def advance(self, time,
time_step): # TOCHECK: can we take advance out of this class?
"""
Advance the surface by one time step.
"""
# move points along point direction
while True:
try:
new_surface = deepcopy(self)
normal_velocities = -new_surface.fluxes / new_surface.material_densities
displacements = normal_velocities * time_step
new_surface.old_positions = copy(new_surface.positions)
new_surface.positions[:,
0] += new_surface.directions[:,
0] * displacements
# change shape direction ?
new_surface.positions[:,
1] += new_surface.directions[:,
1] * displacements
# change shape direction ?
new_pos_x = new_surface.positions[:, 0]
new_pos_z = new_surface.positions[:, 1]
new_surface.material_indexes = self.mat_track.get_materials(
np.array([new_pos_x,
np.zeros(new_pos_x.shape), new_pos_z]))
new_surface.material_names = extract_names(
new_surface.material_indexes)
new_surface.material_densities = extract_densities(
new_surface.material_indexes)
if par.INTERPOLATE:
new_surface.detect_loops()
break
except CrossedPointsError:
time_step = time_step / 2
print_log('time, reduced time step:', time, time_step)
# interpolate surface back to original grid
if par.INTERPOLATE:
new_surface.interpolate_to_grid_of(self)
# refine grid if necessary
if par.ADAPTIVE_GRID:
while True:
try:
refined = new_surface.adapt_grid()
if not refined:
break
except TooLargeSegmentError:
#go back to old surface
new_surface = deepcopy(self)
raise HasUndefinedFluxError
return new_surface, time_step
def write_contour(self, time, linestyle):
"""
Write contour to SURFACE_FILE.
"""
header = 'contour: ' + str(time) + ' ' + str(
self.len_x) + ' ' + linestyle
header += ' x-positions'
if par.SAVE_POSITIONS:
header += ' z-positions'
if par.SAVE_ANGLES:
header += ' angles'
if par.SAVE_FLUXES:
header += ' fluxes'
if par.SAVE_BEAM_FLUXES:
header += ' beam-fluxes'
if par.SAVE_PRECURSOR:
header += ' precursor'
if par.SAVE_MATERIAL_NAMES:
header += ' material(%d)' % (len(par.MATERIAL_NAMES))
header += '\n'
f = open(par.SURFACE_FILE, 'a')
f.write(header)
for position, costheta, flux, beam_flux, precursor, material in \
zip(self.positions, self.costhetas, self.fluxes, self.beam_fluxes, self.coverages, self.material_names):
if par.SAVE_BINARY:
line = str(float(position[0]).hex())
else:
line = str(float(position[0]))
if par.SAVE_POSITIONS:
if par.SAVE_BINARY:
line += ' ' + str(float(position[1]).hex())
else:
line += ' ' + str(float(position[1]))
if par.SAVE_ANGLES:
line += ' ' + str(float(np.degrees(np.arccos(costheta))))
if par.SAVE_FLUXES:
line += ' ' + str(float(flux))
if par.SAVE_BEAM_FLUXES:
line += ' ' + str(float(beam_flux))
if par.SAVE_PRECURSOR:
line += ' ' + str(float(precursor))
if par.SAVE_MATERIAL_NAMES:
line += ' ' + str(material)
line += '\n'
f.write(line)
f.write('end of contour \n')
f.close()
# print information to log file
print_log('time zmin zmax =', \
time, min(self.positions[:,1]), max(self.positions[:,1]))
def generate_movie_show_materials(spin=False):
"""
Generate a movie of the contour evolution using contours from file SURFACE_FILE.
"""
contour = read_contour_from_file_materials()
counter = 1
files = []
fig = plt.figure()
fig.suptitle("Title")
ax = Axes3D(fig)
rotation = 150.0
while True:
try:
x, y, z ,mat= contour.next()
ax.plot_wireframe(x, y, z, color='k')
mat_use = ['Si','W','poly']
color_use = ['b','r','g']
for material,c in zip(mat_use,color_use):
mask = mat == material
ax.scatter(x[mask],y[mask],z[mask],c=c,s=35)
print x.shape, y.shape, z.shape
ax.plot(x[:,-4],y[:,-4],z[:,-4],linewidth=8, color = 'm')
ax.plot(x[:,-21],y[:,-21],z[:,-21],linewidth=8, color = 'y')
#Xstart = (x.min())
#Zstart = (z.min())
#Xend = (x.max())
ax.set_zlim3d(-1000, 0)
ax.view_init(elev=30.0,azim=rotation)
if spin:
rotation += 0.2
#ax.set_zlim3d(Zstart, Zstart+(Xend-Xstart))
tmp_file = '_tmp%012d.png' % counter
files.append(tmp_file)
fig.savefig(tmp_file)
ax.cla()
print_log("Frame", counter)
counter += 1
except StopIteration:
break
basename, ext = os.path.splitext(par.SURFACE_FILE)
if spin: basename = basename + '_spin'
avifile = basename + '.avi'
os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2 -oac copy -o " + avifile)
pngfile = basename + '.png'
os.rename(files[-1], pngfile)
for file in files[:-1]:
os.remove(file)
def generate_movie(spin=False):
"""
Generate a movie of the contour evolution using contours from file SURFACE_FILE.
