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. Two build environments are supported:

Harvard FASRC-style cluster (CMake, GCC ≥ 14, Open MPI modules)
macOS (Conda environment, CMake, Open MPI)

Note

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

Prerequisites (Harvard cluster)

Start an interactive job:
```
salloc -p test --mem 4G -t 0-3:00
```

Load build tools:

module avail    # confirm available module names
module load cmake/3.31.6-fasrc01
module load gcc/14.2.0-fasrc01
module load openmpi/5.0.5-fasrc01

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

Add the patched fix (create the directory if absent):

mkdir -p src/MC
cp /path/to/fix_bond_create_random.cpp src/MC/
cp /path/to/fix_bond_create_random.h   src/MC/

Configure & build (Harvard cluster)

Create a build directory:
```
mkdir build && cd build
```
Configure with CMake (MPI build):
```
cmake ../cmake -DBUILD_MPI=on
```

Enable required packages (old package names):

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

Compile:
```
cmake --build . -j$(nproc)
```
The resulting executable will be in:
```
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]

Prerequisites (macOS)

Install Conda and create a new environment:

# Assumes Miniconda or Anaconda is already installed
conda create -n lammps_env
conda activate lammps_env

Install compilers and tools via Conda:

conda install -c conda-forge cxx-compiler
conda install -c conda-forge cmake=3.31.6
conda install -c conda-forge openmpi

Configure & build (macOS)

Download and unpack LAMMPS 3 Mar 2020 (same as step 3 above):

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

Add the patched fix (same as step 4 above).
Create a build directory:
```
mkdir build && cd build
```
Configure with CMake (specify C++14 standard):
```
cmake ../cmake -DCMAKE_CXX_STANDARD=14
```

Enable required packages:

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

Compile (same as in step 8 above):
```
cmake --build . -j$(sysctl -n hw.ncpu)
```
The executable will be in:
```
build/lmp
```

Optional: Python wrapper

If you plan to control LAMMPS from Jupyter or NumPy, install the Cython wrapper:

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 your maxbond setting in the bond/create/random command or raise extra/special/per/atom in the read_data section.