# created: 20.07.2007 (-1)
from 2022.4 to 2023.1¶
merge pull request #917 from rc/fix-typos
fix typos
merge pull request #918 from rc/convert-mesh-force-3d
convert_mesh.py: new –3d option in main()
merge pull request #919 from rc/resview-camera-position-handling
resview.py: unify camera position handling in animation and normal modes
set default value of –view option to None
–camera-position and –view have precedence over –2d-view
new _get_cpos(), update main()
merge pull request #920 from vlukes/on_screen_animations
fix the off-screen animation issue mentioned in #919
merge pull request #921 from rc/mass-term-amm-rmm
new sfepy/terms/terms_mass.py: new MassTerm (de_mass)
update MassTerm docstring
docs: sync module index of developer guide with current sources
new ReciprocalMassMatrixSolver (ls.rmm) (WIP) - new .__init__(), .init_rmm(), .__call__()
update MassTerm.get_function() for residual mode
rename ReciprocalMassMatrixSolver -> RMMSolver, update docstring
obey active_only in RMMSolver.init_rmm(), update .__call__()
use dedicated NoNLS for RMM in CentralDifferenceTS - update ._create_nlst_a(), .create_nlst()
explain a0 in RMMSolver.__call__()
new output_dir define() argument in elastodynamic.py example
update elastodynamic.py example to show RMMSolver use, support mass lumping - new mass_beta, mass_lumping, fast_rmm define() arguments
set tscedl as default in define() of elastodynamic.py example
new dt, edt_safety define() arguments, update docstring of elastodynamic.py
update docstring of MassTerm
update docstring of RMMSolver
update docstrings of VelocityVerletTS, CentralDifferenceTS
optimize beta == 0 branch in fun() in MassTerm.get_function()
new test_rmm_solver(), update define() in test_ed_solvers.py
improve code for ths storing in test_ed_solvers()
update make_term_args(), _test_single_term() for MassTerm - fixes test_term_call_modes()
merge pull request #922 from rc/variable-has-ebc
new FieldVariable.has_ebc(), update Variables.has_ebc(), add verbose argument
merge pull request #923 from rc/resview-animation-cpos
resview.py: fix and simplify setting camera position in animation mode
merge pull request #924 from vlukes/match_dofs
new MatchDOFsOperator: tie DOFs of two fields
merge pull request #928 from rc/sfepy-view-png-anim
resview.py: support saving animation as PNG sequence in main()
merge pull request #925 from vlukes/multi_topo
new copy_coors argument in CMesh.from_data()
read mesh contaning cells of various topological dimensions
cmesh linked to regions according to the topological dimension of cells
update FEDomain.fix_element_orientation(): check “real” cells only
cleanup: remove six
link cmeshs to fields by topological dimensions
update mappings
update DG field
update IGA domain
update recover_micro_hook()
fix domain.region_leaf(): ‘KW_COG’ -> ‘E_COG’
fix assert_equal(): add nm.number to assert_base_types
move back to cmesh (cmesh_highest -> cmesh)
fix _check_region(): region.cmesh can not be None
update docstrings
merge pull request #929 from vlukes/new_example
add link to ‘reinforced shell beam’ example
merge pull request #930 from vlukes/fix_multi_topo
new tdim argument of function Region.light_copy()
merge pull request #935 from vlukes/update_mirror_regions
fix region.copy(): call light_copy with tdim=self.tdim argument
fig setup_mirror_region(): return mirror_name if ret_name is True
update mirror region: mirror with tdim = dim - 1
replace ‘is_trace’ by ‘trace_region’
fields_base.py clean-up
merge pull request #934 from yosefm/numpy-dep-py39
Fix build dependency for Python 3.9
merge pull request #936 from rc/multilinear-terms-surface-extra
support surface_extra integration in ExpressionBuilder - update .add_virtual_arg(), .add_state_arg(), ExpressionArg.get_bf()
new SurfaceFluxOperatorTerm (de_surface_flux)
merge pull request #939 from yosefm/fix-pyvista-deprecation
Pyvista deprecation: must provide inplace parameter
merge pull request #910 from flothesof/add_github_ci
add CI script
reformat ci file
try other branch name
disable build on push to master and add documentation
add link to CI file in description
add changes proposed by @rc
merge pull request #940 from yosefm/fix-elastodynamic-solver-return
Return last vec from elastodynamic solvers
merge pull request #943 from yosefm/remove-setuptools-limitation
Remove setuptools limitation
merge pull request #946 from rc/update-variable-ts-print-info
use supplied n_step for print info in VariableTimeStepper.set_from_data()
merge pull request #945 from yosefm/explain-missing-odes
Explain the relations between variables in example Elastodynamic problem defines 3 “independent” variables that are dependent by solver magic.
CR tweaks
merge pull request #937 from vlukes/mappings_refactoring
unification of VolumeMapping and SurfaceMapping
element diameters calculated in domain, not in CMapping
remove refmaps.c, replaced by DMapping class and eval_mapping_data_in_qp()
employ DMapping in FE and IGA mappings
update FE fields for new mapping
use CMapping instead of DMapping when callig C functions
translete DMapping to CMapping in fargs for C functions
CMapping.shape removed, use DMapping.n_el instead
add docstring to eval_mapping_data_in_qp()
call einsum with optimize=True
rename DMapping -> PyCMapping
rena coorIn to coor in eval_mapping_data_in_qp()
improve docstrings
clean-up in CMapping
update docstrings
rename (coor, weight) to (coors, weights)
move raise_if_too_large() back
fix PyCMapping.bfg computation
improve calculation efficiency - use dets_fast and invs_fast
use dets_fast() in invs_fast()
fix 2x2 inversion
test_install.py: tweak tolerance to accommodate different rounding errors
merge pull request #947 from rc/fix-surface-region-check
fix region check in Term.setup_integration() for 1D, 2D
merge pull request #950 from rc/fix-region-copy
fix Region.copy() to preserve region kind
merge pull request #949 from vlukes/update_de_grad_term
de_grad term: grad can be multiplied by vector or matrix
more readable code
merge pull request #951 from rc/pass-variable-to-setter
update FieldVariable._get_setter() to pass variable to setter functions
update examples for variable argument of setter functions
docs: update users guide for variable argument of setter functions
merge pull request #952 from rc/fix-typo
fix typo in debug code in divgrad_build_gtg()
merge pull request #953 from rc/seismic-load-example
new apply_ebc argument of Variables.set_state()
apply EBCs in prestep_fun(), poststep_fun() - update Problem.get_tss_functions()
prestep_fun(), poststep_fun() return vec
fixes seismic loading, hyperelastic.py with active_only set to False etc.
update prestep_fun(). poststep_fun() calls to return vec
new sfepy/examples/linear_elasticity/seismic_load.py
update docstring and comments in elastodynamic.py example
gen_gallery.py: add custom view for seismic_load.py example
clean up get_ebcs() in seismic_load.py
test seismic_load.py in test_examples()
merge pull request #954 from vlukes/mappings_refactoring_ii
VolumeMapping and SurfaceMapping -> FEMapping
fix docstring of Field.get_mapping()
fields_base.py: remove six
FEMapping.get_mapping(): simplify handling of bf
fix naming: base function -> basis function
eval_mapping_data_in_qp(): fix docstring
merge pull request #956 from rc/fix-mat-by-region-cell-facet, closes #955
fix get_constants() in ConstantFunctionByRegion for mixed cell/facet regions
make Region.get_cell_indices() consistent with its definition, simplify
merge pull request #957 from vlukes/rename_integration
rename integration: volume->cell, surface->facet, surface_extra->facet_extra
update test_term_call_modes
rename integration II.
update fields and variables
remove unused argument ‘integration’ from get_econn()
update region.set_kind(): edge, face -> facet
fix test: volume -> cell
get_data_shape(): fix docstrings
merge pull request #961 from rc/get-blocks-stats
new get_blocks_stats()
new test_get_blocks_stats()
merge pull request #962 from vlukes/fix_link_to_releases
fix download link: -> https://github.com/sfepy/sfepy/tags
merge pull request #958 from vlukes/unification_of_fefields
unification of VolumeField and SurfaceField, only FEField remains
rearange function ordering in FEField
fix format
replace reference to VolumeField and SurfaceField by FEField
FEField._setup_geoemtry(): fix region.kind check
enable einsum optimization
FEField: setup bubble dofs for surface field
docs: replace volume -> cell, surface -> facet
docs: fix typo
merge pull request #964 from rc/make-any_dof_conn-configurable
update docstrings of Equations.get_graph_conns(), .create_matrix_graph() - volume -> cell, surface -> facet
add any_dof_conn argument to relevant functions, support it in conf.options
update eval_equations()
update Problem.update_equations(), .time_update(), .select_bcs(),
.evaluate(), .eval_equations()
docs: update users guide
merge pull request #966 from rc/resview-plot-on-step-change-only
return early from pv_plot() when step stays the same
merge pull request #967 from rc/plot-times-tight-layout
plot_times.py: use tight layout
merge pull request #969 from lokik/scalar_bar_limits
Allow one side of scalar_bar_limits to be computed in resview
merge pull request #970 from vlukes/update_homogenization
update CoefExprPar class: variable setting is not required
fix recovery for 2D plates
merge pull request #971 from rc/resview-fix-for-no-mat-id
fix pv_plot() for meshes without mat_id array
merge pull request #968 from rc/update-elastodynamics, closes #972
remove Python 2 compatibility code
new TimeSteppingSolver.set_dof_info(), use in Problem.solve()
update gen_multi_vec_packing() for extra variables (multiphysics)
support extra variables in ElastodynamicsBaseTS
update .get_matrices(), .get_a0(), .get_initial_vec()
original unpacking supported in .get_initial_vec() for compatibility
update NewmarkTS for extra variables - remove ._create_nlst_a(), update .create_nlst(), .step()
simplify gen_multi_vec_packing() - update ElastodynamicsBaseTS.get_initial_vec(), NewmarkTS.step()
fix NewmarkTS.create_nlst()
update create_arg_parser() for d+name derivatives, new allow_derivatives arg - update create_bnf() (no change in behaviour)
add allow_derivatives arg to Term.setup(), .setup_formal_args()
update Term.assemble_to() to ignore d+name derivatives
do not setup terms twice when calling Equation.from_desc() - new setup argument of Equation.__init__()
new transform_equations_ed()
support transforming elastodynamics equations in Problem.set_solver()
update ElastodynamicsBasicTSC for extra variables
extra variables are not used for time step control
update .get_scaled_errors, .get_initial_dt(), .__call__()
new sfepy/examples/multi_physics/piezo_elastodynamic.py
test piezo_elastodynamic.py in test_examples()
gen_gallery.py: add custom view for piezo_elastodynamic.py example
docs: update latex_elements in conf.py
remove debug print in transform_equations_ed()
new auto_transform_equations option in Problem.set_solver(), transform only once
docs: update users guide
simplify seismic_load.py example by using equations transformation
fix Problem.set_solver() for setting nls
set default value of auto_transform_equations to False - update seismic_load.py, piezo_elastodynamic.py examples, docs
update docstring of apply_ebc_to_matrix()
apply EBCs to vec in Evaluator when active_only is False
update .eval_residual(), .eval_tangent_matrix()
the tangent matrix is usually computed just after the residual, so in that case applying EBCs there is not needed, but the overhead is minimal
update Problem.get_tss_functions() - do not apply EBCs in prestep_fun()
change default output directory in piezo_elastodynamic.py example
new active_only define() argument in elastodynamics examples - update elastodynamic.py, seismic_load.py, piezo_elastodynamic.py
set default value of allow_derivatives to False - update create_arg_parser(), Term.setup(), .setup_formal_args()
add allow_derivatives argument to Equations.from_conf(), Equation.from_desc() - update Problem.set_equations(), Terms.setup()
update Problem.set_solver() to check for solver.var_names
new ElastodynamicsBaseTS._common_parameters, use in subclasses
new var_names solver option in ElastodynamicsBaseTS._common_parameters - update .__init__(), .get_initial_vec()
add var_names to elastodynamics solver options in elastodynamic.py example
update docstring of elastodynamic.py example
make var_names optional in ElastodynamicsBaseTS._common_parameters - update .__init__(), .get_initial_vec()
add var_names to elastodynamics solver options in test_ed_solvers.py
new test_active_only() in test_ed_solvers.py - update get_ic() in define() for 2D
merge pull request #975 from vlukes/fix_nonlinhomog_example
replace term.integration by term.act_integration
fix MPI logging
from 2022.3 to 2022.4¶
merge pull request #880 from vlukes/update_hdf5meshio_write
update HDF5MeshIO.write(): dump region_name
merge pull request #878 from rc/fix-warnings
fix warning in test_base_functions_delta()
fix file not closed in Mesh3DMeshIO.read()
store connectivity in XYZMeshIO.write() as integers, update xyz meshes
fix sparse matrix comparison warning in test_hdf5_meshio()
fix MumpsSolver.__init__()
fix MUMPSSolver.__init__() for MUMPS not installed
silence SparseEfficiencyWarning in apply_ebc_to_matrix()
update gmres callback setup in ScipyIterative.__call__()
silence SparseEfficiencyWarning in project_to_facets()
silence SparseEfficiencyWarning in ScipyDirect.presolve()
new pytest.ini
clean up coefficients.py
fix remaining invalid escape sequence warnings
update pytest.ini
fix ScipyIterative.__call__() for scipy < 1.4.0
update pytest.ini: do not raise error on warnings
merge pull request #881 from rc/sfepy-test
new sfepy/scripts/run_tests.py
new sfepy-test entry point in setup.py
docs: update installation/testing instructions
merge pull request #888 from rc/allow-mesh-in-place-filename
allow Mesh instance in place of filename in PDESolverApp.setup_output_info()
merge pull request #892 from rc/fix-eig-arguments
rename method argument of eig() to solver_kind, fixes shadowing method parameter
update eig() calls
merge pull request #887 from rc/no-save-in-corrector-calls
do not save results in problem.solve() calls in corrector classes - update CorrNN, CorrN, CorrOne, CorrEqPar
merge pull request #891 from heczis/fix_simple_phonon_args, closes #883, #884
Fix typo in docstring
Do not plot without band gaps or dispersion
Make band-gaps exclusive to dispersion and phase-velocity
Fix AcousticBandGapsApp.setup_options
Use parser.error instead of raise
Make all band-gaps related options available simultaneously
Facelift plotting functions
Remove show and new_axes from plotting functions
Separate log files for band_gaps and dispersion
merge pull request #895 from rc/fix-simplify-log-plot
use plt.tight_layout() in every LogPlotter.apply_commands() call
unregister Log.terminate() in atexit on successful termination
do not use threading in LogPlotter.__call__(), update .apply_commands()
use spawn start method instead of fork in Log.__call__() to start LogPlotter - update .__init__()
merge pull request #897 from rc/fix-log-plotter-labels
plot labels and vlines in every LogPlotter.apply_commands() call - fixes not plotting labels and vlines when show_legends was False
merge pull request #906 from rc/fix-sfepy-test-explicit-paths
fix test() for explicit paths passed to run_tests.py (sfepy-test)
merge pull request #904 from flothesof/transient_poisson_multimaterial_example
first version of example
finish docstring of example
take into account comments from PR
adding post processing
fix line lengths
fix run examples sphinx formatting
make usage path relative to sfepy package dir like in other examples
adding example to list of examples to be tested
removing plt.show call to make example testable
add custom gallery view for time_heat_equation_multi_material.py example
change ordering in test
merge pull request #908 from fix-pyvista-mesh-style
fix pv_plot() for pyvista 0.37.0
show edges with glyphs in pv_plot() only when requested explicitly
merge pull request #902 from rc/elastodynamics-time-step-control
new TimeStepController
add tsc argument to TimeSteppingSolver.__init__(), .__call__()
new FixedTCS, ElastodynamicsBasicTCS in new sfepy/solvers/ts_controllers.py - update solver_table
create VariableTimeStepper in ElastodynamicsBaseTS.__init__() when adapting - for non-fixed TimeStepController subclasses
support time step control in GeneralizedAlphaTS, new .step(), split .__call__()
remove .dts attribute of VariableTimeStepper
de-struct arguments of {TimeStepController,ElastodynamicsBasicTCS}.__call__() - update GeneralizedAlphaTS.__call__()
new TimeStepController.get_initial_dt()
fix adaptive time stepping in GeneralizedAlphaTS.__call__() - do not update dt in-place when the step is accepted
add comment to ElastodynamicsBaseTS.__init__()
new TimesSequenceTCS, new .__init__(), get_initial_dt(), .__call__()
move ElastodynamicsBaseTS._create_nlst_*() to particular classes
move ._create_nlst_a() to NewmarkTS
move ._create_nlst_u() to BatheTS
split/move GeneralizedAlphaTS.__call__() into new ElastodynamicsBaseTS.__call__() - new GeneralizedAlphaTS.__init__(), update .step()
new define(), test_ed_solvers() in new sfepy/tests/test_elastodynamic_solvers.py
pass prestep_fun to .step() in ElastodynamicsBaseTS.__call__() - update GeneralizedAlphaTS.step()
new {VelocityVerletTS, NewmarkTS, BatheTS}.step() replacing .__call__() - use ElastodynamicsBaseTS.__call__() for all elastodynamics solvers
new ElastodynamicsBasicTCS.get_scaled_errors(), update .__call__()
fix typo (TCS -> TSC)
new ElastodynamicsPIDTSC, new .__init__(), .__call__() - update docstrings
rename test_elastodynamic_solvers.py -> test_ed_solvers.py
new ElastodynamicsBaseTS.clear_lin_solver(), update .__call__()
new BatheTS.clear_lin_solver() - fix for adaptive time step control
test time step controllers in test_ed_solvers(), update define()
mark test_ed_solvers() as slow
halve t1, clean up test_ed_solvers()
gen_solver_table.py: update for TimeStepController
docs: sync module index of developer guide with current sources
docs: add time step controllers table to users guide
update Problem.set_conf_solvers(), .init_solvers() for time step controllers
update .__init__()
support time step controllers in problem definition files
simplify test_ed_solvers() by using Problem.init_solvers() - rename _list_elastodynamic_solvers() -> _list_solvers()
illustrate time step control in elastodynamic.py example, new define()
gen_gallery.py: add custom view for elastodynamic.py example
use error_order parameter in ElastodynamicsBasicTSC.__call__() - update ElastodynamicsPIDTSC._parameters
new ElastodynamicsBasicTSC.get_initial_dt(), guess_dt0 parameter - new eval_scaled_norm(), update .get_scaled_errors()
tweak ElastodynamicsBasicTSC parameter description
new ElastodynamicsLinearTSC, new .__init__(), .__call__()
update test_ed_solvers(), define()
show ElastodynamicsLinearTSC use in elastodynamic.py example, update define()
merge pull request #912 from rc/gallery-camera-position
gen_gallery.py: support camera_position option in custom settings - update resview_plot(), generate_images()
merge pull request #909 from flothesof/helmholtz_example, closes #907
first version helmholtz
improve example following review
mesh improvement around source region
add to test_declarative_examples
format long lines
fix LaTeX in docstring
gen_gallery.py: add custom view for helmholtz_apartment.py example
merge materials into a single materials dictionary to reduce number of terms in equations
remove unused import
merge pull request #913 from rc/misc-fixes
fix test_eigenvalue_solvers() to obey can_fail when solving
docs: sync module index of developer guide with current sources
merge pull request #914 from rc/central-difference-tss
new CentralDifferenceTS - new ._create_nlst_a(), .create_nlst(), .step()
test CentralDifferenceTS in test_ed_solvers(), update define()
store u as function in CentralDifferenceTS like in other ED solvers
add ts.central_difference to elastodynamic.py example, fix line lengths
fix line length, update comments in define() of test_ed_solvers.py
update CentralDifferenceTS docstring
merge pull request #915 from rc/fix-multilinear-terms-output-axes-order
fix undefined output axes order in ExpressionBuilder.build()
from 2022.2 to 2022.3¶
merge pull request #839 from rc/fix-active-bcs
fix active BCs in EquationMap.map_equations() for no key set
merge pull request #840 from rc/fix-test-docstring
fix docstring of test()
merge pull request #841 from rc/improve-material-constructor-doc-pr737 - finishes and closes #737 by @burnpanck
tried to improve documentation of Material constructor. Made values= and kwargs completely equivalent instead of almost equivalent
fix Material.__init__() formatting
fix link in Material.__init__() docstring
document special material parameters in Material.__init__() docstring
merge pull request #842 from rc/remove-simple-homog-mpi
simple.py: new bvp-mM mode, new –debug-mpi option
document application kinds in simple.py docstring
remove simple_homog_mpi.py
fix micro_filename path in nonlinear_hyperelastic_mM.py example
update materials in nonlinear_homogenization.py for new Material constructor
see #841 (#737)
fix def_mat()
fix get_slaves() for Python 3
docs: sync module index of developer guide with current sources
add basic description to nonlinear_hyperelastic_mM.py example
merge pull request #843 rc/resview-any-sfepy-format
new make_grid_from_mesh(), use it in read_mesh()
resview.py: update read_mesh() to support any SfePy mesh format
distinguish sfepy and pyvista mesh variables in read_data()
resview.py: update print_camera_position() to work with subprocess.call()
merge pull request #845 from rc/reorganize-scripts-entry-points
remove old scripts edit_identifiers.py, eval_ns_forms.py, eval_tl_forms.py
move script/convert_mesh.py -> sfepy/scripts/convert_mesh.py
new sfepy-convert entry point in setup.py
update docstring of convert_mesh.py
move simple.py -> sfepy/scripts/simple.py
new sfepy-run entry point in setup.py, remove sfepy-run script
update docstring of simple.py
move probe.py -> sfepy/scripts/probe.py
new sfepy-probe entry point in setup.py
update docstring of probe.py
move resview.py -> sfepy/scripts/resview.py
new sfepy-view entry point in setup.py
update docstring of resview.py
move extractor.py -> sfepy/scripts/extractor.py
update docstring of extractor.py
move mesh generator scripts to sfepy/scripts/
move script/blockgen.py -> sfepy/scripts/blockgen.py, script/cylindergen.py -> sfepy/scripts/cylindergen.py, script/gen_iga_patch.py -> sfepy/scripts/gen_iga_patch.py,
blockgen.py: split main() into new gen_block(), add_args()
cylindergen.py: split main() into new gen_cylinder(), add_args()
gen_iga_patch.py: split main() into new gen_iga_patch(), add_args()
new sfepy/scripts/gen_mesh.py
new sfepy-mesh entry point in setup.py
convert_mesh.py: new –extract-edges option in main()
move merge_lines(), extract_edges() into mesh_tools.py
remove extract_edges.py
convert_mesh.py: new –extract-surface, –print-surface options in main()
move _get_facets(), get_surface_faces(), surface_graph(), surface_components() into mesh_tools.py
remove extract_surface.py
convert_mesh.py: new –tile option in main()
remove tile_periodic_mesh.py
move script/show_mesh_info.py -> sfepy/scripts/show_mesh_info.py
show_mesh_info.py: split main() into new show_mesh_info(), add_args()
gen_mesh.py: add show_mesh_info.py as subcommand in main()
move script/dg_plot_1D.py -> sfepy/examples/dg/dg_plot_1D.py
update DG examples for moved dg_plot_1D.py
move script/save_basis.py -> sfepy/scripts/save_basis.py
move script/plot_* scripts into sfepy/scripts/
move script/gen_mesh_prev.py -> sfepy/scripts/gen_mesh_prev.py
to be integrated with resview.py after fixing
rename script/ -> tools/ (not-to-be-installed/development scripts)
move build_helpers.py -> tools/build_helpers.py
move test_install.py -> sfepy/scripts/test_install.py
remove homogen.py compatibility script
update docstrings for script/ -> tools/
new sfepy/scripts/__init__.py, update sfepy/setup.py
update setup.py for reorganized scripts, update get_basic_info()
do not install unnecessary files
test_install.py: update main() for reorganized scripts
update MANIFEST.in
fix get_basic_info() to check for LICENSE instead of generated VERSION
update installed/sdist contents in setup.py, MANIFEST.in
update sphinx extension paths in doc/conf.py
sync_module_docs.py: update for reorganized scripts
docs: sync module index of developer guide with current sources
simple.py: fix phonon options handling in main()
docs: update INSTALL, README.rst for reorganized scripts
docs: update developer guide for reorganized scripts
docs: update FAQ for reorganized scripts
docs: update installation doc for reorganized scripts
docs: update preprocessing doc for reorganized scripts
docs: update primer for reorganized scripts
docs: update tutorial for reorganized scripts
docs: update release tasks for reorganized scripts
docs: update users guide for reorganized scripts
docs: update requirements list
update docstrings of examples for reorganized scripts
gen_gallery.py: update for reorganized scripts
docs: make using salome doc obsolete, update for reorganized scripts
docs: update man pages (sfepy-run, sfepy-view)
merge pull request #849 from rc/update-authors
update AUTHORS
merge pull request #850 from rc/materials-fixes
pass ts to .update_material() in Problem.get_tss_functions()’s prestep_fun()
