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setup_sim.sh removed for innitialize_sim; more usage of templates

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Robin
2025-08-13 14:59:28 +02:00
parent 4fe2ad61a3
commit 2bed210ed8
12 changed files with 227 additions and 292 deletions
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44
polyamorphism_optimization/innitialize_sim.py Normal file
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#!/usr/bin/env python3
import argparse
import os
import subprocess
from pathlib import Path
from importlib.resources import files
import configparser
# --- Core function ---
def innitialize_simulation_dir(directory: Path):
os.chdir(directory)
params = configparser.ConfigParser()
params = params.read('params.ini')
template_path = files("polyamorphism_optimization.templates") / f"topology_{params['model']}.top"
TOPOLOGY = template_path.read_text()
template_path = files("polyamorphism_optimization.templates") / "mdp_parameters.mdp"
MDP_PARAMETERS = template_path.read_text()
# Write files
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)
print(f"finished and simulation directory {directory} created and filled")
for f in os.listdir(directory):
print(f)
# --- CLI entry point ---
def main():
parser = argparse.ArgumentParser(description="Create simulation input files.")
parser.add_argument("-d", "--directory", default=".", help="Base directory")
args = parser.parse_args()
create_simulation_dir(Path(args.directory))
if __name__ == "__main__":
main()

110
polyamorphism_optimization/setup_sim.py
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#!/usr/bin/env python3
import argparse
import os
import subprocess
from pathlib import Path
# --- Template definitions ---
MDP_PARAMETERS = """\
integrator = INTEGRATOR
dt = 0.001
nsteps = NSTEPS
nstcomm = 10
nstlog = NLOG
nstcalcenergy = 10
nstenergy = NENERGY
nstxout-compressed = NSTXOUT
compressed-x-precision = 1000
energygrps = system
rlist = 1.2
nstlist = 10
coulombtype = pme
rcoulomb = 1.2
coulomb-modifier = potential-shift-verlet
vdwtype = pme
rvdw = 1.2
vdw-modifier = potential-shift-verlet
fourierspacing = 0.144
tcoupl = v-rescale
tau_t = TAUT
gen_vel = yes
gen_temp = TEMP
ref_t = TEMP
tc-grps = system
pcoupl = PCOUPL
tau_p = TAUP
ref_p = PRESSURE
compressibility = 4.5e-5
nstpcouple = 10
nsttcouple = 10
"""
PARAMS_EMIN = """\
INTEGRATOR = steep
NSTEPS = 10000
NLOG = 100
NENERGY = 100
NSTXOUT = 100
TAUT = 1.0
TEMP = 300
PCOUPL = no
TCOUPL = no
TAUP = 1.0
"""
PARAMS_AN1 = """\
INTEGRATOR = md
NSTEPS = 2000000
NLOG = 1000
NENERGY = 100
NSTXOUT = 1000
TCOUPL = v-rescale
TAUT = 0.5
TEMP = 10.0
PCOUPL = c-rescale
TAUP = 1.0
"""
TOPOLOGY = """\
[ 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
D 0 0.000 D 0.0 0.0
...
"""
# --- Core function ---
def create_simulation_dir(directory: Path):
directory.mkdir(parents=True, exist_ok=True)
os.chdir(directory)
# Write files
(directory / "mdp_parameters.mdp").write_text(MDP_PARAMETERS)
(directory / "params_emin.ini").write_text(PARAMS_EMIN)
(directory / "params_an1.ini").write_text(PARAMS_AN1)
(directory / "topology.top").write_text(TOPOLOGY)
# ... add the rest of your templates here ...
script_dir = Path(__file__).parent
subprocess.run([script_dir / "create_emin.sh"], check=True)
subprocess.run([script_dir / "create_annealing1.sh"], check=True)
print(f"finished and simulation directory {directory} created and filled")
for f in os.listdir(directory):
print(f)
# --- CLI entry point ---
def main():
parser = argparse.ArgumentParser(description="Create simulation input files.")
parser.add_argument("-d", "--directory", default=".", help="Base directory")
args = parser.parse_args()
create_simulation_dir(Path(args.directory))
if __name__ == "__main__":
main()

