SetGlobas Translation - Final (without ghosts and lp)
Internal methods translations: read_potential, print_potential Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
813
DPpack/.SetGlobals.py
Normal file
813
DPpack/.SetGlobals.py
Normal file
@@ -0,0 +1,813 @@
|
||||
import os, sys
|
||||
import shutil
|
||||
import textwrap
|
||||
|
||||
from DPpack.PTable import *
|
||||
from DPpack.Misc import *
|
||||
|
||||
#### Global hashes that control the behaviour of Diceplayer
|
||||
|
||||
player = {}
|
||||
dice = {}
|
||||
gaussian = {}
|
||||
molcas = {}
|
||||
internal = {}
|
||||
|
||||
#######################################################################
|
||||
#### Global parameters that MAY be given by the user ####
|
||||
#### (If not given by the user, default values will be used) ####
|
||||
#######################################################################
|
||||
|
||||
## Diceplayer:
|
||||
player['maxcyc'] = 1
|
||||
player['initcyc'] = 1 # May restart an optimization (append to geoms.xyz from start)
|
||||
player['nprocs'] = 1
|
||||
player['switchcyc'] = 3 # At which step start doing only one QM calculation (geom & chg)
|
||||
player['altsteps'] = 20000 # Steps for thermalization when starting from previous step
|
||||
player['maxstep'] = 0.3 # Maxstep for geometry relaxation in Bohr
|
||||
player['qmprog'] = "g09"
|
||||
player['opt'] = "yes"
|
||||
player['freq'] = "no"
|
||||
player['readhessian'] = "no"
|
||||
player['lps'] = "no"
|
||||
player['ghosts'] = "no"
|
||||
player['vdwforces'] = "no"
|
||||
player['tol_factor'] = 1.2 # Factor to multiply the default tolerance values
|
||||
|
||||
## Dice:
|
||||
dice['title'] = "Diceplayer run"
|
||||
dice['progname'] = "dice"
|
||||
dice['temp'] = 300.0
|
||||
dice['press'] = 1.0
|
||||
dice['isave'] = 1000 # ASEC construction will take this into account
|
||||
dice['ncores'] = 1
|
||||
|
||||
## Gaussian:
|
||||
gaussian['mem'] = None
|
||||
gaussian['keywords'] = None
|
||||
gaussian['chgmult'] = [0, 1]
|
||||
gaussian['gmiddle'] = None # In each case, if a filename is given, its content will be
|
||||
gaussian['gbottom'] = None # inserted in the gaussian input
|
||||
gaussian['pop'] = "chelpg"
|
||||
gaussian['chglevel'] = None
|
||||
|
||||
## Molcas:
|
||||
molcas['orbfile'] = "input.exporb"
|
||||
molcas['root'] = 1
|
||||
|
||||
|
||||
########################################################################
|
||||
#### Global parameters that MUST be given by the user ####
|
||||
########################################################################
|
||||
|
||||
## Dice:
|
||||
dice['dens'] = None # Investigate the possibility of using 'box = Lx Ly Lz' instead.
|
||||
#dice['box'] = None # So 'geom' would be set by diceplayer and 'cutoff' would be
|
||||
# switched off. One of them must be given.
|
||||
dice['ljname'] = None
|
||||
dice['outname'] = None
|
||||
dice['nmol'] = [] # Up to 4 integer values related to up to 4 molecule types
|
||||
dice['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
|
||||
|
||||
## Gaussian:
|
||||
gaussian['level'] = None
|
||||
|
||||
## Molcas:
|
||||
molcas['mbottom'] = None
|
||||
molcas['basis'] = None
|
||||
|
||||
|
||||
## The following Dice keywords will be handled automatically by Diceplayer:
|
||||
## * init ("yes" in the first thermalization and "yesreadxyz" for thermalizations
|
||||
## starting from a previous step / "no" in subsequent simulations)
|
||||
## * vstep ("0" for NVT simulations and 'nstep'/5 for NPT simulations)
|
||||
## * nstep ('nstep' for NVT and "5" for NPT simulations )
|
||||
## * irdf ("0" for thermalizations and "10*nprocs" for equilibrium)
|
||||
## * seed (will be generated randomly each time a Dice input is created)
|
||||
|
||||
## The following Dice keywords will be set constant by Diceplayer for all simulations
|
||||
## * mstop = 1 (So to guarantee that the ASEC will be correctly built)
|
||||
## * accum = no (There is never a simulation continuation in Diceplayer)
|
||||
## * iprint = 1 (Print energy info every step in Dice output)
|
||||
|
||||
## All the other Dice keywords will not be altered from their default values
|
||||
## and therefore are not mentioned in Diceplayer
|
||||
|
||||
|
||||
#####################################################################
|
||||
#### Global parameters that are not accessible to the user ####
|
||||
#### (Intended to be used only internally by the program) ####
|
||||
#####################################################################
|
||||
|
||||
## Diceplayer:
|
||||
internal['tol_rms_force'] = 3e-4 # Hartree/Bohr
|
||||
internal['tol_max_force'] = 4.5e-4 # Hartree/Bohr
|
||||
internal['tol_rms_step'] = 1.2e-3 # Bohr
|
||||
internal['tol_max_step'] = 1.8e-3 # Bohr
|
||||
internal['trust_radius'] = None
|
||||
|
||||
## Dice:
|
||||
internal['combrule'] = None
|
||||
internal['randominit'] = None
|
||||
|
||||
## Other global variables:
|
||||
molecules = [] # Armazena todas as informacoes sobre cada tipo de molecula
|
||||
# (lbl, na, rx, ry, rz, chg, eps, sig, mass)
|
||||
|
||||
internal['ghost_types'] = []
|
||||
internal['ghost_atoms'] = [] # Store the ghost atoms (off-atom charge sites) in the QM molecule
|
||||
# (rx, ry, rz, chg)
|
||||
internal['lp_types'] = []
|
||||
internal['lp_atoms'] = [] # Store the lone pairs (special off-atom charge sites) in the QM molecule
|
||||
# (rx, ry, rz, chg)
|
||||
|
||||
## Numpy arrays:
|
||||
step = [] ## Values in Bohr
|
||||
internal['position'] = []
|
||||
internal['energy'] = [] ## Values in Hartree
|
||||
internal['gradient'] = [] ## Values in Hartree/Bohr
|
||||
internal['hessian'] = [] ## Values in Hartree/Bohr^2
|
||||
|
||||
## Conversion factors:
|
||||
bohr2ang = 0.52917721092
|
||||
ang2bohr = 1/bohr2ang
|
||||
|
||||
######################################################################
|
||||
#### Environment variables important for executing Diceplayer ####
|
||||
######################################################################
|
||||
|
||||
env = ["OMP_STACKSIZE"]
|
||||
|
||||
####################################### functions ######################################
|
||||
## Functions to process the input files and store the values in the global variables ##
|
||||
##########################################################################################
