Vitor Hideyoshi Nakazone Batista
6017f272b3
Fixed Numerus functions in the SetGlobals file and MolHandling, translated DicePlayer and tested till, such as inertia_tensor, add_type, center_of_mass_to_origin. standard_orientation; and removed chglevel keyword Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
842 lines
30 KiB
Python
842 lines
30 KiB
Python
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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from DPpack.MolHandling import *
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from DPpack.PTable import *
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from DPpack.Misc import *
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class Internal:
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def __init__(self, infile, outfile):
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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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self.randominit = None
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def read_keywords(self):
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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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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 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)
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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):
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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):
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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): # 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 = ljfile.pop(0).split()[0]
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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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nsites = int(nsites)
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self.system.add_type(nsites,Molecule())
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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:
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sys.exit("Error: expected a float in field 5, line {} of file {}".format(line, self.dice.ljname))
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try:
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chg = float(new_atom[5])
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except:
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sys.exit("Error: expected a float in field 6, line {} of file {}".format(line, self.dice.ljname))
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try:
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eps = float(new_atom[6])
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except:
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sys.exit("Error: expected a float in field 7, line {} of file {}".format(line, self.dice.ljname))
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try:
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sig = float(new_atom[7])
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except:
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sys.exit("Error: expected a float in field 8, line {} of file {}".format(line, self.dice.ljname))
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mass = atommass[na]
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if len(new_atom) > 8:
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masskey, mass = new_atom[8].partition("=")[::2]
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if masskey.lower() == 'mass' and len(mass) !=0:
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try:
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new_mass = float(mass)
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if new_mass > 0:
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mass = new_mass
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except:
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sys.exit(
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|
"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):
|
|
|
|
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):
|
|
|
|
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):
|
|
|
|
invhessian = linalg.inv(self.system.molecule[0].hessian)
|
|
pre_step = -1 * np.matmul(invhessian, self.system.molecule[0].gradient.T).T
|
|
maxstep = np.amax(np.absolute(pre_step))
|
|
factor = min(1, self.player.maxstep/maxstep)
|
|
step = factor * pre_step
|
|
|
|
self.player.outfile.write("\nCalculated step:\n")
|
|
pre_step_list = pre_step.tolist()
|
|
|
|
self.player.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.player.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.player.outfile.write("-----------------------------------------------------------------------\n")
|
|
|
|
self.player.outfile.write("Maximum step is {:>11.6}\n".format(maxstep))
|
|
self.player.outfile.write("Scaling factor = {:>6.4f}\n".format(factor))
|
|
self.player.outfile.write("\nFinal step (Bohr):\n")
|
|
step_list = step.tolist()
|
|
|
|
self.player.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.player.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.player.outfile.write("-----------------------------------------------------------------------\n")
|
|
|
|
step_max = np.amax(np.absolute(step))
|
|
step_rms = np.sqrt(np.mean(np.square(step)))
|
|
|
|
self.player.outfile.write(" Max Step = {:>14.9f} RMS Step = {:>14.9f}\n\n".format(
|
|
step_max, step_rms))
|
|
|
|
return step
|
|
|
|
def read_initial_cicle(self):
|
|
|
|
try:
|
|
with open(self.infile) as self.outfile:
|
|
controlfile = self.outfile.readlines()
|
|
except EnvironmentError:
|
|
sys.exit("Error: cannot open file {}".format(self.infile))
|
|
|
|
for line in controlfile:
|
|
|
|
pass
|
|
|
|
### I still have to talk with Herbet about
|
|
def populate_asec_vdw(self, cycle):
|
|
|
|
asec_charges = [] # (rx, ry, rz, chg)
|
|
vdw_meanfield = [] # (rx, ry, rz, 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]) + len(ghost_atoms) + len(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])
|
|
|
|
thickness = []
|
|
picked_mols = []
|
|
|
|
for proc in range(1, self.player.nprocs + 1): ## Run over folders
|
|
|
|
path = "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 = []
|
|
for site in range(len(self.system.molecule[types].atoms)): ## Run over sites of each molecule
|
|
|
|
new_molecule.append({})
|
|
line = xyzfile.pop(0).split()
|
|
|
|
if line[0].title() != atomsymb[molecules[type][site]['na']].strip():
|
|
sys.exit("Error reading file {}".format(file))
|
|
|
|
new_molecule[site]['na'] = molecules[type][site]['na']
|
|
new_molecule[site]['rx'] = float(line[1])
|
|
new_molecule[site]['ry'] = float(line[2])
|
|
new_molecule[site]['rz'] = float(line[3])
|
|
new_molecule[site]['chg'] = molecules[type][site]['chg']
|
|
new_molecule[site]['eps'] = molecules[type][site]['eps']
|
|
new_molecule[site]['sig'] = molecules[type][site]['sig']
|
|
|
|
dist = minimum_distance(molecules[0], 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 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.player.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.player.outfile.write(textwrap.fill(string, 86))
|
|
self.player.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
|
|
|
|
class Player:
|
|
|
|
def __init__(self):
|
|
|
|
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.cyc = 1
|
|
|
|
class Dice:
|
|
|
|
def __init__(self):
|
|
|
|
self.title = "Diceplayer run"
|
|
self.progname = "dice"
|
|
self.path = None
|
|
|
|
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 = [] # Up to 4 integer values related to up to 4 molecule types
|
|
self.nstep = [] # 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
|
|
|
|
|
|
class Gaussian:
|
|
|
|
def __init__(self):
|
|
|
|
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
|
|
|
|
# class Molcas:
|
|
|
|
# def __init(self):
|
|
|
|
# self.orbfile = "input.exporb"
|
|
# self.root = 1
|
|
|
|
# self.mbottom = None
|
|
# self.basis = None |