Vitor Hideyoshi Nakazone Batista
316acf4761
Fixed Numerus functions in the SetGlobals file and MolHandling, translated DicePlayer and tested till printing of initial geometry for cyc==1 Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
327 lines
9.9 KiB
Python
327 lines
9.9 KiB
Python
#!/export/apps/python/361/bin/python3
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import os, sys, time, signal
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import argparse
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import shutil
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from multiprocessing import Process, connection
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import DPpack.Dice as Dice
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import DPpack.Gaussian as Gaussian
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from DPpack.PTable import *
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from DPpack.SetGlobals import *
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from DPpack.MolHandling import *
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from DPpack.Misc import *
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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='%(prog)s 1.0')
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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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outfile = open(args.outfile,'r')
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run_file = outfile.readlines()
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control_sequence = ' Step # '
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for line in run_file:
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if control_sequence in line:
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cyc = int(line[-2]) + 1
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outfile.close()
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os.rename(os.path.abspath(args.outfile),os.path.abspath(args.outfile)+".backup")
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outfile = open(args.outfile,'w')
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if os.path.exists(args.outfile):
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os.rename(os.path.abspath(args.outfile),os.path.abspath(args.outfile)+".backup")
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outfile = open(args.outfile,'w')
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else:
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outfile = open(args.outfile,"w")
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except EnvironmentError 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 EnvironmentError 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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if args.opt_continue:
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internal.player.cyc = cyc
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internal.check_keywords()
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internal.print_keywords()
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# #### Check whether the executables are in the path
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# internal.check_executables()
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# #### Read the potential, store the info in 'molecules' and prints the info in OUTFILE
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internal.read_potential()
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# if internal.player.lps == "yes":
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# read_lps()
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# if internal.player.ghosts == "yes":
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# read_ghosts()
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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))
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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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#### Open the geoms.xyz file and prints the initial geometry if starting from zero
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if internal.player.cyc == 1:
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try:
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geomsfh = open("geoms.xyz", "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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else:
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try:
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geomsfh = open("geoms.xyz", "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.cyc > 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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# for cycle in range(internal.player.cyc, internal.player.cyc + internal.player.maxcyc):
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# internal.outfile.write("\n" + 90 * "-" + "\n")
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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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# if internal.player.altsteps == 0 or cycle == 1:
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# internal.dice.randominit = True
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# else:
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# internal.dice.randominit = False
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# ####
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# #### Start block of parallel simulations
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# ####
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# procs = []
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# sentinels = []
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# for proc in range(1, internal.player.nprocs + 1):
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# p = Process(target=Dice.simulation_process, args=(cycle, proc, internal.outfile))
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# p.start()
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# procs.append(p)
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# sentinels.append(p.sentinel)
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# while procs:
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# finished = connection.wait(sentinels)
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# for proc_sentinel in finished:
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# i = sentinels.index(proc_sentinel)
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# status = procs[i].exitcode
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# procs.pop(i)
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# sentinels.pop(i)
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# if status != 0:
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# for p in procs:
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# p.terminate()
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# sys.exit(status)
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# for proc in range(1, internal.player.nprocs + 1):
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# Dice.print_last_config(cycle, proc)
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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.opt == "yes":
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# ##
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# ## Gaussian block
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# ##
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# if internal.player.qmprog in ("g03", "g09", "g16"):
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# if cycle > 1:
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# src = "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
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# dst = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
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# shutil.copyfile(src, dst)
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# Gaussian.make_force_input(cycle, asec_charges)
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# Gaussian.run_gaussian(cycle, "force", internal.outfile)
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# Gaussian.run_formchk(cycle, internal.outfile)
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# ## Read the gradient
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# file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk"
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# gradient = Gaussian.read_forces(file, internal.outfile)
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# if len(cur_gradient) > 0:
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# old_gradient = cur_gradient
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# cur_gradient = gradient
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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 = Gaussian.read_hessian_fchk(file)
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# else:
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# file = "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.gaussian.read_hessian(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, cur_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.gaussian.print_grad_hessian(cycle, cur_gradient, hessian)
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# ## Calculate the step and update the position
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# step = internal.calculate_step(cur_gradient, hessian, internal.outfile)
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# position += step
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# ## Update the geometry of the reference molecule
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# internal.system.molecule[0].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 = "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 = "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 = "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
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# dst = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
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# shutil.copyfile(src, dst)
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# Gaussian.make_charge_input(cycle, asec_charges)
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# Gaussian.run_gaussian(cycle, "charge", internal.outfile)
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# file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log"
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# Gaussian.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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# ####
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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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# #### |