added pre-commit hooks; fixed whitespace and capitalization dependent parameter replacement; fixed creation of annealing and emin sim directories

.editorconfig

@@ -0,0 +1,12 @@
+# .editorconfig
+root = true
+
+[*]
+trim_trailing_whitespace = true
+
+# Disable for GROMACS template files
+[*.mdp]
+trim_trailing_whitespace = false
+
+[*.top]
+trim_trailing_whitespace = false

.gitignore

@@ -2,6 +2,8 @@
 # gitignore template for Jupyter Notebooks
 # website: http://jupyter.org/
 
+.idea
+
 .ipynb_checkpoints
 */.ipynb_checkpoints/*
 
@@ -187,4 +189,3 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
-

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: '\.(mdp|top)$'
+      - id: end-of-file-fixer
+        exclude: '\.(mdp|top)$'
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 26.5.1
+    hooks:
+      - id: black
+        exclude: '\.(mdp|top)$'
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 9.0.0a3
+    hooks:
+      - id: isort
+        exclude: '\.(mdp|top)$'
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+        exclude: '\.(mdp|top)$'

README.md

@@ -1,3 +1,11 @@
 # polyamorphism_optimization
 
-Code snippets for creation of simulations, analysis, and optimized parameter search for liquids with polyamorphism. Goal is to find parameters for which dynamics is still fast at the critical point and the dynamic anomaly that follows can be studied more easily.
+Code snippets for creation of simulations, analysis, and optimized parameter search for liquids with polyamorphism. Goal is to find parameters for which dynamics is still fast at the critical point and the dynamic anomaly that follows can be studied more easily.
+
+#### Setting up pre-commit hooks
+```
+pip install pre-commit
+pre-commit autoupdate
+pre-commit install
+pre-commit run #--all-files
+```

polyamorphism_optimization/annealing.py

@@ -1,40 +1,50 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python3.12
 import shutil
+from importlib.resources import files
 from pathlib import Path
+
 from generate_annealing import generate_annealing
 from replace_params import replace_params
 
 
 def main(root_dir: Path):
-    simdir = root_dir / "01_an1"
+    sim_dir = root_dir / "01_an1"
 
-    if simdir.exists():
+    if sim_dir.exists():
-        shutil.rmtree(simdir)
+        shutil.rmtree(sim_dir)
-    simdir.mkdir()
+    sim_dir.mkdir()
 
     # Copy topology and replace parameters
-    shutil.copy(root_dir / "topology.top", simdir / "topology.top")
+    shutil.copy(root_dir / "topology.top", sim_dir / "topology.top")
-    replace_params(root_dir / "params.ini", root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params.ini", root_dir / "topology.top", sim_dir / "topology.top", upper=True, space=True)
-    replace_params(root_dir / "params_an1.ini", root_dir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+
-    replace_params(root_dir / "params.ini", simdir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+    replace_params(
+        files("polyamorphism_optimization.templates.params") / "annealing1.ini",
+        root_dir / "mdp_parameters.mdp",
+        sim_dir / "mdp_parameters.mdp",
+        upper=True,
+        space=True,
+    )
+    replace_params(
+        root_dir / "params.ini", sim_dir / "mdp_parameters.mdp", sim_dir / "mdp_parameters.mdp", upper=True, space=True
+    )
 
     # Copy run.sh
-    shutil.copy(root_dir / "run.sh", simdir / "run.sh")
+    shutil.copy(root_dir / "run.sh", sim_dir / "run.sh")
 
     # Generate annealing section
-    annealing = generate_annealing(d=50, l=50, u=1000, s=50, e=2000)
+    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 (simdir / "mdp_parameters.mdp").open("a") as f:
+    with (sim_dir / "mdp_parameters.mdp").open("a") as f:
-        f.write("\n")
         f.write(annealing)
 
-    print(f"Annealing directory {simdir} created and filled.")
+    print(f"Annealing directory {sim_dir} created and filled.")
 
 
 if __name__ == "__main__":
     import sys
+
     if len(sys.argv) != 2:
         print(f"Usage: {sys.argv[0]} ROOT_DIRECTORY")
         sys.exit(1)
     main(Path(sys.argv[1]))
-

polyamorphism_optimization/create_sim.py

@@ -1,14 +1,16 @@
-#!/usr/bin/python3.12
+#!/usr/bin/env python3.12
 import argparse
 import configparser
 import math
 import os
+import shutil
+from importlib.resources import files
+from pathlib import Path
+
 
 def compute_dependent(params):
-    model = params["model"]
-
     # Charge neutrality
-    params["charge_B"] = round(params["charge"]/2, 5)
+    params["charge_B"] = round(params["charge"] / 2, 5)
     params["charge_A"] = -2 * params["charge_B"]
 
