quick fix to test atomistic systems

create_annealing2.sh

@@ -0,0 +1,39 @@
+#!/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 }
+    ' "$file"
+}
+
+simdir="02_an_cooling"
+
+
+rm -r "$simdir" 2>/dev/null
+mkdir "$simdir"
+
+cp topology.top "$simdir/"
+"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
+"$(dirname $0)/replace_params.sh" params_an1.ini mdp_parameters.mdp --output "$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 "00_em/out/out.gro" "$simdir/gro_start.gro"
+
+
+#annealing=$($(dirname $0)/generate_annealing.py -d 50 -l 180 -u 750 -e 2000 -c)
+annealing=$($(dirname $0)/generate_annealing.py -d 20 -l 750 -u 2100 -s 50 -e 10000 -c)
+
+echo "" >> "$simdir/mdp_parameters.mdp"
+echo "$annealing" >> "$simdir/mdp_parameters.mdp"
+
+