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Merge pull request #20 from yskmiyazaki/mod_ions
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Mod ions
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@yskmiyazaki
yskmiyazaki authored Nov 10, 2023
2 parents 975f74d + bed7ba1 commit 06f401c
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Showing 5 changed files with 479 additions and 64 deletions.
15 changes: 13 additions & 2 deletions bin/cg_spica
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ from pathlib import Path
sys.path.append( str(Path(__file__).resolve().parents[1] / "src") )
import gen_top_ENM, gen_top_Go, json_to_top, map_to_cg, map_traj
import wat_to_polar, setup_lmp, setup_gmx, gen_lmp_input, gen_gmx_input
import mod_ion
from argparse import ArgumentParser, RawTextHelpFormatter

def get_option():
Expand All @@ -16,6 +17,7 @@ def get_option():
json2top : make top file from json file
map2cg : map AA configuration to CG (only PDB format)
maptraj : map AA MD trajectory to CG (MDAnalysis module is required)
modion : adjust NaCl salt concentration in CG configuration
ENM : generate top file of protein with elastic network
Go : generate top file of protein with Go model
wat2polar : convert SPICA CG water to pSPICA polar CG water
Expand Down Expand Up @@ -91,6 +93,16 @@ def main():
outfile = args.output
wat2polar = wat_to_polar.wat_to_polar(infile, outfile)
wat2polar.run()
elif args.tool_name == "modion":
args = mod_ion.get_option_script(sub)
infile = args.input
outfile = args.output
conc = args.conc
soluq = args.soluq
pspica = args.pspica
verbose = args.verbose
modion = mod_ion.mod_ion(infile, outfile, conc, soluq, pspica, verbose)
modion.run()
elif args.tool_name == "setup_lmp":
args = setup_lmp.get_option_script(sub)
setup_lmp.run(args)
Expand All @@ -104,9 +116,8 @@ def main():
outfile = args.output
temp = args.T
press = args.P
GPU = args.GPU
pspica = args.pspica
gen_lmpin = gen_lmp_input.gen_lmp_inp(datafile, parmfile, outfile, temp, press, GPU, pspica)
gen_lmpin = gen_lmp_input.gen_lmp_inp(datafile, parmfile, outfile, temp, press, pspica)
gen_lmpin.run()
elif args.tool_name == "gen_gmxin":
args = gen_gmx_input.get_option_script(sub)
Expand Down
97 changes: 52 additions & 45 deletions src/gen_lmp_input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,6 @@ def get_option():
argparser.add_argument('-P', type=float,
default=1.,
help='system pressure [atm] (default: 1.0).')
argparser.add_argument('-GPU', action='store_true',
help='use GPU option for LAMMPS simulation (default: off).')
argparser.add_argument('-pspica', action='store_true',
help='generate LAMMPS input for pSPICA FF (default: for SPICA FF).')
return argparser.parse_args()
Expand All @@ -48,20 +46,17 @@ def get_option_script(argv):
argparser.add_argument('-P', type=float,
default=1.,
help='system pressure [atm] (default: 1.0).')
argparser.add_argument('-GPU', action='store_true',
help='use GPU option for LAMMPS simulation (default: off).')
argparser.add_argument('-pspica', action='store_true',
help='generate LAMMPS input for pSPICA FF (default: for SPICA FF).')
return argparser.parse_args(argv)

class gen_lmp_inp:
def __init__(self, datafile, parmfile, outf, temp, press, GPU, pspica):
def __init__(self, datafile, parmfile, outf, temp, press, pspica):
self.datafile = datafile
self.parmfile = parmfile
self.outf = outf
self.temp = temp
self.press = press
self.GPU = GPU
self.pspica = pspica

def tune_mesh(self, boxl):
Expand Down Expand Up @@ -168,61 +163,71 @@ def run(self):
f = open(self.outf, "w")
if self.pspica:
print("##### Generate LAMMPS input file for pSPICA #####")
else:
print("##### Generate LAMMPS input file for SPICA #####")
print()
if self.pspica:
print("### LAMMPS input for pSPICA FF ###", file=f)
gs = 2
else:
print("##### Generate LAMMPS input file for SPICA #####")
print("### LAMMPS input for SPICA FF ###", file=f)
print(file=f)
gs = 5
print()
print("# Define variables", file=f)
print(f"variable op string run_00", file=f)
print(f"variable nstep equal 1000000", file=f)
print(f"variable nlog equal 1000", file=f)
print(f"variable ndump equal 10000", file=f)
print(f"variable nrest equal 50000", file=f)
print(f"variable t equal {round(self.temp, 2)}", file=f)
print(f"variable p equal {round(self.press, 3)}", file=f)
print(f"variable t equal {round(self.temp, 2)}", file=f)
print(f"variable p equal {round(self.press, 3)}", file=f)
print(f"variable ip index none", file=f)
print(f"variable op index run_00", file=f)
print(f"variable min index no", file=f)
print(f"variable nstep index 100000", file=f)
print(f"variable nlog index 1000", file=f)
print(f"variable ndump index 10000", file=f)
print(f"variable nrest index 50000", file=f)
print(file=f)
print("# Unit and data file style", file=f)
print(f"units real", file=f)
print(f"atom_style full", file=f)
print(file=f)
print("# Set Newton's third law for interactions", file=f)
if self.GPU:
print(f"newton off", file=f)
else:
print(f"newton on off", file=f)
print(f'if "$(is_active(package,gpu))" then &', file=f)
print(f'"newton off" &', file=f)
print(f'else &', file=f)
print(f'"newton on off"', file=f)
print(file=f)
print("# Load data and parameter files", file=f)
print(f"read_data {self.datafile}", file=f)
print('if "${ip} == none" then &', file=f)
print(f'"read_data {self.datafile}" &', file=f)
print(f'else &', file=f)
print('"read_restart ${ip}.rest"', file=f)

