Installation Instructions for FixSymmetry in LAMMPS

Overview

FixSymmetry is a custom LAMMPS fix that enforces crystal symmetry during simulations, porting from ase. It utilizes the spglib library to obtain symmetry operations based on the specified space group.

This guide provides step-by-step instructions to install FixSymmetry into LAMMPS and run a test simulation to verify its functionality.

Prerequisites

• LAMMPS Source Code: Ensure you have the LAMMPS source code available on your system.
• spglib Library: Install spglib (version compatible with your system).

Installation Steps

1. Install spglib

Clone the spglib repository and install it:

git clone https://github.com/spglib/spglib.git
cd spglib
mkdir build
cd build
cmake .. --install-prefix=$HOME/.local
make
sudo make install

Ensure that the spglib header files and libraries are installed in standard system directories or note their installation paths for later use.

2. Modify the instalation related files in lammps for FixSymmetry

Basically, you can use install_fix_symmetry.sh with CMake compiliation in lammps. If you would like to compile manually with Make, please check below.

2-1. Copy FixSymmetry Source Files

Copy fix_symmetry.h and fix_symmetry.cpp into the LAMMPS src directory:

cp fix_symmetry.h /path/to/lammps/src/
cp fix_symmetry.cpp /path/to/lammps/src/

2-2. Update LAMMPS Build Configuration

Use Install_?

Navigate to the LAMMPS src directory:

cd /path/to/lammps/src

For Makefile Build System:

• Add Source File: Append fix_symmetry.cpp and fix_box_relax_symmetry.cpp to the list of source files. Edit Makefile or Makefile.list and include:

  EXTRA_SRCS += fix_symmetry.cpp:fix_box_relax_symmtery.cpp
  

• Include spglib Headers and Libraries: Add the spglib include and library paths. Edit Makefile.lammps and include:

  EXTRA_INC += -I/path/to/spglib/include
  EXTRA_LIB += -L/path/to/spglib/lib -lspglib
  

  Replace /path/to/spglib/include and /path/to/spglib/lib with the actual paths if spglib is not in standard directories.

For CMake Build System:

• Modify CMakeLists.txt: If using CMake, add fix_symmetry.cpp to the source list and link spglib.

  In CMakeLists.txt, add:

  set(SOURCES ${SOURCES} fix_symmetry.cpp:fix_box_relax_symmetry.cpp)
  find_package(spglib REQUIRED)
  include_directories(${SPGLIB_INCLUDE_DIRS})
  target_link_libraries(lammps ${SPGLIB_LIBRARIES})

3. Build LAMMPS

CMake

mkdir build
cd build
cmake ../cmake ...


make -j8

Make

Clean previous builds (optional):

make clean-all

Compile LAMMPS:

make mpi    # Replace 'mpi' with your desired build target

Ensure that the compiler can find spglib headers and libraries. If not in standard locations, you may need to set environment variables or adjust compiler flags.

5. Verify Installation

After successful compilation, verify that FixSymmetry is included:

• Run lmp_mpi -h and check if fix symmetry and fix box/relax/symmetry appears in the list of available fixes.
• Alternatively, proceed to run the test simulation.

Usage Example without box change

In your LAMMPS input script, use FixSymmetry as follows:

fix sym all symmetry <tolerance>

• <tolerance>: Optional. The tolerance for symmetry enforcement (default is 1e-5).

Usage Example with box change

In your LAMMPS input script, use FixSymmetry as follows:

fix sym all box/relax/symmetry symprec <tolerance>

• <tolerance>: Optional. The tolerance for symmetry enforcement (default is 1e-5).

Troubleshooting

• Compilation Errors: Ensure that spglib is correctly installed and that the compiler and linker can find the necessary headers and libraries.
• Runtime Errors: Verify that the space group number and tolerance are correctly specified and appropriate for your simulation.
• Missing Potentials: Ensure that all required potential files are available in your working directory.

License

This code is distributed under the GNU General Public License v2. See the LICENSE file for more details.

Acknowledgments

• spglib: https://github.com/spglib/spglib
• LAMMPS: https://lammps.sandia.gov/