From ac2da2f5c240f80ec47cd077c80933f1cae5faa8 Mon Sep 17 00:00:00 2001
From: Thang Pham <tpham@anl.gov>
Date: Tue, 26 May 2026 11:19:04 -0500
Subject: [PATCH] Add YAML-based gRASPA isotherm batch setup script

Add a Python script and YAML config for setting up gRASPA isotherm
simulations with many temperature/pressure combinations, avoiding
tedious CLI flag repetition. Supports pressure unit conversion
(bar, kPa, atm, Pa).
---
 pyproject.toml                      |  3 +-
 scripts/graspa/isotherm_config.yaml | 42 ++++++++++++++++++
 scripts/graspa/setup_isotherms.py   | 66 +++++++++++++++++++++++++++++
 3 files changed, 110 insertions(+), 1 deletion(-)
 create mode 100644 scripts/graspa/isotherm_config.yaml
 create mode 100644 scripts/graspa/setup_isotherms.py

diff --git a/pyproject.toml b/pyproject.toml
index 0455557..eacd84d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,8 @@ rdkit = ["rdkit"]
 mlip = ["mace-torch"]
 plot = ["matplotlib>=3.5"]
 pacmof2 = ["pacmof2"]
-all = ["rdkit", "mace-torch", "matplotlib>=3.5", "pacmof2"]
+graspa = ["pyyaml>=6.0"]
+all = ["rdkit", "mace-torch", "matplotlib>=3.5", "pacmof2", "pyyaml>=6.0"]
 dev = ["pytest>=7.0", "ruff>=0.4"]
 
 [project.scripts]
diff --git a/scripts/graspa/isotherm_config.yaml b/scripts/graspa/isotherm_config.yaml
new file mode 100644
index 0000000..86e86b4
--- /dev/null
+++ b/scripts/graspa/isotherm_config.yaml
@@ -0,0 +1,42 @@
+# gRASPA isotherm simulation config
+# Usage: python setup_isotherms.py isotherm_config.yaml
+
+cif_dir: ./cifs
+outdir: ./batch_results
+
+adsorbates: [CO2, N2]
+
+temperatures: [283, 293, 313, 333]
+
+pressures:
+  - 0.001
+  - 0.005
+  - 0.01
+  - 0.02
+  - 0.03
+  - 0.04
+  - 0.05
+  - 0.10
+  - 0.15
+  - 0.20
+  - 0.25
+  - 0.30
+  - 0.35
+  - 0.40
+  - 0.45
+  - 0.50
+  - 0.55
+  - 0.60
+  - 0.65
+  - 0.70
+  - 0.75
+  - 0.80
+  - 0.85
+  - 0.90
+  - 0.95
+  - 1.0
+
+pressure_unit: bar  # bar, kPa, atm, or Pa
+
+cutoff: 12.8
+cycles: 1000
diff --git a/scripts/graspa/setup_isotherms.py b/scripts/graspa/setup_isotherms.py
new file mode 100644
index 0000000..4167833
--- /dev/null
+++ b/scripts/graspa/setup_isotherms.py
@@ -0,0 +1,66 @@
+"""Set up gRASPA isotherm simulations from a YAML config file.
+
+Usage:
+    python setup_isotherms.py <config.yaml>
+    python setup_isotherms.py  # defaults to isotherm_config.yaml
+"""
+
+import sys
+from pathlib import Path
+
+import yaml
+
+from matkit.graspa import setup_batch
+
+PRESSURE_TO_PA = {
+    "pa": 1.0,
+    "bar": 1e5,
+    "kpa": 1e3,
+    "atm": 101325.0,
+}
+
+
+def main():
+    if len(sys.argv) > 1:
+        config_path = Path(sys.argv[1])
+    else:
+        config_path = Path(__file__).parent / "isotherm_config.yaml"
+
+    with open(config_path) as f:
+        cfg = yaml.safe_load(f)
+
+    pressure_unit = cfg.get("pressure_unit", "Pa").lower()
+    if pressure_unit not in PRESSURE_TO_PA:
+        raise ValueError(
+            f"Unknown pressure_unit '{cfg['pressure_unit']}'. "
+            f"Supported: {list(PRESSURE_TO_PA.keys())}"
+        )
+    factor = PRESSURE_TO_PA[pressure_unit]
+    pressures_pa = [p * factor for p in cfg["pressures"]]
+
+    adsorbates = [{"MoleculeName": name} for name in cfg["adsorbates"]]
+
+    print(f"Config: {config_path}")
+    print(f"CIF dir: {cfg['cif_dir']}")
+    print(f"Adsorbates: {cfg['adsorbates']}")
+    print(f"Temperatures: {cfg['temperatures']}")
+    print(f"Pressures: {len(pressures_pa)} points "
+          f"({cfg['pressures'][0]}-{cfg['pressures'][-1]} "
+          f"{cfg.get('pressure_unit', 'Pa')})")
+
+    manifest = setup_batch(
+        cif_dir=cfg["cif_dir"],
+        outpath=cfg["outdir"],
+        adsorbates=adsorbates,
+        temperatures=cfg["temperatures"],
+        pressures=pressures_pa,
+        cutoff=cfg.get("cutoff", 12.8),
+        n_cycle=cfg.get("cycles", 1000),
+    )
+
+    print(f"\nSet up {len(manifest)} simulations in {cfg['outdir']}")
+    print(f"Manifest: {cfg['outdir']}/simulations.jsonl")
+
+
+if __name__ == "__main__":
+    main()