docs: fix FAQ example
docs: auto-document special methods to have Material.__init__() in docs
docs: fix typo in FAQ
merge pull request #851 from rc/fix-multilinear-terms-with-computed-arguments
fix ETermBase.make_function() for repeated call of de_non_penetration_p term - treat correctly ExpressionArg arguments
merge pull request #852 from rc/fix-examples
fix default output_dir in define() of stokes_slip_bc.py example
improve plots in main() of linear_viscoelastic.py example
fix solve_problem() in shell10x_cantilever_interactive.py example - use AutoDirect solver
clean up several examples
merge pull request #856 from vlukes/fix_splineregion2d, closes #854
fix SplineRegion2D.find_ts(): depreciated ‘xtol’ parameter
merge pull request #855 from rc/fix-test-install-parsing
test_install.py: fix parsing in report_tests()
merge pull request #853 from rc/support-pip-install, closes #320
new pyproject.toml, update MANIFEST.in
specify install_requires in setup_package() of setup.py
docs: update release tasks
docs: update installation instructions
docs: fix venv testing instructions in release tasks
docs: simplify installation instructions
docs: fix/update TestPyPI upload instructions in release tasks
merge pull request #858 from rc/add-missing-tutorial-image
docs: add missing tutorial image
merge pull request #859 from rc/fix-for-docs-generation
use absolute import in test_dg_terms_calls.py
prepend data_dir to mesh name in recovery_micro() of piezo_elasticity_micro.py
new define() in linear_viscoelastic.py example, silence output on import - update main()
merge pull request #861 from vlukes/update_mumps_interface, closes #860
update interface for mumps library version 5.4.x
fix for library version 5.3
merge pull request #862 from rc/speedup-ls-reuse-unify-presolve
new LinearSolver.clear()
new use_mtx_digest parameter in ScipyDirect, new .clear()
update .__init__(), .__call__(), .presolve()
new use_mtx_digest parameter in ScipySuperLU, ScipyUmfpack
update presolve behaviour
new use_mtx_digest parameter in MUMPSSolver, new .clear()
update .__init__(), .__call__(), .presolve(), .__del__()
new use_mtx_digest parameter in ScipySuperLU, ScipyUmfpack
update presolve behaviour
clear linear solver in ElastodynamicsBaseTS.get_a0() - allows factorization reuse without matrix digest (conf.use_mtx_digest = False)
use separate linear solver instances in BatheTS
update .__init__(), .create_nlst1(), .create_nlst2()
allows factorization reuse without matrix digest (conf.use_mtx_digest = False)
use and describe use_mtx_digest in elastodynamic.py example
merge pull request #863 from rc/fix-generalized-alpha-tss
fix GeneralizedAlphaTS: missing M coefficient, wrong state update
new ._create_nlst_a()
update .create_nlst(), .__call__()
merge pull request #864 from rc/decrease-sdist-size
gen_gallery.py: set screenshot size to (800, 600) in resview_plot()
exclude PDF docs (sfepy_manual.pdf) from source tarball
merge pull request #866 from rc/docs-update-enthought-link, closes #688
docs: replace Enthought Canopy link by Enthought Deployment Manager
merge pull request #867 from rc/fix-primer-interactive, closes #629
docs: fix/update interactive mode part of primer
merge pull request #868 from vlukes/update_homog_recovery
update CorrSolution: new get_output() for exporting states
unify recover_micro_hook() and recover_micro_hook_eps()
new ‘div’ and ‘cauchy_strain’ modes of fields.evaluate_at()
update piezo-elasticity example
fix recover_micro_hook(): slice -> nm.arange
update linear elasticity example
fix micro cell center
fix format
add docstring to ‘recover_micro_hook()’
new mechanics.tensors.get_cauchy_strain()
region_mode and eval_mode as define() arguments
update docstring of recover_micro_hook()
fix typo
add docstring to get_causchy_strain()
merge pull request #869 from vlukes/save_files_per_region
update save_state(): split file by region, file_per_var -> file_split_by
update examples
fix save_state()
change file_split_by to split_results_by
merge pull request #870 from rc/gen-gallery-all-sources
update gen_gallery.py to include all examples sources in docs
new omit_images
update _omit(), generate_images(), generate_rst_files()
merge pull request #871 from vlukes/fix_save_files_by_region
fix ‘extend’ value in save_state()
do not split h5 files
merge pull request #872 from rc/fix-custom-views-files-by-region
fix custom views in gen_gallery.py for files by region
merge pull request #873 from vlukes/update_evaluate_at
update evalauate_at(): return three-dimensional array
merge pull request #874 from vlukes/fix_recovery_micro_hook
use region_name if available
from 2022.1 to 2022.2¶
merge pull request #806 from vlukes/fix_meshio_vtkint64
fix meshio: int64 required by the newer paraview
merge pull request #805 from vlukes/update_ev_div_grad_terms
new EGradTerm
update DivTerm, GradTerm: new optional material parameter
merge pull request #809 from rc/de-lin-convect-term new elinearconvectterm term (de_lin_convect)
new ELinearConvectTerm term (de_lin_convect)
merge pull request #811 from vlukes/suppres_meshio_warnings
suppress meshio warnings
merge pull request #812 from vlukes/suppres_meshio_warnings suppress meshio warnings - update
suppress meshio warnings - update
merge pull request #803 from rc/use-pytest, closes #363
move utility TestCommon methods into module scope - move report(), eval_coor_expression(), compare_vectors(), assert_equal()
update test_assembling.py for pytest
update test_base.py for pytest, clean up
update test_cmesh.py for pytest
new conftest.py: new output_dir fixture
import sfepy.base.testing as tst instead of st
update test_conditions.py for pytest
remove run_tests_py related code in test_dg_field.py, clean up
remove run_tests_py related code in DGTermTestEnvornment - prepare DGTermTestEnvornment using fixture
remove TestCommon, fix compare_vectors(), assert_equal()
new run_declaratice_example(), remove tests/tests_basic.py
move NLSStatus from tests/tests_basic.py to sfepy/base/testing.py
make TestInput.check_conditions() standalone function
remove TestDummy, TestInput, TestInputEvolutionary
remove TestLCBC (WIP)
new test_declarative_examples.py: new test_examples(), test_examples_dg()
remove tests/test_input*, tests/test_dg_input* - replaced by test_declarative_examples.py
fix error checking in updated tests - fix test_assembling.py, test_base.py, test_cmesh.py, test_conditions.py
remove return statements in test_dg_terms_calls.py
update test_domain.py for pytest
update test_eigenvalue_solvers.py for pytest
update test_elasticity_small_strain.py for pytest
update test_fem.py for pytest
update test_functions.py for pytest
update test_high_level.py for pytest
update test_homogenization_engine.py for pytest
update test_homogenization_perfusion.py for pytest
update test_hyperelastic_tlul.py for pytest
update test_io.py for pytest, clean up
update test_laplace_unit_disk.py for pytest, clean up
update test_laplace_unit_square.py for pytest, clean up
fix LCBCOperators.add_from_bc() for no arguments
support output_dir in define() of stokes_slip_bc.py example
support output_dir in run() of laplace_shifted_periodic.py example
update test_lcbcs.py for pytest, use output_dir for all output
new test_elasticity_rigid() in test_lcbcs.py
remove tests/test_lcbc_2d.py, tests/test_lcbc_3d.py - replaced by test_elasticity_rigid()
update MultiProblem solver to use master problem output_dir - update .init_subproblems(), .__call__()
do not save mesh in gen_two_bodies() and log in two_bodies_contact.py example
do not save state twice in test_ebc_functions(), update test_region_functions()
new save_lcbc_vecs argument of define() in stokes_slip_bc.py example
update test_stokes_slip_bc() for save_lcbc_vecs argument
do not save state twice in test_solving()
update test_linalg.py for pytest
update test_linear_solvers.py for pytest
update test_linearization.py for pytest
update test_log.py for pytest
update test_matcoefs.py for pytest
update test_mesh_expand.py for pytest
update test_mesh_generators.py for pytest
update test_mesh_interp.py for pytest
update test_mesh_smoothing.py for pytest
update test_meshio.py for pytest
update test_msm_laplace.py for pytest, clean up
update test_msm_symbolic.py for pytest
update test_normals.py for pytest
update test_parsing.py for pytest
check EPBC application in test_epbcs(), fix error report
remove tests/test_periodic_bc_2d.py, tests/test_periodic_bc_3d.py - covered by test_epbcs()
update test_poly_spaces.py for pytest
do not save state twice in _test_msm_symbolic()
fix return in test_hdf5_meshio()
update test_projections.py for pytest
update test_quadratures.py for pytest
update test_ref_coors.py for pytest
update test_refine_hanging.py for pytest
update test_regions.py for pytest
fix ls_red parameter default in SemismoothNewton parameters
update test_semismooth_newton.py for pytest
update test_sparse.py for pytest
update test_splinebox.py for pytest
update test_tensors.py for pytest
update test_term_call_modes.py for pytest
update test_term_consistency.py for pytest, fix test_surface_evaluate() - clean up
update test_term_sensitivity.py for pytest
update test_units.py for pytest
update test_volume.py for pytest
warnings clean up: do not use numpy.int, numpy.bool
warnings clean up: do not use numpy.object, numpy.float
warnings clean up: update imports in ScipyDirect, ScipyIterative
warnings clean up: update import in LOBPCGEigenvalueSolver
warnings clean up: remove unused arpack_eigs()
warnings clean up: update and simplify dot_sequences() - do not use numpy.core.umath_tests.matrix_multiply()
do not print warp violation messages - only set error in _v_describe(), dq_finite_strain(), dq_tl_finite_strain_surface()
update test_install.py for pytest, clean up - update report_tests(), main()
new pytest_addoption(): new –output-dir option for output_dir fixture
new pytest_configure(): new slow marker
mark slow tests
new test() in sfepy/__init__.py for installed sfepy testing
remove run_tests.py, update setup.py, sfepy-run
move tests/ -> sfepy/tests/
obey output_dir in test_solution() of test_homogenization_perfusion.py
add output_dir argument to homogenization-based material functions - update get_homog_coefs_linear(), get_homog_coefs_nonlinear()
add output_dir argument to homogenization micro recovery functions - update recover_micro_hook_init(), recover_micro_hook(), recover_micro_hook_eps()
obey output_dir in micro-problem of linear_elastic_mM.py example - update post_process(), get_homog()
verify that output_dir is directory in output_dir() fixture
docs: update testing info
new remove_prefix argument of run_declaratice_example()
update test_examples(), test_examples_dg() to remove common name prefix
new inedir(), examples_dir
remove common prefix in examples, examples_dg lists
update docstrings of postproc.py, resview.py for renamed result files and pytest
docs: update users guide for pytest-related changes
docs: update developer guide for moved tests/
move examples/ -> sfepy/examples/
update examples for moved examples/
assume example files relative to sfepy.base_dir in run_declaratice_example() - add comment to examples_dir in test_declarative_examples.py
use sfepy.base_dir in multi-file examples
update tests for moved examples/
update test_install.py for moved tests/ and examples/
update gen_gallery.py, gen_term_table.py for moved examples/
update setup.py for moved tests/ and examples/
docs: update FAQ for moved examples/
update docstrings of examples for moved examples/
use sfepy.base_dir in more multi-file examples
docs: update for moved examples/
update docstrings of simple.py, simple_homog_mpi.py for moved examples/
sync_module_docs.py: omit sfepy/examples/ directory
docs: sync module index of developer guide with current sources, include tests
update MANIFEST.in for moved examples/
CI: update appveyor config for pytest, use Python 3.9
test_install.py: update some output directories
merge pull request #814 from rc/update-testing-docs
docs: update testing instructions
merge pull request #815 from rc/elastic-wave-speeds
new youngpoisson_from_wave_speeds(), wave_speeds_from_youngpoisson()
new test_wave_speeds()
merge pull request #818 from heczis/master
Fix legend placement
merge pull request #820 from rc/remove-phonon
run AcousticBandGapsApp from simple.py, new –app option
add phonon.py-specific options with –phonon- prefix
determine app_mode in main()
remove phonon.py
update scripts for no phonon.py
docs: update for no phonon.py
merge pull request #821 from rc/fix-multilinear-terms-for-complex-args
fix multilinear terms for complex arguments - new ETermBase._eval(), .eval_real(), .eval_complex()
merge pull request #823 from vlukes/issue_760, closes #760
update posprocessing instructions (#760)
examples: update posprocessing instructions (#760)
linear_viscoelastic example: plot deformed mesh
merge pull request #824 from vlukes/resview_isosurface, closes #759
resview isosurfaces (#759)
merge pull request #826 from vlukes/update_resview
resview.py: new ‘camera_position’ and ‘window_size’ options
fix option names: replace ‘_’ by ‘-’
update print of camera position
merge pull request #828 from vlukes/resview_grid
resview.py: new ‘camera_position’ and ‘window_size’ options
fix option names: replace ‘_’ by ‘-’
update print of camera position
resview.py: plot figures in grid
fix spelling
fix settings of position vectors
rename ‘–position-vector’ to ‘–grid-vector’
update users’ guide
merge pull request #829 from vlukes/remove_mayavi_dependency, closes #108, #687
remove mayavi dependent files
update documentation
update setup
update ‘sfepy-run’
update INSTALL instructions
update tutorials
resview.py: report saving figure to file
test resview.py script
remove doc files
update examples
merge pull request #830 from rc/fix-eval-complex
fix weak mode in eval_complex() for two complex arguments
merge pull request #831 from vlukes/term_docs_cleanup, closes #773
update term docs - simplify descriptions
update terms notation
update docs: define evaluation modes
update ‘ev_integrate_mat’ docs: remove ‘el_avg’, ‘qp’ modes
update term docs: replace ‘bar{p}’ with ‘p’
merge pull request #832 from heczis/fix_omit_facets
Fix omit_facets
merge pull request #833 from vlukes/evaluable_EScalarDotMGradScalarTerm
Update EScalarDotMGradScalarTerm to be evaluable
merge pull request #834 from vlukes/fix_homog_phononic
Fix compute_eigenmomenta()
fix: init state on compute_eigenmomenta()
merge pull request #835 from vlukes/fix_multiproblem_output
Fix output setting in subproblems
merge pull request #837 from rc/fix-test-examples-iga
fix igakit-dependent examples list - add navier_stokes2d_iga.py
return pytest result from test()
merge pull request #836 from rc/fix-gen-gallery-resview
resview.py: fix pv_plot() for 1D meshes
script/gen_gallery: fix generate_images() for current resview.py - update custom plots
from 2021.4 to 2022.1¶
merge pull request #762 from rc/newton-step-reduction
new step_red parameter of Newton solver, update .__call__()
merge pull request #765 from rmcgibbo/patch-1
Fix for python3.10 collections.Sequence -> collections.abc.Sequence See for example: https://github.com/wireservice/agate/pull/737/files
merge pull request #767 from rc/fix-auto-solver-dict-conf
fix AutoFallbackSolver.__new__() for dict conf
merge pull request #768 from rc/fix-its2d_5-example
fix stress_strain() in its2D_5.py example
merge pull request #764 from rc/move-state-into-variables, closes #378
rename stripped -> reduced, strip -> reduce in DOF vector context
rename Equations.create_stripped_state_vector() -> .create_reduced_state_vector()
rename Equations.strip_state_vector() -> .reduce_vec()
rename Variables.create_stripped_state_vector() -> .create_reduced_state_vector()
rename Variables.strip_state_vector() -> .reduce_vec()
update Variables.get_indx(), .check_vector_size(), .get_state_part_view(), .set_state_part() argument names
update affected code
new Variables.vec, .rvec attributes to hold state vector, new .init_state()
update .apply_ebc(), .apply_ic(), .has_ebc() - vec argument optional, use self.vec by default
new Equations.init_state(), update .apply_ebc(), .apply_ic()
remove Variables.set_from_state(), update Oseen.__call__() (its only use)
remove unused Equations.state_to_output()
rename state_vector -> vec in DOF vector context
rename Equations.create_state_vector() -> .create_vec(), .create_reduced_state_vector() -> .create_reduced_vec()
rename Variables.create_state_vector() -> .create_vec(), .create_reduced_state_vector() -> .create_reduced_vec()
update affected code
rename state_part{_view} -> vec_part in DOF vector context
rename Variables.get_state_part_view() -> .get_vec_part(), .set_state_part() -> .set_vec_part()
update affected code
rename Variables.state_to_output() -> .create_output() - update affected code
remove unused variable in FieldVariable.save_as_mesh()
fix Variable.advance() for multi-variable problems - replace deque .data attribute by list
add step argument to Variable.set_constant(), use in .init_data()
new .locked attribute of Variable, update .set_data()
implement state handling in Variables, regroup/rename functions
lock state variables in .init_state()
new .fill_state(), .invalidate_evaluate_caches()
invalidate caches in .apply_ebc(), .apply_ic()
new .set_reduced_state(), .get_reduced_state(), .set_full_state(), .set_state(), .get_state(), .set_state_parts()
update .get_state_parts(), .create_output()
rename .check_vector_size() -> .check_vec_size()
update Equations for Variables.set_state()
remove Equations.set_variables_from_state(), .get_state_parts()
use new .set_state() in .eval_residuals(), .eval_tangent_matrices()
update .init_state()
update Problem for Variables replacing State
initialize ics in .__init__(), .create_subproblem(), .set_equations()
remove .setup_ics()
update .create_state() to call .get_initial_state()
update .save_state(), .save_ebc(), .get_tss_functions(), .get_initial_state(), .solve(), .block_solve(), .save_restart(), .load_restart()
update affected code for Variables replacing State
update EVPSolverApp.save_results()
update Evaluator.new_ulf_iteration()
update create_mass_matrix()
update .__call__() of CorrNN, CorrN, CorrSetBCS, CorrEqPar, PressureRHSVector
update MultiProblem.init_subproblems(), .__call__()
update tests for Variables replacing State
update examples for Variables replacing State
do not import State in sfepy/discrete/__init__.py
docs: update users’ guide
update SimpleEVP.save() for Variables replacing State
remove sfepy/discrete/state.py
docs: sync module index of developer guide with current sources
update yet more examples for Variables replacing State
docs: update FAQ for Variables replacing State
docs: update primer for Variables replacing State, Python 3 and current code
simplify and clean up verify_incompressibility()
replace stripped -> reduced in SchurEVP.post_process()
docs: update tutorial, sync it with linear_elastic_interactive.py example
merge pull request #772 from rc/plot-mesh-kwargs
add color, **plot_kwargs arguments to plot_mesh()
merge pull request #775 from rc/pass-eterm-options
add eterm_options argument to Problem.evaluate() - update .create_evaluable(), create_evaluable()
update ETermBase.make_function() for recent jax (0.2.21)
merge pull request #777 from rc/check-errors-in-mesh-graph
check errors in mesh_graph(), exit early
merge pull request #774 from vlukes/new_sensitivity_terms
new multilinear term: ENonSymElasticTerm - nonsymmetric gradient
new multilinear sensitivity term: ESDLinearElasticTerm
new multilinear sensitivity term: ESDPiezoCouplingTerm
new multilinear terms: EDiffusionTerm, ESDDiffusionTerm
new multilinear sensitivity term: ESDStokesTerm
new multilinear sensitivity term: ESDDivGradTerm
new multilinear sensitivity term: ESDDotTerm
update docstrings of multilinear terms, see #773
update docstrings of sensitivity terms, see #773
update term notation table
update term table generator - compact virtual/state/parameter arguments
rename ‘parameter_mesh_velocity’ to ‘parameter_mv’
new multilinear terms: ELinearTractionTerm, ESDLinearTractionTerm
fix term docstring: EIntegrateOperatorTerm
move multilinear sensitivity terms to ‘terms_senstitivity.py’
update test_term_sensitivity: use smaller mesh and gc.collect()
multilinear terms: small fixes
multilinear terms: use v() for nonsymmetric vector storage
use ‘:’ only for symmetric gradient
merge pull request #779 from rc/fix-polyspace-for-0d
fix shape check of quadrature coordinates in PolySpace.eval_base() for 0D - fixes surface integrals in 1D
fix BernsteinSimplexPolySpace._eval_base() for 0D
merge pull request #780 from rc/fix-problem-solve-initial-state-arg
fix initial state argument handling in Problem.solve(), .block_solve() - new .set_default_state()
use Problem.set_default_state() where suitable
add docstring to Problem.set_default_state()
merge pull request #781 from rc/update-faq-structural
docs: update FAQ with structural elements entry
docs: fix indentation in FAQ
merge pull request #783 from rc/multilinear-terms-use-actual-ndarray-args - closes #782
use actual ndarray arguments in ETermBase.make_function()
clean up whitespace
merge pull request #784 from rc/update-faq-element-matrix
docs: update FAQ with element matrix entry
merge pull request #786 from rc/fix-balloon-example
fix extract_time_history() for Python 3
update plot_radius() in balloon.py example for recent matplotlib
merge pull request #787 from rc/array-values-apply-unit-multipliers
support array-like values in apply_unit_multipliers()
remove unused elastic_constants_relations
merge pull request #788 from rc/fix-resview-inf-factor
fix pv_plot() for data with zero norm
merge pull request #789 from vlukes/update_div_grad
DivGradTerm: allow different aprroximations
merge pull request #791 from vlukes/fix_div_grad_term fix divgrad_build_gtg()
fix divgrad_build_gtg()
merge pull request #790 from rc/multilinear-terms-use-actual-mapping-data
use actual reference mapping data in get_einsum_ops()
do not store the mapping data in ExpressionArg
update ExpressionArg.from_term_arg(), .get_dofs()
new ExpressionArg.get_bf()
update ETermBase.make_function()
merge pull request #793 from rc/remove-homogen
run HomogenizationApp from simple.py - update main()
remove homogen.py
update scripts for no homogen.py
docs: update for no homogen.py
new homogen.py proxy for compatibility, calls simple.py - re-add it to setup.py
merge pull request #797 from vlukes/update_to_meshio5
update fem/meshio.py to meshio5
remove meshio version
from 2021.3 to 2021.4¶
merge pull request #729 from brylie/patch-1
Include example Docker compose file for simplicity
Use code/ subdirectory inside of container
merge pull request #735 from burnpanck/patch-1
Clarify orientation of geometry elements
Added a note clarifying that the figure showing geometry elements applies to right-handed coordinate systems.
merge pull request #738 from rc/fix-plot-condition-numbers
script/plot_condition_numbers.py: fix division in main()
script/plot_condition_numbers.py: resolve numpy warning in main()
merge pull request #741 from rc/plot-mass-condition-numbers
script/plot_condition_numbers.py: add smass, vmass types to –matrix option
use choices in –matrix
remove useless dw_laplace coefficient in main()
script/plot_condition_numbers.py: remove order_fix in main()
script/plot_condition_numbers.py: new –output-dir, –no-show options
script/plot_condition_numbers.py: tweak plot parameters in main()
merge pull request #734 from rc/resview-sfepy-h5-no-steps
support sfepy HDF5 meshes with no time steps in read_mesh() - new add_mat_id_to_grid()
update XDMF support in read_mesh() for current meshio, fix 2D meshes
change add_mat_id_to_grid() argument to cell_groups, update read_mesh()
determine default –position-vector from mesh bounding box in pv_plot()
set –position-vector default to None in main()
fixes placement of plots for non-3D meshes
merge pull request #742 from rc/create-faq, closes #413, #706
new doc/faq.rst
docs: link faq.rst in index.rst
docs: add faq.rst to documentation.rst contents
merge pull request #744 from vlukes/update_faq
new advice: use msh22 instead of msh4
merge pull request #747 from rc/fix-plot-mesh-3d
script/plot_mesh.py: do not scale axis in 3D - fixes main() for current matplotlib (3.4.3)
merge pull request #750 from vlukes/multiproc_recovery
update multiproc_proc module: import Pool
new parallel recovery of multiple microstructures
merge pull request #748 from rc/update-faq
docs: add examples of regions by functions (imperative API) into FAQ
docs: add visualization of various FEM-related information into FAQ
docs: fix cell region definition in FAQ
docs: add PYTHONPATH setting for inplace builds into FAQ
merge pull request #751 from flothesof/master
“dry water” flow example
merge pull request #752 from vlukes/reinit_homogenization_engine
allow to reinitialize the homogenization engine
merge pull request #753 from rc/pass-kwargs-conf-to-auto-solver
respect keyword arguments in ‘auto’ solvers - pass kwargs from AutoFallbackSolver.__new__() to use_first_available()
fix AutoFallbackSolver.__new__() to use the original solver configuration
merge pull request #754 from vlukes/resview_streamlines
new streamlines plotting
new option for the XY plane view
update visualization parameters in docstring
relabel option
merge pull request #749 from zitkat/dg-multiple-limiters
Allow multiple limiters for multiple fields.
Fix sfepy imports and remove hardcoded verbose flag.