|
||||
|
||||
# def read_keywords(infile):
|
||||
|
||||
# try:
|
||||
# with open(infile) as fh:
|
||||
# controlfile = fh.readlines()
|
||||
# except EnvironmentError:
|
||||
# sys.exit("Error: cannot open file {}".format(infile))
|
||||
|
||||
# for line in controlfile:
|
||||
|
||||
# key, value = line.partition("=")[::2] # Discards the '='
|
||||
# key = key.strip().lower()
|
||||
# if key in ('title', 'keywords'):
|
||||
# value = value.strip()
|
||||
# else:
|
||||
# value = value.split()
|
||||
|
||||
# #### Read the Diceplayer related keywords
|
||||
# if key in player and len(value) != 0: ## 'value' is not empty!
|
||||
|
||||
# if key == 'qmprog' and value[0].lower() in ("g03", "g09", "g16", "molcas"):
|
||||
# player[key] = value[0].lower()
|
||||
|
||||
# elif key == 'opt' and value[0].lower() in ("yes", "no", "ts"):
|
||||
# player[key] = value[0].lower()
|
||||
|
||||
# #elif key == 'zipprog' and value[0].lower() in ("zip", "gzip", "bzip"):
|
||||
# #player[key] = value[0].lower()
|
||||
|
||||
# elif key in ('lps', 'ghosts') and value[0].lower() in ("yes", "no"):
|
||||
# player[key] = value[0].lower()
|
||||
|
||||
# elif key in ('readhessian', 'vdwforces') and value[0].lower() in ("yes", "no"):
|
||||
# player[key] = value[0].lower()
|
||||
|
||||
# elif key in ('maxcyc', 'initcyc', 'nprocs', 'altsteps', 'switchcyc'):
|
||||
# err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile)
|
||||
# try:
|
||||
# new_value = int(value[0])
|
||||
# if new_value >= 1:
|
||||
# player[key] = new_value
|
||||
# elif key == 'altsteps' and new_value == 0:
|
||||
# player[key] = 0
|
||||
# except ValueError:
|
||||
# sys.exit(err)
|
||||
|
||||
# elif key == 'maxstep': # Cannot be less than 0.01
|
||||
# err = "Error: expected a float greater than 0.01 for keyword {} in file {}".format(key, infile)
|
||||
# try:
|
||||
# new_value = float(value[0])
|
||||
# if new_value < 0.01:
|
||||
# sys.exit(err)
|
||||
# else:
|
||||
# player[key] = new_value
|
||||
# except ValueError:
|
||||
# sys.exit(err)
|
||||
|
||||
# #### Read the Dice related keywords
|
||||
# elif key in dice and len(value) != 0: ## 'value' is not empty!
|
||||
|
||||
# if key == 'title':
|
||||
# dice[key] = value
|
||||
|
||||
# elif key in ('ljname', 'outname', 'progname'):
|
||||
# dice[key] = value[0]
|
||||
|
||||
# elif key in ('ncores', 'isave'):
|
||||
# err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile)
|
||||
# if not value[0].isdigit():
|
||||
# sys.exit(err)
|
||||
# new_value = int(value[0])
|
||||
# if new_value >= 1:
|
||||
# dice[key] = new_value
|
||||
|
||||
# elif key in ('temp', 'press', 'dens'): # Cannot be less than 1e-10
|
||||
# err = "Error: expected a positive float for keyword {} in file {}".format(key, infile)
|
||||
# try:
|
||||
# new_value = float(value[0])
|
||||
# if new_value < 1e-10:
|
||||
# sys.exit(err)
|
||||
# else:
|
||||
# dice[key] = new_value
|
||||
# except ValueError:
|
||||
# sys.exit(err)
|
||||
|
||||
# elif key == 'nmol': # If defined, must be well defined (only positive integer values)
|
||||
# err = "Error: expected 1 to 4 positive integers for keyword {} in file {}".format(key, infile)
|
||||
# args = min(4, len(value))
|
||||
# for i in range(args):
|
||||
# if value[i].isdigit():
|
||||
# new_value = int(value[i])
|
||||
# if new_value < 1:
|
||||
# sys.exit(err)
|
||||
# else:
|
||||
# dice[key].append(new_value)
|
||||
# elif i == 0:
|
||||
# sys.exit(err)
|
||||
# else:
|
||||
# break
|
||||
|
||||
# elif key == 'nstep': # If defined, must be well defined (only positive integer values)
|
||||
# err = "Error: expected 2 or 3 positive integers for keyword {} in file {}".format(key, infile)
|
||||
# if len(value) < 2:
|
||||
# sys.exit(err)
|
||||
# args = min(3, len(value))
|
||||
# for i in range(args):
|
||||
# if value[i].isdigit():
|
||||
# new_value = int(value[i])
|
||||
# if new_value < 1:
|
||||
# sys.exit(err)
|
||||
# else:
|
||||
# dice[key].append(new_value)
|
||||
# elif i < 2:
|
||||
# sys.exit(err)
|
||||
# else:
|
||||
# break
|
||||
|
||||
# #### Read the Gaussian related keywords
|
||||
# elif key in gaussian and len(value) != 0: ## 'value' is not empty!
|
||||
|
||||
# if key == 'mem': # Memory in MB (minimum of 100)
|
||||
# err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile)
|
||||
# if not value[0].isdigit():
|
||||
# sys.exit(err)
|
||||
# new_value = int(value[0])
|
||||
# if new_value >= 100:
|
||||
# gaussian[key] = new_value
|
||||
|
||||
# elif key == 'keywords':
|
||||
# gaussian[key] = value
|
||||
|
||||
# elif key == 'chgmult': # If defined, must be well defined (2 integer values)
|
||||
# err = "Error: expected 2 integers for keyword {} in file {}".format(key, infile)
|
||||
# if len(value) < 2:
|
||||
# sys.exit(err)
|
||||
# for i in range (2):
|
||||
# try:
|
||||
# gaussian[key][i] = int(value[i])
|
||||
# except ValueError:
|
||||
# sys.exit(err)
|
||||
|
||||
# elif key in ('level', 'chglevel'):
|
||||
# gaussian[key] = value[0]
|
||||
|
||||
# elif key in ('gmiddle', 'gbottom'):
|
||||
# gaussian[key] = value[0]
|
||||
|
||||
# elif key == 'pop' and value[0].lower() in ("chelpg", "mk", "nbo"):
|
||||
# gaussian[key] = value[0].lower()
|
||||
|
||||
# #### Read the Molcas related keywords
|
||||
# elif key in molcas and len(value) != 0: ## 'value' is not empty!
|
||||
|
||||
# if key == 'root': # If defined, must be well defined (only positive integer values)
|
||||
# err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile)
|
||||
# if not value[0].isdigit():
|
||||
# sys.exit(err)
|
||||
# new_value = int(value[0])
|
||||
# if new_value >= 1:
|
||||
# molcas[key] = new_value
|
||||
|
||||
# elif key in ('mbottom', 'orbfile'):
|
||||
# molcas[key] = value[0]
|
||||
|
||||
# elif key == 'basis':
|
||||
# molcas[key] = value[0]
|
||||
|
||||
# #### End
|
||||
# return
|
