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
