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SetGlobas Translation - Most

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Internal methods translations: read_keywords, check_keywords, print_keywords, read_potential

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
Vitor Hideyoshi
2021-08-03 16:16:37 -03:00
parent 99b8ee17da
commit d9da04419a
3 changed files with 625 additions and 352 deletions
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8
DPpack/Molhandling.py → DPpack/MolHandling.py
View File

@@ -20,10 +20,12 @@ class System:
def __init__(self): def __init__(self):
self.molecule = [] self.molecule = []
self.nmols = []
def add_molecule(self, m): def add_type(self,nmols, m):
self.molecule.append(m) self.molecule.append(m)
self.nmols = nmols
# Função que calcula a distância entre dois centros de massa # Função que calcula a distância entre dois centros de massa
# e por se tratar de uma função de dois atomos não deve ser # e por se tratar de uma função de dois atomos não deve ser
@@ -192,6 +194,7 @@ class Molecule:
self.gradient = None # Array Numpy self.gradient = None # Array Numpy
self.hessian = None # Array Numpy self.hessian = None # Array Numpy
self.total_mass = 0 self.total_mass = 0
self.com = None
def add_atom(self, a): def add_atom(self, a):
@@ -210,7 +213,7 @@ class Molecule:
com = com / total_mass com = com / total_mass
return com self.com = com
def center_of_mass_to_origin(self): def center_of_mass_to_origin(self):
@@ -477,4 +480,3 @@ class Atom:
self.eps = eps # Double self.eps = eps # Double
self.sig = sig # Double self.sig = sig # Double
self.mass = atommass[self.na] # Double self.mass = atommass[self.na] # Double

814
DPpack/SetGlobals.py
View File

@@ -144,440 +144,440 @@ env = ["OMP_STACKSIZE"]
## Functions to process the input files and store the values in the global variables ## ## Functions to process the input files and store the values in the global variables ##
########################################################################################## ##########################################################################################
def read_keywords(infile): # def read_keywords(infile):
try: # try:
with open(infile) as fh: # with open(infile) as fh:
controlfile = fh.readlines() # controlfile = fh.readlines()
except EnvironmentError: # except EnvironmentError:
sys.exit("Error: cannot open file {}".format(infile)) # sys.exit("Error: cannot open file {}".format(infile))
for line in controlfile: # for line in controlfile:
key, value = line.partition("=")[::2] # Discards the '=' # key, value = line.partition("=")[::2] # Discards the '='
key = key.strip().lower() # key = key.strip().lower()
if key in ('title', 'keywords'): # if key in ('title', 'keywords'):
value = value.strip() # value = value.strip()
else: # else:
value = value.split() # value = value.split()
#### Read the Diceplayer related keywords # #### Read the Diceplayer related keywords
if key in player and len(value) != 0: ## 'value' is not empty! # if key in player and len(value) != 0: ## 'value' is not empty!
if key == 'qmprog' and value[0].lower() in ("g03", "g09", "g16", "molcas"): # if key == 'qmprog' and value[0].lower() in ("g03", "g09", "g16", "molcas"):
player[key] = value[0].lower() # player[key] = value[0].lower()
elif key == 'opt' and value[0].lower() in ("yes", "no", "ts"): # elif key == 'opt' and value[0].lower() in ("yes", "no", "ts"):
player[key] = value[0].lower() # player[key] = value[0].lower()
#elif key == 'zipprog' and value[0].lower() in ("zip", "gzip", "bzip"): # #elif key == 'zipprog' and value[0].lower() in ("zip", "gzip", "bzip"):
#player[key] = value[0].lower() # #player[key] = value[0].lower()
elif key in ('lps', 'ghosts') and value[0].lower() in ("yes", "no"): # elif key in ('lps', 'ghosts') and value[0].lower() in ("yes", "no"):
player[key] = value[0].lower() # player[key] = value[0].lower()
elif key in ('readhessian', 'vdwforces') and value[0].lower() in ("yes", "no"): # elif key in ('readhessian', 'vdwforces') and value[0].lower() in ("yes", "no"):
player[key] = value[0].lower() # player[key] = value[0].lower()
elif key in ('maxcyc', 'initcyc', 'nprocs', 'altsteps', 'switchcyc'): # elif key in ('maxcyc', 'initcyc', 'nprocs', 'altsteps', 'switchcyc'):
err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile) # err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile)
try: # try:
new_value = int(value[0]) # new_value = int(value[0])
if new_value >= 1: # if new_value >= 1:
player[key] = new_value # player[key] = new_value
elif key == 'altsteps' and new_value == 0: # elif key == 'altsteps' and new_value == 0:
player[key] = 0 # player[key] = 0
except ValueError: # except ValueError:
sys.exit(err) # sys.exit(err)
elif key == 'maxstep': # Cannot be less than 0.01 # 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) # err = "Error: expected a float greater than 0.01 for keyword {} in file {}".format(key, infile)
try: # try:
new_value = float(value[0]) # new_value = float(value[0])
if new_value < 0.01: # if new_value < 0.01:
sys.exit(err) # sys.exit(err)
else: # else:
player[key] = new_value # player[key] = new_value
except ValueError: # except ValueError:
sys.exit(err) # sys.exit(err)
#### Read the Dice related keywords # #### Read the Dice related keywords
elif key in dice and len(value) != 0: ## 'value' is not empty! # elif key in dice and len(value) != 0: ## 'value' is not empty!
if key == 'title': # if key == 'title':
dice[key] = value # dice[key] = value
elif key in ('ljname', 'outname', 'progname'): # elif key in ('ljname', 'outname', 'progname'):
dice[key] = value[0] # dice[key] = value[0]
elif key in ('ncores', 'isave'): # elif key in ('ncores', 'isave'):
err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile) # err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile)
if not value[0].isdigit(): # if not value[0].isdigit():
sys.exit(err) # sys.exit(err)
new_value = int(value[0]) # new_value = int(value[0])
if new_value >= 1: # if new_value >= 1:
dice[key] = new_value # dice[key] = new_value
elif key in ('temp', 'press', 'dens'): # Cannot be less than 1e-10 # 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) # err = "Error: expected a positive float for keyword {} in file {}".format(key, infile)
try: # try:
new_value = float(value[0]) # new_value = float(value[0])
if new_value < 1e-10: # if new_value < 1e-10:
sys.exit(err) # sys.exit(err)
else: # else:
dice[key] = new_value # dice[key] = new_value
except ValueError: # except ValueError:
sys.exit(err) # sys.exit(err)
elif key == 'nmol': # If defined, must be well defined (only positive integer values) # 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) # err = "Error: expected 1 to 4 positive integers for keyword {} in file {}".format(key, infile)
args = min(4, len(value)) # args = min(4, len(value))
for i in range(args): # for i in range(args):
if value[i].isdigit(): # if value[i].isdigit():
new_value = int(value[i]) # new_value = int(value[i])
if new_value < 1: # if new_value < 1:
sys.exit(err) # sys.exit(err)
else: # else:
dice[key].append(new_value) # dice[key].append(new_value)
elif i == 0: # elif i == 0:
sys.exit(err) # sys.exit(err)
else: # else:
break # break
elif key == 'nstep': # If defined, must be well defined (only positive integer values) # 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) # err = "Error: expected 2 or 3 positive integers for keyword {} in file {}".format(key, infile)
if len(value) < 2: # if len(value) < 2:
sys.exit(err) # sys.exit(err)
args = min(3, len(value)) # args = min(3, len(value))
for i in range(args): # for i in range(args):
if value[i].isdigit(): # if value[i].isdigit():
new_value = int(value[i]) # new_value = int(value[i])
if new_value < 1: # if new_value < 1:
sys.exit(err) # sys.exit(err)
else: # else:
dice[key].append(new_value) # dice[key].append(new_value)
elif i < 2: # elif i < 2:
sys.exit(err) # sys.exit(err)
else: # else:
break # break
#### Read the Gaussian related keywords # #### Read the Gaussian related keywords
elif key in gaussian and len(value) != 0: ## 'value' is not empty! # elif key in gaussian and len(value) != 0: ## 'value' is not empty!