||||
|
||||
|
||||
|
||||
# def check_keywords(infile):
|
||||
|
||||
# min_steps = 20000
|
||||
|
||||
# if dice['ljname'] == None:
|
||||
# sys.exit("Error: 'ljname' keyword not specified in file {}".format(infile))
|
||||
|
||||
# if dice['outname'] == None:
|
||||
# sys.exit("Error: 'outname' keyword not specified in file {}".format(infile))
|
||||
|
||||
# if dice['dens'] == None:
|
||||
# sys.exit("Error: 'dens' keyword not specified in file {}".format(infile))
|
||||
|
||||
# if len(dice['nmol']) == 0:
|
||||
# sys.exit("Error: 'nmol' keyword not defined appropriately in file {}".format(infile))
|
||||
|
||||
# if len(dice['nstep']) == 0:
|
||||
# sys.exit("Error: 'nstep' keyword not defined appropriately in file {}".format(infile))
|
||||
|
||||
# ## Check only if QM program is Gaussian:
|
||||
# if player['qmprog'] in ("g03", "g09", "g16"):
|
||||
# if gaussian['level'] == None:
|
||||
# sys.exit("Error: 'level' keyword not specified in file {}".format(infile))
|
||||
|
||||
# if gaussian['gmiddle'] != None:
|
||||
# if not os.path.isfile(gaussian['gmiddle']):
|
||||
# sys.exit("Error: file {} not found".format(gaussian['gmiddle']))
|
||||
|
||||
# if gaussian['gbottom'] != None:
|
||||
# if not os.path.isfile(gaussian['gbottom']):
|
||||
# sys.exit("Error: file {} not found".format(gaussian['gbottom']))
|
||||
|
||||
# if gaussian['pop'] != "chelpg" and (player['ghosts'] == "yes" or player['lps'] == "yes"):
|
||||
# sys.exit("Error: ghost atoms or lone pairs only available with 'pop = chelpg')")
|
||||
|
||||
# if gaussian['chglevel'] == None:
|
||||
# gaussian['chglevel'] = gaussian['level']
|
||||
|
||||
# ## Check only if QM program is Molcas:
|
||||
# if player['qmprog'] == "molcas":
|
||||
|
||||
# if molcas['mbottom'] == None:
|
||||
# sys.exit("Error: 'mbottom' keyword not specified in file {}".format(infile))
|
||||
# else:
|
||||
# if not os.path.isfile(molcas['mbottom']):
|
||||
# sys.exit("Error: file {} not found".format(molcas['mbottom']))
|
||||
|
||||
# if molcas['basis'] == None:
|
||||
# sys.exit("Error: 'basis' keyword not specified in file {}".format(infile))
|
||||
|
||||
|
||||
# if player['altsteps'] != 0:
|
||||
|
||||
# ### Verifica se tem mais de 1 molecula QM
|
||||
# ### (No futuro usar o RMSD fit para poder substituir todas as moleculas QM
|
||||
# ### no arquivo outname.xy - Need to change the make_init_file!!)
|
||||
# if dice['nmol'][0] > 1:
|
||||
# sys.exit("Error: altsteps > 0 only possible with 1 QM molecule (nmol = 1 n2 n3 n4)")
|
||||
|
||||
# # if not zero, altsteps cannot be less than min_steps
|
||||
# player['altsteps'] = max(min_steps, player['altsteps'])
|
||||
# # altsteps value is always the nearest multiple of 1000
|
||||
# player['altsteps'] = round(player['altsteps'] / 1000) * 1000
|
||||
|
||||
|
||||
# for i in range(len(dice['nstep'])):
|
||||
# # nstep can never be less than min_steps
|
||||
# dice['nstep'][i] = max(min_steps, dice['nstep'][i])
|
||||
# # nstep values are always the nearest multiple of 1000
|
||||
# dice['nstep'][i] = round(dice['nstep'][i] / 1000) * 1000
|
||||
|
||||
# # isave must be between 100 and 2000
|
||||
# dice['isave'] = max(100, dice['isave'])
|
||||
# dice['isave'] = min(2000, dice['isave'])
|
||||
# # isave value is always the nearest multiple of 100
|
||||
# dice['isave'] = round(dice['isave'] / 100) * 100
|
||||
|
||||
# return
|
||||
|
||||
|
||||
|
||||
# def print_keywords(fh):
|
||||
|
||||
# fh.write("##########################################################################################\n"
|
||||
# "############# Welcome to DICEPLAYER version 1.0 #############\n"
|
||||
# "##########################################################################################\n"
|
||||
# "\n")
|
||||
# fh.write("Your python version is {}\n".format(sys.version))
|
||||
# fh.write("\n")
|
||||
# fh.write("Program started on {}\n".format(weekday_date_time()))
|
||||
# fh.write("\n")
|
||||
# fh.write("Environment variables:\n")
|
||||
# for var in env:
|
||||
# fh.write("{} = {}\n".format(var,
|
||||
# (os.environ[var] if var in os.environ else "Not set")))
|
||||
|
||||
# fh.write("\n==========================================================================================\n"
|
||||
# " CONTROL variables being used in this run:\n"
|
||||
# "------------------------------------------------------------------------------------------\n"
|
||||
# "\n")
|
||||
|
||||
# for key in sorted(player):
|
||||
# if player[key] != None:
|
||||
# if isinstance(player[key], list):
|
||||
# string = " ".join(str(x) for x in player[key])
|
||||
# fh.write("{} = {}\n".format(key, string))
|
||||
# else:
|
||||
# fh.write("{} = {}\n".format(key, player[key]))
|
||||
|
||||
# fh.write("\n")
|
||||
|
||||
# fh.write("------------------------------------------------------------------------------------------\n"
|
||||
# " DICE variables being used in this run:\n"
|
||||
# "------------------------------------------------------------------------------------------\n"
|
||||
# "\n")
|
||||
|
||||
# for key in sorted(dice):
|
||||
# if dice[key] != None:
|
||||
# if isinstance(dice[key], list):
|
||||
# string = " ".join(str(x) for x in dice[key])
|
||||
# fh.write("{} = {}\n".format(key, string))
|
||||
# else:
|
||||
# fh.write("{} = {}\n".format(key, dice[key]))
|
||||
|
||||
# fh.write("\n")
|
||||
|
||||
# if player['qmprog'] in ("g03", "g09", "g16"):
|
||||
|
||||
# fh.write("------------------------------------------------------------------------------------------\n"
|
||||
# " GAUSSIAN variables being used in this run:\n"
|
||||
# "------------------------------------------------------------------------------------------\n"
|
||||
# "\n")
|
||||
|
||||
# for key in sorted(gaussian):
|
||||
# if gaussian[key] != None:
|
||||
# if isinstance(gaussian[key], list):
|
||||
