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debug
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@SangniXun
SangniXun committed May 16, 2024
1 parent ea8349e commit d830cc0
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Showing 2 changed files with 66 additions and 47 deletions.
1 change: 1 addition & 0 deletions autosolvate/FFmetalcomplex.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ def __init__(self, filename,metal_charge, chargefile, solvent,slv_count,folder,
self.basisset = basisset
self.method = method
self.totalcharge = totalcharge
# print('################ totalcharge is ',self.totalcharge)
self.nprocs = nprocs
self.QMexe = QMexe
self.amberhome = amberhome
Expand Down
112 changes: 65 additions & 47 deletions autosolvate/QM_gen.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -129,47 +129,65 @@ def __init__(self, filename,software,caltype,multi,method,basisset,totalcharge,m
self.nprocs = nprocs
self.opt = opt

if self.totalcharge in ['default','Default'] or self.metal in ['default','Default']:
try:
with open(self.info, 'r') as f:
data = f.readlines()
if self.totalcharge in ['default','Default'] :
with open(self.info, 'r') as f:
data = f.readlines()

begin, end = 0, len(data)
for sort, line in enumerate(data):
if '@charges' in line:
begin = sort + 1
elif '@connection_infos' in line:
end = sort
newtotalcharge = 0

for line in data[begin:end]:
if 'LG' not in line:
parts = line.split()
if len(parts) == 2:
new_metal = parts[0].capitalize()
self.metal = new_metal
metalcharge = int(parts[1])
newtotalcharge += metalcharge
else:
parts = line.split()
if len(parts) == 2:
ligand = parts[0].capitalize()
ligandchg = int(parts[1])
newtotalcharge += ligandchg
self.totalcharge = newtotalcharge

except FileNotFoundError:
print('Error, cant find',self.info, ' or the info file is not correct, please assign the metal name and total charge manually')
sys.exit()
except IOError:
print('Error, cant find',self.info, ' or the info file is not correct, please assign the metal name and total charge manually')
sys.exit()
except IndexError:
print('Error, cant find',self.info, ' or the info file is not correct, please assign the metal name and total charge manually')
sys.exit()
except ValueError:
print('Error, cant find',self.info, ' or the info file is not correct, please assign the metal name and total charge manually')
sys.exit()
begin, end = 0, len(data)
for sort, line in enumerate(data):
if '@charges' in line:
begin = sort + 1
elif '@connection_infos' in line:
end = sort
newtotalcharge = 0

for line in data[begin:end]:
if 'LG' not in line:
parts = line.split()
if len(parts) == 2:
new_metal = parts[0].capitalize()
metalcharge = int(float(parts[1]))
newtotalcharge += metalcharge
else:
parts = line.split()
if len(parts) == 2:
ligand = parts[0].capitalize()
ligandchg = int(float(parts[1]))
newtotalcharge += ligandchg
self.totalcharge = newtotalcharge

if self.metal in ['default','Default']:
with open(self.info, 'r') as f:
data = f.readlines()

begin, end = 0, len(data)
for sort, line in enumerate(data):
if '@charges' in line:
begin = sort + 1
elif '@connection_infos' in line:
end = sort

for line in data[begin:end]:
if 'LG' not in line:
parts = line.split()
if len(parts) == 2:
new_metal = parts[0].capitalize()
self.metal = new_metal

# print('########### total charge is ', self.totalcharge)

# except FileNotFoundError:
# print('Error, cant find',self.info, ' or the info file is not correct, please assign the metal name and total charge manually')
# sys.exit()
# except IOError:
# print('Error, cant find',self.info, ' or the info file is not correct, please assign the metal name and total charge manually')
# sys.exit()
# except IndexError:
# print('Error, cant find',self.info, ' or the info file is not correct, please assign the metal name and total charge manually')
# sys.exit()
# except ValueError:
# print('Error, cant find',self.info, ' or the info file is not correct, please assign the metal name and total charge manually')
# sys.exit()

def write_gaussian_opt(self,crds,out,multi,totalcharge,nprocs,basisset,method):
chkfile = self.filename + '_small_opt.chk'
Expand Down Expand Up @@ -326,7 +344,7 @@ def write_orca_mk_old(self,inp,crds,out,multi,totalcharge,basiset,method): #####
basisset=self.basisset,totalcharge=self.totalcharge,
metal=self.metal,nprocs=self.nprocs)
ECPinput.write_orca_mk(crds=crds,multi=multi,
totalcharge=totalcharge,basiset=basiset,method=method,out=out)
totalcharge=self.totalcharge,basiset=basiset,method=method,out=out)

def write_gms_opt(self,inp,out,multi,totalcharge,basiset,method): ## just for 6-31g*
if basiset in ['6-31gs','6-31GS','6-31G*','6-31g*']:
Expand Down Expand Up @@ -355,9 +373,9 @@ def write_gms_opt(self,inp,out,multi,totalcharge,basiset,method): ## just for 6

ofile.write( " $SYSTEM MEMDDI=400 MWORDS=200 $END\n")
if int(multi) > 1:
ofile.write(" $CONTRL SCFTYP=UHF DFTTYP=" + method + " RUNTYP=OPTIMIZE\n ICHARG=" + str(totalcharge) + " MULT=" + str(multi)+" MAXIT=200 $END\n")
ofile.write(" $CONTRL SCFTYP=UHF DFTTYP=" + method + " RUNTYP=OPTIMIZE\n ICHARG=" + str(self.totalcharge) + " MULT=" + str(multi)+" MAXIT=200 $END\n")
else:
ofile.write(" $CONTRL DFTTYP=" + method + " RUNTYP=OPTIMIZE\n ICHARG=" + str(totalcharge) + " MULT=" + str(multi)+" MAXIT=200 $END\n")
ofile.write(" $CONTRL DFTTYP=" + method + " RUNTYP=OPTIMIZE\n ICHARG=" + str(self.totalcharge) + " MULT=" + str(multi)+" MAXIT=200 $END\n")
ofile.write(' $STATPT NSTEP=1000 $END\n')

ofile.write(' $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END\n')
Expand All @@ -373,7 +391,7 @@ def write_gms_opt(self,inp,out,multi,totalcharge,basiset,method): ## just for 6
multi=self.multi,method=self.method,
basisset=self.basisset,totalcharge=self.totalcharge,
metal=self.metal,nprocs=self.nprocs)
ECPinput.write_gms_opt(inp,out,multi,totalcharge,basiset,method)
ECPinput.write_gms_opt(inp,out,multi,self.totalcharge,basiset,method)


def write_gms_fc(self, inp, out, multi, totalcharge, basiset, method):
Expand Down Expand Up @@ -424,9 +442,9 @@ def write_gms_mk(self,crds,out,multi,totalcharge,basiset,method):
if basiset.upper() in ['6-31G','6-31G*','6-31GS']:
ofile = open(out,'w')
ofile.write(' $SYSTEM MEMDDI=400 MWORDS=200 $END\n')
line = ' $CONTRL DFTTYP=' + method.upper() + ' ICHARG=' + str(totalcharge) + ' MULT=1' + ' $END\n'
line = ' $CONTRL DFTTYP=' + method.upper() + ' ICHARG=' + str(self.totalcharge) + ' MULT=1' + ' $END\n'
if int(multi) > 1:
line = ' $CONTRL SCFTYP=UHF DFTTYP=' + method.upper() + ' ICHARG=' + str(totalcharge) + ' MULT=' + str(multi) + '\n MAXIT=200 $END\n'
line = ' $CONTRL SCFTYP=UHF DFTTYP=' + method.upper() + ' ICHARG=' + str(self.totalcharge) + ' MULT=' + str(multi) + '\n MAXIT=200 $END\n'
ofile.write(line)
ofile.write(' $ELPOT IEPOT=1 WHERE=PDC $END\n')
ofile.write(' $PDC PTSEL=CONNOLLY CONSTR=NONE $END\n')
Expand Down Expand Up @@ -577,7 +595,7 @@ def startautoQM(argumentList):
arguments, values = getopt.getopt(argumentList,options,long_options)
software = 'gms'
filename = None
totalcharge = str(0)
totalcharge = 'default'
multi = '1'
caltype = None
metal = 'default'
Expand Down

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