Installation

This guide walks you through compiling LAMMPS 3 Mar 2020 with the custom bond/create/random fix needed for the generate_InitCond polymer-network examples. The steps assume access to an FASRC‐style cluster, but they also work on any system that provides recent CMake, GCC ≥ 14, and Open MPI.

Note

bond/create/random is not part of vanilla 3 Mar 2020. We patch it in manually from the pdebuyl/lammps *fbc_random* branch.

Prerequisites

  1. Start an interactive job

    salloc -p test --mem 4G -t 0-3:00

  2. Load build tools

    module avail  # just to confirm the names below
module load cmake/3.31.6-fasrc01
module load gcc/14.2.0-fasrc01
module load openmpi/5.0.5-fasrc01

Source code

  1. Download and unpack LAMMPS 3 Mar 2020

    wget https://download.lammps.org/tars/lammps-3Mar2020.tar.gz
tar -xf lammps-3Mar2020.tar.gz
cd lammps-3Mar2020

  2. Add the patched fix

    Copy the two files below into src/MC (create the folder if absent):

    cp /path/to/fix_bond_create_random.cpp src/MC/
cp /path/to/fix_bond_create_random.h   src/MC/

    (They come from the fbc_random branch linked above.)

Configure & build

  1. Create a build directory

    mkdir build && cd build

  2. Configure with CMake (MPI build):

    cmake ../cmake -DBUILD_MPI=on

  3. Enable required packages

    The 2020 release still uses old package names:

    cmake -DPKG_MC=on \
      -DPKG_MOLECULE=on \
      -DPKG_USER-MISC=on \
      -DPKG_USER-COLVARS=on .

  4. Compile

    cmake --build . -j$(nproc)

    The resulting executable is:

    lammps-3Mar2020/build/lmp

Sanity check

Verify that the new fix is available:

./lmp -h | grep bond/create/random

Expected output:

bond/create/random       Create bonds (random partner selection)  [MC]

If nothing appears, the patch was not picked up—revisit Step 4 or ensure -DPKG_MC=on was passed to CMake.

Optional: Python wrapper

If you plan to control LAMMPS from Jupyter/NumPy:

pip install --user lammps-cython

Troubleshooting

  • “Package MC is not enabled” Re-run CMake with -DPKG_MC=on and rebuild.

  • “New bond exceeded bonds per atom …” Increase maxbond in your bond/create/random command or raise extra/special/per/atom in the read_data section.

With LAMMPS successfully built you can run the generate_InitCond pipeline and companion analysis notebooks without further modification.