merge pull request #755 from rc/resview-fix-streamlines
resview.py: fix streamline vectors name in pv_plot()
resview.py: use sphere streamlines source in 3D in pv_plot()
merge pull request #756 from vlukes/resview_gallery
update scalar bars positioning and range
update files caching
default glyphs for vector fields, new empty black field
use resview for gallery generation
adjustment of some gallery plots
from 2021.2 to 2021.3¶
merge pull request #709 from vlukes/volume_surface_terms
update term integration: guess integration from region.kind
update terms: unify ev_/dw_ volume/surface terms
update examples, tests, etc.: new term names
update terms: unify dw_volume/surface_dot terms
update examples, tests, etc.: dw_dot
new compatibility file: allow for old term names
rename term: d_region –> ev_volume
update term docstrings: cal{D} stands for a volume or surface domain
unify multilinear terms
update Develeoper Guide
fix User’s Guide
merge pull request #711 from rc/volume-surface-terms-follow-up
docs: use only unified volume/surface terms in users’ guide
fix docstring of poisson_functions.py example
use dw_dot and dw_integrate in interactive examples
merge pull request #710 from vlukes/rename_d_terms
rename evaluation terms starting with d_ to ev_
update user’s guide: Term Overview
rename term: ev_sd_volume_dot to ev_sd_dot
merge pull request #714 from rc/evp-solvers-fixes
fix QuadraticEVPSolver.__init__() for no solver in conf (use default)
fix MatlabEigenvalueSolver.__call__() for None value of eigenvectors arg
merge pull request #716 from livoire13/example-interactive-iga
new iga-interactive example
merge pull request #715 from rc/web-update-citing
web: update citing information
web: update related projects
web: improve plain text citation
merge pull request #718 from rc/update-test-install
fix imperative_burgers_1D.py for unified surface/volume terms - use Term.new() in main()
imperative_burgers_1D.py: new –output-dir, –plot options - new parse_args(), update main()
laplace_iga_interactive.py: rename –output_dir option to –output-dir
test_install.py: test laplace_iga_interactive.py, imperative_burgers_1D.py
merge pull request #719 from vlukes/fix_evp_corrector
fix TCorrectorsViaPressureEVP.setup_equations()
merge pull request #721 from rc/fix-fill-in-message
fix fill-in message in Equations.create_matrix_graph(), Mesh.create_conn_graph()
merge pull request #724 from rc/include-nls-tolerances
include tolerances in error checking in conv_test() - fixes ‘or’ eps mode with eps_a == 0.0 and zero initial residual
merge pull request #725 from vlukes/fix_resview fix resview
fix format
fix colorbar position
merge pull request #726 from rc/resview-auto-factor
resview.py: allow automatic percentage-based scaling factor in pv_plot() - update parse_options() for ‘%’ character
resview.py: update help message and docstring
resview.py: use sentences in docstring, facilitate copy/paste of examples
resview.py: fix factor calculation in pv_plot()
resview.py: report scaling factor in pv_plot()
merge pull request #727 from rc/resview-sfepy-h5
resview.py: new make_cells_from_conn(), used in read_mesh()
resview.py: support custom sfepy .h5, .h5x formats in read_mesh()
support h5x format in Problem.setup_output()
from 2021.1 to 2021.2¶
merge pull request #680 from vlukes/update_doc
new example application
add supporting project
merge pull request #681 from vlukes/new_example_app
new example application
merge pull request #678 from rc/remove-med-mesh-files
remove unused meshes/various_formats/{med_2d_tri_quad.med, med_3d_tet_hex.med}
update filename_meshes in tests/test_meshio.py
merge pull request #682 from vlukes/new_sd_term
d_sd_div_grad: only one optional material paremeter
update from_term_arg(): allow for (ndarray, arg_name) arguments
new SDPiezoCouplingTerm(ETermBase) sensitivity term
new tests of sensitivity terms
merge pull request #683 from vlukes/make_de_convect_evaluable
update multilinear terms: make de_convect evaluable
update sensitivity tests: enable test of convect term
update docstring of de_convect term
merge pull request #684 from vlukes/new_d_sd_surface_ltr
fix geme_mulAVSB3py() for calculating over all cells
new sensitivity term: SDLinearTractionTerm
update tests to check SDLinearTractionTerm
fix formating
update docstring for SDLinearTractionTerm() and rename: nel, nqp -> n_el, n_qp
merge pull request #690 from rc/no-mat-update-in-init-time
do not update materials in Problem.init_time() - allows calling Problem.evaluate() in material update functions in time zero with ‘quasistatic’ set to False
update comments in Problem.solve()
merge pull request #692 from rc/fix-saving-animations, closes #266
update Viewer.encode_animation() for current ffmpeg (4.2.4)
postproc.py: update –ffmpeg-options default, update docstring
docs: update postproc.py help message in users guide
merge pull request #694 from vlukes/new_example_application
new example application
merge pull request #695 from rc/link-example-applications
docs: link example application in index.rst, remove applications section
merge pull request #696 from rc/fix-numpy-indexing-warning
fix numpy future warning in TransformToPlane.tensor_plane_stress() - using a non-tuple sequence for multidimensional indexing
merge pull request #697 from rc/revisit-facet-orientations
describe quad face orientation groups in facets.py docstring
add missing permutations in GeometryElement.get_conn_permutations()
permute common quad face in _gen_common_data(), new _permute_quad_face()
all keys from _quad_ori_groups in sfepy.discrete.fem.facets are tested
update Test.test_continuity(), .test_gradients()
stop after all possible orientations were tested in _gen_common_data()
new _get_possible_oris()
merge pull request #698 from rc/bernstein-basis-new-set-dofs
new BernsteinTensorProductPolySpace
new .__init__(), ._define_nodes(), _eval_base()
check shape of quadrature coordinates in PolySpace.eval_base()
new local argument of VolumeField.get_econn(), create missing surface data
move global basis functions from H1NodalMixin to new GlobalNodalLikeBasis
move ._setup_facet_orientations(), ._setup_edge_dofs(), ._setup_face_dofs(), ._setup_facet_dofs(), ._setup_bubble_dofs()
new H1BernsteinVolumeField, H1BernsteinSurfaceField (WIP)
new H1BernsteinVolumeField.create_basis_context() - same “hack” as in H1HierarchicVolumeField
new local argument of IGField.get_econn()
split/fix IGField.set_dofs(), new Field.set_dofs()
split IGField.set_dofs() into new IGField.get_surface_basis() (IGField- specific) and project_to_facets() (general)
fixes wrong shape of projected function return value
Field.set_dofs() calls project_to_facets()
new GlobalNodalLikeBasis.get_surface_basis()
Field.set_dofs() works with H1BernsteinVolumeField
update H1NodalMixin.set_dofs(), H1HierarchicVolumeField.set_dofs()
according to Field.set_dofs()
update tests/test_poly_spaces.py for Bernstein basis
update _gen_common_data(), test_partition_of_unity(), test_continuity()
new define() in sinbc.py example, update docstring
merge pull request #699 from vlukes/material_shape_update
update materials: allow for (1, N, M) material shape
update terms: replace FMF_SetCell() by FMF_SetCellX1() for material arrays
update piezo term
modify examples to use the newly allowed material shape
update users guide
merge pull request #700 from vlukes/const_material
update material functions
update CMappings
new FMF_PtrCellX1() macro
new make_full_mat_array(): (1, nqp, n, m) -> (nel, nqp, n, m)
update terms
rename and move make_full_mat_array() -> Term.tile_mat()
merge pull request #701 from rc/bernstein-basis-simplex-naive
new BernsteinSimplexPolySpace (naive implementation)
new .__init__(), ._define_nodes(), ._get_barycentric(), _eval_base()
clean up BernsteinTensorProductPolySpace._eval_base()
update tests/test_poly_spaces.py for simplex Bernstein basis
update _gen_common_data(), test_partition_of_unity()
merge pull request #702 from rc/constant-materials-small-fixes
use single cell dummy material in DotProductVolumeTerm.get_fargs()
fix float comparison in PhysicalQPs.get_shape()
merge pull request #703 from vlukes/fix_d_sd_div_grad
fix opt_material in SDDivGradTerm
merge pull request #704 from vlukes/update_coefs_base
update CoefMN.set_variables_default()
merge pull request #705 from rc/fix-more-c-funs-for-const-mats
fix d_of_ns_min_grad() for constant materials
fix dw_st_grad_div() for constant materials
fix actBfT(), sym2nonsym() for constant materials
from 2020.4 to 2021.1¶
merge pull request #664 from vlukes/update_coefs_base
update CoefNN: allow different dimensions for row and column
rename CoefNN to CoefMN
merge pull request #665 from vlukes/update_coefs_phono
fix volumes in DensityVolumeInfo class
merge pull request #668 from rc/multilinear-terms, closes #666
new sfepy/terms/terms_multilinear.py with ETermBase and multilinear terms (see git log)
implemented terms: de_volume_integrate, de_laplace, de_volume_dot, de_surface_dot, de_s_dot_mgrad_s, de_non_penetration_p, de_div_grad, de_convect, de_div, de_stokes, de_lin_elastic, de_cauchy_stress
docs: add multi-linear terms section to developer guide (WIP)
remove tests/test_input_stokes_slip_bc_penalty.py
script/gen_gallery.py: remove stokes_slip_bc_penalty.py custom visualization
script/gen_term_table.py: make new section for multi-linear terms - update typeset_term_tables()
docs: add multi-linear terms section to terms overview, explain de prefix
sync test_stokes_slip_bc() with stokes_slip_bc.py example
merge pull request #675 from rc/fix-term-table
script/gen_term_table.py: fix typeset_term_tables() (de_* terms twice)
merge pull request #671 from rc/propagate-ebcs-via-epbcs
propagate ebcs via epbcs in EquationMap.map_equations()
simplify some expressions in EquationMap.map_equations()
merge pull request #676 from antonykamp/374-doc-link-terms-example - closes #374
get term-example dict, generate links
Added omits, edited reference style
shorten long term argument names to allow line breaks in term table
from 2020.3 to 2020.4¶
merge pull request #648 from rc/fix-mat-init-msg
fix error message in Material.__init__()
merge pull request #650 from vlukes/update_homog_app
add ‘define_args’ argument to get_homog_coefs_nonlinear()
optional multiplier in updating_coors structure
new ‘id’ identifier in micro_states
merge pull request #652 from rc/fix-inline-defs, closes #651
mark private inline functions in mesh.c with static keyword - mark _det3x3(), _tri_area(), _aux_hex()
merge pull request #654 from heczis/add_ogden_term
Add Ogden term
merge pull request #656 from rc/resview-warp-scalar
resview.py: support warp by scalar in pv_plot()
merge pull request #658 from rc/plot-cmesh-label-local-1d
improve 1D mesh entities label placement in label_local_entities()
merge pull request #660 from vlukes/fix_splinebox
fix splinebox - Python3 related issue
merge pull request #661 from vlukes/fix_homog_app
fix HomogenizationApp: Python3 related issue
merge pull request #662 from rc/serendipity-basis
new SerendipityTensorProductPolySpace
new H1SNodalVolumeField, H1SNodalSurfaceField
new H1SNodalVolumeField.create_basis_context() - same “hack” as in H1HierarchicVolumeField
update test_continuity() for serendipity basis
new test_partition_of_unity() in tests/test_poly_spaces.py - tests lagrange, serendipity bases
new script/gen_serendipity_basis.py
new sfepy/discrete/fem/_serendipity.py, generated by script/gen_serendipity_basis.py
clean up sfepy/discrete/fem/poly_spaces.py
limit 3_8 serendipity basis order to 2 in _gen_common_data()
update docstring of tests/test_poly_spaces.py, remove obsolete information
from 2020.2 to 2020.3¶
merge pull request #625 from vlukes/mesh_write_binary
update meshio: pass options in kwargs to meshio library
update mesh conversion script: write mesh in ascii format
merge pull request #626 from rc/fix-elastodynamics-docstring, closes #598
fix equation in docstring of elastodynamic.py example
merge pull request #582 from vlukes/pyvista
new script for visualisations using pyvista
update requirements: pyvista
update users_guide
add pyvista to instalation requirements
update names in installation docs
merge pull request #634 from vlukes/fix_web
various fixes in web doc
merge pull request #635 from vlukes/mumps5.2
update mumps_struc_c for v5.2
absolute import
merge pull request #637 from vlukes/example_bd2b
new example application
merge pull request #638 from vlukes/update_web
links to sfepy_examples: http –> https
merge pull request #639 from heczis/add_gen_yeoh_term
Add generalized Yeoh hyperelastic term (total Lagrangian formulation)
Add example for generalized Yeoh term
merge pull request #640 from vlukes/meshio_file_format_variants
fix meshio interface to accept ascii/binary file format variants
check meshio version, ‘binary’ argument in write() function from v4.0.3
merge pull request #641 from vlukes/fix_meshio
fix #640
merge pull request #643 from rc/get-virtual-dof-conn
update fieldvariable.get_dof_conn() for no primary variable
from 2020.1 to 2020.2¶
merge pull request #589 from heczis/fix_meshio_import
Fix import from meshio
merge pull request #590 from rc/fix-meshio-optional-formats
fix update_supported_formats() to skip optional meshio formats
fix test_read_meshes() to initialize self.meshes and catch read failures
docs: mention installation of meshio dependencies
merge pull request #588 from vlukes/new_web_look
update doc web pages: use sphinx-rtd-theme
drop download.php, link to github releases
use new sfepy logo
web: update gen_gallery.py, use os.path.splitext() to remove suffix
merge branch ‘fix-xyz-mesh-io’
fix xyzmeshio.read() for single entity meshes
merge pull request #591 from vlukes/update_web
web: fix css file
new example application
merge pull request #592 from bubulk/docker-doc
Add simple mention of docker images to installation doc.
merge pull request #594 from zitkat/dg-sfepy-integration
Allow term arguments to be callables.
Add refine for 1D meshes to FEDomain
Ensure propagation of verbose parameter to: * materials update * equation time_update
Override C implementation of mesh_get_facet_normals for 1D mesh.
Rework propagating verbose flag in problem.py: * use self.conf.get instead of get_default_attr * use default values of called methods
Add cell groups treatment to refine for 1D mesh.
merge pull request #599 from rc/docs-problem-description-functions
docs: add problem description functions examples to users guide
merge pull request #596 from zitkat/dg-sfepy-bc-integration
Add mechanism for treating DG BC conditions:
new syntax dgebc and dgepbc for problem description file
new classes and mechanism for parsing BCs including gradient
specific evaluation in map_equations method
merge pull request #600 from vlukes/fix_vtk_1d
fix saving 1D meshes in vtk and vtu formats
merge pull request #595 from rc/gc-hom-engine
force garbage collection (free memory) in HomogenizationWorker.__call__()
merge pull request #602 from vlukes/fix_test_region
fix test_regions: test only existing cell and vertex groups
merge pull request #603 from vlukes/fix_meshio_read_data, closes #601
fix meshio read_data()
merge pull request #604 from rc/gc-run-tests
force garbage collection (free memory) after each test file in run_tests()
merge pull request #611 from zitkat/i610, closes #610
Force nm.int64 in nm.prod in Equations.create_matrix_graph to prevent overflow on win64 platform.
merge pull request #606 from rc/simplify-gitignore
simplify .gitignore - add new non-python files with ‘git add -f’
merge pull request #609 from zitkat/mumps-libname, closes #608
Add fallback to lib*.dll name for loading mumps on win32.
merge pull request #613 from vlukes/fix_coefs
fix saving coefficients
merge pull request #614 from vlukes/fix_meshio_cell_types, closes #607
fix meshio cell_types
update documentation of Preprocessing
merge pull request #593 from zitkat/gmshio-thesecond
Add custom GmshIO class to enable reading and writing of ElementNodeData: * includes reading multiple time steps * omits “gmsh:ref” data to make working with gmsh comfortable
new file_format application option
add gmsh-dg variant description to _supported_formats
use standard vertex and cell group names in MeshioLibIO.read_data()
merge pull request #616 from rc/fix-mesh-generator-scripts
move suffix check from Problem.setup_output() to new check_format_suffix()
script/blockgen.py: check format and suffix, update, fix for current MeshIO
script/cylindergen.py: check format and suffix, update, fix for current MeshIO
merge pull request #618 from vlukes/update_ceofs_phonoic
update coefs_phononic: allow for more general usage
merge pull request #620 from rc/misc-fixes
fix plot_edges() for 1D
move time stamping in Timer.start(), .stop() closer to measured code
merge pull request #621 from rc/guard-memory-fem-mapping
new raise_if_too_large()
guard memory use in VolumeMapping.get_mapping()
CI: add psutil to test environments
new Config.refmap_memory_factor(), update site_cfg_template.py
new PSUTIL_MIN_VERSION in sfepy/version.py, add psutil as optional to setup.py
docs: document optional psutil requirement
merge pull request #619 from rc/speed-up-set-dofs
major speed up by not calling hstack() on Field.get_dofs_in_region() results - update EquationMap.map_equations(), H1NodalMixin.set_dofs(), IGField.set_dofs(), FieldVariable._get_setter()
merge pull request #612 from zitkat/dg-method-main
discontinuous Galerkin method implementation and examples (see git log)
from 2019.4 to 2020.1¶
merge branch ‘dispersion-misc-updates’
dispersion_analysis.py: allow custom save_eigenvectors()
update read_log() for logs prior to int-log-labels branch merge
dispersion_analysis.py: increase log precision to .12e
merge pull request #571 from vlukes/fix_trace_normals
fix dw_surface_dot term: nvec orient. - outwards to the parent region of the virtual variable
merge pull request #575 from rc/fix-splinebox-python-3.7
fix argument type in SplineRegion2D.create_spb() - fixes Travis CI failure for Python 3.7, numpy-1.18.1
merge pull request #574 from rc/docs-update-space-def, closes #572
docs: update function space definition
merge branch ‘fix-comparison’
fix comparison operator in NurbsPatch.elevate()
merge pull request #577 from bubulk/multiprocessing-spawn
Update dirty fix for multiprocessing with default ‘spawn’ method.
merge branch ‘fix-read-log’
fix read_log() for empty log group
merge pull request #579 from rc/drop-python-2.7-support
CI: remove Python 2.7
docs: update installation instructions (drop Python 2.7 support)
remove PysparseEigenvalueSolver (Pytnon 2.7 only), update docs, tests, setup.py
merge branch ‘fix-slepc-eigenvectors’
fix eigenvectors returned by eig.slepc - fix SLEPcEigenvalueSolver.__call__()
merge branch ‘dispersion-dict-pars’
add allow_tuple, free_word arguments to dict_from_string()
new apply_units_to_pars()
dispersion_analysis.py: replace apply_units() by apply_units_to_pars() - new pars_kinds dict - update define() for parameters in Struct
dispersion_analysis.py: reorder definitions
merge pull request #581 from rc/homogenized-coefs-dtype
force dtype in {CoefNN, CoefN, CoefOne}.set_variables_default() - fixes numpy casting TypeError when adding inplace a complex128 array to a float64 one
merge pull request #580 from vlukes/meshio, closes #460
use meshio to read/write mesh files
meshio: update examples
meshio: update tests
fix numpy.savetxt() issue, see https://github.com/numpy/numpy/issues/10018
fix meshes to pass meshio tests
fix comsol writer: flatten mat_ids arrays
update requirements: meshio
update meshio: new handling with file formats
put ansys_cdb back
update script for mesh conversion and add checks to any_from_filename()
new xdmf3 extension to h5 format
CI: install h5py
CI: install netCDF4
CI: install meshio
update installation instructions: add meshio to requirements
fix vtk_cell_types in postprocessing code
update create_file_source()
new MeshioLibIO.read_data(), ._get_dimension()
change format to double in all medit meshes, fixes precision issues
skip meshio write-failed formats in test_write_read_meshes()
hdf5 + xdmf -> hdf5-xdmf format with .h5x and .xdmf suffixes
merge branch ‘misc-fixes’
fix classifiers in setup.py for Python 3
fix count type in get_log_freqs()
merge pull request #583 from rc/fix-ones-dim-saving
fix saving correctors in OnesDim
merge pull request #586 from vlukes/example_poropiezo
new poropiezo example
merge pull request #587 from rc/web-update-front-pages
web: add PUCGen link
web: update support
web: add link to sfepy docker image
from 2019.3 to 2019.4¶
merge pull request #562 from vlukes/fix_mumps, closes #561
fix MUMPSSolver.__init__(): raise if no mpi4py found
check material arguments in Term.classify_args()
use conf.funmod for default user parameters of terms in Problem.set_equations()
use directly conf in Problem.set_equations() to support define()
merge branch ‘1d-surface-mapping’
add 0_1 geometry to geometry_data, new _get_grid_0_1()
skip 0_1 geometry in CMesh.set_local_entities()
create surface facet also for 1D meshes in FEDomain.__init__()
fix n_facet for 1D cells in Region.update_shape()
update Lagrange polynomial spaces for 0_1 geometry
add 0_1 geometry to quadrature_tables, skip it in test_quadratures()
update SurfaceMapping.get_base(), .get_mapping(), _s_describe() for 0_1 geometry
merge pull request #559 from zitkat/misc-updates
Add Functionize decorator Functionize decorator converts python function to sfepy.discrete.functions.Function obejct
Refactor - more descriptive name for Functionize - make_sfepy_function
Add documentation.
merge pull request #560 from zitkat/gmsh-write
Add write mesh method
method for writing element node data.
Add correct interpolation scheme output.
Add msh output to problem ouput_modes.
Update gmsh data reading
Better dimensions treatment when loading meshes from gmsh format
Format and extend documentation.
merge branch ‘xyz-meshio’
new XYZMeshIO
new test meshes in xyz format (2_4, 3_4 cells)
test XYZMeshIO, skip in test_write_read_meshes()
merge pull request #567 from vlukes/update_homog
update homogenization: avoid reloading coefficients and correctors
update CorrEval class: save corrector values
update CoefOne: allow for “Corr1 + Corr2” as in CoefNN
update get_mesh_coors(): add actual parameter which goes into domain.get_mesh_coors()
new updating procedure in nonlinear homogenization
update nonlinear homog. example
fix CorrEval, CoefSum, CoefEval for multiprocessing evaluation
update CoefOne: make set_variables optional
update ‘nls_iter_hook’: simplify hook management
uppdate get_homog_coefs_nonlinear(): store the actual time step to macro_data
update recover_micro_hook_eps(): indicate the total number of recovered microstructures
fix CoefOne and CorrMiniApp classes
update DeformationGradientTerm: allow to choose actual or undeformed reference configuration
merge branch ‘matlab-evp-solver’
new MatlabEigenvalueSolver
new matlab_eig() in sfepy/solvers/matlab_eig.m
update tests/test_eigenvalue_solvers.py for eig.matlab
merge branch ‘matlab-evp-solver-2’
add method parameter to MatlabEigenvalueSolver
update matlab_eig() for method parameter, simplify logic
merge branch ‘misc-fixes’
fix Term.check_shapes() for spaces in shape specifications
fix geme_invert3x3() for very small cells - fixes zero basis gradient (singular matrix) problem in reference mappings for meshes with very small cells (about 1e-6 edge size in 3D and smaller)
merge branch ‘misc-fixes-2’
fix geme_invert4x4() for very small cells, do not throw error
fix dispersion_analysis.py for single requested eigenvalue
fix collect_term(), create_bnf() for leading minus complex term coefficients - example: -1-1j was parsed as -(1-1j) => -1+1j
fix FEField.get_base() for subdomains and basis transform (iels not in key)
do not save results twice in laplace_refine_interactive.py example
add ‘.’ to sys.path in script/show_mesh_info.py
merge branch ‘misc-fixes-3’
fix FEField.create_mapping() for basis transform and subdomains - WIP - raise exception for surface integration
docs: describe active_only option in users guide
merge pull request #569 from rc/verify-tractions
new verify_tractions() post-process hook in linear_elastic_tractions.py example
merge branch ‘speed-up-log-plotter’
update Log, LogPlotter to send/receive last values only
apply plotting commands in LogPlotter just before redrawing canvas
clear axes in LogPlotter.apply_commands()
pass plot_kwargs to LogPlotter.__call__() and in add_axis command
update log parameters in live_plot.py example
merge branch ‘int-log-labels’
use int labels in Log, simplify LogPlotter by passing keys with commands
test multiple groups and lines in test_log_create(), fix test_log_rw()
merge branch ‘fix-qeigen’
fix Timer import
merge branch ‘misc-fixes-4’
fix barycentric array shape in eval_basis_lagrange() for 0_1 geometry
include matlab_eig.m in source tarball
script/gen_release_notes.py: fix for Python 3, improve formatting
update Msh2MeshIO docstrings, fixes PDF documentation build
fix offset in plot_log() for given groups
from 2019.2 to 2019.3¶
merge branch ‘dispersion-brillouin-stepper’
dispersion_analysis.py: update get_stepper() - new BrillouinStepper
dispersion_analysis.py: allow passing wdir as argument to assemble_matrices()
dispersion_analysis.py: new –stepper option - update process_evp_results(), main()
merge branch ‘python3-fixes’
fix enum() for Python 3
fix load_library() for Python 3 - copy dec() from ioutils.py to avoid sfepy modules dependence
remove btrace_python
get python version from site_cfg.py in Makefile
merge branch ‘test-install-fixes’
add ‘.’ to sys.path in interactive examples
test_install.py: update for changing numpy output - add match_numbers argument to report() - clean up
fix Python 3 string encoding problem in save_raw_bg_logs()
fix band_gaps_rigid.py example for Python 3
merge pull request #545 from vlukes/fix_schur_mumps, closes #544
fix ls.schurs_mumps: ‘bloc’ -> ‘block’, use active dof info
merge branch ‘parallel-timing-stats’
new sfepy/base/timing.py, new Timer
store current dt in Timer
use time.perf_counter() in Timer in Python 3
use Timer in poisson_parallel_interactive.py example to gather timing stats
new call_in_rank_order(), update view_petsc_local()
update stats items in poisson_parallel_interactive.py example
poisson_parallel_interactive.py: new –new-stats option - use call_in_rank_order() to save stats - new save_stats()
poisson_parallel_interactive.py: new –stats option
poisson_parallel_interactive.py: fix save_stats() for Python 3
fix partition_mesh() for Python 3
biot_parallel_interactive.py: new –stats, –new-stats options - use Timer, update analogously to poisson_parallel_interactive.py
merge branch ‘fix-for-mayavi-4.7.1’
fix get_data_ranges()
merge branch ‘dispersion-define-kwargs’
dispersion_analysis.py: new –define-kwargs option, update assemble_matrices()
dispersion_analysis.py: new mesh_eps argument in define(), update docstring
merge branch ‘slepc-evp-solver’
update EigenvalueSolver.__init__() to pass on additional arguments
new SLEPcEigenvalueSolver, init_slepc_args()
update tests/test_eigenvalue_solvers.py for eig.slepc
update installation and development docs
check slepc4py version in setup.py, update sfepy/version.py
allow failing of eig.slepc in tests/test_eigenvalue_solvers.py (optional dep.)
merge branch ‘fix-for-numpydoc-0.9.1’
fix See Also sections for numpydoc-0.9.1
merge branch ‘python3-metaclass-update’
remove Python 2 metaclass attributes from Solver subclasses
add SolverMeta metaclass to Solver in Python 3 compatible way - add to base class only
merge pull request #549 from rc/complex-mat-pars, closes #547
update ConstantFunction, ConstantFunctionByRegion for complex dtype
use previously set variables and materials in Problem.set_equations() - initialize default .conf_variables, .conf_materials in .__init__()
fix Region.get_cell_indices() for no common cells
update tests/test_functions.py to test complex material parameters - update test_material_functions()
merge pull request #554 from vlukes/update_convert_mesh, closes #553
update convert_mesh.py: new ‘3d’ option - write only cells of dimension 3
merge pull request #555 from rc/ci-fix-igakit-download
CI: fix igakit download
merge pull request #550 from rc/fix-site-cfg-template-python-version
fix default python_version in site_cfg_template.py to work with Makefile - update Config.python_version()
update Makefile to inform about site_cfg.py Python version setting
report Python version in setup.py
merge pull request #556 from vlukes/update_convert_mesh
update convert_mesh.py: new ‘–cell-dim’ option, write only cells of a given dim
merge pull request #557 from rc/use-timer, closes #548
allow starting Timer on creation in .__init__(), improve .stop() message
use Timer instead of time.clock(), clean up
remove unused mark_time()
merge pull request #558 from rc/fix-set-bcs-corr, closes #551
do not set problem variables in CorrSetBCS
from 2019.1 to 2019.2¶
merge branch ‘allow-zero-eigs’
new EigenvalueSolver._ret_zero(), use it in standard_call()
update test_eigenvalue_solvers() to test zero eigs
merge branch ‘plot-log-nbins’
allow specifying numbers of bins in x, y axes in plot_log()
script/plot_logs.py: new –nbins option
merge branch ‘misc-updates’
fix output_array_stats() for empty arrays
add velocity, acceleration, dyn_viscosity to apply_unit_multipliers()
allow corrector saving in ShapeDim, OnesDim calls
dispersion_analysis.py: attach options to Problem, clean up
dispersion_analysis.py: allow custom steppers, new get_stepper()
fix/update OnesDim, VolumeFractions for complex variables
merge pull request #504 from bubulk/refine-hanging-segfault
fix mei_next()
merge pull request #506 from vlukes/homog_ts
fix ls.py: avoid conflict between presolve option and presolve() method
update coefs: remove obsolote FM coefs, e.g. CoefFMSymSym can be repalced by TSCoef(CoefSymSym)
update set_conf_solvers(): allow to switch off a solver (e.g. ts in homogenization)
fix TSTime coefficient
merge pull request #510 from vlukes/fix_mat_opt, closes #509
fix material_opt.py: Python 2/3 compatibility issue - zip()
merge pull request #511 from vlukes/fix_mat_opt
fix material_opt.py: Python 2/3 compatibility issue - part II.
merge pull request #512 from rc/fallback-solvers-fixes
fix use_first_available() to catch and report all relevant exceptions
clean up AutoFallbackSolver.__new__()
fix use_first_available() for Python 3
merge pull request #513 from vlukes/update_homog
update homogenization: improved saving/dumping of time variable correctors
remove verify_correctors() in TCorrectorsViaPressureEVP class
fix recover_micro_hook_eps()
update saving homog. correctors, remove ‘dump_*’ options
update homog. examples
reimplement matching periodic planes - allow skew geometries
fix match_plane_by_dir() for 2D meshes
merge pull request #515 from vlukes/fix_mumps
fix mumps solver for “small and dense” matrices
merge pull request #516 from vlukes/nonsym_prestress_term
update LinearPrestressTerm term: allow for non-symmetric form
merge pull request #517 from vlukes/fix_meshio
fix VTKMeshIO.write(): incorrect tensor data shape
merge pull request #519 from rc/docs-update-citing-support
docs: update sfepy citing section
docs: update support section, move past support to a separate page
docs: add article full text link
merge pull request #520 from vlukes/fix_mumps_solver
fix SchurMumps and MUMPSParallelSolver: add memory_relaxation parameter
merge pull request #521 from vlukes/fix_splinebox
fix SplineBox: remove forgotten prints
merge pull request #523 from heczis/fix_scipy_misc
Remove use of scipy.misc
merge pull request #525 from vlukes/update_splinebox
update SplineBox.write_control_net(): use control point values as coordinates
merge pull request #526 from vlukes/find_map
reimplement find_map(): use the scipy.spatial.cKDtree implementation
merge pull request #527 from vlukes/remote_mirror
new remote mirror regions: allow mirror regions with no common vertices
merge pull request #528 from vlukes/mirror_region_misc
update User’s Guide: new mesh_eps option
fix get_conn_key() for mirror integration
update User’s Guide: new mirror region option in the regions definition
merge pull request #529 from rc/trace-regions
update create_bnf(), create_arg_parser() for trace regions
update test_parse_equations()
update Term.setup_formal_args() for trace regions
merge pull request #530 from vlukes/mirror_region_misc
update region.setup_mirror_region() for tr(reg, var) syntax
merge pull request #531 from vlukes/multi_traces
allow for multiple traces
merge pull request #532 from vlukes/fix_traces
fix traces for evaluation mode
merge branch ‘misc-fixes’
fix compute_nodal_normals() for higher order nodes
fix PDESolverApp.call() to obey save_results option
merge pull request #533 from bubulk/ci-update
Updated CI .yml config files.
Temporary disable conda update for Windows.
merge pull request #534 from rc/fix-for-python-3.7
fix Material.iter_terms(), get_data_name() for Python 3.7 (PEP 479)
from 2018.4 to 2019.1¶
merge branch ‘change-complex-output-names’
update convert_complex_output(): convert name into real.name, imag.name
merge branch ‘evp-gallery’
update EVPSolverApp.call() to return (problem, evp) tuple
script/gen_gallery.py: make is_scalar_bar configurable in custom views
script/gen_gallery.py: update generate_images() for eigenvalue problems
script/gen_gallery.py: add custom views for quantum examples
add single line descriptions to quantum examples
merge branch ‘plot-log-swap-axes’
add swap_axes argument to plot_log()
script/plot_logs.py: new –swap-axes option
new draw_data(), update LogPlotter.process_command()
update read_log(), plot_log() for complex data - use draw_data()
improve log header saving with empty axes labels in Log.__init__()
merge branch ‘dispersion-kappa-mode’
dispersion_analysis.py: fix kappa mode - mask non-physical eigenmodes - fix saving eigenvectors
dispersion_analysis.py: support logging standard waves in kappa mode - log plot: use viridis colormap, plot points only
dispersion_analysis.py: update logging in omega mode according to kappa mode
dispersion_analysis.py: allow empty regions
dispersion_analysis.py: output eigenvalue indices
dispersion_analysis.py: update docstring, change default range
new square_1m.mesh, square_2m.mesh for kappa mode
merge branch ‘update-import-file’
explicitly name path to remove in import_file()
merge pull request #493 from vlukes/vtk_point_probe
new VTK point probe
merge pull request #495 from bubulk/tests-fix
Misc ASV data changes.
