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>
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662
diceplayer/DPpack/external/Dice.py
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662
diceplayer/DPpack/external/Dice.py
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from diceplayer.DPpack.MolHandling import *
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from diceplayer.DPpack.PTable import *
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from diceplayer.DPpack.Misc import *
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from typing import IO, Tuple, List, TextIO, Union
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from numpy.core.numeric import partition
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from numpy import random
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from multiprocessing import Process, connection
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import setproctitle
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import subprocess
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import os
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import sys
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import shutil
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import textwrap
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import types
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dice_end_flag = "End of simulation" # The normal end flag
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dice_flag_line = -2 # must be in the line before the last
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umaAng3_to_gcm3 = 1.6605 # Conversion between uma/Ang3 to g/cm3
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max_seed = 4294967295 # Maximum allowed value for a seed (numpy)
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class Dice:
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def __init__(self, infile: TextIO, outfile: TextIO) -> None:
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self.title = "Diceplayer run"
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self.progname = "dice"
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self.infile = infile
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self.outfile = outfile
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self.path = None
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self.nprocs: int = None
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self.randominit = 'first'
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self.temp = 300.0
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self.press = 1.0
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self.isave = 1000 # ASEC construction will take this into account
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self.ncores = 1
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# Investigate the possibility of using 'box = Lx Ly Lz' instead.
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self.dens = None
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# self.box = None # So 'geom' would be set by diceplayer and 'cutoff' would be
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# switched off. One of them must be given.
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self.combrule = "*"
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self.ljname = None
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self.outname = None
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# Up to 4 integer values related to up to 4 molecule types
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self.nmol: List[int] = []
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# 2 or 3 integer values related to 2 or 3 simulations
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self.nstep: List[int] = []
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# (NVT th + NVT eq) or (NVT th + NPT th + NPT eq).
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# This will control the 'nstep' keyword of Dice
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self.upbuf = 360
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def __new_density(self, cycle: int, proc: int) -> float:
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sim_dir = "simfiles"
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step_dir = "step{:02d}".format(cycle-1)
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proc_dir = "p{:02d}".format(proc)
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path = sim_dir + os.sep + step_dir + os.sep + proc_dir
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file = path + os.sep + "last.xyz"
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if not os.path.isfile(file):
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sys.exit(
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"Error: cannot find the xyz file {} in main directory".format(file))
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try:
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with open(file) as fh:
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xyzfile = fh.readlines()
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except:
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sys.exit("Error: cannot open file {}".format(file))
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box = xyzfile[1].split()
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volume = float(box[-3]) * float(box[-2]) * float(box[-1])
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total_mass = 0
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for i in range(len(self.molecule)):
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total_mass += self.molecule[i].total_mass * self.nmol[i]
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density = (total_mass / volume) * umaAng3_to_gcm3
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return density
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def __print_last_config(self, cycle: int, proc: int) -> None:
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sim_dir = "simfiles"
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step_dir = "step{:02d}".format(cycle)
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proc_dir = "p{:02d}".format(proc)
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path = sim_dir + os.sep + step_dir + os.sep + proc_dir
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file = path + os.sep + "phb.xyz"
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if not os.path.isfile(file):
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sys.exit("Error: cannot find the xyz file {}".format(file))
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try:
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with open(file) as fh:
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xyzfile = fh.readlines()
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except:
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sys.exit("Error: cannot open file {}".format(file))
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nsites = len(self.molecule[0].atom) * self.nmol[0]
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for i in range(1, len(self.nmol)):
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nsites += self.nmol[i] * len(self.molecule[i].atom)
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nsites += 2 ## To include the comment line and the number of atoms (xyz file format)
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nsites *= -1 ## Become an index to count from the end of xyzfile (list)
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xyzfile = xyzfile[nsites :] ## Take the last configuration
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file = path + os.sep + "last.xyz"
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fh = open(file, "w")
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for line in xyzfile:
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fh.write(line)
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def __make_dice_inputs(self, cycle: int, proc: int) -> None:
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sim_dir = "simfiles"
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step_dir = "step{:02d}".format(cycle)
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proc_dir = "p{:02d}".format(proc)
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path = sim_dir + os.sep + step_dir + os.sep + proc_dir
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num = time.time() # Take the decimal places 7 to 12 of the
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num = (num - int(num)) * 1e6 # time in seconds as a floating point
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# to make an integer in the range 1-1e6
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num = int((num - int(num)) * 1e6)
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random.seed((os.getpid() * num) % (max_seed + 1))
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if (self.randominit == 'first' and cycle > self.initcyc):
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last_step_dir = "step{:02d}".format(cycle-1)
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last_path = sim_dir + os.sep + last_step_dir + os.sep + proc_dir
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xyzfile = last_path + os.sep + "last.xyz"
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self.__make_init_file(path, xyzfile)
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if len(self.nstep) == 2: # Means NVT simulation
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self.__make_nvt_ter(cycle, path)
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self.__make_nvt_eq(path)
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elif len(self.nstep) == 3: # Means NPT simulation
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if (self.randominit == 'first' and cycle > self.initcyc):
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self.dens = self.__new_density(cycle, proc)
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else:
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self.__make_nvt_ter(cycle, path)
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self.__make_npt_ter(cycle, path)
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self.__make_npt_eq(path)
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else:
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sys.exit("Error: bad number of entries for 'nstep'")
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self.__make_potential(path)
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# if (self.randominit == 'first' and cycle > self.initcyc):