     # Relative sigma and epsilon
@@ -25,16 +27,16 @@ def compute_dependent(params):
     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_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"]:
@@ -43,7 +45,8 @@ def clean_params(params):
         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 = [
@@ -72,10 +75,9 @@ def format_directory_name(params):
 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("--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)
@@ -90,7 +92,7 @@ def main():
 
     # 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("--angle_ABA", type=float, default=109.5)  # 104.52
     parser.add_argument("--r_AM", type=float, default=0.4)
 
     # Output
@@ -113,13 +115,14 @@ def main():
         "angle_ABA": args.angle_ABA,
         "r_AM": args.r_AM,
     }
-
+    if params["model"] == "atomistic":
+        params["nmolb"] = 2 * params["nmol"]
 
     # Compute dependent values
     params = compute_dependent(params)
     params = clean_params(params)
-    
+
-    dir_name = format_directory_name(params)
+    dir_name = Path(format_directory_name(params))
     if os.path.exists(dir_name):
         print(f"Directory {dir_name} already exists. Aborting.")
         return
@@ -129,11 +132,14 @@ def main():
     config_path = os.path.join(dir_name, args.output)
     with open(config_path, "w") as f:
         config = configparser.ConfigParser()
+        config.optionxform = str  # keep case sensitivity
         config["params"] = params
         config.write(f)
 
     print(f"Parameter file written to {config_path}")
 
+    shutil.copy(files("polyamorphism_optimization.templates") / "run.sh", dir_name / "run.sh")
+
+
 if __name__ == "__main__":
     main()
-

polyamorphism_optimization/emin.py

@@ -1,35 +1,47 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python3.12
 import shutil
+from importlib.resources import files
 from pathlib import Path
+
 from replace_params import replace_params
 
 
 def main(root_dir: Path):
-    simdir = root_dir / "00_em"
+    sim_dir = root_dir / "00_em"
 
-    if simdir.exists():
+    if sim_dir.exists():
-        shutil.rmtree(simdir)
+        shutil.rmtree(sim_dir)
-    simdir.mkdir()
+    sim_dir.mkdir()
 
     # Copy topology and replace parameters
-    shutil.copy(root_dir / "topology.top", simdir / "topology.top")
+    shutil.copy(root_dir / "topology.top", sim_dir / "topology.top")
-    replace_params(root_dir / "params.ini", root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params.ini", root_dir / "topology.top", sim_dir / "topology.top", upper=True, space=True)
-    replace_params(root_dir / "params_emin.ini", root_dir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+
-    replace_params(root_dir / "params.ini", simdir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+    replace_params(
+        files("polyamorphism_optimization.templates.params") / "emin.ini",
+        root_dir / "mdp_parameters.mdp",
+        sim_dir / "mdp_parameters.mdp",
+        upper=True,
+        space=True,
+    )
+    replace_params(
+        root_dir / "params.ini", sim_dir / "mdp_parameters.mdp", sim_dir / "mdp_parameters.mdp", upper=True, space=True
+    )
 
     # Copy run.sh
-    shutil.copy(root_dir / "run.sh", simdir / "run.sh")
+    shutil.copy(root_dir / "run.sh", sim_dir / "run.sh")
 
     # Add finer emstep
-    with (simdir / "mdp_parameters.mdp").open("a") as f:
+    with (sim_dir / "mdp_parameters.mdp").open("a") as f:
         f.write("\n")
         f.write("emstep                   = 0.001")
 
-    print(f"Energy minimization directory {simdir} created and filled.")
+    print(f"Energy minimization directory {sim_dir} created and filled.")
 
 
 if __name__ == "__main__":
     import sys
+
     if len(sys.argv) != 2:
         print(f"Usage: {sys.argv[0]} ROOT_DIRECTORY")
         sys.exit(1)

polyamorphism_optimization/generate_annealing.py

@@ -1,7 +1,8 @@
-#!/usr/bin/python3.12
+#!/usr/bin/env python3.12
 import argparse
 import math
 
