Export and view a solution¶
There are essentially four ways to view the result of getfem computations:
Scilab, Octave or Matlab, with the interface.
The opensource Paraview, Mayavi2, PyVista or any other VTK/VTU file viewer.
The opensource OpenDX program.
The opensource Gmsh program.
The objects that can be exported are, mesh, mesh_fem objects, and stored_mesh_slice.
Saving mesh and mesh_fem objects for the Matlab interface¶
If you have installed the Scilab, Octave or Matlab interface, you can simply use
mesh_fem::write_to_file
and save the solution as a plain text file, and then,
load them with the interface. For example, supposing you have a solution U
on a mesh_fem
mf
,:
std::fstream f("solution.U",std::ios::out);
for (unsigned i=0; i < gmm::vect_size(U); ++i)
f << U[i] << "\verb+\+n";
// when the 2nd arg is true, the mesh is saved with the mf
mf.write_to_file("solution.mf", true);
and then, under Scilab, Octave or Matlab:
>> U=load('solution.U');
>> mf=gfMeshFem('load','solution.mf');
>> gf_plot(mf,U,'mesh','on');
See the getfemmatlab interface documentation for more details.
Four file formats are supported for export: the VTK and VTU file
formats, the`OpenDX`_ file format and the Gmsh postprocessing file
format. All four can be used for exporting either a getfem::mesh
or getfem::mesh_fem
, and
all except VTU can be used for exporting the more versatile getfem::stored_mesh_slice
.
The corresponding four classes: getfem::vtk_export
, getfem::vtu_export
,
getfem::dx_export
and getfem::pos_export
are contained in the file
getfem/getfem_export.h
.
Examples of use can be found in the examples of the tests directory.
Producing mesh slices¶
GetFEM provides “slicers” objects which are dedicated to generating posttreatment
data from meshes and solutions. These slicers, defined in the file
getfem/getfem_mesh_slicers.h
take a mesh (and sometimes a mesh_fem with a
solution field) on input, and produce a set of simplices after applying some
operations such as intersection with a plane, extraction of the mesh
boundary, refinement of each convex, extraction of isosurfaces, etc. The
output of these slicers can be stored in a getfem::stored_mesh_slice
object (see the file
getfem/getfem_mesh_slice.h
). A stored_mesh_slice object may be considered as a P1
discontinuous FEM on a nonconformal mesh with fast interpolation ability. Slices
are made of segments, triangles and tetrahedrons, so the convexes of the original
mesh are always simplexified.
All slicer operation inherit from getfem::slicer_action
, it is very easy to create a new
slicer. Example of slicers are (some of them use a getfem::mesh_slice_cv_dof_data_base
which is just a
reference to a mesh_fem mf
and a field U
on this mesh_fem).

getfem::slicer_none()¶
empty slicer.

getfem::slicer_boundary(const mesh &m, ldots)¶
extract the boundary of a mesh.

getfem::slicer_apply_deformation(mesh_slice_cv_dof_data_base&)¶
apply a deformation to the mesh , the deformation field is defined on a mesh_fem.

getfem::slicer_half_space(base_node x0, base_node n, int orient)¶
cut the mesh with a half space (if
orient
= 1 or +1), or a plane (iforient
= 0),x0
being a node of the plane, andn
being a normal of the plane.

getfem::slicer_sphere(base_node x0, scalar_type R, int orient)¶
cut with the interior (
orient``=1), boundary (``orient``=0) or exterior (``orient``=+1) or a sphere of center ``x0
and radiusR
.

getfem::slicer_cylinder(base_node x0, base_node x1, scalar_type R, int orient)¶
slice with the interior/boundary/exterior of a cylinder of axis
(x0,x1)
and radiusR
.

getfem::slicer_isovalues(const mesh_slice_cv_dof_data_base &mfU, scalar_type val, int orient)¶
cut with the isosurface defined by the scalar field
mfU
andval
. Keep only simplices where :\(u(x)<val\) (orient``=1), :math:`u(x)=val` (``orient=0
or \(u(x)>val\).

getfem::slicer_mesh_with_mesh(const mesh &m2)¶
cut the convexes with the convexes of the mesh
m2
.

getfem::slicer_union(const slicer_action &sA, const slicer_action &sB)¶
merges the output of two slicer operations.

getfem::slicer_intersect(slicer_action &sA, slicer_action &sB)¶
intersect the output of two slicer operations.

getfem::slicer_complementary(slicer_action &s)¶
return the complementary of a slicer operation.

getfem::slicer_build_edges_mesh(mesh &edges_m)¶
slicer whose sideeffect is to build the mesh
edges_m
with the edges of the sliced mesh.

getfem::slicer_build_mesh(mesh &m)¶
in some (rare) occasions , it might be useful to build a mesh from a slice. Note however that there is absolutely no guaranty that the mesh will be conformal (although it is often the case).

getfem::slicer_build_stored_mesh_slice(stored_mesh_slice &sl)¶
record the output of the slicing operation into a stored_mesh_slice object. Note that it is often more convenient to use the
stored_mesh_slice::build(...)
method to achieve the same result.