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# last_path = sim_dir + os.sep + "step{:02d}".format(cycle-1) + os.sep + proc_dir
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# shutil.copyfile(last_path + os.sep + "phb.dat", path + os.sep + "phb.dat")
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def __make_nvt_ter(self, cycle: int, path: str) -> None:
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file = path + os.sep + "NVT.ter"
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try:
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fh = open(file, "w")
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except:
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sys.exit("Error: cannot open file {}".format(file))
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fh.write("title = {} - NVT Thermalization\n".format(self.title))
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fh.write("ncores = {}\n".format(self.ncores))
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fh.write("ljname = {}\n".format(self.ljname))
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fh.write("outname = {}\n".format(self.outname))
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string = " ".join(str(x) for x in self.nmol)
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fh.write("nmol = {}\n".format(string))
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fh.write("dens = {}\n".format(self.dens))
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fh.write("temp = {}\n".format(self.temp))
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if (self.randominit == 'first' and cycle > self.initcyc):
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fh.write("init = yesreadxyz\n")
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fh.write("nstep = {}\n".format(self.altsteps))
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else:
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fh.write("init = yes\n")
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fh.write("nstep = {}\n".format(self.nstep[0]))
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fh.write("vstep = 0\n")
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fh.write("mstop = 1\n")
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fh.write("accum = no\n")
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fh.write("iprint = 1\n")
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fh.write("isave = 0\n")
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fh.write("irdf = 0\n")
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seed = int(1e6 * random.random())
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fh.write("seed = {}\n".format(seed))
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fh.write("upbuf = {}".format(self.upbuf))
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fh.close()
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def __make_nvt_eq(self, path: str) -> None:
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file = path + os.sep + "NVT.eq"
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try:
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fh = open(file, "w")
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except:
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sys.exit("Error: cannot open file {}".format(file))
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fh.write("title = {} - NVT Production\n".format(self.title))
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fh.write("ncores = {}\n".format(self.ncores))
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fh.write("ljname = {}\n".format(self.ljname))
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fh.write("outname = {}\n".format(self.outname))
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string = " ".join(str(x) for x in self.nmol)
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fh.write("nmol = {}\n".format(string))
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fh.write("dens = {}\n".format(self.dens))
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fh.write("temp = {}\n".format(self.temp))
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fh.write("init = no\n")
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fh.write("nstep = {}\n".format(self.nstep[1]))
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fh.write("vstep = 0\n")
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fh.write("mstop = 1\n")
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fh.write("accum = no\n")
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fh.write("iprint = 1\n")
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fh.write("isave = {}\n".format(self.isave))
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fh.write("irdf = {}\n".format(10 * self.nprocs))
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seed = int(1e6 * random.random())
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fh.write("seed = {}\n".format(seed))
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fh.close()
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def __make_npt_ter(self, cycle: int, path: str) -> None:
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file = path + os.sep + "NPT.ter"
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try:
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fh = open(file, "w")
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except:
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sys.exit("Error: cannot open file {}".format(file))
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fh.write("title = {} - NPT Thermalization\n".format(self.title))
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fh.write("ncores = {}\n".format(self.ncores))
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fh.write("ljname = {}\n".format(self.ljname))
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fh.write("outname = {}\n".format(self.outname))
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string = " ".join(str(x) for x in self.nmol)
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fh.write("nmol = {}\n".format(string))
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fh.write("press = {}\n".format(self.press))
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fh.write("temp = {}\n".format(self.temp))
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if (self.randominit == 'first' and cycle > self.initcyc):
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fh.write("init = yesreadxyz\n")
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fh.write("dens = {:<8.4f}\n".format(self.dens))
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fh.write("vstep = {}\n".format(int(self.altsteps / 5)))
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else:
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# Because there will be a previous NVT simulation
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fh.write("init = no\n")
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fh.write("vstep = {}\n".format(int(self.nstep[1] / 5)))
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fh.write("nstep = 5\n")
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fh.write("mstop = 1\n")
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fh.write("accum = no\n")
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fh.write("iprint = 1\n")
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fh.write("isave = 0\n")
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fh.write("irdf = 0\n")
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seed = int(1e6 * random.random())
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fh.write("seed = {}\n".format(seed))
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fh.close()
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def __make_npt_eq(self, path: str) -> None:
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file = path + os.sep + "NPT.eq"
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try:
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fh = open(file, "w")
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except:
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sys.exit("Error: cannot open file {}".format(file))
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fh.write("title = {} - NPT Production\n".format(self.title))
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fh.write("ncores = {}\n".format(self.ncores))
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fh.write("ljname = {}\n".format(self.ljname))
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fh.write("outname = {}\n".format(self.outname))
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string = " ".join(str(x) for x in self.nmol)
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fh.write("nmol = {}\n".format(string))
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fh.write("press = {}\n".format(self.press))
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fh.write("temp = {}\n".format(self.temp))
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fh.write("nstep = 5\n")
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fh.write("vstep = {}\n".format(int(self.nstep[2] / 5)))
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fh.write("init = no\n")
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fh.write("mstop = 1\n")
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fh.write("accum = no\n")
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fh.write("iprint = 1\n")
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fh.write("isave = {}\n".format(self.isave))
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fh.write("irdf = {}\n".format(10 * self.nprocs))
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seed = int(1e6 * random.random())
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fh.write("seed = {}\n".format(seed))
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fh.close()
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def __make_init_file(self, path: str, file: TextIO) -> None:
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if not os.path.isfile(file):
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sys.exit(
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"Error: cannot find the xyz file {} in main directory".format(file))
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try:
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with open(file) as fh:
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xyzfile = fh.readlines()
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except:
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sys.exit("Error: cannot open file {}".format(file))
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nsites_mm = 0