"""
contour = read_contour_from_file()
counter = 1
files = []
fig = plt.figure()
fig.suptitle("Title")
ax = Axes3D(fig)
rotation = 0.0
while True:
try:
x, y, z = contour.next()
ax.plot_wireframe(x, y, z)
#Xstart = (x.min())
#Zstart = (z.min())
#Xend = (x.max())
ax.set_zlim3d(-400, 0)
if spin:
ax.view_init(elev=30.0,azim=rotation)
rotation += 0.2
#ax.set_zlim3d(Zstart, Zstart+(Xend-Xstart))
tmp_file = '_tmp%012d.png' % counter
files.append(tmp_file)
fig.savefig(tmp_file)
ax.cla()
print_log("Frame", counter)
counter += 1
except StopIteration:
break
basename, ext = os.path.splitext(par.SURFACE_FILE)
if spin: basename = basename + '_spin'
avifile = basename + '.avi'
os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=24 \
-ovc lavc -lavcopts vcodec=msmpeg4v2 -oac copy -o " + avifile)
pngfile = basename + '.png'
os.rename(files[-1], pngfile)
for file in files[:-1]:
os.remove(file)
def write_contour(self, time, linestyle):
"""
Write contour to SURFACE_FILE.
"""
header = 'contour: ' + str(time) + ' ' + linestyle
if par.SAVE_POSITIONS:
header += ' z-positions'
if par.SAVE_ANGLES:
header += ' angles'
if par.SAVE_FLUXES:
header += ' fluxes'
if par.SAVE_BEAM_FLUXES:
header += ' beam-fluxes'
if par.SAVE_PRECURSOR:
header += ' precursor'
header += '\n'
f = open(par.SURFACE_FILE, 'a')
f.write(header)
for position, costheta, flux, beam_flux, precursor in \
zip(self.positions, self.costhetas, self.fluxes, self.beam_fluxes, self.coverages):
line = str(float(position[0]))
if par.SAVE_POSITIONS:
line += ' ' + str(float(position[1]))
if par.SAVE_ANGLES:
line += ' ' + str(float(np.degrees(np.arccos(costheta))))
if par.SAVE_FLUXES:
line += ' ' + str(float(flux))
if par.SAVE_BEAM_FLUXES:
line += ' ' + str(float(beam_flux))
if par.SAVE_PRECURSOR:
line += ' ' + str(float(precursor))
line += '\n'
f.write(line)
f.write('end of contour \n')
f.close()
# print information to log file
print_log('time z= ', time, self.positions[:])
def get_sputter_2D_angular_dist(material_names, cosalpha, costheta,
positive_phi):
"""
Evaluate distribution function (including the sputter yield) using spline function
for given local incidence angles (theta = angle between vertex normal and beam) and
exit angle (alpha = angle between vertex normal and destination of redeposition).
cosalpha: cos of the angle between vertex normal and direction of ejection
costheta: cos of the angle between the beam and the vertex normal
positive_phi: boolean array indicating that phi is positive (i.e. beam source and
direction of ejection are on opposite sides of the vertex normal vector)
All inputs are 1D (masked) arrays.
"""
if False: # Debug
print_log('Unmasked point pairs:', cosalpha.size, ' positive phi:',
cosalpha[positive_phi].size)
if cosalpha.size == 0:
return cosalpha
# determine theta and alpha in rad
theta = np.degrees(np.arccos(costheta))
negative_phi = np.logical_not(
positive_phi) #in numpy !boolean_array = -mask
alpha = np.arccos(cosalpha) * 180 / np.pi
alpha[negative_phi] = -alpha[negative_phi]
dist = np.empty_like(theta)
syields = np.ones_like(theta)
for material_name in par.MATERIAL_NAMES:
mask = (material_names == material_name)
if len(theta[mask]) > 0:
dist[mask] = SPUTTER_ANG_DIST_FUN[material_name](theta[mask],
alpha[mask])
if ANG_DIST_FILE_EXT[material_name] == '.npz':
syields[mask] = SYIELD_FUN[material_name](theta[mask])
dist = np.nan_to_num(dist / syields)
dist *= 180 / np.pi
return dist
def get_new_precursor_coverages(surface, sputter_fluxes, time_step):
"""
Return precursor coverages at surface.positions.
