diff --git a/diceplayer-0.0.1.py b/diceplayer-0.0.1.py deleted file mode 100644 index e9cb51e..0000000 --- a/diceplayer-0.0.1.py +++ /dev/null @@ -1,295 +0,0 @@ -#!/export/apps/python/361/bin/python3 - -import os, sys, time, signal -import argparse -import shutil -from multiprocessing import Process, connection - -import DPpack.Dice as Dice -import DPpack.Gaussian as Gaussian -from DPpack.PTable import * -from DPpack.SetGlobals import * -from DPpack.MolHandling import * -from DPpack.Misc import * - - -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('--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]') - - args = parser.parse_args() - -#### Read and check the keywords in INFILE - - read_keywords(args.infile) - check_keywords(args.infile) - -#### Open OUTFILE for writing and print keywords and initial info - - try: - if player['initcyc'] > 1 and os.path.exists(args.outfile): - oldname = args.outfile + ".old" - os.replace(args.outfile, oldname) - logfh = open(args.outfile, 'w', 1) - except EnvironmentError as err: - sys.exit(err) - - print_keywords(logfh) - -#### Check whether the executables are in the path - - check_executables(logfh) - -#### Read the potential, store the info in 'molecules' and prints the info in OUTFILE - - read_potential(args.infile) - - if player['lps'] == "yes": - read_lps() - - if player['ghosts'] == "yes": - read_ghosts() - - print_potential(logfh) - -#### Bring the molecules to standard orientation and prints info about them - - for i in range(len(molecules)): - logfh.write("\nMolecule type {}:\n\n".format(i + 1)) - print_mol_info(molecules[i], logfh) - logfh.write(" Translating and rotating molecule to standard orientation...") - standard_orientation(molecules[i]) - logfh.write(" Done\n\n New values:\n") - print_mol_info(molecules[i], logfh) - - logfh.write(90 * "=") - logfh.write("\n") - -#### Open the geoms.xyz file and prints the initial geometry if starting from zero - - if player['initcyc'] == 1: - try: - geomsfh = open("geoms.xyz", "w", 1) - except EnvironmentError as err: - sys.exit(err) - print_geom(0, geomsfh) - else: - try: - geomsfh = open("geoms.xyz", "A", 1) - except EnvironmentError as err: - sys.exit(err) - - - logfh.write("\nStarting the iterative process.\n") - - ## Initial position (in Bohr) - position = read_position(molecules[0]) - - ## If restarting, read the last gradient and hessian - if player['initcyc'] > 1: - if 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 - #### - - for cycle in range(player['initcyc'], player['initcyc'] + player['maxcyc']): - - logfh.write("\n" + 90 * "-" + "\n") - logfh.write("{} Step # {}\n".format(40 * " ", cycle)) - logfh.write(90 * "-" + "\n\n") - - make_step_dir(cycle) - - if player['altsteps'] == 0 or cycle == 1: - dice['randominit'] = True - else: - dice['randominit'] = False - - #### - #### Start block of parallel simulations - #### - - procs = [] - sentinels = [] - for proc in range(1, player['nprocs'] + 1): - - p = Process(target=Dice.simulation_process, args=(cycle, proc, logfh)) - 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, player['nprocs'] + 1): - Dice.print_last_config(cycle, proc) - - #### - #### End of parallel simulations block - #### - - ## Make ASEC - logfh.write("\nBuilding the ASEC and vdW meanfields... ") - asec_charges = populate_asec_vdw(cycle, logfh) - - ## After ASEC is built, compress files bigger than 1MB - for proc in range(1, 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 player['opt'] == "yes": - - ## - ## Gaussian block - ## - if player['qmprog'] in ("g03", "g09", "g16"): - - if cycle > 1: - src = "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk" - dst = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk" - shutil.copyfile(src, dst) - - Gaussian.make_force_input(cycle, asec_charges) - Gaussian.run_gaussian(cycle, "force", logfh) - Gaussian.run_formchk(cycle, logfh) - - ## Read the gradient - file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk" - gradient = Gaussian.read_forces(file, logfh) - if len(cur_gradient) > 0: - old_gradient = cur_gradient - cur_gradient = gradient - - ## If 1st step, read the hessian - if cycle == 1: - if player['readhessian'] == "yes": - file = "grad_hessian.dat" - logfh.write("\nReading the hessian matrix from file {}\n".format(file)) - hessian = Gaussian.read_hessian_fchk(file) - else: - file = "step01" + os.sep + "qm" + os.sep + "asec.fchk" - logfh.write("\nReading the hessian matrix from file {}\n".format(file)) - hessian = Gaussian.read_hessian(file) - - ## From 2nd step on, update the hessian - else: - logfh.write("\nUpdating the hessian matrix using the BFGS method... ") - hessian = update_hessian(step, cur_gradient, old_gradient, hessian) - logfh.write("Done\n") - - ## Save gradient and hessian - Gaussian.print_grad_hessian(cycle, cur_gradient, hessian) - - ## Calculate the step and update the position - step = calculate_step(cur_gradient, hessian, logfh) - position += step - - ## Update the geometry of the reference molecule - update_molecule(position, logfh) - - ## If needed, calculate the charges - if cycle < player['switchcyc']: - - Gaussian.make_charge_input(cycle, asec_charges) - Gaussian.run_gaussian(cycle, "charge", logfh) - - ## Read the new charges and update molecules[0] - if cycle < player['switchcyc']: - file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log" - Gaussian.read_charges(file, logfh) - else: - file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.log" - Gaussian.read_charges(file, logfh) - - ## Print new info for molecule[0] - logfh.write("\nNew values for molecule type 1:\n\n") - print_mol_info(molecules[0], logfh) - - ## Print new geometry in geoms.xyz - 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 player['qmprog'] in ("g03", "g09", "g16"): - - if cycle > 1: - src = "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk" - dst = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk" - shutil.copyfile(src, dst) - - Gaussian.make_charge_input(cycle, asec_charges) - Gaussian.run_gaussian(cycle, "charge", logfh) - - file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log" - Gaussian.read_charges(file) - - ## Print new info for molecule[0] - logfh.write("\nNew values for molecule type 1:\n\n") - print_mol_info(molecules[0], logfh) - - #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, ...) - - logfh.write("\nDiceplayer finished normally!\n") - logfh.close() -#### -#### End of the program -#### \ No newline at end of file