def __call__(self, evt, basename, overwrite=True):
if not self.visualize:
return
if self.dim == 1:
u = self.actx.to_numpy(flatten(evt.state_component))
filename = "%s.png" % basename
if not overwrite and os.path.exists(filename):
from meshmode import FileExistsError
raise FileExistsError("output file '%s' already exists" %
filename)
ax = self.fig.gca()
ax.plot(self.x, u, "-")
ax.plot(self.x, u, "k.")
if self.ylim is not None:
ax.set_ylim(self.ylim)
ax.set_xlabel("$x$")
ax.set_ylabel("$u$")
ax.set_title(f"t = {evt.t:.2f}")
self.fig.savefig(filename)
self.fig.clf()
else:
self.vis.write_vtk_file("%s.vtu" % basename,
[("u", evt.state_component)],
overwrite=overwrite)
def __call__(self, evt, basename, overwrite=True):
if not self.visualize:
return
if self.ambient_dim == 2:
u = self.actx.to_numpy(flatten(evt.state_component))
filename = "%s.png" % basename
if not overwrite and os.path.exists(filename):
from meshmode import FileExistsError
raise FileExistsError("output file '%s' already exists" %
filename)
ax = self.fig.gca()
ax.grid()
ax.plot(self.x, u, "-")
ax.plot(self.x, u, "k.")
ax.set_xlabel(r"$\theta$")
ax.set_ylabel("$u$")
ax.set_title(f"t = {evt.t:.2f}")
self.fig.savefig(filename)
self.fig.clf()
elif self.ambient_dim == 3:
self.vis.write_vtk_file("%s.vtu" % basename,
[("u", evt.state_component)],
overwrite=overwrite)
else:
raise ValueError("unsupported dimension")
def __call__(self, evt, basename, overwrite=True):
if not self.visualize:
return
if self.dim == 1:
u = evt.state_component.get(self.queue)
filename = "%s.png" % basename
if not overwrite and os.path.exists(filename):
from meshmode import FileExistsError
raise FileExistsError("output file '%s' already exists" %
filename)
ax = self.fig.gca()
ax.plot(self.x[0], u, '-')
ax.plot(self.x[0], u, 'k.')
if self.ylim is not None:
ax.set_ylim(self.ylim)
ax.set_xlabel("$x$")
ax.set_ylabel("$u$")
ax.set_title("t = {:.2f}".format(evt.t))
self.fig.savefig(filename)
self.fig.clf()
else:
self.vis.write_vtk_file("%s.vtu" % basename,
[("u", evt.state_component)],
overwrite=overwrite)
def write_vertex_vtk_file(mesh, file_name, compressor=None, overwrite=False):
from pyvisfile.vtk import (UnstructuredGrid, DataArray,
AppendedDataXMLGenerator, VF_LIST_OF_COMPONENTS)
# {{{ create cell_types
from pyvisfile.vtk import (VTK_LINE, VTK_TRIANGLE, VTK_TETRA, VTK_QUAD,
VTK_HEXAHEDRON)
from meshmode.mesh import TensorProductElementGroup, SimplexElementGroup
cell_types = np.empty(mesh.nelements, dtype=np.uint8)
cell_types.fill(255)
for egrp in mesh.groups:
if isinstance(egrp, SimplexElementGroup):
vtk_cell_type = {
1: VTK_LINE,
2: VTK_TRIANGLE,
3: VTK_TETRA,
}[egrp.dim]
elif isinstance(egrp, TensorProductElementGroup):
vtk_cell_type = {
1: VTK_LINE,
2: VTK_QUAD,
3: VTK_HEXAHEDRON,
}[egrp.dim]
else:
raise NotImplementedError("mesh vtk file writing for "
"element group of type '%s'" %
type(egrp).__name__)
cell_types[
egrp.element_nr_base:
egrp.element_nr_base + egrp.nelements] = \
vtk_cell_type
assert (cell_types != 255).all()
# }}}
grid = UnstructuredGrid(
(mesh.nvertices,
DataArray(
"points", mesh.vertices, vector_format=VF_LIST_OF_COMPONENTS)),
cells=np.hstack(
[vgrp.vertex_indices.reshape(-1) for vgrp in mesh.groups]),