"""
if par.DIFFUSION:
precursor_consumptions = par.A_PC * par.N_PC * sputter_fluxes
diffusion_matrix, rhs, nx, ny = \
surface.get_precursor_diffusion_matrix(precursor_consumptions, time_step)
new_coverages = solve_equation_system(diffusion_matrix, rhs, nx, ny)
if par.VERBOSE:
print_log('max. precursor:', np.max(new_coverages), '\n')
else:
new_coverages = (surface.coverages + par.A_PC*par.F_PC*par.S_PC*time_step) / \
(1.0 + par.A_PC*(par.F_PC*par.S_PC + sputter_fluxes*par.N_PC)*time_step)
return new_coverages
def adapt_grid(self):
"""
Adapt the grid as to meet the grid criteria.
"""
adapted = False
# check on deletions in x-direction
positions = self.positions.reshape(self.len_x, self.len_y, 3)
x_segment_lengths_after_deletion = distance_between_array(
positions[2:, :], positions[:-2, :])
max_x_segment_lengths_after_deletion = np.amax(
x_segment_lengths_after_deletion, axis=1)
obsolete_x_points = (max_x_segment_lengths_after_deletion <
par.MAX_SEGLEN[0])
obsolete_x_points = np.concatenate(
((False, ), obsolete_x_points, (False, )))
if any(obsolete_x_points):
# points may only be deleted if the two neighbors are not deleted
isolated_x_points = np.logical_not(obsolete_x_points[:-2]) & \
np.logical_not(obsolete_x_points[2:])
isolated_x_points = np.concatenate(
((False, ), isolated_x_points, (False, )))
# if there are consecutive obsolete points, only every second must be deleted
odd_x_points = (np.arange(self.len_x) % 2 == 1)
remove_x_points = obsolete_x_points & (isolated_x_points
| odd_x_points)
indices = np.ravel(np.where(remove_x_points))
print_log('delete at x-indices', indices)
self.remove_points(indices, axis=0)
adapted = True
# check on deletions in y-direction
positions = self.positions.reshape(self.len_x, self.len_y, 3)
y_segment_lengths_after_deletion = distance_between_array(
positions[:, 2:], positions[:, :-2])
max_y_segment_lengths_after_deletion = np.amax(
y_segment_lengths_after_deletion, axis=0)
obsolete_y_points = (max_y_segment_lengths_after_deletion <
par.MAX_SEGLEN[1])
obsolete_y_points = np.concatenate(
((False, ), obsolete_y_points, (False, )))
if any(obsolete_y_points):
# points may only be deleted if the two neighbors are not deleted
isolated_y_points = np.logical_not(obsolete_y_points[:-2]) & \
np.logical_not(obsolete_y_points[2:])
isolated_y_points = np.concatenate(
((False, ), isolated_y_points, (False, )))
# if there are consecutive obsolete points, only every second must be deleted
odd_y_points = (np.arange(self.len_y) % 2 == 1)
remove_y_points = obsolete_y_points & (isolated_y_points
| odd_y_points)
indices = np.ravel(np.where(remove_y_points))
print_log('delete at y-indices', indices)
self.remove_points(indices, axis=1)
adapted = True
# refine segments in x-direction
positions = self.positions.reshape(self.len_x, self.len_y, 3)
x_segment_lengths = distance_between_array(positions[:-1, :],
positions[1:, :])
max_x_segment_lengths = np.amax(x_segment_lengths, axis=1)
too_large_x_segments = (max_x_segment_lengths > (1 + par.GRID_LAZINESS/100)*par.MAX_SEGLEN[0]) & \
self.refine_mask_x[:-1]
if any(too_large_x_segments):
refined_delta_x = (positions[1:, :, 0] - positions[:-1, :, 0]) / 2
min_refined_delta_x = np.amin(np.absolute(refined_delta_x),
axis=1) # minimum of each row
refine_x_segments = too_large_x_segments & (min_refined_delta_x >=
par.MIN_DELTA[0])
if any(refine_x_segments):
indices = np.ravel(np.where(refine_x_segments)) + 1
print_log('refine at x-indices', indices)
self.insert_points(indices, axis=0)
adapted = True
# refine segments in y-direction
positions = self.positions.reshape(self.len_x, self.len_y, 3)
y_segment_lengths = distance_between_array(positions[:, :-1],
positions[:, 1:])
max_y_segment_lengths = np.amax(y_segment_lengths, axis=0)
too_large_y_segments = (max_y_segment_lengths > (1 + par.GRID_LAZINESS/100)*par.MAX_SEGLEN[1]) & \
self.refine_mask_y[:-1]
if any(too_large_y_segments):
refined_delta_y = (positions[:, 1:, 1] - positions[:, :-1, 1]) / 2
min_refined_delta_y = np.amin(np.absolute(refined_delta_y),
axis=0) #minimum of each column
refine_y_segments = too_large_y_segments & (min_refined_delta_y >=
par.MIN_DELTA[1])
if any(refine_y_segments):
indices = np.ravel(np.where(refine_y_segments)) + 1
print_log('refine at y-indices', indices)
self.insert_points(indices, axis=1)
adapted = True
#only remove points if number of points = MAX_POINTS
#if len(self.positions) == par.MAX_POINTS:
# pass
return adapted
def generate_movie_slice_rotate(spin=False, zslice=(float('-Inf'),float('Inf')), xrot=0.0 ):
"""
Generate a movie of the contour evolution using contours from file SURFACE_FILE.
