def run():
print("Running group...")
g = VtkGroup(FILE_PATH)
g.addFile(filepath="sim0000.vtu", sim_time=0.0)
g.addFile(filepath="sim0001.vtu", sim_time=1.0)
g.addFile(filepath="sim0002.vtu", sim_time=2.0)
g.addFile(filepath="sim0003.vtu", sim_time=3.0)
g.save()
def _write_vtu_series(grid, coordinates, connectivity, data, filename_base, last_step, is_cell_data):
steps = last_step + 1 if last_step is not None else len(data)
fn_tpl = "{}_{:08d}"
npoints = len(coordinates[0])
ncells = len(connectivity)
ref = grid.reference_element
if ref is ref is referenceelements.triangle:
points_per_cell = 3
vtk_el_type = VtkTriangle.tid
elif ref is referenceelements.square:
points_per_cell = 4
vtk_el_type = VtkQuad.tid
else:
raise NotImplementedError("vtk output only available for grids with triangle or rectangle reference elments")
connectivity = connectivity.reshape(-1)
cell_types = np.empty(ncells, dtype='uint8')
cell_types[:] = vtk_el_type
offsets = np.arange(start=points_per_cell, stop=ncells*points_per_cell+1, step=points_per_cell, dtype='int32')
group = VtkGroup(filename_base)
for i in range(steps):
fn = fn_tpl.format(filename_base, i)
vtk_data = data[i, :]
w = VtkFile(fn, VtkUnstructuredGrid)
w.openGrid()
w.openPiece(ncells=ncells, npoints=npoints)
w.openElement("Points")
w.addData("Coordinates", coordinates)
w.closeElement("Points")
w.openElement("Cells")
w.addData("connectivity", connectivity)
w.addData("offsets", offsets)
w.addData("types", cell_types)
w.closeElement("Cells")
if is_cell_data:
_addDataToFile(w, cellData={"Data": vtk_data}, pointData=None)
else:
_addDataToFile(w, cellData=None, pointData={"Data": vtk_data})
w.closePiece()
w.closeGrid()
w.appendData(coordinates)
w.appendData(connectivity).appendData(offsets).appendData(cell_types)
if is_cell_data:
_appendDataToFile(w, cellData={"Data": vtk_data}, pointData=None)
else:
_appendDataToFile(w, cellData=None, pointData={"Data": vtk_data})
w.save()
group.addFile(filepath=fn, sim_time=i)
group.save()
def _write_vtu_series(grid, coordinates, connectivity, data, filename_base, last_step, is_cell_data):
steps = last_step + 1 if last_step is not None else len(data)
fn_tpl = "{}_{:08d}"
npoints = len(coordinates[0])
ncells = len(connectivity)
ref = grid.reference_element
if ref is ref is referenceelements.triangle:
points_per_cell = 3
vtk_el_type = VtkTriangle.tid
elif ref is referenceelements.square:
points_per_cell = 4
vtk_el_type = VtkQuad.tid
else:
raise NotImplementedError("vtk output only available for grids with triangle or rectangle reference elments")
connectivity = connectivity.reshape(-1)
cell_types = np.empty(ncells, dtype='uint8')
cell_types[:] = vtk_el_type
offsets = np.arange(start=points_per_cell, stop=ncells*points_per_cell+1, step=points_per_cell, dtype='int32')
group = VtkGroup(filename_base)
for i in range(steps):
fn = fn_tpl.format(filename_base, i)
vtk_data = data[i, :]
w = VtkFile(fn, VtkUnstructuredGrid)
w.openGrid()
w.openPiece(ncells=ncells, npoints=npoints)
w.openElement("Points")
w.addData("Coordinates", coordinates)
w.closeElement("Points")
w.openElement("Cells")
w.addData("connectivity", connectivity)
w.addData("offsets", offsets)
w.addData("types", cell_types)
w.closeElement("Cells")
if is_cell_data:
_addDataToFile(w, cellData={"Data": vtk_data}, pointData=None)
else:
_addDataToFile(w, cellData=None, pointData={"Data": vtk_data})
w.closePiece()
w.closeGrid()
w.appendData(coordinates)
w.appendData(connectivity).appendData(offsets).appendData(cell_types)
if is_cell_data:
_appendDataToFile(w, cellData={"Data": vtk_data}, pointData=None)
else:
_appendDataToFile(w, cellData=None, pointData={"Data": vtk_data})
w.save()
group.addFile(filepath=fn + '.vtu', sim_time=i)
group.save()
# and contact area
# w.openData("Cell")
# w.addData("area", area)
# w.closeData("Cell")
# and heat flux
# w.openData("Cell")
# w.addData("heatflux", heatflux)
# w.closeData("Cell")
# Wrap up
w.closePiece()
w.closeGrid()
