def plotGeom(self, atomSize=0.1, edge=True, ec='k'):
atoms, tmp1, tmp2 = Bu.loadAtoms(
os.path.join(self.paths['inputPath'], 'input_plot.xyz'))
del tmp1, tmp2
self.plotData['geom_plot'] = atoms
plt.fig = plt.gcf()
es = atoms[0]
xs = atoms[1]
ys = atoms[2]
for i in range(len(xs)):
fc = '#%02x%02x%02x' % elements.ELEMENT_DICT[es[i]][
7] #; print "DEBUG: fc", fc ; ##fc = '#FFFFFF' ##
if not edge:
ec = fc
circle = plt.Circle((xs[i], ys[i]), atomSize, fc=fc, ec=ec)
plt.fig.gca().axes.add_artist(circle)
elif (tip_orb == 'dxzyz'):
tc = [0., 0., 0., 0., 0., 0.5, 0.5] # [s, px, py, pz, dz2, dxz, dyz ]
elif (tip_orb == 'px'):
tc = [0., 1., 0., 0., 0., 0., 0.] # [s, px, py, pz, dz2, dxz, dyz ]
elif (tip_orb == 'py'):
tc = [0., 0., 1., 0., 0., 0., 0.] # [s, px, py, pz, dz2, dxz, dyz ]
else:
print("Don't know what kind od tip you mean. I rather going to exit.")
exit()
#print "DEBUG: tc ", tc , " [s, px, py, pz, dz2, dxz, dyz ] "
# --- Reading geometry for plotting (if necessary) --- #
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)