"""
contour = read_contour_from_file()
counter = 1
files = []
top_files =[]
spin_files = []
back_files = []
left_files = []
comp_files = []
flat_2D_files = []
fig_spin = plt.figure(figsize=(8,6),dpi=100)
fig_back = plt.figure(figsize=(8,6),dpi=100)
fig_top = plt.figure(figsize=(8,6),dpi=100)
fig_left = plt.figure(figsize=(8,6),dpi=100)
fig_2D = plt.figure(figsize=(8,6),dpi=100)
fig_left.suptitle("Left Side")
fig_spin.suptitle("Rotating")
fig_back.suptitle("Front View")
fig_top.suptitle("Top View")
ax_spin = Axes3D(fig_spin)
ax_left = Axes3D(fig_left)
ax_back = Axes3D(fig_back)
ax_top = Axes3D(fig_top)
front_2D = fig_2D.add_subplot(2,2,1)
top_2D = fig_2D.add_subplot(2,2,3)
side_2D = fig_2D.add_subplot(1,2,2)
rotation = 140.0
basename, ext = os.path.splitext(par.SURFACE_FILE)
while True:
try:
x, y, z = contour.next()
x,y,z = rotate_by_angle(x,y,z,xrot)
newx = []
newy = []
newz = []
for x_in in range(z.shape[0]):
x_run =[]
y_run =[]
z_run =[]
for y_in in range(z.shape[1]):
element = z[x_in,y_in]
test = (element >= zslice[0]) and (element <= zslice[1])
if test:
x_run.append(x[x_in,y_in])
y_run.append(y[x_in,y_in])
z_run.append(element)
if len(z_run)>0:
if len(z_run) == z.shape[1]:
newx.append(x_run)
newy.append(y_run)
newz.append(z_run)
n_x = np.array(newx, object)
n_y = np.array(newy, object)
n_z = np.array(newz, object)
#z_mask = np.bitwise_and((z>=zslice[0]) , (z<=zslice[1]))
#ax_spin.plot_wireframe(x, y, z)
ax_spin.plot_surface(x,y,z,rstride=1, cstride=1, linewidth=0,shade=True, antialiased=False)
samples = 5
#print n_z.shape
if n_z.shape[0]>samples and n_z.shape[1]>samples:
#ax_spin.plot_wireframe(n_x, n_y, n_z, linewidth=5.0).set_color('red')
for index in range(samples):
fraction = float(index)/float(samples-1)
indexY = np.ceil(n_z.shape[0]*fraction)
indexX = np.ceil(n_z.shape[1]*fraction)
if indexY == n_z.shape[0]:indexY+=-1
if indexX == n_z.shape[1]:indexX+=-1
front_2D.plot(n_y[indexY,],n_z[indexY,])
top_2D.plot(n_y[indexY],n_x[indexY]-77.89,label= 'z=%4d'%(n_z[indexY,0]))
side_2D.plot(n_x.T[indexX,]-77.893,n_z.T[indexX,], label= 'y=%4d'%(n_y.T[indexX,0]))
tmp_left_file = '_%s_left_tmp%012d.png' % (basename,counter)
front_2D.set_title('\nY-Z Plot')
front_2D.set_ylabel('Z(nm)')
front_2D.set_xlabel('Y(nm)')
top_2D.set_title('\nY-X Plot')
top_2D.set_ylabel('X(nm)')
top_2D.set_xlabel('Y(nm)')
side_2D.set_title('\nX-Z Plot')
side_2D.set_ylabel('Z(nm)')
side_2D.set_xlabel('X(nm)')
thelegend=side_2D.legend(loc='best')
if thelegend != None:
thelegend.get_frame().set_alpha(0.6)
for t in thelegend.get_texts():
t.set_fontsize('x-small')
thetoplegend=top_2D.legend(loc='best')
if thetoplegend != None:
thetoplegend.get_frame().set_alpha(0.6)
for t in thetoplegend.get_texts():
t.set_fontsize('xx-small')
fig_2D.tight_layout()
fig_2D.savefig(tmp_left_file)
front_2D.cla()
top_2D.cla()
side_2D.cla()
#fig_2D.clf()
ax_back.plot_wireframe(x, y, z)
ax_top.plot_wireframe(x, y, z)
#ax_left.plot_wireframe(x, y, z)
#Xstart = (x.min())
#Zstart = (z.min())
#Xend = (x.max())
#ax.set_zlim3d(-400, 0)
ax_spin.set_zlim3d(-1000, 0)
ax_back.set_zlim3d(-1000, 0)
ax_top.set_zlim3d(-1000, 0)
ax_left.set_zlim3d(-1000, 0)
ax_back.view_init(elev=0.0,azim=180.0)
ax_top.view_init(elev=80.0,azim=180.0)
ax_left.view_init(elev=0.0,azim=90.0)
#if spin:
ax_spin.view_init(elev=30.0,azim=rotation)
rotation += 0.000
#ax.set_zlim3d(Zstart, Zstart+(Xend-Xstart))
tmp_spin_file = '_%s_spin_tmp%012d.png' % (basename,counter)
tmp_back_file = '_%s_back_tmp%012d.png' % (basename,counter)
tmp_top_file = '_%s_top_tmp%012d.png' % (basename,counter)
tmp_left_file = '_%s_left_tmp%012d.png' % (basename,counter)
files.append(tmp_spin_file)
files.append(tmp_back_file)
files.append(tmp_top_file)
files.append(tmp_left_file)
spin_files.append(tmp_spin_file)
back_files.append(tmp_back_file)
top_files.append(tmp_top_file)
left_files.append(tmp_left_file)
ax_back.grid(False)
ax_top.grid(False)
ax_spin.grid(False)
fig_spin.savefig(tmp_spin_file)
fig_back.savefig(tmp_back_file)
fig_top.savefig(tmp_top_file)
#fig_left.savefig(tmp_left_file)
ax_spin.cla()
ax_back.cla()
ax_top.cla()
ax_left.cla()
#fig_spin.clf()
#fig_back.clf()
#fig_top.clf()
#plt.close(fig_spin)
#plt.close(fig_back)
#plt.close(fig_top)
#plt.close(fig_2D)
#del front_2D
#del side_2D
#del top_2D
#del ax_spin
#del ax_back
#del ax_top
tmp_comp = composite_frame(tmp_spin_file, tmp_top_file, tmp_left_file, tmp_back_file)
comp_files.append(tmp_comp)
files.append(tmp_comp)
print_log("Frame", counter)
counter += 1
except StopIteration:
break
#basename, ext = os.path.splitext(par.SURFACE_FILE)
#if spin: basename = basename + '_spin'
avifile = basename + '.avi'
spinfile = basename + '_spin' + '.avi'
topfile = basename + '_top' + '.avi'
leftfile = basename + '_left' + '.avi'
backfile = basename + '_back' + '.avi'
os.system("mencoder 'mf://*_%s_comp_tmp*.png' -mf type=png:fps=24 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=4800 -oac copy -o "%basename + avifile)
os.system("mencoder 'mf://*_%s_spin_tmp*.png' -mf type=png:fps=24 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=4800 -oac copy -o "%basename + spinfile)
os.system("mencoder 'mf://*_%s_top_tmp*.png' -mf type=png:fps=24 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=4800 -oac copy -o "%basename + topfile)
os.system("mencoder 'mf://*_%s_left_tmp*.png' -mf type=png:fps=24 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=4800 -oac copy -o "%basename + leftfile)
os.system("mencoder 'mf://*_%s_back_tmp*.png' -mf type=png:fps=24 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=4800 -oac copy -o "%basename + backfile)
pngfile = basename + '.png'
os.rename(files[-1], pngfile)
for file in files[:-1]:
os.remove(file)
def generate_movie_slice(spin=False, zslice=(float('-Inf'),float('Inf')) ):
"""
Generate a movie of the contour evolution using contours from file SURFACE_FILE.
