setup_sim.sh removed for innitialize_sim; more usage of templates
This commit is contained in:
Robin
44
polyamorphism_optimization/innitialize_sim.py
Normal file
44
polyamorphism_optimization/innitialize_sim.py
Normal file
@@ -0,0 +1,44 @@
|
||||
#!/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()
|
||||
|
||||
@@ -1,110 +0,0 @@
|
||||
#!/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()
|
||||
|
||||
@@ -1,182 +0,0 @@
|
||||
#!/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
9
polyamorphism_optimization/templates/NPT.ini
Normal file
@@ -0,0 +1,9 @@
|
||||
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
9
polyamorphism_optimization/templates/NVT.ini
Normal file
@@ -0,0 +1,9 @@
|
||||
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
31
polyamorphism_optimization/templates/mdp_parameters.mdp
Normal file
@@ -0,0 +1,31 @@
|
||||
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
10
polyamorphism_optimization/templates/params/annealing1.ini
Normal file
@@ -0,0 +1,10 @@
|
||||
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
10
polyamorphism_optimization/templates/params/annealing2.ini
Normal file
@@ -0,0 +1,10 @@
|
||||
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
10
polyamorphism_optimization/templates/params/emin.ini
Normal file
@@ -0,0 +1,10 @@
|
||||
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
33
polyamorphism_optimization/templates/top_3point.top
Normal file
@@ -0,0 +1,33 @@
|
||||
[ 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
40
polyamorphism_optimization/templates/top_4point.top
Normal file
@@ -0,0 +1,40 @@
|
||||
[ 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
31
polyamorphism_optimization/templates/top_atomistic.top
Normal file
@@ -0,0 +1,31 @@
|
||||
[ 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
|
||||
Reference in New Issue
Block a user