# string = " ".join(str(x) for x in gaussian[key])
|
||||
# fh.write("{} = {}\n".format(key, string))
|
||||
# else:
|
||||
# fh.write("{} = {}\n".format(key, gaussian[key]))
|
||||
|
||||
# fh.write("\n")
|
||||
|
||||
# elif player['qmprog'] == "molcas":
|
||||
|
||||
# fh.write("------------------------------------------------------------------------------------------\n"
|
||||
# " MOLCAS variables being used in this run:\n"
|
||||
# "------------------------------------------------------------------------------------------\n"
|
||||
# "\n")
|
||||
|
||||
# for key in sorted(molcas):
|
||||
# if molcas[key] != None:
|
||||
# if isinstance(molcas[key], list):
|
||||
# string = " ".join(str(x) for x in molcas[key])
|
||||
# fh.write("{} = {}\n".format(key, string))
|
||||
# else:
|
||||
# fh.write("{} = {}\n".format(key, molcas[key]))
|
||||
|
||||
# fh.write("\n")
|
||||
|
||||
# return
|
||||
|
||||
|
||||
|
||||
# def read_potential(infile): # Deve ser atualizado para o uso de
|
||||
|
||||
# try:
|
||||
# with open(dice['ljname']) as file:
|
||||
# ljfile = file.readlines()
|
||||
# except EnvironmentError as err:
|
||||
# sys.exit(err)
|
||||
|
||||
# combrule = ljfile.pop(0).split()[0]
|
||||
# if combrule not in ("*", "+"):
|
||||
# sys.exit("Error: expected a '*' or a '+' sign in 1st line of file {}".format(dice['ljname']))
|
||||
# dice['combrule'] = combrule
|
||||
|
||||
# ntypes = ljfile.pop(0).split()[0]
|
||||
# if not ntypes.isdigit():
|
||||
# sys.exit("Error: expected an integer in the 2nd line of file {}".format(dice['ljname']))
|
||||
# ntypes = int(ntypes)
|
||||
|
||||
# if ntypes != len(dice['nmol']):
|
||||
# sys.exit("Error: number of molecule types in file {} must match that of 'nmol' keyword in file {}".format(
|
||||
# dice['ljname'], infile))
|
||||
|
||||
# line = 2
|
||||
# for i in range(ntypes):
|
||||
# line += 1
|
||||
# nsites = ljfile.pop(0).split()[0]
|
||||
# if not nsites.isdigit():
|
||||
# sys.exit("Error: expected an integer in line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# nsites = int(nsites)
|
||||
# molecules.append([])
|
||||
|
||||
# for j in range(nsites):
|
||||
# line += 1
|
||||
# new_atom = ljfile.pop(0).split()
|
||||
|
||||
# if len(new_atom) < 8:
|
||||
# sys.exit("Error: expected at least 8 fields in line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# molecules[i].append({})
|
||||
|
||||
# if not new_atom[0].isdigit():
|
||||
# sys.exit("Error: expected an integer in field 1, line {} of file {}".format(line, dice['ljname']))
|
||||
# molecules[i][j]['lbl'] = int(new_atom[0])
|
||||
|
||||
# if not new_atom[1].isdigit():
|
||||
# sys.exit("Error: expected an integer in field 2, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# 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, dice['ljname']))
|
||||
# molecules[i][j]['na'] = atnumber
|
||||
|
||||
# try:
|
||||
# molecules[i][j]['rx'] = float(new_atom[2])
|
||||
# except:
|
||||
# sys.exit("Error: expected a float in field 3, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# try:
|
||||
# molecules[i][j]['ry'] = float(new_atom[3])
|
||||
# except:
|
||||
# sys.exit("Error: expected a float in field 4, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# try:
|
||||
# molecules[i][j]['rz'] = float(new_atom[4])
|
||||
# except:
|
||||
# sys.exit("Error: expected a float in field 5, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# try:
|
||||
# molecules[i][j]['chg'] = float(new_atom[5])
|
||||
# except:
|
||||
# sys.exit("Error: expected a float in field 6, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# try:
|
||||
# molecules[i][j]['eps'] = float(new_atom[6])
|
||||
# except:
|
||||
# sys.exit("Error: expected a float in field 7, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# try:
|
||||
# molecules[i][j]['sig'] = float(new_atom[7])
|
||||
# except:
|
||||
# sys.exit("Error: expected a float in field 8, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
# molecules[i][j]['mass'] = atommass[molecules[i][j]['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:
|
||||
# molecules[i][j]['mass'] = new_mass
|
||||
# except:
|
||||
# sys.exit(
|
||||
# "Error: expected a positive float after 'mass=' in field 9, line {} of file {}".format(
|
||||
# line, dice['ljname']))
|
||||
|
||||
# return
|
||||
|
||||
|
||||
|
||||
def read_ghosts():
|
||||
|
||||
max_atom_number = len(molecules[0])
|
||||
|
||||
try:
|
||||
with open("ghosts.in") as fh:
|
||||
ghostfile = fh.readlines()
|
||||
except EnvironmentError:
|
||||
sys.exit("Error: cannot open file ghosts.in")
|
||||
|
||||
for line in ghostfile:
|
||||
|
||||
if len(line.split()) > 1: # Discard lines with less than 2 fields
|
||||
|
||||
key, *atom_numbers = line.split()
|
||||
key = key.lower()
|
||||
|
||||
if key in ("g", "m", "z"): # Discard lines that do not start with g|m|z
|
||||
ghost_types.append({})
|
||||
ghost_types[-1]['type'] = key
|
||||
ghost_types[-1]['numbers'] = []
|
||||
|
||||
for num in atom_numbers:
|
||||
if not num.isdigit():
|
||||
sys.exit("Error: in file ghosts.in: only positive integers allowed after letter g|m|z")
|
||||
new_num = int(num)
|
||||
if new_num > max_atom_number:
|
||||
sys.exit("Error: in file ghosts.in: there is no atom number {}".format(new_num))
|
||||
else:
|
||||
ghost_types[-1]['numbers'].append(new_num)
|
||||
|
||||
if len(ghost_types[-1]['numbers']) < 2:
|
||||
sys.exit("Error: in file ghosts.in: at least 2 atoms are necessary to make a ghost")
|
||||
|
||||
if len(ghost_types) == 0:
|
||||
sys.exit("Error: no ghost atom found in ghosts.in")
|
||||
|
||||
return
|
||||
|
||||
|
||||
|
||||
def read_lps():
|
||||
|
||||
lp_alpha = 104.0 # Default values
|
||||
lp_dist = 0.7 #
|
||||
max_lp_type = 2
|
||||
min_alpha = 90.0
|
||||
max_alpha = 150.0
|
||||
min_dist = 0.5
|
||||
max_dist = 1.5
|
||||
max_atom_number = len(molecules[0])
