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[Getfem-commits] [getfem-commits] devel-logari81 updated (494de10 -> 632
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From: |
Konstantinos Poulios |
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Subject: |
[Getfem-commits] [getfem-commits] devel-logari81 updated (494de10 -> 63276e8) |
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Date: |
Wed, 20 Jun 2018 04:23:46 -0400 (EDT) |
logari81 pushed a change to branch devel-logari81.
from 494de10 fix bug in simplexification of pyramid elements
adds 06d2af2 Remove commented out lines.
adds 030923a Remove cvpts.
adds 8b6c956 Use linear mapping to find initial guess.
adds 7e20e2c Reimplement Newton method.
adds d538ee7 Use analytic formula, if matrix is well-conditioned.
adds 27e02f9 Return linear flag correctly.
adds acb2428 Move bgeot namespace into new file.
adds f2980db Make nonlinear inversion work for axisymmetry.
adds 385c385 Use factored out transformation instead of original one.
adds 0346c9e Check complexity_ instead of degree.
adds 4693f8c Revert change of is_lin, since also first-order product
transformations are nonlinear.
adds 557d17f Check explicitly whether point is in convex.
adds 27bc633 Add missing node.
adds 142c759 Add flag for projection into convex.
adds 46919bd Create linear transformation only, if complexity is
larger than one.
adds e67a8ac Also check nodes of element for good initial guess.
adds d3109a2 Use Newton method with adaptive damping.
adds cf76f1b adding bgeot_torus.h and bgeot_torus.cc to the Makefile
adds 1fc1f56 Fix a conflict
adds f237af9 Use dir_points for creation of linearised transformation.
adds 89c0bd0 Some bug fixing.
adds c49a018 * rewrite direct modifications to the hfs object from std
containers in order to make the code compatible with INTEL2017 c++ compiler
update 5
adds dc685a3 * remove unnecessary comments * fix styling: remove
spaces before and after +-*/ operations
adds 9a26a21 change initiation order and simplification
adds ec53c5b Merge from master.
adds 1872d5b Fix sizes for lower-dimensional elements.
adds 599b43f Merge branch 'mb-transInversion' of
ssh://git.sv.gnu.org:/srv/git/getfem into mb-transInversion
adds 06b29a6 modifications for compilation problems on g++ and
cosmetic changes
adds 4c201aa Small modification of the mesh file format
adds 6061ebd minor fix
adds 561b155 minor change : preload of the blas if found
adds 96f5398 In case of axisymmetry, resize G to original dimension.
Pass original transformation to convex_quality_estimate.
adds b7a7994 Merge remote-tracking branch
'origin/mb_convex_quality_torus'
adds b33589a minor fix
adds 76c1f5c fix valgrind warning about unitialized variable
adds d435d97 fix memleak
adds 638cf10 code simplification
adds c82245f code simplification
adds 42a3e5f use nullptr instead of 0
adds f710f52 add few new assertions inside ga_tree
adds b8350c8 Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem
adds 92d3170 scripts and installer for matlab and python interface on
windows
adds 788157a minor fix
adds 5c22991 Merge remote-tracking branch 'origin/devel-yves'
adds 8df3383 minor modification
adds 36565e0 Don't change current cvs, since it is a const function.
adds d1f8db2 Create cvs in the constructor and set auto_basic flag.
adds 9ad22f9 Also for 0-dimensional convex, auto_basic has to be true.
adds 2b4e0ca Add getter for auto_basic.
adds eadab4c Pass correct flag.
adds 931b69d Revert moving the assert.
adds 5a30fb5 Create simplexified_convex only, if auto_basic.
adds cf5355f use qhull to simplexify unlisted reference elements
adds 3a7755f Change the use of mex -v for getting dynamic library
extension which is not valid anymore
adds c4f9550 Fix for compatibility with 64 bit integer BLAS and LAPACK
versions
adds d6b12f9 suppress lu_solve lapack interface
adds 6e85ffe minor change
adds a8190e1 Merge branch 'devel-yves-fix-matlab-pb' of
ssh://git.sv.gnu.org:/srv/git/getfem into devel-yves-fix-matlab-pb
adds 203a16f fix copy_node problem
adds f52a236 Merge branch 'devel-yves-fix-matlab-pb'
adds a06ee06 Another adaptation for 64 bit integer blas/lapack, ipvt
interface structure. Change a bit the call of some factorization functions
adds 28b4546 adding a comment on difficulties with MKL ILP64
adds 6ea64bd minor change
adds eca2c61 minor fix on matlab detection
adds 8404197 doc fixes for std::vector output with gmm
adds adb1011 minor fix
adds c0d0c62 Set number of DoFs correctly.
adds 9d7b168 Add the max_dof update at he interpolate_test cases
adds 23b7259 Fix compilation error under Windows.
adds d40f292 Merge remote-tracking branch
'origin/mb-win_compilation_error'
adds 438d13e revert introduction of inconsistent assert condition
adds 545272b Fix a little problem with non integral bricks
adds 33e8b61 Bug fixes for MPI parallelization
adds 3743716 minor fixes
adds 399f4f3 remove a dependance of Gmm library with a GetFEM include
which brokes the standalone version of Gmm
adds 3836fcb fix a bug in the derivative of the Normalized operator
adds d603f27 Change of approx_method needs the update of pgp.
adds 9c140e2 Merge remote-tracking branch
'origin/inpterpolation_im_data_fix'
adds 7b4907b declare element_K as a vector for 1D elements
adds d834c69 fix a problem affecting the use of variable groups
adds fa1c299 minor change
adds 771dd1b minor change
adds 14fc43e improve dynamic contact tests
adds c27b401 some corrections
adds 2e8d01b gamma -> 1/gamma and minor changes
adds 31609c8 a small experimentation
adds 53783bf Merge remote-tracking branch
'origin/devel-yves-dyn-contact'
adds ba95c87 Adding the possibility to print gfsparse matrices
adds e453705 Add missing includes.
adds aeee811 Add missing definition of GETFEM_HAVE_OPENMP.
adds f732ed4 Take the maximum of previous number and end of interval,
since variables are not necessarily ordered in ascending ordering starting from
0.
adds 660f33f Remove duplicated functions that are already defined in
getfem_omp.h
adds 1db28fa Revert "Remove duplicated functions that are already
defined in getfem_omp.h"
adds abcd05d adding gmm_arch_config.h
adds 58d4a70 Merge remote-tracking branch
'origin/mb-fix_compilation_error'
adds 3dde20c dynamic contact test
adds a464152 minor fixes
adds ebf4c7d Increase maximal number of subdivisions.
adds 19f8373 fix inconsistencies for small strain plasticity brick
adds bcfdfaa bug fix on max_dof computation
adds d8c94f4 A attempt for a Newton algorithm with step control : work
in progress
adds f62d8dd minor changes
adds 121fc57 work in progress
adds 9ae91b0 Merge remote-tracking branch
'origin/devel-yves-ctrl-newton'
adds 6363945 minor changes
adds e5587d5 simplifaction for access to a component of a sparse
matrix in the interface
adds 0224f9b minor fixes
adds 15c6d5c delete an debug output
adds 0299ac1 adding reg_pos_part a regularised positive part in the
assembly language
adds 630870e Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem
adds 70daa5d Authorization of test function interpolation
adds ffc87a3 Added a bounding box method to mesh_region class.
adds 1539d40 Fix a little problem on Mac Os
adds dec612c Use the project_into_element option when extrapolation of
interpolation function option is disabled so that points very close to the
boundary can be handled properly.
adds 4712064 Minor modifications
adds d8ba058 Merge branch 'master' of git.sv.gnu.org:/srv/git/getfem
into interpolation_with_projection_into_element
adds 764aa53 splitting of the giant file getfem_generic_assembly.cc,
work in progress
adds ee8ed29 split of getfem_generic_assembly.cc done
adds d9128be adding the definition of macros with parameters, work in
progress
adds 60a7341 Macro expansion
adds a29bbf0 macro interface
adds ced932d better error messages
adds f52a242 adaptation of the macro documtenation
adds 3a284f7 Adding a Diff(expression, variable) operator in the
assembly language
adds 3269bff Grad operator, a first step
adds 039ca29 Grad operator, work in progress
adds 716a4e9 Adding operator Contract to the assembly language : some
specific tensor contractions
adds f9c54c1 Allowing integration of tensor quantities
adds 1258d62 Minor fixes
adds 203047f extend transpose operation a bit
adds f97aa44 ga_grad, work in progress
adds 9d11af0 adding Swap_indices operation in the assembly language
adds 808a09e adding Swap_indices operation in the assembly language
adds 7df7e67 work in progress
adds 6862d40 grad(expression), work in progress
adds 8a7be52 grad(expression), work in progress
adds aa44084 Change in the storage of explicit tensor : natural order.