cell_types=cell_types)
import os
from meshmode import FileExistsError
if os.path.exists(file_name):
if overwrite:
os.remove(file_name)
else:
raise FileExistsError("output file '%s' already exists" %
file_name)
with open(file_name, "w") as outf:
AppendedDataXMLGenerator(compressor)(grid).write(outf)
def write_nodal_adjacency_vtk_file(file_name, mesh,
compressor=None,
overwrite=False):
from pyvisfile.vtk import (
UnstructuredGrid, DataArray,
AppendedDataXMLGenerator,
VTK_LINE,
VF_LIST_OF_COMPONENTS)
centroids = np.empty(
(mesh.ambient_dim, mesh.nelements),
dtype=mesh.vertices.dtype)
for grp in mesh.groups:
iel_base = grp.element_nr_base
centroids[:, iel_base:iel_base+grp.nelements] = (
np.sum(mesh.vertices[:, grp.vertex_indices], axis=-1)
/ grp.vertex_indices.shape[-1])
adj = mesh.nodal_adjacency
nconnections = len(adj.neighbors)
connections = np.empty((nconnections, 2), dtype=np.int32)
nb_starts = adj.neighbors_starts
for iel in range(mesh.nelements):
connections[nb_starts[iel]:nb_starts[iel+1], 0] = iel
connections[:, 1] = adj.neighbors
grid = UnstructuredGrid(
(mesh.nelements,
DataArray("points",
centroids,
vector_format=VF_LIST_OF_COMPONENTS)),
cells=connections.reshape(-1),
cell_types=np.asarray([VTK_LINE] * nconnections,
dtype=np.uint8))
import os
from meshmode import FileExistsError
if os.path.exists(file_name):
if overwrite:
os.remove(file_name)
else:
raise FileExistsError("output file '%s' already exists" % file_name)
with open(file_name, "w") as outf:
AppendedDataXMLGenerator(compressor)(grid).write(outf)
def write_vtk_file(self, file_name, names_and_fields,
compressor=None, real_only=False, overwrite=False,
use_high_order=None,
par_manifest_filename=None, par_file_names=None):
"""Write a Vtk XML file (typical extension ``.vtu``) containing
the visualization data in *names_and_fields*. Can optionally also write
manifests for distributed memory simulation (typical extension
``.pvtu``). See also :meth:`write_parallel_vtk_file` for a convenience
wrapper.
:arg names_and_fields: A list of tuples ``(name, value)``, where
*name* is a string and *value* is a
:class:`~meshmode.dof_array.DOFArray` or a constant,
or an object array of those.
:arg overwrite: If *True*, silently overwrite existing
files.
:arg use_high_order: Writes arbitrary order Lagrange VTK elements.
These elements are described in
`this blog post <https://blog.kitware.com/modeling-arbitrary-order-lagrange-finite-elements-in-the-visualization-toolkit/>`__
and are available in VTK 8.1 and newer.
:arg par_manifest_filename: If not *None* write a distributed-memory
manifest with this file name if *file_name* matches the first entry in
*par_file_names*.
:arg par_file_names: A list of file names of visualization files to
include in the distributed-memory manifest.
.. versionchanged:: 2020.2
- Added *par_manifest_filename* and *par_file_names*.
- Added *use_high_order*.
""" # noqa
if use_high_order is None:
use_high_order = False
if use_high_order:
if not self.is_equidistant:
raise RuntimeError("Cannot visualize high-order Lagrange elements "
"using a non-equidistant visualizer. "
"Call 'make_visualizer' with 'force_equidistant=True'.")
connectivity = self._vtk_lagrange_connectivity
else:
connectivity = self._vtk_connectivity
from pyvisfile.vtk import (
UnstructuredGrid, DataArray,
AppendedDataXMLGenerator,
ParallelXMLGenerator,
VF_LIST_OF_COMPONENTS)
nodes = self._vis_nodes_numpy()
names_and_fields = [
(name, resample_to_numpy(self.connection, fld))
for name, fld in names_and_fields]
# {{{ create cell_types
nsubelements = sum(vgrp.nsubelements for vgrp in connectivity.groups)
cell_types = np.empty(nsubelements, dtype=np.uint8)
cell_types.fill(255)
for vgrp in connectivity.groups:
isubelements = np.s_[
vgrp.subelement_nr_base:
vgrp.subelement_nr_base + vgrp.nsubelements]
cell_types[isubelements] = vgrp.vtk_cell_type
assert (cell_types < 255).all()
# }}}
# {{{ shrink elements
if abs(self.element_shrink_factor - 1.0) > 1.0e-14:
node_nr_base = 0
for vgrp in self.vis_discr.groups:
nodes_view = (
nodes[:, node_nr_base:node_nr_base + vgrp.ndofs]
.reshape(nodes.shape[0], vgrp.nelements, vgrp.nunit_dofs))
el_centers = np.mean(nodes_view, axis=-1)
nodes_view[:] = (
(self.element_shrink_factor * nodes_view)
+ (1-self.element_shrink_factor)
* el_centers[:, :, np.newaxis])
node_nr_base += vgrp.ndofs
# }}}
# {{{ create grid
nodes = nodes.reshape(self.vis_discr.ambient_dim, -1)
points = DataArray("points", nodes, vector_format=VF_LIST_OF_COMPONENTS)
grid = UnstructuredGrid(
(nodes.shape[1], points),
cells=connectivity.cells,
cell_types=cell_types)
for name, field in separate_by_real_and_imag(names_and_fields, real_only):
grid.add_pointdata(
DataArray(name, field, vector_format=VF_LIST_OF_COMPONENTS)
)
# }}}
# {{{ write
import os
from meshmode import FileExistsError
# {{{ write either both the vis file and the manifest, or neither
if os.path.exists(file_name):
if overwrite:
# we simply overwrite below, no need to remove
pass
else:
raise FileExistsError("output file '%s' already exists"
% file_name)
if par_manifest_filename is not None:
if os.path.exists(par_manifest_filename):
if overwrite:
# we simply overwrite below, no need to remove
pass
else:
raise FileExistsError("output file '%s' already exists"
% par_manifest_filename)
else:
pass
# }}}
with open(file_name, "w") as outf:
generator = AppendedDataXMLGenerator(
compressor=compressor,
vtk_file_version=connectivity.version)
generator(grid).write(outf)
if par_file_names is not None:
if par_manifest_filename is None:
raise ValueError("must specify par_manifest_filename if "
"par_file_names are given")
if par_file_names[0] == file_name:
with open(par_manifest_filename, "w") as outf:
generator = ParallelXMLGenerator(par_file_names)
generator(grid).write(outf)
def write_vtk_file(self,
file_name,
names_and_fields,
compressor=None,
real_only=False,
overwrite=False):
from pyvisfile.vtk import (UnstructuredGrid, DataArray,
AppendedDataXMLGenerator,
VF_LIST_OF_COMPONENTS)
with cl.CommandQueue(self.vis_discr.cl_context) as queue:
nodes = self.vis_discr.nodes().with_queue(queue).get()
names_and_fields = [(name, self._resample_and_get(queue, fld))
for name, fld in names_and_fields]
vc_groups = self._vis_connectivity()
# {{{ create cell_types
nsubelements = sum(vgrp.nsubelements for vgrp in vc_groups)
cell_types = np.empty(nsubelements, dtype=np.uint8)
cell_types.fill(255)
for vgrp in vc_groups:
cell_types[
vgrp.subelement_nr_base:
vgrp.subelement_nr_base + vgrp.nsubelements] = \
vgrp.vtk_cell_type
assert (cell_types < 255).all()
# }}}
if self.element_shrink_factor != 1:
for vgrp in self.vis_discr.groups:
nodes_view = vgrp.view(nodes)
el_centers = np.mean(nodes_view, axis=-1)
nodes_view[:] = ((self.element_shrink_factor * nodes_view) +
(1 - self.element_shrink_factor) *
el_centers[:, :, np.newaxis])
grid = UnstructuredGrid(
(self.vis_discr.nnodes,
DataArray("points",
nodes.reshape(self.vis_discr.ambient_dim, -1),
vector_format=VF_LIST_OF_COMPONENTS)),
cells=np.hstack(
[vgrp.vis_connectivity.reshape(-1) for vgrp in vc_groups]),
cell_types=cell_types)
# for name, field in separate_by_real_and_imag(cell_data, real_only):
# grid.add_celldata(DataArray(name, field,
# vector_format=VF_LIST_OF_COMPONENTS))
for name, field in separate_by_real_and_imag(names_and_fields,
real_only):
grid.add_pointdata(
DataArray(name, field, vector_format=VF_LIST_OF_COMPONENTS))
import os
from meshmode import FileExistsError
if os.path.exists(file_name):
if overwrite:
os.remove(file_name)
else:
raise FileExistsError("output file '%s' already exists" %
file_name)
with open(file_name, "w") as outf:
AppendedDataXMLGenerator(compressor)(grid).write(outf)