mattergen-generation

name	mattergen-generation
description	Generate inorganic crystal structures with MatterGen, supporting unconditional sampling, property-conditioned generation, and sampling from custom trained or finetuned checkpoints.
tags	["MatterGen","crystal generation","inverse design"]
tools	["run_bash"]
dependent_skills	[]

MatterGen Skill

Use this skill to generate inorganic crystal structures with MatterGen through the official CLI. Prefer direct shell commands.

Available Pre-trained Checkpoints

Common upstream checkpoint names include:

• mattergen_base
• mp_20_base
• chemical_system with --properties-to-condition-on "{'chemical_system': 'Li-O'}"
• space_group with --properties-to-condition-on "{'space_group': 62}"
• dft_mag_density with --properties-to-condition-on "{'dft_mag_density': 0.5}"
• dft_band_gap with --properties-to-condition-on "{'dft_band_gap': 1.5}"
• ml_bulk_modulus with --properties-to-condition-on "{'ml_bulk_modulus': 120.0}"
• dft_mag_density_hhi_score with --properties-to-condition-on "{'dft_mag_density': 0.5, 'hhi_score': 2000.0}"
• chemical_system_energy_above_hull with --properties-to-condition-on "{'chemical_system': 'Li-O', 'energy_above_hull': 0.05}"

Generation on local

Invocation note:

• For local execution, it is fine to use an explicit environment-prefixed path such as "${MATTERGEN_ENV}/bin/mattergen-generate" when you need to pin the executable.
• For remote submission through the bohrium skill, use the CLI name directly in the task command, such as mattergen-generate, mattergen-evaluate, mattergen-finetune, or mattergen-train. Do not prepend ${MATTERGEN_ENV}/bin/ or any local environment path, because the command should resolve inside the remote runtime environment.

Parameter rule:

• If --pretrained-name mattergen_base is used, --properties-to-condition-on is optional and generation can be unconditional.
• If any other pre-trained checkpoint is used, --properties-to-condition-on must be provided and should match the property or properties expected by that checkpoint.
• If you want to sample from a model trained or finetuned by yourself, replace --pretrained-name ... with --model_path /abs/path/to/model_dir, following the official README.

Unconditional generation

ts=$(date +"%Y%m%d%H%M%S")
outdir="mattergen/${ts}.mattergen_generate"
"${MATTERGEN_ENV}/bin/mattergen-generate" "$outdir" \
  --pretrained-name mattergen_base \
  --batch_size=16 \
  --num_batches=1

Property or Multi-property conditioned generation

ts=$(date +"%Y%m%d%H%M%S")
outdir="/tmp/mattergen/${ts}.mattergen_generate"
"${MATTERGEN_ENV}/bin/mattergen-generate" "$outdir" \
  --pretrained-name chemical_system_energy_above_hull \
  --batch_size=16 \
  --num_batches=1 \
  --properties_to_condition_on="{'energy_above_hull': 0.05, 'chemical_system': 'Li-O'}" \
  --diffusion_guidance_factor=2.0

Generation from a local trained or finetuned model

Use --model_path when sampling from a model you trained or finetuned yourself.

Example for property-conditioned generation:

ts=$(date +"%Y%m%d%H%M%S")
outdir="/tmp/mattergen/${ts}.mattergen_generate"
"${MATTERGEN_ENV}/bin/mattergen-generate" "$outdir" \
  --model_path /abs/path/to/model_dir \
  --batch_size=16 \
  --num_batches=1 \
  --properties_to_condition_on="{'dft_band_gap': 1.5}" \
  --diffusion_guidance_factor=2.0

Report at minimum:

• The generated extxyz path
• The exact output directory

Generation on Bohrium

When submitting MatterGen jobs to Bohrium through the bohrium skill, Bohrium-specific submission settings, including authentication, project, image, and machine type, can be read from environment variables such as BOHRIUM_MAT_IMAGE and BOHRIUM_MAT_MACHINE.

• When using Bohrium, forward_files should include the pretrained model directory. The local pretrained model path can be obtained from the environment variable mattergen_model, with one folder per pretrained model name, such as mattergen_base. Users can also specify the model path.
• backward_files should include the generated result path so outputs are retrieved, for example the generation output directory.

Prepare a writable local job directory first:

ts=$(date +"%Y%m%d%H%M%S")
outdir="matg/${ts}.mattergen_generate"
mkdir -p "$outdir"
cd "$outdir"

Then copy the pretrained MatterGen model directory into "$outdir".

In submission.json:

• set forward_files to the model directory name inside "$outdir", for example mattergen_base
• set backward_files to the generation output directory, for example results
• set command to a generation command such as:

mattergen-generate results/ \
  --model_path=model \
  --batch_size=16 \
  --num_batches=1 \
  --properties_to_condition_on="{'dft_band_gap': 1.5}" \
  --diffusion_guidance_factor=2.0

--model_path must point to the actual model location available inside the submitted job, so after copying the checkpoint into "$outdir" it should usually be a relative path such as mattergen_base.

Expected Outputs

When running generation on Bohrium, make sure backward_files includes the generated result directory from the command line, for example the timestamped output directory created as ${outdir}.