#!/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"