"""
contour = read_contour_from_file()
counter = 1
files = []
top_files =[]
spin_files = []
back_files = []
left_files = []
comp_files = []
flat_2D_files = []
fig_spin = plt.figure(figsize=(8,6),dpi=100)
fig_back = plt.figure(figsize=(8,6),dpi=100)
fig_top = plt.figure(figsize=(8,6),dpi=100)
fig_left = plt.figure(figsize=(8,6),dpi=100)
fig_2D = plt.figure(figsize=(8,6),dpi=100)
fig_spin.suptitle("Rotating")
fig_back.suptitle("Back View")
fig_top.suptitle("Top View")
fig_left.suptitle("Left Side")
ax_spin = Axes3D(fig_spin)
ax_back = Axes3D(fig_back)
ax_top = Axes3D(fig_top)
ax_left = Axes3D(fig_left)
front_2D = fig_2D.add_subplot(2,2,1)
top_2D = fig_2D.add_subplot(2,2,3)
side_2D = fig_2D.add_subplot(1,2,2)
rotation = 0.0
basename, ext = os.path.splitext(par.SURFACE_FILE)
while True:
try:
x, y, z = contour.next()
newx = []
newy = []
newz = []
for x_in in range(z.shape[0]):
x_run =[]
y_run =[]
z_run =[]
for y_in in range(z.shape[1]):
element = z[x_in,y_in]
test = (element >= zslice[0]) and (element <= zslice[1])
if test:
x_run.append(x[x_in,y_in])
y_run.append(y[x_in,y_in])
z_run.append(element)
if len(z_run)>0:
if len(z_run) == z.shape[1]:
newx.append(x_run)
newy.append(y_run)
newz.append(z_run)
n_x = np.array(newx, object)
n_y = np.array(newy, object)
n_z = np.array(newz, object)
#z_mask = np.bitwise_and((z>=zslice[0]) , (z<=zslice[1]))
ax_spin.plot_wireframe(x, y, z)
print n_z.shape
if len(newz)>0:
ax_spin.plot_wireframe(n_x, n_y, n_z, linewidth=5.0).set_color('red')
samples = 5
for index in range(samples):
fraction = float(index)/float(samples)
indexY = np.ceil(n_z.shape[0]*fraction)
indexX = np.ceil(n_z.shape[1]*fraction)
front_2D.plot(n_y[indexY,],n_z[indexY,])
top_2D.plot(n_y[indexY],n_x[indexY])
side_2D.plot(n_x.T[indexX,],n_z.T[indexX,])
tmp_left_file = '_%s_left_tmp%012d.png' % (basename,counter)
fig_2D.savefig(tmp_left_file)
front_2D.cla()
top_2D.cla()
side_2D.cla()
ax_back.plot_wireframe(x, y, z)
ax_top.plot_wireframe(x, y, z)
ax_left.plot_wireframe(x, y, z)
#Xstart = (x.min())
#Zstart = (z.min())
#Xend = (x.max())
#ax.set_zlim3d(-400, 0)
ax_spin.set_zlim3d(-1000, 0)
ax_back.set_zlim3d(-1000, 0)
ax_top.set_zlim3d(-1000, 0)
ax_left.set_zlim3d(-1000, 0)
ax_back.view_init(elev=0.0,azim=180.0)
ax_top.view_init(elev=80.0,azim=0.0)
ax_left.view_init(elev=0.0,azim=90.0)
#if spin:
ax_spin.view_init(elev=30.0,azim=rotation)
rotation += 0.2
#ax.set_zlim3d(Zstart, Zstart+(Xend-Xstart))
tmp_spin_file = '_%s_spin_tmp%012d.png' % (basename,counter)
tmp_back_file = '_%s_back_tmp%012d.png' % (basename,counter)
tmp_top_file = '_%s_top_tmp%012d.png' % (basename,counter)
tmp_left_file = '_%s_left_tmp%012d.png' % (basename,counter)
files.append(tmp_spin_file)
files.append(tmp_back_file)
files.append(tmp_top_file)
files.append(tmp_left_file)
spin_files.append(tmp_spin_file)
back_files.append(tmp_back_file)
top_files.append(tmp_top_file)
left_files.append(tmp_left_file)
fig_spin.savefig(tmp_spin_file)
fig_back.savefig(tmp_back_file)
fig_top.savefig(tmp_top_file)
#fig_left.savefig(tmp_left_file)
ax_spin.cla()
ax_back.cla()
ax_top.cla()
ax_left.cla()
tmp_comp = composite_frame(tmp_spin_file, tmp_top_file, tmp_left_file, tmp_back_file)
comp_files.append(tmp_comp)
files.append(tmp_comp)
print_log("Frame", counter)
counter += 1
except StopIteration:
break
#basename, ext = os.path.splitext(par.SURFACE_FILE)
#if spin: basename = basename + '_spin'
avifile = basename + '.avi'
spinfile = basename + '_spin' + '.avi'
topfile = basename + '_top' + '.avi'
leftfile = basename + '_left' + '.avi'
backfile = basename + '_back' + '.avi'
os.system("mencoder 'mf://*_%s_comp_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + avifile)
os.system("mencoder 'mf://*_%s_spin_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + spinfile)
os.system("mencoder 'mf://*_%s_top_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + topfile)
os.system("mencoder 'mf://*_%s_left_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + leftfile)
os.system("mencoder 'mf://*_%s_back_tmp*.png' -mf type=png:fps=24 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + backfile)
pngfile = basename + '.png'
os.rename(files[-1], pngfile)
for file in files[:-1]:
os.remove(file)
def generate_movie_windowed(spin=False):
"""
Generate a movie of the contour evolution using contours from file SURFACE_FILE.
