if options.input == None:
sys.exit(
"ERROR!!! Please, specify the input file with the '-i' option \n\n" +
HELP_MSG)
print " >> OVEWRITING SETTINGS by params.ini "
PPU.loadParams('params.ini')
print "--- Compute Lennard-Jones Force-filed ---"
atoms, lvec = PPH.importGeometries(options.input)
FFparams = None
if os.path.isfile('atomtypes.ini'):
print ">> LOADING LOCAL atomtypes.ini"
FFparams = PPU.loadSpecies('atomtypes.ini')
else:
FFparams = PPU.loadSpecies(cpp_utils.PACKAGE_PATH +
'/defaults/atomtypes.ini')
PBC = False if not options.noPBC else PPU.params['PBC']
iZs, Rs, Qs = PPH.parseAtoms(atoms,
autogeom=False,
PBC=options.noPBC,
FFparams=FFparams)
# This function returns the following information:
# iZs - 1D array, containing the numbers of the elements, which corresponds to
# their position in the atomtypes.ini file (Number of line - 1)
# Rs - 2D array, containing the coordinates of the atoms:
# [ [x1,y1,z1],
atoms, nDim, lvec = basUtils.loadXSFGeom( options.input )
PPU.params['gridN'] = nDim
PPU.params['gridA'] = lvec[1]
PPU.params['gridB'] = lvec[2]
PPU.params['gridC'] = lvec[3]
else:
sys.exit("ERROR!!! Unknown format of geometry system. Supported "
"formats are: .xyz, .cube, .xsf \n\n")
FFparams=None
if os.path.isfile( 'atomtypes.ini' ):
print ">> LOADING LOCAL atomtypes.ini"
FFparams=PPU.loadSpecies( 'atomtypes.ini' )
else:
FFparams = PPU.loadSpecies( cpp_utils.PACKAGE_PATH+'/defaults/atomtypes.ini' )
iZs,Rs,Qs=PPH.parseAtoms(atoms, autogeom = False, PBC = options.noPBC,
FFparams=FFparams )
# This function returns the following information:
# iZs - 1D array, containing the numbers of the elements, which corresponds to
# their position in the atomtypes.ini file (Number of line - 1)
# Rs - 2D array, containing the coordinates of the atoms:
# [ [x1,y1,z1],
# [x2,y2,z2],
# ...
# [xn,yn,zn]]
# Qs - 1D array, containing the atomic charges