Vitor Hideyoshi
2a4e9eff0c
This commit adds the methods that were present in the Gaussian.py file into the SetGlobals.py file and packages the program into a diceplayer module so it can be ran using 'python3 -m diceplayer' Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
343 lines
10 KiB
Python
343 lines
10 KiB
Python
#!/usr/bin/python3
|
|
|
|
import os, sys, time, signal
|
|
import setproctitle
|
|
import argparse
|
|
import shutil
|
|
from multiprocessing import Process, connection
|
|
|
|
from diceplayer.DPpack.PTable import *
|
|
from diceplayer.DPpack.SetGlobals import *
|
|
from diceplayer.DPpack.MolHandling import *
|
|
from diceplayer.DPpack.Misc import *
|
|
|
|
_version = 'dev'
|
|
setproctitle.setproctitle("diceplayer-{}".format(_version))
|
|
|
|
if __name__ == '__main__':
|
|
#### Read and store the arguments passed to the program ####
|
|
#### and set the usage and help messages ####
|
|
|
|
parser = argparse.ArgumentParser(prog='Diceplayer')
|
|
parser.add_argument('--continue', dest='opt_continue' , default=False, action='store_true')
|
|
parser.add_argument('--version', action='version', version='%(prog)s 1.0')
|
|
parser.add_argument('-i', dest='infile', default='control.in', metavar='INFILE',
|
|
help='input file of diceplayer [default = control.in]')
|
|
parser.add_argument('-o', dest='outfile', default='run.log', metavar='OUTFILE',
|
|
help='output file of diceplayer [default = run.log]')
|
|
## Study the option of a parameter for continuing the last process via data from control.in and run.log files
|
|
|
|
args = parser.parse_args()
|
|
|
|
#### Open OUTFILE for writing and print keywords and initial info
|
|
|
|
try:
|
|
|
|
if args.opt_continue and os.path.exists(args.outfile):
|
|
|
|
outfile = open(args.outfile,'r')
|
|
run_file = outfile.readlines()
|
|
control_sequence = ' Step # '
|
|
sucessfull_sequence = '+----------------------------------------------------------------------------------------+'
|
|
|
|
for line in run_file:
|
|
if control_sequence in line:
|
|
cyc = int(line[-2])
|
|
if sucessfull_sequence in line:
|
|
cyc += 1
|
|
|
|
|
|
outfile.close()
|
|
|
|
if os.path.isfile(args.outfile+".backup"):
|
|
os.remove(args.outfile+".backup")
|
|
|
|
os.rename(args.outfile,args.outfile+".backup")
|
|
outfile = open(args.outfile,'w',1)
|
|
|
|
elif os.path.exists(args.outfile):
|
|
os.rename(args.outfile, args.outfile+".backup")
|
|
outfile = open(args.outfile,'w',1)
|
|
else:
|
|
outfile = open(args.outfile,"w",1)
|
|
|
|
except EnvironmentError as err:
|
|
sys.exit(err)
|
|
|
|
try:
|
|
|
|
if os.path.exists(args.infile):
|
|
infile = open(args.infile,"r")
|
|
|
|
except EnvironmentError as err:
|
|
sys.exit(err)
|
|
|
|
#### Read and check the keywords in INFILE
|
|
|
|
internal = Internal(infile, outfile)
|
|
|
|
internal.read_keywords()
|
|
|
|
if args.opt_continue:
|
|
try:
|
|
internal.player.initcyc = cyc
|
|
except:
|
|
sys.exit("Error: There is no sutable run.log file to continue the previous process")
|
|
|
|
internal.check_keywords()
|
|
internal.print_keywords()
|
|
|
|
# #### Check whether the executables are in the path
|
|
|
|
internal.check_executables()
|
|
|
|
# #### Read the potential, store the info in 'molecules' and prints the info in OUTFILE
|
|
|
|
internal.read_potential()
|
|
|
|
# if internal.player.lps == "yes":
|
|
# read_lps()
|
|
|
|
# if internal.player.ghosts == "yes":
|
|
# read_ghosts()
|
|
|
|
internal.print_potential()
|
|
|
|
#### Bring the molecules to standard orientation and prints info about them
|
|
|
|
for i in range(len(internal.system.molecule)):
|
|
|
|
internal.outfile.write("\nMolecule type {} - {}:\n\n".format(i + 1, internal.system.molecule[i].molname))
|
|
internal.system.molecule[i].print_mol_info(internal.outfile)
|
|
internal.outfile.write(" Translating and rotating molecule to standard orientation...")
