/LAMMPS_wrapper

Primary LanguageC

LAMMPS_wrapper

LAMMPS_wrapper makes LAMMPS calculation easier by using POSCAR directly with simple INPUT files. If you activate the calculation type you want to do, LAMMPS_wrapper converts INPUT and POSCAR files internally. LAMMPS_wrapper supports oneshot calculation, relaxation, NEB method, dynamical matrix calculation, and NVT MD simulation. Be free from writing complex input files and tedious conversion between POSCAR and LAMMPS data format!

Requirement

  • CMake >= 3.13
  • LAMMPS >= 23Jun2022

Installation

  1. Build LAMMPS as shared library. [link]
cd lammps
mkdir build; cd build
cmake ../cmake -D BUILD_SHARED_LIBS=yes -D PKG_REPLICA=yes PKG_PHONON=yes
cmake --build . --target install
  1. Build LAMMPS_wrapper. Please check compiler type in CMakeLists.txt.
cd LAMMPS_wrapper
mkdir build; cd build
cmake ../src
cmake --build .

Usage

For oneshot, relaxation, NEB, dynamical matrix, and NVT MD simulation, single POSCAR file is needed.

mpirun -np $numproc ./LAMMPS_wrapper POSCAR

For NEB calculation, two POSCAR files are needed.

mpirun -np $numproc ./LAMMPS_wrapper POSCAR_initial POSCAR_final

$numproc stands for the number of CPU cores in parallel computation.

Input

Potential parameter

  • NELEMENT [integer]
    • NELEMENT is the number of elements
  • ATOM_TYPE [strings]
    • ATOM_TYPE is the symbols of elements
  • PAIR_STYLE [strings]
    • PAIR_STYLE stands for the pair style in LAMMPS input.
  • PAIR_COEFF [strings]
    • PAIR_COEFF stands for the pair coeff in LAMMPS input.

oneshot

  • ONESHOT [0/1]
    • ONESHOT determines whether oneshot calculation runs.

relaxation

  • ATOM_RELAX [0/1]
    • ATOM_RELAX determines whether atomic coordinates are optimized.
  • CELL_RELAX [0/1]
    • CELL_RELAX determines whether lattice vectors are also optimized.
  • MAX_FORCE [real]
    • MAX_FORCE sets the force tolerance for relaxation (in eV/Angst).

neb

  • NEB [0/1]
    • NEB determines whether the nudged-elastic band method runs.
  • NIMAGES [integer]
    • NIMAGES sets the number of images during the NEB emthod.
  • MIN_DIST [real]
    • MIN_DIST sets the minimum bond distance between atoms when generating images with interpolation.

dynamic matrix

  • DYNMAT [0/1]
    • DYNMAT determines whether the dynamical matrix is calculated.
  • FINITE_DIFF [real]
    • FINITE_DIFF sets the displacement in finite difference method (in Angst).

NVT MD

  • NVT_MD [0/1]
    • NVT_MD determines whether NVT molecular dynamics run.
  • TIMESTEP [real]
    • TIMESTEP sets the timestep for time integration (in fs).
  • MAX_STEP [integer]
    • MAX_STEP sets the maximum MD step.
  • TEMPERATURE [real]
    • TEMPERATURE sets the temperature of system (in K).

TARGET (only for DYNMAT)

It contains the atom indices or types to be the targets of dynamical matrix.

I 0 1 2 3
T 1
A
  • I: Index (starting from 0)
  • T: Type (starting from 1)
  • A: All

Tips

  1. LAMMPS_wrapper supports only units metal currently.
  2. TARGET file is only needed for calculating dynamical matrix.
  3. Output of dynamical matrix is written as dynmat.dat.