Getting Started

Obtaining the code

LLNL Employees:

Please see the special Bitbucket instructions

GitHub Users:

Please see the special Github instructions

Compiling and running the code

As described above, the chimes_calculator comprises library tools for evaluating ChIMES interactions. Further information about the model architecture can be found in ChIMES Calculator. chimesFF.h and chimesFF.cpp are the source files that implement the core logic of calculating ChIMES interactions given the cluster of atoms. When the class defined therein is instantiated, it read in a ChIMES parameter file. It then can be used to evaluate individual terms in the many-body cluster expansion that defines the ChIMES potential. Specifically, it contains functions to compute energy, stress tensor, and per-atom forces for an individual 2-, 3- or 4-body cluster of atoms, given their coordinates.

For most applications, chimesFF should be integrated into a simulation code that can take a full system configuration, extract all n-body clusters while respecting periodic boundary conditions, and feed them into chimesFF. An example to do this is provided in ChIMES Calculator Serial Interface, which demonstrates how to use the chimes_calculator for an overall system evaluation. We also provide an implementation of chimesFF as a pair_style in lammps in the The ChIMES Calculator with LAMMPS page.

These examples can be compiled by navigating to a given example subdirectory (e.g. chimesFF/examples/cpp/) and typing make.

You can compile and install the entire software suite in different computing environments. All require C, C++ and Fortran compilers:

  • Standard Installation (Local Machine or Basic Environment)

    • If your environment is correctly configured, you can simply execute ./install.sh in the outer most directory.

  • Installation on an HPC cluster

    • You need to load pre-configured module files first. Module files are already configured for a handful of HPC in /modfiles/ ; verify if yours is listed. If it is (e.g., LLNL-LC.mod), execute export hosttype=LLNL-LC; ./install.sh to install. Otherwise, load the appropriate modules by hand before running the install script.

  • CMake-Based Installation

    • You can execute the appropriate CMake commands by simply running ./install.sh from the base chimes_calculator directory. If this option is used, a list of generated executables/library files and their respective install locations can be found in the generated build/install_manifest.txt file.

Note

Consider submitting module files and corresponding install.sh changes as a PR, for your HPC!

Sample ChIMES parameter and input files are provided in the serial_interface/tests/force_fields and serial_interface/tests/configurations directories, allowing compiled executables to be tested via, e.g.:

serial_interface/examples/cpp/chimescalc \
serial_interface/tests/force_fields/published_params.liqC.2b.cubic.txt \
serial_interface/tests/configurations/liqC.2.5gcc_6000K.OUTCAR_#000.xyz | tee my_test.log

Compiling the ChIMES Calculator with LAMMPS

We implemented the CHIMES in the LAMMPS and detailed information regarding Compiling and running can be found in The ChIMES Calculator with LAMMPS.

For additional details on using, integrating, compiling, and contributing, see: