Vitor Hideyoshi
2f9cecee34
Internal methods fixes: check_executables Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
660 lines
22 KiB
Python
660 lines
22 KiB
Python
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, self.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, self.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, self.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, self.dice.ljname))
|
|
na = atnumber
|
|
|
|
try:
|
|
rx = float(new_atom[2])
|
|
except:
|
|
sys.exit("Error: expected a float in field 3, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
try:
|
|
ry = float(new_atom[3])
|
|
except:
|
|
sys.exit("Error: expected a float in field 4, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
try:
|
|
rz = float(new_atom[4])
|
|
except:
|
|
sys.exit("Error: expected a float in field 5, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
try:
|
|
chg = float(new_atom[5])
|
|
except:
|
|
sys.exit("Error: expected a float in field 6, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
try:
|
|
eps = float(new_atom[6])
|
|
except:
|
|
sys.exit("Error: expected a float in field 7, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
try:
|
|
sig = float(new_atom[7])
|
|
except:
|
|
sys.exit("Error: expected a float in field 8, line {} of file {}".format(line, self.dice.ljname))
|
|
|
|
mass = atommass[na]
|
|
|
|
if len(new_atom) > 8:
|
|
masskey, mass = new_atom[8].partition("=")[::2]
|
|
if masskey.lower() == 'mass' and len(mass) !=0:
|
|
try:
|
|
new_mass = float(mass)
|
|
if new_mass > 0:
|
|
mass = new_mass
|
|
except:
|
|
sys.exit(
|
|
"Error: expected a positive float after 'mass=' in field 9, line {} of file {}".format(
|
|
line, self.dice.ljname))
|
|
|
|
self.system.molecule[i].add_atom(Atom(lbl,na,rx,ry,rz,chg,eps,sig,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}')
|
|
|
|
|
|
def print_potential(self, 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(self.dice.ljname))
|
|
fh.write("------------------------------------------------------------------------------------------\n"
|
|
"\n")
|
|
|
|
fh.write("Combination rule: {}\n".format(self.dice.combrule))
|
|
fh.write("Types of molecules: {}\n\n".format(len(self.system.molecule)))
|
|
|
|
i = 0
|
|
for mol in self.system.molecule:
|
|
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.atom:
|
|
|
|
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 self.player.ghosts == "yes" or self.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
|
|
|
|
|
|
def check_executables(self, fh):
|
|
|
|
fh.write("\n")
|
|
fh.write(90 * "=")
|
|
fh.write("\n\n")
|
|
|
|
dice_path = shutil.which(self.dice.progname)
|
|
if dice_path != None:
|
|
fh.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:
|
|
fh.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:
|
|
fh.write("Program formchk found at {}\n".format(formchk_path))
|
|
else:
|
|
sys.exit("Error: cannot find formchk executable")
|
|
|
|
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.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.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.chglevel = None
|
|
|
|
self.level = None
|
|
|
|
# class Molcas:
|
|
|
|
# def __init(self):
|
|
|
|
# self.orbfile = "input.exporb"
|
|
# self.root = 1
|
|
|
|
# self.mbottom = None
|
|
# self.basis = None |