From bcf9d98932abdbfbbcecf4a79e3bc649f9bb0569 Mon Sep 17 00:00:00 2001
From: robrobo <robin.horstmann@gmx.net>
Date: Fri, 26 Jun 2026 18:28:34 +0200
Subject: [PATCH] small fixes on numbers to make it run for now

---
 polyamorphism_optimization/annealing.py  | 1 +
 polyamorphism_optimization/create_sim.py | 9 +++++----
 polyamorphism_optimization/emin.py       | 1 +
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/polyamorphism_optimization/annealing.py b/polyamorphism_optimization/annealing.py
index fb03a70..87c14b6 100755
--- a/polyamorphism_optimization/annealing.py
+++ b/polyamorphism_optimization/annealing.py
@@ -33,6 +33,7 @@ def main(root_dir: Path):
     shutil.copy(root_dir / "run.sh", sim_dir / "run.sh")
 
     # Generate annealing section
+    # TODO go higher than 1000
     annealing = generate_annealing(dT=50, Tmin=50, Tmax=1000, start_time=50, end_time=2000)
     # -d 20 -l 750 -u 2100 -s 50 -e 10000 -c
     with (sim_dir / "mdp_parameters.mdp").open("a") as f:
diff --git a/polyamorphism_optimization/create_sim.py b/polyamorphism_optimization/create_sim.py
index f35c1e7..b88627c 100755
--- a/polyamorphism_optimization/create_sim.py
+++ b/polyamorphism_optimization/create_sim.py
@@ -15,7 +15,7 @@ def compute_dependent(params):
 
     # Relative sigma and epsilon
     params["sigma_A"] = params["sigma"]
-    params["epsilon_A"] = params["sigma"]
+    params["epsilon_A"] = params["epsilon"]
     sigma_A = params["sigma"]
     epsilon_A = params["epsilon"]
     params["sigma_B"] = round(params["sigma_rel"] * sigma_A, 5)
@@ -28,7 +28,7 @@ def compute_dependent(params):
         # 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
+        m_atom = m_total / 2 * 5  # TODO remove the 5 again
         params["mass"] = round(m_atom, 5)
 
     params["d_BB"] = round(2 * params["d_AB"] * math.sin(math.radians(params["angle_ABA"]) / 2), 5)
@@ -84,8 +84,8 @@ def main():
     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)
+    parser.add_argument("--sigma_rel", type=float, default=0.5)
+    parser.add_argument("--epsilon_rel", type=float, default=0.5)
 
     # Mass (optional, will be calculated if omitted)
     parser.add_argument("--mass", type=float, default=None)
@@ -139,6 +139,7 @@ def main():
     print(f"Parameter file written to {config_path}")
 
     shutil.copy(files("polyamorphism_optimization.templates") / "run.sh", dir_name / "run.sh")
+    shutil.copy(files("polyamorphism_optimization.templates") / "gro_atomistic.gro", dir_name / "gro_start.gro")
 
 
 if __name__ == "__main__":
diff --git a/polyamorphism_optimization/emin.py b/polyamorphism_optimization/emin.py
index fce5051..fa73a46 100755
--- a/polyamorphism_optimization/emin.py
+++ b/polyamorphism_optimization/emin.py
@@ -30,6 +30,7 @@ def main(root_dir: Path):
 
     # Copy run.sh
     shutil.copy(root_dir / "run.sh", sim_dir / "run.sh")
+    shutil.copy(root_dir / "gro_start.gro", sim_dir / "gro_start.gro")
 
     # Add finer emstep
     with (sim_dir / "mdp_parameters.mdp").open("a") as f: