import pyProbeParticle.GridUtils as GU
from optparse import OptionParser
parser = OptionParser()
parser.add_option( "--dfrange", action="store", type="float", help="Range of plotted frequency shift (df)", nargs=2)
parser.add_option( "--npy" , action="store_true" , help="load and save fields in npy instead of xsf" , default=False)
(options, args) = parser.parse_args()
if options.npy:
format ="npy"
else:
format ="xsf"
dfs,lvec,nDim=GU.load_scal_field('df',format=format)
#print lvec
#print nDim
print " # ============ Plot Relaxed Scan 3D "
slices = range( 0, len(dfs) )
#print slices
extent=( 0.0, lvec[1][0], 0.0, lvec[2][1])
for ii,i in enumerate(slices):
print " plotting ", i
plt.figure( figsize=( 10,10 ) )
if(options.dfrange != None):
fmin = options.dfrange[0]
fmax = options.dfrange[1]
plt.imshow( dfs[i], origin='image', interpolation='bicubic', vmin=fmin, vmax=fmax, cmap='gray', extent=extent)
for i in range(len(Voltages)):
if didv_b:
print("Importing dIdV data for V:", namez[i])
#print("DEBUG:WF:", WorkFunction , "Voltages[i]:", Voltages[i], "WF_decay", WF_decay )
name_file1 = 'didv_' + namez[
i] + "_tip_" + tip_type + "-" + tip_orb1 + "_WF_" + str(
WorkFunction - Voltages[i] * WF_decay
) + "_eta_" + str(
eta
) # WorkFunction gets higher with lower (higher negative) sample bias
name_file2 = 'didv_' + namez[
i] + "_tip_" + tip_type + "-" + tip_orb2 + "_WF_" + str(
WorkFunction - Voltages[i] * WF_decay) + "_eta_" + str(eta)
#print ("DEBUG: name_file1", name_file1)
tmp_dIdV1, lvec1, nDim1 = GU.load_scal_field(files_path + name_file1,
data_format=data_format)
didv1 = np.array([tmp_dIdV1]) if i == 0 else np.append(
didv1, np.array([tmp_dIdV1]), axis=0)
#print "DEBUG: name_file2", name_file2
tmp_dIdV2, lvec2, nDim2 = GU.load_scal_field(files_path + name_file2,
data_format=data_format)
didv2 = np.array([tmp_dIdV2]) if i == 0 else np.append(
didv2, np.array([tmp_dIdV2]), axis=0)
assert np.array(lvec1).all() == np.array(
lvec2).all(), "lvec1 != lvec2 control your input files"
assert np.array(nDim2).all() == np.array(
nDim2).all(), "nDim1 != nDim2 control your input files"
print("dIdV for V:", namez[i], " imported")
#print "DEBUG: didv1.shape", didv1.shape
if STM_b:
print("Importing STM data for V:", namez[i])
# Amps
if opt_dict['arange'] is not None:
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']]
for iq, Q in enumerate(Qs):
for ik, K in enumerate(Ks):
dirname = "Q%1.2fK%1.2f" % (Q, K)
print "Working in {} directory".format(dirname)
fzs, lvec, nDim = GU.load_scal_field(dirname + '/OutFz',
data_format=data_format)
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])
slices=list(range(0, len(denomin))))
GU.saveWSxM_3D(dirname + "/IETS",
IETS,
extent,
slices=list(range(0, len(IETS))))
del eigvalK
del Evib
del IETS
del denomin
#except:
# print "error: ", sys.exc_info()
# print "cannot load : " + ( dirname+'/eigvalKs_?.' + data_format )
if ((opt_dict['df'] or opt_dict['save_df'] or opt_dict['WSxM']
or opt_dict['2Dnp'])):
try:
fzs, lvec, nDim = GU.load_scal_field(dirname + '/OutFz',
data_format=data_format)
if not ((len(TbQs) == 1) and (TbQs[0] == 0.0)):
print("loading tip_base forces")
try:
fzt, lvect, nDimt = GU.load_scal_field(
'./OutFzTip_base', data_format=data_format)
except:
print("error: ", sys.exc_info())
print("cannot load : ",
'./OutFzTip_base.' + data_format)
for iA, Amp in enumerate(Amps):
for iT, TbQ in enumerate(TbQs):
if (TbQ == 0.0):
AmpStr = "/Amp%2.2f" % Amp
print("Amp= ", AmpStr)
dirNameAmp = dirname + AmpStr
parser.add_option( "--npy" , action="store_true" , help="load and save fields in npy instead of xsf" , default=False)
(options, args) = parser.parse_args()
try:
points = np.genfromtxt( options.p ,dtype='int')
print("plotting in points", points)
except:
print(options.p+" not found => exiting ...")
sys.exit()
if options.npy:
data_format ="npy"
else:
data_format ="xsf"
fzs,lvec,nDim=GU.load_scal_field(options.i,data_format=data_format)
#xs = lvec[3,2]/*np.array( range(nDim[0]) )
xs = np.linspace( 0, lvec[3,2], nDim[0] )
#print nDim
print(xs)
plt.imshow( fzs[options.iz], origin='imgage', cmap='gray' )
for point in points:
plt.plot(point[0],point[1],'o')
plt.xlim(0,nDim[2])
plt.ylim(0,nDim[1])
plt.savefig( options.i+'_zcurves_legend.png', bbox_inches='tight')
plt.figure()
curves = np.zeros((len(points)+1,len(xs)))
if opt_dict['arange'] is not None:
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'] ]
for iq,Q in enumerate( Qs ):
for ik,K in enumerate( Ks ):
dirname = "Q%1.2fK%1.2f" %(Q,K)
print "Working in {} directory".format(dirname)
fzs,lvec,nDim=GU.load_scal_field(dirname+'/OutFz',format=format)
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])
extent = (lvec[0,0],lvec[0,0]+xl,lvec[0,1],lvec[0,1]+yl)
tip_r2 = RS.mkSpaceGrid(lvec[0,0],lvec[0,0]+xl,dx,lvec[0,1],lvec[0,1]+yl,dy,lvec[0,2],lvec[0,2]+zl,dz)
# --- specification on which voltages the STM (dI/dV ...) calculations are performed - two methods - direct specification or sequence of voltages
Voltages=[-0.338, -0.09406976, 0., 2.422684]
namez=['H**O-3-2','H**O-1','H**O','LUMO++1']
#Voltages=np.arange(-1.0,+1.0+0.01,0.1) # this part is important for scans over slabs at different voltages
#namez = []
#for V in Voltages:
# namez.append(str(round(V,1)))
# --- downloading the df data
df, lvec2, nDim2 = GU.load_scal_field( path_df+'df' ,data_format=data_format)
# --- the Main Loop - for different WorkFunction (exponential z-decay of current), sample bias Voltages & eta - lorentzian FWHM
i=0;
for V in Voltages:
current0 = PS.dIdV( V, WorkFunction, eta, eigEn, tip_r2, Ratin, coefs, orbs=orbs, s=1.0, px=0.0, py=0.0, pz = 0.0)
current1 = PS.dIdV( V, WorkFunction, eta, eigEn, tip_r1, Ratin, coefs, orbs=orbs, s=1.0, px=0.0, py=0.0, pz = 0.0)
current2 = PS.dIdV( V, WorkFunction, eta, eigEn, tip_r1, Ratin, coefs, orbs=orbs, s=0.0, px=0.5, py=0.5, pz = 0.0)
# --- plotting part here, plots all calculated signals:
print(" plotting ")
for k in [3,11]:
dff = np.array(df[k,:,:]).copy()
curr0 = np.array(current0[k,:,:]).copy()
curr1 = np.array(current1[k,:,:]).copy()
curr2 = np.array(current2[k,:,:]).copy()
nx=PPdisp.shape[2]
ny=PPdisp.shape[1]
nz=PPdisp.shape[0]
test=np.meshgrid(xTips,yTips,zTips)
#print "TEST SHAPE", np.array(test).shape
#print nx,ny,nz
i=0
while i<nx:
j=0
while j<ny:
k=0
while k<nz:
PPdisp[k][j][i]-=np.array([xTips[i],xTips[j],zTips[k]])+ np.array([PPU.params['r0Probe'][0],PPU.params['r0Probe'][1],-PPU.params['r0Probe'][2]])
k+=1
j+=1
i+=1
GU.save_vec_field( dirname+'/PPdisp', PPdisp, lvecScan, format=format )
if opt_dict['pos']:
GU.save_vec_field( dirname+'/PPpos', PPpos, lvecScan, format=format )
if options.bI:
print "Calculating current from tip to the Boltzmann particle:"
I_in, lvec, nDim = GU.load_scal_field('I_boltzmann', format=format)
I_out = GU.interpolate_cartesian( I_in, PPpos, cell=lvec[1:,:], result=None )
del I_in;
GU.save_scal_field( dirname+'/OutI_boltzmann', I_out, lvecScan, format=format)
# the rest is done in plot_results.py; For df, go to plot_results.py
print " ***** ALL DONE ***** "
#plt.show()
beta = 1/(kBoltz*T) # [eV]
print("T= ", T, " [K] => beta ", beta/1000.0, "[meV] ")
#E_cutoff = 32.0 * beta
E_cutoff = 18.0 * beta
wGauss = 2.0
Egauss = -0.01
# =============== main
if options.noProbab :
print(" ==== calculating probabilties ====")
# --- tip
V_tip, lvec, nDim = GU.load_scal_field('tip/VLJ',data_format=data_format)
#cell = np.array( [ lvec[1],lvec[2],lvec[3] ] ); print "nDim ", nDim, "\ncell ", cell
#X,Y,Z = getXYZ( nDim, cell )
#V_tip = V_tip*0 + Egauss * getProbeDensity( (cell[0,0]/2.+cell[1,0]/2.,cell[1,1]/2,cell[2,2]/2.-3.8), X, Y, Z, wGauss ) # works for tip (the last flexible tip apex atom) in the middle of the cell
limitE( V_tip, E_cutoff )
W_tip = np.exp( -beta * V_tip )
#W_tip = W_cut(W_tip,nz=95,side='down',sm=5)
del V_tip;
GU.save_scal_field ( 'W_tip', W_tip, lvec, data_format=data_format)
# --- sample
V_surf, lvec, nDim = GU.load_scal_field('sample/VLJ',data_format=data_format)
limitE( V_surf, E_cutoff )
W_surf = np.exp( -beta * V_surf )
#W_surf=W_cut(W_surf,nz=50,side='up',sm=1)
del V_surf;
data_format=data_format)
#print "SHAPE", PPpos.shape, xTips.shape, yTips.shape, zTips.shape
if opt_dict['disp']:
GU.save_vec_field(dirname + '/PPdisp',
rPPs - rTips + PPU.params['r0Probe'][0],
lvecScan,
data_format=data_format)
if (opt_dict['pos'] or opt_dict['stm']):
GU.save_vec_field(dirname + '/PPpos',
rPPs,
lvecScan,
data_format=data_format)
# Please do not change this procedure, especialy the lvecScan - it is important for the STM calculations!
if options.bI:
print("Calculating current from tip to the Boltzmann particle:")
I_in, lvec, nDim = GU.load_scal_field('I_boltzmann',
data_format=data_format)
I_out = GU.interpolate_cartesian(I_in,
rPPs,
cell=lvec[1:, :],
result=None)
del I_in
GU.save_scal_field(dirname + '/OutI_boltzmann',
I_out,
lvecScan,
data_format=data_format)
if tip_base:
print(
"Interpolating FFel_tip_z in position of the tip_base. Beware, this is higher than the PP."
)
Ftip_in, lvec, nDim = GU.load_scal_field('FFel_tip',
data_format=data_format)
beta = 1/(kBoltz*T) # [eV]
print "T= ", T, " [K] => beta ", beta/1000.0, "[meV] "
#E_cutoff = 32.0 * beta
E_cutoff = 18.0 * beta
wGauss = 2.0
Egauss = -0.01
# =============== main
if options.noProbab :
print " ==== calculating probabilties ===="
# --- tip
V_tip, lvec, nDim = GU.load_scal_field('tip/VLJ',format=format)
#cell = np.array( [ lvec[1],lvec[2],lvec[3] ] ); print "nDim ", nDim, "\ncell ", cell
#X,Y,Z = getXYZ( nDim, cell )
#V_tip = V_tip*0 + Egauss * getProbeDensity( (cell[0,0]/2.+cell[1,0]/2.,cell[1,1]/2,cell[2,2]/2.-3.8), X, Y, Z, wGauss ) # works for tip (the last flexible tip apex atom) in the middle of the cell
limitE( V_tip, E_cutoff )
W_tip = np.exp( -beta * V_tip )
#W_tip = W_cut(W_tip,nz=95,side='down',sm=5)
del V_tip;
GU.save_scal_field ( 'W_tip', W_tip, lvec, format=format)
# --- sample
V_surf, lvec, nDim = GU.load_scal_field('sample/VLJ',format=format)
limitE( V_surf, E_cutoff )
W_surf = np.exp( -beta * V_surf )
#W_surf=W_cut(W_surf,nz=50,side='up',sm=1)
del V_surf;
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 )
dfs = PPU.Fz2df( fzs, dz = dz, k0 = PPU.params['kCantilever'], f0=PPU.params['f0Cantilever'], n=Amp/dz )
if opt_dict['save_df']:
GU.save_scal_field( dirNameAmp+'/df', dfs, lvec, format=format )
if opt_dict['df']:
print " plotting df : "
PPPlot.plotImages(
dirNameAmp+"/df"+atoms_str+cbar_str,
dfs, slices = range( 0,
len(dfs) ), zs=zTips, extent=extent, atoms=atoms, bonds=bonds, atomSize=atomSize, cbar=opt_dict['cbar'] )
action="store",
type="float",
help="Range of plotted frequency shift (df)",
nargs=2)
parser.add_option("--npy",
action="store_true",
help="load and save fields in npy instead of xsf",
default=False)
(options, args) = parser.parse_args()
if options.npy:
data_format = "npy"
else:
data_format = "xsf"
dfs, lvec, nDim = GU.load_scal_field('df', data_format=data_format)
#print lvec
#print nDim
print " # ============ Plot Relaxed Scan 3D "
slices = range(0, len(dfs))
#print slices
extent = (0.0, lvec[1][0], 0.0, lvec[2][1])
for ii, i in enumerate(slices):
print " plotting ", i
plt.figure(figsize=(10, 10))
if (options.dfrange != None):
fmin = options.dfrange[0]
fmax = options.dfrange[1]
plt.imshow(dfs[i],
parser.add_option( "--npy" , action="store_true" , help="load and save fields in npy instead of xsf" , default=False)
(options, args) = parser.parse_args()
try:
points = np.genfromtxt( options.p )
print "plotting in points", points
except:
print options.p+" not found => exiting ..."
sys.exit()
if options.npy:
format ="npy"
else:
format ="xsf"
fzs,lvec,nDim=GU.load_scal_field(options.i,format=format)
#xs = lvec[3,2]/*np.array( range(nDim[0]) )
xs = np.linspace( 0, lvec[3,2], nDim[0] )
#print nDim
print xs
plt.imshow( fzs[options.iz], origin='imgage', cmap='gray' )
for point in points:
plt.plot(point[0],point[1],'o')
plt.xlim(0,nDim[2])
plt.ylim(0,nDim[1])
plt.savefig( options.i+'_zcurves_legend.png', bbox_inches='tight')
plt.figure()
curves = np.zeros((len(points)+1,len(xs)))
