Vitor Hideyoshi Nakazone Batista
7d74c3fb3e
Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
295 lines
8.1 KiB
Python
295 lines
8.1 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('--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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args = parser.parse_args()
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#### Read and check the keywords in INFILE
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read_keywords(args.infile)
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check_keywords(args.infile)
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#### Open OUTFILE for writing and print keywords and initial info
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try:
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if player['initcyc'] > 1 and os.path.exists(args.outfile):
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oldname = args.outfile + ".old"
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os.replace(args.outfile, oldname)
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logfh = open(args.outfile, 'w', 1)
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except EnvironmentError as err:
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sys.exit(err)
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print_keywords(logfh)
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#### Check whether the executables are in the path
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check_executables(logfh)
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#### Read the potential, store the info in 'molecules' and prints the info in OUTFILE
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read_potential(args.infile)
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if player['lps'] == "yes":
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read_lps()
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if player['ghosts'] == "yes":
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read_ghosts()
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print_potential(logfh)
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#### Bring the molecules to standard orientation and prints info about them
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for i in range(len(molecules)):
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logfh.write("\nMolecule type {}:\n\n".format(i + 1))
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print_mol_info(molecules[i], logfh)
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logfh.write(" Translating and rotating molecule to standard orientation...")
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standard_orientation(molecules[i])
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logfh.write(" Done\n\n New values:\n")
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print_mol_info(molecules[i], logfh)
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logfh.write(90 * "=")
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logfh.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 player['initcyc'] == 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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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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logfh.write("\nStarting the iterative process.\n")
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## Initial position (in Bohr)
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position = read_position(molecules[0])
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## If restarting, read the last gradient and hessian
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if player['initcyc'] > 1:
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if 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(player['initcyc'], player['initcyc'] + player['maxcyc']):
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logfh.write("\n" + 90 * "-" + "\n")
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logfh.write("{} Step # {}\n".format(40 * " ", cycle))
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logfh.write(90 * "-" + "\n\n")
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make_step_dir(cycle)
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if player['altsteps'] == 0 or cycle == 1:
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dice['randominit'] = True
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else:
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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, player['nprocs'] + 1):
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p = Process(target=Dice.simulation_process, args=(cycle, proc, logfh))
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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, 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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logfh.write("\nBuilding the ASEC and vdW meanfields... ")
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asec_charges = populate_asec_vdw(cycle, logfh)
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## After ASEC is built, compress files bigger than 1MB
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for proc in range(1, 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 player['opt'] == "yes":
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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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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", logfh)
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Gaussian.run_formchk(cycle, logfh)
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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, logfh)
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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 player['readhessian'] == "yes":
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file = "grad_hessian.dat"
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logfh.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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logfh.write("\nReading the hessian matrix from file {}\n".format(file))
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hessian = Gaussian.read_hessian(file)
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## From 2nd step on, update the hessian
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else:
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logfh.write("\nUpdating the hessian matrix using the BFGS method... ")
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hessian = update_hessian(step, cur_gradient, old_gradient, hessian)
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logfh.write("Done\n")
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## Save gradient and hessian
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Gaussian.print_grad_hessian(cycle, cur_gradient, hessian)
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## Calculate the step and update the position
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step = calculate_step(cur_gradient, hessian, logfh)
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position += step
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## Update the geometry of the reference molecule
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update_molecule(position, logfh)
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## If needed, calculate the charges
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if cycle < player['switchcyc']:
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Gaussian.make_charge_input(cycle, asec_charges)
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Gaussian.run_gaussian(cycle, "charge", logfh)
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## Read the new charges and update molecules[0]
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if cycle < player['switchcyc']:
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file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log"
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Gaussian.read_charges(file, logfh)
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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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Gaussian.read_charges(file, logfh)
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## Print new info for molecule[0]
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logfh.write("\nNew values for molecule type 1:\n\n")
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print_mol_info(molecules[0], logfh)
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## Print new geometry in geoms.xyz
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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 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", logfh)
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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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logfh.write("\nNew values for molecule type 1:\n\n")
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print_mol_info(molecules[0], logfh)
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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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logfh.write("\nDiceplayer finished normally!\n")
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logfh.close()
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####
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#### End of the program
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#### |