Accepts now higher order tensors with the nested format
adds 1b14a1d making [1,2,3] and [1;2;3] equivalents
adds c628572 Grad(expression) working
adds 5b026af Operator Diff(expression, variable, direction)
adds d561544 minor fixes
adds eedb4e8 Merge remote-tracking branch
'origin/devel-yves-generic-assembly-modifs'
adds f62201b A very small modifications, improving error messages
adds 45d24ca Smaller empty point tolerance.
adds 005de20 Ignore zero weighted points in the assembly.
adds d7006a6 fix a problem in macro expansion
adds 790caff Merge branch 'master' of git.sv.gnu.org:/srv/git/getfem
into ignore_empty_integration_points
adds 2863438 fix a problem on the level of threshold
adds d517c0a Option to add zero weighted integration points.
adds d5cebf0 Use consistent type.
adds dd3cd21 minor change
adds 8926cf6 reverting a copy file error
adds 350bab4 minor correction
adds e930335 Fix kinematic hardening coefficient error in small strain
plasticity
adds ca00b69 Fix kinematic hardening modulus definition in small
strain plasticity documentation
adds a621a31 Merge remote-tracking branch
'origin/devel-logari81-plasticity'
adds 7cc126f name simplification: add_linear_assembly_brick ->
add_linear_term and the same for similar operations.
adds f1fc36b Making 'Normal' refering to the unit vector to a
level-set when integrating on a level-set
adds b8af863 fix a bug in transpose
adds 9f47ed8 Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem
adds 10b2744 minor fixes in xfem enrichment function evaluation
adds 7bfbfd0 Very minor changes
adds 3b13164 Merge branch 'master' of git.sv.gnu.org:/srv/git/getfem
into uniform_composite_fem
adds f269855 Use single polynomial if mesh is uniform.
adds e2db190 Revert "Use single polynomial if mesh is uniform."
adds 6d47867 Use map instead of vector to reduce the memory
consumption on composite fem.
adds d21a14d Save memory usage by storing polynomial as
static_stored_object and store its convex and key in a map.
adds c50c588 Merge remote-tracking branch
'origin/uniform_composite_fem'
adds f450689 remove undesirable ';'
adds 6a5e4f8 White space and typo fixes
adds 3a1c26a Add target region option to interpolate transformation
from expression
adds 987b363 Minor code simplifications
adds 8d65fe7 White space, file enconding and other minor changes
adds e9c45ff Renaming of geotrans and fem types
adds 4d70d1d Minor cosmetic changes
adds 3480c3b Account for pyramid elements in classic integration
methods
adds b7ba5d1 Improve support for incomplete (serendipity) elements and
add discontinuous versions
adds 440cca6 minor fix after name change of incomplete prism
transformation
adds ffcd11d For compatibility with python3
adds 020c608 Replace the mean unit normal vector on face nodes by the
unit normal vector on the mean of face nodes : for pyramid element
adds 93ea20c fix a problem in inverting transformation for pyramids
adds 42f6488 Merge branch 'master' of
ssh://git.sv.gnu.org:/srv/git/getfem
adds b98e9b5 minor modifications for 5.3 release
adds f862cc8 Fix compilation problems on MACOS
adds ca3d0aa Still some minor modification for the 5.3 release
new 63276e8 Merge branch 'master' into devel-logari81
Summary of changes:
.gitignore | 381 +-
bin/extract_doc | 4 +-
bin/upload_documentation | 3 +
bin/upload_html | 3 +
bin/upload_misc | 3 +
bin/upload_version | 3 +
configure.ac | 22 +-
.../test_plasticity/test_small_strain_plasticity.m | 10 +-
.../test_small_strain_plasticity.py | 10 +-
doc/doxygen/Doxyfile | 2 +-
doc/sphinx/source/.templates/download.html | 27 +-
doc/sphinx/source/.templates/indexcontent.html | 12 +-
doc/sphinx/source/biblio.rst | 2 +-
doc/sphinx/source/gmm/blas.rst | 4 +-
doc/sphinx/source/gmm/denselu.rst | 2 +-
doc/sphinx/source/gmm/first-step.rst | 4 +-
doc/sphinx/source/gmm/misc.rst | 2 +-
doc/sphinx/source/install/install_linux.rst | 7 +
doc/sphinx/source/install/install_windows.rst | 2 +-
doc/sphinx/source/links.rst | 44 +-
doc/sphinx/source/project/contribute.rst | 14 +-
doc/sphinx/source/project/femdesc.rst | 2 +-
.../source/project/libdesc_high_gen_assemb.rst | 16 +-
doc/sphinx/source/project/libdesc_mim.rst | 2 +-
doc/sphinx/source/replaces.txt | 4 +-
doc/sphinx/source/tutorial/basic_usage.rst | 2 +-
doc/sphinx/source/tutorial/thermo_coupling.rst | 31 +-
doc/sphinx/source/tutorial/wheel.rst | 14 +-
doc/sphinx/source/userdoc/bmesh.rst | 2 +-
doc/sphinx/source/userdoc/gasm_high.rst | 166 +-
doc/sphinx/source/userdoc/interMM.rst | 8 +-
doc/sphinx/source/userdoc/model_Mindlin_plate.rst | 4 +-
doc/sphinx/source/userdoc/model_Nitsche.rst | 16 +-
.../model_contact_friction_large_sliding.rst | 16 +-
doc/sphinx/source/userdoc/model_fourier_robin.rst | 3 +-
.../source/userdoc/model_generic_assembly.rst | 17 +-
.../source/userdoc/model_generic_elliptic.rst | 2 +-
.../source/userdoc/model_nonlinear_elasticity.rst | 2 +-
.../userdoc/model_plasticity_small_strain.rst | 26 +-
doc/sphinx/source/userdoc/model_source_term.rst | 2 +-
.../source/userdoc/model_time_integration.rst | 8 +-
doc/sphinx/source/userdoc/xfem.rst | 2 +-
doc/sphinx/source/whatsnew/4.2.rst | 4 +-
doc/sphinx/source/whatsnew/4.3.rst | 6 +-
doc/sphinx/source/whatsnew/5.0.rst | 11 +-
doc/sphinx/source/whatsnew/5.1.rst | 6 +-
doc/sphinx/source/whatsnew/5.2.rst | 6 +-
doc/sphinx/source/whatsnew/5.3.rst | 21 +
doc/sphinx/source/whatsnew/index.rst | 1 +
extract_gmm++ | 47 +-
interface/src/gf_asm.cc | 13 +-
interface/src/gf_mesh.cc | 4 +-
interface/src/gf_mesh_fem_set.cc | 87 +-
interface/src/gf_model_get.cc | 7 +-
interface/src/gf_model_set.cc | 101 +-
interface/src/gf_spmat_get.cc | 54 +-
interface/src/python/getfem_python.c | 4 +-
interface/src/python/setup.py.in | 2 +-
interface/tests/matlab/check_all.sh | 11 +-
interface/tests/matlab/check_plasticity.m | 6 +-
.../tests/matlab/demo_Mindlin_Reissner_plate.m | 10 +-
.../tests/matlab/demo_Nitsche_contact_by_hand.m | 25 +-
interface/tests/matlab/demo_continuation.m | 3 +-
interface/tests/matlab/demo_crack.m | 4 +-
interface/tests/matlab/demo_dynamic_contact.m | 314 +-
interface/tests/matlab/demo_dynamic_plasticity.m | 2 +-
.../matlab/demo_dynamic_plasticity_with_contact.m | 2 +-