print(f"include {self.parmfile}", file=f)
print(file=f)
boxl = self.read_box()
if self.check_coul():
print("# Coulomb interaction", file=f)
print(f"variable gs equal {gs}", file=f)
print("variable nx equal round(lx/${gs})", file=f)
print("variable ny equal round(ly/${gs})", file=f)
print("variable nz equal round(lz/${gs})", file=f)
if self.pspica:
print(f"kspace_style pppm 1.0e-5", file=f)
print("kspace_style pppm 1.0e-5", file=f)
else:
print(f"kspace_style pppm/cg 1.0e-5", file=f)
mesh = self.tune_mesh(boxl)
print("kspace_style pppm/cg 1.0e-5", file=f)
#mesh = self.tune_mesh(boxl)
if self.pspica:
print(f"kspace_modify mesh {mesh[0]} {mesh[1]} {mesh[2]} order 5", file=f)
print("kspace_modify mesh ${nx} ${ny} ${nz}", file=f)
else:
print(f"kspace_modify mesh {mesh[0]} {mesh[1]} {mesh[2]} order 3", file=f)
print("kspace_modify mesh ${nx} ${ny} ${nz} order 3", file=f)
print(file=f)
print("# Neighbor list setup", file=f)
print(f"neighbor 2.0 bin", file=f)
print(f"neigh_modify delay 5", file=f)
print(f"neigh_modify delay 4", file=f)
print(file=f)
print("# Minimization", file=f)
print(f"min_style cg", file=f)
print(f"minimize 1.0e-4 1.0e-6 100 1000", file=f)
print('if "${min} == yes" then &', file=f)
print('"min_style cg" &', file=f)
print('"minimize 1.0e-4 1.0e-6 100 1000" &', file=f)
print('"velocity all create $t 12345 dist gaussian rot yes"', file=f)
print(file=f)
print("# Zero timestep and assign initial velocity", file=f)
print("# Zero timestep", file=f)
print(f"reset_timestep 0", file=f)
print(f"velocity all create $t 12345 mom yes rot yes dist gaussian", file=f)
print(file=f)
print("# Timestep for integration [fs]", file=f)
print(f"timestep 10", file=f)
Expand All @@ -234,13 +239,13 @@ def run(self):
print(f"fix 0 all shake 1.0e-5 10 0 b {polarbond}", file=f)
print(f"fix 1 all momentum 1 linear 1 1 1", file=f)
if len(set(boxl)) == 1:
print(f"fix 2 all npt temp $t $t 500. iso $p $p 5000. drag 0.1", file=f)
print(f"fix 2 all npt temp $t $t 500. iso $p $p 5000.", file=f)
cpl = "isotropic"
elif boxl[0] == boxl[1] and boxl[0] != boxl[2]:
print(f"fix 2 all npt temp $t $t 500. aniso $p $p 5000. couple xy drag 0.1", file=f)
print(f"fix 2 all npt temp $t $t 500. aniso $p $p 5000. couple xy", file=f)
cpl = "semiisotropic"
else:
print(f"fix 2 all npt temp $t $t 500. aniso $p $p 5000. drag 0.1", file=f)
print(f"fix 2 all npt temp $t $t 500. aniso $p $p 5000.", file=f)
cpl = "anisotropic"
print(file=f)
print("# Output log information", file=f)
Expand All @@ -257,20 +262,23 @@ def run(self):
print("# Number of steps to integrate and Perform MD", file=f)
print("run ${nstep}", file=f)
print(file=f)
print("# Output the final snapshot", file=f)
print("write_dump all xtc ${op}.fin.xtc modify unwrap yes", file=f)
print(file=f)
f.close()
print(f"-Pressure coupling is predicted to be '{cpl}' from the simulation box symmetry")
print()
if self.pspica:
print(f"##### LAMMPS input file '{self.outf}' for pSPICA has been generated! #####")
print(f"NOTE: '{self.outf}' is just to run 1 ns LAMMPS MD with NPT using pSPICA.")
else:
print(f"##### LAMMPS input file '{self.outf}' for SPICA has been generated! #####")
print()
if self.pspica:
print(f"NOTE: '{self.outf}' is just to run 100 ns LAMMPS MD with NPT using pSPICA.")
else:
print(f"NOTE: '{self.outf}' is just to run 100 ns LAMMPS MD with NPT using SPICA.")
print(f"NOTE: Please check and modify the input for your simulation purpose.")
print("NOTE: When using GPU, please add '-sf gpu -pk gpu {#ofGPU}' option on command line.")
print(f"NOTE: '{self.outf}' is just to run 1 ns LAMMPS MD with NPT using SPICA.")
print("NOTE: Please check and modify the input for your simulation purpose.")
print("NOTE: Please check and modify the input for your simulation purpose.")
print("Command-line Example:")
print(f"$ lmp_mpi -in {self.outf} -v min yes -v op npt_00 -v nstep 50000 -sf gpu -pk gpu 2")
print(f"$ lmp_mpi -in {self.outf} -v ip npt_00 -v op npt_01 -v nstep 100000 -v -nlog 5000")

if __name__ == "__main__":
args = get_option()
Expand All @@ -279,7 +287,6 @@ def run(self):
outf = args.output
temp = args.T
press = args.P
GPU = args.GPU
pspica = args.pspica
obj = gen_lmp_inp(datafile, parmfile, outf, temp, press, GPU, pspica)
obj = gen_lmp_inp(datafile, parmfile, outf, temp, press, pspica)
obj.run()
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