|
||||
|
||||
try:
|
||||
with open("lps.in") as fh:
|
||||
lpfile = fh.readlines()
|
||||
except EnvironmentError:
|
||||
sys.exit("Error: cannot open file lps.in")
|
||||
|
||||
for line in lpfile:
|
||||
|
||||
if len(line.split()) > 1: # Discard lines with less than 2 fields
|
||||
|
||||
type, *atom_numbers = line.split()
|
||||
|
||||
if type.isdigit(): # Discard lines that do not start with an integer
|
||||
new_type = int(type)
|
||||
if new_type > max_lp_type:
|
||||
sys.exit("Error: in file lps.in: allowed LP types from 1 to {}".format(max_lp_type))
|
||||
lp_types.append({})
|
||||
lp_types[-1]['type'] = new_type
|
||||
lp_types[-1]['numbers'] = []
|
||||
|
||||
# Read types 1 and 2
|
||||
if new_type in (1, 2):
|
||||
|
||||
if len(atom_numbers) < 3:
|
||||
sys.exit("Error: in file lps.in: at least 3 atoms are necessary to make LPs type 1 and 2")
|
||||
for i in range(3):
|
||||
num = atom_numbers.pop(0)
|
||||
if not num.isdigit():
|
||||
sys.exit("Error: in file lps.in: expected 3 atom numbers after LPs type 1 and 2")
|
||||
new_num = int(num)
|
||||
if new_num > max_atom_number or new_num < 1:
|
||||
sys.exit("Error: in file lps.in: there is no atom number {}".format(new_num))
|
||||
else:
|
||||
lp_types[-1]['numbers'].append(new_num)
|
||||
|
||||
lp_types[-1]['alpha'] = lp_alpha
|
||||
lp_types[-1]['dist'] = lp_dist
|
||||
|
||||
if len(atom_numbers) != 0:
|
||||
try:
|
||||
alpha = float(atom_numbers.pop(0))
|
||||
if alpha > min_alpha and alpha < max_alpha:
|
||||
lp_types[-1]['alpha'] = alpha
|
||||
else:
|
||||
atom_numbers = []
|
||||
except:
|
||||
atom_numbers = []
|
||||
|
||||
if len(atom_numbers) != 0:
|
||||
try:
|
||||
dist = float(atom_numbers.pop(0))
|
||||
if dist > min_dist and dist < max_dist:
|
||||
lp_types[-1]['dist'] = dist
|
||||
except:
|
||||
None
|
||||
# End of types 1 and 2
|
||||
|
||||
if len(lp_types) == 0:
|
||||
sys.exit("Error: no lone pair found in lps.in")
|
||||
|
||||
return
|
||||
|
||||
|
||||
|
||||
# def print_potential(fh):
|
||||
|
||||
# formatstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}\n"
|
||||
# fh.write("\n"
|
||||
# "==========================================================================================\n")
|
||||
# fh.write(" Potential parameters from file {}:\n".format(dice['ljname']))
|
||||
# fh.write("------------------------------------------------------------------------------------------\n"
|
||||
# "\n")
|
||||
|
||||
# fh.write("Combination rule: {}\n".format(dice['combrule']))
|
||||
# fh.write("Types of molecules: {}\n\n".format(len(molecules)))
|
||||
|
||||
# i = 0
|
||||
# for mol in molecules:
|
||||
# i += 1
|
||||
# fh.write("{} atoms in molecule type {}:\n".format(len(mol), i))
|
||||
# fh.write("---------------------------------------------------------------------------------\n"
|
||||
# "Lbl AN X Y Z Charge Epsilon Sigma Mass\n")
|
||||
# fh.write("---------------------------------------------------------------------------------\n")
|
||||
|
||||
# for atom in mol:
|
||||
# fh.write(formatstr.format(atom['lbl'], atom['na'], atom['rx'], atom['ry'], atom['rz'],
|
||||
# atom['chg'], atom['eps'], atom['sig'], atom['mass']))
|
||||
|
||||
# fh.write("\n")
|
||||
|
||||
# if player['ghosts'] == "yes" or player['lps'] == "yes":
|
||||
# fh.write("\n"
|
||||
# "------------------------------------------------------------------------------------------\n"
|
||||
# " Aditional potential parameters:\n"
|
||||
# "------------------------------------------------------------------------------------------\n")
|
||||
|
||||
# if player['ghosts'] == "yes":
|
||||
|
||||
# fh.write("\n")
|
||||
# fh.write("{} ghost atoms appended to molecule type 1 at:\n".format(len(ghost_types)))
|
||||
# fh.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":
|
||||
# fh.write(textwrap.fill("* Geometric center of atoms {}".format(atoms_string), 80))
|
||||
# elif ghost['type'] == "m":
|
||||
# fh.write(textwrap.fill("* Center of mass of atoms {}".format(atoms_string), 80))
|
||||
# elif ghost['type'] == "z":
|
||||
# fh.write(textwrap.fill("* Center of atomic number of atoms {}".format(atoms_string), 80))
|
||||
|
||||
# fh.write("\n")
|
||||
|
||||
# if player['lps'] == 'yes':
|
||||
|
||||
# fh.write("\n")
|
||||
# fh.write("{} lone pairs appended to molecule type 1:\n".format(len(lp_types)))
|
||||
# fh.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()
|
||||
|
||||
# fh.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))
|
||||
# fh.write("\n")
|
||||
|
||||
# # Other LP types
|
||||
|
||||
# fh.write("\n"
|
||||
# "==========================================================================================\n")
|
||||
|
||||
# return
|
||||
|
||||
## Creation of continue_function
|
||||
|
||||
# def check_executables(fh):
|
||||
|
||||
# fh.write("\n")
|
||||
# fh.write(90 * "=")
|
||||
# fh.write("\n\n")
|
||||
|
||||
# dice_path = shutil.which(dice['progname'])
|
||||
# if dice_path != None:
|
||||
# fh.write("Program {} found at {}\n".format(dice['progname'], dice_path))
|
||||
# else:
|
||||
# sys.exit("Error: cannot find dice executable")
|
||||
|
||||
# qmprog_path = shutil.which(player['qmprog'])
|
||||
# if qmprog_path != None:
|
||||
# fh.write("Program {} found at {}\n".format(player['qmprog'], qmprog_path))
|
||||
# else:
|
||||
# sys.exit("Error: cannot find {} executable".format(player['qmprog']))
|
||||
|
||||
# if player['qmprog'] in ("g03", "g09", "g16"):
|
||||
# formchk_path = shutil.which("formchk")
|
||||
# if formchk_path != None:
|
||||
# fh.write("Program formchk found at {}\n".format(formchk_path))
|
||||
# else:
|
||||
# sys.exit("Error: cannot find formchk executable")
|
||||
|
||||
|
||||
# return
|
||||
|
||||
|
||||
|
||||
@@ -480,3 +480,5 @@ class Atom:
|
||||
self.eps = eps # Double
|
||||
self.sig = sig # Double
|
||||