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for i in range(1, len(self.nmol)):
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nsites_mm += self.nmol[i] * len(self.molecule[i].atom)
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# Become an index to count from the end of xyzfile (list)
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nsites_mm *= -1
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# Only the MM atoms of the last configuration remains
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xyzfile = xyzfile[nsites_mm:]
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file = path + os.sep + self.outname + ".xy"
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try:
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fh = open(file, "w", 1)
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except:
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sys.exit("Error: cannot open file {}".format(file))
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for atom in self.molecule[0].atom:
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fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(
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atom.rx, atom.ry, atom.rz))
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# for i in self.molecule[0].ghost_atoms:
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# with self.molecule[0].atom[i] as ghost:
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# fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(ghost.rx, ghost.ry, ghost.rz))
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# for i in self.molecule[0].lp_atoms:
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# with self.molecule[0].atom[i] as lp:
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# fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(lp.rx, lp.ry, lp.rz))
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for line in xyzfile:
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atom = line.split()
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rx = float(atom[1])
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ry = float(atom[2])
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rz = float(atom[3])
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fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(rx, ry, rz))
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fh.write("$end")
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fh.close()
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def __make_potential(self, path: str) -> None:
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fstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f}\n"
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file = path + os.sep + self.ljname
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try:
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||||
fh = open(file, "w")
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||||
except:
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||||
sys.exit("Error: cannot open file {}".format(file))
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||||
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||||
fh.write("{}\n".format(self.combrule))
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fh.write("{}\n".format(len(self.nmol)))
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nsites_qm = len(self.molecule[0].atom) + len(
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self.molecule[0].ghost_atoms) + len(self.molecule[0].lp_atoms)
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# Print the sites of the QM self.molecule
|
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fh.write("{} {}\n".format(nsites_qm, self.molecule[0].molname))
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for atom in self.molecule[0].atom:
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||||
fh.write(fstr.format(atom.lbl, atom.na, atom.rx, atom.ry, atom.rz,
|
||||
atom.chg, atom.eps, atom.sig))
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||||
|
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ghost_label = self.molecule[0].atom[-1].lbl + 1
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||||
for i in self.molecule[0].ghost_atoms:
|
||||
fh.write(fstr.format(ghost_label, ghost_number, self.molecule[0].atom[i].rx, self.molecule[0].atom[i].ry,
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self.molecule[0].atom[i].rz, self.molecule[0].atom[i].chg, 0, 0))
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||||
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ghost_label += 1
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for lp in self.molecule[0].lp_atoms:
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fh.write(fstr.format(ghost_label, ghost_number, lp['rx'], lp['ry'], lp['rz'],
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lp['chg'], 0, 0))
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# Print the sites of the other self.molecules
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for mol in self.molecule[1:]:
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fh.write("{} {}\n".format(len(mol.atom), mol.molname))
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for atom in mol.atom:
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fh.write(fstr.format(atom.lbl, atom.na, atom.rx, atom.ry,
|
||||
atom.rz, atom.chg, atom.eps, atom.sig))
