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):
for ik, K in enumerate(Ks):
dirname = "Q%1.2fK%1.2f" % (Q, K)
if opt_dict['pos']:
try:
PPpos, lvec, nDim = GU.load_vec_field(dirname + '/PPpos',
data_format=data_format)
print(" plotting PPpos : ")
atoms_str="_atoms"
atoms = basUtils.loadAtoms( 'input_plot.xyz' )
# 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 = options.noPBC,
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 ):
for ik,K in enumerate( Ks ):
dirname = "Q%1.2fK%1.2f" %(Q,K)
if opt_dict['pos']:
try:
PPpos, lvec, nDim = GU.load_vec_field( dirname+'/PPpos' ,format=format)
print " plotting PPpos : "
PPPlot.plotDistortions( dirname+"/xy"+atoms_str+cbar_str, PPpos[:,:,:,0], PPpos[:,:,:,1], slices = range( 0, len(PPpos) ), BG=PPpos[:,:,:,2], extent=extent, atoms=atoms, bonds=bonds, atomSize=atomSize, markersize=2.0, cbar=opt_dict['cbar'] )