Vitor Hideyoshi
926ffc5c6b
This commit temporarily uses Gaussian Heassian for step calculations, fixes fchk file reading, fixes step calculation, fixes log file and geoms formation. Also this commit adds type hinting to improve and facilitate the program development.
1722 lines
59 KiB
Python
1722 lines
59 KiB
Python
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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import setproctitle
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import subprocess
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import os, 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 Internal:
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def __init__(self, infile: TextIO, outfile: TextIO) -> None:
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self.cyc = 1
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self.infile = infile
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self.outfile = outfile
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self.system = System()
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self.player = self.Player()
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self.player_keywords = [a for a in dir(self.player) if not a.startswith('__') and not callable(getattr(self.player, a))]
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self.dice = self.Dice()
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self.dice_keywords = [a for a in dir(self.dice) if not a.startswith('__') and not callable(getattr(self.dice, a))]
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self.gaussian = self.Gaussian()
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self.gaussian_keywords = [a for a in dir(self.gaussian) if not a.startswith('__') and not callable(getattr(self.gaussian, a))]
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# self.molcas = self.Molcas()
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# self.molcas_keywords = [a for a in dir(self.molcas) if not a.startswith('__') and not callable(getattr(self.molcas, a))]
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## Constanst that shall be set for global use
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self.tol_rms_force = 3e-4 # Hartree/Bohr
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self.tol_max_force = 4.5e-4 # Hartree/Bohr
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self.tol_rms_step = 1.2e-3 # Bohr
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self.tol_max_step = 1.8e-3 # Bohr
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self.trust_radius = None
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## Dice:
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self.combrule = None
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def read_keywords(self) -> None:
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try:
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controlfile = self.infile.readlines()
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except EnvironmentError:
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sys.exit("Error: cannot read file {}".format(self.infile))
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for line in controlfile:
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key, value = line.partition("=")[::2] # Discards the '='
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key = key.strip().lower()
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if key in ('title', 'keywords'):
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value = value.strip()
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else:
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value = value.split()
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#### Read the Diceplayer related keywords
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if key in self.player_keywords and len(value) != 0: ## 'value' is not empty!
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if key == 'qmprog' and value[0].lower() in ("g03", "g09", "g16", "molcas"):
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setattr(self.player, key, value[0].lower())
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if self.player.qmprog in ("g03","g09","g16"):
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self.gaussian.qmprog = self.player.qmprog
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# if self.player.qmprog == "molcas":
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# pass
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elif key == 'opt' and value[0].lower() in ("yes", "no", "ts"):
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setattr(self.player, key, value[0].lower())
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#elif key == 'zipprog' and value[0].lower() in ("zip", "gzip", "bzip"):
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#player[key] = value[0].lower()
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elif key in ('lps', 'ghosts') and value[0].lower() in ("yes", "no"):
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setattr(self.player, key, value[0].lower())
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elif key in ('readhessian', 'vdwforces') and value[0].lower() in ("yes", "no"):
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setattr(self.player, key, value[0].lower())
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elif key in ('maxcyc', 'nprocs', 'altsteps', 'switchcyc'):
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err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
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try:
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new_value = int(value[0])
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if new_value >= 1:
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setattr(self.player, key, new_value)
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elif key == 'altsteps' and new_value == 0:
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setattr(self.player, key, 0)
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except ValueError:
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sys.exit(err)
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elif key == 'maxstep': # Cannot be less than 0.01
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err = "Error: expected a float greater than 0.01 for keyword {} in file {}".format(key, self.infile)
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try:
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new_value = float(value[0])
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if new_value < 0.01:
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sys.exit(err)
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else:
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setattr(self.player, key, new_value)
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except ValueError:
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sys.exit(err)
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#### Read the Dice related keywords
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elif key in self.dice_keywords and len(value) != 0: ## 'value' is not empty!
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if key == 'title':
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setattr(self.dice, key, value)
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elif key in ('ljname', 'outname', 'progname'):
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setattr(self.dice, key, value[0])
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elif key == 'randominit':
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if value in ('always','first'):
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setattr(self.dice,key,value[0])
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elif key in ('ncores', 'isave'):
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err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
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if not value[0].isdigit():
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sys.exit(err)
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new_value = int(value[0])
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if new_value >= 1:
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setattr(self.dice, key, new_value)
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elif key in ('temp', 'press', 'dens'): # Cannot be less than 1e-10
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err = "Error: expected a positive float for keyword {} in file {}".format(key, self.infile)
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try:
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new_value = float(value[0])
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if new_value < 1e-10:
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sys.exit(err)
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else:
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setattr(self.dice, key, new_value)
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except ValueError:
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sys.exit(err)
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elif key == 'nmol': # If defined, must be well defined (only positive integer values)
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err = "Error: expected 1 to 4 positive integers for keyword {} in file {}".format(key, self.infile)
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args = min(4, len(value))
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for i in range(args):
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if value[i].isdigit():
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new_value = int(value[i])
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if new_value < 1:
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sys.exit(err)
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else:
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getattr(self.dice, key).append(new_value)
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elif i == 0:
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sys.exit(err)
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else:
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break
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elif key == 'nstep': # If defined, must be well defined (only positive integer values)
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err = "Error: expected 2 or 3 positive integers for keyword {} in file {}".format(key, self.infile)
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if len(value) < 2:
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sys.exit(err)
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args = min(3, len(value))
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for i in range(args):
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if value[i].isdigit():
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new_value = int(value[i])
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if new_value < 1:
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sys.exit(err)
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else:
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getattr(self.dice, key).append(new_value)
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elif i < 2:
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sys.exit(err)
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else:
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break
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#### Read the Gaussian related keywords
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elif key in self.gaussian_keywords and len(value) != 0: ## 'value' is not empty!
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if key == 'mem': # Memory in MB (minimum of 100)
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err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
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if not value[0].isdigit():
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sys.exit(err)
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new_value = int(value[0])
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if new_value >= 100:
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setattr(self.gaussian, key, new_value)
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elif key == 'keywords':
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setattr(self.gaussian, key, value)
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elif key == 'chgmult': # If defined, must be well defined (2 integer values)
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err = "Error: expected 2 integers for keyword {} in file {}".format(key, self.infile)
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if len(value) < 2:
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sys.exit(err)
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for i in range (2):
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try:
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getattr(self.gaussian, key)[i] = int(value[i])
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except ValueError:
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sys.exit(err)
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elif key == 'level':
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setattr(self.gaussian, key, value[0])
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elif key in ('gmiddle', 'gbottom'):
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setattr(self.gaussian, key, value[0])
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elif key == 'pop' and value[0].lower() in ("chelpg", "mk", "nbo"):
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setattr(self.gaussian, key, value[0].lower())
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# #### Read the Molcas related keywords
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# elif key in self.molcas_keywords and len(value) != 0: ## 'value' is not empty!
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# if key == 'root': # If defined, must be well defined (only positive integer values)
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# err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
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# if not value[0].isdigit():
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# sys.exit(err)
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# new_value = int(value[0])
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# if new_value >= 1:
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# setattr(self.molcas, key, new_value)
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# elif key in ('mbottom', 'orbfile'):
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# setattr(self.molcas, key, value[0])
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# elif key == 'basis':
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# setattr(self.molcas ,key, value[0])
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# #### End
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def check_keywords(self) -> None:
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min_steps = 20000
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if self.dice.ljname == None:
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sys.exit("Error: 'ljname' keyword not specified in file {}".format(self.infile))
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if self.dice.outname == None:
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sys.exit("Error: 'outname' keyword not specified in file {}".format(self.infile))
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if self.dice.dens == None:
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sys.exit("Error: 'dens' keyword not specified in file {}".format(self.infile))
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if self.dice.nmol == 0:
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sys.exit("Error: 'nmol' keyword not defined appropriately in file {}".format(self.infile))
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if self.dice.nstep == 0:
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sys.exit("Error: 'nstep' keyword not defined appropriately in file {}".format(self.infile))
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## Check only if QM program is Gaussian:
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if self.player.qmprog in ("g03", "g09", "g16"):
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if self.gaussian.level == None:
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sys.exit("Error: 'level' keyword not specified in file {}".format(self.infile))
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if self.gaussian.gmiddle != None:
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if not os.path.isfile(self.gaussian.gmiddle):
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sys.exit("Error: file {} not found".format(self.gaussian.gmiddle))
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if self.gaussian.gbottom != None:
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if not os.path.isfile(self.gaussian.gbottom):
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sys.exit("Error: file {} not found".format(self.gaussian.gbottom))
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if self.gaussian.pop != "chelpg" and (self.player.ghosts == "yes" or self.player.lps == "yes"):
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sys.exit("Error: ghost atoms or lone pairs only available with 'pop = chelpg')")
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## Check only if QM program is Molcas:
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# if self.player.qmprog == "molcas":
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# if self.molcas.mbottom == None:
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# sys.exit("Error: 'mbottom' keyword not specified in file {}".format(self.infile))
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# else:
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# if not os.path.isfile(self.molcas.mbottom):
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# sys.exit("Error: file {} not found".format(self.molcas.mbottom))
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# if self.molcas.basis == None:
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# sys.exit("Error: 'basis' keyword not specified in file {}".format(self.infile))
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if self.player.altsteps != 0:
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### Verifica se tem mais de 1 molecula QM
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### (No futuro usar o RMSD fit para poder substituir todas as moleculas QM
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### no arquivo outname.xy - Need to change the make_init_file!!)
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if self.dice.nmol[0] > 1:
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sys.exit("Error: altsteps > 0 only possible with 1 QM molecule (nmol = 1 n2 n3 n4)")
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# if not zero, altsteps cannot be less than min_steps
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self.player.altsteps = max(min_steps, self.player.altsteps)
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# altsteps value is always the nearest multiple of 1000
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self.player.altsteps = round(self.player.altsteps / 1000) * 1000
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for i in range(len(self.dice.nstep)):
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# nstep can never be less than min_steps
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self.dice.nstep[i] = max(min_steps, self.dice.nstep[i])
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# nstep values are always the nearest multiple of 1000
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self.dice.nstep[i] = round(self.dice.nstep[i] / 1000) * 1000
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# isave must be between 100 and 2000
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self.dice.isave = max(100, self.dice.isave)
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self.dice.isave = min(2000, self.dice.isave)
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# isave value is always the nearest multiple of 100
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self.dice.isave = round(self.dice.isave / 100) * 100
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def print_keywords(self) -> None:
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self.outfile.write("##########################################################################################\n"
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"############# Welcome to DICEPLAYER version 1.0 #############\n"
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"##########################################################################################\n"
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"\n")
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self.outfile.write("Your python version is {}\n".format(sys.version))
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self.outfile.write("\n")
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self.outfile.write("Program started on {}\n".format(weekday_date_time()))
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self.outfile.write("\n")
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self.outfile.write("Environment variables:\n")
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for var in env:
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self.outfile.write("{} = {}\n".format(var,
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(os.environ[var] if var in os.environ else "Not set")))
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self.outfile.write("\n==========================================================================================\n"
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" CONTROL variables being used in this run:\n"
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"------------------------------------------------------------------------------------------\n"
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"\n")
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for key in sorted(self.player_keywords):
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if getattr(self.player,key) != None:
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if isinstance(getattr(self.player,key), list):
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string = " ".join(str(x) for x in getattr(self.player,key))
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self.outfile.write("{} = {}\n".format(key, string))
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else:
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self.outfile.write("{} = {}\n".format(key, getattr(self.player,key)))
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self.outfile.write("\n")
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self.outfile.write("------------------------------------------------------------------------------------------\n"
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" DICE variables being used in this run:\n"
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"------------------------------------------------------------------------------------------\n"
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"\n")
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for key in sorted(self.dice_keywords):
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if getattr(self.dice,key) != None:
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if isinstance(getattr(self.dice,key), list):
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string = " ".join(str(x) for x in getattr(self.dice,key))
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self.outfile.write("{} = {}\n".format(key, string))
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else:
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self.outfile.write("{} = {}\n".format(key, getattr(self.dice,key)))
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self.outfile.write("\n")
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if self.player.qmprog in ("g03", "g09", "g16"):
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self.outfile.write("------------------------------------------------------------------------------------------\n"
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" GAUSSIAN variables being used in this run:\n"
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"------------------------------------------------------------------------------------------\n"
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"\n")
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for key in sorted(self.gaussian_keywords):
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if getattr(self.gaussian,key) != None:
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if isinstance(getattr(self.gaussian,key), list):
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string = " ".join(str(x) for x in getattr(self.gaussian,key))
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self.outfile.write("{} = {}\n".format(key, string))
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else:
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self.outfile.write("{} = {}\n".format(key, getattr(self.gaussian,key)))
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self.outfile.write("\n")
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# elif self.player.qmprog == "molcas":
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# self.outfile.write("------------------------------------------------------------------------------------------\n"
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# " MOLCAS variables being used in this run:\n"
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# "------------------------------------------------------------------------------------------\n"
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# "\n")
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# for key in sorted(molcas):
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# if molcas[key] != None:
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# if isinstance(molcas[key], list):
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# string = " ".join(str(x) for x in molcas[key])
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# self.outfile.write("{} = {}\n".format(key, string))
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# else:
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# self.outfile.write("{} = {}\n".format(key, molcas[key]))
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# self.outfile.write("\n")
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def read_potential(self) -> None: # Deve ser atualizado para o uso de
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try:
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with open(self.dice.ljname) as file:
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ljfile = file.readlines()
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except EnvironmentError as err:
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sys.exit(err)
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combrule = ljfile.pop(0).split()[0]
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if combrule not in ("*", "+"):
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sys.exit("Error: expected a '*' or a '+' sign in 1st line of file {}".format(self.dice.ljname))
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self.dice.combrule = combrule
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ntypes = ljfile.pop(0).split()[0]
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if not ntypes.isdigit():
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sys.exit("Error: expected an integer in the 2nd line of file {}".format(self.dice.ljname))
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ntypes = int(ntypes)
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if ntypes != len(self.dice.nmol):
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sys.exit("Error: number of molecule types in file {} must match that of 'nmol' keyword in file {}".format(
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self.dice.ljname, self.infile))
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line = 2
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for i in range(ntypes):
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line += 1
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nsites, molname = ljfile.pop(0).split()[:2]
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if not nsites.isdigit():
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sys.exit("Error: expected an integer in line {} of file {}".format(line, self.dice.ljname))
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if molname is None:
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sys.exit("Error: expected a molecule name in line {} of file {}".format(line, self.dice.ljname))
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nsites = int(nsites)
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self.system.add_type(nsites, Molecule(molname))
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for j in range(nsites):
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line += 1