"""
contour = read_contour_from_file()
counter = 1
files = []
top_files =[]
spin_files = []
back_files = []
left_files = []
comp_files = []
fig_spin = plt.figure(figsize=(8,6),dpi=100)
fig_back = plt.figure(figsize=(8,6),dpi=100)
fig_top = plt.figure(figsize=(8,6),dpi=100)
fig_left = plt.figure(figsize=(8,6),dpi=100)
fig_spin.suptitle("Rotating")
fig_back.suptitle("Back View")
fig_top.suptitle("Top View")
fig_left.suptitle("Left Side")
ax_spin = Axes3D(fig_spin)
ax_back = Axes3D(fig_back)
ax_top = Axes3D(fig_top)
ax_left = Axes3D(fig_left)
rotation = 0.0
basename, ext = os.path.splitext(par.SURFACE_FILE)
while True:
try:
x, y, z = contour.next()
ax_spin.plot_wireframe(x, y, z)
ax_back.plot_wireframe(x, y, z)
ax_top.plot_wireframe(x, y, z)
ax_left.plot_wireframe(x, y, z)
#Xstart = (x.min())
#Zstart = (z.min())
#Xend = (x.max())
#ax.set_zlim3d(-400, 0)
ax_spin.set_zlim3d(-1000, 0)
ax_back.set_zlim3d(-1000, 0)
ax_top.set_zlim3d(-1000, 0)
ax_left.set_zlim3d(-1000, 0)
ax_back.view_init(elev=0.0,azim=180.0)
ax_top.view_init(elev=80.0,azim=0.0)
ax_left.view_init(elev=0.0,azim=90.0)
#if spin:
ax_spin.view_init(elev=30.0,azim=rotation)
rotation += 0.2
#ax.set_zlim3d(Zstart, Zstart+(Xend-Xstart))
tmp_spin_file = '_%s_spin_tmp%012d.png' % (basename,counter)
tmp_back_file = '_%s_back_tmp%012d.png' % (basename,counter)
tmp_top_file = '_%s_top_tmp%012d.png' % (basename,counter)
tmp_left_file = '_%s_left_tmp%012d.png' % (basename,counter)
files.append(tmp_spin_file)
files.append(tmp_back_file)
files.append(tmp_top_file)
files.append(tmp_left_file)
spin_files.append(tmp_spin_file)
back_files.append(tmp_back_file)
top_files.append(tmp_top_file)
left_files.append(tmp_left_file)
fig_spin.savefig(tmp_spin_file)
fig_back.savefig(tmp_back_file)
fig_top.savefig(tmp_top_file)
fig_left.savefig(tmp_left_file)
ax_spin.cla()
ax_back.cla()
ax_top.cla()
ax_left.cla()
tmp_comp = composite_frame(tmp_spin_file, tmp_top_file, tmp_left_file, tmp_back_file)
comp_files.append(tmp_comp)
files.append(tmp_comp)
print_log("Frame", counter)
counter += 1
except StopIteration:
break
#basename, ext = os.path.splitext(par.SURFACE_FILE)
#if spin: basename = basename + '_spin'
avifile = basename + '.avi'
spinfile = basename + '_spin' + '.avi'
topfile = basename + '_top' + '.avi'
leftfile = basename + '_left' + '.avi'
backfile = basename + '_back' + '.avi'
os.system("mencoder 'mf://*_%s_comp_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + avifile)
os.system("mencoder 'mf://*_%s_spin_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + spinfile)
os.system("mencoder 'mf://*_%s_top_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + topfile)
os.system("mencoder 'mf://*_%s_left_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + leftfile)
os.system("mencoder 'mf://*_%s_back_tmp*.png' -mf type=png:fps=60 \
-ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=2400 -oac copy -o "%basename + backfile)
pngfile = basename + '.png'
os.rename(files[-1], pngfile)
for file in files[:-1]:
os.remove(file)
def main():
"""
Main function of TopSim.