if key == 'mem': # Memory in MB (minimum of 100) # if key == 'mem': # Memory in MB (minimum of 100)
err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile) # err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile)
if not value[0].isdigit(): # if not value[0].isdigit():
sys.exit(err) # sys.exit(err)
new_value = int(value[0]) # new_value = int(value[0])
if new_value >= 100: # if new_value >= 100:
gaussian[key] = new_value # gaussian[key] = new_value
elif key == 'keywords': # elif key == 'keywords':
gaussian[key] = value # gaussian[key] = value
elif key == 'chgmult': # If defined, must be well defined (2 integer values) # elif key == 'chgmult': # If defined, must be well defined (2 integer values)
err = "Error: expected 2 integers for keyword {} in file {}".format(key, infile) # err = "Error: expected 2 integers for keyword {} in file {}".format(key, infile)
if len(value) < 2: # if len(value) < 2:
sys.exit(err) # sys.exit(err)
for i in range (2): # for i in range (2):
try: # try:
gaussian[key][i] = int(value[i]) # gaussian[key][i] = int(value[i])
except ValueError: # except ValueError:
sys.exit(err) # sys.exit(err)
elif key in ('level', 'chglevel'): # elif key in ('level', 'chglevel'):
gaussian[key] = value[0] # gaussian[key] = value[0]
elif key in ('gmiddle', 'gbottom'): # elif key in ('gmiddle', 'gbottom'):
gaussian[key] = value[0] # gaussian[key] = value[0]
elif key == 'pop' and value[0].lower() in ("chelpg", "mk", "nbo"): # elif key == 'pop' and value[0].lower() in ("chelpg", "mk", "nbo"):
gaussian[key] = value[0].lower() # gaussian[key] = value[0].lower()
#### Read the Molcas related keywords # #### Read the Molcas related keywords
elif key in molcas and len(value) != 0: ## 'value' is not empty! # 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) # 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) # err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile)
if not value[0].isdigit(): # if not value[0].isdigit():
sys.exit(err) # sys.exit(err)
new_value = int(value[0]) # new_value = int(value[0])
if new_value >= 1: # if new_value >= 1:
molcas[key] = new_value # molcas[key] = new_value
elif key in ('mbottom', 'orbfile'): # elif key in ('mbottom', 'orbfile'):
molcas[key] = value[0] # molcas[key] = value[0]
elif key == 'basis': # elif key == 'basis':
molcas[key] = value[0] # molcas[key] = value[0]
#### End # #### End
return # return
def check_keywords(infile): # def check_keywords(infile):
min_steps = 20000 # min_steps = 20000
if dice['ljname'] == None: # if dice['ljname'] == None:
sys.exit("Error: 'ljname' keyword not specified in file {}".format(infile)) # sys.exit("Error: 'ljname' keyword not specified in file {}".format(infile))
if dice['outname'] == None: # if dice['outname'] == None:
sys.exit("Error: 'outname' keyword not specified in file {}".format(infile)) # sys.exit("Error: 'outname' keyword not specified in file {}".format(infile))
if dice['dens'] == None: # if dice['dens'] == None:
sys.exit("Error: 'dens' keyword not specified in file {}".format(infile)) # sys.exit("Error: 'dens' keyword not specified in file {}".format(infile))
if len(dice['nmol']) == 0: # if len(dice['nmol']) == 0:
sys.exit("Error: 'nmol' keyword not defined appropriately in file {}".format(infile)) # sys.exit("Error: 'nmol' keyword not defined appropriately in file {}".format(infile))
if len(dice['nstep']) == 0: # if len(dice['nstep']) == 0:
sys.exit("Error: 'nstep' keyword not defined appropriately in file {}".format(infile)) # sys.exit("Error: 'nstep' keyword not defined appropriately in file {}".format(infile))
## Check only if QM program is Gaussian: # ## Check only if QM program is Gaussian:
if player['qmprog'] in ("g03", "g09", "g16"): # if player['qmprog'] in ("g03", "g09", "g16"):
if gaussian['level'] == None: # if gaussian['level'] == None:
sys.exit("Error: 'level' keyword not specified in file {}".format(infile)) # sys.exit("Error: 'level' keyword not specified in file {}".format(infile))
if gaussian['gmiddle'] != None: # if gaussian['gmiddle'] != None:
if not os.path.isfile(gaussian['gmiddle']): # if not os.path.isfile(gaussian['gmiddle']):
sys.exit("Error: file {} not found".format(gaussian['gmiddle'])) # sys.exit("Error: file {} not found".format(gaussian['gmiddle']))
if gaussian['gbottom'] != None: # if gaussian['gbottom'] != None:
if not os.path.isfile(gaussian['gbottom']): # if not os.path.isfile(gaussian['gbottom']):
sys.exit("Error: file {} not found".format(gaussian['gbottom'])) # sys.exit("Error: file {} not found".format(gaussian['gbottom']))
if gaussian['pop'] != "chelpg" and (player['ghosts'] == "yes" or player['lps'] == "yes"): # 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')") # sys.exit("Error: ghost atoms or lone pairs only available with 'pop = chelpg')")
if gaussian['chglevel'] == None: # if gaussian['chglevel'] == None:
gaussian['chglevel'] = gaussian['level'] # gaussian['chglevel'] = gaussian['level']
## Check only if QM program is Molcas: # ## Check only if QM program is Molcas:
if player['qmprog'] == "molcas": # if player['qmprog'] == "molcas":
if molcas['mbottom'] == None: # if molcas['mbottom'] == None:
sys.exit("Error: 'mbottom' keyword not specified in file {}".format(infile)) # sys.exit("Error: 'mbottom' keyword not specified in file {}".format(infile))
else: # else:
if not os.path.isfile(molcas['mbottom']): # if not os.path.isfile(molcas['mbottom']):
sys.exit("Error: file {} not found".format(molcas['mbottom'])) # sys.exit("Error: file {} not found".format(molcas['mbottom']))
if molcas['basis'] == None: # if molcas['basis'] == None:
sys.exit("Error: 'basis' keyword not specified in file {}".format(infile)) # sys.exit("Error: 'basis' keyword not specified in file {}".format(infile))
if player['altsteps'] != 0: # if player['altsteps'] != 0:
### Verifica se tem mais de 1 molecula QM # ### Verifica se tem mais de 1 molecula QM
### (No futuro usar o RMSD fit para poder substituir todas as moleculas 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!!) # ### no arquivo outname.xy - Need to change the make_init_file!!)
if dice['nmol'][0] > 1: # if dice['nmol'][0] > 1:
sys.exit("Error: altsteps > 0 only possible with 1 QM molecule (nmol = 1 n2 n3 n4)") # 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 # # if not zero, altsteps cannot be less than min_steps
player['altsteps'] = max(min_steps, player['altsteps']) # player['altsteps'] = max(min_steps, player['altsteps'])
# altsteps value is always the nearest multiple of 1000 # # altsteps value is always the nearest multiple of 1000
player['altsteps'] = round(player['altsteps'] / 1000) * 1000 # player['altsteps'] = round(player['altsteps'] / 1000) * 1000
for i in range(len(dice['nstep'])): # for i in range(len(dice['nstep'])):
# nstep can never be less than min_steps # # nstep can never be less than min_steps
dice['nstep'][i] = max(min_steps, dice['nstep'][i]) # dice['nstep'][i] = max(min_steps, dice['nstep'][i])
# nstep values are always the nearest multiple of 1000 # # nstep values are always the nearest multiple of 1000
dice['nstep'][i] = round(dice['nstep'][i] / 1000) * 1000 # dice['nstep'][i] = round(dice['nstep'][i] / 1000) * 1000
# isave must be between 100 and 2000 # # isave must be between 100 and 2000
dice['isave'] = max(100, dice['isave']) # dice['isave'] = max(100, dice['isave'])
dice['isave'] = min(2000, dice['isave']) # dice['isave'] = min(2000, dice['isave'])
# isave value is always the nearest multiple of 100 # # isave value is always the nearest multiple of 100
dice['isave'] = round(dice['isave'] / 100) * 100 # dice['isave'] = round(dice['isave'] / 100) * 100
return # return
def print_keywords(fh): # def print_keywords(fh):
fh.write("##########################################################################################\n" # fh.write("##########################################################################################\n"
"############# Welcome to DICEPLAYER version 1.0 #############\n" # "############# Welcome to DICEPLAYER version 1.0 #############\n"
"##########################################################################################\n" # "##########################################################################################\n"
"\n") # "\n")
fh.write("Your python version is {}\n".format(sys.version)) # fh.write("Your python version is {}\n".format(sys.version))
fh.write("\n") # fh.write("\n")
fh.write("Program started on {}\n".format(weekday_date_time())) # fh.write("Program started on {}\n".format(weekday_date_time()))
fh.write("\n") # fh.write("\n")
fh.write("Environment variables:\n") # fh.write("Environment variables:\n")