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new_atom = ljfile.pop(0).split()
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if len(new_atom) < 8:
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sys.exit("Error: expected at least 8 fields in line {} of file {}".format(line, self.dice.ljname))
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if not new_atom[0].isdigit():
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sys.exit("Error: expected an integer in field 1, line {} of file {}".format(line, self.dice.ljname))
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lbl = int(new_atom[0])
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if not new_atom[1].isdigit():
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sys.exit("Error: expected an integer in field 2, line {} of file {}".format(line, self.dice.ljname))
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atnumber = int(new_atom[1])
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if atnumber == ghost_number and i == 0: # Ghost atom not allowed in the QM molecule
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sys.exit("Error: found a ghost atom in line {} of file {}".format(line, self.dice.ljname))
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na = atnumber
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try:
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rx = float(new_atom[2])
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except:
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sys.exit("Error: expected a float in field 3, line {} of file {}".format(line, self.dice.ljname))
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try:
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ry = float(new_atom[3])
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except:
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sys.exit("Error: expected a float in field 4, line {} of file {}".format(line, self.dice.ljname))
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try:
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rz = float(new_atom[4])
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except:
|
|
sys.exit("Error: expected a float in field 5, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
try:
|
|
chg = float(new_atom[5])
|
|
except:
|
|
sys.exit("Error: expected a float in field 6, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
try:
|
|
eps = float(new_atom[6])
|
|
except:
|
|
sys.exit("Error: expected a float in field 7, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
try:
|
|
sig = float(new_atom[7])
|
|
except:
|
|
sys.exit("Error: expected a float in field 8, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
mass = atommass[na]
|
|
|
|
if len(new_atom) > 8:
|
|
masskey, mass = new_atom[8].partition("=")[::2]
|
|
if masskey.lower() == 'mass' and len(mass) !=0:
|
|
try:
|
|
new_mass = float(mass)
|
|
if new_mass > 0:
|
|
mass = new_mass
|
|
except:
|
|
sys.exit(
|
|
"Error: expected a positive float after 'mass=' in field 9, line {} of file {}".format(
|
|
line, self.dice.ljname))
|
|
|
|
self.system.molecule[i].add_atom(Atom(lbl,na,rx,ry,rz,chg,eps,sig))
|
|
|
|
to_delete = ['lbl','na','rx','ry','rz','chg','eps','sig','mass']
|
|
for _var in to_delete:
|
|
if _var in locals() or _var in globals():
|
|
exec(f'del {_var}')
|
|
|
|
def print_potential(self) -> None:
|
|
|
|
formatstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}\n"
|
|
self.outfile.write("\n"
|
|
"==========================================================================================\n")
|
|
self.outfile.write(" Potential parameters from file {}:\n".format(self.dice.ljname))
|
|
self.outfile.write("------------------------------------------------------------------------------------------\n"
|
|
"\n")
|
|
|
|
self.outfile.write("Combination rule: {}\n".format(self.dice.combrule))
|
|
self.outfile.write("Types of molecules: {}\n\n".format(len(self.system.molecule)))
|
|
|
|
i = 0
|
|
for mol in self.system.molecule:
|
|
i += 1
|
|
self.outfile.write("{} atoms in molecule type {}:\n".format(len(mol.atom), i))
|
|
self.outfile.write("---------------------------------------------------------------------------------\n"
|
|
"Lbl AN X Y Z Charge Epsilon Sigma Mass\n")
|
|
self.outfile.write("---------------------------------------------------------------------------------\n")
|
|
|
|
for atom in mol.atom:
|
|
|
|
self.outfile.write(formatstr.format(atom.lbl, atom.na, atom.rx, atom.ry, atom.rz,
|
|
atom.chg, atom.eps, atom.sig, atom.mass))
|
|
|
|
self.outfile.write("\n")
|
|
|
|
if self.player.ghosts == "yes" or self.player.lps == "yes":
|
|
self.outfile.write("\n"
|
|
"------------------------------------------------------------------------------------------\n"
|
|
" Aditional potential parameters:\n"
|
|
"------------------------------------------------------------------------------------------\n")
|
|
|
|
# if player['ghosts'] == "yes":
|
|
|
|
# self.outfile.write("\n")
|
|
# self.outfile.write("{} ghost atoms appended to molecule type 1 at:\n".format(len(ghost_types)))
|
|
# self.outfile.write("---------------------------------------------------------------------------------\n")
|
|
|
|
# atoms_string = ""
|
|
# for ghost in ghost_types:
|
|
# for atom in ghost['numbers']:
|
|
# atom_sym = atomsymb[ molecules[0][atom - 1]['na'] ].strip()
|
|
# atoms_string += "{}{} ".format(atom_sym,atom)
|
|
|
|
# if ghost['type'] == "g":
|
|
# self.outfile.write(textwrap.fill("* Geometric center of atoms {}".format(atoms_string), 80))
|
|
# elif ghost['type'] == "m":
|
|
# self.outfile.write(textwrap.fill("* Center of mass of atoms {}".format(atoms_string), 80))
|
|
# elif ghost['type'] == "z":
|
|
# self.outfile.write(textwrap.fill("* Center of atomic number of atoms {}".format(atoms_string), 80))
|
|
|
|
# self.outfile.write("\n")
|
|
|
|
# if player['lps'] == 'yes':
|
|
|
|
# self.outfile.write("\n")
|
|
# self.outfile.write("{} lone pairs appended to molecule type 1:\n".format(len(lp_types)))
|
|
# self.outfile.write("---------------------------------------------------------------------------------\n")
|
|
|
|
# for lp in lp_types:
|
|
# # LP type 1 or 2
|
|
# if lp['type'] in (1, 2):
|
|
# atom1_num = lp['numbers'][0]
|
|
# atom1_sym = atomsymb[ molecules[0][atom1_num - 1]['na'] ].strip()
|
|
# atom2_num = lp['numbers'][1]
|
|
# atom2_sym = atomsymb[ molecules[0][atom2_num - 1]['na'] ].strip()
|
|
# atom3_num = lp['numbers'][2]
|
|
# atom3_sym = atomsymb[ molecules[0][atom3_num - 1]['na'] ].strip()
|
|
|
|
# self.outfile.write(textwrap.fill(
|
|
# "* Type {} on atom {}{} with {}{} {}{}. Alpha = {:<5.1f} Deg and D = {:<4.2f} Angs".format(
|
|
# lp['type'], atom1_sym, atom1_num, atom2_sym, atom2_num, atom3_sym, atom3_num, lp['alpha'],
|
|
# lp['dist']), 86))
|
|
# self.outfile.write("\n")
|
|
|
|
# # Other LP types
|
|
|
|
self.outfile.write("\n"
|
|
"==========================================================================================\n")
|
|
|
|
def check_executables(self) -> None:
|
|
|
|
self.outfile.write("\n")
|
|
self.outfile.write(90 * "=")
|
|
self.outfile.write("\n\n")
|
|
|
|
dice_path = shutil.which(self.dice.progname)
|
|
if dice_path != None:
|
|
self.outfile.write("Program {} found at {}\n".format(self.dice.progname, dice_path))
|
|
self.dice.path = dice_path
|
|
else:
|
|
sys.exit("Error: cannot find dice executable")
|
|
|
|
qmprog_path = shutil.which(self.gaussian.qmprog)
|
|
if qmprog_path != None:
|
|
self.outfile.write("Program {} found at {}\n".format(self.gaussian.qmprog, qmprog_path))
|
|
self.gaussian.path = qmprog_path
|
|
else:
|
|
sys.exit("Error: cannot find {} executable".format(self.gaussian.qmprog))
|
|
|
|
if self.gaussian.qmprog in ("g03", "g09", "g16"):
|
|
formchk_path = shutil.which("formchk")
|
|
if formchk_path != None:
|
|
self.outfile.write("Program formchk found at {}\n".format(formchk_path))
|
|
else:
|
|
sys.exit("Error: cannot find formchk executable")
|
|
|
|
def calculate_step(self, cycle: int, gradient: np.ndarray,
|
|
hessian: np.ndarray) -> np.ndarray:
|
|
|
|
invhessian = np.linalg.inv(hessian)
|
|
pre_step = -1 * np.matmul(invhessian, gradient.T).T
|
|
maxstep = np.amax(np.absolute(pre_step))
|
|
factor = min(1, self.player.maxstep/maxstep)
|
|
step = factor * pre_step
|
|
|
|
self.outfile.write("\nCalculated step-{}:\n".format(cycle))
|
|
pre_step_list = pre_step.tolist()
|
|
|
|
self.outfile.write("-----------------------------------------------------------------------\n"
|
|
"Center Atomic Step (Bohr)\n"
|
|
"Number Number X Y Z\n"
|
|
"-----------------------------------------------------------------------\n")
|
|
for i in range(len(self.system.molecule[0].atom)):
|
|
self.outfile.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format(
|
|
i + 1, self.system.molecule[0].atom[i].na,
|
|
pre_step_list.pop(0), pre_step_list.pop(0), pre_step_list.pop(0)))
|
|
|
|
self.outfile.write("-----------------------------------------------------------------------\n")
|
|
|
|
self.outfile.write("Maximum step is {:>11.6}\n".format(maxstep))
|
|
self.outfile.write("Scaling factor = {:>6.4f}\n".format(factor))
|
|
self.outfile.write("\nFinal step (Bohr):\n")
|
|
step_list = step.tolist()
|
|
|
|
self.outfile.write("-----------------------------------------------------------------------\n"
|
|
"Center Atomic Step (Bohr)\n"
|
|
"Number Number X Y Z\n"
|
|
"-----------------------------------------------------------------------\n")
|
|
for i in range(len(self.system.molecule[0].atom)):
|
|
self.outfile.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format(
|
|
i + 1, self.system.molecule[0].atom[i].na,
|
|
step_list.pop(0), step_list.pop(0), step_list.pop(0)))
|
|
|
|
self.outfile.write("-----------------------------------------------------------------------\n")
|
|
|
|
step_max = np.amax(np.absolute(step))
|
|
step_rms = np.sqrt(np.mean(np.square(step)))
|
|
|
|
self.outfile.write(" Max Step = {:>14.9f} RMS Step = {:>14.9f}\n\n".format(
|
|
step_max, step_rms))
|
|
|
|
return step
|
|
|
|
### I still have to talk with Herbet about this function
|
|
def populate_asec_vdw(self, cycle):
|
|
|
|
## Both asec_charges and vdw_meanfield will utilize the Molecule() class and Atoms() with some None elements
|
|
|
|
asec_charges = Molecule() # (lbl=None, na=None, rx, ry, rz, chg, eps=None, sig=None)
|
|
vdw_meanfield = Molecule() # (lbl=None, na=None, rx, ry, rz, chg=None, eps, sig)
|
|
|
|
if self.dice.nstep[-1] % self.dice.isave == 0:
|
|
nconfigs = round(self.dice.nstep[-1] / self.dice.isave)
|
|
else:
|
|
nconfigs = int(self.dice.nstep[-1] / self.dice.isave)
|
|
|
|
norm_factor = nconfigs * self.player.nprocs
|
|
|
|
nsitesref = len(self.system.molecule[0].atom) + len(self.system.molecule[0].ghost_atoms) + len(self.system.molecule[0].lp_atoms)
|
|
|
|
nsites_total = self.dice.nmol[0] * nsitesref
|
|
for i in range(1, len(self.dice.nmol)):
|
|
nsites_total += self.dice.nmol[i] * len(self.system.molecule[i].atom)
|
|
|
|
thickness = []
|
|
picked_mols = []
|
|
|
|
for proc in range(1, self.player.nprocs + 1): ## Run over folders
|
|
|
|
simdir = "simfiles"
|
|
path = simdir + os.sep + "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
|
|
file = path + os.sep + self.dice.outname + ".xyz"
|
|
if not os.path.isfile(file):
|
|
sys.exit("Error: cannot find file {}".format(file))
|
|
try:
|
|
with open(file) as xyzfh:
|
|
xyzfile = xyzfh.readlines()
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
for config in range(nconfigs): ## Run over configs in a folder
|
|
|
|
if int( xyzfile.pop(0).split()[0] ) != nsites_total:
|
|
sys.exit("Error: wrong number of sites in file {}".format(file))
|
|
|
|
box = xyzfile.pop(0).split()[-3:]
|
|
box = [ float(box[0]), float(box[1]), float(box[2]) ]
|
|
sizes = self.system.molecule[0].sizes_of_molecule()
|
|
thickness.append( min([ (box[0] - sizes[0])/2, (box[1] - sizes[1])/2,
|
|
(box[2] - sizes[2])/2 ]) )
|
|
|
|
xyzfile = xyzfile[nsitesref:] ## Skip the first (reference) molecule
|
|
mol_count = 0
|
|
for type in range(len(self.dice.nmol)): ## Run over types of molecules
|
|
|
|
if type == 0:
|
|
nmols = self.dice.nmol[0] - 1
|
|
else:
|
|
nmols = self.dice.nmol[type]
|
|
|
|
for mol in range(nmols): ## Run over molecules of each type
|
|
|
|
new_molecule = Molecule(self.system.molecule[type].molnale)
|
|
for site in range(len(self.system.molecule[types].atom)): ## Run over sites of each molecule
|
|
|
|
new_molecule.append({})
|
|
line = xyzfile.pop(0).split()
|
|
|
|
if line[0].title() != atomsymb[self.system.molecule[type].atom[site].na.strip()]:
|
|
sys.exit("Error reading file {}".format(file))
|
|
|
|
new_molecule.add_atom(Atom(self.system.molecule[type].atom[site].lbl,
|
|
self.system.molecule[type].atom[site].na,
|
|
self.system.molecule[type].atom[site].float(line[1]),
|
|
self.system.molecule[type].atom[site].float(line[2]),
|
|
self.system.molecule[type].atom[site].float(line[3]),
|
|
self.system.molecule[type].atom[site].chg,
|
|
self.system.molecule[type].atom[site].eps,
|
|
self.system.molecule[type].atom[site].sig))
|
|
|
|
dist = self.system.molecule[0].minimum_distance(new_molecule)
|
|
if dist < thickness[-1]:
|
|
mol_count += 1
|
|
for atom in new_molecule:
|
|
asec_charges.append({})
|
|
vdw_meanfield.append({})
|
|
|
|
asec_charges[-1]['rx'] = atom['rx']
|
|
asec_charges[-1]['ry'] = atom['ry']
|
|
asec_charges[-1]['rz'] = atom['rz']
|
|
asec_charges[-1]['chg'] = atom['chg'] / norm_factor
|
|
|
|
if self.player.vdwforces == "yes":
|
|
vdw_meanfield[-1]['rx'] = atom['rx']
|
|
vdw_meanfield[-1]['ry'] = atom['ry']
|
|
vdw_meanfield[-1]['rz'] = atom['rz']
|
|
vdw_meanfield[-1]['eps'] = atom['eps']
|
|
vdw_meanfield[-1]['sig'] = atom['sig']
|
|
|
|
# #### Read lines with ghosts or lps in molecules of type 0 (reference)
|
|
# #### and, if dist < thickness, appends to asec
|
|
# if type == 0:
|
|
# for ghost in ghost_atoms:
|
|
# line = xyzfile.pop(0).split()
|
|
# if line[0] != dice_ghost_label:
|
|
# sys.exit("Error reading file {}".format(file))
|
|
# if dist < thickness[-1]:
|
|
# asec_charges.append({})
|
|
# asec_charges[-1]['rx'] = float(line[1])
|
|
# asec_charges[-1]['ry'] = float(line[2])
|
|
# asec_charges[-1]['rz'] = float(line[3])
|
|
# asec_charges[-1]['chg'] = ghost['chg'] / norm_factor
|
|
|
|
# for lp in lp_atoms:
|
|
# line = xyzfile.pop(0).split()
|
|
# if line[0] != dice_ghost_label:
|
|
# sys.exit("Error reading file {}".format(file))
|
|
# if dist < thickness[-1]:
|
|
# asec_charges.append({})
|
|
# asec_charges[-1]['rx'] = float(line[1])
|
|
# asec_charges[-1]['ry'] = float(line[2])
|
|
# asec_charges[-1]['rz'] = float(line[3])
|
|
# asec_charges[-1]['chg'] = lp['chg'] / norm_factor
|
|
|
|
picked_mols.append(mol_count)
|
|
|
|
self.outfile.write("Done\n")
|
|
|
|
string = "In average, {:^7.2f} molecules ".format(sum(picked_mols)/norm_factor)
|
|
string += "were selected from each of the {} configurations ".format(len(picked_mols))
|
|
string += "of the production simulations to form the ASEC, comprising a shell with "
|
|
string += "minimum thickness of {:>6.2f} Angstrom\n".format(sum(thickness)/norm_factor)
|
|
|
|
self.outfile.write(textwrap.fill(string, 86))
|
|
self.outfile.write("\n")
|
|
|
|
otherfh = open("ASEC.dat", "w")
|
|
for charge in asec_charges:
|
|
otherfh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format(
|
|
charge['rx'], charge['ry'], charge['rz'], charge['chg']))
|
|
otherfh.close()
|
|
|
|
return asec_charges
|
|
|
|
## Dice related Upper fuctions
|
|
|
|
def print_last_config(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
|
|
file = path + os.sep + self.dice.outname + ".xyz"
|
|
if not os.path.isfile(file):
|
|
sys.exit("Error: cannot find the xyz file {}".format(file))
|
|
try:
|
|
with open(file) as fh:
|
|
xyzfile = fh.readlines()
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
nsites = len(self.system.molecule[0].atom) * self.dice.nmol[0]
|
|
for i in range(1, len(self.dice.nmol)):
|
|
nsites += self.dice.nmol[i] * len(self.system.molecule[i].atom)
|
|
|
|
nsites += 2 ## To include the comment line and the number of atoms (xyz file format)
|
|
|
|
nsites *= -1 ## Become an index to count from the end of xyzfile (list)
|
|
xyzfile = xyzfile[nsites :] ## Take the last configuration
|
|
|
|
|
|
file = path + os.sep + "last.xyz"
|
|
fh = open(file, "w")
|
|
for line in xyzfile:
|
|
fh.write(line)
|
|
|
|
def new_density(self, cycle: int, proc: int) -> float:
|
|
|
|
sim_dir = "simfiles"
|
|
step_dir = "step{:02d}".format(cycle-1)
|
|
proc_dir = "p{:02d}".format(proc)
|
|
path = sim_dir + os.sep + step_dir + os.sep + proc_dir
|
|
file = path + os.sep + "last.xyz"
|
|
if not os.path.isfile(file):
|
|
sys.exit("Error: cannot find the xyz file {} in main directory".format(file))
|
|
try:
|
|
with open(file) as fh:
|
|
xyzfile = fh.readlines()
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
box = xyzfile[1].split()
|
|
volume = float(box[-3]) * float(box[-2]) * float(box[-1])
|
|
|
|
total_mass = 0
|
|
for i in range(len(self.system.molecule)):
|
|
|
|
total_mass += self.system.molecule[i].total_mass * self.system.nmols[i]
|
|
|
|
density = (total_mass / volume) * umaAng3_to_gcm3
|
|
|
|
return density
|
|
|
|
def simulation_process(self, cycle: int, proc: int) -> None:
|
|
|
|
setproctitle.setproctitle("diceplayer-step{:0d}-p{:0d}".format(cycle,proc))
|
|
|
|
try:
|
|
self.dice.make_proc_dir(cycle, proc)
|
|
self.make_dice_inputs(cycle, proc)
|
|
self.dice.run_dice(cycle, proc, self.outfile)
|
|
except Exception as err:
|
|
sys.exit(err)
|
|
|
|
def make_dice_inputs(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
|
|
|
|
num = time.time() ## Take the decimal places 7 to 12 of the
|
|
num = (num - int(num)) * 1e6 ## time in seconds as a floating point
|
|
num = int((num - int(num)) * 1e6) ## to make an integer in the range 1-1e6
|
|
random.seed( (os.getpid() * num) % (max_seed + 1) )
|
|
|
|
if self.dice.randominit == 'first' and cycle > 1:
|
|
step_dir = "step{:02d}".format(cycle-1)
|
|
last_path = sim_dir + os.sep + step_dir + os.sep + proc_dir
|
|
xyzfile = last_path + os.sep + "last.xyz"
|
|
self.make_init_file(path, xyzfile)
|
|
|
|
if len(self.dice.nstep) == 2: ## Means NVT simulation
|
|
|
|
self.make_nvt_ter(cycle, path)
|
|
self.make_nvt_eq(path)
|
|
|
|
elif len(self.dice.nstep) == 3: ## Means NPT simulation
|
|
|
|
if self.dice.randominit == 'first' and cycle > 1:
|
|
self.dens = self.new_density(cycle, proc)
|
|
else:
|
|
self.make_nvt_ter(cycle, path)
|
|
|
|
self.make_npt_ter(cycle, path)
|
|
self.make_npt_eq(path)
|
|
|
|
else:
|
|
sys.exit("Error: bad number of entries for 'nstep'")
|
|
|
|
self.make_potential(path)
|
|
|
|
# if (self.dice.randominit == 'first' and cycle > 1):
|
|
|
|
# last_path = sim_dir + os.sep + "step{:02d}".format(cycle-1) + os.sep + proc_dir
|
|
# shutil.copyfile(last_path + os.sep + "phb.dat", path + os.sep + "phb.dat")
|
|
|
|
|
|
def make_nvt_ter(self,cycle: int, path: str) -> None:
|
|
|
|
file = path + os.sep + "NVT.ter"
|
|
try:
|
|
fh = open(file, "w")
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
fh.write("title = {} - NVT Thermalization\n".format(self.dice.title))
|
|
fh.write("ncores = {}\n".format(self.dice.ncores))
|
|
fh.write("ljname = {}\n".format(self.dice.ljname))
|
|
fh.write("outname = {}\n".format(self.dice.outname))
|
|
|
|
string = " ".join(str(x) for x in self.dice.nmol)
|
|
fh.write("nmol = {}\n".format(string))
|
|
|
|
fh.write("dens = {}\n".format(self.dice.dens))
|
|
fh.write("temp = {}\n".format(self.dice.temp))
|
|
|
|
if self.dice.randominit == 'first' and cycle > 1:
|
|
fh.write("init = yesreadxyz\n")
|
|
fh.write("nstep = {}\n".format(self.player.altsteps))
|
|
else:
|
|
fh.write("init = yes\n")
|
|
fh.write("nstep = {}\n".format(self.dice.nstep[0]))
|
|
|
|
fh.write("vstep = 0\n")
|
|
fh.write("mstop = 1\n")
|
|
fh.write("accum = no\n")
|
|
fh.write("iprint = 1\n")
|
|
fh.write("isave = 0\n")
|
|
fh.write("irdf = 0\n")
|
|
|
|
seed = int(1e6 * random.random())
|
|
fh.write("seed = {}\n".format(seed))
|
|
fh.write("upbuf = {}".format(self.dice.upbuf))
|
|
|
|
|
|
fh.close()
|
|
|
|
def make_nvt_eq(self, path: str) -> None:
|
|
|
|
file = path + os.sep + "NVT.eq"
|
|
try:
|
|
fh = open(file, "w")
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
fh.write("title = {} - NVT Production\n".format(self.dice.title))
|
|
fh.write("ncores = {}\n".format(self.dice.ncores))
|
|
fh.write("ljname = {}\n".format(self.dice.ljname))
|
|
fh.write("outname = {}\n".format(self.dice.outname))
|
|
|
|
string = " ".join(str(x) for x in self.dice.nmol)
|
|
fh.write("nmol = {}\n".format(string))
|
|
|
|
fh.write("dens = {}\n".format(self.dice.dens))
|
|
fh.write("temp = {}\n".format(self.dice.temp))
|
|
fh.write("init = no\n")
|
|
fh.write("nstep = {}\n".format(self.dice.nstep[1]))
|
|
fh.write("vstep = 0\n")
|
|
fh.write("mstop = 1\n")
|
|
fh.write("accum = no\n")
|
|
fh.write("iprint = 1\n")
|
|
fh.write("isave = {}\n".format(self.dice.isave))
|
|
fh.write("irdf = {}\n".format(10 * self.player.nprocs))
|
|
|
|
seed = int(1e6 * random.random())
|
|
fh.write("seed = {}\n".format(seed))
|
|
|
|
fh.close()
|
|
|
|
def make_npt_ter(self, cycle: int, path: str) -> None:
|
|
|
|
file = path + os.sep + "NPT.ter"
|
|
try:
|
|
fh = open(file, "w")
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
fh.write("title = {} - NPT Thermalization\n".format(self.dice.title))
|
|
fh.write("ncores = {}\n".format(self.dice.ncores))
|
|
fh.write("ljname = {}\n".format(self.dice.ljname))
|
|
fh.write("outname = {}\n".format(self.dice.outname))
|
|
|
|
string = " ".join(str(x) for x in self.dice.nmol)
|
|
fh.write("nmol = {}\n".format(string))
|
|
|
|
fh.write("press = {}\n".format(self.dice.press))
|
|
fh.write("temp = {}\n".format(self.dice.temp))
|
|
|
|
|
|
if self.dice.randominit == 'first' and cycle > 1:
|
|
fh.write("init = yesreadxyz\n")
|
|
fh.write("dens = {:<8.4f}\n".format(self.dice.dens))
|
|
fh.write("vstep = {}\n".format(int(self.player.altsteps / 5)))
|
|
else:
|
|
fh.write("init = no\n") ## Because there will be a previous NVT simulation
|
|
fh.write("vstep = {}\n".format(int(self.dice.nstep[1] / 5)))
|
|
|
|
fh.write("nstep = 5\n")
|
|
fh.write("mstop = 1\n")
|
|
fh.write("accum = no\n")
|
|
fh.write("iprint = 1\n")
|
|
fh.write("isave = 0\n")
|
|
fh.write("irdf = 0\n")
|
|
|
|
seed = int(1e6 * random.random())
|
|
fh.write("seed = {}\n".format(seed))
|
|
|
|
fh.close()
|
|
|
|
def make_npt_eq(self, path: str) -> None:
|
|
|
|
file = path + os.sep + "NPT.eq"
|
|
try:
|
|
fh = open(file, "w")
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
fh.write("title = {} - NPT Production\n".format(self.dice.title))
|
|
fh.write("ncores = {}\n".format(self.dice.ncores))
|
|
fh.write("ljname = {}\n".format(self.dice.ljname))
|
|
fh.write("outname = {}\n".format(self.dice.outname))
|
|
|
|
string = " ".join(str(x) for x in self.dice.nmol)
|
|
fh.write("nmol = {}\n".format(string))
|
|
|
|
fh.write("press = {}\n".format(self.dice.press))
|
|
fh.write("temp = {}\n".format(self.dice.temp))
|
|
|
|
fh.write("nstep = 5\n")
|
|
|
|
fh.write("vstep = {}\n".format(int(self.dice.nstep[2] / 5)))
|
|
fh.write("init = no\n")
|
|
fh.write("mstop = 1\n")
|
|
fh.write("accum = no\n")
|
|
fh.write("iprint = 1\n")
|
|
fh.write("isave = {}\n".format(self.dice.isave))
|
|
fh.write("irdf = {}\n".format(10 * self.player.nprocs))
|
|
|
|
seed = int(1e6 * random.random())
|
|
fh.write("seed = {}\n".format(seed))
|
|
|
|
fh.close()
|
|
|
|
def make_init_file(self, path: str, file: TextIO) -> None:
|
|
|
|
if not os.path.isfile(file):
|
|
sys.exit("Error: cannot find the xyz file {} in main directory".format(file))
|
|
try:
|
|
with open(file) as fh:
|
|
xyzfile = fh.readlines()
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
nsites_mm = 0
|
|
for i in range(1, len(self.dice.nmol)):
|
|
nsites_mm += self.dice.nmol[i] * len(self.system.molecule[i].atom)
|
|
|
|
nsites_mm *= -1 ## Become an index to count from the end of xyzfile (list)
|
|
xyzfile = xyzfile[nsites_mm :] ## Only the MM atoms of the last configuration remains
|
|
|
|
file = path + os.sep + self.dice.outname + ".xy"
|
|
|
|
try:
|
|
fh = open(file, "w", 1)
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
for atom in self.system.molecule[0].atom:
|
|
fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(atom.rx, atom.ry, atom.rz))
|
|
|
|
# for i in self.system.molecule[0].ghost_atoms:
|
|
# with self.system.molecule[0].atom[i] as ghost:
|
|
# fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(ghost.rx, ghost.ry, ghost.rz))
|
|
|
|
# for i in self.system.molecule[0].lp_atoms:
|
|
# with self.system.molecule[0].atom[i] as lp:
|
|
# fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(lp.rx, lp.ry, lp.rz))
|
|
|
|
for line in xyzfile:
|
|
atom = line.split()
|
|
rx = float(atom[1])
|
|
ry = float(atom[2])
|
|
rz = float(atom[3])
|
|
fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(rx, ry, rz))
|
|
|
|
fh.write("$end")
|
|
|
|
fh.close()
|
|
|
|
def make_potential(self, path: str) -> None:
|
|
|
|
fstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f}\n"
|
|
|
|
file = path + os.sep + self.dice.ljname
|
|
try:
|
|
fh = open(file, "w")
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
fh.write("{}\n".format(self.dice.combrule))
|
|
fh.write("{}\n".format(len(self.dice.nmol)))
|
|
|
|
nsites_qm = len(self.system.molecule[0].atom) + len(self.system.molecule[0].ghost_atoms) + len(self.system.molecule[0].lp_atoms)
|
|
|
|
## Print the sites of the QM molecule
|
|
fh.write("{} {}\n".format(nsites_qm, self.system.molecule[0].molname))
|
|
for atom in self.system.molecule[0].atom:
|
|
fh.write(fstr.format(atom.lbl, atom.na, atom.rx, atom.ry, atom.rz,
|
|
atom.chg, atom.eps, atom.sig))
|
|
|
|
ghost_label = self.system.molecule[0].atom[-1].lbl + 1
|
|
for i in self.system.molecule[0].ghost_atoms:
|
|
fh.write(fstr.format(ghost_label, ghost_number, self.system.molecule[0].atom[i].rx, self.system.molecule[0].atom[i].ry,
|
|
self.system.molecule[0].atom[i].rz, self.system.molecule[0].atom[i].chg, 0, 0))
|
|
|
|
ghost_label += 1
|
|
for lp in self.system.molecule[0].lp_atoms:
|
|
fh.write(fstr.format(ghost_label, ghost_number, lp['rx'], lp['ry'], lp['rz'],
|
|
lp['chg'], 0, 0))
|
|
|
|
## Print the sites of the other molecules
|
|
for mol in self.system.molecule[1:]:
|
|
fh.write("{} {}\n".format(len(mol.atom), mol.molname))
|
|
for atom in mol.atom:
|
|
fh.write(fstr.format(atom.lbl, atom.na, atom.rx, atom.ry,
|
|
atom.rz, atom.chg, atom.eps, atom.sig))
|
|
|
|
#----------------------------------------------------------------------------------------------------------------------------------------
|
|
# Gaussian related methods
|
|
#----------------------------------------------------------------------------------------------------------------------------------------
|
|
def read_forces_fchk(self, file: str, fh: TextIO) -> np.ndarray:
|
|
|
|
forces = []
|
|
try:
|
|
with open(file) as tmpfh:
|
|
fchkfile = tmpfh.readlines()
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
start = fchkfile.pop(0).strip()
|
|
while start.find("Cartesian Gradient") != 0: ## expression in begining of line
|
|
start = fchkfile.pop(0).strip()
|
|
|
|
degrees = 3 * len(self.system.molecule[0].atom)
|
|
count = 0
|
|
while len(forces) < degrees:
|
|
values = fchkfile.pop(0).split()
|
|
forces.extend([ float(x) for x in values ])
|
|
count += len(values)
|
|
if count >= degrees:
|
|
forces = forces[:degrees]
|
|
break
|
|
|
|
gradient = np.array(forces)
|
|
|
|
fh.write("\nGradient read from file {}:\n".format(file))
|
|
fh.write("-----------------------------------------------------------------------\n"
|
|
"Center Atomic Forces (Hartree/Bohr)\n"
|
|
"Number Number X Y Z\n"
|
|
"-----------------------------------------------------------------------\n")
|
|
for i in range(len(self.system.molecule[0].atom)):
|
|
fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format(
|
|
i + 1, self.system.molecule[0].atom[i].na, forces.pop(0), forces.pop(0), forces.pop(0)))
|
|
|
|
fh.write("-----------------------------------------------------------------------\n")
|
|
|
|
force_max = np.amax(np.absolute(gradient))
|
|
force_rms = np.sqrt(np.mean(np.square(gradient)))
|
|
|
|
fh.write(" Max Force = {:>14.9f} RMS Force = {:>14.9f}\n\n".format(
|
|
force_max, force_rms))
|
|
|
|
return gradient
|
|
|
|
def read_hessian_fchk(self, file: str) -> np.ndarray:
|
|
|
|
force_const = []
|
|
try:
|
|
with open(file) as tmpfh:
|
|
fchkfile = tmpfh.readlines()
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
start = fchkfile.pop(0).strip()
|
|
while start.find("Cartesian Force Constants") != 0:
|
|
start = fchkfile.pop(0).strip()
|
|
|
|
degrees = 3 * len(self.system.molecule[0].atom)
|
|
last = round(degrees * (degrees + 1) / 2)
|
|
count = 0
|
|
|
|
while len(force_const) < last:
|
|
|
|
value = fchkfile.pop(0).split()
|
|
force_const.extend([ float(x) for x in value ])
|
|
|
|
# while len(force_const) < last:
|
|
|
|
# values = fchkfile.pop(0).split()
|
|
# force_const.extend([ float(x) for x in values ])
|
|
# count += len(values)
|
|
# if count >= last:
|
|
# force_const = force_const[:last]
|
|
# break
|
|
|
|
hessian = np.zeros((degrees, degrees))
|
|
for i in range(degrees):
|
|
for j in range(i + 1):
|
|
hessian[i,j] = force_const.pop(0)
|
|
hessian[j,i] = hessian[i,j]
|
|
|
|
return hessian
|
|
|
|
def read_hessian_log(self, file: str) -> np.ndarray:
|
|
|
|
try:
|
|
with open(file) as tmpfh:
|
|
logfile = tmpfh.readlines()
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
start = logfile.pop(0).strip()
|
|
while start.find("The second derivative matrix:") != 0:
|
|
start = logfile.pop(0).strip()
|
|
|
|
degrees = 3 * len(self.system.molecule[0].atom)
|
|
hessian = np.zeros((degrees, degrees))
|
|
|
|
k = 0
|
|
while k < degrees:
|
|
logfile.pop(0)
|
|
for i in range(k, degrees):
|
|
values = logfile.pop(0).split()[1:]
|
|
for j in range(k, min(i + 1, k + 5)):
|
|
hessian[i,j] = float(values.pop(0))
|
|
hessian[j,i] = hessian[i,j]
|
|
k += 5
|
|
|
|
return hessian
|
|
|
|
def print_grad_hessian(self, cycle: int,
|
|
cur_gradient: np.ndarray, hessian: np.ndarray
|
|
) -> None:
|
|
|
|
try:
|
|
fh = open("grad_hessian.dat", "w")
|
|
except:
|
|
sys.exit("Error: cannot open file grad_hessian.dat")
|
|
|
|
fh.write("Optimization cycle: {}\n".format(cycle))
|
|
fh.write("Cartesian Gradient\n")
|
|
degrees = 3 * len(self.system.molecule[0].atom)
|
|
for i in range(degrees):
|
|
fh.write(" {:>11.8g}".format(cur_gradient[i]))
|
|
if (i + 1) % 5 == 0 or i == degrees - 1:
|
|
fh.write("\n")
|
|
|
|
fh.write("Cartesian Force Constants\n")
|
|
n = int(np.sqrt(2*degrees))
|
|
last = degrees * (degrees + 1) / 2
|
|
count = 0
|
|
for i in range(n):
|
|
for j in range(i + 1):
|
|
count += 1
|
|
fh.write(" {:>11.8g}".format(hessian[i,j]))
|
|
if count % 5 == 0 or count == last:
|
|
fh.write("\n")
|
|
|
|
fh.close()
|
|
|
|
## Change the name to make_gaussian_input
|
|
def make_gaussian_input(self, cycle: int, asec_charges=None) -> None:
|
|
|
|
simdir="simfiles"
|
|
stepdir="step{:02d}".format(cycle)
|
|
path = simdir + os.sep + stepdir + os.sep + "qm"
|
|
|
|
file = path + os.sep + "asec.gjf"
|
|
|
|
try:
|
|
fh = open(file, "w")
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
fh.write("%Chk=asec.chk\n")
|
|
if self.gaussian.mem != None:
|
|
fh.write("%Mem={}MB\n".format(self.gaussian.mem))
|
|
fh.write("%Nprocs={}\n".format(self.player.nprocs * self.dice.ncores))
|