interface/tests/matlab/demo_elasticity.m | 2 +-
interface/tests/matlab/demo_laplacian.m | 2 +-
interface/tests/matlab/demo_laplacian_DG.m | 10 +-
interface/tests/matlab/demo_laplacian_pyramid.m | 2 +-
.../tests/matlab/demo_large_sliding_contact.m | 24 +-
interface/tests/matlab/demo_nonlinear_elasticity.m | 43 +-
interface/tests/matlab/demo_periodic_laplacian.m | 4 +-
interface/tests/matlab/demo_plasticity.m | 6 +-
.../demo_thermo_elasticity_electrical_coupling.m | 6 +-
.../tests/matlab/test1_nitsche_large_sliding.m | 8 +-
.../tests/matlab/test2_nitsche_large_sliding.m | 30 +-
interface/tests/matlab/tutorial1.m | 4 +-
interface/tests/matlab/uAnalytic.m | 110 +
interface/tests/python/Makefile.am | 4 +
interface/tests/python/check_asm.py | 238 +
interface/tests/python/check_export.py | 2 +-
interface/tests/python/demo_crack.py | 4 +-
.../python/demo_cracked_thermo_elastic_body.py | 284 +
interface/tests/python/demo_dynamic_contact_1D.py | 501 +
interface/tests/python/demo_laplacian_DG.py | 2 +-
.../tests/python/demo_large_sliding_contact.py | 20 +-
interface/tests/python/demo_navier_stokes.py | 4 +-
.../tests/python/demo_nonlinear_elasticity.py | 12 +-
interface/tests/python/demo_plasticity.py | 2 +-
.../demo_thermo_elasticity_electrical_coupling.py | 6 +-
interface/tests/python/demo_wheel_contact.py | 6 +-
internal_tools/getfem-matlab-interface-script.iss | 124 +
internal_tools/getfem-python-interface-script.iss | 104 +
internal_tools/simplexification_refelt.cc | 2 +-
src/Makefile.am | 16 +-
src/bgeot_convex_ref.cc | 232 +-
src/bgeot_convex_ref_simplexified.cc | 17 +-
src/bgeot_convex_structure.cc | 42 +-
src/bgeot_geometric_trans.cc | 102 +-
src/bgeot_geotrans_inv.cc | 293 +-
src/bgeot_mesh_structure.cc | 4 +-
src/bgeot_poly_composite.cc | 254 +-
src/bgeot_sparse_tensors.cc | 8 +-
src/bgeot_torus.cc | 213 +
src/getfem/bgeot_convex_ref.h | 32 +-
src/getfem/bgeot_convex_structure.h | 15 +-
src/getfem/bgeot_geometric_trans.h | 30 +-
src/getfem/bgeot_geotrans_inv.h | 76 +-
src/getfem/bgeot_poly.h | 366 +-
src/getfem/bgeot_poly_composite.h | 16 +-
src/getfem/{getfem_torus.h => bgeot_torus.h} | 164 +-
src/getfem/getfem_assembling.h | 8 +-
src/getfem/getfem_fem.h | 40 +-
src/getfem/getfem_generic_assembly.h | 137 +-
.../getfem_generic_assembly_compile_and_exec.h | 214 +
...tfem_generic_assembly_functions_and_operators.h | 116 +
src/getfem/getfem_generic_assembly_semantic.h | 117 +
src/getfem/getfem_generic_assembly_tree.h | 470 +
src/getfem/getfem_im_list.h | 2 +-
src/getfem/getfem_integration.h | 3 +-
src/getfem/getfem_interpolation.h | 13 +-
src/getfem/getfem_mesh.h | 4 +-
src/getfem/getfem_mesh_fem.h | 44 +-
src/getfem/getfem_mesh_im_level_set.h | 4 +
src/getfem/getfem_mesh_region.h | 25 +-
src/getfem/getfem_mesher.h | 57 +-
src/getfem/getfem_model_solvers.h | 182 +-
src/getfem/getfem_models.h | 48 +-
src/getfem/getfem_torus.h | 95 +-
src/getfem_assembling_tensors.cc | 11 +-
src/getfem_contact_and_friction_common.cc | 2 +-
src/getfem_contact_and_friction_integral.cc | 583 +-
