mattersim

name	mattersim
description	Run MatterSim workflows for batch structure relaxation, molecular dynamics, model finetuning, and post-MD ionic conductivity analysis on crystal structure datasets..
tags	["MatterSim","relaxation","molecular dynamics","MSD","Mean Squared Displacement"]
tools	["run_bash"]
dependent_skills	[]

Script	Role
mattersim_moldyn.py	Supports a two-stage molecular dynamics workflow with an NPT stage followed by an NVT stage

Script: mattersim_moldyn.py (in the skill's scripts/ directory).

MatterSim Skill

Default format

• Use extxyz as the default input and output format.
• For batch jobs, prefer a multi-frame extxyz file as input.

Relaxation and Molecular Dynamics on local

Perform structure optimization and molecular dynamics simulations locally using MatterSim.

Batch relaxation

Use the MatterSim CLI relax subcommand.

Example:

ts=$(date +"%Y%m%d%H%M%S")
workdir="matsim/${ts}.mattersim_relax"
mkdir -p "$workdir"
cd "$workdir"
source ${MATTERGEN_ENV}/bin/activate

python -m mattersim.cli.mattersim_app relax \
  --structure-file /abs/path/to/structures.extxyz \
  --device cuda \
  --work-dir results \
  --filter EXPCELLFILTER \
  --fmax 0.01 \
  --steps 1000

Important options

• --structure-file: one or more structure files; prefer one multi-frame extxyz
• --mattersim-model: optional:["mattersim-v1.0.0-1m", "mattersim-v1.0.0-5m"], default:"mattersim-v1.0.0-1m"
• --device: cpu or cuda
• --work-dir: working directory for relaxation outputs
• --save-csv: output table for relaxation results
• --filter: optional cell filter
• --constrain-symmetry: optional enable symmetry constraints when needed
• --pressure-in-GPa: optional target pressure
• --fmax: force convergence threshold
• --steps: maximum relaxation steps，default:1000

After relaxation, extract the structures from results.csv.gz and save them as an extxyz file.

Batch molecular dynamics

Recommended workflow:

1. Create a timestamped workdir:

ts=$(date +"%Y%m%d%H%M%S")
workdir="matsim/${ts}.mattersim_batch_md"
mkdir -p "$workdir"

2. Prepare the input structures. If the input is a multi-frame extxyz, split it into single-frame structure files, create numerically indexed subdirectories under workdir, and place one extxyz file in each directory. Also determine the starting and ending indices, num_start and num_end.
3. Run mattersim moldyn once for each structure directory.

Example:

source "${MATTERGEN_ENV}/bin/activate"
for i in $(seq "$num_start" "$num_end"); do
  python mattersim_moldyn.py \
    --stru "$workdir/$i/structure.extxyz" \
    --model mattersim-v1.0.0-5M.pth \
    --temp 300 \
    --npt_steps 1000 \
    --nvt_steps 100000 \
    --timestep 2
done

Important options

• --stru: a single structure file for each MD run
• --model: a real model path
• --temp: simulation temperature in Kelvin
• --npt_steps: number of NPT steps
• --nvt_steps: number of NVT steps
• --timestep: MD timestep in fs, default 2

Generated files

• CONTCAR_min.vasp: minimized structure in VASP format
• log.npt, md_npt.xyz: NPT log and trajectory frames
• log.nvt, md_nvt.xyz, <temp>_nvt.traj: NVT log and trajectory outputs

Notes

• Molecular dynamics should not be run on multiple structures in a single call.
• If the input is a multi-frame extxyz, split it into multiple single-structure extxyz files and run them one by one.
• Use separate output directories and trajectory files for different structures.

Relaxation and Molecular Dynamics on Bohrium

Perform structure optimization and molecular dynamics simulations on Bohrium platform using MatterSim.

When submitting MatterSim jobs to Bohrium through the bohrium skill, the image and machine required by MatterSim are obtained from the environment variables BOHRIUM_MAT_IMAGE and BOHRIUM_MAT_MACHINE.

Batch relaxation

ts=$(date +"%Y%m%d%H%M%S")
workdir="matsim/${ts}.mattersim_relax"
mkdir -p "$workdir"
cd "$workdir"

Then copy the structure to be relaxed into the workdir.

In submission.json:

• set command to a generation command such as:

/opt/mattergen/.venv/bin/python -m mattersim.cli.mattersim_app relax \
  --structure-file structures.extxyz \
  --device cuda \
  --work-dir results \
  --filter EXPCELLFILTER \
  --fmax 0.01 \
  --steps 2000

• forward_files should include the structures , such as generated.extxyz.
• backward_files can be results.

After relaxation, extract the structures from results.csv.gz and save them as an extxyz file.

Batch molecular dynamics

1. Create a timestamped workdir:

ts=$(date +"%Y%m%d%H%M%S")
workdir="matsim/${ts}.mattersim_batch_md"
mkdir -p "$workdir"
cd "$workdir"

2. Prepare the input structures. If the input is a multi-frame extxyz, split it into single-frame structure files, create numerically indexed subdirectories under workdir, and place one extxyz file in each directory. Also determine the starting and ending indices, num_start and num_end.

3. Copy the model file into workdir. The model path can be obtained from the mattersim_model environment variable. Also copy the mattersim_moldyn.py into workdir.

4. Example of submission.json:

• Example of submission.json can refer to bohrium-moldyn.md.

Finetune MatterSim

Finetune the pre-trained MatterSim model on a custom dataset。

Recommended workflow:

1. Create a timestamped workdir:

ts=$(date +"%Y%m%d%H%M%S")
workdir="matsim/${ts}.mattersim_finetune"
mkdir -p "$workdir"

2. Prepare the training and validation datasets in extxyz format, and copy them into workdir.

Also copy the model file into workdir. The model path can be obtained from the mattersim_model environment variable.

3. Example of submission.json:

• Example of submission.json can refer to finetune.md.

Compute Ionic Conductivity

After molecular dynamics, estimate the ionic conductivity of the target mobile ion species such as Li or other ions from the MD trajectory.

• For detailed procedures and code examples for conductivity calculation, refer to conductivity.md.

What to report

Report at minimum:

• for batch relaxation: the number of input structures, optimizer, filter, fmax, steps, and the absolute path to the relaxation work directory and CSV results
• for batch MD: the number of input structures, whether the input was split before running, temperature, timestep, number of MD steps, ensemble, and the absolute path to each MD work directory, trajectory file
• for ionic conductivity analysis: the target ion species, temperature, the trajectory used, the selected trajectory frame window, time_step_fs, step_skip, the estimated diffusivity and conductivity with their standard deviations and units, and the absolute paths to the exported MSD data and plot files