chem-sorption-gcmc

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

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价格未确认★ 161 GitHub Stars目录更新于 · 2026年9月6日agent-skill

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

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chem-sorption-gcmc

Goal

To predict the macroscopic adsorption uptake of a gas (or gas mixture) in a porous material at a specific temperature and pressure. The skill relies on Grand Canonical Monte Carlo (GCMC) simulations where the host-guest and guest-guest interactions are calculated using a Machine Learning Interatomic Potential (MLIP: MACE, FairChem, MatGL).

Prerequisites

  • Input: A relaxed framework structure in CIF (or XYZ) format. The structure should ideally be processed by chem-sorption-relax to ensure proper supercell dimensions.
  • Conda environment: Depends on the MLIP used (e.g., fairchem-agent, mace-agent, matgl-agent).

Instructions

  1. Perform Single-Component GCMC (Optional): If you are investigating a single gas species, use run_gcmc.py.
# Env: fairchem-agent (or other MLIP-specific env)
python .agents/skills/chem-sorption-gcmc/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
  1. Perform Multi-Component GCMC (Optional): If you are simulating a gas mixture (e.g. flue gas separation 15% CO2 / 85% N2), use run_gcmc_multi.py.
# Env: fairchem-agent
python .agents/skills/chem-sorption-gcmc/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
Key Parameters
  • --cif: Path to the relaxed host framework.
  • --calculator: The backend MLIP (fairchem, mace, matgl).
  • --model-name: Name or path to the MLIP weights (e.g., uma-s-1p1.pt, MACE-MH-1).
  • --task-name: Optional, required by some models (omol for UMA and MACE-MH).
  • --steps: Number of Monte Carlo steps (minimum 50,000 recommended for equilibration).
  • --temperature-K: Sim temperature.
  • --pressure-bar (Single): Gas pressure in bar.
  • --p-total-bar (Multi): Total mixture pressure in bar.
  • --gases / --y (Multi): Species list and corresponding mole fractions in the vapor phase.

Examples

Example 1: Generating an Isotherm Point (CO2, 0.1 bar, 298K) with UMA:

# Env: fairchem-agent
python .agents/skills/chem-sorption-gcmc/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

Constraints

  • Simulation Time: GCMC with MLIPs can be computationally intensive. Use GPUs when available (--device cuda).
  • Equilibration: You MUST check the generated nmols.png and energy.png inside the output-dir to visually confirm that the number of molecules and energy have plateaued (equilibrated). If the trend is still rising/falling at the end of the simulation, you must re-run with more --steps (or restart the trajectory).
  • Restarting: You can pass --restart-traj ./out/mc.traj to continue a previous run.

Author: Artur Lyssenko Contact: GitHub @arturlyssenko12

文件元数据
name: chem-sorption-gcmc
description: Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.
category: [materials, chemistry]
查看原始文本
---
name: chem-sorption-gcmc
description: Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.
category: [materials, chemistry]
---

# chem-sorption-gcmc

## Goal

To predict the macroscopic adsorption uptake of a gas (or gas mixture) in a porous material at a specific temperature and pressure. The skill relies on Grand Canonical Monte Carlo (GCMC) simulations where the host-guest and guest-guest interactions are calculated using a Machine Learning Interatomic Potential (MLIP: MACE, FairChem, MatGL).

## Prerequisites

- **Input**: A relaxed framework structure in CIF (or XYZ) format. The structure should ideally be processed by [chem-sorption-relax](../chem-sorption-relax/SKILL.md) to ensure proper supercell dimensions.
- **Conda environment**: Depends on the MLIP used (e.g., `fairchem-agent`, `mace-agent`, `matgl-agent`).

## Instructions

1. **Perform Single-Component GCMC (Optional)**: If you are investigating a single gas species, use `run_gcmc.py`.

```bash
# Env: fairchem-agent (or other MLIP-specific env)
python .agents/skills/chem-sorption-gcmc/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
```

2. **Perform Multi-Component GCMC (Optional)**: If you are simulating a gas mixture (e.g. flue gas separation 15% CO2 / 85% N2), use `run_gcmc_multi.py`.

```bash
# Env: fairchem-agent
python .agents/skills/chem-sorption-gcmc/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
```

### Key Parameters
- `--cif`: Path to the relaxed host framework.
- `--calculator`: The backend MLIP (`fairchem`, `mace`, `matgl`).
- `--model-name`: Name or path to the MLIP weights (e.g., `uma-s-1p1.pt`, `MACE-MH-1`).
- `--task-name`: Optional, required by some models (`omol` for UMA and MACE-MH).
- `--steps`: Number of Monte Carlo steps (minimum 50,000 recommended for equilibration).
- `--temperature-K`: Sim temperature.
- `--pressure-bar` (Single): Gas pressure in bar.
- `--p-total-bar` (Multi): Total mixture pressure in bar.
- `--gases` / `--y` (Multi): Species list and corresponding mole fractions in the vapor phase.