Removed ASV data.
Add tests for missing igalib module to tests suite.
“Fixed” NamedTemporyryFile behaviour on windows platform.
Fix py27/win64/numpy numpy.array.shape[] type inconsistency (int-long).
Add fix for broken multipocessing implementation on windows platform.
Updated appveryor.yml
Fixed appveryor.yml #2
Updated appveryor.yml (#3): trying to fix IGAkit build.
merge pull request #482 from {vlukes,rc}/update_linear_solvers
update MUMPS solver: consider matrix symmetry, verbose flag, …
update linear direct solvers: new scipy_superlu, scipy_umfpack
new ‘fallback’ option to linear solvers, new ‘auto_direct’ solver
update examples: use fallback option and AutoDirect/AutoIterative solvers
update doc: new “virtual” solver and fallback option
fix ls.schur_mumps: convert matrix to COO format
rename ls_fallback() -> use_first_available(), improve failure reporting
merge pull request #499 from rc/block-compat
add block() from NumPy 1.14.1 to compat.py
use block() in _build_cauchy_strain_op()
merge pull request #500 from rc/surface-integrate-mat-term
new IntegrateSurfaceMatTerm (ev_surface_integrate_mat)
fix docstring of IntegrateMatTerm
new alias of ev_integrate_mat: IntegrateVolumeMatTerm (ev_volume_integrate_mat)
rename IntegrateMatTerm -> IntegrateVolumeMatTerm (remove the alias) - ev_integrate_mat -> ev_volume_integrate_mat
update for ev_volume_integrate_mat
docs: update users guide for ev_volume_integrate_mat
merge pull request #501 from vlukes/update_micmac
update get_correctors_from_file() - allow corrector file names to be different from corrector names
merge pull request #502 from bubulk/fix-c-defs
Removed “obsolete” (and trouble-making) __SDIR__ C pre-processor cmd line defs.
merge branch ‘update-show-authors’
fix script/show_authors.py for unicode, update for several names
merge branch ‘write-log’
new write_log()
move header writing from write_log() to new _write_header() - update Log.__init__()
new tests/test_log.py - new test_log_create(), test_log_rw()
merge branch ‘fix-log-plot-kwargs’
fix saving plot kwargs in Log.__init__()
update test_log_create()
merge branch ‘quadratic-evp’
new sfepy/solvers/qeigen.py: QuadraticEVPSolver, LQuadraticEVPSolver - new standard_call()
update solver_table
update script/gen_solver_table.py
docs: update users guide
docs: sync module index of developer guide with current sources
dispersion_analysis.py: update for LQuadraticEVPSolver
dispersion_analysis.py: move _max_diff_csr() to sfepy/linalg/utils.py
add debug parameter to LQuadraticEVPSolver
move QuadraticEVPSolver into sfepy/solvers/solvers.py
merge branch ‘dispersion-split’
dispersion_analysis.py: move assembling to new assemble_matrices()
dispersion_analysis.py: put coefficients other than omega, kappa into equations
dispersion_analysis.py: remove _le suffix from problem-dependent functions
dispersion_analysis.py: update symmetry checks in assemble_matrices()
merge branch ‘quadratic-evp-status’
update LQuadraticEVPSolver to store matrix info in status in debug mode
update LQuadraticEVPSolver to store solution errors in status in debug mode
merge branch ‘dispersion-generalize’
dispersion_analysis.py: use new build_evp_matrices() - assemble_matrices() returns dict of blocks
dispersion_analysis.py: use new process_eigs()
dispersion_analysis.py: set output_dir to problem in assemble_matrices()
dispersion_analysis.py: set wave vector direction using material function - new get_wdir() - update define(), set_wave_dir(), assemble_matrices()
dispersion_analysis.py: use new setup_n_eigs()
dispersion_analysis.py: update, rename process_eigs() -> process_evp_results()
fix Term.get_str() for complex coefficients
do not check argument count when saving figures in Log.__call__()
merge branch ‘lin-convect2-term’
new LinearConvect2Term (dw_lin_convect2)
merge pull request #503 from vlukes/update_homog
update homog. app - call setup_options() properly
update CorrEval
from 2018.3 to 2018.4¶
merge branch ‘fix-viewer-for-mayavi-4.6.2’, closes #466
fix get_data_ranges() for Mayavi 4.6.2
fix hanging of ClosingHandler.object_button_quit_changed()
merge pull request #468 from vlukes/mumps_update
fix mumps solver and update for mumps library version 5.1.2
merge pull request #467 from vlukes/update_homog_example
update linear_homogenization.py: set option ‘is_linear’ to True for speed-up
merge pull request #470 from bubulk/ci-appveyor, closes #469
Changed ‘version’ statement.
merge pull request #471 from vlukes/coefs_update
update coeffficients.py: saving of complex valued coefficients to .txt
merge pull request #472 from vlukes/fix_splinebox
fix scipy FutureWarning warning in scipy.linalg.lstsq()
merge pull request #473 from vlukes/fix_homperf_example
fix the url of the cited paper in examples/homogenization/perfusion_micro.py
merge pull request #474 from vlukes/new_schur
update mumps solver - rename functions: set_b -> set_rhs, set_A_* -> set_mtx_*
new schur_mumps linear solver
remove old Schur linear solver
update mumps wrapper - fix various library versions
merge pull request #475 from vlukes/update_mumps_sym
update mumps: use a symmetric solver if the matrix is symmetric
merge pull request #480 from vlukes/fix_gallery_link
fix links to the gallery
merge pull request #481 from vlukes/fix_download_page
fix downloads counter after HW upgrade
merge branch ‘fix-refmaps-small-cells’
fix reference mappings in C for cells with very small volumes - update _v_describe(), dq_finite_strain(), dq_tl_finite_strain_surface()
merge branch ‘dispersion-post-processing’
dispersion_analysis.py: support eigenvector post-processing - update save_eigenvectors()
dispersion_analysis.py: new –post-process option - new compute_von_mises(), update define_le()
support complex arrays in output_array_stats()
dispersion_analysis.py: output nonzero stats of matrices
dispersion_analysis.py: new –save-regions option
merge branch ‘example-boundary-fluxes’
new meshes/2d/cross-51-0.34.mesh
update poisson_neumann.py example to compute boundary fluxes, change mesh
merge branch ‘example-material-opt-clean-up’
remove matplotlib backend selection (Log does not need it anymore)
add a rudimentary docstring to material_opt.py example
merge pull request #484 from vlukes/fix_mumps
fix ls.mumps for symmetric complex valued matrices
merge branch ‘log-complex-values’
support str.format() style string formatting in Log - enables logging complex values - update .__init__(), .add_group(), .__call__()
fix default plot_kwargs in Log.add_group()
fix Log.add_group() use in live_plot.py example
use str.format() style format in live_plot.py example
log and plot complex values in live_plot.py example
automatically plot and label real and imaginary parts in LogPlotter - the imaginary part line has alpha reduced to one half of the real part - update Log.plot_data(), LogPlotter.process_command()
merge pull request #485 from lokik/parse_conf
Allow empty dict in dict_from_string
parse_conf grammar improvments
Code cleaning
merge branch ‘evp-solver-app’, closes #479
new EVPSolverApp, based on SchroedingerApp
simple.py: update for EVPSolverApp
tweak EVPSolverApp output
update examples/quantum/ for EVPSolverApp - new get_exact() in examples - new report_eigs() in quantum_common.py
add usage examples to quantum_common.py example
remove schroedinger.py - quantum examples can be run using simple.py
remove sfepy/physics/ - SchroedingerApp obsoleted by EVPSolverApp
update setup.py files
update sfepy-run
update test_install.py
docs: update for no schroedinger.py and sfepy/physics/
preserve dtype in EVPSolverApp.make_full()
docs: sync module index of developer guide with current sources
add rudimentary docstrings to quantum examples
use short syntax in quantum_common.py, replace eig.pysparse with eig.scipy
docs: update Pysparse description
update solve_pde() for EVPSolverApp, support status arg in EVPSolverApp.call()
new tests/test_input_{boron,hydrogen,oscillator,well}.py
merge branch ‘fix-extend-cell-data’
fix extend_cell_data() for complex values
merge pull request #488 from rc/mumps-parallel-check-main-scope
do not execute code in ls_mumps_parallel.py on import - add main scope check
merge branch ‘update-plot-mesh’
update text alignment in label_global_entities(), label_local_entities()
script/plot_mesh.py: new –{vertex,edge,face,cell,wireframe}-opts options
script/plot_mesh.py: new –no-axes, –no-show, figname options
merge pull request #489 from rc/http-to-https
docs: http -> https in sfepy-related links
merge pull request #490 from heczis/update_docstring
Update example in the docstring of Problem.create_evaluable
merge pull request #492 from vlukes/fix_mumps_presolve
fix presolve() in mumps solver
merge branch ‘allow-n-eigs-none’
allow unspecified n_eigs in EVPSolverApp.solve_eigen_problem()
update saving complex eigs in EVPSolverApp.save_results() for easier loading
split dense and sparse solvers in ScipyEigenvalueSolver - ‘method’ can be {‘eig’, ‘eigh’, ‘eigs’, ‘eigsh’}, default is ‘eigs’ - basic support of n_eigs argument for dense problems
update tests and examples for current ScipyEigenvalueSolver
from 2018.2 to 2018.3¶
merge branch ‘update-contacts’
update ContactTerm.get_fargs() to use field approximation for basis gradient
new ContactInfo.__init__(), .update(), ContactTerm.get_contact_info(), update ContactTerm.get_fargs() to use ContactInfo
update ContactTerm.get_fargs() to return gap function in evaluation mode
update .call_function(), .eval_real()
rename .function() -> .function_weak()
new .integrate(), .function(), .get_eval_shape()
fix surface region case in extend_cell_data()
two_bodies_contact.py: save gap function in new post_process()
fix actual order of tensor product rules in QuadraturePoints
plot_quadrature.py: print info in _get_bqp()
merge branch ‘misc-updates’
new structify()
new triangulate()
script/convert_mesh.py: use triangulate()
merge branch ‘update-term-implementation-docs’
docs: remove NewTerm references from developer guide
docs: update text
docs: describe dw_s_dot_mgrad_s term implementation in developer guide
merge branch ‘fix-vtk-write’
fix tensor reshaping in VTKMeshIO.write() for single cell meshes
merge branch ‘set-variable-from-function’
new FieldVariable.set_from_function()
move FieldVariable.set_from_mesh_vertices()
rename FieldVariable.set_data_from_qp() -> .set_from_qp()
rename Variables.set_data_from_state() -> .set_from_state()
update for renames
test FieldVariable.set_from_qp(), .set_from_function() in test_variables()
shorten FieldVariable.set_from_function()
merge pull request #463 from vlukes/fix_extract_surface
fix extract_surface.py: remove useless semicolon
merge pull request #462 from vlukes/fix_ofn_trunk
fix Problem.setup_output(): allow dots in domain name
merge pull request #464 from vlukes/new_extract_edges
new_extract_edges.py: extract outline edges of a given mesh
update setup.py: add extract_edges.py to aux_scripts list
merge pull request #461 from vlukes/piezo_homog_example
new example - homogenization of a piezoelectric heterogeneous structure
update recover_micro_hook*(): suppress outputs when recovering microstructures
merge pull request #465 from vlukes/update_recovery
update recovery_micro_hook*()
merge branch ‘update-term-for-no-cells’
update Term.evaluate() for no cells in region - do not call term functions
merge branch ‘gen-release-notes’
new script/gen_release_notes.py
docs: update release tasks
add gen_release_notes.py into scripts to install in setup.py
from 2018.1 to 2018.2¶
merge branch ‘new-time-stepping-solvers’
new GeneralizedAlphaTS
fix cache name in ElastodynamicsBaseTS._create_nlst_a()
new VelocityVerletTS
new is_string(), fix IsSave.__call__() for future NumPy
add new solvers to elastodynamic.py example, use save_times option
merge branch ‘update-ntc-links’
update links to NTC web pages
merge branch ‘stokes-wave-terms’
new StokesWaveTerm (dw_stokes_wave), StokesWaveDivTerm (dw_stokes_wave_div)
new expand_basis()
use expand_basis() in terms
merge branch ‘remove-rcm’
remove CloseNodesIterator
remove sfepy/linalg/extmods/
update setup.py, __init__.py in sfepy/linalg/
update FieldVariable.set_from_other() for no CloseNodesIterator
remove tests/test_permutations.py
docs: sync module index of developer guide with current sources
merge branch ‘misc-updates’
update apply_unit_multipliers() for compressibility
fix ScipyIterative.__call__() to use eps_a from configuration options - update for future SciPy (1.1.x, atol argument)
change default eps_a of ScipyIterative
set eps_a of iterative scipy solvers in test_linear_solvers.py
merge branch ‘fix-dw_lin_elastic_iso’
simplify stiffness_from_lame() to consistently add two dimensions
update LinearElasticIsotropicTerm.get_fargs() for current stiffness_from_lame() - fixes wrong material shape in single quadrature point per cell case
update get_pars() in material_nonlinearity.py example
merge pull request #451 from BubuLK/gen-solvers-table, closes #447
add gen_solver_table extension.
add preliminary version of gen_solver_table.py
updated ‘Solvers’ section in users guide. Changed “SfePy” typography according to (updated) install guide…
add solver_table.rst (gen_solver_table.py output) to .gitignore.
added generated solver_table (per-partes) to solvers section.
update/fix docstrings of time-stepping solvers for solver table
update docstrings of nonlinear solvers for solver table
update docstrings of eigenvalue problem solvers for solver table
docs: update introductory paragraphs of solver descriptions in users guide
add link to the corresponding solver class documentation.
merge branch ‘remove-google-analytics’
remove google analytics code
merge branch ‘fix-orient-small-cells’
fix orient_elements() for cells with very small volumes
merge branch ‘fix-allow-empty-regions’
fix Region.finalize() to set .is_empty also for non-cell regions
update Region.finalize() to check for emptiness in any case
update test_operators()
merge branch ‘cache-refcoors-in-probes’
reuse reference coordinates in probes if possible - new Probe.get_actual_cache(), update .__init__(), .probe()
share geometry in probes in time_poisson_interactive.py - update gen_lines()
add docstring to Probe.get_actual_cache(), clean up
clean up time_poisson_interactive.py
rename gen_lines() -> gen_probes()
show the last figure with –show option
merge pull request #452 from vlukes/new_mumps
MUMPS linear solver: new wrapper for C library using ctypes
update installation instructions
merge branch ‘dispersion-analysis3’
dispersion_analysis.py: new –no-show option
dispersion_analysis.py: quote command line in saved options
dispersion_analysis.py: free unused memory after each step - allows running several examples in parallel without hogging memory
dispersion_analysis.py: support custom standard waves logs - new save_materials_le(), get_std_wave_fun_le()
dispersion_analysis.py: update docstring, update defaults for –range option
add show_legends argument to plot_log(), Log.__init__(), update .plot_data()
script/plot_logs.py: new –no-legends option
dispersion_analysis.py: new –no-legends option
dispersion_analysis.py: fix eigensolver calls for all eigenvalues case
merge pull request #457 from vlukes/upadte_micro_recovery
update recover_micro_hook_eps()
merge pull request #458 from lokik/mmaster
fix in script/gen_iga_patch.py
from 2017.4 to 2018.1¶
merge branch ‘fix-vc++-9-compilation’
fix for Visual C++ for Python 9.0
merge branch ‘fix-mtx-comparison’
fix matrix comparisons for in-place changes - use sha1 hash instead of only id
initialize .mtx_digest in LinearSolver.__init__()
new _get_cs_matrix_hash(), _is_new_matrix()
fix ScipyDirect, PyAMGSolver, PETScKrylovSolver
update PyAMGKrylovSolver
fix _is_new_matrix() for non-CSR matrices (e.g. PETSc.Mat)
merge branch ‘petsc-ls-options’
allow setting additional PETSc options in PETScKrylovSolver
update biot_short_syntax.py example
merge branch ‘force-reuse-ls-option’
new force_reuse option of PyAMGSolver, PETScKrylovSolver
update _is_new_matrix()
allow reusing solver objects without checking matrix digests
new test_ls_reuse() in tests/test_linear_solvers.py
fix linear solver call in poisson_parallel_interactive.py example
merge pull request #441 from vlukes/fix_recovery
fix recover_micro_hook_eps()
merge branch ‘reimplement-advect-div-free-term’
new ScalarDotMGradScalarTerm (dw_s_dot_mgrad_s)
subclass AdvectDivFreeTerm from ScalarDotMGradScalarTerm, update docstring
merge branch ‘dispersion-analysis2’
dispersion_analysis.py: new –conf option for alternative problem descriptions
new apply_units_le(), set_wave_dir_le()
rename define() -> define_le()
dispersion_analysis.py: eliminate zeros in matrices
merge branch ‘fix-self-contacts’
fix evaluateContactConstraints() for self-contacts
turn on global search in ContactTerm.get_fargs()
merge branch ‘numpy-1.14.0-fixes’
fix einsum() call in add_eas_dofs()
fix transform_basis(), workaround for NumPy 1.14.0
use _cmp() in test_consistent_sets() to fix float comparison
merge pull request #444 from vlukes/mumps_solver
new interface to MUMPS linear solver
update User’s Guide: MUMPS linear solver
fix Solver.process_conf()
merge pull request #443 from heczis/add_hyper_example
Add new interactive hyperelastic example
merge pull request #446 from rc/rewrite-time-stepping-add-dynamics
set initial conditions of parameter variables using setter functions
update Variables.setup_initial_conditions()
new FieldVariable._get_setter()
update FieldVariable.time_update() for ._get_setter()
new ZeroTerm (dw_zero)
update TimeSteppingSolver arguments
new examples/linear_elasticity/elastodynamic.py + test
new NewmarkTS
set quasistatic option of default ts_conf in Problem.set_conf_solvers()
update Problem.get_time_solver(), NewmarkTS.__init__() for context argument
new output_array_stats()
update TimeSteppingSolver to have a generic interface
update TimeSteppingSolver.__init__(), .__call__() signatures
remove .init_time()
update PDESolverApp.call() for generic interface (WIP)
new init_fun(), prestep_fun(), poststep_fun()
remove init_hook(), step_hook()
update StationarySolver for generic interface
update PDESolverApp.call() for active_only, new get_vec(), set_state() (WIP)
update PDESolverApp.call(): presolve, update init_fun() to return vector (WIP)
update SimpleTimeSteppingSolver for generic interface
new .solve_step0()
remove .init_time(), .solve_step()
update SimpleTimeSteppingSolver to be base for AdaptiveTimeSteppingSolver
new .solve_step(), .output_step_info()
update AdaptiveTimeSteppingSolver for generic interface
adapt_fun in options has to be a function, not a function name string
update .solve_step()
remove .__call__()
new .output_step_info()
update adapt_time_step()
update VariableTimeStepper for current AdaptiveTimeSteppingSolver
allow setting current step in .set_step()
update .advance(), .iter_from_current()
new .iter_from()
fix Equations.time_update() for no active_only and changing EBC DOFs - update Problem.update_equations()
fix error reporting in test_term_call_modes()
update extract_time_history() to use actual step times
update linear_elastic_damping.py example for current TS solvers - use HDF5 for output
update balloon.py example to use ts.adaptive
update adapt_time_step() docstring
update laplace_time_ebcs.py example for current TS solvers
new standard_ts_call(), decorate .__call__() of TS solvers
fix FieldVariable.__init__() to initialize .history attribute
use quasistatic TimeStepper in StationarySolver.__init__()
add status argument to TimeSteppingSolver.__init__() for consistence
move prepare_save_data(), prepare_matrix() into problem.py
move get_initial_state() -> Problem.get_initial_state()
move time-stepping solver management from PDESolverApp to Problem
update PDESolverApp.call()
replace Problem.nls with Problem.solver - a TS solver instance
update .solve()
new .get_tss(), .get_tss_functions(), .get_nls(), .get_ls()
update Problem.__init__(), .reset() .set_equations(), .set_equations_instance(), .set_conf_solvers(), .set_solver(), .try_presolve(), .get_solver(), .is_linear(), .set_linear()
update .init_solvers() - add ts_conf argument
remove .get_time_solver()
new State.get_vec(), .set_vec()
unite BasicEvaluator with LCBCEvaluator in Evaluator, clean up
update Problem.get_evaluator(), PETScParallelEvaluator for Evaluator
update tests to use nls.fun() instead of (Basic)Evaluator
update solve_pde(), PDESolverApp.call() to have status argument
remove nls, ls, ts, auto_solvers arguments of Problem.__init__() - update .from_conf(), .copy(), .create_subproblem()
initialize solver configuration attributes in Problem.__init__()
update Problem.set_solver() to set nonlinear solver functions - new .get_nls_functions()
initialize .ts in Problem.reset(), .set_solver()
update Evaluator to check for LCBCs at run-time (remove .has_lcbc, .mtx_lcbc)
update tests for new solver status handling
remove make_implicit_step()
update SchurGeneralized for no active DOF indices at solver creation time - update SchurComplement parameters initialization
new Problem.block_solve() replacing EquationSequenceSolver - update Problem.solve()
update make_l2_projection_data(), make_h1_projection_data() for current Problem
update tests for current Problem
update (interactive) examples for current Problem
update test_install.py for changed output
update MultiProblem for no active DOF indices at solver creation time
update for not passing time stepper in user argument in Problem.set_equations() - update Term.assign_args(), .time_update(), create_evaluable()
replace prepare_save_data() with new make_is_save() - new IsSave
update is_sequence()
update Problem.get_tss_functions()
update examples for save_times option and time-stepper default verbosity change
docs: update users guide for save_times option
new TimeStepper.set_substep_time(), .restore_step_time()
new BatheTS
simplify NewmarkTS, BatheTS by subclassing new ElastodynamicsBaseTS
docs: update tutorial
docs: update solvers sections in users guide
clean up: move solver related-functions together in Problem
docs: tweak for users guide changes in master
merge branch ‘fix-test-ls-reuse’
update test_ls_reuse() for #446
merge branch ‘remove-petsc-worker’
remove unused sfepy/solvers/petsc_worker.py - see 125d59dd82c0f2e4c88031c7c58e2dfa255c8cf8
update sfepy/solvers/__init__.py
docs: sync module index of developer guide with current sources
merge pull request #448 from vlukes/update_nonlin_homog_example
update Problem.get_evaluator(): allow a user evaluator Class specified in problem options
update nonlinear homog. example: adapt to the altered solvers
merge branch ‘fix-hdf5-saving-only-some-steps’, closes #445
allow saving without step 0 in HDF5MeshIO.write()
update HDF5MeshIO for not saving all steps
new HDF5MeshIO._get_step_group_names()
update .read_times()
update ._get_step_group() .read_data_header() for no step 0
update .read_time_history() for missing steps
merge pull request #449 from heczis/update_interactive_example
update hyperelastic_tl_up_interactive.py example for current Problem
merge branch ‘update-web-docs’
docs: update support section
docs: move (old) featured applications under examples
update script/gen_gallery.py for current Problem
from 2017.3 to 2017.4¶
merge pull request #418 from lokik/python3-compatibility
Python 3 compatibility: region.py
Python 3 compatibility: update_dict_recursively
merge pull request #420 from lokik/master
sfepy.base.parse_conf: fix and test
merge branch ‘contacts’
implements a penalty based contact term
new examples/linear_elasticity/two_bodies_contact2d.py
new sfepy/terms/terms_contact.py - new ContactTerm
allow strings as special material arguments in Term.check_shapes()
new sfepy/mechanics/extmods/__init__.py
new sfepy/mechanics/extmods/contres.{c, h}
new sfepy/mechanics/extmods/ccontres.pyx
new sfepy/mechanics/extmods/setup.py
new get_longest_edge_and_gps() cython function
new get_AABB() cython function
new init_global_search() cython function
new evaluate_contact_constraints() cython function
new assemble_contact_residual_and_stiffness() cython function
update Term.evaluate(), .assemble_to() for sparse vector data
clean up sfepy/base/plotutils.py
fix print_matrix_diff() for matrices in CSC format
update spy(): make dots visible, fix axes limits, do not shift points - with matplotlib 1.5.1
return extra matrix from Term.assemble_to(), do not assemble it there
update Equations, Equation for extra matrices
update Equations.evaluate(), .eval_tangent_matrices()
update Equation.evaluate()
rename two_bodies_contact2d.py -> two_bodies_contact.py
update two_bodies_contact.py for 3D, generate bodies by new gen_two_bodies()
update/fix contres.{c, h} for 3D
update ContactTerm for 3D
add docstring to Term.assemble_to(), clean up
new test for two_bodies_contact.py example
move active DOF treatment from ContactTerm.get_fargs() to Term.assemble_to()
update _test_single_term() for dynamic connectivity terms - test_term_call_modes() tests pass for dw_contact
docs: sync module index of developer guide with current sources
merge branch ‘plot-boundary-quadratures’
script/plot_quadratures.py: new –boundary option, update _get_bqp(), plot_quadrature()
script/plot_quadratures.py: new —show-labels, –print-qp options, new label_points(), update plot_quadrature()
merge pull request #422 from vlukes/update_doc
update users_guide: add links to PyAMG and PETSc documentation
update users_guide: remove ‘ls.petsc_parallel’ section
merge branch ‘solver-context’
update Solver.__init__() and subclasses: add context argument, update LinearSolver.__call__() signature
update Problem.init_solvers() to pass self as context
update linear solvers for context argument
update standard_call(), petsc_call() decorators
update ScipyIterative, PyAMGKrylovSolver, PETScKrylovSolver, SchurGeneralized, MultiProblem
update Oseen for context argument
update setup_precond() in biot_short_syntax.py example for context argument
merge branch ‘embed-shell’
add frame argument to python_shell()
new shell(), ipython_shell()
merge pull request #424 from BubuLK/c-cython-warnings, closes #406
Updated array/pointer cdef to follow new Cython parser conventions (removed Cython warnings).
Removed unused variables definitions.
Replace abs()->fabs().
Updated cmesh.{c,h} explicit casting.
Updated explicit casting (discrete/common).
Updated explicit casting (iga), fixed typo.
Added cython explicit type casting (to remove warnings).
Add “unreachable code” explicit marks () to disable warnings.
Removed duplicated compiler options defines (sfepy_common).
Fixed comparsion bug (from unreachable code).
Cleanup mesh.c explicit type casting.
Updated OS detection defs.
