#!/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="01_an1"


rm -r "$simdir" 2>/dev/null
mkdir "$simdir"

cp topology.top "$simdir/"
../replace_params.sh params.ini topology.top --output "$simdir/topology.top"
../replace_params.sh params_an1.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
../replace_params.sh params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
cp ../run.sh "$simdir/"
cp "00_em/out/out.gro" "$simdir/gro_start.gro"


annealing=$(../generate_annealing.py -d 50 -l 50 -u 1000 -s 100 -e 2000)

annealing=$(../generate_annealing.py -d 30 -l 400 -u 950 -s 50 -e 2000)

echo "" >> "$simdir/mdp_parameters.mdp"
echo "annealing                = single" >> "$simdir/mdp_parameters.mdp"
echo "$annealing" >> "$simdir/mdp_parameters.mdp"