|
|
internal.system.molecule[i].standard_orientation()
|
|
internal.outfile.write(" Done\n\n New values:\n")
|
|
internal.system.molecule[i].print_mol_info(internal.outfile)
|
|
|
|
internal.outfile.write(90 * "=")
|
|
internal.outfile.write("\n")
|
|
|
|
if not args.opt_continue:
|
|
make_simulation_dir()
|
|
else:
|
|
simdir = "simfiles"
|
|
stepdir = "step{:02d}".format(internal.player.initcyc)
|
|
if os.path.exists(simdir+os.sep+stepdir):
|
|
shutil.rmtree(simdir+os.sep+stepdir)
|
|
|
|
#### Open the geoms.xyz file and prints the initial geometry if starting from zero
|
|
|
|
if internal.player.initcyc == 1:
|
|
try:
|
|
path = "geoms.xyz"
|
|
geomsfh = open(path, "w", 1)
|
|
except EnvironmentError as err:
|
|
sys.exit(err)
|
|
internal.system.print_geom(0, geomsfh)
|
|
else:
|
|
try:
|
|
path = "geoms.xyz"
|
|
geomsfh = open(path, "a", 1)
|
|
except EnvironmentError as err:
|
|
sys.exit(err)
|
|
|
|
internal.outfile.write("\nStarting the iterative process.\n")
|
|
|
|
## Initial position (in Bohr)
|
|
position = internal.system.molecule[0].read_position()
|
|
|
|
## If restarting, read the last gradient and hessian
|
|
# if internal.player.initcyc > 1:
|
|
# if internal.player.qmprog in ("g03", "g09", "g16"):
|
|
# Gaussian.read_forces("grad_hessian.dat")
|
|
# Gaussian.read_hessian_fchk("grad_hessian.dat")
|
|
|
|
#if player['qmprog'] == "molcas":
|
|
#Molcas.read_forces("grad_hessian.dat")
|
|
#Molcas.read_hessian("grad_hessian.dat")
|
|
|
|
###
|
|
### Start the iterative process
|
|
###
|
|
|
|
internal.outfile.write("\n" + 90 * "-" + "\n")
|
|
|
|
for cycle in range(internal.player.initcyc, internal.player.initcyc + internal.player.maxcyc):
|
|
|
|
internal.outfile.write("{} Step # {}\n".format(40 * " ", cycle))
|
|
internal.outfile.write(90 * "-" + "\n\n")
|
|
|
|
make_step_dir(cycle)
|
|
|
|
####
|
|
#### Start block of parallel simulations
|
|
####
|
|
|
|
procs = []
|
|
sentinels = []
|
|
for proc in range(1, internal.player.nprocs + 1):
|
|
|
|
p = Process(target=internal.simulation_process, args=(cycle, proc))
|
|
p.start()
|
|
procs.append(p)
|
|
sentinels.append(p.sentinel)
|
|
|
|
while procs:
|
|
finished = connection.wait(sentinels)
|
|
for proc_sentinel in finished:
|
|
i = sentinels.index(proc_sentinel)
|
|
status = procs[i].exitcode
|
|
procs.pop(i)
|
|
sentinels.pop(i)
|
|
if status != 0:
|
|
for p in procs:
|
|
p.terminate()
|
|
sys.exit(status)
|
|
|
|
for proc in range(1, internal.player.nprocs + 1):
|
|
internal.print_last_config(cycle, proc)
|
|
|
|
internal.outfile.write("\n+" + 88 * "-" + "+\n")
|
|
|
|
###
|
|
### End of parallel simulations block
|
|
###
|
|
|
|
## Make ASEC
|
|
# internal.outfile.write("\nBuilding the ASEC and vdW meanfields... ")
|
|
# asec_charges = internal.populate_asec_vdw(cycle)
|
|
|
|
# ## After ASEC is built, compress files bigger than 1MB
|
|
# for proc in range(1, internal.player.nprocs + 1):
|
|
# path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
|
|
# compress_files_1mb(path)
|
|
|
|
###
|
|
### Start QM calculation
|
|
###
|
|
|
|
make_qm_dir(cycle)
|
|
|
|
if internal.player.qmprog in ("g03", "g09", "g16"):
|
|
|
|
if cycle > 1:
|
|
src = "simfiles" + os.sep + "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
|
|
dst = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
|
|
shutil.copyfile(src, dst)
|
|
|
|
internal.make_gaussian_input(cycle)
|
|
internal.gaussian.run_gaussian(cycle, "force", internal.outfile)
|
|
# internal.gaussian.run_formchk(cycle, internal.outfile)
|
|
|
|
# ## Read the gradient
|
|
# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk"
|
|
# gradient = internal.read_forces(file, internal.outfile)
|
