MoSDeF + Engines + CP2K Installer — README

This README explains how to install, activate, and test a full MoSDeF stack with optional engines (LAMMPS, HOOMD, GROMACS) and CP2K. It also includes validation commands and troubleshooting tips.

Do not run with sudo. Install per-user into ~/miniforge3 by default. If you previously installed conda as root under /root/miniforge3, remove it or ignore it.

1) Prerequisites

Linux or macOS shell with:
- bash, curl
No existing requirements for Python or CUDA (handled by conda/mamba).
Sufficient disk space (~10–20 GB depending on engines and caches).

2) Get the installer

Save your script as install-mosdef-cp2k.sh and make it executable:

chmod +x install-mosdef-cp2k.sh

Optionally choose a local conda prefix (default is ~/miniforge3):

export CONDA_HOME="$HOME/miniforge3"

3) Quick install (CPU-only)

./install-mosdef-cp2k.sh

What it does:

Installs/updates Miniforge to $CONDA_HOME
Ensures mamba in base
Creates env mosdef-env (Python 3.11)
Installs MoSDeF stack + LAMMPS, HOOMD, GROMACS, CP2K
Ensures CP2K data and sets CP2K_DATA_DIR
Creates one-shot activator: ~/miniforge3/envs/mosdef-env/activate.sh
Runs smoke checks and prints versions

4) Optional flags

Toggle via env vars before running install-mosdef-cp2k.sh:

Engines Skip LAMMPS/HOOMD/GROMACS:

INSTALL_ENGINES=false ./install-mosdef-cp2k.sh

CUDA (toolkit only; engine GPU builds are not configured here)
```
ENABLE_CUDA=true CUDA_VERSION=12.4 ./install-mosdef-cp2k.sh
```

Conda prefix

CONDA_HOME="$HOME/miniforge3" ./install-mosdef-cp2k.sh

Don’t modify your shell startup files (skip conda init; use the activator script instead)
```
INIT_SHELL=false ./install-mosdef-cp2k.sh
```

5) Activate the environment

One-shot activator (recommended):

~/miniforge3/envs/mosdef-env/activate.sh

Or, load conda in this shell and activate:

eval "$($HOME/miniforge3/bin/conda shell.bash hook)"
conda activate mosdef-env

Persistent (new terminals):

$HOME/miniforge3/bin/conda init bash
# reopen terminal, then:
conda activate mosdef-env

6) Validate MoSDeF install

Imports (should print NumPy & ParmEd versions):

python - <<'PY'
mods = ["numpy","parmed","mbuild","foyer","gmso","unyt","signac","nglview","openmm"]
bad = []
for m in mods:
    try:
        __import__(m)
    except Exception as e:
        bad.append((m, repr(e)))
if bad:
    print("Import failures:")
    for m,e in bad: print(f" - {m}: {e}")
    raise SystemExit(1)
import numpy, parmed
print("✓ MoSDeF imports OK | NumPy", numpy.__version__, "| ParmEd", parmed.__version__)
PY

7) Validate engines

# LAMMPS
lmp -h | head -n 1

# GROMACS
gmx --version | head -n 1

# HOOMD (Python module)
python - <<'PY'
try:
    import hoomd, importlib.metadata as im
    print("HOOMD:", getattr(hoomd,"__version__", None) or im.version("hoomd"))
except Exception as e:
    print("[!] HOOMD import failed:", e)
PY

Note: HOOMD may be CPU-only; GPU builds require a separate env.

8) Validate CP2K (binary + data + runs)

8.1 Ensure a binary is present

which cp2k.psmp || true
which cp2k.popt || true
which cp2k.ssmp || true   # conda-forge commonly ships this one
which cp2k.sopt || true

# Version
cp2k.ssmp --version

8.2 Ensure data directory

The installer sets CP2K_DATA_DIR. Verify:

# Prefer .../share/cp2k/data; else .../share/cp2k
if [ -d "$CONDA_PREFIX/share/cp2k/data" ]; then
  export CP2K_DATA_DIR="$CONDA_PREFIX/share/cp2k/data"
else
  export CP2K_DATA_DIR="$CONDA_PREFIX/share/cp2k"
fi

ls -l "$CP2K_DATA_DIR"/{BASIS_MOLOPT,POTENTIAL}

8.3 Minimal ENERGY test

cat > h2o_energy.inp <<'EOF'
&GLOBAL
  PROJECT H2O-test
  RUN_TYPE ENERGY
  PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
  METHOD Quickstep
  &DFT
    BASIS_SET_FILE_NAME  BASIS_MOLOPT
    POTENTIAL_FILE_NAME  POTENTIAL
    &MGRID
      CUTOFF 100
    &END MGRID
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
  &SUBSYS
    &CELL
      ABC 10.0 10.0 10.0
    &END CELL
    &COORD
      O 0.000 0.000 0.000
      H 0.757 0.586 0.000
      H -0.757 0.586 0.000
    &END COORD
    &KIND H
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND
    &KIND O
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
  &END SUBSYS
&END FORCE_EVAL
EOF

cp2k.ssmp -i h2o_energy.inp -o h2o_energy.out
grep -n "ENERGY|" h2o_energy.out | head

