Compiling

Quick start instructions using pre-compiled binaries can be found in the section here.

Compiling the source codes may require downloading and installing a few dependent packages. To ensure compatibility, we also list the versions that were used during development and testing.

Package Dependence

For lammps you may also need the lastest versions of libpng and libjpeg and other packages (depending on the options you choose for compilation), see lammps documentation for details.

Scripts and Makefiles have been put together to help with compilation within lammps. This may require further reading of the lammps compilation steps and editing the makefiles to adjust the source and library installation locations. We have put together prototype makefiles and scripts for both serial and mpi builds.

Compiling mlmod-lammps involves the following steps:

  • Download lammps from https://lammps.org/, pytorch libtorch from http://pytorch.org/, and install the other dependencies. All the mlmod scripts also can be downloaded from the mlmod_github.

  • Copy mlmod files into the lammps distribution at location $lammps_dir. The $lammps_dir gives the base directory for lammps ./src, ./lib. We put together an automated script copy_src_to_lammps.sh (also available from mlmod_github/src). This is run by specifying the lammps directory:

    ./copy_src_to_lammps.sh -l $lammps_dir

    To install instead manually the mlmod files, copy the mlmod ./lib directory to the lammps ./lib/mlmod directory. Copy the mlmod ./src/USER-MLMOD directory to the lammps ./src directory. Copy the mlmod ./src/USER-MLMOD/MAKE to the lammps ./src/MAKE/MINE directory. Copy any other needed makefiles to corresponding locations.

  • You may need to adjust paths and settings in makefiles. For example, for libtorch, we use directory naming conventions for chosen CXX11 ABIs libtorch_cxx11 or libtorch_no_cxx11. The Makefiles are located in $lammps_dir/lib/mlmod/MAKE, $lammps_dir/lib/vtk, and $lammps_dir/src/MAKE/MINE.

  • Activate the mlmod and related packages in lammps by:

    cd $lammps_dir/src
make yes-user-mlmod yes-molecule yes-vtk

Build using scripts

  • Build the mlmod shared library libmlmod.so by going to the lammps ./lib/mlmod directory and running ./build_mlmod_serial.sh or ./build_mlmod_mpi.sh. You may need to adjust the makefiles for your system’s dependencies for the locations of the installed libraries and include files. We will discuss below primarily the serial version, but the mpi build proceeds similarly.

  • Build the main executable lmp_mlmod_serial by:

    cd $lammps_dir/src
./build_mlmod_lammps.sh

    You may need to adjust the makefiles.

  • You can test the build by calling:

    echo "info system" >& test.in && lmp_mlmod_serial -in test.in

    Given shared library dependencies, you may need to adjust the LD_LIBRARY_PATH. For example:

    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$lammps_dir:$lammps_dir/../lib/mlmod:$lammps_dir/../lib/mlmod/libtorch_cxx11/lib

Build manually

  • While the scripts above automate some of the build process, the makfiles also can be used more directly for serial and mpi compilation. We give the manual steps for building the package, which might be helpful in trouble-shooting or for other target environments.

  • Be sure to activate the mlmod package in lammps:

    cd $lammps_dir/src
make yes-user-mlmod yes-molecule yes-vtk

  • For mpi builds, you may need to adjust the makefiles to point to the libraries for your system configuration. For serial builds, compile the MPI stubs by going into lammps $lammps_dir/src/STUBS and running make. You may need to adjust the ABI_CXX11 interface used for consistency on your system.

  • Build the mlmod library by:

    cd $lammps_dir/lib/mlmod
make -f ./MAKE/Makefile.lib.mlmod_serial lib_shared

    This should result in the shared library libmlmod.so. Similarly you can use ./MAKE/Makefile.lib.mlmod_mpi for building an mpi version of the library.

  • Copy the lammps related makefile information into place for mlmod with:

    cd $lammps_dir/lib/mlmod
cp ./MAKE/Makefile.lammps.mlmod_serial Makefile.lammps

    Or similarly, copy ./MAKE/Makefile.lammps.mlmod_mpi for mpi builds.

  • Copy the lammps related makefile information into place for vtk with:

    cd $lammps_dir/lib/vtk
cp Makefile.lammps.mlmod_serial Makefile.lammps

    Or similarly, copy ./MAKE/Makefile.lammps.mlmod_mpi for mpi builds.

  • Build the main executable lmp_mlmod_serial using:

    cd $lammps_dir/src
make mlmod_serial

    Similarly, make mlmod_mpi for mpi builds. You may need to adjust the makefiles for your particular platform.

  • You can test the build by calling:

    echo "info system" >& test.in && lmp_mlmod_serial -in test.in

    For mpi builds be sure to use mpirun when testing and running simulations:

    echo "info system" >& test.in && mpirun -n 4 lmp_mlmod_mpi -in test.in

    Given shared library dependencies, you may need to adjust the LD_LIBRARY_PATH. For example:

    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$lammps_dir:$lammps_dir/../lib/mlmod:$lammps_dir/../lib/mlmod/libtorch_cxx11/lib

How to use the package is discussed briefly here.

Unit Tests for the mlmod package can be found in the $mlmod_git/tests folder. Tests are performed with the scripts ./run_test.sh and uses the pytest package.

Examples: For further details on setting up models and running simulations, see the examples folder and mlmod website.

Additional Information

For more details, see the lammps documentation pages https://lammps.org/ and http://atzberger.org/.

For installation of pre-compiled binaries, see the quick start instructions.