Diindeks di Registry
chem-sorption-gcmc
Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.
Ringkasan
Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.
Baca dokumentasi lengkap
Dokumentasi sumber, bukan instruksi untuk situs ini. Periksa izin sebelum menjalankan perintah.
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
- 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
- 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 (omolfor 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.pngandenergy.pnginside theoutput-dirto 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.trajto continue a previous run.
Author: Artur Lyssenko Contact: GitHub @arturlyssenko12
Metadata berkas
name: chem-sorption-gcmc description: Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP. category: [materials, chemistry]
Lihat teks asli
---
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)
Tinjau sumber
Harga dan biaya penggunaan
- Dapatkan skill
- Harga belum dikonfirmasi
- Jalankan
- Persyaratan belum dikonfirmasi. Periksa biaya agen, API, dan layanan di sumbernya.
- Lisensi
- MIT
- Harga belum dikonfirmasi
- Harga belum dikonfirmasi. Tautan sumber dan instalasi yang ada tetap tersedia.
Gratis diperoleh bukan berarti gratis dijalankan. Harga bukan penilaian keamanan. Kirim informasi harga →
Sumber skill tercatat
Jalur instruksi telah dicatat. Ini bukan uji eksekusi, jaminan keamanan, atau sertifikasi kompatibilitas.
Tinjau sebelum memasang: Hindari pemasangan otomatis
Lisensi: 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
Daftar alat adalah petunjuk metadata, bukan kompatibilitas teruji. Prompt adalah saran.
Mulai dengan tugas kecil
- 1Baca sumber dan pastikan masukan, keluaran, dependensi, serta izin.
- 2Minta rencana dari agent. Setujui pengaturan dan biaya sebelum uji terisolasi.
- 3Periksa hasil dan berkas yang berubah. Laporkan hanya yang dijalankan dan simpan revisi sumber.
Periksa dependensi, kunci API, dan biaya layanan pihak ketiga pada sumber. Repositori publik tidak berarti semua layanan gratis.
Sumber dan catatan penggunaan
Metadata dan tinjauan bersifat saran. Popularitas, penemuan sumber, dan keberhasilan eksekusi adalah fakta berbeda.
- Repositori sumber
- learningmatter-mit/AtomisticSkills
- Lisensi
- MIT
- Versi
- 1.0.0
- Push GitHub terakhir
- 3 Sep 2026
- Direktori diperbarui
- 6 Sep 2026
- Jalur instruksi
- .agents/skills/chem-sorption-gcmc/SKILL.md @ d1f7ecfda2cd
Versi dilaporkan dalam metadata direktori; periksa rilis sumber.
Kualitas
66/100
Menjanjikan
Kepercayaan
57/100
Do not auto-install
Audit
73/100
Perlu ditinjau
- 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
- Verified installs
- —
- Hasil
- —
Menyalin bukan memasang. Jumlah instalasi memerlukan laporan berhasil dan bukan jaminan kualitas menyeluruh.
Akses agent
API Registry menyediakan sinyal keputusan, kepercayaan, audit, use case, dan pemasangan tanpa mengikis UI.
Detail lainnya
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"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"
}
}Untuk kreator
Sumber listing
Diindeks Registry
Listing ini diindeks dari sumber publik dan belum ditandai resmi hingga klaim pemelihara disetujui.
- Kreator
- learningmatter-mit
- Diindeks oleh
- Indeks komunitas OpenAgentSkill
Atribusi menautkan ke repositori publik atau profil kreator. Kreator dapat mengklaim listing untuk memperbarui sinyal kepemilikan.
Klaim skill iniKlaim pemilik
Klaim listing skill ini
Listing Diindeks Registry ini dikaitkan dengan learningmatter-mit, tetapi belum ditandai resmi. Klaim untuk menambahkan sinyal pemilik terverifikasi dan membuat pembaruan peluncuran, pemasangan, serta audit berikutnya lebih tepercaya.
Kit berbagi
Kit backlink kreator
Tambahkan badge bukti ke README Anda
Tampilkan listing kanonis, sinyal kepercayaan dan audit saat ini, serta bukti Agent-Proven nyata di tempat pengembang mengevaluasi repositori.
[](https://www.openagentskill.com/skills/learningmatter-mit-chem-sorption-gcmc?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[](https://www.openagentskill.com/skills/learningmatter-mit-chem-sorption-gcmc?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[](https://www.openagentskill.com/skills/learningmatter-mit-chem-sorption-gcmc/audit)
[](https://www.openagentskill.com/skills/learningmatter-mit-chem-sorption-gcmc?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)Sinyal komunitas
Bagikan apakah skill ini bermanfaat untuk alur kerja Agent Anda. Masukan gabungan meningkatkan peringkat dari waktu ke waktu.
