atoms_str = ""
atoms = None
bonds = None
if opt_dict['atoms'] or opt_dict['bonds']:
atoms_str = "_atoms"
atoms, tmp1, tmp2 = basUtils.loadAtoms('input_plot.xyz')
del tmp1, tmp2
# print "atoms ", atoms
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, Qstmp = PPH.parseAtoms(atoms,
autogeom=False,
PBC=False,
FFparams=FFparams)
atom_colors = basUtils.getAtomColors(iZs, FFparams=FFparams)
Rs = Rs.transpose().copy()
atoms = [iZs, Rs[0], Rs[1], Rs[2], atom_colors]
#print "atom_colors: ", atom_colors
if opt_dict['bonds']:
bonds = basUtils.findBonds(atoms, iZs, 1.0, FFparams=FFparams)
#print "bonds ", bonds
atomSize = 0.15
cbar_str = ""
if opt_dict['cbar']:
cbar_str = "_cbar"
for iq, Q in enumerate(Qs):
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],
# [x2,y2,z2],
# ...
# [xn,yn,zn]]
# Qs - 1D array, containing the atomic charges
FFLJ, VLJ = PPH.computeLJ(Rs,
iZs,
FFLJ=None,
FFparams=FFparams,
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
FFLJ, VLJ=PPH.computeLJ( Rs, iZs, FFLJ=None, FFparams=FFparams, Vpot=options.energy )
# This function computes the LJ forces experienced by the ProbeParticle
# FFparams either read from the local "atomtypes.ini" file, or will be read from
# the default one inside the computeLJ function