|
||||
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||||
def __make_proc_dir(self, cycle: int, proc: int) -> None:
|
||||
|
||||
sim_dir = "simfiles"
|
||||
step_dir = "step{:02d}".format(cycle)
|
||||
proc_dir = "p{:02d}".format(proc)
|
||||
path = sim_dir + os.sep + step_dir + os.sep + proc_dir
|
||||
try:
|
||||
os.makedirs(path)
|
||||
except:
|
||||
sys.exit("Error: cannot make directory {}".format(path))
|
||||
|
||||
def __run_dice(self, cycle: int, proc: int, fh: str) -> None:
|
||||
|
||||
sim_dir = "simfiles"
|
||||
step_dir = "step{:02d}".format(cycle)
|
||||
proc_dir = "p{:02d}".format(proc)
|
||||
|
||||
try:
|
||||
fh.write("Simulation process {} initiated with pid {}\n".format(
|
||||
sim_dir + os.sep + step_dir + os.sep + proc_dir, os.getpid()))
|
||||
|
||||
except Exception as err:
|
||||
print("I/O error({0}): {1}".format(err))
|
||||
|
||||
path = sim_dir + os.sep + step_dir + os.sep + proc_dir
|
||||
working_dir = os.getcwd()
|
||||
os.chdir(path)
|
||||
|
||||
if len(self.nstep) == 2: # Means NVT simulation
|
||||
|
||||
if (self.randominit == 'first' and cycle > self.initcyc):
|
||||
string_tmp = 'previous'
|
||||
else:
|
||||
string_tmp = 'random'
|
||||
|
||||
# NVT thermalization
|
||||
string = "(from " + string_tmp + " configuration)"
|
||||
fh.write("p{:02d}> NVT thermalization finished {} on {}\n".format(proc, string,
|
||||
date_time()))
|
||||
|
||||
infh = open("NVT.ter")
|
||||
outfh = open("NVT.ter.out", "w")
|
||||
|
||||
if shutil.which("bash") != None:
|
||||
exit_status = subprocess.call(
|
||||
["bash", "-c", "exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
|
||||
else:
|
||||
exit_status = subprocess.call(
|
||||
self.progname, stin=infh.name, stout=outfh.name)
|
||||
|
||||
infh.close()
|
||||
outfh.close()
|
||||
|
||||
if os.getppid() == 1: # Parent process is dead
|
||||
sys.exit()
|
||||
|
||||
if exit_status != 0:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
else:
|
||||
# Open again to seek the normal end flag
|
||||
outfh = open("NVT.ter.out")
|
||||
flag = outfh.readlines()[dice_flag_line].strip()
|
||||
outfh.close()
|
||||
if flag != dice_end_flag:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
|
||||
# NVT production
|
||||
fh.write("p{:02d}> NVT production initiated on {}\n".format(
|
||||
proc, date_time()))
|
||||
|
||||
infh = open("NVT.eq")
|
||||
outfh = open("NVT.eq.out", "w")
|
||||
|
||||
if shutil.which("bash") != None:
|
||||
exit_status = subprocess.call(
|
||||
["bash", "-c", "exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
|
||||
else:
|
||||
exit_status = subprocess.call(
|
||||
self.progname, stin=infh.name, stout=outfh.name)
|
||||
|
||||
infh.close()
|
||||
outfh.close()
|
||||
|
||||
if os.getppid() == 1: # Parent process is dead
|
||||
sys.exit()
|
||||
|
||||
if exit_status != 0:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
else:
|
||||
# Open again to seek the normal end flag
|
||||
outfh = open("NVT.eq.out")
|
||||
flag = outfh.readlines()[dice_flag_line].strip()
|
||||
outfh.close()
|
||||
if flag != dice_end_flag:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
|
||||
fh.write("p{:02d}> ----- NVT production finished on {}\n".format(proc,
|
||||
date_time()))
|
||||
|
||||
elif len(self.nstep) == 3: # Means NPT simulation
|
||||
|
||||
# NVT thermalization if randominit
|
||||
if self.randominit == 'always' or (self.randominit == 'first' and cycle == 1) or self.continued:
|
||||
string = "(from random configuration)"
|
||||
fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc,
|
||||
string, date_time()))
|
||||
infh = open("NVT.ter")
|
||||
outfh = open("NVT.ter.out", "w")
|
||||
|
||||
if shutil.which("bash") != None:
|
||||
exit_status = subprocess.call(
|
||||
["bash", "-c", "exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
|
||||
else:
|
||||
exit_status = subprocess.call(
|
||||
self.progname, stin=infh.name, stout=outfh.name)
|
||||
|
||||
infh.close()
|
||||
outfh.close()
|
||||
|
||||
if os.getppid() == 1: # Parent process is dead
|
||||
sys.exit()
|
||||
|
||||
if exit_status != 0:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
else:
|
||||
# Open again to seek the normal end flag
|
||||
outfh = open("NVT.ter.out")
|
||||
flag = outfh.readlines()[dice_flag_line].strip()
|
||||
outfh.close()
|
||||
if flag != dice_end_flag:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
|
||||
# NPT thermalization
|
||||
if not self.randominit == 'always' or ((self.randominit == 'first' and cycle > self.initcyc)):
|
||||
string = " (from previous configuration) "
|
||||
else:
|
||||
string = " "
|
||||
fh.write("p{:02d}> NPT thermalization finished {} on {}\n".format(proc, string,
|
||||
date_time()))
|
||||
|
||||
infh = open("NPT.ter")
|
||||
outfh = open("NPT.ter.out", "w")
|
||||
|
||||
if shutil.which("bash") != None:
|
||||
exit_status = subprocess.call(
|
||||
["bash", "-c", "exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
|
||||
else:
|
||||
exit_status = subprocess.call(
|
||||
self.progname, stin=infh.name, stout=outfh.name)
|
||||
|
||||
infh.close()
|
||||
outfh.close()
|
||||
|
||||
if os.getppid() == 1: # Parent process is dead
|
||||
sys.exit()
|
||||
|
||||
if exit_status != 0:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
else:
|
||||
# Open again to seek the normal end flag
|
||||
outfh = open("NPT.ter.out")
|
||||
flag = outfh.readlines()[dice_flag_line].strip()
