print " >> OVEWRITING SETTINGS by params.ini " PPU.loadParams( 'params.ini' ) lvec=np.zeros((4,3)) lvec[ 1,: ] = PPU.params['gridA'].copy() lvec[ 2,: ] = PPU.params['gridB'].copy() lvec[ 3,: ] = PPU.params['gridC'].copy() #PPU.params['gridN'] = nDim.copy() print "--- Compute Lennard-Jones Force-filed ---" if(is_xyz): atoms = basUtils.loadAtoms(options.input) elif(is_cube): atoms = basUtils.loadAtomsCUBE(options.input) lvec = basUtils.loadCellCUBE(options.input) nDim = basUtils.loadNCUBE(options.input) PPU.params['gridN'] = nDim PPU.params['gridA'] = lvec[1] PPU.params['gridB'] = lvec[2] PPU.params['gridC'] = lvec[3] elif(is_xsf): 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:
print("TbQs =", TbQs) #sys.exit(" STOPPED ") print(" ============= RUN ") dz = PPU.params['scanStep'][2] xTips, yTips, zTips, lvecScan = PPU.prepareScanGrids() extent = (xTips[0], xTips[-1], yTips[0], yTips[-1]) 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 "Amps =", Amps #sys.exit(" STOPPED ") print " ============= RUN " dz = PPU.params['scanStep'][2] xTips,yTips,zTips,lvecScan = PPU.prepareScanGrids( ) extent = ( xTips[0], xTips[-1], yTips[0], yTips[-1] ) 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