WorkDir = os.getcwd().strip()
HomeDir = os.getenv('HOME')
if os.getenv('IGOR_MODULES_PATH'): # STRING, private module DIR
ModuDir = os.getenv('IGOR_MODULES_PATH')
sys.path.append(ModuDir) # Append it into "sys.path"
import gaussian_manage as gaum # Import private modules
else:
print('\n'+\
'Error in getting grobal environment '+\
'\"$IGOR_MODULES_PATH\" which is the direction to private modules')
os.exit()
IOut = file('test.out', 'w')
TmpGau = gaum.GauIO(IOut, fn=None, bugctrl=1)
Form = '%5s%16.8f%16.8f%16.8f'
counter = 0
for line in file(sys.argv[1]):
counter += 1
if counter == 1 or counter == 2:
pass
else:
tmpList = line.split()
geomList = map(float, tmpList[1:])
geomList = [parse_atom_name(tmpList[0].lower())] + geomList
TmpGau.GeomList.append(Form % tuple(geomList))
TmpGau.Charge = 0
TmpGau.Spin = 1
TmpGau.CartesianFlag = True
#!/usr/bin/python2.7
import gaussian_manage
output = open("Output", "w")
ff = gaussian_manage.GauIO(output, "NH3-force.gjf")
ff.get_MachAndOpt()
print(ff.MachineList)
print(ff.OptionList)
ff.get_TCSGR()
print(ff.TitleList)
print("Spin of this system is %5i" % ff.Spin)
print("Charge of this system is %5i" % ff.Charge)
for xx in ff.GeomList:
print(xx)
print(ff.RestList)
ff.form_Inp()
import cp2k_manage as cp2k
from my_io import print_Error
from my_io import print_List
from my_io import print_String
else:
print '\n'+\
'Error in getting grobal environment '+\
'\"$IGOR_MODULES_PATH\" which is the direction to private modules'
sys.exit(1)
lf = file('../chage.log','w')
p1 = re.compile(' *\d+[ \t]+[\d]+ *\n')
os.listdir('%s' %WorkDir)
for inp in os.listdir('./'):
name, postfix = os.path.splitext(inp)
tmpGau = gaum.GauIO(lf,inp,bugctrl=1)
tmpGau.get_MachAndOpt()
tmpGau.ctrl_Option()
tmpGau.get_TCSGR()
tmpCP2K = cp2k.CP2KIO(lf,fn=None,bugctrl=1)
tmpCP2K.JobName = name
tmpCP2K.InpuDict={}
tmpCP2K.InpuDict['force_eval'] = dict(index=['force_eval'],content=[],rest='')
ProjName = 'PROJECT %s' % name
tmpCP2K.InpuDict['global'] = dict(index=['global'], content=[ProjName],rest='')
Spin = 'MULTIPLICITY %i' % tmpGau.Spin
Charge = 'CHARGE %i' % tmpGau.Charge
tmpCP2K.InpuDict['dft'] = dict(index=['force_eval','dft'], content=[Spin,Charge],rest='')
def run_xDH(argv=None):
from os import remove
from os.path import isfile
import sys
import gaussian_manage as gaum # Import private modules
import xDH_module as xDH # Import private modules
from gaussian_manage import print_Error
from gaussian_manage import print_List
from gaussian_manage import print_String
if argv is None: argv = sys.argv
FileName = argv[-1]
Path, FileName = os.path.split(os.path.abspath(FileName))
Name, Extension = os.path.splitext(FileName)
__info__ = prepare_Info(__version__)
if isfile('%s.xDH' % Name): # Open the output file
iout = open('%s.xDH' % Name, 'a')
else:
iout = open('%s.xDH' % Name, 'w')
print_List(iout, __info__, 2,
'%s' % '-' * 76 + '==') # Writing the package info.
print_String(
iout, 'Start the job of "%s" using the Gaussian %02i package' %
(FileName, __gaussian__), 2)
MainIO = gaum.GauIO(iout, '%s%s' % (Name, extension), iprint)
MainIO.KickOptionList = ['extraoverlay', 'oniom',
'opt'] # Disable options for xDH
MainIO.get_MachAndOpt()
MainIO.ctrl_Option()
MainIO.get_TCSGR()
OptClass = gaum.OptHandle(iout, MainIO, iprint)
R5Class = xDH.xDH(iout, MainIO, OptClass, iprint, __gaussian__,
syncinterval)
#if not MainIO.CartesianFlag:
# MainIO.collect_Geom()
#DFTDClass = gaum.DFTD(iout,MainIO,OptClass,iprint)
#if DFTDClass.PureDisp:
# DFTDClass.DispClass.get_EngyReal() # Get classical disp. engy.
# return
iout.flush() # Flush the output
if R5Class.TurnOn:
#R5Class.gen_OptionList()
EngyPos = iout.tell()
iout.write('%s\n' % (' ' * 640))
print_String(
iout,
'The following is the output for preparing KS orbitals and density ::',
2)
iout.flush() # Flush the output
R5Class.run_Job(sync=True)
R5Class.collect_EngyReal(EngyPos) # Bring energy print to front
if not OptClass.Opt:
if iprint >= 1:
print_String(iout, 'Job Type :: Single-Point Calculation', 1)
else:
os.remove('Job_%s.log' % MainIO.JobName)
iout.write('=' * 80 + '\n')
iout.write('**%s**\n' % (' ' * 76))
iout.write('** THE JOB OF \"%s\" IS DONE%s**\n' %
(Name, (' ' * (54 - len(Name)))))
iout.write('**%s**\n' % (' ' * 76))
iout.write('=' * 80 + '\n')
#del DFTDClass
del R5Class
del OptClass
del MainIO
return
else:
print_Error(iout,'Geom. optimization is not supported'\
+' in this version')
else:
print_Error(iout,
'Normal Gaussian job does not need the xDH4Gau package')
return