8.4 Forces test (optional)

cat > h2o_force.inp <<'EOF'
&GLOBAL
  PROJECT H2O-test
  RUN_TYPE ENERGY_FORCE
  PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
  METHOD Quickstep
  &DFT
    BASIS_SET_FILE_NAME  BASIS_MOLOPT
    POTENTIAL_FILE_NAME  POTENTIAL
    &MGRID
      CUTOFF 100
    &END MGRID
    &SCF
      MAX_SCF 50
      &OT
        PRECONDITIONER FULL_SINGLE_INVERSE
        MINIMIZER DIIS
      &END OT
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
  &SUBSYS
    &CELL
      ABC 10.0 10.0 10.0
    &END CELL
    &COORD
      O 0.000 0.000 0.000
      H 0.757 0.586 0.000
      H -0.757 0.586 0.000
    &END COORD
    &KIND H
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND
    &KIND O
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
  &END SUBSYS
  &PRINT
    &FORCES ON
    &END FORCES
  &END PRINT
&END FORCE_EVAL
EOF

cp2k.ssmp -i h2o_force.inp -o h2o_force.out
grep -n "ATOMIC FORCES" h2o_force.out

If something is odd, try export OMP_NUM_THREADS=1 first.

9) CUDA sanity (optional)

If you installed the CUDA toolkit (ENABLE_CUDA=true):

python - <<'PY'
try:
    from openmm import Platform
    print([Platform.getPlatform(i).getName() for i in range(Platform.getNumPlatforms())])
except Exception as e:
    print("[!] OpenMM GPU check failed:", e)
PY

Seeing “CUDA” in the platforms requires compatible drivers + GPU. Engines (HOOMD/GROMACS/LAMMPS) GPU builds are not installed by this script.

10) Troubleshooting

“conda: command not found” (in a new shell) Either use the one-shot activator:
```
~/miniforge3/envs/mosdef-env/activate.sh
```
or initialize conda for future shells:
```
$HOME/miniforge3/bin/conda init bash
exec bash
```

Permission denied using /root/miniforge3/... You ran as root previously. Reinstall to your home:

sudo rm -rf /root/miniforge3   # optional cleanup
CONDA_HOME="$HOME/miniforge3" ./install-mosdef-cp2k.sh

CP2K aborts reading BASIS_MOLOPT/POTENTIAL Ensure data exists and CP2K_DATA_DIR is set (installer handles this; validate with):
```
echo "$CP2K_DATA_DIR"
ls -l "$CP2K_DATA_DIR"/{BASIS_MOLOPT,POTENTIAL}
```
Solver memory issues during engine installs The script retries sequentially with pins and MAMBA_NUM_THREADS=1. If it still fails, re-run with:
```
INSTALL_ENGINES=false ./install-mosdef-cp2k.sh
# later: conda activate mosdef-env && mamba install -c conda-forge lammps hoomd gromacs
```

11) Uninstall / Cleanup

# Remove the environment
eval "$($HOME/miniforge3/bin/conda shell.bash hook)"
conda env remove -n mosdef-env

# Remove Miniforge (only if you don’t need it)
rm -rf "$HOME/miniforge3"

12) Quick reference

# Install
./install-mosdef-cp2k.sh

# Activate now
~/miniforge3/envs/mosdef-env/activate.sh

# Test MoSDeF
python -c "import mbuild,foyer,gmso; print('MoSDeF ready')"

# Test engines
lmp -h | head -n 1
gmx --version | head -n 1
python -c "import hoomd, importlib.metadata as im; print('HOOMD', getattr(hoomd,'__version__',None) or im.version('hoomd'))"

# Test CP2K
cp2k.ssmp --version
echo "$CP2K_DATA_DIR"
ls -l "$CP2K_DATA_DIR"/{BASIS_MOLOPT,POTENTIAL}

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MoSDeF + Engines + CP2K Installer — README

1) Prerequisites

2) Get the installer

3) Quick install (CPU-only)

4) Optional flags

5) Activate the environment

6) Validate MoSDeF install

7) Validate engines

8) Validate CP2K (binary + data + runs)

8.1 Ensure a binary is present

8.2 Ensure data directory

8.3 Minimal ENERGY test

8.4 Forces test (optional)

9) CUDA sanity (optional)

10) Troubleshooting

11) Uninstall / Cleanup

12) Quick reference

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Name		Name	Last commit message	Last commit date
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README.md		README.md
h2o_energy.inp		h2o_energy.inp
install-mosdef-cp2k.sh		install-mosdef-cp2k.sh

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MoSDeF + Engines + CP2K Installer — README

1) Prerequisites

2) Get the installer

3) Quick install (CPU-only)

4) Optional flags

5) Activate the environment

6) Validate MoSDeF install

7) Validate engines

8) Validate CP2K (binary + data + runs)

8.1 Ensure a binary is present

8.2 Ensure data directory

8.3 Minimal ENERGY test

8.4 Forces test (optional)

9) CUDA sanity (optional)

10) Troubleshooting

11) Uninstall / Cleanup

12) Quick reference

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