|
||||
outfh.close()
|
||||
if flag != dice_end_flag:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
|
||||
# NPT production
|
||||
fh.write("p{:02d}> NPT production initiated on {}\n".format(
|
||||
proc, date_time()))
|
||||
|
||||
infh = open("NPT.eq")
|
||||
outfh = open("NPT.eq.out", "w")
|
||||
|
||||
if shutil.which("bash") != None:
|
||||
exit_status = subprocess.call(
|
||||
["bash", "-c", "exec -a dice-step{}-p{} {} < {} > {}".format(cycle, proc, self.progname, infh.name, outfh.name)])
|
||||
else:
|
||||
exit_status = subprocess.call(
|
||||
self.progname, stin=infh.name, stout=outfh.name)
|
||||
|
||||
infh.close()
|
||||
outfh.close()
|
||||
|
||||
if os.getppid() == 1: # Parent process is dead
|
||||
sys.exit()
|
||||
|
||||
if exit_status != 0:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
else:
|
||||
# Open again to seek the normal end flag
|
||||
outfh = open("NPT.eq.out")
|
||||
flag = outfh.readlines()[dice_flag_line].strip()
|
||||
outfh.close()
|
||||
if flag != dice_end_flag:
|
||||
sys.exit(
|
||||
"Dice process step{:02d}-p{:02d} did not exit properly".format(cycle, proc))
|
||||
|
||||
fh.write("p{:02d}> ----- NPT production finished on {}\n".format(proc,
|
||||
date_time()))
|
||||
|
||||
os.chdir(working_dir)
|
||||
|
||||
def __simulation_process(self, cycle: int, proc: int):
|
||||
setproctitle.setproctitle(
|
||||
"diceplayer-step{:0d}-p{:0d}".format(cycle, proc))
|
||||
|
||||
try:
|
||||
self.__make_proc_dir(cycle, proc)
|
||||
self.__make_dice_inputs(cycle, proc)
|
||||
self.__run_dice(cycle, proc, self.outfile)
|
||||
except Exception as err:
|
||||
sys.exit(err)
|
||||
|
||||
def configure(self, initcyc: int, nprocs: int, altsteps: int, nmol: List[int], molecule: List[Molecule]):
|
||||
|
||||
self.initcyc = initcyc
|
||||
|
||||
self.nprocs = nprocs
|
||||
self.altsteps = altsteps
|
||||
|
||||
self.molecule = molecule
|
||||
|
||||
def start(self, cycle: int) -> None:
|
||||
|
||||
procs = []
|
||||
sentinels = []
|
||||
|
||||
for proc in range(1, self.nprocs + 1):
|
||||
|
||||
p = Process(target=self.__simulation_process, args=(cycle, proc))
|
||||
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, self.nprocs + 1):
|
||||
self.__print_last_config(cycle, proc)
|
||||
|
||||
def reset(self):
|
||||
|
||||
del self.nprocs
|
||||
del self.altsteps
|
||||
del self.molecule
|
||||
@@ -1,11 +1,12 @@
|
||||
#!/usr/bin/python3
|
||||
|
||||
from multiprocessing import Process, connection
|
||||
import os, sys, time, signal
|
||||
import setproctitle
|
||||
import numpy as np
|
||||
import argparse
|
||||
import shutil
|
||||
from multiprocessing import Process, connection
|
||||
import pickle
|
||||
|
||||
from diceplayer.DPpack.PTable import *
|
||||
from diceplayer.DPpack.SetGlobals import *
|
||||
@@ -23,9 +24,9 @@ if __name__ == '__main__':
|
||||
parser.add_argument('--continue', dest='opt_continue' , default=False, action='store_true')
|
||||
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]')
|
||||
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]')
|
||||
help='output file of diceplayer [default = run.log]')
|
||||
## Study the option of a parameter for continuing the last process via data from control.in and run.log files
|
||||
|
||||
args = parser.parse_args()
|
||||
@@ -36,19 +37,7 @@ if __name__ == '__main__':
|
||||
|
||||
if args.opt_continue and os.path.exists(args.outfile):
|
||||
|
||||
outfile = open(args.outfile,'r')
|
||||
run_file = outfile.readlines()
|
||||
control_sequence = ' Step # '
|
||||
sucessfull_sequence = '+----------------------------------------------------------------------------------------+'
|
||||
|
||||
for line in run_file:
|
||||
if control_sequence in line:
|
||||
cyc = int(line[-2])
|
||||
if sucessfull_sequence in line:
|
||||
cyc += 1
|
||||
|
||||
|
||||
outfile.close()
|
||||
save = pickle.load(open("latest-step.pkl","rb"))
|
||||
|
||||
if os.path.isfile(args.outfile+".backup"):
|
||||
os.remove(args.outfile+".backup")
|
||||
@@ -62,7 +51,7 @@ if __name__ == '__main__':
|
||||
else:
|
||||
outfile = open(args.outfile,"w",1)
|
||||
|
||||
except EnvironmentError as err:
|
||||
except Exception as err:
|
||||
sys.exit(err)
|
||||
|
||||
try:
|
||||
@@ -70,7 +59,7 @@ if __name__ == '__main__':
|
||||
if os.path.exists(args.infile):
|
||||
infile = open(args.infile,"r")
|
||||
|
||||
except EnvironmentError as err:
|
||||
except Exception as err:
|
||||
sys.exit(err)
|
||||
|
||||
#### Read and check the keywords in INFILE
|
||||
@@ -79,29 +68,20 @@ if __name__ == '__main__':
|
||||
|
||||
internal.read_keywords()
|
||||
|
||||
if args.opt_continue:
|
||||
try:
|
||||
internal.player.initcyc = cyc
|
||||
except:
|
||||
sys.exit("Error: There is no sutable run.log file to continue the previous process")
|
||||
|
||||
internal.check_keywords()
|
||||
internal.print_keywords()
|
||||
|
||||
# #### Check whether the executables are in the path
|
||||
if args.opt_continue:
|
||||
internal.player.initcyc = save[0] + 1
|
||||
internal.system = save[1]
|
||||
else:
|
||||
internal.read_potential()
|
||||
|
||||
#### Check whether the executables are in the path
|
||||
#### and print potential to Log File
|
||||
|
||||
internal.check_executables()
|
||||
|
||||
# #### Read the potential, store the info in 'molecules' and prints the info in OUTFILE
|
||||
|
||||
internal.read_potential()
|
||||
|
||||
# if internal.player.lps == "yes":
|
||||