src/getfem_contact_and_friction_large_sliding.cc | 2 +-
src/getfem_export.cc | 27 +-
src/getfem_fem.cc | 321 +-
src/getfem_fem_composite.cc | 8 +-
src/getfem_fem_level_set.cc | 4 +-
src/getfem_generic_assembly.cc | 14320 -------------------
src/getfem_generic_assembly_compile_and_exec.cc | 6880 +++++++++
...fem_generic_assembly_functions_and_operators.cc | 749 +
src/getfem_generic_assembly_interpolation.cc | 935 ++
src/getfem_generic_assembly_semantic.cc | 4762 ++++++
src/getfem_generic_assembly_tree.cc | 1952 +++
src/getfem_generic_assembly_workspace.cc | 969 ++
src/getfem_global_function.cc | 38 +-
src/getfem_import.cc | 23 +-
src/getfem_integration.cc | 29 +-
src/getfem_integration_composite.cc | 4 +-
src/getfem_interpolation.cc | 2 +
src/getfem_level_set.cc | 30 +-
src/getfem_mat_elem.cc | 11 +-
src/getfem_mesh.cc | 269 +-
src/getfem_mesh_fem.cc | 92 +-
src/getfem_mesh_im_level_set.cc | 31 +-
src/getfem_mesh_level_set.cc | 4 +-
src/getfem_mesh_region.cc | 266 +-
src/getfem_mesher.cc | 93 +-
src/getfem_model_solvers.cc | 11 +-
src/getfem_models.cc | 144 +-
src/getfem_plasticity.cc | 82 +-
src/getfem_regular_meshes.cc | 4 +-
src/getfem_torus.cc | 190 +-
src/gmm/gmm_blas.h | 64 +
src/gmm/gmm_blas_interface.h | 72 +-
src/gmm/gmm_dense_lu.h | 66 +-
src/gmm/gmm_lapack_interface.h | 213 +-
src/gmm/gmm_opt.h | 63 +-
src/gmm/gmm_std.h | 15 +-
tests/elastostatic.param | 4 +-
tests/laplacian_with_bricks.cc | 6 +-
tests/nonlinear_elastostatic.param | 4 +-
tests/plasticity.cc | 5 +-
tests/test_assembly.cc | 7 +-
tests/test_continuation.cc | 3 +-
tests/test_gmm_matrix_functions.cc | 26 +-
tests/thermo_elasticity_electrical_coupling.cc | 6 +-
178 files changed, 22491 insertions(+), 17593 deletions(-)
create mode 100644 doc/sphinx/source/whatsnew/5.3.rst
create mode 100644 interface/tests/matlab/uAnalytic.m
create mode 100644 interface/tests/python/check_asm.py
create mode 100644 interface/tests/python/demo_cracked_thermo_elastic_body.py
create mode 100644 interface/tests/python/demo_dynamic_contact_1D.py
create mode 100755 internal_tools/getfem-matlab-interface-script.iss
create mode 100755 internal_tools/getfem-python-interface-script.iss
create mode 100644 src/bgeot_torus.cc
copy src/getfem/{getfem_torus.h => bgeot_torus.h} (57%)
create mode 100644 src/getfem/getfem_generic_assembly_compile_and_exec.h
create mode 100644 src/getfem/getfem_generic_assembly_functions_and_operators.h
create mode 100644 src/getfem/getfem_generic_assembly_semantic.h
create mode 100644 src/getfem/getfem_generic_assembly_tree.h
delete mode 100644 src/getfem_generic_assembly.cc
create mode 100644 src/getfem_generic_assembly_compile_and_exec.cc
create mode 100644 src/getfem_generic_assembly_functions_and_operators.cc
create mode 100644 src/getfem_generic_assembly_interpolation.cc
create mode 100644 src/getfem_generic_assembly_semantic.cc
create mode 100644 src/getfem_generic_assembly_tree.cc
create mode 100644 src/getfem_generic_assembly_workspace.cc
- [Getfem-commits] [getfem-commits] devel-logari81 updated (494de10 -> 63276e8),
Konstantinos Poulios <=