From 870dd224fc7d040b8e4713211f01c5989866292c Mon Sep 17 00:00:00 2001
From: Robin Horstmann <robin.horstmann@pkm.tu-darmstadt.de>
Date: Wed, 13 Aug 2025 15:34:52 +0200
Subject: [PATCH] type in init; emin to python

---
 polyamorphism_optimization/annealing.py       |  0
 polyamorphism_optimization/create_emin.sh     | 35 --------------
 polyamorphism_optimization/emin.py            | 36 ++++++++++++++
 .../{innitialize_sim.py => initialize_sim.py} | 10 ++--
 polyamorphism_optimization/replace_params.py  |  0
 polyamorphism_optimization/replace_params.sh  | 47 -------------------
 pyproject.toml                                |  2 +-
 7 files changed, 43 insertions(+), 87 deletions(-)
 mode change 100644 => 100755 polyamorphism_optimization/annealing.py
 delete mode 100755 polyamorphism_optimization/create_emin.sh
 create mode 100755 polyamorphism_optimization/emin.py
 rename polyamorphism_optimization/{innitialize_sim.py => initialize_sim.py} (83%)
 mode change 100644 => 100755 polyamorphism_optimization/replace_params.py
 delete mode 100755 polyamorphism_optimization/replace_params.sh

diff --git a/polyamorphism_optimization/annealing.py b/polyamorphism_optimization/annealing.py
old mode 100644
new mode 100755
diff --git a/polyamorphism_optimization/create_emin.sh b/polyamorphism_optimization/create_emin.sh
deleted file mode 100755
index be37706..0000000
--- a/polyamorphism_optimization/create_emin.sh
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/bin/bash
-
-get_ini_value() {
-    local file=$1
-    local section=$2
-    local key=$3
-
-    awk -F '=' -v section="$section" -v key="$key" '
-    $0 ~ "\\[" section "\\]" { in_section = 1; next }
-    in_section && $1 ~ "^" key"[[:space:]]*$" {
-        gsub(/[[:space:]]+/, "", $2)
-        print $2
-        exit
-    }
-    $0 ~ /^\[/ { in_section = 0 }
-    ' "$file"
-}
-
-
-simdir="00_em"
-
-
-rm -r "$simdir" 2>/dev/null
-mkdir "$simdir"
-
-cp topology.top "$simdir/"
-"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
-"$(dirname $0)/replace_params.sh" params_emin.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
-"$(dirname $0)/replace_params.sh" params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
-cp "$(dirname $0)/run.sh" "$simdir/"
-cp "$(dirname $0)/templates/gro_$(get_ini_value params.ini params model).gro" "$simdir/gro_start.gro"
-
-echo "emstep                   = 0.001" >> $simdir/mdp_parameters.mdp
-
-
diff --git a/polyamorphism_optimization/emin.py b/polyamorphism_optimization/emin.py
new file mode 100755
index 0000000..2b2aa6a
--- /dev/null
+++ b/polyamorphism_optimization/emin.py
@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+import shutil
+from pathlib import Path
+from replace_params import replace_params
+
+
+def main(root_dir: Path):
+    simdir = root_dir / "00_em"
+
+    if simdir.exists():
+        shutil.rmtree(simdir)
+    simdir.mkdir()
+
+    # Copy topology and replace parameters
+    shutil.copy(root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params.ini", root_dir / "topology.top", simdir / "topology.top")
+    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")
+
+    # Copy run.sh
+    shutil.copy(root_dir / "run.sh", simdir / "run.sh")
+
+    # Add finer emstep
+    with (simdir / "mdp_parameters.mdp").open("a") as f:
+        f.write("\n")
+        f.write("emstep                   = 0.001")
+
+    print(f"Energy minimization directory {simdir} 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]))
diff --git a/polyamorphism_optimization/innitialize_sim.py b/polyamorphism_optimization/initialize_sim.py
similarity index 83%
rename from polyamorphism_optimization/innitialize_sim.py
rename to polyamorphism_optimization/initialize_sim.py
index bd9b470..79fd347 100755
--- a/polyamorphism_optimization/innitialize_sim.py
+++ b/polyamorphism_optimization/initialize_sim.py
@@ -6,9 +6,12 @@ from pathlib import Path
 from importlib.resources import files
 import configparser
 
+from annealing import main as annealing
+from emin import main as emin
+
 
 # --- Core function ---
-def innitialize_simulation_dir(directory: Path):
+def initialize_simulation_dir(directory: Path):
     os.chdir(directory)
     
     params = configparser.ConfigParser()
@@ -23,9 +26,8 @@ def innitialize_simulation_dir(directory: Path):
     Path("mdp_parameters.mdp").write_text(MDP_PARAMETERS)
     Path("topology.top").write_text(TOPOLOGY)
 
-    script_dir = Path(__file__).parent
-    subprocess.run([script_dir / "create_emin.sh"], check=True)
-    subprocess.run([script_dir / "create_annealing1.sh"], check=True)
+    emin(directory)
+    annealing(directory)
 
     print(f"finished and simulation directory {directory} created and filled")
     for f in os.listdir(directory):
diff --git a/polyamorphism_optimization/replace_params.py b/polyamorphism_optimization/replace_params.py
old mode 100644
new mode 100755
diff --git a/polyamorphism_optimization/replace_params.sh b/polyamorphism_optimization/replace_params.sh
deleted file mode 100755
index 37d810c..0000000
--- a/polyamorphism_optimization/replace_params.sh
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-if [[ $# -lt 2 ]]; then
-    echo "Usage: $0 <params.ini> <template> [--output <output_file>]"
-    exit 1
-fi
-
-PARAMS_FILE="$1"
-TEMPLATE_FILE="$2"
-OUTPUT_FILE="${TEMPLATE_FILE}.out"
-
-# Optional --output <filename>
-if [[ "$3" == "--output" && -n "$4" ]]; then
-    OUTPUT_FILE="$4"
-fi
-
-declare -A PARAMS
-
-# Load params.ini (ignore [section] headers)
-while IFS='=' read -r key value; do
-    # Trim whitespace and ignore comments/sections
-    key="${key%%\#*}"   # remove inline comments
-    value="${value%%\#*}"
-    key="$(echo "$key" | xargs)"     # trim leading/trailing whitespace
-    value="$(echo "$value" | xargs)"
-    [[ -z "$key" || "$key" =~ ^\[.*\]$ ]] && continue
-
-    key_upper=$(echo "$key" | tr '[:lower:]' '[:upper:]')
-    PARAMS["$key_upper"]="$value"
-done < "$PARAMS_FILE"
-
-# Read template into a variable
-template=$(<"$TEMPLATE_FILE")
-
-# Replace placeholders (only when surrounded by spaces)
-for key in "${!PARAMS[@]}"; do
-    val="${PARAMS[$key]}"
-    # Use sed to do space-surrounded substitution
-    template=$(echo "$template" | sed -E "s/([[:space:]])$key([[:space:]])/$val/g")
-done
-
-# Save to output file
-echo "$template" > "$OUTPUT_FILE"
-echo "Wrote output to $OUTPUT_FILE"
-
diff --git a/pyproject.toml b/pyproject.toml
index ac4522b..14f5eb2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ dependencies = [
 ]
 
 [project.scripts]
-po_init_sim = "polyamorphism_optimization.innitialize_sim:main"
+po_init_sim = "polyamorphism_optimization.initialize_sim:main"
 
 [tool.setuptools.package-data]
 polyamorphism_optimization = ["templates/*"]