self.mass = atommass[self.na] # Double
|
||||
|
||||
|
||||
|
||||
1339
DPpack/SetGlobals.py
1339
DPpack/SetGlobals.py
File diff suppressed because it is too large
Load Diff
@@ -1,543 +0,0 @@
|
||||
import os, sys
|
||||
import shutil
|
||||
import textwrap
|
||||
|
||||
from DPpack.MolHandling import *
|
||||
from DPpack.PTable import *
|
||||
from DPpack.Misc import *
|
||||
|
||||
env = ["OMP_STACKSIZE"]
|
||||
|
||||
bohr2ang = 0.52917721092
|
||||
ang2bohr = 1/bohr2ang
|
||||
|
||||
class Internal:
|
||||
|
||||
def __init__(self, infile):
|
||||
|
||||
self.infile = infile
|
||||
self.system = System()
|
||||
|
||||
self.player = self.Player()
|
||||
self.player_keywords = [a for a in dir(self.player) if not a.startswith('__') and not callable(getattr(self.player, a))]
|
||||
|
||||
self.dice = self.Dice()
|
||||
self.dice_keywords = [a for a in dir(self.dice) if not a.startswith('__') and not callable(getattr(self.dice, a))]
|
||||
|
||||
self.gaussian = self.Gaussian()
|
||||
self.gaussian_keywords = [a for a in dir(self.gaussian) if not a.startswith('__') and not callable(getattr(self.gaussian, a))]
|
||||
|
||||
# self.molcas = self.Molcas()
|
||||
# self.molcas_keywords = [a for a in dir(self.molcas) if not a.startswith('__') and not callable(getattr(self.molcas, a))]
|
||||
|
||||
## Constanst that shall be set for global use
|
||||
|
||||
self.tol_rms_force = 3e-4 # Hartree/Bohr
|
||||
self.tol_max_force = 4.5e-4 # Hartree/Bohr
|
||||
self.tol_rms_step = 1.2e-3 # Bohr
|
||||
self.tol_max_step = 1.8e-3 # Bohr
|
||||
self.trust_radius = None
|
||||
|
||||
## Dice:
|
||||
self.combrule = None
|
||||
self.randominit = None
|
||||
|
||||
def read_keywords(self):
|
||||
|
||||
try:
|
||||
with open(self.infile) as fh:
|
||||
controlfile = fh.readlines()
|
||||
except EnvironmentError:
|
||||
sys.exit("Error: cannot open file {}".format(self.infile))
|
||||
|
||||
for line in controlfile:
|
||||
|
||||
key, value = line.partition("=")[::2] # Discards the '='
|
||||
key = key.strip().lower()
|
||||
if key in ('title', 'keywords'):
|
||||
value = value.strip()
|
||||
else:
|
||||
value = value.split()
|
||||
|
||||
#### Read the Diceplayer related keywords
|
||||
if key in self.player_keywords and len(value) != 0: ## 'value' is not empty!
|
||||
|
||||
if key == 'qmprog' and value[0].lower() in ("g03", "g09", "g16", "molcas"):
|
||||
setattr(self.player, key, value[0].lower())
|
||||
|
||||
elif key == 'opt' and value[0].lower() in ("yes", "no", "ts"):
|
||||
setattr(self.player, key, value[0].lower())
|
||||
|
||||
#elif key == 'zipprog' and value[0].lower() in ("zip", "gzip", "bzip"):
|
||||
#player[key] = value[0].lower()
|
||||
|
||||
elif key in ('lps', 'ghosts') and value[0].lower() in ("yes", "no"):
|
||||
setattr(self.player, key, value[0].lower())
|
||||
|
||||
elif key in ('readhessian', 'vdwforces') and value[0].lower() in ("yes", "no"):
|
||||
setattr(self.player, key, value[0].lower())
|
||||
|
||||
elif key in ('maxcyc', 'initcyc', 'nprocs', 'altsteps', 'switchcyc'):
|
||||
err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
|
||||
try:
|
||||
new_value = int(value[0])
|
||||
if new_value >= 1:
|
||||
setattr(self.player, key, new_value)
|
||||
elif key == 'altsteps' and new_value == 0:
|
||||
setattr(self.player, key, 0)
|
||||
except ValueError:
|
||||
sys.exit(err)
|
||||
|
||||
elif key == 'maxstep': # Cannot be less than 0.01
|
||||
err = "Error: expected a float greater than 0.01 for keyword {} in file {}".format(key, self.infile)
|
||||
try:
|
||||
new_value = float(value[0])
|
||||
if new_value < 0.01:
|
||||
sys.exit(err)
|
||||
else:
|
||||
setattr(self.player, key).append(new_value)
|
||||
except ValueError:
|
||||
sys.exit(err)
|
||||
|
||||
#### Read the Dice related keywords
|
||||
elif key in self.dice_keywords and len(value) != 0: ## 'value' is not empty!
|
||||
|
||||
if key == 'title':
|
||||
setattr(self.dice, key, value)
|
||||
|
||||
elif key in ('ljname', 'outname', 'progname'):
|
||||
setattr(self.dice, key, value[0])
|
||||
|
||||
elif key in ('ncores', 'isave'):
|
||||
err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
|
||||
if not value[0].isdigit():
|
||||
sys.exit(err)
|
||||
new_value = int(value[0])
|
||||
if new_value >= 1:
|
||||
setattr(self.dice, key, new_value)
|
||||
|
||||
elif key in ('temp', 'press', 'dens'): # Cannot be less than 1e-10
|
||||
err = "Error: expected a positive float for keyword {} in file {}".format(key, self.infile)
|
||||
try:
|
||||
new_value = float(value[0])
|
||||
if new_value < 1e-10:
|
||||
sys.exit(err)
|
||||
else:
|
||||
setattr(self.dice, key, new_value)
|
||||
except ValueError:
|
||||
sys.exit(err)
|
||||
|
||||
elif key == 'nmol': # If defined, must be well defined (only positive integer values)
|
||||
err = "Error: expected 1 to 4 positive integers for keyword {} in file {}".format(key, self.infile)
|
||||
args = min(4, len(value))
|
||||
for i in range(args):
|
||||
if value[i].isdigit():
|
||||
new_value = int(value[i])
|
||||
if new_value < 1:
|
||||
sys.exit(err)
|
||||
else:
|
||||
setattr(self.dice, key, new_value)
|
||||
elif i == 0:
|
||||
sys.exit(err)
|
||||
else:
|
||||
break
|
||||
|
||||
elif key == 'nstep': # If defined, must be well defined (only positive integer values)
|
||||
err = "Error: expected 2 or 3 positive integers for keyword {} in file {}".format(key, self.infile)
|
||||
if len(value) < 2:
|
||||
sys.exit(err)
|
||||
args = min(3, len(value))
|
||||
for i in range(args):
|
||||
if value[i].isdigit():
|
||||
new_value = int(value[i])
|
||||
if new_value < 1:
|
||||
sys.exit(err)
|
||||
else:
|
||||
setattr(self.dice, key, new_value)
|
||||
elif i < 2:
|
||||
sys.exit(err)
|
||||
else:
|
||||
break
|
||||
|
||||
#### Read the Gaussian related keywords
|
||||
elif key in self.gaussian_keywords and len(value) != 0: ## 'value' is not empty!
