quick fix to test atomistic systems

create_annealing1.sh

@@ -23,19 +23,18 @@ rm -r "$simdir" 2>/dev/null
 mkdir "$simdir"
 
 cp topology.top "$simdir/"
-../replace_params.sh params.ini topology.top --output "$simdir/topology.top"
+"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
-../replace_params.sh params_an1.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
+"$(dirname $0)/replace_params.sh" params_an1.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
-../replace_params.sh params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
+"$(dirname $0)/replace_params.sh" params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
-cp ../run.sh "$simdir/"
+cp "$(dirname $0)/run.sh" "$simdir/"
 cp "00_em/out/out.gro" "$simdir/gro_start.gro"
 
 
-annealing=$(../generate_annealing.py -d 50 -l 50 -u 1000 -s 100 -e 2000)
+annealing=$($(dirname $0)/generate_annealing.py -d 50 -l 50 -u 1000 -s 50 -e 2000)
 
-annealing=$(../generate_annealing.py -d 30 -l 400 -u 950 -s 50 -e 2000)
+#annealing=$($(dirname $0)/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"
 
 

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"
+
+

create_emin.sh

@@ -24,11 +24,11 @@ rm -r "$simdir" 2>/dev/null
 mkdir "$simdir"
 
 cp topology.top "$simdir/"
-../replace_params.sh params.ini topology.top --output "$simdir/topology.top"
+"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
-../replace_params.sh params_emin.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
+"$(dirname $0)/replace_params.sh" params_emin.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
-../replace_params.sh params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
+"$(dirname $0)/replace_params.sh" params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
-cp ../run.sh "$simdir/"
+cp "$(dirname $0)/run.sh" "$simdir/"
-cp "../gro_$(get_ini_value params.ini params model).gro" "$simdir/gro_start.gro"
+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
 

generate_annealing.py

@@ -51,8 +51,8 @@ def generate_temperature_list_dynamic(dT=10, Tmin=10, Tmax=5000, rel_tol=5e-3):
     return rounded_T
     
 def generate_temperature_list(dT=10, Tmin=10, Tmax=5000, rel_tol=5e-3):
-    dT = (Tmax - Tmin) / 20
+    r = (Tmax/Tmin)**(1/20)
-    all_T = [i*dT+Tmin 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]
@@ -80,7 +80,7 @@ def main():
 
     #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)
-    if not args.cooling:
+    if args.cooling:
         temps = list(reversed(temps))
 
     if args.start_time > 0:

setup_sim.sh

@@ -135,9 +135,44 @@ L  1
 L                 NMOL 
 EOF
 
+cat > topology.top << EOF
+[ defaults ]
+; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+  1             2               yes              1.0     1.0
+
+[atomtypes]
+;name     mass      charge   ptype    sigma        epsilon
+A     MASS       0.000       A      SIGMA_A         EPSILON_A 
+B     MASS       0.000       A      SIGMA_B         EPSILON_B 
+
+[moleculetype]
+; name nrexcl
+A  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     A   1     L  A   1    CHARGE_A      MASS 
+
+[moleculetype]
+; name nrexcl
+B  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     B   1     L  B   1    CHARGE_B      MASS 
+
+[system]
+ MODEL 
+
+[molecules]
+A                1000
+B                2000
+EOF
+
 #=====================================================================================
-bash ../create_emin.sh
+echo $(dirname $0)
-bash ../create_annealing1.sh
+bash ".$(dirname $0)/create_emin.sh"
+bash ".$(dirname $0)/create_annealing1.sh"
 
 
 #=====================================================================================

templates/A.gro

@@ -0,0 +1,4 @@
+SOL tip4p/2005 t= 8254.00000 step= 4127000
+    1
+    1SOL     OW    1   1.982   1.987   2.025
+   4.00000   4.00000   4.00000

templates/B.gro

@@ -0,0 +1,4 @@
+SOL tip4p/2005 t= 8254.00000 step= 4127000
+    1
+    1SOL      N    1   1.982   1.987   2.025
+   4.00000   4.00000   4.00000