|
# if len(cur_gradient) > 0:
|
|
# old_gradient = cur_gradient
|
|
# cur_gradient = gradient
|
|
|
|
# ## If 1st step, read the hessian
|
|
# if cycle == 1:
|
|
# if internal.player.readhessian == "yes":
|
|
# file = "grad_hessian.dat"
|
|
# internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
|
|
# hessian = internal.read_hessian_fchk(file)
|
|
# else:
|
|
# file = "simfiles" + os.sep + "step01" + os.sep + "qm" + os.sep + "asec.fchk"
|
|
# internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
|
|
# hessian = internal.gaussian.read_hessian(file)
|
|
|
|
# ## From 2nd step on, update the hessian
|
|
# else:
|
|
# internal.outfile.write("\nUpdating the hessian matrix using the BFGS method... ")
|
|
# hessian = internal.system.molecule[0].update_hessian(step, cur_gradient, old_gradient, hessian)
|
|
# internal.outfile.write("Done\n")
|
|
|
|
# ## Save gradient and hessian
|
|
# internal.gaussian.print_grad_hessian(cycle, cur_gradient, hessian)
|
|
|
|
# ## Calculate the step and update the position
|
|
# step = internal.calculate_step(cur_gradient, hessian, internal.outfile)
|
|
# position += step
|
|
|
|
# ## Update the geometry of the reference molecule
|
|
# internal.system.molecule[0].update_molecule(position, internal.outfile)
|
|
|
|
# ## If needed, calculate the charges
|
|
# if cycle < internal.player.switchcyc:
|
|
|
|
# # internal.gaussian.make_charge_input(cycle, asec_charges)
|
|
# internal.gaussian.run_gaussian(cycle, "charge", internal.outfile)
|
|
|
|
# ## Read the new charges and update molecules[0]
|
|
# if cycle < internal.player.switchcyc:
|
|
# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log"
|
|
# internal.gaussian.read_charges(file, internal.outfile)
|
|
# else:
|
|
# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.log"
|
|
# internal.gaussian.read_charges(file, internal.outfile)
|
|
|
|
# ## Print new info for molecule[0]
|
|
# internal.outfile.write("\nNew values for molecule type 1:\n\n")
|
|
# internal.system.molecule[0].print_mol_info()
|
|
|
|
# ## Print new geometry in geoms.xyz
|
|
# internal.system.molecule[0].print_geom(cycle, geomsfh)
|
|
|
|
# ##
|
|
# ## Molcas block
|
|
# ##
|
|
# #if player['qmprog'] == "molcas":
|
|
|
|
|
|
# #elif player['opt'] == "ts":
|
|
|
|
# ##
|
|
# ## Gaussian block
|
|
# ##
|
|
# #if player['qmprog'] in ("g03", "g09", "g16"):
|
|
|
|
|
|
|
|
# ##
|
|
# ## Molcas block
|
|
# ##
|
|
# #if player['qmprog'] == "molcas":
|
|
|
|
|
|
# else: ## Only relax the charge distribution
|
|
|
|
# if internal.player.qmprog in ("g03", "g09", "g16"):
|
|
|
|
# if cycle > 1:
|
|
# src = "simfiles" + os.sep + "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
|
|
# dst = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
|
|
# shutil.copyfile(src, dst)
|
|
|
|
# # internal.gaussian.make_charge_input(cycle, asec_charges)
|
|
# internal.gaussian.run_gaussian(cycle, "charge", internal.outfile)
|
|
|
|
# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log"
|
|
# internal.read_charges(file)
|
|
|
|
# ## Print new info for molecule[0]
|
|
# internal.outfile.write("\nNew values for molecule type 1:\n\n")
|
|
# internal.system.molecule[0].print_mol_info()
|
|
|
|
# #if player['qmprog'] == "molcas":
|
|
|
|
|
|
|
|
# ####
|
|
# #### End of the iterative process
|
|
# ####
|
|
|
|
# # ## imprimir ultimas mensagens, criar um arquivo de potencial para ser usado em eventual
|
|
# # ## continuacao, fechar arquivos (geoms.xyz, run.log, ...)
|
|
|
|
# # internal.outfile.write("\nDiceplayer finished normally!\n")
|
|
# # internal.outfile.close()
|
|
# # ####
|
|
# # #### End of the program
|
|
# # ####
|