Indexado en Registry
chem-sorption-relax
Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.
Resumen
Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.
Leer documentación completa
Documentación de origen, no instrucciones para este sitio. Revisa los permisos antes de ejecutar comandos.
chem-sorption-relax
Goal
To process porous frameworks (e.g., MOFs, COFs) for downstream molecular sorption calculations. It checks if the unit cell's interplanar distances are large enough (usually ≥ 12 Å for typical gases) to avoid self-interaction of gas molecules across periodic boundaries. If not, it builds an appropriate supercell. Finally, it uses a standard Machine Learning Interatomic Potential (MLIP) workflow to relax the structure.
Prerequisites
- Input: A framework structure in CIF (or XYZ) format.
- MLIP MCP Tool: A relaxation tool such as
mcp_fairchem_relax_structure,mcp_mace_relax_structure, ormcp_matgl_relax_structure. - Conda environment:
base-agentfor the supercell builder logic, followed by the specific environment for the chosen MLIP (e.g.,fairchem-agent).
Instructions
- Build Supercell (if necessary): Determine if the input framework needs to be expanded. Use the provided utility to read the input CIF, check interplanar distances, build a supercell if they are below the threshold, and save the result.
# Env: base-agent
python .agents/skills/chem-sorption-relax/scripts/build_supercell.py \
--structure path/to/framework.cif \
--min-plane-dist 12.0 \
--output-cif ./out/framework_supercell.cif
[!TIP] If the script output indicates a
1x1x1supercell was created (i.e. no expansion needed), you can just use your original CIF or the output CIF, as they will be identical.
- Relax the Framework: Relax the output structure using the MCP server environment. Ensure that the correct MLIP is loaded first.
# Env: fairchem-agent (via MCP server)
mcp_fairchem_load_model(
model_name="uma-s-1p2",
device="auto"
)
mcp_fairchem_relax_structure(
structure_data="./out/framework_supercell.cif",
fmax=0.05,
steps=500,
optimizer="LBFGS",
relax_cell=True,
output_dir="./out/relaxed_framework"
)
relax_structure.py Parameters
--structure: Path to input CIF or XYZ.--name: Identifier used in output filenames.--calculator: Backend MLIP (fairchem,mace,matgl).--model-name: Named model (e.g.uma-s-1p2) or full path to checkpoint.--task-name: Multi-task head (omol,omat,odac,oc20,omc).--optimizer:LBFGS(default) orFIRE.--fmax: Force convergence threshold in eV/Å (default: 0.05).--steps: Maximum optimizer steps (default: 500).--relax-cell: Relax unit cell (default: True). Use--fixed-cellto fix cell.--output-dir: Directory to save<name>.relaxed.cifandrelax_results.json.
- Proceed to downstream tasks:
The relaxed CIF file (e.g.
./out/relaxed_framework/<name>.relaxed.cif) from step 2 is now ready for use in chem-sorption-widom and chem-sorption-gcmc.
Examples
Full workflow:
- Build supercell:
# Env: base-agent
python .agents/skills/chem-sorption-relax/scripts/build_supercell.py \
--structure my_cof.cif \
--min-plane-dist 12.0 \
--output-cif ./results/COF-1_supercell.cif
- Relax with UMA-S-1p2 via MCP Tool:
mcp_fairchem_load_model(
model_name="uma-s-1p2",
device="auto"
)
mcp_fairchem_relax_structure(
structure_data="./results/COF-1_supercell.cif",
fmax=0.05,
steps=500,
optimizer="LBFGS",
output_dir="./results/relaxed"
)
Constraints
- Input Structure: The initial framework should be somewhat reasonable; highly distorted structures might fail during relaxation.
- Minimum Distance: The
--min-plane-distshould be at least 2 × (cut-off radius) of the probe gas interaction length (typically 12 Å for CO2 or N2).
Authors: Artur Lyssenko, Sauradeep Majumdar Contact: GitHub @arturlyssenko12, GitHub @sauradeep93
Metadatos del archivo
name: chem-sorption-relax description: Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools. category: [materials, chemistry]
Ver texto original
---
name: chem-sorption-relax
description: Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.
category: [materials, chemistry]
---
# chem-sorption-relax
## Goal
To process porous frameworks (e.g., MOFs, COFs) for downstream molecular sorption calculations. It checks if the unit cell's interplanar distances are large enough (usually ≥ 12 Å for typical gases) to avoid self-interaction of gas molecules across periodic boundaries. If not, it builds an appropriate supercell. Finally, it uses a standard Machine Learning Interatomic Potential (MLIP) workflow to relax the structure.
## Prerequisites
- **Input**: A framework structure in CIF (or XYZ) format.
- **MLIP MCP Tool**: A relaxation tool such as `mcp_fairchem_relax_structure`, `mcp_mace_relax_structure`, or `mcp_matgl_relax_structure`.
- **Conda environment**: `base-agent` for the supercell builder logic, followed by the specific environment for the chosen MLIP (e.g., `fairchem-agent`).
## Instructions
1. **Build Supercell (if necessary)**: Determine if the input framework needs to be expanded. Use the provided utility to read the input CIF, check interplanar distances, build a supercell if they are below the threshold, and save the result.
