Matthias Maier [Wed, 26 Nov 2014 22:38:39 +0000 (23:38 +0100)]
Code cleanup and several bugfixes
Refactor the creation of the final (possibly rotated) interpolation matrix
in make_periodicity_constraints into its own function. Add some additional
asserts to catch corner cases.
Return early if nothing to do (fixes dof_tools_21* tests)
Include mpi.h in base/config.h to avoid Intel compile error
On my system with Intel compiler, I used to get the following error:
In file included from /lrz/sys/intel/mpi_41_3_048/intel64/include/mpi.h(1279),
from [...]/deal.II/include/deal.II/base/mpi.h(23),
from [...]/deal.II/include/deal.II/base/utilities.h(21),
from [...]/deal.II/include/deal.II/base/index_set.h(20),
from [...]/deal.II/include/deal.II/lac/vector.h(24),
from [...]/deal.II/source/numerics/data_out_faces.cc(18):
/lrz/sys/intel/mpi_41_3_048/intel64/include/mpicxx.h(99): error: #error directive: "SEEK_CUR is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
#error "SEEK_CUR is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
^
This is Intel compiler 15.0 with Intel MPI. The solution to this problem is to include mpi.h early enough, which for us means to include it in base/config.h before we include types.h.
Timo Heister [Mon, 24 Nov 2014 13:04:03 +0000 (08:04 -0500)]
Fix mathjax on website broken due to https
The dealii.org webserver now tries to serve https sites. This breaks mathjax because of:
Mixed Content: The page at 'https://www.dealii.org/developer/doxygen/deal.II/step_31.html' was loaded over HTTPS, but requested an insecure resource 'http://cdn.mathjax.org/mathjax/latest/MathJax.js'. This request has been blocked;
We have a number of tests that use p4est output functionality, but the
format p4est writes in has changed in recent p4est versions. Delete the
lines that differ in normalize.pl and adjust stored test output files
accordingly.
A new way to initialize an FEEvaluation object (fast tensor product evaluation routines) has been introduced.
It takes the same arguments as the initialization method of FEValues, namely a Mapping, a FiniteElement, a
one-dimensional Quadrature<1> object, and update flags. This enables using FEEvaluation on the fly just as
FEValues. Since FEEvaluation treats objects of one base element only, this class can select which components
to read.
The concept is explained in the documentation of the FEEvaluation class and an example for the Laplace matrix
is given. However, it also works for the Stokes operator as shown by the test program assemble_matrix_02.
Improved comparison operators for TriaAccessorBase
The previous commit was a bit too aggressive because it is still useful to catch the case when comparing iterators to two different triangulations (leading to infinite loops).
Therefore, I now merely extended the assertion to not trigger when one of the two objects is default constructed, i.e., does contain a null pointer to tria. The comparison then does not need tria == a.tria because invalid iterators use invalid cell and level index, too (leading to !=).
Allow comparison == and != of TriaAccessorBase with different tria
It is well-defined to check for equality and inequality of TriaAccessorBase (cell_iterator types) that belong to different triangulations. Those are simply unequal. This is necessary e.g. for comparing with a default constructed cell_iterator variable. Of course, operator < is still undefined.
Daniel Arndt [Wed, 19 Nov 2014 20:14:12 +0000 (21:14 +0100)]
Implement rotation for vector valued dofs on periodic bc
This commit completes the interface for periodic boundary conditions. It
exposes the interpolation matrix (that is internally used to satisfy
hanging node constraints on periodic boundaries) and provides a possibility
to generate it from a rotation matrix and an index for the vector component
in question (in a similar vein as we already do this for different vector
valued finite elements).
Enable vectorization of vector updates in Chebyshev preconditioner
Use DEAL_II_OPENMP_SIMD_PRAGMA annotation. To avoid a bug in gcc, use an additional
boolean in the 'if' statement that avoids checking factor1 == Number().
Denis Davydov [Thu, 13 Nov 2014 09:17:55 +0000 (10:17 +0100)]
fixed a bug in set_matrix_mode.
STSetMatMode shall be called only after transformation_data->st
is initialised. Thus, we need to store the desired STMatMode
untill set_context is called from the solver object.
For historical reason, GridTools::distort_random() is not deterministic in that if
you call it twice on the same mesh, it will produce different results. This is because
we call rand() which carries around internal state. On the other hand, for the newly
implemented parallel algorithm, we can ensure that this isn't the case by creating
our own random number generator that we start from the same seed every time.
Andrea Mola [Wed, 12 Nov 2014 13:30:55 +0000 (14:30 +0100)]
added namespace and () to the read_STEP and write_STEP name functions in the doc/changes.h file; removed some extra empty line from the function implementation in utilities.cc
Matthias Maier [Wed, 12 Nov 2014 00:37:20 +0000 (01:37 +0100)]
Allow default paths for opencascade detection
OPENCASCADE_DIR is just a hint and might be invalid.
(In FindTRILINOS.cmake the full path is known due to the inclusion of the
Trilinos project configuration. Thus, those options ensure that no wrong
library is accidentally picked up.)
This was supposed to work in a backward compatible way but I broke
it for everyone who didn't explicitly #included the old base/std_cxx1x/*h
headers but got stuff through indirect #includes.
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