## Examples

**Example 1: Generating an Isotherm Point (CO2, 0.1 bar, 298K) with UMA:**
```bash
# Env: fairchem-agent
python .agents/skills/chem-sorption-gcmc/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
```

## Constraints
- **Simulation Time**: GCMC with MLIPs can be computationally intensive. Use GPUs when available (`--device cuda`).
- **Equilibration**: You MUST check the generated `nmols.png` and `energy.png` inside the `output-dir` to visually confirm that the number of molecules and energy have plateaued (equilibrated). If the trend is still rising/falling at the end of the simulation, you must re-run with more `--steps` (or restart the trajectory).
- **Restarting**: You can pass `--restart-traj ./out/mc.traj` to continue a previous run.

---

**Author:** Artur Lyssenko
**Contact:** [GitHub @arturlyssenko12](https://github.com/arturlyssenko12)

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许可证: MIT

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The SKILL.md does not explain the output file formats (e.g., gcmc_results.json, multi_gcmc.json) or how to interpret the results (e.g., uptake units, selectivity).
  • The example uses only 100 Monte Carlo steps, which is far below the recommended minimum of 50,000 for real simulations; this could mislead users into thinking such short runs are sufficient.
  • The term 'BVT' is used without explanation; users unfamiliar with the ensemble may be confused.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
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仓库元数据和审核信号仅供参考。受欢迎、已发现来源、成功运行是不同的事实。

来源仓库
learningmatter-mit/AtomisticSkills
许可证
MIT
版本
1.0.0
最近 GitHub 推送
2026年9月3日
目录更新于
2026年9月6日

版本来自目录元数据,使用前请核实来源发布记录。

质量

66/100

有潜力

信任

57/100

Do not auto-install

审计

73/100

需审查

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The SKILL.md does not explain the output file formats (e.g., gcmc_results.json, multi_gcmc.json) or how to interpret the results (e.g., uptake units, selectivity).
  • The example uses only 100 Monte Carlo steps, which is far below the recommended minimum of 50,000 for real simulations; this could mislead users into thinking such short runs are sufficient.
  • The term 'BVT' is used without explanation; users unfamiliar with the ensemble may be confused.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
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  },
  "outcome_feedback": {
    "endpoint": "https://www.openagentskill.com/api/agent/outcome",
    "method": "POST",
    "requires_resolve_event_id": true,
    "event_id_source": "Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.",
    "expected_outcomes": [
      "success",
      "failed",
      "not_relevant",
      "blocked_by_risk",
      "setup_required"
    ],
    "payload_template": {
      "event_id": "<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>",
      "skill_slug": "learningmatter-mit-chem-sorption-gcmc",
      "task": "Use chem-sorption-gcmc in an agent workflow",
      "agent": "codex",
      "outcome": "success",
      "install_used": true,
      "risk_blocked": false,
      "setup_required": false,
      "task_success": true,
      "output_quality": 4,
      "error_type": null,
      "human_review_required": false,
      "workspace": "sandbox",
      "time_to_useful_ms": 120000,
      "notes": "Report the smallest successful task, setup friction, files touched, and risk notes."
    }
  },
  "endpoints": {
    "web": "https://www.openagentskill.com/skills/learningmatter-mit-chem-sorption-gcmc",
    "api": "https://www.openagentskill.com/api/agent/skills/learningmatter-mit-chem-sorption-gcmc",
    "audit": "https://www.openagentskill.com/skills/learningmatter-mit-chem-sorption-gcmc/audit",
    "eval": "https://www.openagentskill.com/api/agent/evals?slug=learningmatter-mit-chem-sorption-gcmc&task=Use%20chem-sorption-gcmc%20in%20an%20agent%20workflow&max_risk=medium",
    "resolve": "https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-sorption-gcmc%20in%20an%20agent%20workflow&agent=codex&max_risk=medium",
    "receipt": "https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-sorption-gcmc%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text",
    "install": "https://www.openagentskill.com/api/skills/learningmatter-mit-chem-sorption-gcmc/install",
    "manifest": "https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-sorption-gcmc"
  }
}

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