1262 lines
51 KiB
Python
1262 lines
51 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 diceplayer.DPpack.external.Dice 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
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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 Internal:
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def __init__(self, infile: TextIO, outfile: TextIO) -> None:
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self.infile = infile
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self.outfile = outfile
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self.continued: bool = None
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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(
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'__') and not callable(getattr(self.player, a))]
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self.dice = Dice(infile, outfile)
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self.dice_keywords = [a for a in dir(self.dice) if not a.startswith(
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'__') 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(
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'__') 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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# 'value' is not empty!
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if key in self.player_keywords and len(value) != 0:
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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(
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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(
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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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# 'value' is not empty!
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elif key in self.dice_keywords and len(value) != 0:
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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(
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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(
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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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# If defined, must be well defined (only positive integer values)
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elif key == 'nmol':
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err = "Error: expected 1 to 4 positive integers for keyword {} in file {}".format(
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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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# If defined, must be well defined (only positive integer values)
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elif key == 'nstep':
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err = "Error: expected 2 or 3 positive integers for keyword {} in file {}".format(
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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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# 'value' is not empty!
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elif key in self.gaussian_keywords and len(value) != 0:
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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(
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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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# If defined, must be well defined (2 integer values)
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elif key == 'chgmult':
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err = "Error: expected 2 integers for keyword {} in file {}".format(
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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(
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"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(
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"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(
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"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(
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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(
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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(
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"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(
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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(
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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(
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"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(
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"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(
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"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)
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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(
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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(
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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)
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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(
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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(
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"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(
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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(
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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(
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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(
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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(
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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(
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line, self.dice.ljname))
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|
|
atnumber = int(new_atom[1])
|
|
if atnumber == ghost_number and i == 0: # Ghost atom not allowed in the QM molecule
|
|
sys.exit("Error: found a ghost atom in line {} of file {}".format(
|
|
line, self.dice.ljname))
|
|
na = atnumber
|
|
|
|
try:
|
|
rx = float(new_atom[2])
|
|
except:
|
|
sys.exit("Error: expected a float in field 3, line {} of file {}".format(
|
|
line, self.dice.ljname))
|
|
|
|
try:
|
|
ry = float(new_atom[3])
|
|
except:
|
|
sys.exit("Error: expected a float in field 4, line {} of file {}".format(
|
|
line, self.dice.ljname))
|
|
|
|
try:
|
|
rz = float(new_atom[4])
|
|
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 dice_start(self, cycle: int):
|
|
|
|
self.dice.configure(self.player.initcyc,
|
|
self.player.nprocs,
|
|
self.player.altsteps,
|
|
self.system.nmols,
|
|
self.system.molecule)
|
|
|
|
self.dice.start(cycle)
|
|
|
|
self.dice.reset()
|
|
|
|
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]))
|
|
|
|
# Skip the first (reference) molecule
|
|
xyzfile = xyzfile[nsitesref:]
|
|
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)
|
|
# Run over sites of each molecule
|
|
for site in range(len(self.system.molecule[types].atom)):
|
|
|
|
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
|
|
|
|
# ----------------------------------------------------------------------------------------------------------------------------------------
|
|
# 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 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
|