315 lines
9.5 KiB
Python
315 lines
9.5 KiB
Python
#!/usr/bin/python3
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from multiprocessing import Process, connection
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import os, sys, time, signal
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import setproctitle
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import numpy as np
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import argparse
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import shutil
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import pickle
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from diceplayer.DPpack.PTable import *
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from diceplayer.DPpack.SetGlobals import *
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from diceplayer.DPpack.MolHandling import *
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from diceplayer.DPpack.Misc import *
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__version = 'dev'
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setproctitle.setproctitle("diceplayer-{}".format(__version))
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if __name__ == '__main__':
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#### Read and store the arguments passed to the program ####
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#### and set the usage and help messages ####
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parser = argparse.ArgumentParser(prog='Diceplayer')
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parser.add_argument('--continue', dest='opt_continue' , default=False, action='store_true')
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parser.add_argument('--version', action='version', version= "diceplayer-"+__version)
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parser.add_argument('-i', dest='infile', default='control.in', metavar='INFILE',
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help='input file of diceplayer [default = control.in]')
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parser.add_argument('-o', dest='outfile', default='run.log', metavar='OUTFILE',
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help='output file of diceplayer [default = run.log]')
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## Study the option of a parameter for continuing the last process via data from control.in and run.log files
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args = parser.parse_args()
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#### Open OUTFILE for writing and print keywords and initial info
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try:
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if args.opt_continue and os.path.exists(args.outfile):
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save = pickle.load(open("latest-step.pkl","rb"))
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if os.path.isfile(args.outfile+".backup"):
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os.remove(args.outfile+".backup")
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os.rename(args.outfile,args.outfile+".backup")
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outfile = open(args.outfile,'w',1)
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elif os.path.exists(args.outfile):
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os.rename(args.outfile, args.outfile+".backup")
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outfile = open(args.outfile,'w',1)
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else:
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outfile = open(args.outfile,"w",1)
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except Exception as err:
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sys.exit(err)
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try:
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if os.path.exists(args.infile):
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infile = open(args.infile,"r")
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except Exception as err:
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sys.exit(err)
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#### Read and check the keywords in INFILE
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internal = Internal(infile, outfile)
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internal.read_keywords()
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internal.check_keywords()
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internal.print_keywords()
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if args.opt_continue:
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internal.player.initcyc = save[0] + 1
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internal.system = save[1]
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else:
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internal.read_potential()
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#### Check whether the executables are in the path
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#### and print potential to Log File
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internal.check_executables()
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internal.print_potential()
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#### Bring the molecules to standard orientation and prints info about them
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for i in range(len(internal.system.molecule)):
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internal.outfile.write("\nMolecule type {} - {}:\n\n".format(i + 1, internal.system.molecule[i].molname))
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internal.system.molecule[i].print_mol_info(internal.outfile)
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internal.outfile.write(" Translating and rotating molecule to standard orientation...")
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internal.system.molecule[i].standard_orientation()
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internal.outfile.write(" Done\n\n New values:\n")
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internal.system.molecule[i].print_mol_info(internal.outfile)
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internal.outfile.write(90 * "=")
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internal.outfile.write("\n")
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if not args.opt_continue:
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make_simulation_dir()
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else:
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simdir = "simfiles"
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stepdir = "step{:02d}".format(internal.player.initcyc)
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if os.path.exists(simdir+os.sep+stepdir):
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shutil.rmtree(simdir+os.sep+stepdir)
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#### Open the geoms.xyz file and prints the initial geometry if starting from zero
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if internal.player.initcyc == 1:
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try:
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path = "geoms.xyz"
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geomsfh = open(path, "w", 1)
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except EnvironmentError as err:
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sys.exit(err)
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internal.system.print_geom(0, geomsfh)
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geomsfh.write(40 * "-"+"\n")
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else:
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try:
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path = "geoms.xyz"
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geomsfh = open(path, "a", 1)
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except EnvironmentError as err:
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sys.exit(err)
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internal.outfile.write("\nStarting the iterative process.\n")
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## Initial position (in Bohr)
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position = internal.system.molecule[0].read_position()
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## If restarting, read the last gradient and hessian
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# if internal.player.initcyc > 1:
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# if internal.player.qmprog in ("g03", "g09", "g16"):
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# Gaussian.read_forces("grad_hessian.dat")
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# Gaussian.read_hessian_fchk("grad_hessian.dat")
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#if player['qmprog'] == "molcas":
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#Molcas.read_forces("grad_hessian.dat")
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#Molcas.read_hessian("grad_hessian.dat")
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###
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### Start the iterative process
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###
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internal.outfile.write("\n" + 90 * "-" + "\n")
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for cycle in range(internal.player.initcyc, internal.player.initcyc + internal.player.maxcyc):
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internal.outfile.write("{} Step # {}\n".format(40 * " ", cycle))
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internal.outfile.write(90 * "-" + "\n\n")
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make_step_dir(cycle)
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####
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#### Start block of parallel simulations