for var in env: # for var in env:
fh.write("{} = {}\n".format(var, # fh.write("{} = {}\n".format(var,
(os.environ[var] if var in os.environ else "Not set"))) # (os.environ[var] if var in os.environ else "Not set")))
fh.write("\n==========================================================================================\n" # fh.write("\n==========================================================================================\n"
" CONTROL variables being used in this run:\n" # " CONTROL variables being used in this run:\n"
"------------------------------------------------------------------------------------------\n" # "------------------------------------------------------------------------------------------\n"
"\n") # "\n")
for key in sorted(player): # for key in sorted(player):
if player[key] != None: # if player[key] != None:
if isinstance(player[key], list): # if isinstance(player[key], list):
string = " ".join(str(x) for x in player[key]) # string = " ".join(str(x) for x in player[key])
fh.write("{} = {}\n".format(key, string)) # fh.write("{} = {}\n".format(key, string))
else: # else:
fh.write("{} = {}\n".format(key, player[key])) # fh.write("{} = {}\n".format(key, player[key]))
fh.write("\n") # fh.write("\n")
fh.write("------------------------------------------------------------------------------------------\n" # fh.write("------------------------------------------------------------------------------------------\n"
" DICE variables being used in this run:\n" # " DICE variables being used in this run:\n"
"------------------------------------------------------------------------------------------\n" # "------------------------------------------------------------------------------------------\n"
"\n") # "\n")
for key in sorted(dice): # for key in sorted(dice):
if dice[key] != None: # if dice[key] != None:
if isinstance(dice[key], list): # if isinstance(dice[key], list):
string = " ".join(str(x) for x in dice[key]) # string = " ".join(str(x) for x in dice[key])
fh.write("{} = {}\n".format(key, string)) # fh.write("{} = {}\n".format(key, string))
else: # else:
fh.write("{} = {}\n".format(key, dice[key])) # fh.write("{} = {}\n".format(key, dice[key]))
fh.write("\n") # fh.write("\n")
if player['qmprog'] in ("g03", "g09", "g16"): # if player['qmprog'] in ("g03", "g09", "g16"):
fh.write("------------------------------------------------------------------------------------------\n" # fh.write("------------------------------------------------------------------------------------------\n"
" GAUSSIAN variables being used in this run:\n" # " GAUSSIAN variables being used in this run:\n"
"------------------------------------------------------------------------------------------\n" # "------------------------------------------------------------------------------------------\n"
"\n") # "\n")
for key in sorted(gaussian): # for key in sorted(gaussian):
if gaussian[key] != None: # if gaussian[key] != None:
if isinstance(gaussian[key], list): # if isinstance(gaussian[key], list):
string = " ".join(str(x) for x in gaussian[key]) # string = " ".join(str(x) for x in gaussian[key])
fh.write("{} = {}\n".format(key, string)) # fh.write("{} = {}\n".format(key, string))
else: # else:
fh.write("{} = {}\n".format(key, gaussian[key])) # fh.write("{} = {}\n".format(key, gaussian[key]))
fh.write("\n") # fh.write("\n")
elif player['qmprog'] == "molcas": # elif player['qmprog'] == "molcas":
fh.write("------------------------------------------------------------------------------------------\n" # fh.write("------------------------------------------------------------------------------------------\n"
" MOLCAS variables being used in this run:\n" # " MOLCAS variables being used in this run:\n"
"------------------------------------------------------------------------------------------\n" # "------------------------------------------------------------------------------------------\n"
"\n") # "\n")
for key in sorted(molcas): # for key in sorted(molcas):
if molcas[key] != None: # if molcas[key] != None:
if isinstance(molcas[key], list): # if isinstance(molcas[key], list):
string = " ".join(str(x) for x in molcas[key]) # string = " ".join(str(x) for x in molcas[key])
fh.write("{} = {}\n".format(key, string)) # fh.write("{} = {}\n".format(key, string))
else: # else:
fh.write("{} = {}\n".format(key, molcas[key])) # fh.write("{} = {}\n".format(key, molcas[key]))
fh.write("\n") # fh.write("\n")
return # return
def read_potential(infile): # Deve ser atualizado para o uso de # def read_potential(infile): # Deve ser atualizado para o uso de
try: # try:
with open(dice['ljname']) as file: # with open(dice['ljname']) as file:
ljfile = file.readlines() # ljfile = file.readlines()
except EnvironmentError as err: # except EnvironmentError as err:
sys.exit(err) # sys.exit(err)
combrule = ljfile.pop(0).split()[0] # combrule = ljfile.pop(0).split()[0]
if combrule not in ("*", "+"): # if combrule not in ("*", "+"):
sys.exit("Error: expected a '*' or a '+' sign in 1st line of file {}".format(dice['ljname'])) # sys.exit("Error: expected a '*' or a '+' sign in 1st line of file {}".format(dice['ljname']))
dice['combrule'] = combrule # dice['combrule'] = combrule
ntypes = ljfile.pop(0).split()[0] # ntypes = ljfile.pop(0).split()[0]
if not ntypes.isdigit(): # if not ntypes.isdigit():
sys.exit("Error: expected an integer in the 2nd line of file {}".format(dice['ljname'])) # sys.exit("Error: expected an integer in the 2nd line of file {}".format(dice['ljname']))
ntypes = int(ntypes) # ntypes = int(ntypes)
if ntypes != len(dice['nmol']): # if ntypes != len(dice['nmol']):
sys.exit("Error: number of molecule types in file {} must match that of 'nmol' keyword in file {}".format( # sys.exit("Error: number of molecule types in file {} must match that of 'nmol' keyword in file {}".format(
dice['ljname'], infile)) # dice['ljname'], infile))
line = 2 # line = 2
for i in range(ntypes): # for i in range(ntypes):
line += 1 # line += 1
nsites = ljfile.pop(0).split()[0] # nsites = ljfile.pop(0).split()[0]
if not nsites.isdigit(): # if not nsites.isdigit():
sys.exit("Error: expected an integer in line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected an integer in line {} of file {}".format(line, dice['ljname']))
nsites = int(nsites) # nsites = int(nsites)
molecules.append([]) # molecules.append([])
for j in range(nsites): # for j in range(nsites):
line += 1 # line += 1
new_atom = ljfile.pop(0).split() # new_atom = ljfile.pop(0).split()
if len(new_atom) < 8: # if len(new_atom) < 8:
sys.exit("Error: expected at least 8 fields in line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected at least 8 fields in line {} of file {}".format(line, dice['ljname']))
molecules[i].append({}) # molecules[i].append({})
if not new_atom[0].isdigit(): # if not new_atom[0].isdigit():
sys.exit("Error: expected an integer in field 1, line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected an integer in field 1, line {} of file {}".format(line, dice['ljname']))
molecules[i][j]['lbl'] = int(new_atom[0]) # molecules[i][j]['lbl'] = int(new_atom[0])
if not new_atom[1].isdigit(): # if not new_atom[1].isdigit():
sys.exit("Error: expected an integer in field 2, line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected an integer in field 2, line {} of file {}".format(line, dice['ljname']))
atnumber = int(new_atom[1]) # atnumber = int(new_atom[1])
if atnumber == ghost_number and i == 0: # Ghost atom not allowed in the QM molecule # 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'])) # sys.exit("Error: found a ghost atom in line {} of file {}".format(line, dice['ljname']))
molecules[i][j]['na'] = atnumber # molecules[i][j]['na'] = atnumber
try: # try:
molecules[i][j]['rx'] = float(new_atom[2]) # molecules[i][j]['rx'] = float(new_atom[2])
except: # except:
sys.exit("Error: expected a float in field 3, line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected a float in field 3, line {} of file {}".format(line, dice['ljname']))
try: # try:
molecules[i][j]['ry'] = float(new_atom[3]) # molecules[i][j]['ry'] = float(new_atom[3])
except: # except:
sys.exit("Error: expected a float in field 4, line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected a float in field 4, line {} of file {}".format(line, dice['ljname']))
try: # try:
molecules[i][j]['rz'] = float(new_atom[4]) # molecules[i][j]['rz'] = float(new_atom[4])
except: # except:
sys.exit("Error: expected a float in field 5, line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected a float in field 5, line {} of file {}".format(line, dice['ljname']))
try: # try:
molecules[i][j]['chg'] = float(new_atom[5]) # molecules[i][j]['chg'] = float(new_atom[5])
except: # except:
sys.exit("Error: expected a float in field 6, line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected a float in field 6, line {} of file {}".format(line, dice['ljname']))
try: # try:
molecules[i][j]['eps'] = float(new_atom[6]) # molecules[i][j]['eps'] = float(new_atom[6])
except: # except:
sys.exit("Error: expected a float in field 7, line {} of file {}".format(line, dice['ljname'])) # sys.exit("Error: expected a float in field 7, line {} of file {}".format(line, dice['ljname']))
try: # try:
molecules[i][j]['sig'] = float(new_atom[7]) # molecules[i][j]['sig'] = float(new_atom[7])
except: # except:
sys.exit("Error: expected a float in field 8, line {} of file {}".format(line, dice['ljname'])) # 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']] # molecules[i][j]['mass'] = atommass[molecules[i][j]['na']]
if len(new_atom) > 8: # if len(new_atom) > 8:
masskey, mass = new_atom[8].partition("=")[::2] # masskey, mass = new_atom[8].partition("=")[::2]
if masskey.lower() == 'mass' and len(mass) !=0: # if masskey.lower() == 'mass' and len(mass) !=0:
try: # try:
new_mass = float(mass) # new_mass = float(mass)
if new_mass > 0: # if new_mass > 0:
molecules[i][j]['mass'] = new_mass # molecules[i][j]['mass'] = new_mass
except: # except:
sys.exit( # sys.exit(
"Error: expected a positive float after 'mass=' in field 9, line {} of file {}".format( # "Error: expected a positive float after 'mass=' in field 9, line {} of file {}".format(
line, dice['ljname'])) # line, dice['ljname']))
return # return

293
DPpack/SetGlobalsClass.py
View File

@@ -2,14 +2,21 @@ import os, sys
import shutil import shutil
import textwrap import textwrap
from DPpack.MolHandling import *
from DPpack.PTable import * from DPpack.PTable import *
from DPpack.Misc import * from DPpack.Misc import *
env = ["OMP_STACKSIZE"]
bohr2ang = 0.52917721092
ang2bohr = 1/bohr2ang
class Internal: class Internal:
def __init__(self, infile): def __init__(self, infile):
self.infile = infile self.infile = infile
self.system = System()
self.player = self.Player() 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.player_keywords = [a for a in dir(self.player) if not a.startswith('__') and not callable(getattr(self.player, a))]
@@ -20,8 +27,8 @@ class Internal:
self.gaussian = self.Gaussian() 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.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 = self.Molcas()
self.molcas_keywords = [a for a in dir(self.molcas) if not a.startswith('__') and not callable(getattr(self.molcas, a))] # 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 ## Constanst that shall be set for global use
@@ -189,7 +196,7 @@ class Internal:
elif key in self.molcas_keywords and len(value) != 0: ## 'value' is not empty! 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) 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) err = "Error: expected a positive integer for keyword {} in file {}".format(key, self.infile)
if not value[0].isdigit(): if not value[0].isdigit():
sys.exit(err) sys.exit(err)
new_value = int(value[0]) new_value = int(value[0])
@@ -204,12 +211,276 @@ class Internal:
#### End #### 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: class Player:
def __init__(self): def __init__(self):
self.maxcyc = None self.maxcyc = None
self.initcyc = 1 # self.initcyc = 1 Eliminated
self.nprocs = 1 self.nprocs = 1
self.switchcyc = 3 self.switchcyc = 3
self.altsteps = 20000 self.altsteps = 20000
@@ -237,7 +508,7 @@ class Internal:
self.ncores = 1 self.ncores = 1
self.dens = None # Investigate the possibility of using 'box = Lx Ly Lz' instead. self.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 # self.box = None # So 'geom' would be set by diceplayer and 'cutoff' would be
# switched off. One of them must be given. # switched off. One of them must be given.
self.ljname = None self.ljname = None
self.outname = None self.outname = None
@@ -261,12 +532,12 @@ class Internal:
self.level = None self.level = None
class Molcas: # class Molcas:
def __init(self): # def __init(self):
self.orbfile = "input.exporb" # self.orbfile = "input.exporb"
self.root = 1 # self.root = 1
self.mbottom = None # self.mbottom = None
self.basis = None # self.basis = None