Updated defs/casting according to issue comments.
remove unused variables in C code - closes pull request #423 from vlukes/c_clean_up
resolve remaining warnings
merge branch ‘scikit-umfpack-version’
update _scikit_umfpack_version()
merge pull request #425 from BubuLK/c-compiler-flags
Fixed typo in sfepy_common library macros.
merge branch ‘allow-empty-regions-option’
new allow_empty_regions Problem configuration option, update Problem.from_conf(), .set_regions()
docs: update users guide
merge pull request #428 from BubuLK/Appveyor-IGA
Add IGAkit install/build to Appveyor config.
merge pull request #426 from rc/small-fixes
fix real definition in parse_conf.py, new cmplx definition
initialize time_stats in Newton.__call__()
fix spelling: rezidual -> residual
print time_stats in fixed order in Newton.__call__()
fix LogPlotter.__call__() docstring
merge branch ‘small-fixes-2’
add show_mesh_info.py into scripts to install in setup.py
script/show_mesh_info.py: fix misleading description, show real centre
clean up sfepy/mechanics/units.py
fix density definition in units_of_quantities, more num_prefixes
improve value shape checking, error reporting in H1NodalMixin.set_dofs()
merge branch ‘active-only-option’
new active_only Problem configuration option - update Problem.from_conf()
obey active_only in Problem.copy(), .create_subproblem()
add active_only argument to Problem.evaluate() and related functions
update Problem.create_evaluable(), .eval_equations()
update create_evaluable(), eval_equations(), eval_in_els_and_qp(), assemble_by_blocks()
new Problem.get_ebc_indices()
update PETScParallelEvaluator() for Problem.get_ebc_indices()
fix matrix diagonal in BasicEvaluator.eval_tangent_matrix() for no active_only
fix Problem.solve() for no active_only
fix making full vector in BasicEvaluator for no active_only, fix .eval_residual(), .eval_tangent_matrix()
update PETScParallelEvaluator for apply_ebc_to_matrix() call in BasicEvaluator
fix create_adof_conns(), apply_ebc_to_matrix() for EPBCs
update Problem.get_ebc_indices()
update BasicEvaluator.eval_tangent_matrix()
fix equations in poisson_periodic_boundary_condition.py example
set active_only to False in poisson_periodic_boundary_condition.py example
move apply_ebc_to_matrix() into sfepy/discrete/evaluate.py
update Problem docstring
merge pull request #430 from rc/update-convert-mesh
script/convert_mesh.py: new –2d option
docs: document –2d option in preprocessing section
docs: add data files
docs: mention legacy VTK reader 2D detection feature
fix printing writable mesh formats in for_format()
merge branch ‘fix-poisson_parallel_interactive’
poisson_parallel_interactive.py: fix for moved apply_ebc_to_matrix() - see active-only-option branch
merge pull request #431 from vlukes/new_surface_grad_term
new ev_surface_grad and ev_surface_div terms
merge pull request #432 from vlukes/update_complex_eval_at
update fields.evaluate_at() for evaluating complex fields
new test for fields.evaluate_at()
merge branch ‘small-fixes-3’
output last step KSP stats in PETScNonlinearSolver
fix ANSYSCDBMeshIO for meshes with both tetrahedra and hexahedra
merge pull request #433 from vlukes/save_mesh_per_matid
update mesh conversion: extract cells by material id
update preprocessing tutorial - new “save-per-mat” arugment to conversion script
merge pull request #434 from heczis/abaqus_ax_elm
Add reading of axisymmetric elements to AbaqusMeshIO
merge branch ‘show-mesh-info-euler-ncomp’
script/show_mesh_info.py: show Euler characteristic
script/show_mesh_info.py: show medians of volumes, update formatting
script/show_mesh_info.py: show Euler characteristics of mesh volume and surface
script/show_mesh_info.py: show numbers of volume/surface components
script/show_mesh_info.py: update output formatting
merge pull request #436 from vlukes/new_vtk_probe
new ProbeFromFile class: init VTK probe using a given file
merge pull request #437 from vlukes/recovery_eps
new recover_micro_hook_eps(): recover a real sized microstructure
merge pull request #435 from rc/tetgen-remesh-option
script/convert_mesh.py: new –remesh option
merge pull request #438 from vlukes/update_recovery
update calls of microproblems: pass arguments to define() at the microlevel
fix recover_micro_hook_eps(): fix for incorrect microstructure size
let the code be friedly to pep8
merge branch ‘small-fixes-4’
check that all facets are on surface in SurfaceField._check_region(), improve messages
allow quoting command line items in save_options() - new quote_command_line argument
fix Mesh.create_conn_graph() to obey verbose argument
merge branch ‘dispersion-analysis’
new ElasticWaveTerm (dw_elastic_wave), _build_wave_strain_op()
new ElasticWaveCauchyTerm (dw_elastic_wave_cauchy), _build_cauchy_strain_op()
new which option instead of hard-coded value in ScipyEigenvalueSolver
new examples/linear_elasticity/dispersion_analysis.py
new apply_unit_multipliers()
new lame_from_stiffness(), youngpoisson_from_stiffness()
update test_stiffness_tensors()
update Log, LogPlotter for plots with varying line properties
update Log.__init__(), .add_group(), .plot_data()
update LogPlotter.process_command()
save plot properties header in Log.__init__(), update read_log(), plot_log()
add raw_log_save_name option to BandGaps
new save_raw_bg_logs(), update AcousticBandGapsApp.call() for saving raw logs
update plot_log() for plotting to given list of axes
script/plot_logs.py: update –rc option, update ParseRc to use eval()
values with commas work
update for current plot_log()
improve BandGaps.save_log()
script/plot_logs.py: new –groups option, update plot_log()
fix dense eigh() call in ScipyEigenvalueSolver.__call__()
set accuracy for periodic vertex matching in band_gaps_conf.py
use basic SI units in band_gaps.py example, small updates
use basic SI units in band_gaps_rigid.py example, small updates
update test_install.py for updated units in phononic examples
from 2017.2 to 2017.3¶
merge branch ‘regions-update’
allow ‘-’ in region names - update parsing code + test
fix reading of vertex sets (nodal bcs) in HDF5MeshIO.read_mesh_from_hdf5() - group argument is no longer overwritten
merge pull request #395 from lokik/master
svec (output buffer) argument for variables.strip_state_vector
code lint in discrete/variables
merge branch ‘improve-parallel’
improve information outputs
speed-up assemble_rhs_to_petsc(), assemble_mtx_to_petsc() by removing loops
measure and report global domain/fields setup time in parallel examples
merge pull request #403 from vlukes/homog_mpi
update homog. engine - rearrange functions, define new class HomogenizationWorker
update engine.py to comply pep8
update homog. engine: define numdeps as dict instead of list
new sfepy/base/multiproc_mpi.py - classes and functions for MPI parallelization
update sfepy/base/multiproc.py - unify multiproc. modules
update homog. engine and application for MPI computation
update sfepy/base/multiproc.py and sfepy/homogenization/homogen_app.py to comply pep8
fix test_homogenization_engine.py - new structure of homog. engine
merge branch ‘iterative-ls-precond’
make preconditioners for ScipyIterative solver actually usable - change option precond (a matrix-like) to setup_precond (a callable)
add iteration callback to ScipyIterative, calls user callback if provided
fix PETScKrylovSolver.__call__() for no initial guess
simple.py: allow additional options (to use with PETSc options)
new init_petsc_args(), used in PETScKrylovSolver.__init__()
new Solver.set_field_split()
allow slices in PETScKrylovSolver.set_field_split()
set field split data in Problem.solve()
obey verbose option in ScipyIterative
new examples/multi_physics/biot_short_syntax.py + test
update PETScNonlinearSolver to return same status information as Newton
set manually the solution from the update in case the KSP did not converge
merge branch ‘expand-nodes-node-by-node’, closes #404
arrayize function values in {H1HierarchicVolumeField, H1NodalMixin}.set_dofs()
fix shape for NumPy 1.13.0 in EquationMap.map_equations()
fix shape for NumPy 1.13.0 in FieldVariable.setup_initial_conditions()
update expand_nodes_to_equations() to use node-by-node ordering of DOFs
unify shape of values returned by Field.set_dofs() implementations
update H1HierarchicVolumeField, H1NodalMixin, IGField
update for node-by-node ordering: use (n_nodes, n_components)
update MRLCBCOperator.setup() for node-by-node ordering
update EBC/LCBC functions in examples for node-by-node ordering
update test_ebc_functions() for vector variables
docs: update users guide for node-by-node ordering
merge pull request #407 from BubuLK/doc-tutorial, closes #379, #401
updated tutorial.rst accordint to issue #379.
updated primer.rst
updated linear_elasticity_interactive.py according to tutorial.rst
added sfepy-wrapper label to user_guide.rst.
updated tutorial/installation.rst.
updated tutorial/basic-usage.rst
removed “$” from cli examples.
merge pull request #409 from BubuLK/Sphinx-conf
replaced custom ‘ipython_console_highlighting.py’ with standard one. Corrected IPython console outputs in tutorial.rst.
replaced deprecated pngmath extension with imgmath.
updated conf.py to new LaTeX customization scheme (latex_preamble->latex_elements).
merge branch ‘docs-fix-term-table’, closes #399
force longtable in script/gen_term_table.py
add LaTeX page breaks around tables in script/gen_term_table.py
merge pull request #410 from vlukes/tri_tetra_elements
new option to convert_mesh.py script: ‘-t’ convert quad/hexa elements to tri/tetra
merge branch ‘improve-ls’
add solver name to messages in ScipyIterative.__call__()
reuse KSP instance in PETScKrylovSolver for multiple solves with one matrix
speed-up, especially for direct solver preconditioning
update .__init__(), .__call__()
allow additional options in ScipyIterative
prepare ScipyIterative for future scipy support of both rtol and atol
tweak verbosity levels in ScipyIterative, print number of iterations
fix ScipyDirect to obey presolve option
do not store matrix in ScipyDirect
update PyAMGSolver to use id of matrix for solver reuse check - do not store matrix
remove bit-rotten/obsolete PETScParallelKrylovSolver
update standard_call(), petsc_call() to return number of iterations in status
update ScipyIterative.__call__()
supported where possible, closes #216
return total number of linear solver iterations in status - update Newton, PETScNonlinearSolver
update test_solvers() to report numbers of linear solver iterations
update test_install.py for updated nls status
merge branch ‘fix-for-sympy-1.1’
fix Quantity.__init__() for sympy 1.1
merge pull request #412 from vlukes/homog_mpi
update parallel MPI homogenization - add features for solution of multiscale problems
update get_homog_coefs_nonlinear() for MPI parallel computation
update MPI homogenization - improve efficiency of MPI communication
update multiproc_mpi.py: update classes RemoteDict and RemoteDictMaster, fix typos in logs
rearrange multiprocessing modules
update homog. functions - reaaranged multiprocessing modules
update save_mappings() and get_mappings() - rearranged multiprocessing modules
new simple_homog_mpi solver - allows to run parallel micro-macro coupled simulation
merge branch ‘misc-updates’
improve error message in Term.check_shapes() to include actual shapes
fix PETScNonlinearSolver.__call__() for no SNES.getFunctionNorm() - see https://bitbucket.org/petsc/petsc4py/commits/1ffe3970457cf66c4354ca2d4601852ea06999b5
merge pull request #414 from vlukes/homog_mpi_fix
fix get_homog_coefs_nonlinear() in homogenization/micmac.py - mpi switch
merge branch ‘mesh-entity-volumes’
new mesh_get_volumes() C function - new _det3x3(), _tri_area(), _aux_hex()
new CMesh.get_volumes()
script/show_mesh_info.py: show only names of nodal BCs
script/show_mesh_info.py: new –detailed option, shows entity volumes
update mesh_get_volumes() for approximate bilinear face area computation
new test_entity_volumes() in tests/test_cmesh.py
merge pull request #415 from vlukes/homog_mpi_fix
update homog. engine - replace ‘chunk_size’ option by ‘chunks_per_worker’
update nonlin. homog. example - pep8 code style
update multiproc. code - ‘thread’ in names is obsolete, replaced by ‘proc’
merge branch ‘pyamg-krylov’
allow additional method/solve options in PyAMGSolver, support callbacks - add iteration callback to PyAMGSolver, calls user callback if provided
new PyAMGKrylovSolver - interface to PyAMG Krylov solvers
update tests/test_linear_solvers.py
merge branch ‘petsc-user-precond’
support user-defined preconditioners in PETScKrylovSolver - new setup_precond option
update tests/test_linear_solvers.py
merge pull request #417 from BubuLK/deployment-CI, closes #350
add updated configs for Travis/AppVeyor testing.
changed run_test.py call (ps->cmd).
removed (obsolete) x86 arch to speedup test.
merge branch ‘remove-shaper’
remove obsolete shaper.py
remove obsolete sfepy/optimize/ - remove __init__.py, free_form_def.py, setup.py, shape_optim.py
update setup.py, sfepy-run for no shaper.py
update problem description file transforms
docs: update users guide for no shaper.py
update sfepy/setup.py for no sfepy/optimize/
merge branch ‘update-log-live-plot’, closes #131
use threading in LogPlotter.__call__() to call .poll_draw() - update.poll_draw() to sleep between canvas updates (replaces gobject timeout)
allow plt.tight_layout() failure in LogPlotter.process_command()
update Log.__init__() for no fixed matplotlib backend dependence
update LogPlotter for new sleep argument
update Log for new sleep argument
update live_plot.py example to use aggregate, sleep options, clean up
miscellaneous updates:
docs: sync module index of developer guide with current sources
update version string in get_basic_info() to conform with PEP 440
from 2017.1 to 2017.2¶
merge pull request #369 from rc/fix-variable-history-advance
initialize history of variables in get_initial_state()
update make_implicit_step()
update SimpleTimeSteppingSolver, AdaptiveTimeSteppingSolver
fix Variable.advance() to initialize current step data
merge pull request #370 from heczis/master
remove the unused method Problem.init_variables
merge pull request #368 from vlukes/update_homogen
update: simplified and unified implementation of some homogenized coefficients
fix the homogenization example: perfusion_micro.py
merge pull request #372 from vlukes/fix_material_shape_change
fix changing of the material shape
merge pull request #373 from vlukes/piezo_strain
new PiezoStrainTerm
update piezo-elasticity example
merge pull request #376 from vlukes/fix_truncation
fix: avoid number truncation in region definitions
merge branch ‘docs-main-page’
update support section
remove link to obsolete wiki pages
add link to anaconda installation instructions to main page
merge branch ‘fix-vtk-source-mayavi-4.4’, closes #292
update VTKMeshIO.read_data() to read cell data, small tweaks
fix GenericFileSource._reshape() for single-axis data
fix GenericSequenceFileSource
update .read_common()
remove .create_source()
new .file_changed()
initialize .io in GenericFileSource.__init__()
update create_file_source() to work around a Mayavi 4.4.x issue
merge branch ‘fix-coefs-to-latex’
fix Coefficients._save_dict_latex() for scalars and general data
clean up: raise exception with message
merge pull request #377 from rc/fix-variable-state-data-sharing
fix data copying in Variable.advance() - bad interaction with State
merge pull request #380 from heczis/fix_doc_python3
fix things to be compatible with both python 2 and 3
merge branch ‘term-report-missing-virtual’
new Term.get_str()
use Term.get_str() in Term, Equations
update Term.evaluate() to report missing virtual variable in ‘weak’ mode
merge pull request #383 from vlukes/update_homog_doc
update homogenization examples, add references
merge pull request #385 from vlukes/change_shape_ev_grad
change the shape of the gradient array provided by ‘ev_grad’, now: (n_el, n_qp, dim, n_c)
merge pull request #386 from vlukes/replace_copydata_corr
replace corrector CopyData by the more general one with name CorrEval
merge pull request #388 from vlukes/fix_meshio_msh
fix Msh2MeshIO.read() to discard ‘2_2’ elements
merge pull request #390 from rc/docs-sfepy-at-python-org
docs: update for sfepy(at)python.org
merge pull request #391 from rc/fix-project-by-component
fix project_by_component() for general tensor shape
new test_project_tensors()
merge branch ‘fix-ansys-cdb’
fix ANSYSCDBMeshIO.read(), convert tetras as degenerate hexas to tetras
new look_ahead_line()
update ANSYSCDBMeshIO.read() to determine true number of fields
fixes reading files with wrong nblock/eblock information
update make_format()
fix remapping of nodal bcs in ANSYSCDBMeshIO.read() for qtetras, qhexas
merge branch ‘misc-updates’
copying subclasses of problem
numpy compatibility
problem.make_full_vec accept vec argument.
new Container.__add__(), .__iadd__(), test_container_add()
update Viewer.build_mlab_pipeline() to add mat_id to source if not filtered
merge pull request #375 from {lokik,rc}/save-custom-data-to-hdf5
saving custom structured data to h5 file in problem.save_state
ioutils.enc and ioutils.dec utf strings compatibility
HDF5ContextManager
IGDomain reading and writing from HDF5 file
asserting equality of complex structures
HDF5 reading and writing
faster assert_equals.
default mesh argument for HDF5MeshIo.read()
storing data to hd5 using softlinks.
clean up iga/domain.py, iga/io.py
clean up and reorganize HDF5MeshIO
clean up ioutils.py, reorganize new functions/classes
move assert_equals() into TestCommon.assert_equal(), update
clean up and update test_hdf5_meshio()
merge branch ‘docs-devel-page’
update development tab, new topics section
update copyright info
add more topics to development tab
merge pull request #393 from heczis/fix_generators_next
fix generators’ next method calls in script/gen_gallery.py
fix generators’ next method calls in sfepy/base/log.py
fix generators’ next method calls in sfepy/application/application.py
merge branch ‘band-gaps-ranges’
new get_gap_ranges(), use in BandGaps.__call__()
simplify plot_gap() by using gap_ranges, move text output to plot_gaps() - update AcousticBandGapsApp.plot_band_gaps(), .plot_dispersion(), use tight layout
fix plot resources for matplotlib >= 1.5.1
merge pull request #398 from vlukes/tutorial_preproc
new tutorial: preparing meshes using FreeCAD/OpenSCAD and Gmsh
new “merge” option in convert_mesh.py - remove duplicate vertices
merge pull request #400 from vlukes/update_homog
update homogenization to allow saving “pi” correctors
merge pull request #397 from BubuLK/doc-install, closes #366, #382
updated Install doc: - issue #382 - issue #366 (?) - other misc doc cleanup
doc cleanup - bugfixes - updates according to PR comments - updated sections structure
updated and re-structured install doc
updated Anaconda instructions
add link to conda-forge on downloads page
add link to install doc
add direct link conda-forge SfePy packages
miscellaneous updates:
update mailing lists addresses in release tasks
from 2016.4 to 2017.1¶
merge pull request #355 from heczis/dont_redefine_help
fix redefining help
merge pull request #354 from lokik/master
new numpy version compatibility
merge pull request #359 from heczis/python_cmd_in_test_install
python -> python2 in test_install.py
merge pull request #360 from heczis/logging_in_test_install
use the logging module for output in test_install.py
merge branch ‘fix-data-from-qp-shape’
fix caching in Integrals.get()
fix vertex data reshaping in GenericFileSource.add_data_to_dataset() - new GenericFileSource._reshape()
fix data shape in FieldVariable.set_data_from_qp()
update nodal_stress() in its2D_3.py example
merge pull request #361 from vlukes/fix_doc_splinebox
fix splinebox example - “Mesh parametrization”
merge pull request #362 from vlukes/update_splinebox
update splinebox - parameterization of an arbitrary field
update splinebox.py to pass the pep8 check
new splinebox test - check field parametrization
merge pull request #356 from rc/docs-conda-forge-install
docs: update installation instructions for conda-forge releases
merge branch ‘python-3.6-fixes’
update .travis.yml to test with Python 3.5, 3.6
fix integer division errors in shapes/indices
fix errclear() for Python 3.6, remove useless line from errput()
catch ValueError in Term.call_get_fargs(), .call_function()
fix more integer division errors
merge branch ‘fix-petsc-sub-precond-type’
fix default sub_precond value in PETScKrylovSolver
fix sub_precond argument in parallel examples
report number of iterations in PETScKrylovSolver, PETScParallelKrylovSolver
merge branch ‘fix-integer-divisions’
fix integer division errors
merge branch ‘problem-docstring’
improve active_only description in Problem docstring
describe arguments of Problem.__init__() in class docstring
merge pull request #364 from vc12345679/master
fix bug: “Python.h” Include Path Error - use sysconfig.get_config_var(‘INCLUDEPY’), instead of sys.prefix+’include’+’python’+version, to obtain include path of ‘Python.h’
merge pull request #365 from vlukes/fix_save_regions
fix saving surface regions
miscellaneous updates:
docs: update release tasks
from 2016.3 to 2016.4¶
merge branch ‘fix-lcbc-several-fields’
fix _s_describe() for zero area facets
fix/improve geme_invert3x3(), geme_invert4x4() for singular matrices
fix LCBCOperators.finalize() to keep correct ordering of variables - update _dict_to_di()
new test_stokes_slip_bc() in tests/test_lcbcs.py
merge pull request #343 from ‘rc/debug-on-error’
new debug_on_error()
run_tests.py: rename –debug option to –raise
run_tests.py: new –debug option - run debugger on exception
docs: update for updated options of run_tests.py
update .travis.yml for –raise
new –debug option in top level scripts - update extractor.py, homogen.py, phonon.py, postproc.py, probe.py, schroedinger.py, shaper.py, simple.py
merge branch ‘empty-fe-surface’
update FESurface.__init__() for empty region
update CMapping.describe() for empty region
update FieldVariable.evaluate() for empty region
merge branch ‘non-penetration-penalty-term’
new NonPenetrationPenaltyTerm (dw_non_penetration_p)
new examples/navier_stokes/stokes_slip_bc_penalty.py + test
small tweaks in stokes_slip_bc.py example, reference stokes_slip_bc_penalty.py
parallel support:
update Domain.create_regions() for empty regions - new allow_empty argument
update Mesh.from_region() to preserve nodal BCs
update Region.setup_from_highest() to always succeed when allowed empty
update create_task_dof_maps() for easier debugging of partitioning problems
new save_inter_regions, output_dir arguments
update distribute_fields_dofs()
merge branch ‘parallel-examples-update’
new remove_files_patterns()
new save_options()
poisson_parallel_interactive.py: new –save-inter-regions options, save options
biot_parallel_interactive.py: new –save-inter-regions options, save options
merge pull request #340 from ‘lokik/master’
equations.add_equation method
merge pull request #348 from vlukes/fix_pt_open, closes #342
fix pytables compatibility issue: openFile -> open_file, createGroup -> create_group, …
merge pull request #346 from vlukes/fix_set_coors
fix setting field coordinates for higher order elements
merge pull request #337 from vlukes/update_tests
display the test file numbers and test numbers to get a better view in a debug mode
merge pull request #347 from vlukes/nonsym_biot
new nonsymmetric mode of BiotTerm
merge pull request #349 from rc/fix-biot-ccode
fix op_nonsym_biot()
fix dw_biot_grad() for compiling on windows
merge pull request #351 from rc/he-clean-up
remove obsolete CorrectorsPermeability
fix insert_sub_reqs() for arbitrary order of leaf requirements
simplify insert_sub_reqs() - remove too strict circular dependency check
new tests/test_homogenization_engine.py: new test_dependencies()
merge branch ‘hanging-nodes’
conflicts: sfepy/discrete/fem/fields_base.py
support basis transforms in FEField, VolumeMapping, PolySpace
new FEField.basis_transform attribute, FEField.set_basis_transform()
update FEField.get_base(), .create_mapping()
update VolumeMapping.get_mapping()
new transform_basis()
update PolySpace.eval_base()
new sfepy/discrete/fem/refine_hanging.py - initial 2D version, WIP
new find_level_interface(), refine_region(), find_facet_substitutions(), refine(), do_connectivity_substitutions(), eval_basis_transform()
manage connectivity substitutions and unused DOFs in FEField
move do_connectivity_substitutions() into new FEField.substitute_dofs()
new FEField.econn0, .unused_dofs attributes
new FEField.restore_dofs(), .restore_substituted()
update EquationMap.map_equations() to omit unused field DOFs from active DOFs
update FieldVariable.get_full() to restore unused field DOFs
fix Region.cells setter for empty cell regions
fix CMesh.get_incident() for no incident entities
update FEField._setup_esurface() to setup .eedges in 3D
fix refine_edges_3_8
update Variable._set_kind() to always initialize .dof_name
use the variable name as the DOF name for parameter variables without a primary
update ._setup_dofs()
update EquationMap.map_equations() to obey unused DOFs in no EBC case
update ._init_empty()
new ._mark_unused()
fix PointsProbe.__init__() to force C-contiguous order
new tests/test_refine_hanging.py: new test_continuity() test
new eval_fun(), _gen_lines_2_4(), _gen_grid_3_8(), _build_filenames()
move body of FEField.substitute_dofs() into new H1NodalMixin._substitute_dofs()
move eval_basis_transform() -> H1NodalMixin._eval_basis_transform()
update FEField.substitute_dofs(), .restore_dofs() for storing substitutions
new .stored_subs
evaluate and set basis transform in FEField.substitute_dofs()
preserve indices of non-refined cells
update refine_region() - new _interleave_refined()
update find_level_interface(), find_facet_substitutions(), refine()
update refine_region() to preserve vertex groups of non-refined cells
new test_preserve_coarse_entities() in tests/test_refine_hanging.py
new examples/diffusion/laplace_refine_interactive.py
update test_install.py to test laplace_refine_interactive.py example
merge branch ‘hessian-lagrange-basis’
new LagrangeSimplexPolySpace._eval_hessian()
new LagrangeTensorProductPolySpace._eval_hessian(), update .__init__()
update PolySpace.eval_base(), LagrangePolySpace._eval_base() for 2. derivatives
new test_hessians() in tests/test_poly_spaces.py
merge pull request #352 from vlukes/ulf_homog
fix set_mesh_coors() - initiate coors_act array
update Problem.solve() to allow disabling materials update in a given time step
update periodic.match_() for caching matching coordinates
clean-up: periodic.py
new multiproc module - global multiprocessing management
update saving of field mappings, allow sharing data among processes
update homog. engine - compute coefficients for multiple micro configurations at once
clean up in homogenization modules
update homogenization engine: volumes are calculated as the coefficients
fix the test of homogenization_perfusion.py
new non-linear homogenization example
update homogenization engine test: check splitting/merging chunks
fix band_gaps_app.py and the related test
merge pull request #353 from vlukes/update_homog_example
update linear homogenization examples
miscellaneous updates:
docs: update latest snapshot link, closes #344
add custom view for stokes_slip_bc_penalty.py example to script/gen_gallery.py
fix streamline position in plot_velocity() - regression by 63171ad
sfepy-run: fix –version option for Python 3
fix SurfaceMomentTerm - add .arg_shapes, make shift special material parameter
fix AcousticBandGapsApp.__init__() for non-file problem configuration
fix typo in phononic examples
docs: sync module index of developer guide with current sources
do not omit linear_elastic_mM.py in script/gen_gallery.py
docs: update release tasks
from 2016.2 to 2016.3¶
merge pull request #330 from ‘vlukes/fixdoc’
fix docstrings in DotProductVolumeTerm, VectorDotGradScalarTerm
merge pull request #331 from ‘takluyver/py3’ and ‘rc/py3’, closes #164
Python 2.7 and 3.4 support with the same code
manually fix syntax in some support files
run python-modernize relative import fixer
run python-modernize print syntax fixer
run 2to3 exec syntax fixer
run python-modernize raise and except syntax fixers
fix dynamic creation of new methods
run python-modernize dict iteration fixers
fix Python version comparison
switch from deprecated os.path.walk to os.walk
import reload() on Python 3
run python-modernize dict.has_key fixer
fix StringIO import for test on Python 3