182
polyamorphism_optimization/setup_sim.sh
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#!/bin/bash -l
usage() { echo "Usage: $0 [-d basedirectory ]" 1>&2; exit 1; }
DIRECTORY="."
while getopts "d:" opt; do
case $opt in
d )
DIRECTORY=$OPTARG
;;
h )
usage
;;
\? )
usage
;;
esac
done
cd $DIRECTORY
#=====================================================================================
cat > mdp_parameters.mdp << EOF
integrator = INTEGRATOR
dt = 0.001
nsteps = NSTEPS
nstcomm = 10
nstlog = NLOG
nstcalcenergy = 10
nstenergy = NENERGY
nstxout-compressed = NSTXOUT
compressed-x-precision = 1000
energygrps = system
rlist = 1.2
nstlist = 10
coulombtype = pme
rcoulomb = 1.2
coulomb-modifier = potential-shift-verlet
vdwtype = pme
rvdw = 1.2
vdw-modifier = potential-shift-verlet
fourierspacing = 0.144
tcoupl = v-rescale
tau_t = TAUT
gen_vel = yes
gen_temp = TEMP
ref_t = TEMP
tc-grps = system
pcoupl = PCOUPL
tau_p = TAUP
ref_p = PRESSURE
compressibility = 4.5e-5
nstpcouple = 10
nsttcouple = 10
EOF
#=====================================================================================
cat > params_emin.ini << EOF
INTEGRATOR = steep
NSTEPS = 10000
NLOG = 100
NENERGY = 100
NSTXOUT = 100
TAUT = 1.0
TEMP = 300
PCOUPL = no
TCOUPL = no
TAUP = 1.0
EOF
cat > params_an1.ini << EOF
INTEGRATOR = md
NSTEPS = 2000000
NLOG = 1000
NENERGY = 100
NSTXOUT = 1000
TCOUPL = v-rescale
TAUT = 0.5
TEMP = 10.0
PCOUPL = c-rescale
TAUP = 1.0
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
D 0 0.000 D 0.0 0.0
[moleculetype]
; name nrexcl
L 1
[atoms]
; nr type resnr residu atom cgnr charge
1 A 1 L A 1 0 MASS
2 B 1 L B1 1 CHARGE_B MASS
3 B 1 L B2 1 CHARGE_B MASS
4 D 1 L D 1 CHARGE_A 0.0
[settles]
;i funct doh dhh
1 1 D_AB D_BB
[dummies3]
; Dummy from funct a b
4 1 2 3 1 DUMMY_AB DUMMY_AB
[exclusions]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
[system]
MODEL
[molecules]
L NMOL
EOF
cat > topology_atomistic.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
#=====================================================================================
echo $(dirname $0)
bash ".$(dirname $0)/create_emin.sh"
bash ".$(dirname $0)/create_annealing1.sh"
#=====================================================================================
echo "finished and simulation directory $DIRECTORY created and filled"
ls
exit 0

9
polyamorphism_optimization/templates/NPT.ini Normal file
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INTEGRATOR = md
NSTEPS = 2000000
NLOG = 1000
NENERGY = 100
NSTXOUT = 1000
TCOUPL = v-rescale
TAUT = 1.0
PCOUPL = c-rescale
TAUP = 1.0

9
polyamorphism_optimization/templates/NVT.ini Normal file
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INTEGRATOR = md
NSTEPS = 2000000
NLOG = 1000
NENERGY = 100
NSTXOUT = 1000
TCOUPL = v-rescale
TAUT = 1.0
PCOUPL = no
TAUP = 1.0

31
polyamorphism_optimization/templates/mdp_parameters.mdp Normal file
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integrator = INTEGRATOR
dt = 0.001
nsteps = NSTEPS
nstcomm = 10
nstlog = NLOG
nstcalcenergy = 10
nstenergy = NENERGY
nstxout-compressed = NSTXOUT
compressed-x-precision = 1000
energygrps = system
rlist = 1.2
nstlist = 10
coulombtype = pme
rcoulomb = 1.2
coulomb-modifier = potential-shift-verlet
vdwtype = pme
rvdw = 1.2
vdw-modifier = potential-shift-verlet
fourierspacing = 0.144
tcoupl = v-rescale
tau_t = TAUT
gen_vel = yes
gen_temp = TEMP
ref_t = TEMP
tc-grps = system
pcoupl = PCOUPL
tau_p = TAUP
ref_p = PRESSURE
compressibility = 4.5e-5
nstpcouple = 10
nsttcouple = 10

10
polyamorphism_optimization/templates/params/annealing1.ini Normal file
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INTEGRATOR = md
NSTEPS = 2000000
NLOG = 1000
NENERGY = 100
NSTXOUT = 1000
TCOUPL = v-rescale
TAUT = 0.5
TEMP = 10.0
PCOUPL = c-rescale
TAUP = 1.0

10
polyamorphism_optimization/templates/params/annealing2.ini Normal file
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INTEGRATOR = md
NSTEPS = 5000000
NLOG = 1000
NENERGY = 100
NSTXOUT = 1000
TCOUPL = v-rescale
TAUT = 0.5
TEMP = 10.0
PCOUPL = c-rescale
TAUP = 1.0

10
polyamorphism_optimization/templates/params/emin.ini Normal file
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INTEGRATOR = steep
NSTEPS = 10000
NLOG = 100
NENERGY = 100
NSTXOUT = 100
TAUT = 1.0
TEMP = 300
PCOUPL = no
TCOUPL = no
TAUP = 1.0

33
polyamorphism_optimization/templates/top_3point.top Normal file
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[ 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
L 1
[atoms]
; nr type resnr residu atom cgnr charge
1 A 1 L A 1 CHARGE_A MASS
2 B 1 L B1 1 CHARGE_B MASS
3 B 1 L B2 1 CHARGE_B MASS
[settles]
;i funct doh dhh
1 1 D_AB D_BB
[exclusions]
1 2 3
2 1 3
3 1 2
[system]
MODEL
[molecules]
L NMOL

40
polyamorphism_optimization/templates/top_4point.top Normal file
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[ 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
D 0 0.000 D 0.0 0.0
[moleculetype]
; name nrexcl
L 1
[atoms]
; nr type resnr residu atom cgnr charge
1 A 1 L A 1 0 MASS
2 B 1 L B1 1 CHARGE_B MASS
3 B 1 L B2 1 CHARGE_B MASS
4 D 1 L D 1 CHARGE_A 0.0
[settles]
;i funct doh dhh
1 1 D_AB D_BB
[dummies3]
; Dummy from funct a b
4 1 2 3 1 DUMMY_AB DUMMY_AB
[exclusions]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
[system]
MODEL
[molecules]
L NMOL

31
polyamorphism_optimization/templates/top_atomistic.top Normal file
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[ 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 NMOL
B NMOLB