|
|
|
kword_line = "#P " + str(self.gaussian.level)
|
|
|
|
if self.gaussian.keywords != None:
|
|
kword_line += " " + self.gaussian.keywords
|
|
|
|
if self.player.opt == 'yes':
|
|
kword_line += " Force"
|
|
|
|
# kword_line += " Charge"
|
|
kword_line += " NoSymm"
|
|
kword_line += " Pop={} Density=Current".format(self.gaussian.pop)
|
|
|
|
if cycle > 1:
|
|
kword_line += " Guess=Read"
|
|
|
|
fh.write(textwrap.fill(kword_line, 90))
|
|
fh.write("\n")
|
|
|
|
fh.write("\nForce calculation - Cycle number {}\n".format(cycle))
|
|
fh.write("\n")
|
|
fh.write("{},{}\n".format(self.gaussian.chgmult[0], self.gaussian.chgmult[1]))
|
|
|
|
for atom in self.system.molecule[0].atom:
|
|
symbol = atomsymb[atom.na]
|
|
fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol,
|
|
atom.rx, atom.ry, atom.rz))
|
|
|
|
# ## If also performing charge fit in the same calculation
|
|
# if cycle >= self.player.switchcyc:
|
|
# for ghost in ghost_atoms:
|
|
# fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
|
|
# ghost['rx'], ghost['ry'], ghost['rz']))
|
|
|
|
# for lp in lp_atoms:
|
|
# fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
|
|
# lp['rx'], lp['ry'], lp['rz']))
|
|
|
|
# fh.write("\n")
|
|
|
|
## If gmiddle file was informed, write its contents in asec.gjf
|
|
# if self.gaussian.gmiddle != None:
|
|
# if not os.path.isfile(self.gaussian.gmiddle):
|
|
# sys.exit("Error: cannot find file {} in main directory".format(
|
|
# self.gaussian.gmiddle))
|
|
# try:
|
|
# with open(self.gaussian.gmiddle) as gmiddlefile:
|
|
# gmiddle = gmiddlefile.readlines()
|
|
# except:
|
|
# sys.exit("Error: cannot open file {}".format(self.gaussian.gmiddle))
|
|
|
|
# for line in gmiddle:
|
|
# fh.write(line)
|
|
|
|
# fh.write("\n")
|
|
|
|
# ## Write the ASEC:
|
|
# for charge in asec_charges:
|
|
# fh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format(
|
|
# charge['rx'], charge['ry'], charge['rz'], charge['chg']))
|
|
|
|
fh.write("\n")
|
|
|
|
# ## If gbottom file was informed, write its contents in asec.gjf
|
|
# if self.gaussian.gbottom != None:
|
|
# if not os.path.isfile(self.gaussian.gbottom):
|
|
# sys.exit("Error: cannot find file {} in main directory".format(
|
|
# self.gaussian.gbottom))
|
|
# try:
|
|
# with open(self.gaussian.gbottom) as gbottomfile:
|
|
# gbottom = gbottomfile.readlines()
|
|
# except:
|
|
# sys.exit("Error: cannot open file {}".format(self.gaussian.gbottom))
|
|
|
|
# for line in gbottom:
|
|
# fh.write(line)
|
|
|
|
# fh.write("\n")
|
|
|
|
# fh.close()
|
|
|
|
def read_charges(self, file: str, fh: TextIO) -> None:
|
|
|
|
try:
|
|
with open(file) as tmpfh:
|
|
glogfile = tmpfh.readlines()
|
|
except:
|
|
sys.exit("Error: cannot open file {}".format(file))
|
|
|
|
start = glogfile.pop(0).strip()
|
|
while start != "Fitting point charges to electrostatic potential":
|
|
start = glogfile.pop(0).strip()
|
|
|
|
glogfile = glogfile[3:] ## Consume 3 more lines
|
|
|
|
fh.write("\nAtomic charges:\n")
|
|
fh.write("------------------------------------\n")
|
|
for atom in self.system.molecule[0].atom:
|
|
line = glogfile.pop(0).split()
|
|
atom_str = line[1]
|
|
charge = float(line[2])
|
|
atom.chg = charge
|
|
fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge))
|
|
|
|
# if self.gaussian.pop == "chelpg":
|
|
# for ghost in ghost_atoms:
|
|
# line = glogfile.pop(0).split()
|
|
# atom_str = line[1]
|
|
# charge = float(line[2])
|
|
# ghost['chg'] = charge
|
|
# fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge))
|
|
|
|
# for lp in lp_atoms:
|
|
# line = glogfile.pop(0).split()
|
|
# atom_str = line[1]
|
|
# charge = float(line[2])
|
|
# lp['chg'] = charge
|
|
# fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge))
|
|
|
|
fh.write("------------------------------------\n")
|
|
|
|
class Player:
|
|
|
|
def __init__(self) -> None:
|
|
|
|
self.maxcyc = None
|
|
self.nprocs = 1
|
|
self.switchcyc = 3
|
|
self.altsteps = 20000
|
|
self.maxstep = .3
|
|
self.opt = "yes"
|
|
self.freq = "no"
|
|
self.readhessian = "no"
|
|
self.lps = "no"
|
|
self.ghosts = "no"
|
|
self.vdwforces = "no"
|
|
self.tol_factor = 1.2
|
|
self.qmprog = "g16"
|
|
|
|
self.initcyc = 1
|
|
|
|
class Dice:
|
|
|
|
def __init__(self) -> None:
|
|
|
|
self.title = "Diceplayer run"
|
|
self.progname = "dice"
|
|
self.path = None
|
|
|
|
|
|
self.randominit = 'first'
|
|
self.temp = 300.0
|
|
self.press = 1.0
|
|
self.isave = 1000 # ASEC construction will take this into account
|
|
self.ncores = 1
|
|
|
|
self.dens = None # Investigate the possibility of using 'box = Lx Ly Lz' instead.
|
|
# self.box = None # So 'geom' would be set by diceplayer and 'cutoff' would be
|
|
# switched off. One of them must be given.
|
|
self.combrule = "*"
|
|
self.ljname = None
|
|
self.outname = None
|
|
self.nmol: List[int] = [] # Up to 4 integer values related to up to 4 molecule types
|
|
self.nstep: List[int] = [] # 2 or 3 integer values related to 2 or 3 simulations
|
|
# (NVT th + NVT eq) or (NVT th + NPT th + NPT eq).
|
|
# This will control the 'nstep' keyword of Dice
|
|
self.upbuf = 360
|
|
|
|
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 == 'no' or (self.randominit == 'first' and cycle > 1):
|
|
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:
|
|
outfh = open("NVT.ter.out") ## Open again to seek the normal end flag
|
|
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:
|
|
outfh = open("NVT.eq.out") ## Open again to seek the normal end flag
|
|
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):
|
|
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:
|
|
outfh = open("NVT.ter.out") ## Open again to seek the normal end flag
|
|
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 == 1):
|
|
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:
|
|
outfh = open("NPT.ter.out") ## Open again to seek the normal end flag
|
|
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:
|
|
outfh = open("NPT.eq.out") ## Open again to seek the normal end flag
|
|
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)
|
|
|
|
class Gaussian:
|
|
|
|
def __init__(self) -> None:
|
|
|
|
self.qmprog = "g09"
|
|
self.path = None
|
|
|
|
self.mem = None
|
|
self.keywords = None
|
|
self.chgmult = [0, 1]
|
|
self.gmiddle = None # In each case, if a filename is given, its content will be
|
|
self.gbottom = None # inserted in the gaussian input
|
|
self.pop = "chelpg"
|
|
self.level = None
|
|
|
|
def run_gaussian(self, cycle: int, type: str, fh: TextIO) -> None:
|
|
|
|
simdir="simfiles"
|
|
stepdir="step{:02d}".format(cycle)
|
|
path = simdir + os.sep + stepdir + os.sep + "qm"
|
|
work_dir = os.getcwd()
|
|
os.chdir(path)
|
|
|
|
# if type == "force":
|
|
# infile = "asec.gjf"
|
|
# elif type == "charge":
|
|
# infile = "asec2.gjf"
|
|
|
|
infile = "asec.gjf"
|
|
|
|
fh.write("\nCalculation of {}s initiated with Gaussian on {}\n".format(type, date_time()))
|
|
|
|
if shutil.which("bash") != None:
|
|
exit_status = subprocess.call(["bash","-c","exec -a {}-step{} {} {}".format(self.qmprog, cycle, self.qmprog, infile)])
|
|
else:
|
|
exit_status = subprocess.call([self.qmprog, infile])
|
|
|
|
if exit_status != 0:
|
|
sys.exit("Gaussian process did not exit properly")
|
|
|
|
fh.write("Calculation of {}s finished on {}\n".format(type, date_time()))
|
|
|
|
os.chdir(work_dir)
|
|
|
|
def run_formchk(self, cycle: int, fh: TextIO):
|
|
|
|
simdir="simfiles"
|
|
stepdir="step{:02d}".format(cycle)
|
|
path = simdir + os.sep + stepdir + os.sep + "qm"
|
|
|
|
work_dir = os.getcwd()
|
|
os.chdir(path)
|
|
|
|
fh.write("Formatting the checkpoint file... \n")
|
|
|
|
exit_status = subprocess.call(["formchk", "asec.chk"], stdout=fh)
|
|
|
|
fh.write("Done\n")
|
|
|
|
os.chdir(work_dir)
|
|
|
|
# class Molcas:
|
|
|
|
# def __init(self):
|
|
|
|
# self.orbfile = "input.exporb"
|
|
# self.root = 1
|
|
|
|
# self.mbottom = None
|
|
# self.basis = None |