|
||||
|
||||
if key == 'mem': # Memory in MB (minimum of 100)
|
||||
err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
|
||||
if not value[0].isdigit():
|
||||
sys.exit(err)
|
||||
new_value = int(value[0])
|
||||
if new_value >= 100:
|
||||
setattr(self.gaussian, key, new_value)
|
||||
|
||||
elif key == 'keywords':
|
||||
setattr(self.gaussian, key, value)
|
||||
|
||||
elif key == 'chgmult': # If defined, must be well defined (2 integer values)
|
||||
err = "Error: expected 2 integers for keyword {} in file {}".format(key, self.infile)
|
||||
if len(value) < 2:
|
||||
sys.exit(err)
|
||||
for i in range (2):
|
||||
try:
|
||||
setattr(self.gaussian, key)[i] = int(value[i])
|
||||
except ValueError:
|
||||
sys.exit(err)
|
||||
|
||||
elif key in ('level', 'chglevel'):
|
||||
setattr(self.gaussian, key, value[0])
|
||||
|
||||
elif key in ('gmiddle', 'gbottom'):
|
||||
setattr(self.gaussian, key, value[0])
|
||||
|
||||
elif key == 'pop' and value[0].lower() in ("chelpg", "mk", "nbo"):
|
||||
setattr(self.gaussian, key, value[0].lower())
|
||||
|
||||
#### Read the Molcas related keywords
|
||||
elif key in self.molcas_keywords and len(value) != 0: ## 'value' is not empty!
|
||||
|
||||
if key == 'root': # If defined, must be well defined (only positive integer values)
|
||||
err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
|
||||
if not value[0].isdigit():
|
||||
sys.exit(err)
|
||||
new_value = int(value[0])
|
||||
if new_value >= 1:
|
||||
setattr(self.molcas, key, new_value)
|
||||
|
||||
elif key in ('mbottom', 'orbfile'):
|
||||
setattr(self.molcas, key, value[0])
|
||||
|
||||
elif key == 'basis':
|
||||
setattr(self.molcas ,key, value[0])
|
||||
|
||||
#### End
|
||||
|
||||
|
||||
def check_keywords(self):
|
||||
|
||||
min_steps = 20000
|
||||
|
||||
if self.dice.ljname == None:
|
||||
sys.exit("Error: 'ljname' keyword not specified in file {}".format(self.infile))
|
||||
|
||||
if self.dice.outname == None:
|
||||
sys.exit("Error: 'outname' keyword not specified in file {}".format(self.infile))
|
||||
|
||||
if self.dice.dens == None:
|
||||
sys.exit("Error: 'dens' keyword not specified in file {}".format(self.infile))
|
||||
|
||||
if len(self.dice.nmol) == 0:
|
||||
sys.exit("Error: 'nmol' keyword not defined appropriately in file {}".format(self.infile))
|
||||
|
||||
if len(self.dice.nstep) == 0:
|
||||
sys.exit("Error: 'nstep' keyword not defined appropriately in file {}".format(self.infile))
|
||||
|
||||
## Check only if QM program is Gaussian:
|
||||
if self.player.qmprog in ("g03", "g09", "g16"):
|
||||
|
||||
if self.gaussian.level == None:
|
||||
sys.exit("Error: 'level' keyword not specified in file {}".format(self.infile))
|
||||
|
||||
if self.gaussian.gmiddle != None:
|
||||
if not os.path.isfile(self.gaussian.gmiddle):
|
||||
sys.exit("Error: file {} not found".format(self.gaussian.gmiddle))
|
||||
|
||||
if self.gaussian.gbottom != None:
|
||||
if not os.path.isfile(self.gaussian.gbottom):
|
||||
sys.exit("Error: file {} not found".format(self.gaussian.gbottom))
|
||||
|
||||
if self.gaussian.pop != "chelpg" and (self.player.ghosts == "yes" or self.player.lps == "yes"):
|
||||
sys.exit("Error: ghost atoms or lone pairs only available with 'pop = chelpg')")
|
||||
|
||||
if self.gaussian.chglevel == None:
|
||||
self.gaussian.chglevel = self.gaussian.level
|
||||
|
||||
## Check only if QM program is Molcas:
|
||||
# if self.player.qmprog == "molcas":
|
||||
|
||||
# if self.molcas.mbottom == None:
|
||||
# sys.exit("Error: 'mbottom' keyword not specified in file {}".format(self.infile))
|
||||
# else:
|
||||
# if not os.path.isfile(self.molcas.mbottom):
|
||||
# sys.exit("Error: file {} not found".format(self.molcas.mbottom))
|
||||
|
||||
# if self.molcas.basis == None:
|
||||
# sys.exit("Error: 'basis' keyword not specified in file {}".format(self.infile))
|
||||
|
||||
|
||||
if self.player.altsteps != 0:
|
||||
|
||||
### Verifica se tem mais de 1 molecula QM
|
||||
### (No futuro usar o RMSD fit para poder substituir todas as moleculas QM
|
||||
### no arquivo outname.xy - Need to change the make_init_file!!)
|
||||
if self.dice.nmol[0] > 1:
|
||||
sys.exit("Error: altsteps > 0 only possible with 1 QM molecule (nmol = 1 n2 n3 n4)")
|
||||
|
||||
# if not zero, altsteps cannot be less than min_steps
|
||||
self.player.altsteps = max(min_steps, self.player.altsteps)
|
||||
# altsteps value is always the nearest multiple of 1000
|
||||
self.player.altsteps = round(self.player.altsteps / 1000) * 1000
|
||||
|
||||
|
||||
for i in range(len(self.dice.nstep)):
|
||||
# nstep can never be less than min_steps
|
||||
self.dice.nstep[i] = max(min_steps, self.dice.nstep[i])
|
||||
# nstep values are always the nearest multiple of 1000
|
||||
self.dice.nstep[i] = round(self.dice.nstep[i] / 1000) * 1000
|
||||
|
||||
# isave must be between 100 and 2000
|
||||
self.dice.isave = max(100, self.dice.isave)
|
||||
self.dice.isave = min(2000, self.dice.isave)
|
||||
# isave value is always the nearest multiple of 100
|
||||
self.dice.isave = round(self.dice.isave / 100) * 100
|
||||
|
||||
def print_keywords(self, fh):
|
||||
|
||||
fh.write("##########################################################################################\n"
|
||||
"############# Welcome to DICEPLAYER version 1.0 #############\n"
|
||||
"##########################################################################################\n"
|
||||
"\n")
|
||||
fh.write("Your python version is {}\n".format(sys.version))
|
||||
fh.write("\n")
|
||||
fh.write("Program started on {}\n".format(weekday_date_time()))
|
||||
fh.write("\n")
|
||||
fh.write("Environment variables:\n")
|
||||
for var in env:
|
||||
fh.write("{} = {}\n".format(var,
|
||||
(os.environ[var] if var in os.environ else "Not set")))
|
||||
|
||||
fh.write("\n==========================================================================================\n"
|
||||
" CONTROL variables being used in this run:\n"
|
||||
"------------------------------------------------------------------------------------------\n"
|
||||
"\n")
|
||||
|
||||
for key in sorted(self.player_keywords):
|
||||
if getattr(self.player,key) != None:
|
||||
if isinstance(getattr(self.player,key), list):
|
||||