# read_lps()
|
||||
|
||||
# if internal.player.ghosts == "yes":
|
||||
# read_ghosts()
|
||||
|
||||
internal.print_potential()
|
||||
|
||||
#### Bring the molecules to standard orientation and prints info about them
|
||||
@@ -175,29 +155,7 @@ if __name__ == '__main__':
|
||||
#### Start block of parallel simulations
|
||||
####
|
||||
|
||||
procs = []
|
||||
sentinels = []
|
||||
for proc in range(1, internal.player.nprocs + 1):
|
||||
|
||||
p = Process(target=internal.simulation_process, args=(cycle, proc))
|
||||
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, internal.player.nprocs + 1):
|
||||
internal.print_last_config(cycle, proc)
|
||||
internal.dice_start(cycle)
|
||||
|
||||
###
|
||||
### End of parallel simulations block
|
||||
@@ -216,67 +174,62 @@ if __name__ == '__main__':
|
||||
### Start QM calculation
|
||||
###
|
||||
|
||||
make_qm_dir(cycle)
|
||||
# make_qm_dir(cycle)
|
||||
|
||||
if internal.player.qmprog in ("g03", "g09", "g16"):
|
||||
# if internal.player.qmprog in ("g03", "g09", "g16"):
|
||||
|
||||
if cycle > 1:
|
||||
# if cycle > 1:
|
||||
|
||||
src = "simfiles" + os.sep + "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
|
||||
dst = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
|
||||
shutil.copyfile(src, dst)
|
||||
# src = "simfiles" + os.sep + "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk"
|
||||
# dst = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk"
|
||||
# shutil.copyfile(src, dst)
|
||||
|
||||
internal.make_gaussian_input(cycle)
|
||||
internal.gaussian.run_gaussian(cycle, "force", internal.outfile)
|
||||
internal.gaussian.run_formchk(cycle, internal.outfile)
|
||||
# internal.make_gaussian_input(cycle)
|
||||
# internal.gaussian.run_gaussian(cycle, "force", internal.outfile)
|
||||
# internal.gaussian.run_formchk(cycle, internal.outfile)
|
||||
|
||||
## Read the gradient
|
||||
file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk"
|
||||
# ## Read the gradient
|
||||
# file = "simfiles" + os.sep + "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk"
|
||||
|
||||
try:
|
||||
gradient
|
||||
old_gradient = gradient
|
||||
except:
|
||||
pass
|
||||
# try:
|
||||
# gradient
|
||||
# old_gradient = gradient
|
||||
# except:
|
||||
# pass
|
||||
|
||||
gradient = internal.read_forces_fchk(file, internal.outfile)
|
||||
# gradient = internal.read_forces_fchk(file, internal.outfile)
|
||||
|
||||
print(type(gradient),"\n",gradient.shape,"\n",gradient)
|
||||
# # If 1st step, read the hessian
|
||||
# if cycle == 1:
|
||||
|
||||
# If 1st step, read the hessian
|
||||
if cycle == 1:
|
||||
# if internal.player.readhessian == "yes":
|
||||
|
||||
if internal.player.readhessian == "yes":
|
||||
# file = "grad_hessian.dat"
|
||||
# internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
|
||||
# hessian = internal.read_hessian_log(file)
|
||||
|
||||
file = "grad_hessian.dat"
|
||||
internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
|
||||
hessian = internal.read_hessian_log(file)
|
||||
# else:
|
||||
|
||||
else:
|
||||
# file = "simfiles" + os.sep + "step01" + os.sep + "qm" + os.sep + "asec.fchk"
|
||||
# internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
|
||||
# hessian = internal.read_hessian_fchk(file)
|
||||
|
||||
file = "simfiles" + os.sep + "step01" + os.sep + "qm" + os.sep + "asec.fchk"
|
||||
internal.outfile.write("\nReading the hessian matrix from file {}\n".format(file))
|
||||
hessian = internal.read_hessian_fchk(file)
|
||||
# # From 2nd step on, update the hessian
|
||||
# else:
|
||||
# internal.outfile.write("\nUpdating the hessian matrix using the BFGS method... ")
|
||||
# hessian = internal.system.molecule[0].update_hessian(step, gradient, old_gradient, hessian)
|
||||
# internal.outfile.write("Done\n")
|
||||
|
||||
print(type(hessian), "\n", hessian.shape, "\n", hessian)
|
||||
# # Save gradient and hessian
|
||||
# internal.print_grad_hessian(cycle, gradient, hessian)
|
||||
|
||||
# From 2nd step on, update the hessian
|
||||
else:
|
||||
internal.outfile.write("\nUpdating the hessian matrix using the BFGS method... ")
|
||||
hessian = internal.system.molecule[0].update_hessian(step, gradient, old_gradient, hessian)
|
||||
internal.outfile.write("Done\n")
|
||||
# # Calculate the step and update the position
|
||||
# step = internal.calculate_step(cycle, gradient, hessian)
|
||||
|
||||
# Save gradient and hessian
|
||||
internal.print_grad_hessian(cycle, gradient, hessian)
|
||||
# position += step
|
||||
|
||||
# Calculate the step and update the position
|
||||
step = internal.calculate_step(cycle, gradient, hessian)
|
||||
|
||||
print(type(step), "\n", step.shape, "\n", step)
|
||||
position += step
|
||||
|
||||
# ## Update the geometry of the reference molecule
|
||||
internal.system.update_molecule(position, internal.outfile)
|
||||
# # ## Update the geometry of the reference molecule
|
||||
# internal.system.update_molecule(position, internal.outfile)
|
||||
|
||||
# ## If needed, calculate the charges
|
||||
# if cycle < internal.player.switchcyc:
|
||||
@@ -345,6 +298,8 @@ if __name__ == '__main__':
|
||||
geomsfh.write(40 * "-"+"\n")
|
||||
|
||||
internal.outfile.write("\n+" + 88 * "-" + "+\n")
|
||||
|
||||
pickle.dump([cycle,internal.system], open("latest-step.pkl", "wb"))
|
||||
####
|
||||
#### End of the iterative process
|
||||
####
|
||||
|
||||
Reference in New Issue
Block a user