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####
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internal.dice_start(cycle)
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###
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### End of parallel simulations block
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###
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## Make ASEC
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# internal.outfile.write("\nBuilding the ASEC and vdW meanfields... ")
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# asec_charges = internal.populate_asec_vdw(cycle)
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# ## After ASEC is built, compress files bigger than 1MB
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# for proc in range(1, internal.player.nprocs + 1):
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# path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
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# compress_files_1mb(path)
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###
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### Start QM calculation
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###
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# make_qm_dir(cycle)
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# if internal.player.qmprog in ("g03", "g09", "g16"):
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# if cycle > 1:
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# src = "simfiles" + os.sep + "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
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# dst = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
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# shutil.copyfile(src, dst)
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# internal.make_gaussian_input(cycle)
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# internal.gaussian.run_gaussian(cycle, "force", internal.outfile)
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# internal.gaussian.run_formchk(cycle, internal.outfile)
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# ## Read the gradient
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# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk"
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# try:
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# gradient
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# old_gradient = gradient
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# except:
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# pass
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# gradient = internal.read_forces_fchk(file, internal.outfile)
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# # If 1st step, read the hessian
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# if cycle == 1:
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# if internal.player.readhessian == "yes":
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# file = "grad_hessian.dat"
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# internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
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# hessian = internal.read_hessian_log(file)
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# else:
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# file = "simfiles" + os.sep + "step01" + os.sep + "qm" + os.sep + "asec.fchk"
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# internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
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# hessian = internal.read_hessian_fchk(file)
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# # From 2nd step on, update the hessian
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# else:
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# internal.outfile.write("\nUpdating the hessian matrix using the BFGS method... ")
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# hessian = internal.system.molecule[0].update_hessian(step, gradient, old_gradient, hessian)
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# internal.outfile.write("Done\n")
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# # Save gradient and hessian
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# internal.print_grad_hessian(cycle, gradient, hessian)
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# # Calculate the step and update the position
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# step = internal.calculate_step(cycle, gradient, hessian)
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# position += step
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# # ## Update the geometry of the reference molecule
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# internal.system.update_molecule(position, internal.outfile)
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# ## If needed, calculate the charges
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# if cycle < internal.player.switchcyc:
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# # internal.gaussian.make_charge_input(cycle, asec_charges)
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# internal.gaussian.run_gaussian(cycle, "charge", internal.outfile)
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# ## Read the new charges and update molecules[0]
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# if cycle < internal.player.switchcyc:
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# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log"
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# internal.gaussian.read_charges(file, internal.outfile)
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# else:
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# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.log"
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# internal.gaussian.read_charges(file, internal.outfile)
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# ## Print new info for molecule[0]
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# internal.outfile.write("\nNew values for molecule type 1:\n\n")
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# internal.system.molecule[0].print_mol_info()
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# ## Print new geometry in geoms.xyz
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# internal.system.molecule[0].print_geom(cycle, geomsfh)
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# ##
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# ## Molcas block
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# ##
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# #if player['qmprog'] == "molcas":
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# #elif player['opt'] == "ts":
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# ##
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# ## Gaussian block
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# ##
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# #if player['qmprog'] in ("g03", "g09", "g16"):
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# ##
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# ## Molcas block
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# ##
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# #if player['qmprog'] == "molcas":
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# else: ## Only relax the charge distribution
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# if internal.player.qmprog in ("g03", "g09", "g16"):
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# if cycle > 1:
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# src = "simfiles" + os.sep + "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
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# dst = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
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# shutil.copyfile(src, dst)
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# # internal.gaussian.make_charge_input(cycle, asec_charges)
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# internal.gaussian.run_gaussian(cycle, "charge", internal.outfile)
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# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log"
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# internal.read_charges(file)
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# ## Print new info for molecule[0]
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# internal.outfile.write("\nNew values for molecule type 1:\n\n")
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# internal.system.molecule[0].print_mol_info()
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# #if player['qmprog'] == "molcas":
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internal.system.print_geom(cycle, geomsfh)
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geomsfh.write(40 * "-"+"\n")
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internal.outfile.write("\n+" + 88 * "-" + "+\n")
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pickle.dump([cycle,internal.system], open("latest-step.pkl", "wb"))
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####
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#### End of the iterative process
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####
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## imprimir ultimas mensagens, criar um arquivo de potencial para ser usado em eventual
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## continuacao, fechar arquivos (geoms.xyz, run.log, ...)
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internal.outfile.write("\nDiceplayer finished normally!\n")
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internal.outfile.close()
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####
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#### End of the program
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####
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