+
 def round_dynamic(x, rel_tol=1e-3, max_decimals=6, max_negative_decimals=3):
     """
     Dynamically round x so that the relative error is within rel_tol.
@@ -23,6 +24,7 @@ def round_dynamic(x, rel_tol=1e-3, max_decimals=6, max_negative_decimals=3):
         factor = 10 ** (-decimals)
         return round(x / factor) * factor
 
+
 def generate_temperature_list_dynamic(dT=10, Tmin=10, Tmax=5000, rel_tol=5e-3):
     r = (300 - dT) / 300.0
 
@@ -49,16 +51,18 @@ def generate_temperature_list_dynamic(dT=10, Tmin=10, Tmax=5000, rel_tol=5e-3):
     rounded_T = [round_dynamic(t, rel_tol=rel_tol) for t in all_T]
 
     return rounded_T
-    
+
+
 def generate_temperature_list(dT=10, Tmin=10, Tmax=5000, rel_tol=5e-3):
-    r = (Tmax/Tmin)**(1/20)
+    r = (Tmax / Tmin) ** (1 / 20)
-    all_T = [Tmin*r**i for i in range(21)]
+    all_T = [Tmin * r**i for i in range(21)]
 
     # Apply dynamic rounding
     rounded_T = [round_dynamic(t, rel_tol=rel_tol) for t in all_T]
 
     return rounded_T
 
+
 def generate_times_list(npoints, start_time, end_time):
     if npoints == 1:
         return [0.0]
@@ -66,6 +70,7 @@ def generate_times_list(npoints, start_time, end_time):
     interval = duration / (npoints - 1)
     return [round(start_time + i * interval, 3) for i in range(npoints)]
 
+
 def main():
     parser = argparse.ArgumentParser(description="Generate annealing times and temperatures for GROMACS.")
     parser.add_argument("-d", "--dT", type=float, default=20.0, help="Temperature step size")
@@ -74,25 +79,35 @@ def main():
     parser.add_argument("-r", "--rel_tol", type=float, default=5e-3, help="Relative tolerance for rounding")
     parser.add_argument("-s", "--start_time", type=float, default=0, help="Start time in fs")
     parser.add_argument("-e", "--end_time", type=float, required=True, help="End time in fs")
-    parser.add_argument("-c", "--cooling", action='store_true', help="Do cooling instead of heating")
+    parser.add_argument("-c", "--cooling", action="store_true", help="Do cooling instead of heating")
 
     args = parser.parse_args()
+    annealing = generate_annealing(args.e, args.d, args.l, args.u, args.r, args.c, args.s)
+    print(annealing)
 
-    #temps = generate_temperature_list_dynamic(args.dT, args.Tmin, args.Tmax, args.rel_tol)
+
-    temps = generate_temperature_list(args.dT, args.Tmin, args.Tmax, args.rel_tol)
+def generate_annealing(end_time, dT=20, Tmin=10, Tmax=5000, rel_tol=5e-3, cooling=False, start_time=0):
-    if args.cooling:
+
+    # temps = generate_temperature_list_dynamic(args.dT, args.Tmin, args.Tmax, args.rel_tol)
+    temps = generate_temperature_list(dT, Tmin, Tmax, rel_tol)
+    if cooling:
         temps = list(reversed(temps))
 
-    if args.start_time > 0:
+    if start_time > 0:
         temps = [temps[0]] + temps  # hold first temperature
-        times = [0.0] + generate_times_list(len(temps) - 1, args.start_time, args.end_time)
+        times = [0.0] + generate_times_list(len(temps) - 1, start_time, end_time)
     else:
-        times = generate_times_list(len(temps), args.start_time, args.end_time)
+        times = generate_times_list(len(temps), start_time, end_time)
+
+    annealing_config = f"""
+annealing                = single
+annealing-npoints        = {len(times)}
+annealing-time           = {"  ".join(f'{t:.3f}' for t in times)}
+annealing-temp           = {"  ".join(f'{t:.2f}' for t in temps)}
+"""
+
+    return annealing_config
 
