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NOTE: If you are using LAMMPS < 07Sep16, you will need to replace list->ghost by list->ghostflag in pair_atomistica.cpp.

To compile the LAMMPS-Atomistica interface do the following:

  1. Extract the current version of Atomistica to a directory outside of your LAMMPS source directory. Alternative: clone the git-repository directly via

    git clone https://github.com/Atomistica/atomistica.git

    Cloning the git-repository will download the latest development version, not the latest release. It may be safer to download the release tarball.

    This should give the following directory hierachy

    atomistica/
   build/
   build_lammps/
   build_standalone/
   build_unittests/
   ...

  2. Change to the atomistica/build_lammps directory. This directory contains makefiles for compilation with the GNU compiler suite (Makefile.gnu), for compilation with the Intel compiler suite (Makefile.intel) and for compilation with the XL compiler suite on Blue Gene (Makefile.xl). It is recommended to use the same compiler used for compiling LAMMPS. Copy one of the Makefile.* to Makefile and edit if necessary. Then compile with

    make lammps_factories
make atomistica

    The final output of this procedure is the file libatomistica.a.

  3. Copy the files pair_atomistica.cpp and pair_atomistica.h from the atomistica/src/lammps/pair_style directory to LAMMPS' src directory.

  4. Modify your LAMMPS Makefile to link the main executable with libatomistica.a created by step 2. Add

    -L/path/to/atomistica/build_lammps -latomistica

    to the link flags of LAMMPS.

    pair_atomistica.h additionally needs to be able to find the files ptrdict.h and potentials_factory_c.h during from the atomistica source directory during compilation. These files are located here:

    atomistica/src/support/ptrdict.h 
atomistica/build_lammps/potentials_factory_c.h

    Modify your LAMMPS Makefile to add these paths to the header search path by adding

    -I/path/to/atomistica/src/support -I/path/to/atomistica/build_lammps

    to the compile flags of LAMMPS.

    Atomistica additionally needs to be linked with some LAPACK implementation, the Fortran runtime and the MPI library, the details depend on the compiler and MPI version.

    The following instructions are for Intel compilers only. To link with LAPACK, add

    -mkl=sequential

    to the link flags of LAMMPS. It will additionally be necessary to link to a Fortran runtime library. Failing to link to a Fortran runtime will result in undefined symbols when building LAMMPS. For the Intel compiler suite add

    -lifcore -lifport

    to the link flags of LAMMPS. Finally, it will be necessary to link with the Fortran MPI bindings. Try adding

    -l<f77_mpi_library>

    to the link line of LAMMPS. Common names for <f77_mpi_library> are mpi_f77 or mpi_mpifh; this depends on the MPI implementation that you are using.

    The atomistica/src/lammps/MAKE subdirectory of the atomistica source packages contains a sample makefile, but it is likely outdated. It is recommended to modify your LAMMPS makefile by hand!

  5. Compile LAMMPS.

Atomistica potentials are available via the "atomistica" pair style. A typical LAMMPS script looks like

  ... units metal ... pair_style atomistica Tersoff # Tersoff potential pair_coeff * * Si # LAMMPS atom id 1 is Silicon ...  

If you need to modify the potential parameters create an Atomistica parameter file.

  Tersoff { A = "1000, 1000, 1000"; };  

In the LAMMPS control file use:

  pair_style atomistica Tersoff params.dat pair_coeff * * Si    

where "params.dat" is the above file.

Troubleshooting

Undefined symbols error:

If, during LAMMPS compilation, you get an error which looks like this:

...
./liblammps_mpi.so: error: undefined reference to 'atomistica_startup'
./liblammps_mpi.so: error: undefined reference to 'particles_set_element'
./liblammps_mpi.so: error: undefined reference to 'neighbors_set_pointers'
./liblammps_mpi.so: error: undefined reference to 'ptrdict_read'
...

It is possible that you have linked the libraries in an incorrect order. As of 05/12/2023, for a build using make mpi with GCC and mode = shared, the following lines lead to correct compilation:

LMPLINK= -L. -llammps_$@ -L/path/to/atomistica/build_lammps -latomistica -L/path/to/OpenBLAS/0.3.18-GCC-11.2.0/lib/ -lgomp -lgfortran -lstdc++ -lopenblas -lmpi_mpifh

in Makefile, and

CCFLAGS =	-g -O3 -std=c++11 -I/path/to/atomistica/src/support -I/path/to/atomistica/build_lammps


LIB = -L/path/to/atomistica/build_lammps -latomistica -L/path/to/OpenBLAS/0.3.18-GCC-11.2.0/lib/ -lgomp -lgfortran -lstdc++ -lopenblas -lmpi_mpifh

in makefile.mpi.