Separated Completely Dice in Dice.py and Fixed Continue Feature in Dice
This commit separates the Dice class in a Dice.py file stored in DPacks/external, also fixes the continue feature in the Dice class. Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
@@ -1,11 +1,12 @@
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#!/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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from multiprocessing import Process, connection
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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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@@ -23,9 +24,9 @@ if __name__ == '__main__':
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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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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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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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@@ -36,19 +37,7 @@ if __name__ == '__main__':
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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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sucessfull_sequence = '+----------------------------------------------------------------------------------------+'
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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])
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if sucessfull_sequence in line:
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cyc += 1
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outfile.close()
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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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@@ -62,7 +51,7 @@ if __name__ == '__main__':
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else:
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outfile = open(args.outfile,"w",1)
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except EnvironmentError as err:
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except Exception as err:
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sys.exit(err)
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try:
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@@ -70,7 +59,7 @@ if __name__ == '__main__':
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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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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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@@ -79,29 +68,20 @@ if __name__ == '__main__':
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internal.read_keywords()
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if args.opt_continue:
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try:
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internal.player.initcyc = cyc
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except:
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sys.exit("Error: There is no sutable run.log file to continue the previous process")
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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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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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# #### 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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@@ -175,29 +155,7 @@ if __name__ == '__main__':
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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=internal.simulation_process, args=(cycle, proc))
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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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internal.print_last_config(cycle, proc)
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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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@@ -216,67 +174,62 @@ if __name__ == '__main__':
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### Start QM calculation
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###
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make_qm_dir(cycle)
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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 internal.player.qmprog in ("g03", "g09", "g16"):
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if cycle > 1:
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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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# 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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# 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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# ## 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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# 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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# gradient = internal.read_forces_fchk(file, internal.outfile)
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print(type(gradient),"\n",gradient.shape,"\n",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 = 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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# If 1st step, read the hessian
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if cycle == 1:
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# # Save gradient and hessian
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# internal.print_grad_hessian(cycle, gradient, hessian)
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if internal.player.readhessian == "yes":
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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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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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print(type(hessian), "\n", hessian.shape, "\n", hessian)
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# position += step
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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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print(type(step), "\n", step.shape, "\n", step)
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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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# # ## 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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@@ -344,7 +297,9 @@ if __name__ == '__main__':
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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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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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