run 2to3 tuple parameters fixer
run python-modernize xrange fixer
update use of string functions
reverse type check of filename - ‘file’ is not a reliable type
run python-modernize reduce fixer
use six.integer_types to check for integers
misc fixes in sfepy.discrete
misc fixes in sfepy.discrete.fem.meshio
run python-modernize print syntax fixer on scripts and examples
run python-modernize relative import fixer on scripts, examples and tests
run python-modernize dict iteration fixers on scripts and examples
run python-modernize xrange fixer on scripts and examples
do not use six.iteritems() with Container subclasses
do not use relative imports in examples - fixes SystemError: Parent module ‘’ not loaded, cannot perform relative import
change cmp= to key= when sorting lists
fix VariableTimeStepper.set_step()
fix exception instance not defined outside except block
implement point.__truediv__()
new enc(), dec() encoding utility functions
fix string IO in HDF5MeshIO
fix string IO in HDF5 (pytables) related functions
update test_install.py for Python 3
fix integer division
fix comparison of strings containing floats in test_units()
fix reporting of failed tests in test_install.py with Python 3 - new report_tests()
docs: update installation instructions for Python 3
merge pull request #332 from ‘rc/travis-ci’, closes #321
automatic testing on Python 2.7 and 3.4 using Travis CI
new .travis.yml
update run_tests.py to return status
do not require DISPLAY in linear_elastic_probes.py example
allow failing of evp0 in tests/test_eigenvalue_solvers.py - update linear_elastic_probes.py example to run without vtk probes
update linear_elastic_mM.py example to regenerate coefficients - fixes race condition with several travis runs
merge branch ‘readme-rst’
show travis build status on github
rename README -> README.rst
update setup.py, sfepy/version.py for README.rst
README.rst: show travis status, update and fix text and links
merge branch ‘plot-cmesh’
fix plot_wireframe()
new plot_cmesh(), support **kwargs in plotting functions
script/plot_mesh.py: use plot_cmesh()
merge pull request #333 from ‘vlukes/hyperelast’
new term: NonsymElasticTerm - non-symmetric gradient
fix Term.get_approximation()
update hyperelastic terms - new “family data” implementation
new sym2nonsym() function in terms_op.c
new classes for homogenized coefficients: CoefNonSymNonSym and CoefNonSym
update “ev_integrate_mat” term - allow arbitrary shaped material
merge branch ‘remove-get-approximation’
remove FieldVariable.get_approximation(), Term.get_approximation()
update terms for no Term.get_approximation()
merge pull request #334 from ‘vlukes/fixdocs’
fix docstring of SDDotVolumeTerm, SDDivTerm, SDDivGradTerm, SDConvectTerm, SDGradDivStabilizationTerm, SDDiffusionTerm
merge pull request #336 from ‘heczis/issue_281_argparse’, closes #281
use argparse instead of optparse in:
examples/linear_elasticity/its2D_interactive.py
examples/linear_elasticity/linear_elastic_interactive.py
examples/linear_elasticity/linear_viscoelastic.py
examples/linear_elasticity/modal_analysis.py
examples/homogenization/rs_correctors.py
examples/diffusion/laplace_shifted_periodic.py
examples/diffusion/time_poisson_interactive.py
examples/large_deformation/compare_elastic_materials.py
test_install.py
script/blockgen.py
script/gen_term_table.py
script/gen_mesh_prev.py
script/plot_mesh.py
script/plot_quadratures.py
script/plot_times.py
script/tile_periodic_mesh.py
script/save_basis.py
script/convert_mesh.py
script/cylindergen.py
script/extract_surface.py
script/plot_logs.py
script/gen_iga_patch.py
script/show_terms_use.py
script/gen_lobatto1d_c.py
script/sync_module_docs.py
script/gen_gallery.py
script/plot_condition_numbers.py
run_tests.py
extractor.py
probe.py
simple.py
schroedinger.py
homogen.py
postproc.py
phonon.py
shaper.py
fix import path
fix usage in examples/linear_elasticity/shell10x_cantilever_interactive.py
miscellaneous updates:
support numeric prefixes in Quantity, Unit.get_prefix(), update prefixes
update script/show_authors.py for Python 3
fix docstring of get_local_ids(), add comments in mesh_build()
fix regression in FieldVariable.get_element_diameters()
add support for os.walk() keyword arguments to locate_files(), remove_files()
fix _gen_common_data() in tests/test_poly_spaces.py to permute connectivity
from 2016.1 to 2016.2¶
merge pull request #309 from ‘vlukes/splines’
bsplines: update to_ndarray(), fix draw() - evaluate curve/surface coordinates, if needed
merge branch ‘fix-gradient-items-ordering’
fix ordering of gradient items in evaluate_in_rc() - ordering corresponds to (n_coor, n_components, dim) as described in Field.evaluate_at() docstring
fix docstring of FieldVariable.evaluate_at()
change data shape of GradTerm values to correspond to Field.evaluate_at() - update GradTerm.get_fargs(), .get_eval_shape()
update test_field_gradient() to test fields with more than one component
test proportions of component gradients
update prepare_variable() so that components are multiples of the first one
merge pull request #310 from ‘vlukes/meshio_msh’
update meshio.py: support for msh file format (gmsh) - reading
MSH mesh format: update tests, add test meshes
merge pull request #315 from ‘vlukes/terms_cleanup’
rename ‘d_diffusion_sa’ term to ‘d_sd_diffusion’, remove unused functions
remove terms_acoustic from doc
make dw_lin_elastic_iso as the shortcut to dw_lin_elastic + stiffness_from_lame()
fix docstring of assemble_by_blocks()
update examples: replace dw_lin_elastic_iso
update tests and scripts: linear elastic terms
rename di_surface_moment to d_surface_moment
term table divided into: basic, sensitivity, large deformation, special terms
merge pull request #316 from ‘vlukes/parallel_homog’
new: parallel computation of homogenized coefficients
examples/phononic/band_gaps.py: no multiprocessing
update test_install.py - new test to check presence of lines in the output
new flush() method in OutputFilter class - needed for multiprocessing
merge branch ‘shell10x’
partial shell10x element implementation
new sfepy/discrete/structural/ for structural elements
fix docstring of IGField.get_data_shape()
replace ‘plate’ integration with ‘custom’
update Field.from_conf() to scan sfepy/discrete/structural/
new sfepy/mechanics/shell10x.py - shell10x element implementation functions
new create_elastic_tensor(), create_transformation_matrix(), transform_asm_matrices(), create_local_bases(), create_rotation_ops(), create_strain_transform(), get_mapping_data(), get_dsg_strain(), create_strain_matrix(), add_eas_dofs(), rotate_elastic_tensor(), create_drl_transform(), lock_drilling_rotations()
new sfepy/discrete/structural/mappings.py - new Shell10XMapping
new sfepy/discrete/structural/fields.py - new Shell10XField
new sfepy/terms/terms_shells.py - new Shell10XTerm (dw_shell10x)
update ConcentratedPointLoadTerm.arg_shapes for general number of components
fix PhysicalQPs.get_shape() for no quadrature points (point integration terms)
fix Term.check_shapes() for scalar ‘N’ values
new Shell10XTerm.poly_space_base class attribute
update tests/test_term_call_modes.py to report shapes of all values
update tests/test_term_call_modes.py to test Shell10XTerm
update make_term_args(), Test
support custom integration and dim != tdim geometry
obey optional Term.poly_space_base attribute
use identity for 2D material matrix
new examples/linear_elasticity/shell10x_cantilever_interactive.py
update Term.from_desc() to pass integral to term constructor
new examples/linear_elasticity/shell10x_cantilever.py + test
add custom view for shell10x_cantilever.py example to script/gen_gallery.py
merge branch ‘mayavi-dataset-manager’
remove sfepy/postprocess/dataset_manager.py
use dataset_manager.py from mayavi
merge branch ‘no-symlinks’
remove scripts-common/
update setup.py to install main scripts into sfepy/script/
sfepy-run: update for no scripts-common/ symlinks, use explicit script names
docs: update for no posix only sfepy-run
merge branch ‘fix-windows-build’ - closes #317, #318, #325
setup.py: import setuptools in setup_package() to find a C compiler on windows
fix __SDIR__ definition, new inline definition for windows in setup.py files
allow long shape in parse_shape()
remove inline directive for ravel_multi_index() on windows - fixes linker error
materials:
merge pull request #311 from ‘vlukes/sd_elastic’
remove unused variables in terms_[elastic, diffusion, basic].c
update d_sd_lin_elastic term: new, much faster implementation
fix .arg_shapes class attribute of DivGradTerm for no material
use special material for index in ScalarDotGradIScalarTerm - update .arg_shapes, .dw_fun()
fix arg_shapes in SDDotVolumeTerm
docs:
remove no longer used terms_acoustic.rst
update support section
sync module index of developer guide with current sources
miscellaneous updates:
fix mesh_get_centroids() for cells of lower topological dimension
fix VTKMeshIO.read() for cells of lower topological dimension than space - simplify vtk_inverse_cell_types
obey linearization kind in FEField.create_output() - allows adaptive linearization also for, e.g., Q1 fields
add common sources to dependencies of igac extension module
from 2015.4 to 2016.1¶
merge pull request #307 from ‘vlukes/mesh_generators’
fix gen_mesh_from_voxels()
new tests of gen_mesh_from_geom(), gen_tiled_mesh(), gen_mesh_from_voxels()
merge branch ‘auto-check-material-shapes’
implement general Term.check_shapes() - check term argument shapes at run-time
update terms to use generic variable size in .arg_shapes where appropriate
update IntegrateVolumeTerm, IntegrateSurfaceTerm, VolumeTerm, SurfaceTerm, VolumeSurfaceTerm, IntegrateMatTerm, SumNodalValuesTerm, GradTerm
remove .check_shapes() from all terms having it
remove it from DotProductVolumeTerm, BCNewtonTerm, VectorDotGradScalarTerm, VectorDotScalarTerm, LinearElasticIsotropicTerm, LinearPrestressTerm, LinearStrainFiberTerm, SurfaceTractionTLTerm, VolumeSurfaceTLTerm, ConcentratedPointLoadTerm
new .arg_shapes class attribute in DotProductSurfaceTerm, ConcentratedPointLoadTerm
update LinearPointSpringTerm for new .arg_shapes class attribute
change special material argument to a single float
update tests/test_elasticity_small_strain.py
update get_arg_kinds() to distinguish ‘ts’ argument, new _match_ts
update tests/test_term_call_modes.py for TimeStepper (‘ts’) term argument - update make_term_args()
new/fill-in .arg_shapes class attributes in time history terms
update BiotTHTerm, BiotETHTerm, DotSProductVolumeOperatorWTHTerm, DotSProductVolumeOperatorWETHTerm, LinearElasticTHTerm, LinearElasticETHTerm, CauchyStressTHTerm, CauchyStressETHTerm
change ‘N’ value to 1 in _parse_scalar_shape() in make_term_args() - fix for time history terms
merge pull request #306 from ‘vlukes/fix-gen_mesh_from_geom’
fix to_poly_file() in geom_tools.py
fix gen_mesh_from_geom(), remove gen_mesh_from_poly()
merge branch ‘remove-ts-explicit’
remove make_explicit_step(), ExplicitTimeSteppingSolver
remove MassOperator and sfepy/discrete/mass_operator.py
update time_poisson_explicit.py to use ts.simple
merge pull request #304 from ‘vlukes/splines’
new documentation to SplineBox and SplineRegion2D classes
update bspline.py, new SplineRegion2D in splinebox.py
merge branch ‘no-fea’
replace Interpolant by PolySpace in GeometryElement
GeometryElement.interp -> .poly_space
update FEDomain.__init__() and affected code
move set_mesh_coors() into sfepy/discrete/fem/fields_base.py - update Problem.set_mesh_coors()
move Approximation into FEField and subclasses, part 1
update volume fields
prepare for volume-only PolySpace in fields
remove imports of fea.py
sfepy/discrete/fem/fea.py:
move eval_nodal_coors(), _interp_to_faces() into sfepy/discrete/fem/fields_base.py
remove Interpolant
remove Approximation.eval_extra_coor(), .get_connectivity(), .get_poly_space()
move into FEField:
Approximation.clear_qp_base(), .get_qp(), .get_base()
Approximation._create_bqp(), .create_bqp() into new FEField.create_bqp()
Approximation.describe_geometry() into FEField.create_mapping()
new FEField attributes:
from Approximation .surface_data, .point_data, .ori, .efaces, .econn
.poly_space
update FEField.__init__(), ._setup_esurface(), .setup_coors(), .get_data_shape(), .linearize(), .interp_to_qp()
replace Interpolant by PolySpace in VolumeField
update VolumeField._create_interpolant(), ._init_econn(), ._setup_vertex_dofs(), .setup_extra_data(), .get_econn()
remove VolumeField._setup_approximations()
rename VolumeField._setup_surface_data(), ._setup_point_data() to .setup_surface_data(), .setup_point_data(), merge with Approximation.setup_surface_data(), .setup_point_data()
update H1NodalMixin._setup_facet_orientations(), ._setup_facet_dofs(), ._setup_bubble_dofs(), .create_basis_context()
update H1NodalVolumeField.interp_v_vals_to_n_vals()
update H1HierarchicVolumeField._init_econn(), ._setup_facet_orientations(), ._setup_facet_dofs(), ._setup_bubble_dofs(), .create_basis_context()
update eval_in_els_and_qp(), create_expression_output()
move Approximation into FEField and subclasses, part 2
update surface integration/mappings for volume-only PolySpace in fields
update FEField.get_data_shape(), .create_bqp(), .create_mapping()
update FEMapping.__init__() - new .indices attribute
new SurfaceMapping.set_basis_indices(), .get_base()
move Approximation into FEField and subclasses, part 3
update FEField.create_mesh(), VolumeField.average_qp_to_vertices()
update compute_nodal_normals()
update FieldVariable.get_element_diameters()
update describe_geometry() in membranes.py
move Approximation into FEField and subclasses, part 4
remove H1DiscontinuousField._setup_approximations()
update H1DiscontinuousField._setup_global_base()
move Approximation into FEField and subclasses, part 5
update surface fields
fix .surface_data, .point_data initialization in FEField.__init__()
update FEField.get_qp(), .create_mapping()
update SurfaceField._create_interpolant(), .setup_extra_data(), ._init_econn(), ._setup_vertex_dofs(), .get_econn(), .average_qp_to_vertices()
remove SurfaceField._setup_approximations()
remove sfepy/discrete/fem/fea.py
update FieldVariable.get_approximation() to return Field
new FEField.get_connectivity() convenience alias
update sfepy/parallel/ code for no Approximation
update create_task_dof_maps(), distribute_field_dofs(), distribute_fields_dofs(), get_local_ordering(), plot_partitioning(), plot_local_dofs()
script/save_basis.py: update save_basis_on_mesh() for no Approximation
update tests/test_poly_spaces.py for no Approximation
merge branch ‘active-fibres-update’
update HyperElasticBase to pass kwargs to stress and tangent modulus functions - update HyperElasticBase.compute_stress(), .compute_tan_mod()
new create_omega(), compute_fibre_strain()
update FibresActiveTLTerm - move fibre_function() into the class, cache data
remove fibre_function()
new _setdefault_fibre_data()
update FibresActiveTLTerm.get_fargs(), .stress_function(), tan_mod_function()
merge branch ‘parallel-pc-fieldsplit’
support ‘fieldsplit’ preconditioner in PETScKrylovSolver
new .set_field_split()
update .__init__(), .create_ksp()
setup ‘fieldsplit’ preconditioner in biot_parallel_interactive.py example
update docstring of biot_parallel_interactive.py example
docs:
sync IGA section with current state
document refinement_level configuration option in users guide
stop omitting time_poisson_explicit.py in script/gen_gallery.py
sync module index of developer guide with current sources
scripts:
new script/show_mesh_info.py
script/convert_mesh.py: update –list option to list also readable formats
rename & update output_writable_meshes() -> output_mesh_formats()
examples and tests:
parallel examples: fix race condition when output directory does not exist
adjust final time in time_poisson_explicit.py
miscellaneous updates:
merge branch ‘fix-mat-by-region-for-surfaces2’
update Region.get_cells() to obey parent region
fix Region.get_cell_indices() for non-disjoint, non-subset cells
remove useless FEField._create_interpolant()
remove obsolete SurfaceLaplaceLayerTerm, SurfaceCoupleLayerTerm
update Problem.from_conf() to support refinement_level configuration option
fix argument name in docstring of FieldVariable.evaluate()
fix NEUMeshIO.read() for empty lines and 3_8 cells
fix Region.get_facet_indices() for safe numpy casting on windows10
from 2015.3 to 2015.4¶
basic support for restart files
merge branch restart-files
simple.py: new –save-restart, –load-restart options
new Problem.get_restart_filename(), .save_restart(), .load_restart() - update .init_time() to initialize new ._restart_filenames attribute
update Problem.__init__(): update default conf to have options attribute
fix Variables.set_data() to use step argument
update SimpleTimeSteppingSolver.__call__() to support restart files
update Problem for restarting stationary problems - update .reset() to initialize ._restart_filenames attribute
update StationarySolver.__call__() to support restart files
new TimeStepper.get_state(), .set_state()
new VariableTimeStepper.get_state(), .set_state()
update VariableTimeStepper to have current state stored in .times, .dts
new .advance(), .iter_from_current()
update .set_step(), .__iter__()
update AdaptiveTimeSteppingSolver.__call__() to support restart files
update SimpleTimeSteppingSolver.__call__() for variables with history
update TimeStepper.iter_from(), new .advance()
check step in Variable.set_data()
docs: update user’s guide - introduce restart files
linear combination boundary conditions:
improve docstrings of MRLCBCOperator, ShiftedPeriodicOperator
update ShiftedPeriodicOperator.__init__() for pyflakes
support general linear combination of DOFs in a node
merge branch nodal-lcbcs
update LCBCOperators.make_global_operator() for rhs without column variable
new NodalLCOperator - general linear combination of DOFs in a node
new examples/linear_elasticity/nodal_lcbcs.py + test
fix IntegralMeanValueOperator for several DOFs per node
examples and tests:
merge branch example-balloon
new meshes/3d/unit_ball.mesh
new examples/large_deformation/balloon.py + test
miscellaneous updates:
do not check facet-only meshes in FEDomain.fix_element_orientation() - fixes segfault
remove unused doc/images/sfepy_gui.png
fix Mesh.copy() to provide default name
fix bubble DOFs setup in H1DiscontinuousField._setup_global_base() - initialize .bubble_remap attribute
clean up sfepy/postprocess/time_history.py
fix extract_time_history() for no element groups
docs: fix Green strain definitions
allow None as problem argument in MiniAppBase.__init__()
lib.lapack import bug fix (merge pull request #301 from rexfuzzle/master)
fix output order of scipy.linalg.lapack functions in ScipySGEigenvalueSolver
fix version comparison in dets_fast()
set SYMPY_MIN_VERSION to 0.7.3 in sfepy/version.py (merge branch sympy-lcbc-compat)
fix describe_geometry() to initialize base functions in membrane_geo
merge branch fix-mat-by-region-for-surfaces
allow non-cell regions in ConstantFunctionByRegion.get_constants()
update Region.get_cell_indices() to allow cells to be sutperset of region cells
fix access to mat_id in GenericFileSource.create_source(), .get_mat_id()
from 2015.2 to 2015.3¶
preliminary support for parallel computing
merge branch parallel
allow constructing empty regions
update Domain.create_region(), Region.setup_from_highest(), .finalize()
new allow_empty argument
new sfepy/parallel/__init__.py
new sfepy/parallel/setup.py, update sfepy/setup.py
new sfepy/parallel/parallel.py - start PETSc-based parallelization
new get_inter_facets(), create_task_dof_maps(), distribute_field_dofs(), get_local_ordering(), get_sizes(), expand_dofs(), create_petsc_matrix(), apply_ebc_to_matrix(), assemble_to_petsc()
use cmesh.tdim in get_inter_facets()
new create_prealloc_data()
new partition_mesh()
new petsc_call() linear solver decorator
update PETScKrylovSolver for parallel use
allow passing in PETSc matrices and vectors
new sub_precond option
update .__init__() - new comm argument, setup converged_reasons there
update .create_ksp()
remove .set_matrix(), new .create_petsc_matrix()
update .__call__() - new comm argument, use petsc_call() decorator, return PETSc solution vector for PETSc right-hand side vector
update docstring
new view_petsc_local()
new create_local_petsc_vector()
new create_gather_scatter(), create_gather_to_zero()
new verify_task_dof_maps()
new is_matrix argument in Problem.time_update(), .update_equations()
update PETScKrylovSolver.__call__() to output actual solver and preconditioner
new distribute_fields_dofs() - support multiple fields
new get_composite_sizes()
split assemble_to_petsc() - new assemble_rhs_to_petsc(), assemble_mtx_to_petsc()
remove debug() call in Equations.get_graph_conns()
support non-reduced (full size) system assembling in Equations and Variables
update Equations.time_update(), .get_graph_conns(), .create_matrix_graph() - new active_only argument
update create_adof_conns(), Variables.equation_mapping() - new active_only argument
update Problem for non-reduced (full size) system assembling
new .active_only attribute
update .__init__(), .update_equations() - new active_only argument
new PETScNonlinearSolver
new sfepy/parallel/evaluate.py - new PETScParallelEvaluator
new setup_composite_dofs()
new create_petsc_system()
update setup.py - new petsc4py and pymetis version checks - update sfepy/version.py
filter-out -h, –help from sys.argv options passed to petsc4py
-h, –help is avaliable for user options, -help can be used to show PETSc options
new sfepy/parallel/plot_parallel_dofs.py - new mark_subdomains(), label_dofs(), plot_partitioning(), plot_local_dofs()
new examples/diffusion/poisson_parallel_interactive.py
new examples/multi_physics/biot_parallel_interactive.py
update setup.py - new mpi4py version check - update sfepy/version.py
docs:
sync module index of developer guide with current sources
parallel examples: add mpi4py requirement
update installation requirements
update user’s guide - add basic parallel problem solving description - update developer guide, doc/index.rst
update test_install.py to test parallel examples
(mostly) fix finding of reference coordinates
merge branch fix-find-ref-coors - (almost) solves #285
TODO: make get_xi_tensor() robust w.r.t. multiple solutions, prefer those inside a cell
rename get_ref_coors() -> get_ref_coors_convex(), refc_find_ref_coors() -> refc_find_ref_coors_convex(), find_ref_coors() -> find_ref_coors_convex()
new refc_find_ref_coors() C function, new find_ref_coors()
new get_potential_cells(), get_ref_coors_general()
remove strategy argument of get_ref_coors_convex(), use extrapolate flag
new get_ref_coors() - support ‘general’ and ‘convex’ strategies
update .evaluate_at() and its calls for new get_ref_coors()
update H1HierarchicVolumeField.evaluate_at()
update H1NodalMixin.evaluate_at()
update FieldVariable.evaluate_at(), .set_from_other()
update Probe.probe()
fix comment in get_xi_tensor()
new tests/test_ref_coors.py + cross3d.mesh
allow field gradient evaluation in arbitrary points
merge branch evaluate-gradient
update evaluate_in_rc() for gradients
update .evaluate_at() and its calls - new mode argument, support gradients
update H1HierarchicVolumeField.evaluate_at()
update H1NodalMixin.evaluate_at()
update FieldVariable.evaluate_at(), .set_from_other()
update Probe.probe()
update test_invariance_qp() in tests/test_mesh_interp.py - test field gradients, increase field approximation order to 2
fix eval_lagrange_simplex() - initialize properly gradient output to zeros
make vector field gradient in evaluate_in_rc() compatible with ev_grad term - define ib type
update test_invariance_qp() to test several meshes with different cell types
update test_invariance_qp() for new prepare_variable(), update reporting
new test_field_gradient() in tests/test_mesh_interp.py
unify evaluation of basis functions using basis-specific contexts, part 1
merge branch basis-context
hide basis-specific arguments in lagrange.c into new LagrangeContext struct
update get_barycentric_coors(), get_xi_simplex(), get_xi_tensor(), eval_lagrange_simplex(), eval_lagrange_tensor_product() C functions
update get_barycentric_coors(), eval_lagrange_simplex(), eval_lagrange_tensor_product(), evaluate_in_rc() cython functions
update evaluate_in_rc() for merged ‘evaluate-gradient’ branch
new print_context_lagrange() C function
update find_ref_coors_convex, find_ref_coors() (cython) for LagrangeContext - update refc_find_ref_coors_convex(), refc_find_ref_coors() C functions
new get_xi_dist() C function, update LagrangeContext - add tdim attribute
new CLagrangeContext cython class, wraps LagrangeContext C struct
update LagrangeContext cython definition
new CLagrangeContext.__cinit__(), .__dealloc__(), .__str__(), .cprint()
update refc_find_ref_coors_convex(), refc_find_ref_coors() - new qp_eps argument
new abstract BasisContext C struct
remove _get_xi_dist()
no more dependence on lagrange.h
new abstract CBasisContext cython class
update find_ref_coors_convex, find_ref_coors() (cython) for CBasisContext - and for updated refc_find_ref_coors_convex(), refc_find_ref_coors()
new H1NodalMixin.create_basis_context()
update get_ref_coors_convex(), get_ref_coors_general() - use Field.create_basis_context()
new H1HierarchicVolumeField.create_basis_context()
move common extension modules to sfepy/discrete/common/extmods
merge branch ‘common-extmods’
new sfepy/discrete/common/extmods/ - move common extension modules there
move sfepy/discrete/fem/extmods/{_fmfield.pxd, _fmfield.pyx, _geommech.pxd, _geommech.pyx, assemble.pyx, cmesh.pxd, cmesh.pyx, common.h, common_python.c, crefcoors.pyx, fmfield.c}
new sfepy/discrete/common/extmods/__init__.py
update setup.py files, new sfepy/discrete/common/extmods/setup.py
update imports
unify evaluation of basis functions using basis-specific contexts, part 2
merge branch basis-context2
update LagrangeContext
add .eval_basis, .order, .is_bubble attributes
new .iel, .geo_ctx, .mesh_coors, .mesh_conn, .n_cell, .n_cp attributes
change .bc attribute type
new .mbfg attribute
update print_context_lagrange()
update CLagrangeContext
update for current LagrangeContext
update .__cinit__(), new .is_bubble property
new .evaluate()
update .__cinit__()
new ._geo_ctx, .mesh_coors, .mesh_conn, .base1d attributes
new .iel, .geo_ctx properties
new .mbfg attribute
new LagrangePolySpace
new .create_context()
new ._eval_base(), update derived classes
update LagrangeSimplexPolySpace:
update .__init__() - new init_context argument
remove ._eval_base()
update LagrangeSimplexBPolySpace:
update .__init__() - new init_context argument
update .create_context() - support **kwargs
remove ._eval_base()
update LagrangeTensorProductPolySpace:
update .__init__() - new init_context argument
remove ._eval_base()
update LagrangeSimplexPolySpace, LagrangeTensorProductPolySpace
inherit from LagrangePolySpace
new LagrangeSimplexBPolySpace.create_context()
new fmf_set_qp() C function
new eval_basis_lagrange() C function, update eval_lagrange_simplex() - support only a single point
update get_xi_dist() for current LagrangeContext - update get_xi_simplex(), get_xi_tensor()
update H1NodalMixin.create_basis_context()
update BasisContext - new .eval_basis, .iel attributes
move evaluate_in_rc() from bases.pyx to crefcoors.pyx, update for BasisContext - great simplification by using abstract BasisContext.eval_basis()
remove cython functions replaced by CLagrangeContext.evaluate()
remove get_barycentric_coors(), eval_lagrange_simplex(), eval_lagrange_tensor_product()
remove unused definitions in bases.pyx
move global_interp.py into sfepy/discrete/common/
move H1NodalMixin.evaluate_at() -> Field.evaluate_at(), remove H1HierarchicVolumeField.evaluate_at()
update imports
improve error message in fmf_copy()
allow higher-order cell-vertex connectivities in CMesh.from_data()
move buffer for cell coordinates into context
update BasisContext, LagrangeContext - new e_coors_max attribute
update CLagrangeContext - new e_coors_max attribute, update .__cinit__()
split meaning of .iel into .iel and new .is_dx attribute of BasisContext
update BasisContext, LagrangeContext - new .is_dx attribute
update CLagrangeContext.__cinit__()
update evaluate_in_rc()
update refc_find_ref_coors_convex(), refc_find_ref_coors() C functions - set ctx->is_dx and ctx->iel
update eval_basis_lagrange()
update evaluate_in_rc() - add basic shape check of output buffer
improve handling of get_xi_dist() failure in refc_find_ref_coors() - initialize imin, imin and d_min are in sync