"""
CPU_start_time = TTT.clock()
# initialize input parameters and closely related parameters
init_input_parameters()
# further initializations
init_physical_properties()
time = 0.0 # time at beginning of time step
old_time = 0.0 # time at beginning of previous time step
time_step = get_timestep(time)
n_write = 1
surface = init_surface()
if par.ADAPTIVE_GRID:
while True:
refined = surface.adapt_grid()
if not refined:
break
beam = TiltedScannedBeam()
old_surface = deepcopy(surface)
surface.write_contour(time, 'bx-')
surface.calc_point_directions()
surface.calc_point_areas()
surface, time_step = surface.advance(
0.0, 0.0) #initialize and subdivide if necessary
surface.calc_point_directions()
surface.calc_point_areas()
surface.calc_thetas(beam)
surface.write_contour(time, 'bx-')
# loop over time steps
while True:
# update surface properties
surface.calc_point_directions()
surface.calc_point_areas()
# beam fluxes
try:
beam.update_angle()
surface.beam_fluxes, time_step = beam.get_fluxes(
surface.positions, time, time_step)
except StopIteration:
# exit loop when there is no more beam
break
# update local incidence angles
surface.calc_thetas(beam)
# calculate fluxes
try:
time_step = calc_fluxes(surface, old_surface, beam, time,
time_step)
# remember surface, so we can later revert to it
old_surface = deepcopy(surface)
except TooLargeFluxVariationsError: #not implemented
# reject surface and revert to old_surface
surface = deepcopy(old_surface)
time = old_time
time_step = time_step / 2
# advance surface
while True:
try:
surface, time_step = surface.advance(time, time_step)
break
except HasUndefinedFluxError:
print 'WARNING: undefined_fluxes not yet implemented.'
#calc_undefined_fluxes(surface)
# increment time and get new time step
old_time = time
time += time_step
if par.VERBOSE:
print_log('time=', time)
if time >= 0.9999999 * n_write * par.WRITE_TIME_STEP:
n_write += 1
surface.write_contour(time, 'bx-')
time_step = get_timestep(time)
surface.write_contour(time, 'bx-')
if par.DISPLAY_SURFACE:
surface.plot_contour()
#f.close()
print_log('\nCPU time:', TTT.clock() - CPU_start_time)
def adapt_grid(self):
"""
Adapt the grid as to meet the grid criteria.
"""
adapted = False
# check on deletions
segment_lengths_after_deletion = distance_between(
self.positions[2:], self.positions[:-2])
obsolete_points = (segment_lengths_after_deletion < par.MAX_SEGLEN[0])
obsolete_points = np.concatenate(
((False, ), obsolete_points, (False, )))
if any(obsolete_points):
# points may only be deleted if the two neighbors are not deleted
isolated_points = np.logical_not(obsolete_points[:-2]) & \
np.logical_not(obsolete_points[2:])
isolated_points = np.concatenate(
((False, ), isolated_points, (False, )))
# if there are consecutive obsolete points, only every second must be deleted
odd_points = (np.arange(self.len_x) % 2 == 1)
remove_points = obsolete_points & (isolated_points | odd_points)
indices = np.ravel(np.where(remove_points))
print_log('delete at indices', indices)
self.remove_points(indices)
adapted = True
# check on insertions
segment_lengths = distance_between(self.positions[1:],
self.positions[:-1])
too_large_segments = (segment_lengths > (1.0 + par.GRID_LAZINESS/100.0)*par.MAX_SEGLEN[0]) & \
self.refine_mask[:-1]
#too_small_segments = (segment_lengths > (1 - par.GRID_LAZINESS/100)*par.MAX_SEGLEN) & \
# self.refine_mask[:-1]
#reject = (segment_lengths > (1 + 2*par.GRID_LAZINESS/100)*par.MAX_SEGLEN) & \
# self.refine_mask[:-1]
if any(too_large_segments):
refined_delta_x = (self.positions[1:, 0] -
self.positions[:-1, 0]) / 2
refine_segments = too_large_segments & \
(np.absolute(refined_delta_x) >= par.MIN_DELTA[0]) #comparing a 2d distance to a 1d distance
if any(refine_segments):
indices = np.ravel(np.where(refine_segments)) + 1
print_log('refine at indices', indices)
self.insert_points(indices)
adapted = True
#if any(reject): raise TooLargeSegmentError
#only remove points if number of points = MAX_POINTS
#if len(self.positions) == par.MAX_POINTS:
# segment_lengths = distance_between(self.positions[1:,:], self.positions[:-1,:])
# if any(too_small_segments):
# error = segment_lengths[too_small_segments] - par.MAX_SEGLEN
# second_next_points = np.insert(too_small_segments, (0,0), (False, False), 0)
# new_segment_lengths = distance_between(self.positions[too_small_segments],
# self.positions[second_next_points])
# new_error = new_segment_lengths - par.MAX_SEGLEN
# remove = (abs(new_error) < abs(error))
# indices = np.ravel(np.where(remove == True))
# self.remove_points(indices)
# old_surface.remove_points(indices)
return adapted