initial commit

create_sim.py

@@ -0,0 +1,139 @@
+#!/usr/bin/python3.12
+import argparse
+import configparser
+import math
+import os
+
+def compute_dependent(params):
+    model = params["model"]
+
+    # Charge neutrality
+    params["charge_B"] = round(params["charge"]/2, 5)
+    params["charge_A"] = -2 * params["charge_B"]
+
+    # Relative sigma and epsilon
+    params["sigma_A"] = params["sigma"]
+    params["epsilon_A"] = params["sigma"]
+    sigma_A = params["sigma"]
+    epsilon_A = params["epsilon"]
+    params["sigma_B"] = round(params["sigma_rel"] * sigma_A, 5)
+    params["epsilon_B"] = round(params["epsilon_rel"] * epsilon_A, 5)
+    params["d_AB"] = round(params["r_AB"] * sigma_A, 5)
+    params["d_AM"] = round(params["r_AM"] * sigma_A, 5)
+
+    # Mass: either specified or computed to give τ ≈ 0.1
+    if params["mass"] is None:
+        # Let total mass m = 2 * m_A, solve: τ = σ * sqrt(m/ε) ≈ 0.1
+        tau_target = 0.05 * 10
+        m_total = (tau_target / sigma_A)**2 * epsilon_A
+        m_atom = m_total / 2
+        params["mass"] = round(m_atom, 5)
+
+
+    params["d_BB"] = round(2 * params["d_AB"] * math.sin(math.radians(params["angle_ABA"]) / 2), 5)
+    params["dummy_ab"] = round(params["d_AM"] / (2 * math.cos(math.radians(params["angle_ABA"]) / 2)), 5)
+
+    return params
+    
+def clean_params(params):
+    if params["model"] != "4point":
+        for k in ["r_AM", "d_AM", "d_BB", "dummy_ab"]:
+            params.pop(k)
+    if params["model"] != "3point" and params["model"] != "4point":
+        for k in ["r_AB", "d_AB", "angle_ABA"]:
+            params.pop(k)
+    return params
+    
+def format_directory_name(params):
+    """Generate a short directory name from active parameters."""
+    keys_order = [
+        ("sigma", "s"),
+        ("epsilon", "e"),
+        ("charge", "q"),
+        ("sigma_rel", "sr"),
+        ("epsilon_rel", "er"),
+        ("r_AB", "d"),
+        ("angle_ABA", "a"),
+        ("r_AM", "m"),
+    ]
+
+    parts = [params["model"]]
+    parts.append(f"P{params['pressure']}")
+
+    for key, prefix in keys_order:
+        if key in params:
+            val = params[key]
+            parts.append(f"{prefix}{val:.5f}".rstrip("0").rstrip("."))
+
+    parts.append(f"v{params['version']}")
+    return "_".join(parts)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Generate directory and parameter file for A-B molecular systems.")
+    parser.add_argument("--version", type=int, default=1, help="Version identifier for parameter sweep")
+    parser.add_argument("--model", choices=["atomistic", "3point", "4point"], default='atomistic')
+    parser.add_argument("--pressure", type=float, default=1.0)
+
+
+    # Independent parameters
+    parser.add_argument("--sigma", type=float, default=0.3)
+    parser.add_argument("--epsilon", type=float, default=0.8)
+    parser.add_argument("--q", type=float, default=1.0)
+
+    # Relative parameters
+    parser.add_argument("--sigma_rel", type=float, default=0.1)
+    parser.add_argument("--epsilon_rel", type=float, default=0.1)
+
+    # Mass (optional, will be calculated if omitted)
+    parser.add_argument("--mass", type=float, default=None)
+
+    # Geometry for bonded/virtual_site
+    parser.add_argument("--r_AB", type=float, default=0.33334)
+    parser.add_argument("--angle_ABA", type=float, default=109.5) # 104.52
+    parser.add_argument("--r_AM", type=float, default=0.4)
+
+    # Output
+    parser.add_argument("--output", type=str, default="params.ini")
+
+    args = parser.parse_args()
+
+    params = {
+        "version": args.version,
+        "model": args.model,
+        "nmol": 1000,
+        "pressure": args.pressure,
+        "sigma": args.sigma,
+        "sigma_rel": args.sigma_rel,
+        "epsilon": args.epsilon,
+        "epsilon_rel": args.epsilon_rel,
+        "charge": args.q,
+        "mass": args.mass,
+        "r_AB": args.r_AB,
+        "angle_ABA": args.angle_ABA,
+        "r_AM": args.r_AM,
+    }
+
+
+    # Compute dependent values
+    params = compute_dependent(params)
+    params = clean_params(params)
+    
+    dir_name = format_directory_name(params)
+    if os.path.exists(dir_name):
+        print(f"Directory {dir_name} already exists. Aborting.")
+        return
+    os.makedirs(dir_name)
+
+    # Save to file
+    config_path = os.path.join(dir_name, args.output)
+    with open(config_path, "w") as f:
+        config = configparser.ConfigParser()
+        config["params"] = params
+        config.write(f)
+
+    print(f"Parameter file written to {config_path}")
+
+if __name__ == "__main__":
+    main()
+