice parameters of multiple VASP jobs; Conversion of coordinate systems (Fractional/Cartesian);
• Job management: Processing of multiple VASP jobs automatically; Write task summary/report of multiple VASP jobs.

Wannier tools

• Retrieving data from Wannier results and data visualization.

Three-dimensional atom probe tomography (APT) postprocessing tools

• Extract information from the concentration profile.csv file.
• Visualization of the concentration profile across the interface.

DVM tools

• Read the .input, .incar, .otput files
• Write the .input, .incar, IND.DAT files
• Ouput the interatomic energy (IE) files (including the IEs of the first nearest neighbor atoms)
• The .incar file can also be prepared by atom selection from the vasp_build function in the vasp module

PMS tools

• Job management: Processing of multiple VASP jobs automatically
• Write task summary (of VASP jobs)

Others tools

• file format conversion
• fig2pdf (converting multiple images to a single .pdf file)

Installation

pip install matsdp

Release note

• version 0.2.4

• Date: 20210629

Usage

Graphical User Interface (GUI)

• matsdp_gui.exe (part of the functions are realized in the GUI version)

Running with Python environment

modules that may be imported before using the vasp package

• from matsdp.vasp import vasp_read
• from matsdp.vasp import vasp_build
• from matsdp.vasp import vasp_plot
• from matsdp.vasp import vasp_analyze
• from matsdp.vasp import vasp_write
• from matsdp.vasp import vasp_tools
• from matsdp.vasp import vasp_default
• from matsdp.vasp import vasp_help

modules that may be imported before using the apt package

• from matsdp.apt import apt_read
• from matsdp.apt import apt_plot

modules that may be imported before using the dvm package

• from matsdp.dvm import dvm_read
• from matsdp.dvm import dvm_build
• from matsdp.dvm import dvm_analyze
• from matsdp.dvm import dvm_write
• from matsdp.dvm import dvm_default
• from matsdp.dvm import dvm_help

modules that may be imported before using the pms package

• from matsdp.pms import project_manager
• from matsdp.pms import task_manager

Tests

To run the tests, please run the runtests.py in the "tests" directory.