patch_lammps.sh

#!/bin/bash

lammps_root=$1
cxx_standard=$2 # 14, 17
d3_support=$3 # 1, 0
SCRIPT_DIR=$(dirname "${BASH_SOURCE[0]}")

###########################################
# Check if the given arguments are valid  #
###########################################

# Check the number of arguments
if [ "$#" -ne 3 ]; then
    echo "Usage: sh patch_lammps.sh {lammps_root} {cxx_standard} {d3_support}"
    echo "  {lammps_root}: Root directory of LAMMPS source"
    echo "  {cxx_standard}: C++ standard (14, 17)"
    echo "  {d3_support}: Support for pair_d3 (1, 0)"
    exit 1
fi

# Check if the lammps_root directory exists
if [ ! -d "$lammps_root" ]; then
    echo "Error: No such directory: $lammps_root"
    exit 1
fi

# Check if the given directory is the root of LAMMPS source
if [ ! -d "$lammps_root/cmake" ] && [ ! -d "$lammps_root/potentials" ]; then
    echo "Error: Given $lammps_root is not a root of LAMMPS source"
    exit 1
fi

# Check if the script is being run from the root of SevenNet
if [ ! -f "${SCRIPT_DIR}/pair_e3gnn.cpp" ]; then
    echo "Error: Script executed in a wrong directory"
    exit 1
fi

# Check if the patch is already applied
if [ -f "$lammps_root/src/pair_e3gnn.cpp" ]; then
    echo "----------------------------------------------------------"
    echo "Seems like given LAMMPS is already patched."
    echo "Try again after removing src/pair_e3gnn.cpp to force patch"
    echo "----------------------------------------------------------"
    echo "Example build commands, under LAMMPS root"
    echo "  mkdir build; cd build"
    echo "  cmake ../cmake -DCMAKE_PREFIX_PATH=$(python -c 'import torch;print(torch.utils.cmake_prefix_path)')"
    echo "  make -j 4"
    exit 0
fi

# Check if OpenMPI exists and if it is CUDA-aware
if command -v ompi_info &> /dev/null; then
    cuda_support=$(ompi_info --parsable --all | grep mpi_built_with_cuda_support:value)
    if [[ -z "$cuda_support" ]]; then
        echo "OpenMPI not found, parallel performance is not optimal"
    elif [[ "$cuda_support" == *"true" ]]; then
        echo "OpenMPI is CUDA aware"
    else
        echo "This system's OpenMPI is not 'CUDA aware', parallel performance is not optimal"
    fi
else
    echo "OpenMPI not found, parallel performance is not optimal"
fi

# Extract LAMMPS version and update
lammps_version=$(grep "#define LAMMPS_VERSION" $lammps_root/src/version.h | awk '{print $3, $4, $5}' | tr -d '"')

# Combine version and update
detected_version="$lammps_version"
required_version="2 Aug 2023"  # Example required version

# Check if the detected version is compatible
if [[ "$detected_version" != "$required_version" ]]; then
    echo "Warning: Detected LAMMPS version ($detected_version) may not be compatible. Required version: $required_version"
fi

###########################################
# Backup original LAMMPS source code      #
###########################################

# Create a backup directory if it doesn't exist
backup_dir="$lammps_root/_backups"
mkdir -p $backup_dir

# Copy comm_* from original LAMMPS source as backup
cp $lammps_root/src/comm_brick.cpp $backup_dir/
cp $lammps_root/src/comm_brick.h $backup_dir/

# Copy cmake/CMakeLists.txt from original source as backup
cp $lammps_root/cmake/CMakeLists.txt $backup_dir/CMakeLists.txt

###########################################
# Patch LAMMPS source code: e3gnn         #
###########################################

# 1. Copy pair_e3gnn files to LAMMPS source
cp $SCRIPT_DIR/{pair_e3gnn,pair_e3gnn_parallel,comm_brick}.cpp $lammps_root/src/
cp $SCRIPT_DIR/{pair_e3gnn,pair_e3gnn_parallel,comm_brick}.h $lammps_root/src/

# 2. Patch cmake/CMakeLists.txt
sed -i "s/set(CMAKE_CXX_STANDARD 11)/set(CMAKE_CXX_STANDARD $cxx_standard)/" $lammps_root/cmake/CMakeLists.txt
cat >> $lammps_root/cmake/CMakeLists.txt << "EOF"

find_package(Torch REQUIRED)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
target_link_libraries(lammps PUBLIC "${TORCH_LIBRARIES}")
EOF

###########################################
# Patch LAMMPS source code: d3            #
###########################################

if [ "$d3_support" -ne 0 ]; then

# 1. Copy pair_d3 files to LAMMPS source
cp $SCRIPT_DIR/pair_d3.cu $lammps_root/src/
cp $SCRIPT_DIR/pair_d3.h $lammps_root/src/
cp $SCRIPT_DIR/pair_d3_pars.h $lammps_root/src/

# 2. Patch cmake/CMakeLists.txt
sed -i "s/project(lammps CXX)/project(lammps CXX CUDA)/" $lammps_root/cmake/CMakeLists.txt
sed -i "s/\${LAMMPS_SOURCE_DIR}\/\[\^.\]\*\.cpp/\${LAMMPS_SOURCE_DIR}\/\[\^.\]\*\.cpp  \${LAMMPS_SOURCE_DIR}\/\[\^.\]\*\.cu/" $lammps_root/cmake/CMakeLists.txt
cat >> $lammps_root/cmake/CMakeLists.txt << "EOF"

find_package(CUDA)
set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -fmad=false -O3")
string(REPLACE "-gencode arch=compute_50,code=sm_50" "" CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS}")
target_link_libraries(lammps PUBLIC ${CUDA_LIBRARIES} cuda)
EOF

fi

###########################################
# Print changes and backup file locations #
###########################################

# Print changes and backup file locations
echo "Changes made:"
echo "  - Original LAMMPS files (src/comm_brick.*, cmake/CMakeList.txt) are in {lammps_root}/_backups"
echo "  - Copied contents of pair_e3gnn to $lammps_root/src/"
echo "  - Patched CMakeLists.txt: include LibTorch, CXX_STANDARD $cxx_standard"
if [ "$d3_support" -ne 0 ]; then
    echo "  - Copied contents of pair_d3 to $lammps_root/src/"
    echo "  - Patched CMakeLists.txt: include CUDA"
fi

# Provide example cmake command to the user
echo "Example build commands, under LAMMPS root"
echo "  mkdir build; cd build"
echo "  cmake ../cmake -DCMAKE_PREFIX_PATH=$(python -c 'import torch;print(torch.utils.cmake_prefix_path)')"
echo "  make -j 4"

exit 0