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:
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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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,
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atom.chg, atom.eps, atom.sig))
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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:
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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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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,
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atom.rz, atom.chg, atom.eps, atom.sig))
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def __make_proc_dir(self, cycle: int, proc: int) -> None:
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||||
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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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||||
try:
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||||
os.makedirs(path)
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||||
except:
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||||
sys.exit("Error: cannot make directory {}".format(path))
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||||
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||||
def __run_dice(self, cycle: int, proc: int, fh: str) -> None:
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||||
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||||
sim_dir = "simfiles"
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||||
step_dir = "step{:02d}".format(cycle)
|
||||
proc_dir = "p{:02d}".format(proc)
|
||||
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||||
try:
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||||
fh.write("Simulation process {} initiated with pid {}\n".format(
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||||
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()
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||||
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
|
||||
Reference in New Issue
Block a user