update eval_basis_lagrange() for bubble functions. update eval_lagrange_simplex()
new NURBSContext C struct
new print_context_nurbs(), get_xi_dist(), eval_basis_nurbs()
update eval_bspline_basis_tp(), eval_nurbs_basis_tp() - new is_dx argument
new CNURBSContext cython class, wraps NURBSContext C struct
new CNURBSContext.__cinit__(), .__dealloc__(), .__str__(), .cprint(), .evaluate()
update eval_mapping_data_in_qp(), eval_variable_in_qp(), eval_in_tp_coors() for is_dx argument
update IGDomain - new .eval_mesh attribute, update .__init__()
new IGField.create_mesh(), .create_eval_mesh(), .create_basis_context()
new Field.create_eval_mesh()
fix Field.evaluate_at() - do not use FEM-specific attributes
update get_ref_coors_general() for field.create_eval_mesh()
update sfepy/discrete/common/__init__.py - import Field
rename & update test_ref_coors() -> test_ref_coors_fem()
remove field creation from Test.from_conf()
use basis context for basis evaluation
fix typo
new test_ref_coors_iga() in tests/test_ref_coors.py
update IGField to have approx_order attribute (make projections work)
new test_projection_iga_fem() in tests/test_projections.py
merge pull request #298 from vlukes/el_eval
new evaluation mode ‘el_eval’, ‘el’ mode removed
update equations.evaluate()
merge pull request #300 from vlukes/mat_optim
new example: material identification - multiscale analysis
new example: material identification - mesh
new tutorial: material identification
merge branch test-conditions
move tests/test_ebcs.py -> tests/test_conditions.py
tests/test_conditions.py: remove configuration
new test_ebcs() in tests/test_conditions.py, update Test.from_conf()
new test_epbcs() in tests/test_conditions.py
update test_save_ebc() in tests/test_conditions.py
move checking of applied conditions from test_ebcs() into new check_vec()
new test_ics() in tests/test_conditions.py
merge branch how-to-contribute
update generic installation instructions, add two section labels
update how to contribute instructions in developer guide
remove gitwash section from developer guide
remove doc/dev/gitwash/
update script/sync_module_docs.py
update developer guide with Vladimir’s suggestions
postprocessing and visualization:
fix VTK version issue related to SetSource()
fix VTK version issue related to Update()
fix plot_dofs option in save_basis_on_mesh() for no element groups
remove show argument of plot functions, use single code for 2D and 3D
support 1D where applicable
update plot_control_mesh()
update plot_wireframe(), plot_entities(), label_global_entities(), label_local_entities()
update plot_points(), plot_mesh(), plot_global_dofs(), plot_local_dofs(), plot_nodes()
update plot_geometry(), plot_edges(), plot_faces()
update plot_weighted_points(), plot_quadrature()
update import in script/plot_mesh.py
fix tetrahedralize_vtk_mesh()
use tight bounding box in figure.savefig() calls in plot_parallel_dofs.py
postproc.py: new –colormap option
new set_colormap()
update Viewer.build_mlab_pipeline(), .call_mlab()
allow user-defined file sources in place of filename in create_file_source()
probes:
update Probe.__call__() to support keyword arguments
update Probe.probe() - new ret_points argument, update docstring
update VTK Probe.__call__() - new ret_points argument, update docstring, new .dim attribute
materials:
remove unused Material.set_data_from_variable()
use expression materials when copy_materials=True in Problem.create_evaluable()
fixes evaluation of terms with materials not present in Problem.equations
initialize Problem.conf.materials in Problem.__init__()
remove unused Materials.semideep_copy()
regions:
fix Region.get_facet_indices() for inner cell “corners”
fix “Cannot cast array data …” (Windows 8.1, Numpy 1.8.2)
terms:
new PiezoStressTerm (ev_piezo_stress)
new AdvectDivFreeTerm (dw_advect_div_free)
setup:
remove unused IPYTHON_MIN_VERSION
update package_check() - new show_only argument, update messages and docstring
update setup.py to show names and versions of dependencies at the end - new check_versions()
update Clean.run() build helper to clean *.pyd files (dynamic libs on windows)
increase SYMPY_MIN_VERSION to 0.7.2
new scikits.umfpack and pysparse version checks - update sfepy/version.py
docs:
update installation requirements - add scikit-umfpack
fix label of theoretical background section
fix indentation, include links.inc in user’s guide
examples and tests:
fix time_poisson_interactive.py for new copy_materials semantics
time_poisson_interactive.py: update circle probe parameters in gen_lines()
fix –show option in poisson_parallel_interactive.py example - update for c985650d356bcc1eb3608f4144fc84299e67c458
clean up piezo_elasticity.py example, use short syntax
update piezo_elasticity.py example to compute stresses - new post_process()
fix its2D_interactive.py for new copy_materials semantics, update stress_strain(), nodal_stress()
modal_analysis.py:
new –axis option
support optional positional argument for user-provided mesh
fix –show option with user-provided mesh
fix –n-eigs help message
fix paths in help/docstring
update –bc-kind option - new fixed mode, rename clamped -> cantilever
new –ignore option
improve reporting results
update test_install.py for current modal_analysis.py
fix line lengths
new examples/diffusion/time_advection_diffusion.py + test
miscellaneous updates:
remove whitespaces in linalg/utils.py
replace dets_fast based on lapack_lite by numpy.linalg.det for numpy version >= 1.8
fix expand2d()
remove duplicate line in get_ref_coors()
fix docstring of DiffusionCoupling term
fix sympy.zeros() call for sympy 0.7.6
fix FieldVariable.setup_initial_conditions() for multiple conditions
fix test_eigenvalue_solvers() to obey Test.can_fail
clean up tests/test_msm_symbolic.py
move tests/sympy_operators.py -> sfepy/linalg/sympy_operators.py
new HDF5MeshIO.read_dimension()
fix docstring of configure_output()
fix exception message in FEDomain.fix_element_orientation()
update PysparseEigenvalueSolver to support extra options
script/show_authors.py: merge by names, show commit counts
from 2015.1 to 2015.2¶
update time stepping solvers for interactive use
merge branch ts-interactive
rename Problem.set_solvers() -> .set_conf_solvers()
rename Problem.set_solvers_instances() -> .set_solver()
work only with nonlinear solver
remove .solvers, new .nls (the nonlinear solver instance)
rename .get_solvers() -> .get_solver()
update Problem.is_linear(), .set_linear() to use nonlinear solver instance
update ScipyDirect to presolve in new .presolve()
new LinearSolver.presolve()
remove {ScipyDirect, SchurGeneralized, MultiProblem}._presolve()
update Problem.init_solvers() to only create instances, new .try_presolve()
update Problem.time_update() to reuse existing conditions by default
make functions argument optional in Equations.setup_initial_conditions()
remove Problem.setup_ic(), new .set_ics(), .setup_ics()
new Problem.ics attribute - update .copy(), .clear_equations()
update get_initial_state()
make generator from .__call__() of time stepping solvers - yield step, time, state
move initial step initialization of time stepping solvers to new .init_time()
update StationarySolver, EquationSequenceSolver, SimpleTimeSteppingSolver, new .init_time() - call Problem.init_solvers() there
update make_implicit_step() - use Problem.try_presolve()
update make_explicit_step()
new TimeSteppingSolver.init_time()
updates for time stepping solvers as generators and .init_time()
move project_by_component() from example into sfepy code
new examples/diffusion/time_poisson_interactive.py
solvers:
fix PETSc Krylov solvers for reusing with different matrices
new PETScKrylovSolver.create_ksp(), update .set_matrix(), .__call__()
update PETScParallelKrylovSolver.__call__()
reorganize examples:
merge branch reorganize-examples
move Biot, piezo-, thermo-elasticity examples into examples/multi_physics/
move compare_elastic_materials.py into examples/large_deformation/, remove el3.mesh
clean up compare_elastic_materials.py, generate mesh, use short syntax, make it an executable script
move rs_correctors.py into examples/homogenization/, move osteonT1_11.mesh into meshes/2d/special/
clean up rs_correctors.py, use short syntax, add docstring, make it an executable script, change output to current directory
move laplace_shifted_periodic.py into examples/diffusion/
move linear_elasticity.py into examples/linear_elasticity/ - rename to linear_elastic_interactive.py
move modal_analysis.py into examples/linear_elasticity/
remove examples/standalone/interactive/__init__.py
move live_plot.py into examples/miscellaneous/
move thermal_electric.py into examples/multi_physics/
remove examples/standalone/__init__.py
update tests for moved examples
update test_install.py for moved examples
script/gen_gallery.py: update for moved examples
docs: update tutorial for moved examples
remove element groups - major code simplification
merge branch no-ig
update CMesh and Mesh:
new CMesh.from_data(), new .vertex_groups attribute
start using CMesh internally in Mesh to store mesh data, no element groups - update Mesh._set_data(), ._set_shape_info()
remove CMesh.from_mesh(), .get_from_cell_group(), .get_igs()
new CMesh.create_new()
remove unused Mesh.setup_done attribute
remove unused make_point_cells()
remove unused write_bb()
rename Mesh._set_data() -> ._set_io_data(), update MeditMeshIO.read()
remove Mesh.mat_ids, .ngroups, make .coors @property alias to .cmesh.coors
update ._set_io_data()
new .coors() property
new Mesh.get_conn()
new Mesh._get_io_data()
update Mesh.write() - remove coors, igs arguments
update Mesh.from_data() for no element groups
remove unused Mesh.get_element_coors()
update Mesh.__init__() for CMesh
new cmesh argument, remove filename, prefix_dir, kwargs arguments
new Mesh._collect_descs()
update Mesh docstring
update Mesh.from_region(), .copy() for CMesh.create_new()
do not add facet entities in Mesh.from_region()
remove unused Mesh._append_region_faces(), .localize()
remove unused Mesh.from_surface()
update merge_mesh(), Mesh.__add__(), .create_conn_graph() for no element groups
remove unused get_min_edge_size()
remove unused Mesh.explode_groups()
remove unused make_inverse_connectivity()
mesh generators:
update tiled_mesh1d(), gen_tiled_mesh() for no element groups
update gen_extended_block_mesh() for no element groups
update MeshIO and subclasses:
do not split connectivities by mat_id in MeditMeshIO.read()
update MeditMeshIO.write(), VTKMeshIO.write() for Mesh._get_io_data()
do not split connectivities by mat_id in VTKMeshIO.read()
clean up tests/test_meshio.py
new split_conns_mat_ids(), update MeditMeshIO.read()
update MeshIO and remaining subclasses for current Mesh
do not split connectivities by mat_id in *.read()
use Mesh._get_io_data() in *.write()
update MeshIO docstring
update TetgenMeshIO.read()
update ComsolMeshIO.read(), .write()
update HDF5MeshIO.read(), .write()
update MEDMeshIO.read()
update Mesh3DMeshIO.read()
update mesh_from_groups()
update BDFMeshIO.read(), .write()
update NEUMeshIO.read()
remove unused meshio functions related to element groups
remove sort_by_mat_id(), sort_by_mat_id2(), split_by_mat_id(), join_conn_groups()
update Domain, FEDomain:
update FEDomain__init__() for CMesh in Mesh and no element groups
remove .setup_groups(), .iter_groups(), .get_cell_offsets()
remove .groups, .mat_ids_to_i_gs, .cell_offsets attributes
update orient_elements() C function for C Mesh, update cmesh.pyx
update FEDomain.fix_element_orientation() for CMesh
update FEDomain__init__() - set self.shape.n_el
update region_leaf() for no element groups, use CMesh
update create_bnf(): remove E_CI2, rename E_CI1 -> E_CI
update tests/test_regions.py
fix element orientation in FEDomain.__init__() before setting local entities
new FEDomain.get_conn(), update .__init__() to disallow multiple cell kinds
update remaining FEDomain methods for no element groups - update .get_element_diameters(), .create_surface_group(), .refine()
update refine_*() for no element groups
update refine_2_3(), refine_2_4(), refine_3_4(), refine_3_8()
update FEDomain.refine() for current refine_*()
update Domain.save_regions_as_groups() for no element groups
update FEDomain.get_evaluate_cache() for CMesh
update Region:
update Region for no element groups
update .__init__(), .set_kind(), .update_shape(), .get_entities(), .get_cells(), .get_facet_indices(), .setup_mirror_region(), .get_mirror_region(), .get_n_cells()
remove .igs property, ._igs, .ig_map, .ig_map_i attributes
remove .get_vertices(), .get_edges(), .get_faces(), .get_facets(), .iter_cells(), .get_cell_offsets()
remove unused _try_delete()
fix Region.get_facet_indices() to setup required connectivity
new Region.get_cell_indices()
remove unused Region.get_vertices_of_cells()
fields:
update VolumeField._check_region(), ._setup_geometry() for no element groups
remove unused FEField._setup_approximations() (re-implemented in subclasses)
update FEField and subclasses for no element groups
setup of global basis of volume nodal fields works
remove FEField.igs, .aps attributes
new FEField.ap attribute
update FEField._setup_global_base(), .setup_coors()
update VolumeField._setup_approximations(), ._init_econn(), ._setup_vertex_dofs()
update H1NodalMixin._setup_facet_orientations(), ._setup_facet_dofs(), ._setup_bubble_dofs()
update Field.get_mapping()
update FEField._setup_esurface(), ._get_facet_dofs(), .get_data_shape(), .interp_to_qp(), .create_mapping()
rename & update FEField.get_dofs_in_region_group() -> .get_dofs_in_region()
update VolumeField._setup_surface_data(), ._setup_point_data(), .get_econn(), .average_qp_to_vertices()
update H1HierarchicVolumeField._init_econn(), ._setup_facet_dofs(), ._setup_bubble_dofs(), .set_dofs()
update H1NodalMixin.set_dofs()
remove Field.get_dofs_in_region()
remove facet_desc argument of H1HierarchicVolumeField._setup_facet_dofs()
update FEField linearization functions for no element groups
update eval_in_els_and_qp()
update get_eval_expression(), create_expression_output()
update FEField.linearize()
update SurfaceField for no element groups
update ._check_region(), ._setup_geometry(), ._setup_approximations(), .setup_extra_data(), ._init_econn(), ._setup_vertex_dofs(), ._setup_bubble_dofs(), .get_econn(), .average_qp_to_vertices()
update H1DiscontinuousField for no element groups - update ._setup_approximations(), ._setup_global_base()
update FEField.create_mesh() for no element groups
update H1NodalVolumeField.interp_v_vals_to_n_vals() for no element groups
update get_facet_dof_permutations() for no element groups
update find_ref_coors(), evaluate_in_rc() for no element groups
update H1NodalMixin.evaluate_at() for no element groups - update get_ref_coors()
IGA:
update IGDomain.__init__() for no element groups
update IGField for no element groups
update .__init__(), .get_econn(), .get_data_shape(), .set_dofs(), .create_mapping()
rename and update .get_dofs_in_region_group() -> .get_dofs_in_region()
Term, Terms:
update ConnInfo for no element groups - remove ConnInfo.iter_igs()
remove vector_chunk_generator(), CharacteristicFunction()
remove unused Term.__call__(), ._call()
remove Terms.set_current_group()
update Term for no element groups
remove .char_fun attribute
remove .get_current_group(), .set_current_group(), .igs(), .iter_groups()
update .setup(), .get_conn_info(), .get_args(), .get_approximation(), .get_physical_qps(), .get_mapping(), .get_data_shape(), .get(), .evaluate(), .assemble_to()
update docstring of .assign_args(), .check_args()
fix Term.eval_complex() - force complex output also for real arguments
remove sfepy/terms/terms_new.py - NewTerm and subclasses
update FieldVariable for no NewTerm
remove .clear_bases(), .setup_bases(), .clear_current_group(), .set_current_group(), .val(), .val_qp(), .grad(), .grad_qp(), .iter_dofs(), .get_element_zeros(), .get_component_indices()
update .__init__()
remove compare_scalar_terms.py, compare_vector_terms.py examples
update PhysicalQPs for no element groups
update .__init__(), .get_shape()
remove .get_merged_values()
update Material for no element groups
update .set_data(), .set_data_from_variable(), .update_data(), .get_data(), ._get_data(), .get_constant_data(), .reduce_on_datas()
update eval_nodal_coors() for no element groups
update Approximation and subclasses for no element groups
update Approximation.__init__(), .eval_extra_coor(), .setup_surface_data(), .setup_point_data(), .get_connectivity(), .describe_geometry()
remove Approximation.ig attribute
update DiscontinuousApproximation.eval_extra_coor()
update SurfaceApproximation.__init__()
update FESurface for no element groups - update .__init__(), .setup_mirror_connectivity()
update Equations.get_graph_conns() for no element groups
update EquationMap.map_equations() for no element groups
update create_adof_conns() for no element groups
update Mapping.from_args() for no element groups - update get_physical_qps(), get_mapping_data()
update FieldVariable for no element groups
update .get_mapping(), .get_dof_conn(), .time_update(), .setup_initial_conditions(), .get_approximation(), .get_data_shape(), .evaluate(), .get_state_in_region(), .get_element_diameters()
miscellaneous updates:
clean up meshutils.[ch]
clean up sfepy/discrete/fem/fea.py
update set_mesh_coors() for current Mesh
update refine_reference() for no element groups
update compute_nodal_normals(), extend_cell_data() for no element groups
update StabilizationFunction.__call__() for no element groups
update ConstantFunctionByRegion.__init__() for no element groups
scripts:
script/extract_surface.py: update for no element groups
use Mesh.from_region()
allow surface mesh saving also for 2D meshes
script/save_basis.py: update save_basis_on_mesh() for no element groups
update homogenization recovery functions for no element groups
update get_output_suffix(), .recover_bones(), .recover_paraflow(), .recover_micro_hook()
terms:
update membrane describe_geometry() for no element groups
update TLMembraneTerm for no element groups - update .__init__(), .get_fargs()
update hyperelastic terms for no element groups
update HyperElasticBase.__init__(), .get_fargs()
update BulkPressureTLTerm.get_fargs()
update BulkPressureULTerm.get_fargs()
update contact surface terms for no element groups
update ContactPlaneTerm.get_fargs()
update ContactSphereTerm.get_fargs()
remove commented-out code in hyperelastic terms
examples and tests:
fix mesh_hook() in examples/diffusion/laplace_1d.py
update examples/linear_elasticity/its2D_3.py for no element groups
update examples/homogenization/rs_correctors.py for no element groups, use cells of channels regions directly
update tests for no element groups and current Mesh
add docstring to FieldVariable.get_state_in_region()
docs: update for current sources
improve finding reference element coordinates of physical points
merge branch improve-find-ref-coors - partially fixes #285
update gtr_normalize_v3() for 2D - add dim argument
new mesh_get_facet_normals() C function
new CMesh.get_facet_normals()
update gtr_dot_v3() for 2D - add dim argument
update orient_elements() for current gtr_dot_v3()
fix tensor-product mode in inverse_element_mapping()
split cmesh.pyx -> cmesh.pyx + cmesh.pxd
add verbose argument to gtr_normalize_v3()
new refc_find_ref_coors() C function in new refcoors.c
new sfepy/discrete/fem/extmods/refcoors.[ch]
new _mul_c_add_v3(), _intersect_line_plane(), _intersect_line_triangle(), _get_cell_coors(), _get_tri_coors(), _get_xi_dist()
new find_ref_coors() in new crefcoors.pyx extension module
new sfepy/discrete/fem/extmods/crefcoors.pyx
update sfepy/discrete/fem/extmods/setup.py
update get_ref_coors() for new find_ref_coors() C function
remove old find_ref_coors() Cython function
move FEDomain.get_evaluate_cache() -> FEField.get_evaluate_cache() - update for new find_ref_coors()
set failed values to nan in H1NodalMixin.evaluate_at() if not returning status, fix and update docstring
update Probe.probe() for current code
reorganize main scripts
merge branch reorganize-scripts
add main sfepy-run wrapper and scripts-common dir
add sfepy.in_source_tree dependency
update doc build scripts for man builder, add sfepy manpage
add scripts-common links and modify setup call parameters
update user’s guide for sfepy-run command
scripts:
postproc.py: new –parallel-projection option - update Viewer.call_mlab(), .render_scene()
miscellaneous updates:
change default verbose value to False in FieldVariable.evaluate_at() + related
update FEDomain.get_evaluate_cache() for new verbose argument
force solution in make_l2_projection_data() by decreasing absolute tolerance
add boilerplate in eval_ns_forms.py
fix probe constructors to obey share_geometry - fix PointsProbe, LineProbe, RayProbe, CircleProbe
new Probe.get_evaluate_cache(), update .probe()
add nonlinear solver options argument to projection functions - project_by_component(), update make_l2_projection(), make_l2_projection_data()
fix memory leak - new CMesh.__dealloc__(), new mesh_free() C function
fix graph_components() (according to cs_graph_components() in scipy.sparse)
add igakit as optional dependency in setup.py, update sfepy/version.py
new mesh function: expand2d - converts tri/quad mesh to tetra/hexa
allow matrix_hook to handle residual vector
update splinebox.py: number of segments as an input argument to __init__()
remove unused variable in evaluate_in_rc()
update plot_wireframe() for non-string color specifications
fix DOWNLOAD_URL
fix has_several_times, has_several_steps in Viewer.call_mlab()
speed up GenericFileSource.create_dataset()
check number of dimensions of material array in Material.set_data()
examples and tests:
clean up tests/test_linear_solvers.py
new example: Darcy flow in multiple compartments
new tests/test_input_darcy_flow_multicomp.py
update test_install.py to test postproc.py with HDF5 output files
terms:
update LinearTractionTerm docstring - explain load shapes
new term: dw_vm_dot_s
replace mulATB_integrate() by mulAB_integrate() with multiple modes; new: actBfT()
docs:
sync module index of developer guide with current sources
update release tasks for sfepy-run
from 2014.4 to 2015.1¶
support multiple fields in IGA
merge branch iga-multifield
move NurbsPatch-related code in IGDomain.__init__() to NurbsPatch.__init__()
update IGMapping for nurbs patch other than domain.nurbs
update IGMapping.__init__() - new nurbs argument
update docstring
allow ‘iga*’ approximation order in parse_approx_order()
new NurbsPatch.elevate()
update IGField.__init__() for degree elevation of NURBS basis
new approx_order argument in IGField.__init__()
new parse_approx_order()
use self.nurbs instead of self.domain.nurbs in IGField
update .get_econn(), .set_dofs(), .create_mapping(), .create_output()
new ._get_facets()
remove IGDomain.facets
new meshes/iga/block2d.iga
new examples/navier_stokes/navier_stokes2d_iga.py + test
IGA:
new eval_bspline_basis_tp() - use if all weights are one - new is_nurbs(), update igac.pyx
pre-compute Bernstein basis in eval_mapping_data_in_qp(), eval_variable_in_qp() - update eval_bspline_basis_tp(), eval_nurbs_basis_tp()
fix get_facet_axes() in 2D
fix get_surface_degrees()
fix connectivity types in create_connectivity_1d()
update get_bezier_element_entities() to return also vertices
new create_from_igakit(), update gen_patch_block_domain()
new NurbsPatch._to_igakit(), ._from_igakit(), update .elevate()
update IGField.__init__() for str or None approx_order values
redesign handling of solver parameters
merge branch solver-parameters
new SolverMeta
new format_next(), typeset_to_indent(), make_option_docstring()
new par_template
update Solver to use SolverMeta, new generic Solver.process_conf()
update LinearSolver.get_tolerance() for no tolerances in conf, clean up
update basic linear solvers for SolverMeta, new ._parameters class attribute
update ScipyDirect, ScipyIterative, PyAMGSolver, PETScKrylovSolver, PETScParallelKrylovSolver - remove .process_conf()
update nonlinear solvers for SolverMeta, new ._parameters class attribute
update Newton, ScipyBroyden, Oseen - remove .process_conf()
support extra parameters in Solver.process_conf() - marked by ‘*’ name in _parameters solver attribute
update optimization solvers for SolverMeta, new ._parameters class attribute
update FMinSteepestDescent, ScipyFMinSolver - remove .process_conf()
update remaining linear solvers for SolverMeta, new ._parameters class attribute
update SchurGeneralized, SchurComplement, MultiProblem - remove .process_conf()
remove ‘needs_problem_instance’ solver parameter
remove ‘needs_problem_instance’ from examples
rename Newton parameter ‘problem’ -> ‘is_linear’
update Newton.parameters, .__call__()
update Problem.is_linear(), .set_linear()
docs: update for ‘is_linear’
update examples for ‘is_linear’ (remove default setting, reformat if needed)
update SemismoothNewton for SolverMeta, new ._parameters class attribute - remove .process_conf()
update time-stepping solvers for SolverMeta, new ._parameters class attribute
update StationarySolver, EquationSequenceSolver, SimpleTimeSteppingSolver, ExplicitTimeSteppingSolver, AdaptiveTimeSteppingSolver - remove .process_conf()
update eigenvalue solvers for SolverMeta, new ._parameters class attribute
update ScipyEigenvalueSolver, ScipySGEigenvalueSolver, LOBPCGEigenvalueSolver, PysparseEigenvalueSolver - remove .process_conf()
use SchurComplement solver in linear_elastic_up.py example
solvers:
remove ls.umfpack solver (class Umfpack), replace by ls.scipy_direct
clean up sfepy/solvers/ls.py
remove unneeded code in make_implicit_step()
fix default i_max of LOBPCGEigenvalueSolver, use verbose option
obey verbose option and eigenvectors argument in PysparseEigenvalueSolver
fix default i_max, eps_a
move imports to .__init__() for early failure
new Solver.build_solver_kwargs()
refactor ScipyEigenvalueSolver, ScipySGEigenvalueSolver
ScipyEigenvalueSolver uses dense or sparse scipy linalg functions, new method option, support extra options
ScipySGEigenvalueSolver uses dense lapack functions, remove force_n_eigs option
imports moved to .__init__() for early failure
use Solver.build_solver_kwargs() in ScipyFMinSolver
clean up sfepy/solvers/optimize.py
clean up sfepy/solvers/oseen.py
clean up sfepy/solvers/semismooth_newton.py
scripts:
script/gen_iga_patch.py: new –cp-mode option, update gen_patch_block_domain()
script/gen_gallery.py: update views for centered scene
miscellaneous updates:
new Region.from_cells()
clean up tests/sympy_operators.py
fix get_mem_usage() (workaround of pyparsing object with iteritems of str type)
update units_of_quantities (add density), prefixes (add ‘p’, ‘T’)
fix GenericFileSource.get_bounding_box()
fix mappings, QP and base function key collisions
use integral order instead of name in mapping keys, in QP and base function keys
make region name the first item in mapping keys
update Approximation, SurfaceApproximation, Field, FieldVariable, Term, NewTerm
update QuadraturePoints docstring
support all QuadraturePoints.__init__() arguments in Integral.__init__() - update Integral.get_qp()
update actor positions in Viewer.build_mlab_pipeline() to center scene
fix sympy.zeros() calls for sympy 0.7.6
new bspline functions (curve and surface)
update SplineBox: use bspline.py functions, new test
update BSpline.basis_function_dg() for degree 0
add linear solver argument to make_l2_projection(), make_l2_projection_data()
fix SchroedingerApp.solve_eigen_problem() to request eigenvectors - fix for updated PysparseEigenvalueSolver
tests and examples:
new examples/standalone/interactive/modal_analysis.py
update test_install.py to test modal_analysis.py example
update examples/navier_stokes/navier_stokes2d.py - generated domain, new BC
remove unused rectangle_fine_quad.mesh, rectangle_fine_tri.mesh
regenerate IGA meshes with greville control points mode
new tests/test_input_linear_elastic_iga.py, tests/test_input_poisson_iga.py
new tests/test_eigenvalue_solvers.py
docs:
sync module index of developer guide with current sources
update citing section
update list of applications
update list of IGA examples
update description of IGA field definition
update installation notes:
add Anaconda distribution info
update tested versions
bux-fixes
minor reorganization and clean up
from 2014.3 to 2014.4¶
preliminary support for 1D problems
merge branch 1d
update CMesh for 1D (preliminary support)
update Region, Domain and FEDomain for 1D, update orient_elements() - update geometry_data
update diffusion and Navier-Stokes terms for 1D