-    print("annealing                = single")
-    print(f"annealing-npoints        = {len(times)}")
-    print("annealing-time           = " + "  ".join(f"{t:.3f}" for t in times))
-    print("annealing-temp           = " + "  ".join(f"{t:.2f}" for t in temps))
 
 if __name__ == "__main__":
     main()

polyamorphism_optimization/initialize_sim.py

@@ -1,10 +1,9 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python3.12
 import argparse
-import os
-import subprocess
-from pathlib import Path
-from importlib.resources import files
 import configparser
+import os
+from importlib.resources import files
+from pathlib import Path
 
 from annealing import main as annealing
 from emin import main as emin
@@ -12,19 +11,19 @@ from emin import main as emin
 
 # --- Core function ---
 def initialize_simulation_dir(directory: Path):
-    os.chdir(directory)
+    directory = Path(directory)
-    
-    params = configparser.ConfigParser()
-    params = params.read('params.ini')
 
-    template_path = files("polyamorphism_optimization.templates") / f"topology_{params['model']}.top"
+    params = configparser.ConfigParser()
+    params.read(directory / "params.ini")
+
+    template_path = files("polyamorphism_optimization.templates") / f"top_{params['params']['model']}.top"
     TOPOLOGY = template_path.read_text()
     template_path = files("polyamorphism_optimization.templates") / "mdp_parameters.mdp"
     MDP_PARAMETERS = template_path.read_text()
-    
+
     # Write files
-    Path("mdp_parameters.mdp").write_text(MDP_PARAMETERS)
+    Path(directory / "mdp_parameters.mdp").write_text(MDP_PARAMETERS)
-    Path("topology.top").write_text(TOPOLOGY)
+    Path(directory / "topology.top").write_text(TOPOLOGY)
 
     emin(directory)
     annealing(directory)
@@ -33,14 +32,16 @@ def initialize_simulation_dir(directory: Path):
     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))
+    # create_simulation_dir(Path(args.directory))
+    initialize_simulation_dir(Path(args.directory))
+
 
 if __name__ == "__main__":
     main()
-

polyamorphism_optimization/replace_params.py

@@ -1,10 +1,10 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python3.12
-import sys
 import configparser
+import sys
 from pathlib import Path
 
 
-def replace_params(param_file: Path, template_file: Path, output_file: Path):
+def replace_params(param_file: Path, template_file: Path, output_file: Path, upper=False, space=False):
     """Replace placeholders in template_file with values from an INI file."""
     config = configparser.ConfigParser()
     config.optionxform = str  # keep case sensitivity
@@ -14,7 +14,15 @@ def replace_params(param_file: Path, template_file: Path, output_file: Path):
     params = {}
     for section in config.sections():
         for key, value in config.items(section):
-            params[key] = value
+            if upper:
+                params[key.upper()] = value
+            else:
+                params[key] = value
+
+    if space:
+        for key, value in dict(params.items()).items():
+            params[f" {key} "] = value
+            params.pop(key)
 
     content = template_file.read_text()
 
@@ -38,4 +46,3 @@ def main():
 
 if __name__ == "__main__":
     main()
-

polyamorphism_optimization/templates/NPT.ini

@@ -1,3 +1,4 @@
+[mdp]
 INTEGRATOR = md
 NSTEPS = 2000000
 NLOG = 1000

polyamorphism_optimization/templates/NVT.ini

@@ -1,3 +1,4 @@
+[mdp]
 INTEGRATOR = md
 NSTEPS = 2000000
 NLOG = 1000

polyamorphism_optimization/templates/mdp_parameters.mdp

@@ -1,11 +1,11 @@
-integrator               =  INTEGRATOR
+integrator               =  INTEGRATOR 
 dt                       = 0.001
-nsteps                   =  NSTEPS
+nsteps                   =  NSTEPS 
 nstcomm                  = 10
-nstlog                   =  NLOG
+nstlog                   =  NLOG 
 nstcalcenergy            = 10
-nstenergy                =  NENERGY
+nstenergy                =  NENERGY 
-nstxout-compressed       =  NSTXOUT
+nstxout-compressed       =  NSTXOUT 
 compressed-x-precision   = 1000
 energygrps               = system
 rlist                    = 1.2
@@ -18,14 +18,14 @@ rvdw                     = 1.2
 vdw-modifier             = potential-shift-verlet
 fourierspacing           = 0.144
 tcoupl                   = v-rescale
-tau_t                    =  TAUT
+tau_t                    =  TAUT 
 gen_vel                  = yes
-gen_temp                 =  TEMP
+gen_temp                 =  TEMP 
-ref_t                    =  TEMP
+ref_t                    =  TEMP 
 tc-grps                  = system
-pcoupl                   =  PCOUPL
+pcoupl                   =  PCOUPL 
-tau_p                    =  TAUP
+tau_p                    =  TAUP 
-ref_p                    =  PRESSURE
+ref_p                    =  PRESSURE 
 compressibility          = 4.5e-5
 nstpcouple               = 10
 nsttcouple               = 10