# Append binary data
w.appendData( (x,y,z) )
w.appendData(connections).appendData(offset).appendData(celltype)
w.appendData(forceClean).appendData(connectionLengthClean)
w.save()
# Add this file to the group of all timesteps
groupfile.addFile(filepath = os.path.relpath(vtufile,inputdir), sim_time = timestep)
fileindex += 1
timestep = forcedata.next()
# end of main loop - close group file
groupfile.save()
# * *
# * 2. Redistributions in binary form must reproduce the above copyright notice, *
# * this list of conditions and the following disclaimer in the documentation *
# * and/or other materials provided with the distribution. *
# * *
# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR *
# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF *
# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO *
# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, *
# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, *
# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, *
# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY *
# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING *
# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS *
# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
# ************************************************************************
# **************************************************************
# * Example of how to create a VTK group to visualize time *
# * dependent data. *
# **************************************************************
from evtk.vtk import VtkGroup
g = VtkGroup("./group")
g.addFile(filepath="sim0000.vtu", sim_time=0.0)
g.addFile(filepath="sim0001.vtu", sim_time=1.0)
g.addFile(filepath="sim0002.vtu", sim_time=2.0)
g.addFile(filepath="sim0003.vtu", sim_time=3.0)
g.save()
# and contact area
# w.openData("Cell")
# w.addData("area", area)
# w.closeData("Cell")
# and heat flux
# w.openData("Cell")
# w.addData("heatflux", heatflux)
# w.closeData("Cell")
# Wrap up
w.closePiece()
w.closeGrid()
# Append binary data
w.appendData((x, y, z))
w.appendData(connections).appendData(offset).appendData(celltype)
w.appendData(forceClean).appendData(connectionLengthClean)
w.save()
# Add this file to the group of all timesteps
groupfile.addFile(filepath=os.path.relpath(vtufile, inputdir),
sim_time=timestep)
fileindex += 1
timestep = forcedata.next()
# end of main loop - close group file
groupfile.save()
del edens
try:
del spindens
except NameError:
pass
t = instance.transmission(instance.grl)
transmissions[i] = t
np.save(filepath + '/' + name + '_transmission', transmissions)
print 'Calculated transmission: ', t
del instance.grl
transmissions[i] = t
gc.collect()
#dens = instance.dorrgm(energy_multi*instance.t0)
#dens = -dens.imag/(instance.a**2)*instance.fermifunction(energy_multi*instance.t0, instance.mu)
#intdens = intdens + spindens
g.addFile(filepath=filename + '.vtr', sim_time=i)
# plt.figure(figsize=(3,3))
# plt.imshow(edens)
# plt.colorbar()
# plt.title('Page '+str(i))
# pdf.savefig()
#close()
# i+=1
g.save()
# plt.figure(figsize=(3,3))
# plt.plot(transmissions)
# pdf.savefig()
# pdf.close()
#import pudb; pudb.set_trace()
return transmissions
#NOTE: In order for this to work it needs a folder called 'meshes' in the directory where this file is located.
def saveVTK(filename, i, j):
ind = numpy.arange(0, len(i)*len(j), dtype = 'uint32')
temp = numpy.zeros((1), dtype = 'int32')
def fun(x,y):
array = numpy.zeros((len(x),len(y)))
for i in range(len(x)):
array[i, :] = x[i]*y
return array
dictionary = {'whatever': fun(i,j)[:,None]}
evtk.gridToVTK(filename, i, j, temp, pointData = dictionary)
i = numpy.arange(2, 10.5, 0.5)
j = numpy.arange(-4, 4.5, 0.5)
saveVTK("./meshes/test-1", i,j)
i = numpy.arange(2, 5.25, 0.25)
j = numpy.arange(-4, 4.25, 0.25)
saveVTK("./meshes/test-2", i,j)
g = VtkGroup("./group")
g.addFile(filepath = "./meshes/test-1.vtr", sim_time = 0.0)
g.addFile(filepath = "./meshes/test-2.vtr", sim_time = 0.0)
g.save()