getfem::slicer_explode(c)¶
shrink or expand each convex with respect to its gravity center.
In order to apply these slicers, a getfem::mesh_slicer(mesh&)
object should be
created, and the getfem::slicer_action
are then stacked with
mesh_slicer::push_back_action(slicer_action&)
and
mesh_slicer::push_front_action(slicer_action&)
. The slicing operation is
finally executed with mesh_slicer::exec(int nrefine)
(or
mesh_slicer::exec(int nrefine, const mesh_region &cvlst)
to apply the operation
to a subset of the mesh, or its boundary etc.).
The nrefine
parameter is very important, as the “precision” of the final result
will depend on it: if the data that is represented on the final slice is just P1
data on convexes with a linear geometric transformation, nrefine = 1
is the
right choice, but for P2, P3, non linear transformation etc, it is better to refine
each convex of the original mesh during the slicing operation. This allows an
accurate representation of any finite element field onto a very simple structure
(linear segment/triangles/tetrahedrons with P1 discontinuous data on them) which is
what most visualization programs (gmsh, mayavi, opendx, scilab, octave, matlab, etc.) expect.
Example of use (cut the boundary of a mesh m
with a halfspace, and save the
result into a stored_mesh_slice):
getfem::slicer_boundary a0(m);
getfem::slicer_half_space a1(base_node(0,0), base_node(1, 0), 1);
getfem::stored_mesh_slice sl;
getfem::slicer_build_stored_mesh_slice a2(sl);
getfem::mesh_slicer slicer(m);
slicer.push_back_action(a1);
slicer.push_back_action(a2);
int nrefine = 3;
slicer.exec(nrefine);
In order to build a getfem::stored_mesh_slice
object during the slicing operation, the stored_mesh_slice::build()
method is often more convenient than using explicitly the slicer_build_stored_mesh_slice
slicer:
getfem::stored_mesh_slice sl;
sl.build(m, getfem::slicer_boundary(m),
getfem::slicer_half_space(base_node(0,0), base_node(1, 0), 1),
nrefine);
The simplest way to use these slices is to export them to VTK, OpenDX, or Gmsh.
Exporting mesh, mesh_fem or slices to VTK/VTU¶
VTK/VTU files can handle data on segment, triangles, quadrangles, tetrahedrons and hexahedrons of first or second degree.
For example, supposing that a stored_mesh_slice sl
has already been built:
// an optional the 2nd argument can be set to true to produce
// a text file instead of a binary file
vtk_export exp("output.vtk");
exp.exporting(sl); // will save the geometrical structure of the slice
exp.write_point_data(mfp, P, "pressure"); // write a scalar field
exp.write_point_data(mfu, U, "displacement"); // write a vector field
In this example, the fields P
and U
are interpolated on the slice
nodes and then written into the VTK field.
It is also possible to export a mesh_fem mfu
without having to build a slice:
// an optional the 2nd argument can be set to true to produce
// a text file instead of a binary file
vtk_export exp("output.vtk");
exp.exporting(mfu);
exp.write_point_data(mfp, P, "pressure"); // write a scalar field
exp.write_point_data(mfu, U, "displacement"); // write a vector field
An mesh_fem mfu
can also be exported in the VTU format with:
vtu_export exp("output.vtu);
exp.exporting(mfu); // will save the geometrical structure of the mesh_fem
exp.write_point_data(mfp, P, "pressure"); // write a scalar field
exp.write_point_data(mfu, U, "displacement"); // write a vector field
Note however that when exporing a mesh_fem with vtk_export
or vtu_export
each convex/fem of mfu
will be mapped to a VTK/VTU element type. As
VTK/VTU does not handle elements of degree greater than 2, there will be a
loss of precision for higher degree FEMs.
Exporting mesh, mesh_fem or slices to OpenDX¶
The OpenDX data file is more versatile than the VTK one. It is able to store more
that one mesh, any number of fields on these meshes etc. However, it does only
handle elements of degree 1 and 0 (segments, triangles, tetrahedrons, quadrangles
etc.). And each mesh can only be made of one type of element, it cannot mix
triangles and quadrangles in a same object. For that reason, it is generally
preferable to export getfem::stored_mesh_slice
objects (in which non simplex elements are
simplexified, and which allows refinement of elements) than getfem::mesh_fem
and getfem::mesh
objects.
The basic usage is very similar to getfem::vtk_export
:
getfem::dx_export exp("output.dx");
exp.exporting(sl);
exp.write_point_data(mfu, U, "displacement");
Moreover, getfem::dx_export
is able to reopen a ‘.dx’ file and append new data into
it. Hence it is possible, if many timesteps are to be saved, to view intermediate
results in OpenDX during the computations. The prototype of the constructor is:
dx_export(const std::string& filename, bool ascii = false, bool append = false);
dx_export(std::ostream &os_, bool ascii = false);
An example of use, with multiple time steps (taken from
tests/dynamic_friction.cc
):
getfem::stored_mesh_slice sl;
getfem::dx_export exp("output.dx", false);
if (N <= 2) sl.build(mesh, getfem::slicer_none(),4);
else sl.build(mesh, getfem::slicer_boundary(mesh),4);
exp.exporting(sl,true);
// for each mesh object, a corresponding ``mesh'' object will be
// created in the data file for the edges of the original mesh
exp.exporting_mesh_edges();
while (t <= T) {
...
exp.write_point_data(mf_u, U0);
exp.serie_add_object("deformation");
exp.write_point_data(mf_vm, VM);
exp.serie_add_object("von_mises_stress");
}
In this example, an OpenDX “time series” is created, for each time step, two data fields are saved: a vector field called “deformation”, and a scalar field called “von_mises_stress”.
Note also that the dx_export::exporting_mesh_edges()
function has been called.
It implies that for each mesh exported, the edges of the original mesh are also
exported (into another OpenDX mesh). In this example, you have access in OpenDX to
4 data fields: “deformation”, “deformation_edges”, “von_mises_stress” and
“von_mises_stress_edges”.
The tests/dynamic_friction.net
is an example of OpenDX program for these data
(run it with cd tests; dx edit dynamic_friction.net
, menu
“Execute/sequencer”).