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): for ik, K in enumerate(Ks): dirname = "Q%1.2fK%1.2f" % (Q, K)
atoms_str="" atoms = None bonds = None if opt_dict['atoms'] or opt_dict['bonds']: 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)