polyamorphism_optimization/templates/params/annealing1.ini

@@ -1,3 +1,4 @@
+[mdp]
 INTEGRATOR = md
 NSTEPS = 2000000
 NLOG = 1000

polyamorphism_optimization/templates/params/annealing2.ini

@@ -1,3 +1,4 @@
+[mdp]
 INTEGRATOR = md
 NSTEPS = 5000000
 NLOG = 1000

polyamorphism_optimization/templates/params/emin.ini

@@ -1,3 +1,4 @@
+[mdp]
 INTEGRATOR = steep
 NSTEPS = 10000
 NLOG = 100

polyamorphism_optimization/templates/top_3point.top

@@ -3,15 +3,15 @@
   1             2               yes              1.0     1.0
 [atomtypes]
 ;name     mass      charge   ptype    sigma        epsilon
-A     MASS       0.000       A      SIGMA_A         EPSILON_A
+A     MASS       0.000       A      SIGMA_A         EPSILON_A 
-B     MASS       0.000       A      SIGMA_B         EPSILON_B
+B     MASS       0.000       A      SIGMA_B         EPSILON_B 
 
 [moleculetype]
 ; name nrexcl
 L  1
 
 [atoms]
-; nr type resnr residu atom cgnr charge
+; nr type resnr residu atom cgnr charge mass
 1     A   1     L  A    1    CHARGE_A      MASS 
 2     B   1     L  B1   1    CHARGE_B      MASS 
 3     B   1     L  B2   1    CHARGE_B      MASS 

polyamorphism_optimization/templates/top_4point.top

@@ -3,8 +3,8 @@
   1             2               yes              1.0     1.0
 [atomtypes]
 ;name     mass      charge   ptype    sigma        epsilon
-A     MASS       0.000       A      SIGMA_A         EPSILON_A
+A     MASS       0.000       A      SIGMA_A         EPSILON_A 
-B     MASS       0.000       A      SIGMA_B         EPSILON_B
+B     MASS       0.000       A      SIGMA_B         EPSILON_B 
 D     0          0.000       D   0.0           0.0
 
 [moleculetype]
@@ -12,7 +12,7 @@ D     0          0.000       D   0.0           0.0
 L  1
 
 [atoms]
-; nr type resnr residu atom cgnr charge
+; nr type resnr residu atom cgnr charge mass
 1     A   1     L  A    1     0        MASS 
 2     B   1     L  B1   1    CHARGE_B      MASS 
 3     B   1     L  B2   1    CHARGE_B      MASS 

polyamorphism_optimization/templates/top_atomistic.top

@@ -12,7 +12,7 @@ B     MASS       0.000       A      SIGMA_B         EPSILON_B
 A  1
 
 [atoms]
-; nr type resnr residu atom cgnr charge
+; nr type resnr residu atom cgnr charge mass
 1     A   1     L  A   1    CHARGE_A      MASS 
 
 [moleculetype]
@@ -20,12 +20,12 @@ A  1
 B  1
 
 [atoms]
-; nr type resnr residu atom cgnr charge
+; nr type resnr residu atom cgnr charge mass
 1     B   1     L  B   1    CHARGE_B      MASS 
 
 [system]
  MODEL 
 
 [molecules]
-A                NMOL
+A                NMOL 
-B                NMOLB
+B                NMOLB 

pyproject.toml

@@ -22,3 +22,17 @@ po_init_sim = "polyamorphism_optimization.initialize_sim:main"
 [tool.setuptools.package-data]
 polyamorphism_optimization = ["templates/*"]
 
+[tool.black]
+line-length = 120
+target-version = ["py312"]
+exclude = '''
+(
+  \.mdp
+  | \.top
+)
+'''
+
+[tool.isort]
+profile = "black"  # Makes isort compatible with black's formatting
+line_length = 120
+extend_skip_glob = ["*.mdp", "*.top"]

setup.cfg

@@ -0,0 +1,5 @@
+[flake8]
+max-line-length = 120
+exclude =
+    *.mdp,
+    *.top