added setup and toml file; first preliminary script; moved templates

polyamorphism_optimization/setup_sim.py

@@ -0,0 +1,110 @@
+#!/usr/bin/env python3
+import argparse
+import os
+import subprocess
+from pathlib import Path
+
+# --- Template definitions ---
+MDP_PARAMETERS = """\
+integrator               =  INTEGRATOR
+dt                       = 0.001
+nsteps                   =  NSTEPS
+nstcomm                  = 10
+nstlog                   =  NLOG
+nstcalcenergy            = 10
+nstenergy                =  NENERGY
+nstxout-compressed       =  NSTXOUT
+compressed-x-precision   = 1000
+energygrps               = system
+rlist                    = 1.2
+nstlist                  = 10
+coulombtype              = pme
+rcoulomb                 = 1.2
+coulomb-modifier         = potential-shift-verlet
+vdwtype                  = pme
+rvdw                     = 1.2
+vdw-modifier             = potential-shift-verlet
+fourierspacing           = 0.144
+tcoupl                   = v-rescale
+tau_t                    =  TAUT
+gen_vel                  = yes
+gen_temp                 =  TEMP
+ref_t                    =  TEMP
+tc-grps                  = system
+pcoupl                   =  PCOUPL
+tau_p                    =  TAUP
+ref_p                    =  PRESSURE
+compressibility          = 4.5e-5
+nstpcouple               = 10
+nsttcouple               = 10
+"""
+
+PARAMS_EMIN = """\
+INTEGRATOR = steep
+NSTEPS = 10000
+NLOG = 100
+NENERGY = 100
+NSTXOUT = 100
+TAUT = 1.0
+TEMP = 300
+PCOUPL = no
+TCOUPL = no
+TAUP = 1.0
+"""
+
+PARAMS_AN1 = """\
+INTEGRATOR = md
+NSTEPS = 2000000
+NLOG = 1000
+NENERGY = 100
+NSTXOUT = 1000
+TCOUPL = v-rescale
+TAUT = 0.5
+TEMP = 10.0
+PCOUPL = c-rescale
+TAUP = 1.0
+"""
+
+TOPOLOGY = """\
+[ defaults ]
+; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+  1             2               yes              1.0     1.0
+[atomtypes]
+;name     mass      charge   ptype    sigma        epsilon
+A     MASS       0.000       A      SIGMA_A         EPSILON_A
+B     MASS       0.000       A      SIGMA_B         EPSILON_B
+D     0          0.000       D   0.0           0.0
+...
+"""
+
+# --- Core function ---
+def create_simulation_dir(directory: Path):
+    directory.mkdir(parents=True, exist_ok=True)
+    os.chdir(directory)
+
+    # Write files
+    (directory / "mdp_parameters.mdp").write_text(MDP_PARAMETERS)
+    (directory / "params_emin.ini").write_text(PARAMS_EMIN)
+    (directory / "params_an1.ini").write_text(PARAMS_AN1)
+    (directory / "topology.top").write_text(TOPOLOGY)
+    # ... add the rest of your templates here ...
+
+    script_dir = Path(__file__).parent
+    subprocess.run([script_dir / "create_emin.sh"], check=True)
+    subprocess.run([script_dir / "create_annealing1.sh"], check=True)
+
+    print(f"finished and simulation directory {directory} created and filled")
+    for f in os.listdir(directory):
+        print(f)
+
+# --- CLI entry point ---
+def main():
+    parser = argparse.ArgumentParser(description="Create simulation input files.")
+    parser.add_argument("-d", "--directory", default=".", help="Base directory")
+    args = parser.parse_args()
+
+    create_simulation_dir(Path(args.directory))
+
+if __name__ == "__main__":
+    main()
+

polyamorphism_optimization/setup_sim.sh

@@ -135,7 +135,7 @@ L  1
 L                 NMOL 
 EOF
 
-cat > topology.top << EOF
+cat > topology_atomistic.top << EOF
 [ defaults ]
 ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
   1             2               yes              1.0     1.0

pyproject.toml

@@ -0,0 +1,24 @@
+[build-system]
+requires = ["setuptools>=80.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "polyamorphism_optimization"
+version = "0.1.0"
+requires-python = ">=3.12"
+
+dependencies = [
+    "pip>=25",
+    "wheel>=0.45",
+    "numpy>=2.3",
+    "scipy>=1.16",
+    "pandas>=2.3",
+    "mdevaluate @ git+ssh://git@gitea.pkm.physik.tu-darmstadt.de/IPKM/mdevaluate.git@feature/compatibility_robin",
+]
+
+[project.scripts]
+po_setup_sim = "polyamorphism_optimization.setup_sim:main"
+
+[tool.setuptools.package-data]
+polyamorphism_optimization = ["templates/*"]
+

setup_env.sh

@@ -0,0 +1,5 @@
+python3.12 -m venv .venv
+source .venv/bin/activate
+pip install -e .
+# pip install --upgrade --force-reinstall .
+