elif opt_dict['tip_base_q'] is not None:
TbQs = [opt_dict['tip_base_q']]
else:
TbQs = [float(PPU.params['tip_base'][1])]
print("Ks =", Ks)
print("Qs =", Qs)
print("Amps =", Amps)
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 +
#PPPlot.params = PPU.params # now we dont use PPPlot here
if ( charged_system == True):
print " load Electrostatic Force-field "
FFel, lvec, nDim = GU.load_vec_field( "FFel" ,format=format)
if (options.boltzmann or options.bI) :
print " load Boltzmann Force-field "
FFboltz, lvec, nDim = GU.load_vec_field( "FFboltz", format=format)
print " load Lenard-Jones Force-field "
FFLJ, lvec, nDim = GU.load_vec_field( "FFLJ" , format=format)
PPU.lvec2params( lvec )
PPC.setFF( FFLJ )
xTips,yTips,zTips,lvecScan = PPU.prepareScanGrids( )
for iq,Q in enumerate( Qs ):
if ( charged_system == True):
FF = FFLJ + FFel * Q
else:
FF = FFLJ
if options.boltzmann :
FF += FFboltz
PPC.setFF_Fpointer( FF )
for ik,K in enumerate( Ks ):
dirname = "Q%1.2fK%1.2f" %(Q,K)
print " relaxed_scan for ", dirname
if not os.path.exists( dirname ):
os.makedirs( dirname )
PPC.setTip( kSpring = np.array((K,K,0.0))/-PPU.eVA_Nm )