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[Getfem-commits] [getfem-commits] devel-tetsuo-code-cleanup updated (aad
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From: |
Tetsuo Koyama |
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Subject: |
[Getfem-commits] [getfem-commits] devel-tetsuo-code-cleanup updated (aaddb20 -> 65ebcac) |
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Date: |
Wed, 20 Feb 2019 08:20:32 -0500 (EST) |
tkoyama010 pushed a change to branch devel-tetsuo-code-cleanup.
from aaddb20 Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-tetsuo-code-cleanup
adds ab95e5c optimizing gmm::add for small vectors
adds 98b56a3 adding the scaled case
adds f56e01a comparing pconvex_structure by keys everywhere
adds e9270a8 further refining comparison for convex_structure pointers
adds 45c3f1b Add a ball shell structured mesh generator (tested in 2D
and 3D)
adds a14b31c Code clean up
adds f054185 Let the tolerance sign determine if added points to a
mesh are merged with existing ones or not
adds b462708 Add merge_convexes_from_mesh method to the mesh object
adds 3e2655b New implementation of project_into_convex as a geotrans
class function
adds 5e91d08 Fix projected_fem
adds 4001a79 Fix copyright header
adds aa91194 Add format option to GMM's vecsave
adds 5b0ebff Fix vecsave format option
adds 11638ff Avoid creation of some temporary objects.
adds 3326ae3 minor fix
adds 4fe9963 Fix python script by 2to3
adds 18bcf86 Add initial support for gmsh mesh format version 4
adds d33eb66 Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-tetsuo-2to3check
adds c7b7ac1 minor change
adds f88ba52 minor change
adds b3bf69b [update] svn -> git
adds e26a31f Fix typo in docs
adds 980a9c8 Fix typo in docs
adds f606123 Fix typo in docs
adds 3fcba5a Fix typo in docs
adds 366dcee Fix typo in docs
adds 4d22c9a Merge remote-tracking branch 'origin/fixmisspell'
adds d4e6de7 Add getfem_tutorial.pdf
adds e68cc96 Merge remote-tracking branch
'origin/devel-tetsuo-add-tutorial-pdf'
adds 1124491 Fix bug
adds 7db9249 fixed SEH exceptions created by a wrong optimization by
the INTEL c++ 2019 compiler
adds 59ae132 Merge remote-tracking branch
'origin/devel-tunc_bahcecioglu_intel2019_fix'
adds 407e1d8 Macro that encapsulates the parallel Open MP run
adds 059c201 Merge branch 'master' of git.sv.gnu.org:/srv/git/getfem
into consistent_partitioning_for_open_mp
adds df43516 Besides doing some basic clean up in the Open MP related
partitioning and global storage the main purpose is to make region and
subsequently assembly partitioning independent from the number of parallel
threads being used. For instance, if we choose to partition the whole
calculation into 8 partitions, but use only 2 parallel threads, then each
thread will be looping through 4 independent partitions. This way, no matter
how many threads we choose we partition the reg [...]
adds 69ba642 Adaptations for Scilab 6.0
adds 9770d9d Some small fixes for consistent partionning for open_mp
adds f217241 fixing segmentation fault caused by the fact that
omp_distribute for singletons was destroyed before the objects from it were
deleted. Fixed by creating it dynamically and deleting only when its content
was emptied
adds 56a1522 removing commented out or GCC specific pragmas
adds de60c3d partitions_updated proper initialization
adds e4f9900 Merge branch 'consistent_partitioning_for_open_mp'
adds 012ff70 minor fix
adds efdbaac Fix typos (also in class name) and code cleanup
adds dda317b returning accidentally removed #pragma omp
adds b83e2f9 Optional argument of the sub-element, to improve
performance by avoiding space search.
adds f821dce Add projected_fem to the scripting interface
adds 0b2282d initializing singleton_instance pointer as a static
variable to prevent initialization in parallel open_mp blocks
adds dcd7d39 improving multi-threaded performance by reducing the
usage of muteces when the shared data hasn't changed.
adds f04b73d Add asm_lumped_mass_matrix
adds b6a52a7 Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-tetsuo-asm_lumped_mass_matrix
adds ff6df87 Fix by two loops which can be very inefficient for large
matrices
adds b878a0b Minor Fix
adds 7d8db6b Merge branch 'devel-tetsuo-asm_lumped_mass_matrix' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-tetsuo-asm_lumped_mass_matrix
adds 7e1082f Merge branch 'master' of git.sv.gnu.org:/srv/git/getfem
into static_initialization_for_singleton_instance_pointer
adds ed69b3f fixing the issue when singleton pointer is not
initialized before the other global objects
adds d58721c Clean code by using -Werror option
adds 05b4b36 Fix typo lamda to lambda
adds b17723e Merge remote-tracking branch
'origin/devel-tetsuo-code-cleanup-by-werror'
adds 9b4bc96 minor change
adds 9961a1c Add struct lumped_mass_brick_for_first_order
adds c2f2204 Add convexes_in_box function to the scripting interface
adds b3583f9 remove the projection for invert_lin
adds c744abd Merge remote-tracking branch
'origin/devel-arsha-remove-projection-in-invert-lin'
adds 6501f90 Fix ANSYS mesh import when ANSYS skips the last
coordinate of a node being zero
adds d57b018 Fix test error
adds 4b53edb Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-tetsuo-model_lumped_mass_matrix
adds 72783ed Fix skipped pfp update due to interpolate filter
adds 8a4a34b Minor coding style and whitespace changes
adds 76a8dc6 Fix printing of interpolate filter nodes in ga_print_node
adds 69583e8 warning fixes
adds 94dad7f Fix warning: this statement may fall through
[-Wimplicit-fallthrough=]
adds 86a54a3 minor fixes
adds 7d37202 Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-tetsuo-model_lumped_mass_matrix
adds 6fbdde8 add add_lumped_mass_brick_for_first_order function
adds 75a1155 allowing to have lower number of partitions than
max_concurrency
adds 53a1931 - safer omp_distribute component extraction (in Debug) -
default number of threads and partitions is 1, increasing threads automatically
increases partitions unless specific number of partitions was requested. -
corrected constructions with universal references
adds 8bd82f1 thread based partitioning: - flag in mesh region needs
to atomic, not distributed, not to depend on the thread policy used -
initializing threads to 1, to be able to expand it to the desired number
(setting them to any large number prevents later setting to 1, as shrinking
partitions is not possible)
adds 467ae55 1) partitioning can be changed only once; 2) flag in the
region should be atomic; 3) starting from one thread, if more desired, this
should be specified
adds 5d3e796 Merge branch 'master' of git.sv.gnu.org:/srv/git/getfem
into partitions_initiation
adds 55089b9 cleaner error messages syntax
adds 383842d update the information of "Interpolation of a finite
element method on non-matching meshes"
adds 8516041 add model object description ``add_filtered_fem_variable``
adds 710de08 some documentation improvements
adds 664b86e Fix layout of sphinx source
adds 6df7941 minor change
adds 57f174f Merge branch 'master' of git.sv.gnu.org:/srv/git/getfem
into partitions_initiation
adds 0254182 Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-tetsuo-model_lumped_mass_matrix
adds d45f136 Fix bug introduced in #69583e8b
adds 21c9098 Type naming simplifications
adds f374fd7 Whitespace, typos, file encodings
new fe2a357 Simplify disable_variable and enable_variable
new 65ebcac Merge branch 'devel-tetsuo-code-cleanup' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-tetsuo-code-cleanup
Summary of changes:
.gitignore | 4 +
configure.ac | 14 +-
doc/sphinx/source/.templates/download.html | 4 +-
doc/sphinx/source/conf.py | 3 +
doc/sphinx/source/project/femdesc.rst | 4 +-
doc/sphinx/source/project/libdesc_cont.rst | 2 +-
doc/sphinx/source/project/libdesc_gmm.rst | 2 +-
.../source/project/libdesc_high_gen_assemb.rst | 2 +-
doc/sphinx/source/project/libdesc_mesh.rst | 4 +-
doc/sphinx/source/tutorial/basic_usage.rst | 2 +-
doc/sphinx/source/tutorial/install.rst | 6 +-
doc/sphinx/source/tutorial/intro.rst | 4 +-
doc/sphinx/source/tutorial/thermo_coupling.rst | 53 +-
doc/sphinx/source/userdoc/appendixA.rst | 2 +-
doc/sphinx/source/userdoc/appendixB.rst | 2 +-
doc/sphinx/source/userdoc/gasm_high.rst | 1 +
doc/sphinx/source/userdoc/gasm_low.rst | 4 +-
doc/sphinx/source/userdoc/interNMM.rst | 31 +-
doc/sphinx/source/userdoc/model_ALE_rotating.rst | 4 +-
doc/sphinx/source/userdoc/model_Mindlin_plate.rst | 2 +-
doc/sphinx/source/userdoc/model_Nitsche.rst | 2 +-
doc/sphinx/source/userdoc/model_dirichlet.rst | 2 +-
.../source/userdoc/model_linear_elasticity.rst | 2 +-
doc/sphinx/source/userdoc/model_object.rst | 11 +
.../source/userdoc/model_time_integration.rst | 2 +-
interface/src/getfemint.h | 1 +
interface/src/gf_asm.cc | 82 +-
interface/src/gf_fem.cc | 70 +-
interface/src/gf_mesh_get.cc | 26 +
interface/src/scilab/builder.sce | 4 +-
.../src/scilab/macros/gf_compute_Q1grid_interp.sci | 2 +-
interface/src/scilab/macros/gf_plot_slice.sci | 2 +-
interface/src/scilab/macros/init_pde.sci | 3 +-
interface/src/scilab/sci_gateway/c/gfm_common.c | 6 +-
interface/src/scilab/sci_gateway/c/gfm_common.h | 4 +-
interface/src/scilab/sci_gateway/c/gfm_scilab.cpp | 4 +-
interface/src/scilab/sci_gateway/c/sci_cgne.c | 4 +-
interface/src/scilab/sci_gateway/c/sci_cgs.c | 4 +-
interface/src/scilab/sci_gateway/c/sci_gmres.c | 4 +-
interface/src/scilab/sci_gateway/c/sci_mgcr.c | 4 +-
interface/src/scilab/sci_gateway/c/sci_spchol.c | 6 +-
interface/src/scilab/sci_gateway/c/sci_spcholinc.c | 4 +-
interface/src/scilab/sci_gateway/c/sci_spchsolve.c | 4 +-
interface/src/scilab/sci_gateway/c/sci_splu.c | 4 +-
interface/src/scilab/sci_gateway/c/sci_spluinc.c | 4 +-
interface/src/scilab/sci_gateway/c/sci_splusolve.c | 4 +-
interface/tests/matlab/check_all.sh | 8 +-
interface/tests/python/check_levelset.py | 2 +-
.../python/demo_cracked_thermo_elastic_body.py | 2 +-
interface/tests/python/demo_dynamic_contact_1D.py | 38 +-
.../tests/python/demo_large_sliding_contact.py | 2 +-
interface/tests/python/demo_mortar.py | 2 +-
interface/tests/python/demo_plasticity.py | 4 +-
interface/tests/python/demo_stokes_3D_tank.py | 4 +-
interface/tests/python/demo_tripod.py | 4 +-
interface/tests/python/demo_tripod_alt.py | 4 +-
interface/tests/python/demo_wave.py | 4 +-
interface/tests/python/getfem_tvtk.py | 22 +-
src/Makefile.am | 29 +-
src/bgeot_convex_ref.cc | 66 +
src/bgeot_convex_structure.cc | 26 +
src/bgeot_ftool.cc | 13 +-
src/bgeot_geometric_trans.cc | 35 +-
src/bgeot_geotrans_inv.cc | 7 +-
src/bgeot_node_tab.cc | 26 +-
src/bgeot_poly.cc | 23 +-
src/bgeot_poly_composite.cc | 59 -
src/bgeot_torus.cc | 15 +-
src/dal_singleton.cc | 61 +-
src/dal_static_stored_objects.cc | 514 +-
src/getfem/bgeot_convex_ref.h | 7 +
src/getfem/bgeot_convex_structure.h | 16 +-
src/getfem/bgeot_geometric_trans.h | 5 +
src/getfem/bgeot_geotrans_inv.h | 3 +-
src/getfem/bgeot_mesh.h | 18 +-
src/getfem/bgeot_mesh_structure.h | 6 +-
src/getfem/bgeot_node_tab.h | 9 +-
src/getfem/bgeot_poly_composite.h | 76 +-
src/getfem/bgeot_small_vector.h | 4 +-
src/getfem/bgeot_torus.h | 3 +-
src/getfem/dal_naming_system.h | 9 +-
src/getfem/dal_singleton.h | 169 +-
src/getfem/dal_static_stored_objects.h | 41 +-
src/getfem/getfem_accumulated_distro.h | 223 +
src/getfem/getfem_assembling.h | 30 +-
src/getfem/getfem_context.h | 2 +-
src/getfem/getfem_deformable_mesh.h | 2 +-
src/getfem/getfem_fem.h | 38 +-
src/getfem/getfem_generic_assembly.h | 12 +-
.../getfem_generic_assembly_compile_and_exec.h | 16 +-
src/getfem/getfem_generic_assembly_semantic.h | 34 +-
src/getfem/getfem_generic_assembly_tree.h | 20 +-
src/getfem/getfem_im_list.h | 6072 ++++++++++----------
src/getfem/getfem_interpolation.h | 19 +-
src/{gmm/gmm.h => getfem/getfem_locale.h} | 38 +-
src/getfem/getfem_mesh.h | 7 +
src/getfem/getfem_mesh_fem.h | 2 +-
src/getfem/getfem_mesh_region.h | 139 +-
src/getfem/getfem_models.h | 70 +-
src/getfem/getfem_omp.h | 634 +-
src/getfem/getfem_partial_mesh_fem.h | 2 +-
src/getfem/getfem_projected_fem.h | 8 +-
src/getfem/getfem_regular_meshes.h | 22 +
src/getfem_assembling_tensors.cc | 10 +-
src/getfem_contact_and_friction_common.cc | 96 +-
src/getfem_contact_and_friction_large_sliding.cc | 2 +-
src/getfem_error_estimate.cc | 9 +-
src/getfem_generic_assembly_compile_and_exec.cc | 199 +-
...fem_generic_assembly_functions_and_operators.cc | 25 +-
src/getfem_generic_assembly_semantic.cc | 41 +-
src/getfem_generic_assembly_tree.cc | 741 +--
src/getfem_generic_assembly_workspace.cc | 37 +-
src/getfem_import.cc | 468 +-
.../gf_mesh_levelset.cc => src/getfem_locale.cc | 66 +-
src/getfem_mesh.cc | 41 +
src/getfem_mesh_im_level_set.cc | 1 +
src/getfem_mesh_region.cc | 502 +-
src/getfem_models.cc | 474 +-
src/getfem_omp.cc | 424 +-
src/getfem_projected_fem.cc | 88 +-
src/getfem_regular_meshes.cc | 168 +-
src/gmm/gmm_blas_interface.h | 102 +-
src/gmm/gmm_inoutput.h | 14 +-
src/gmm/gmm_matrix.h | 330 +-
src/gmm/gmm_opt.h | 101 +-
src/gmm/gmm_real_part.h | 1 +
src/gmm/gmm_std.h | 75 +-
127 files changed, 7030 insertions(+), 6126 deletions(-)
create mode 100644 src/getfem/getfem_accumulated_distro.h
copy src/{gmm/gmm.h => getfem/getfem_locale.h} (73%)
copy interface/src/gf_mesh_levelset.cc => src/getfem_locale.cc (52%)
- [Getfem-commits] [getfem-commits] devel-tetsuo-code-cleanup updated (aaddb20 -> 65ebcac),
Tetsuo Koyama <=