Chem Sorption Gcmc

What it does

Example prompts

• “Use the chem-sorption-gcmc skill to calculate gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP”
• “/chem-sorption-gcmc”

Requirements

• Python 3
• A Bash shell

Workflow steps

2 steps, taken from the first numbered list in SKILL.md.

1. 1Perform Single-Component GCMC (Optional): If you are investigating a single gas species, use run_gcmc.py.
2. 2Perform Multi-Component GCMC (Optional): If you are simulating a gas mixture (e.g. flue gas separation 15% CO2 / 85% N2), use…

What it can do on your machine

Read from SKILL.md and the folder at commit 6257444. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships 11 files in scripts/ (Python and Shell), which the agent can run.

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • github.com

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Chem Sorption Gcmc loads about 926 tokens when it runs. Until then it costs about 31 tokens; SKILL.md has 299 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~31

When it runs · the whole SKILL.md, loaded when a task matches

~926

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 299 words, ~926 tokens.

name

chem-sorption-gcmc

description

Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.

metadata.category

materials, chemistry

metadata.venv

fairchem

# (or other MLIP-specific env)
${CLAUDE_SKILL_DIR}/../../venv/run fairchem python ${CLAUDE_SKILL_DIR}/scripts/run_gcmc.py \
    --cif path/to/relaxed_supercell.cif \
    --calculator fairchem \
    --model-name uma-s-1p1 \
    --task-name omol \
    --steps 50000 \
    --temperature-K 298 \
    --pressure-bar 1.0 \
    --adsorbate CO2 \
    --output-dir ./results/single_gcmc

${CLAUDE_SKILL_DIR}/../../venv/run fairchem python ${CLAUDE_SKILL_DIR}/scripts/run_gcmc_multi.py \
    --cif path/to/relaxed_supercell.cif \
    --calculator fairchem \
    --model-name uma-s-1p1 \
    --task-name omol \
    --steps 50000 \
    --temperature-K 298 \
    --gases CO2 N2 \
    --y 0.15 0.85 \
    --p-total-bar 1.0 \
    --output-dir ./results/multi_gcmc

${CLAUDE_SKILL_DIR}/../../venv/run fairchem python ${CLAUDE_SKILL_DIR}/scripts/run_gcmc.py \
    --cif ./data/MOF-5_supercell.cif \
    --calculator fairchem \
    --model-name uma-s-1p1 \
    --task-name omol \
    --steps 50000 \
    --temperature-K 298 \
    --pressure-bar 0.1 \
    --adsorbate CO2 \
    --output-dir ./out/0.1_bar

© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 15 other files (scripts) in skills/chem-sorption-gcmc of learningmatter-mit/AtomisticSkills.

• SKILL.md
• examples/README.md
• examples/multi_gas/input_configs.yaml
• examples/single_gas/input_configs.yaml
• examples/test_gcmc.sh
• scripts/ase_mc/AtomisticSkills.code-workspace
• scripts/ase_mc/__init__.py
• scripts/ase_mc/ensembles.py
• scripts/ase_mc/logger.py
• scripts/ase_mc/mc.py
• scripts/ase_mc/moves.py
• scripts/ase_mc/moveset.py
• scripts/ase_mc/utility.py
• scripts/gcmc_common.py
• scripts/run_gcmc.py
• scripts/run_gcmc_multi.py

Open the folder on GitHubat commit 6257444