n=Amp / dz)
# print "TYT", fzs.shape
for p in options.points:
xmin = float(p[0].split('x')[0])
ymin = float(p[0].split('x')[1])
zmin = float(p[0].split('x')[2])
xmax = float(p[1].split('x')[0])
ymax = float(p[1].split('x')[1])
zmax = float(p[1].split('x')[2])
npoints = float(p[2])
print opt_dict['disp']
if opt_dict['disp']:
print "Displacment {}".format(opt_dict['disp'][0])
disp_all, lvec, nDim, head = GU.load_vec_field(dirname +
'/PPdisp_')
disp_x, disp_y, disp_z = GU.unpackVecGrid(disp_all)
del disp_all
if (opt_dict['disp'][0] == 'x'):
disp = disp_x
del disp_y, disp_z
elif (opt_dict['disp'][0] == 'y'):
disp = disp_y
del disp_x, disp_z
elif (opt_dict['disp'][0] == 'z'):
disp = disp_z
del disp_x, disp_y
DSPplot = selectLine(BIGarray=disp,
MIN=scan_min,
MAX=scan_max,
startingPoint=np.array([xmin, ymin,
if (plot_atoms):
geom_plot, tmp1, tmp2 = Bu.loadAtoms('input_plot.xyz')
del tmp1, tmp2
#print "DEBUG: geom_plot", geom_plot
else:
geom_plot = None
# --- the grid on which the STM signal is calculated --- #
if ((tip_type == 'relaxed') or (tip_type == 'r')):
print(
"Importing positions of PP from the PP-AFM calculations. Path for the data:"
)
path_pos = "Q%1.2fK%1.2f/" % (Q, K)
print(path_pos)
tip_r, lvec, nDim = GU.load_vec_field(path_pos + 'PPpos',
data_format=data_format)
extent = (lvec[0, 0], lvec[0, 0] + lvec[1, 0], lvec[0, 1],
lvec[0, 1] + lvec[2, 1])
#print "DEBUG: extent", extent
print("PP postions imported")
dx = lvec[1, 0] / (nDim[2] - 1)
dy = lvec[2, 1] / (nDim[1] - 1)
dz = lvec[3, 2] / (nDim[0] - 1)
tip_r0 = RS.mkSpaceGrid(lvec[0, 0], lvec[0, 0] + lvec[1, 0], dx,
lvec[0, 1], lvec[0, 1] + lvec[2, 1], dy,
lvec[0, 2], lvec[0, 2] + lvec[3, 2], dz)
#print "DEBUG: dx, dy, dz", dx, dy, dz
#print "DEBUG: tip_r.shape, tip_r0.shape", tip_r.shape, tip_r0.shape
else:
print("Priparing the scan grid for fixed scan")
extent = (x[0], x[1], y[0], y[1])
dfs = PPU.Fz2df( fzs, dz = dz, k0 = PPU.params['kCantilever'], f0=PPU.params['f0Cantilever'], n=Amp/dz )
# print "TYT", fzs.shape
for p in options.points:
xmin=float(p[0].split('x')[0])
ymin=float(p[0].split('x')[1])
zmin=float(p[0].split('x')[2])
xmax=float(p[1].split('x')[0])
ymax=float(p[1].split('x')[1])
zmax=float(p[1].split('x')[2])
npoints=float(p[2])
print opt_dict['disp']
if opt_dict['disp'] :
print "Displacment {}".format(opt_dict['disp'][0])
disp_all,lvec,nDim,head=GU.load_vec_field(dirname+'/PPdisp_')
disp_x,disp_y,disp_z = GU.unpackVecGrid( disp_all ); del disp_all;
if (opt_dict['disp'][0]=='x'):
disp = disp_x; del disp_y, disp_z;
elif (opt_dict['disp'][0]=='y'):
disp = disp_y; del disp_x, disp_z;
elif (opt_dict['disp'][0]=='z'):
disp = disp_z; del disp_x, disp_y;
DSPplot=selectLine(BIGarray=disp, MIN=scan_min,
MAX=scan_max,startingPoint=np.array([xmin,ymin,zmin]),
endPoint=np.array([xmax,ymax,zmax]),
nsteps=npoints)
DSPplt=np.transpose(DSPplot)[1].copy()
Lplot=np.transpose(DSPplot)[0].copy()
DSP_interp=interp1d(Lplot, DSPplt,kind='cubic')
plt.plot(Lplot, DSPplt, 'ko',Lplot, DSP_interp(Lplot),'k--')
#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 : ")
PPPlot.plotDistortions(dirname + "/xy" + atoms_str + cbar_str,
PPpos[:, :, :, 0],
PPpos[:, :, :, 1],
slices=list(range(0, len(PPpos))),
BG=PPpos[:, :, :, 2],
extent=extent,
atoms=atoms,
bonds=bonds,
atomSize=atomSize,
markersize=2.0,
cbar=opt_dict['cbar'])
del PPpos
except:
print("error: ", sys.exc_info())
del V_surf;
GU.save_scal_field ( 'W_surf', W_surf, lvec, data_format=data_format)
#=================== Force
if options.noForces :
print(" ==== calculating Forces ====")
if (options.noProbab==False) :
print(" ==== loading probabilties ====")
# --- tip
W_tip, lvec, nDim = GU.load_scal_field('W_tip',data_format=data_format)
# --- sample
W_surf, lvec, nDim = GU.load_scal_field('W_surf',data_format=data_format)
W_tip = np.roll(np.roll(np.roll(W_tip,nDim[0]/2, axis=0),nDim[1]/2, axis=1),nDim[2]/2, axis=2) # works for tip (the last flexible tip apex atom) in the middle of the cell
FF_tmp, lvec, nDim = GU.load_vec_field('tip/FFLJ',data_format=data_format)
Fx_tip, Fy_tip, Fz_tip = GU.unpackVecGrid( FF_tmp )
del FF_tmp;
# Fz:
Fz_tip = np.roll(np.roll(np.roll(Fz_tip,nDim[0]/2, axis=0),nDim[1]/2, axis=1),nDim[2]/2, axis=2) # works for tip (the last flexible tip apex atom) in the middle of the cell
F1=fFFT.Average_tip( Fz_tip , W_surf, W_tip )
#GU.saveXSF ( 'FFboltz_z.xsf', F1, lvec)#, echo=True )
# Fx:
Fx_tip = np.roll(np.roll(np.roll(Fx_tip,nDim[0]/2, axis=0),nDim[1]/2, axis=1),nDim[2]/2, axis=2) # works for tip (the last flexible tip apex atom) in the middle of the cell
F2=fFFT.Average_tip( Fx_tip , W_surf, W_tip )
#GU.saveXSF ( 'FFboltz_x.xsf', F1, lvec)#, echo=True )
# Fy:
Fy_tip = np.roll(np.roll(np.roll(Fy_tip,nDim[0]/2, axis=0),nDim[1]/2, axis=1),nDim[2]/2, axis=2) # works for tip (the last flexible tip apex atom) in the middle of the cell
# Amps = np.linspace( opt_dict['arange'][0], opt_dict['arange'][1], opt_dict['arange'][2] )
#elif opt_dict['a'] is not None:
# Amps = [ opt_dict['a'] ]
#else:
# Amps = [ PPU.params['Amplitude'] ]
print "Ks =", Ks
print "Qs =", Qs
#print "Amps =", Amps
print " ============= RUN "
#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):
sys.exit()
tip_base = options.tip_base
if not tip_base:
tip_base = True if ((PPU.params["tip_base"][0] != 'None') and
(PPU.params["tip_base"][0] != None)) else False
print("Ks =", Ks)
print("Qs =", Qs)
print("tip_base =", tip_base)
print(" ============= RUN ")
if (charged_system == True):
print(" load Electrostatic Force-field ")
FFel, lvec, nDim = GU.load_vec_field("FFel", data_format=data_format)
if (options.boltzmann or options.bI):
print(" load Boltzmann Force-field ")
FFboltz, lvec, nDim = GU.load_vec_field("FFboltz", data_format=data_format)
print(" load Lenard-Jones Force-field ")
FFLJ, lvec, nDim = GU.load_vec_field("FFLJ", data_format=data_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
del V_surf;
GU.save_scal_field ( 'W_surf', W_surf, lvec, format=format)
#=================== Force
if options.noForces :
print " ==== calculating Forces ===="
if (options.noProbab==False) :
print " ==== loading probabilties ===="
# --- tip
W_tip, lvec, nDim = GU.load_scal_field('W_tip',format=format)
# --- sample
W_surf, lvec, nDim = GU.load_scal_field('W_surf',format=format)
W_tip = np.roll(np.roll(np.roll(W_tip,nDim[0]/2, axis=0),nDim[1]/2, axis=1),nDim[2]/2, axis=2) # works for tip (the last flexible tip apex atom) in the middle of the cell
FF_tmp, lvec, nDim = GU.load_vec_field('tip/FFLJ',format=format)
Fx_tip, Fy_tip, Fz_tip = GU.unpackVecGrid( FF_tmp )
del FF_tmp;
# Fz:
Fz_tip = np.roll(np.roll(np.roll(Fz_tip,nDim[0]/2, axis=0),nDim[1]/2, axis=1),nDim[2]/2, axis=2) # works for tip (the last flexible tip apex atom) in the middle of the cell
F1=fFFT.Average_tip( Fz_tip , W_surf, W_tip )
#GU.saveXSF ( 'FFboltz_z.xsf', F1, lvec)#, echo=True )
# Fx:
Fx_tip = np.roll(np.roll(np.roll(Fx_tip,nDim[0]/2, axis=0),nDim[1]/2, axis=1),nDim[2]/2, axis=2) # works for tip (the last flexible tip apex atom) in the middle of the cell
F2=fFFT.Average_tip( Fx_tip , W_surf, W_tip )
#GU.saveXSF ( 'FFboltz_x.xsf', F1, lvec)#, echo=True )
# Fy:
Fy_tip = np.roll(np.roll(np.roll(Fy_tip,nDim[0]/2, axis=0),nDim[1]/2, axis=1),nDim[2]/2, axis=2) # works for tip (the last flexible tip apex atom) in the middle of the cell
#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'] ) del PPpos except: print "error: ", sys.exc_info() print "cannot load : " + ( dirname+'/PPpos_?.' + format ) if ( ( opt_dict['df'] or opt_dict['save_df'] or opt_dict['WSxM'] ) ): try : fzs, lvec, nDim = GU.load_scal_field( dirname+'/OutFz' , format=format) for iA,Amp in enumerate( Amps ): AmpStr = "/Amp%2.2f" %Amp print "Amp= ",AmpStr dirNameAmp = dirname+AmpStr if not os.path.exists( dirNameAmp ): os.makedirs( dirNameAmp )