```bash
# Env: base-agent
python .agents/skills/chem-sorption-relax/scripts/build_supercell.py \
--structure path/to/framework.cif \
--min-plane-dist 12.0 \
--output-cif ./out/framework_supercell.cif
```
> [!TIP]
> If the script output indicates a `1x1x1` supercell was created (i.e. no expansion needed), you can just use your original CIF or the output CIF, as they will be identical.
2. **Relax the Framework**: Relax the output structure using the MCP server environment. Ensure that the correct MLIP is loaded first.
```python
# Env: fairchem-agent (via MCP server)
mcp_fairchem_load_model(
model_name="uma-s-1p2",
device="auto"
)
mcp_fairchem_relax_structure(
structure_data="./out/framework_supercell.cif",
fmax=0.05,
steps=500,
optimizer="LBFGS",
relax_cell=True,
output_dir="./out/relaxed_framework"
)
```
### relax_structure.py Parameters
- `--structure`: Path to input CIF or XYZ.
- `--name`: Identifier used in output filenames.
- `--calculator`: Backend MLIP (`fairchem`, `mace`, `matgl`).
- `--model-name`: Named model (e.g. `uma-s-1p2`) or full path to checkpoint.
- `--task-name`: Multi-task head (`omol`, `omat`, `odac`, `oc20`, `omc`).
- `--optimizer`: `LBFGS` (default) or `FIRE`.
- `--fmax`: Force convergence threshold in eV/Å (default: 0.05).
- `--steps`: Maximum optimizer steps (default: 500).
- `--relax-cell`: Relax unit cell (default: True). Use `--fixed-cell` to fix cell.
- `--output-dir`: Directory to save `<name>.relaxed.cif` and `relax_results.json`.
3. **Proceed to downstream tasks**:
The relaxed CIF file (e.g. `./out/relaxed_framework/<name>.relaxed.cif`) from step 2 is now ready for use in [chem-sorption-widom](../chem-sorption-widom/SKILL.md) and [chem-sorption-gcmc](../chem-sorption-gcmc/SKILL.md).
## Examples
**Full workflow:**
1. Build supercell:
```bash
# Env: base-agent
python .agents/skills/chem-sorption-relax/scripts/build_supercell.py \
--structure my_cof.cif \
--min-plane-dist 12.0 \
--output-cif ./results/COF-1_supercell.cif
```
2. Relax with UMA-S-1p2 via MCP Tool:
```python
mcp_fairchem_load_model(
model_name="uma-s-1p2",
device="auto"
)
mcp_fairchem_relax_structure(
structure_data="./results/COF-1_supercell.cif",
fmax=0.05,
steps=500,
optimizer="LBFGS",
output_dir="./results/relaxed"
)
```
## Constraints
- **Input Structure**: The initial framework should be somewhat reasonable; highly distorted structures might fail during relaxation.
- **Minimum Distance**: The `--min-plane-dist` should be at least 2 × (cut-off radius) of the probe gas interaction length (typically 12 Å for CO2 or N2).
---
**Authors:** Artur Lyssenko, Sauradeep Majumdar
**Contact:** [GitHub @arturlyssenko12](https://github.com/arturlyssenko12), [GitHub @sauradeep93](https://github.com/sauradeep93)
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- Licencia
- MIT
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Revisar antes de instalar: Evitar instalación automática
Licencia: MIT
- Dependency or permission surface needs review
- Permission surface may require sandboxing
- 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
Las herramientas son indicios de metadatos, no compatibilidad probada. Los prompts son sugerencias.
Empieza con una tarea pequeña
- 1Lee la fuente y confirma entradas, resultados, dependencias y permisos.
- 2Pide un plan al agente. Aprueba la configuración y los costes antes de probar en un entorno aislado.
- 3Comprueba resultados y archivos modificados. Informa solo de lo ejecutado y conserva la revisión de la fuente.
Consulta dependencias, claves API y costes externos en la fuente. Un repositorio público no implica servicios gratuitos.
Fuente y notas de uso
Los metadatos y revisiones son orientativos. Popularidad, descubrimiento y ejecución correcta son hechos distintos.
- Repositorio fuente
- learningmatter-mit/AtomisticSkills
- Licencia
- MIT
- Versión
- 1.0.0
- Último push de GitHub
- 3 sept 2026
- Registro actualizado
- 6 sept 2026
- Ruta de instrucciones
- .agents/skills/chem-sorption-relax/SKILL.md @ d1f7ecfda2cd
Versión declarada en el registro; consulta las versiones de la fuente.
Calidad
66/100
Prometedor
Confianza
65/100
Solo sandbox
Auditoría
76/100
Requiere revisión
- Dependency or permission surface needs review
- Permission surface may require sandboxing
- 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
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Más detalles
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}Para el creador
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Esta ficha Indexado por Registry se atribuye a learningmatter-mit, pero aún no está marcada como oficial. Reclámala para añadir una señal de propietario verificado y hacer más fiables futuras actualizaciones de lanzamiento, instalación y auditoría.
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Comparte si este skill resulta útil para tu flujo de Agent. Los comentarios agregados mejoran la clasificación con el tiempo.
