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 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 __init__(self, path, mesh, submesh):
'''Prebuild and then only receive data'''
comm = mesh.mpi_comm()
rank = comm.rank
size = comm.size
dirname, basaname = os.path.dirname(path), os.path.basename(path)
if dirname:
not os.path.exists(dirname) and comm.rank == 0 and os.mkdir(
dirname)
local_has_piece = np.zeros(comm.size, dtype=bool)
if submesh.num_cells() == 0:
self.write_vtu_piece = lambda data, counter, path=path, rank=rank, size=size: (
"%s_p%d_of%d_%06d.vtu" % (path, rank, size, counter))
else:
local_has_piece[comm.rank] = True
x, y, z = map(np.array, submesh.coordinates().T)
cells = submesh.cells()
ncells, nvertices_cell = cells.shape
assert nvertices_cell == 3
connectivity = cells.flatten()
offsets = np.cumsum(np.repeat(3, ncells))
connectivity = connectivity.astype(offsets.dtype)
cell_types = VtkTriangle.tid * np.ones(ncells)
self.write_vtu_piece = lambda data, counter, path=path, rank=rank, size=size: (
unstructuredGridToVTK("%s_p%d_of%d_%06d" %
(path, rank, size, counter),
x,
y,
z,
connectivity,
offsets,
cell_types,
cellData=data))
# Root will write the group file
global_has_piece = sum(comm.allgather(local_has_piece),
np.zeros_like(local_has_piece))
self.has_piece, = np.where(global_has_piece)
# Only other piece to remember is for parallel writeing on root
self.counter = 0 # Of times write_vtu_piece was called
self.path = path
self.world_rank = comm.rank
self.world_size = comm.size
# Also group file goes into the directory
self.world_rank == 0 and setattr(self, 'group', VtkGroup(path))
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()
# create a sub-directory for the output .vtu files
outputdir = os.path.join(inputdir,fileprefix)
try:
os.mkdir(outputdir)
except:
pass
# Read in the dump file - since we can have many contacts (i.e. >> nparticles)
# and many timesteps I will deal with one timestep at a time in memory,
# write to the appropriate .vtu file for a single timestep, then move on.
forcedata = bdump(filename,0)
groupfile = fileprefix
groupfile = os.path.join(inputdir,groupfile)
groupfile = VtkGroup(groupfile)
fileindex = 0
timestep = forcedata.next()
# check that we have the right number of colums (>11)
#
# NOTE: the first timesteps are often blank, and then natoms returns 0, so this doesn't really work...
#
if forcedata.snaps[fileindex].natoms !=0 and len(forcedata.snaps[0].atoms[0]) < 12:
print "Error - dump file requires at least all parameters from a compute pair/gran/local id pos force (12 in total)"
sys.exit()
# loop through available timesteps
#
while timestep >= 0:
# * *
# * 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()
# create a sub-directory for the output .vtu files
outputdir = os.path.join(inputdir, fileprefix)
try:
os.mkdir(outputdir)
except:
pass
# Read in the dump file - since we can have many contacts (i.e. >> nparticles)
# and many timesteps I will deal with one timestep at a time in memory,
# write to the appropriate .vtu file for a single timestep, then move on.
forcedata = bdump(filename, 0)
groupfile = fileprefix
groupfile = os.path.join(inputdir, groupfile)
groupfile = VtkGroup(groupfile)
fileindex = 0
timestep = forcedata.next()
# check that we have the right number of colums (>11)
#
# NOTE: the first timesteps are often blank, and then natoms returns 0, so this doesn't really work...
#
if forcedata.snaps[fileindex].natoms != 0 and len(
forcedata.snaps[0].atoms[0]) < 12:
print "Error - dump file requires at least all parameters from a compute pair/gran/local id pos force (12 in total)"
sys.exit()
# loop through available timesteps
#
# create a sub-directory for the output .vtu files
outputdir = os.path.join(inputdir, fileprefix)
try:
os.mkdir(outputdir)
except:
pass
# Read in the dump file - since we can have many contacts (i.e. >> nparticles)
# and many timesteps I will deal with one timestep at a time in memory,
# write to the appropriate .vtu file for a single timestep, then move on.
forcedata = dump(filename, 0)
groupfile = fileprefix
groupfile = os.path.join(inputdir, groupfile)
groupfile = VtkGroup(groupfile)
fileindex = 0
timestep = forcedata.next()
# check that we have the right number of colums (>11)
#
# NOTE: the first timesteps are often blank, and then natoms returns 0, so this doesn't really work...
#
#if forcedata.snaps[fileindex].natoms !=0 and len(forcedata.snaps[0].atoms[0]) < 11:
# print "Error - dump file requires at least all parameters from a compute pair/gran/local id pos force (12 in total)"
# sys.exit()
# loop through available timesteps
while timestep >= 0:
name = time.strftime('%b-%d-%Y-%H.%M')
import os, errno
home = os.environ['HOME']
filepath = home + '/spinr/output/' + str(
instance.atlas[-15:-4]) + '-' + str(instance.p.task_id)
try:
print 'trying to create dir', filepath
os.makedirs(filepath)
except OSError, e:
if e.errno != errno.EEXIST:
raise
# from matplotlib.backends.backend_pdf import PdfPages
#from pylab import plot,figure,title,close,imshow
# import matplotlib.pyplot as plt
print 'creating group file'
g = VtkGroup(filepath + "/group" + name)
print 'finished creating group file'
# i=0
# pdf = PdfPages('Density_and_Conductivity'+name+'.pdf')
sweep_range = 400
transmissions = np.zeros(sweep_range, dtype=complex128)
print 'Setting mode to graph'
instance.setmode('spin_graph')
print 'done setting mode to spin_graph'
# shift = -140
#charge = 8
slope = 0
for i in range(sweep_range):
print '---------------------------------------------------------'
print 'Step Number: ', i
print '---------------------------------------------------------'
#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()