string = " ".join(str(x) for x in getattr(self.player,key))
|
||||
fh.write("{} = {}\n".format(key, string))
|
||||
else:
|
||||
fh.write("{} = {}\n".format(key, getattr(self.player,key)))
|
||||
|
||||
fh.write("\n")
|
||||
|
||||
fh.write("------------------------------------------------------------------------------------------\n"
|
||||
" DICE variables being used in this run:\n"
|
||||
"------------------------------------------------------------------------------------------\n"
|
||||
"\n")
|
||||
|
||||
for key in sorted(self.dice_keywords):
|
||||
if getattr(self.dice,key) != None:
|
||||
if isinstance(getattr(self.dice,key), list):
|
||||
string = " ".join(str(x) for x in getattr(self.dice,key))
|
||||
fh.write("{} = {}\n".format(key, string))
|
||||
else:
|
||||
fh.write("{} = {}\n".format(key, getattr(self.dice,key)))
|
||||
|
||||
fh.write("\n")
|
||||
|
||||
if self.player.qmprog in ("g03", "g09", "g16"):
|
||||
|
||||
fh.write("------------------------------------------------------------------------------------------\n"
|
||||
" GAUSSIAN variables being used in this run:\n"
|
||||
"------------------------------------------------------------------------------------------\n"
|
||||
"\n")
|
||||
|
||||
for key in sorted(self.gaussian_keywords):
|
||||
if getattr(self.gaussian,key) != None:
|
||||
if isinstance(getattr(self.gaussian,key), list):
|
||||
string = " ".join(str(x) for x in getattr(self.gaussian,key))
|
||||
fh.write("{} = {}\n".format(key, string))
|
||||
else:
|
||||
fh.write("{} = {}\n".format(key, getattr(self.gaussian,key)))
|
||||
|
||||
fh.write("\n")
|
||||
|
||||
# elif self.player.qmprog == "molcas":
|
||||
|
||||
# fh.write("------------------------------------------------------------------------------------------\n"
|
||||
# " MOLCAS variables being used in this run:\n"
|
||||
# "------------------------------------------------------------------------------------------\n"
|
||||
# "\n")
|
||||
|
||||
# for key in sorted(molcas):
|
||||
# if molcas[key] != None:
|
||||
# if isinstance(molcas[key], list):
|
||||
# string = " ".join(str(x) for x in molcas[key])
|
||||
# fh.write("{} = {}\n".format(key, string))
|
||||
# else:
|
||||
# fh.write("{} = {}\n".format(key, molcas[key]))
|
||||
|
||||
# fh.write("\n")
|
||||
|
||||
def read_potential(self): # Deve ser atualizado para o uso de
|
||||
|
||||
try:
|
||||
with open(self.dice.ljname) as file:
|
||||
ljfile = file.readlines()
|
||||
except EnvironmentError as err:
|
||||
sys.exit(err)
|
||||
|
||||
combrule = ljfile.pop(0).split()[0]
|
||||
if combrule not in ("*", "+"):
|
||||
sys.exit("Error: expected a '*' or a '+' sign in 1st line of file {}".format(self.dice.ljname))
|
||||
self.dice.combrule = combrule
|
||||
|
||||
ntypes = ljfile.pop(0).split()[0]
|
||||
if not ntypes.isdigit():
|
||||
sys.exit("Error: expected an integer in the 2nd line of file {}".format(self.dice.ljname))
|
||||
ntypes = int(ntypes)
|
||||
|
||||
if ntypes != len(self.dice.nmol):
|
||||
sys.exit("Error: number of molecule types in file {} must match that of 'nmol' keyword in file {}".format(
|
||||
self.dice.ljname, self.infile))
|
||||
|
||||
line = 2
|
||||
for i in range(ntypes):
|
||||
|
||||
line += 1
|
||||
nsites = ljfile.pop(0).split()[0]
|
||||
if not nsites.isdigit():
|
||||
sys.exit("Error: expected an integer in line {} of file {}".format(line, self.dice.ljname))
|
||||
|
||||
nsites = int(nsites)
|
||||
self.system.add_type(Molecule())
|
||||
|
||||
for j in range(nsites):
|
||||
|
||||
line += 1
|
||||
new_atom = ljfile.pop(0).split()
|
||||
|
||||
if len(new_atom) < 8:
|
||||
sys.exit("Error: expected at least 8 fields in line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
self.system.molecule[i].add_atom()
|
||||
|
||||
if not new_atom[0].isdigit():
|
||||
sys.exit("Error: expected an integer in field 1, line {} of file {}".format(line, dice['ljname']))
|
||||
lbl = int(new_atom[0])
|
||||
|
||||
if not new_atom[1].isdigit():
|
||||
sys.exit("Error: expected an integer in field 2, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
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, 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, dice['ljname']))
|
||||
|
||||
try:
|
||||
ry = float(new_atom[3])
|
||||
except:
|
||||
sys.exit("Error: expected a float in field 4, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
try:
|
||||
rz = float(new_atom[4])
|
||||
except:
|
||||
sys.exit("Error: expected a float in field 5, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
try:
|
||||
chg = float(new_atom[5])
|
||||
except:
|
||||
sys.exit("Error: expected a float in field 6, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
try:
|
||||
eps = float(new_atom[6])
|
||||
except:
|
||||
sys.exit("Error: expected a float in field 7, line {} of file {}".format(line, dice['ljname']))
|
||||
|
||||
try:
|
||||
sig = float(new_atom[7])
|
||||
except:
|
||||
sys.exit("Error: expected a float in field 8, line {} of file {}".format(line, 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, dice['ljname']))
|
||||
|
||||
self.system.molecule[i].add_atom(Atom(lbl,na,rx,ry,rz,chg,eps,sig,mass))
|
||||
|
||||
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}')
|
||||
|
||||
class Player:
|
||||
|
||||
def __init__(self):
|
||||
|
||||
self.maxcyc = None
|
||||
# self.initcyc = 1 Eliminated
|
||||
self.nprocs = 1
|
||||
self.switchcyc = 3
|
||||
self.altsteps = 20000
|
||||
self.maxstep = .3
|
||||
self.qmprog = "g09"
|
||||
self.opt = "yes"
|
||||
self.freq = "no"
|
||||
self.readhessian = "no"
|
||||
self.lps = "no"
|
||||
self.ghosts = "no"
|
||||
self.vdwforces = "no"
|
||||
self.tol_factor = 1.2
|
||||
|
||||
|
||||
|
||||
class Dice:
|
||||
|
||||
def __init__(self):
|
||||
|
||||
self.title = "Diceplayer run"
|
||||
self.progname = "dice"
|
||||
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.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.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.chglevel = None
|
||||
|
||||
self.level = None
|
||||
|
||||
# class Molcas:
|
||||
|
||||
# def __init(self):
|
||||
|
||||
# self.orbfile = "input.exporb"
|
||||
# self.root = 1
|
||||
|
||||
# self.mbottom = None
|
||||
# self.basis = None
|
||||
Reference in New Issue
Block a user