update Term.geometries
update tests/test_term_call_modes.py for 1D
update C implementation of hyperelasticity for 1D
update VTKMeshIO.write() for 1D
add 1D reference elements meshes (1_2_1.mesh, 1_2_2.mesh)
new examples/diffusion/laplace_1d.py + test
update SDLinearElasticTerm for 1D
support custom material parameter values in tests/test_term_call_modes.py
update make_term_args()
add custom value for ‘dw_s_dot_grad_i_s’ in Test._test_single_term()
add custom view for laplace_1d.py example to script/gen_gallery.py
update GenericFileSource.get_bounding_box(), .create_dataset() for 1D
merge pull request #276 (VTK probes)
simplify probes, use pyVTK library
Primer - use VTK probes
new postrocessing function based on VTK, example
update User’s guide - postrocessing filters
interactive example for Primer
merge branch its-interactive-example
update nodal_stress() to accept user-provided integrals
new examples/linear_elasticity/its2D_interactive.py
docs: add interactive example section to primer
scripts:
script/gen_iga_patch.py: report number of DOFs per axis
fix path in script/gen_lobatto1d_c.py - bug introduced in ec186b8c69b0719f483e11a864092a21a608a203
clean up script/edit_identifiers.py
fix sys.path in auxiliary scripts and standalone examples - for cases where the current directory (i.e. top level sfepy directory) is not added automatically
script/gen_gallery.py:
omit examples that use VTK probes - bad interaction, probably with Mayavi, leads to segfault
simplify section titles, generate better labels
miscellaneous updates:
fix number of returned values for no refinement in refine_reference()
fix make_l2_projection_data() for parameter variables
IGA: update plot_iso_lines() for curves in 2D
tests and examples:
update test_install.py for current linear_elastic_probes.py
prevent modifying linear_elastic.py namespace in derived examples
new tests/test_input_linear_elastic_probes.py
docs:
fix testing instructions for installed build
update user’s guide for interactive probing example in primer
fix IGA section for current sources
clean up script/gen_term_table.py, use common help and docstring
update script/gen_term_table.py: simpler table, correct links to term classes
update doc/index.rst for 1D and new gallery labels
sync doc/introduction.rst with doc/index.rst
from 2014.2 to 2014.3¶
speed-up IGA by C implementation of NURBS basis evaluation
merge branches iga-c and iga-c-2
new eval_bernstein_basis() in C in sfepy/discrete/iga/extmods/
new sfepy/discrete/iga/extmods/nurbs.[ch]
new sfepy/discrete/iga/extmods/igac.pyx
new setup.py files
support DEBUG_FMF define in sfepy/discrete/iga/extmods/setup.py
update IGDomain.__init__() to have nurbs.cs in FMField compatible shape
new ravel_multi_index(), unravel_index() in C
new eval_nurbs_basis_tp() in C
new array2puint2(), array2puint1() helper functions
change return value of compute_bezier_extraction_1d() to 3D array
change nurbs.degrees dtype to int32 in IGDomain.__init__()
new eval_mapping_data_in_qp(), eval_variable_in_qp() in C - use in sfepy/discrete/iga/mappings.py
new eval_in_tp_coors() in C
update NurbsPatch.__call__() to use eval_in_tp_coors()
generalize linear combination boundary conditions to work between different fields/variables and to support non-homogeneous periodic conditions (non-zero right-hand side or shift)
merge branch ‘lcbc’ - closes #179, #267
update transform_lcbcs() for new LCBC syntax
the syntax: region[, times], dofs, dof_map_fun, kind[, other arguments]
update Conditions.from_conf(), LinearCombinationBC.__init__() for new syntax
new LinearCombinationBC.canonize_dof_names()
new are_disjoint()
new LinearCombinationBC.get_var_names()
check that regions are disjoint in Variables.setup_lcbc_operators()
update Variables.setup_lcbc_operators() for new operators (to be done)
remove FieldVariable.create_lcbc_operators()
new kind attribute of LCBC operators
update LCBCOperator for two variables in two regions
rename & update LCBCOperator -> MRLCBCOperator (model reduction)
new general LCBCOperator for tying two variables in two regions
reimplement LCBCOperators, use common LCBCOperator constructor signature
update .__init__(), .add_from_bc(), .append(), .finalize()
move make_global_lcbc_operator() -> new LCBCOperators.make_global_operator()
new ShiftedPeriodicOperator
provide some defaults for long syntax in transform_lcbcs()
store field in MRLCBCOperator
update LCBC operators new base classes - update IntegralMeanValueOperator, RigidOperator, NoPenetrationOperator, NormalDirectionOperator
fix MRLCBCOperator active equation map for non-scalar variables
update MRLCBCOperator.treat_pbcs()
update Variables.setup_lcbc_operators(), .__init__(), FieldVariable.__init__()
new Variables.has_lcbc_rhs
rename Variables.op_lcbc, .rhs_lcbc -> .mtx_lcbc, .vec_lcbc
remove FieldVariable.has_lcbc
set vec_lc to None in LCBCOperators.make_global_operator() when no rhs
update LCBCEvaluator, eval_equations() for renamed operators
add comment to State.get_reduced()
update meshes/2d/square_quad.mesh to have two cell groups
simplify transform_conditions() - LCBCs treated in transform_lcbcs()
docs: update essential boundary conditions description, add EPBCs, LCBCs
tests and examples:
update examples and tests for new LCBC syntax
new examples/diffusion/laplace_coupling_lcbcs.py + test
new examples/linear_elasticity/elastic_shifted_periodic.py + test
new examples/standalone/interactive/laplace_shifted_periodic.py
new tests/test_lcbcs.py, test_laplace_shifted_periodic()
add custom views for laplace_coupling_lcbcs.py, elastic_shifted_periodic.py to script/gen_gallery.py
support non-constant essential boundary conditions given by a function in IGA
merge branch ‘iga-ebc’
update IGField.get_econn() for surface connectivities
simplify IGField.get_dofs_in_region_group() by using .get_econn()
new get_facet_axes()
new solve() convenience wrapper
new create_boundary_qp()
new get_surface_degrees()
update IGField.set_dofs() for DOFs given by function, update docstring - initial implementation
examples:
update examples/linear_elasticity/linear_elastic_iga.py for EBCs by function
update custom view for linear_elastic_iga.py example in script/gen_gallery.py
IGA:
fix IGDomain.__init__() for standalone use - reset regions
fix IGField.create_output() for no key argument
new sfepy/discrete/iga/domain_generators.py - new gen_patch_block_domain()
fix plot_nurbs_basis_1d to use ax argument
regions:
new Region.kind_tdim attribute, new .set_kind_tdim(), update .set_kind()
make ig argument optional in Region.get_entities(), signature change
update Region.contains() to use other region kind entities
make sure entities are initialized in Region.get_entities()
update Region.setup_from_highest() - new allow_lower argument
works also when the highest dimension of entities is lower than requested
fixes selectors like ‘vertices of surface *f vertices in (x < 0.0)’
new Region.finalize(), update Domain.create_region()
fix region definitions in tests and examples as reported by Region.finalize()
postprocessing and visualization:
remove import lines from sfepy/postprocess/__init__.py, update affected imports
update Viewer.call_mlab(): do not show GUI if show option is False
applications:
update SchroedingerApp.save_results() for custom mesh in out[‘__mesh__’]
relax too strict assertion in DensityVolumeInfo.__call__()
new: micro-recovery hook allows to return some values to the “master” macro-problem
scripts:
script/gen_iga_patch.py: use gen_patch_block_domain()
script/gen_iga_patch.py: plot 1D basis along patch mid-line
miscellaneous updates:
remove prints and config.py file generation from setup.py files
support user-specified ebcs, epbcs in Problem.save_ebc(), update docstring
fix Newton.__init__(), Oseen.__init__() to obey log plot option
normalize paths in top_dir, data_dir and base_dir
update import_file() to use full package paths for sfepy modules - prevents name clashes for different fields.py files
add can_reload argument to import_file()
do not force module reload in load_classes()
fix issue #263, ConstantFunctionByRegion
clean up sfepy/discrete/conditions.py
use os.sep instead of ‘/’ for the pathname separator in import_file() - fix portability issue
fix extend_cell_data() for several groups, new average_surface argument
change keys in transform_epbcs()
report unknown LCBC kind in LCBCOperators.add_from_bc()
clean up run_tests.py, sfepy/base/testing.py, sfepy/discrete/materials.py, tests/tests_basic.py, sfepy/mechanics/matcoefs.py
fix set_mesh_coors() - update also cmesh coordinates
update get_debug() to allow frame specification in debug()
update MED file support, fix this issue: https://groups.google.com/forum/#!msg/sfepy-devel/z1e83Xgl1_U/884jDfKzKPsJ
fix setup.py - add missing plot_logs.py script
remove unused sfepy/physics/energy.py
examples:
do not force examples to be in a package - update import_file(), ProblemConf.from_file()
remove examples/diffusion/octahedron.py + test - no added value w.r.t. other diffusion examples
update examples/linear_elasticity/linear_elastic.py: comments -> docstring
docs:
module index of developer guide with current sources
fix docs generation without igakit
fix typeset_term_table() for import_file() using full package paths
add missing figure
replace alphas8bit with alphas - word_free with alphas8bit as default argument value in get_standard_type_defs() and list_dict() breaks sphinx docs generation on platforms with non utf-8 locale
new section on exploring the code in developer guide
fix download page
migrate tutorial “Using Salome with SfePy” from google site, see #171
merge branch ‘theory-docs’
new doc/ebcs_implementation.rst - explanation of EBCs implementation
move IGA section from tutorial to user’s guide
new doc/theory.rst
move notes on solving PDEs from doc/tutorial.rst to new doc/solving_pdes_by_fem.rst
add doc/ebcs_implementation.rst to doc/theory.rst
update doc/index.rst
remove doc/notes.rst
simplify paragraph in doc/index.rst
simplify doc/introduction.rst
put Primer under Examples
merge pull request #275 (short syntax)
remove long syntax from the user’s guide
new doc page with long syntax
tutorial with short syntax of keywords, closes #272
add introductory paragraph to examples
from 2014.1 to 2014.2¶
preliminary support for isogeometric analysis
merge branch ‘iga’
new iga.py: compute_bezier_extraction_1d(), _get_knots_tuple(), eval_bernstein_basis(), compute_bezier_extraction(), get_raveled_index(), tensor_product(), combine_bezier_extraction(), create_connectivity_1d(), create_connectivity(), compute_bezier_control(), get_unraveled_indices(), eval_nurbs_basis_tp(), eval_variable_in_qp(), get_bezier_topology(), get_patch_box_regions(), get_bezier_element_entities(), eval_mapping_data_in_qp()
new plot_nurbs.py: plot_parametric_mesh(), plot_control_mesh(), plot_iso_lines(), plot_nurbs_basis_1d(), plot_bezier_mesh(), _get_edges(), plot_bezier_nurbs_basis_1d()
new utils.py: create_linear_fe_mesh(), create_mesh_and_output(), save_basis()
new io.py: write_iga_data(), read_iga_data()
add filename_domain as alternative to required keywords
update PDESolverApp.setup_output_info() for filename_domain keyword
simplify Domain.has_faces()
remove unused Domain.get_conns()
initialize shape in Domain.__init__()
move common Domain code into new sfepy/discrete/common/domain.py
move & update region_leaf()
move region_op(), Domain.get_centroids(), .has_faces(), .reset_regions(), .create_region(), .create_regions(), .save_regions(), .save_regions_as_groups()
rename original Domain -> FEDomain, update FEDomain.__init__()
new Domain.__init__()
new sfepy/discrete/iga/domain.py - new IGDomain
new .from_file(), .__init__()
update Problem.from_conf() for FEDomain, IGDomain
new NurbsPatch - ._get_ref_coors_1d(), .__call__(), .evaluate()
move common Field code into new sfepy/discrete/common/fields.py
move Field.from_args(), .from_conf(), ._setup_kind()
move parse_approx_order(), setup_extra_data(), fields_from_conf()
rename original Field -> FEField, update FEField.__init__()
update VolumeField, SurfaceField parent class
new parse_shape(), update FEField.__init__()
new sfepy/discrete/iga/fields.py - new IGField
new .__init__(), .get_true_order(), .is_higher_order()
new .get_econn(), .setup_extra_data() - volume only
new IGField.get_dofs_in_region_group()
new IGField.set_dofs() - only for a constant value over an entire patch side
new IGField.create_mapping()
new IGField.create_output() - initial version with hard-coded values
output mesh corresponding to uniform parametric mesh is returned as out[‘__mesh__’]
update Problem.save_state() for custom mesh in out[‘__mesh__’]
update parse_approx_order(), Field.from_conf() for IGField
get dimension from domain in FieldVariable._set_field()
move FEField.get_dofs_in_region() into Field
move common Mappings code into new sfepy/discrete/common/mappings.py
move PhysicalQPs, get_mapping_data(), get_jacobian(), get_normals()
replace create_mapping() by new Mapping.from_args()
rename original Mapping -> FEMapping - move .get_physical_qps()
update VolumeMapping, SurfaceMapping parent class
move mapping handling code from FEField to Field
move .clear_mappings(), .save_mappings(), .get_mapping()
update Field.get_mapping() to use .create_mapping(), fix docstring
update FEField.create_mapping() to return both CMapping and Mapping
do not use domain shape in Field.get_mapping() - remove sharing of full group mappings
do not use mesh coordinates in Material.update_special_data()
new sfepy/discrete/iga/mappings.py - new IGMapping
new .__init__(), .get_geometry(), .get_physical_qps(), .get_mapping()
update Mapping.from_args() for IGMapping
use Field.get_econn() in FieldVariable.evaluate()
do not use Approximation.get_connectivity()
update VolumeField.get_econn() - add integration argument
update signature of SurfaceField.get_econn(), IGField.get_econn()
move FieldVariable.get_data_shape() functionality to Field subclasses
new FEField.get_data_shape(), IGField.get_data_shape()
remove Approximation.get_v_data_shape(), .get_s_data_shape()
update H1DiscontinuousField.extend_dofs(), .remove_extra_dofs() for FEField
new is_surface attribute of fields
update VolumeField._setup_geometry(), SurfaceField._setup_geometry()
update FieldVariable._set_field() - does not import SurfaceField from sfepy.discrete
update sfepy/discrete/__init__.py for common Domain, Field
update sfepy/discrete/fem/__init__.py for FEDomain
update domain creating code for FEDomain
update ‘surface_extra’ assembling cells in Term.get_assembling_cells()
for Field.get_econn() in FieldVariable.evaluate() - surface regions have no more a complete group DOF connectivity
update ‘volume’ Term.get_assembling_cells() for subdomains
for Field.get_econn() in FieldVariable.evaluate() - subdomain volume regions have no more a complete group DOF connectivity
trivial now, could be removed
update FieldVariable.setup_initial_conditions() to use Field.set_dofs()
tests and examples:
fix get_pars() in tests/test_functions.py for None in coors argument
update import in _integrate() in tests/test_term_consistency.py
new meshes/iga/patch2d.iga
new examples/diffusion/poisson_iga.py
new meshes/iga/block3d.iga
new examples/linear_elasticity/linear_elastic_iga.py
update test_install.py to test poisson_iga.py example
scripts:
new script/gen_iga_patch.py
add custom view for poisson_iga.py example to script/gen_gallery.py, sort custom dict by keys
add custom view for linear_elastic_iga.py example to script/gen_gallery.py
docs:
update developer guide for IGA, split sfepy.discrete contents list
new IGA section in tutorial, update links and index
update optional installation dependencies
postprocessing and visualization:
postproc.py: update –layout option for row#n, col#n layouts - update get_position_counts(), Viewer.get_size_hint()
always use cell-to-point filter for domain-specific plots
point scalars work as color_name
update Viewer.build_mlab_pipeline()
update file sources for providing both steps and times
update FileSource.reset(), .get_step_range()
remove FileSource.set_step(), VTKFileSource.get_step_range(), VTKSequenceFileSource.get_step_range(), GenericFileSource.get_step_range() GenericSequenceFileSource.get_step_range()
update GenericFileSource.__init__(), .read_common(), .file_changed()
new FileSource.get_step_time(), .get_ts_info()
new VTKSequenceFileSource.__init__()
new GenericSequenceFileSource.read_common()
update postproc.py, Viewer for updated file sources, add slider for times
update Viewer.call_mlab()
update SetStep - new ._time_editor, .time, .time_low, .time_high, .is_adjust ._time_changed()
update .__source_changed(), ._step_changed(), ._file_changed_changed()
update Viewer.save_animation() for selected steps or times
update Viewer.get_animation_info(), .encode_animation()
remove FileSource.get_step_range()
remove animate, anim_format arguments from Viewer.__init__()
update view_file(), postproc.py
update Viewer.call_mlab(), make_animation()
update Viewer, ViewerGUI for saving snapshots in given ranges of steps/times
update Viewer.call_mlab(), make_animation()
update SetStep:
new .seq_* traits
new .init_seq_selection(), ._seq_n_step_changed(), ._seq_dt_changed()
new ClosingHandler
update ViewerGUI:
custom quit button
remove button_make_animation, button_make_snapshots buttons
new button_make_animation_steps, button_make_snapshots_steps button_make_animation_times, button_make_snapshots_times buttons + their handlers
postproc.py: new –time option
change default of –step to None, –step has precedence over –time
update view_file(), Viewer.call_mlab()
postproc.py: improve –list-ranges
for HDF5 result files, output union of ranges for all steps if –step or –time are not given
output in form suitable for –ranges
fix suffix returned by Viewer.get_animation_info()
remove auto_screenshot argument of Viewer.__init__() - update .call_mlab()
postproc.py: update –output option behaviour, update docstring
input-output:
update defaults for missing output data attributes in HDF5MeshIO.write() - only mode and data are required
provide better default values in MeshIO.read_times()
scripts:
new script/plot_logs.py - plot text file logs of variables saved by Log
update schroedinger.py: remove mesh generation options, simplify
remove –create-mesh, –2d, –mesh, –mesh-dir options
new –n-eigs, –tau options for updated examples/quantum/
update docstring
script/extract_surface.py: fix default value of –mesh option
update script/gen_gallery.py for current Viewer - save image explicitly
fix docstring formatting of script/convert_mesh.py
terms:
make material argument of dw_tl_surface_traction optional - update SurfaceTractionTLTerm, dw_tl_surface_traction()
new VolumeSurfaceTLTerm (d_tl_volume_surface) - new d_tl_volume_surface()
move SurfaceTractionTLTerm.compute_family_data() to new common class
new HyperElasticSurfaceTLBase
update SurfaceTractionTLTerm, VolumeSurfaceTLTerm
new SurfaceFluxTLTerm (d_tl_surface_flux) - new d_tl_surface_flux()
fix setting cells of normals in dw_surface_v_dot_n_s(), dw_surface_s_v_dot_n()
fix arg_shapes of LaplaceTerm
new SurfaceFluxOperatorTerm (dw_surface_flux) - new dw_surface_flux()
fix mat_le_stress() for heterogeneous parameters in 2D
solvers:
update cm_pb solver: add “master problem” to kwargs
improve linear solution precision warning message in Newton.__call__()
new eps_mode parameter of Newton solver, update conv_test()
clean up sfepy/solvers/nls.py, add module and conv_test() docstrings
update PETScParallelKrylovSolver - new log_dir option - closes #250
remove obsolete is_plot option from Newton and Oseen solvers
miscellaneous updates:
fix create_adof_conns(): problem with trace
fix docstring of Region.get_facet_indices()
new get_simplex_volumes()
update read_log() for general (float) x values
fix read_log() for vlines before actual data
fix solve_pde() to preserve conf.options class
use tight layout in LogPlotter.process_command() after plotting labels
fix surface mode in extend_cell_data()
fix Problem.create_evaluable() to use copies of problem variables
update test_install.py for meshes/quantum/ and schroedinger.py changes
use tempfile in gen_misc_mesh()
remove mesh coordinate transformation code in Problem.from_conf()
remove tmp/.ignore
update make_l2_projection_data() for array data, new order argument, fix overwriting of target._variables
new get_condition_value(), update EquationMap.map_equations()
update EquationMap.map_equations() to use get_condition_value() for EPBCs
tests and examples:
increase required precision in examples/acoustics/acoustics3d.py
allow trying mesh refinement in tests/test_linear_solvers.py
clean up tests/test_volume.py
update tests/test_volume.py to test TL volume terms, new test_volume_tl()
update examples/quantum/ - use meshes/quantum/square.mesh
update quantum_common.py to use square.mesh, add docstring, increase approximation order to 2, update common() arguments
new arguments to define() in examples: n_eigs, tau
remove unused meshes in meshes/quantum/
update meshes/quantum/square.geo
new meshes/quantum/square.mesh (corresponds to meshes/quantum/square.geo)
docs:
update developer guide for sfepy/discrete/
update support section
update years in LICENSE
replace link by contents of LICENSE, new doc/license.rst
update year in doc/conf.py
remove obsolete Intel Mac installation instructions
update platform-specific notes
simplify INSTALL, update installation and links
new citing section in index
from 2013.4 to 2014.1¶
new handling of field and variable shapes:
use region space dimension instead of field shape in vector LCBC operators
use DOF per node count instead of field shape in IntegralMeanValueOperator
update Field.from_args(), __init__() docstrings (shape parameter)
update Field: new n_components, val_shape attributes, new H1Mixin
inherit H1NodalMixin from H1Mixin, update .set_dofs()
inherit H1HierarchicVolumeField from H1Mixin, update .set_dofs()
remove n_components argument in Variable, FieldVariable constructors
update Variable.__init__(), FieldVariable.__init__()
update Variable._setup_dofs() - new n_components, val_shape arguments
update FieldVariable._set_field() - set n_components, val_shape from field
update sfepy.fem modules for no n_components argument
update scripts, examples and tests for no n_components argument
update docs for no n_components argument
remove Field.setup_dof_conns() (duplicated in VolumeField.setup_dof_conns())
remove dpn argument of {VolumeField, SurfaceField}.setup_dof_conns()
create active DOF connectivities directly from field connectivities:
fields have no dof_conns dict
remove create_dof_conn(), setup_dof_conns(), Field.clear_dof_conns() VolumeField.setup_dof_conns(), SurfaceField.setup_dof_conns()
new VolumeField.get_econn(), SurfaceField.get_econn()
update Field.__init__()
remove Variables.setup_adof_conns(), FieldVariable.setup_adof_conns()
new create_adof_conns(), Variables.set_adof_conns()
update create_adof_conn(), Variable.__init__()
update sfepy.fem for create_adof_conns()
remove Equations.setup()
remove setup, make_virtual, verbose arguments of Equations.__init__()
remove setup, make_virtual arguments of Equations.from_conf()
update Equations.time_update(), create_evaluable(), ProblemDefinition.set_equations()
update Term.standalone_setup() for create_adof_conns()
variables, equations:
update active DOF connectivities only when needed in Equations.time_update()
initialize adof_conns in Variables.__init__()
remove active argument of FieldVariable.get_dof_conn()
update Variable.get_primary(), .get_dual() for incomplete variables
selective equations evaluation - new ProblemDefinition.eval_equations()
update Equations.evaluate() - split weak branch, fix/update docstring
add verbosity argument to FieldVariable.evaluate_at()
terms:
update LinearTractionTerm: new eval mode
regions:
fix passing region kind argument in Region.from_facets()
add parent argument to Region.from_facets()
report no entities error in Region.setup_from_highest()
solvers:
update ProblemDefinition to provide and store default nls_status
update .__init__(), .init_solvers() to use .set_solvers_instances()
update .set_solvers_instances() to set .nls_status
update .solve() to use nls_status and set .nls_status
fix make_implicit_step() to use nls_status argument in all time steps
fix time step decrease in adapt_time_step() - update current time
update VariableTimeStepper.set_time_step() - new update_time argument
mechanics:
new get_t4_from_t2s() helper function
clean up, update tests/test_tensors.py
homogenization:
clean up sfepy/homogenization/engine.py
clean up homogen.py
large deformation:
prevent false memory errors after warp violation in dq_finite_strain()
fix false memory errors after warp violation in dq_tl_finite_strain_surface()
fix error reporting of finite strain family functions
mesh generation:
vectorize gen_block_mesh(), new get_tensor_product_cells()
scripts:
new script/plot_times.py - taken from plant cell mechanics project
miscellaneous updates:
fix transform_asm_vectors()
re-add ‘2_2’, ‘3_2’ to vtk_cell_types
remove unused filename argument of IntegralMeanValueOperator.__init__()
save LCBC data only in the initial time step of LCBC application
fix ProblemDefinition.save_ebc() for no equations (–solve-not option)
move sfepy/physics/radial_mesh.py into specialized repository
new sfepy/base/mem_usage.py - get_mem_usage(), print_mem_usage()
new ProblemConf.update_conf(), .add_missing()
fix link in docstring of ProblemDefinition.update_materials()
update parsing lexical elements of problem configuration - new list_dict()
fix approx_order description in Field.__init__() docstring
update QuadraturePoints.from_table() docstring
fix IndexError in Mesh.from_region() / detected on Win8
update plot_dofs.py for 1D
update ConstantFunctionByRegion.get_constants() to use Region.get_cells()
update SplineBox.__init__(), new coors_shape attribute
tests and examples:
fix typo in examples/piezo_elasticity/piezo.py
fix docstring of examples/navier_stokes/stokes_slip_bc.py
update test_install.py to test mesh generation/conversion scripts
update test_install.py to test probe.py, extractor.py
general clean up:
remove kill_* shell scripts
remove unused Variable.get_full_state()
remove .hgignore
remove sfepy/mesh/femlab.py, sfepy/mesh/meshutils.py
remove friction_slip.py, sfepy/mechanics/friction.py
remove isfepy, sfepy/interactive/ - update Viewer docstring, docs
remove plotPerfusionCoefs.py
remove script/config.py
remove sfepy/base/progressbar.py - update sfepy/ for no progress bar
split sfepy.fem - separate FEM-specific and general modules:
merge branch ‘split_fem’
rename sfepy/fem/ -> sfepy/discrete/fem/
move general files from sfepy/discrete/fem/ to sfepy/discrete/
update setup.py files for new paths
split fem/dof_info.py -> common/dof_info.py, fem/lcbc_operators.py
update sfepy/discrete/__init__.py, sfepy/discrete/fem/__init__.py
update sfepy/ for new paths
update top level scripts for new paths
update examples for new paths
update tests for new paths
update scripts for new paths
update docs for new paths
update docstrings for new paths
update MANIFEST.in for new paths
require integral argument in Approximation.describe_geometry()
make Region.create_mapping() a standalone function create_mapping()
update get_physical_qps()
fix Region.iter_cells() for subdomains
add cell_offsets attribute to Domain, use it in Region
simplify Domain.get_cell_offsets()
move fem/region.py -> common/region.py
new Domain.get_evaluate_cache()
remove mesh argument from probe constructors, remove all mesh references
update Probe.probe() to use Domain.get_evaluate_cache()
simplify Probe.__init__()
move discrete/fem/probes.py -> discrete/probes.py
update examples for moved and updated probes
rename ProblemDefinition -> Problem
rename many modules (fix according to naming conventions):
genPerMesh.py -> script/tile_periodic_mesh.py
findSurf.py -> script/extract_surface.py
script/evalForms.py -> script/eval_ns_forms.py
runTests.py -> run_tests.py
sfepy/optimize/shapeOptim.py -> sfepy/optimize/shape_optim.py
sfepy/optimize/freeFormDef.py -> sfepy/optimize/free_form_def.py
termsAcoustic.{py, c, h} -> terms_acoustic.{py, c, h}
termsAdjointNavierStokes.{py, c, h} -> terms_adj_navier_stokes.{py, c, h}
termsBasic.{py, c, h} -> terms_basic.{py, c, h}
termsBiot.{py, c, h} -> terms_biot.{py, c, h}
termsElectric.{py, c, h} -> terms_electric.{py, c, h}
termsLaplace.{py, c, h} -> terms_diffusion.{py, c, h}
termsLinElasticity.{py, c, h} -> terms_elastic.{py, c, h}
termsNavierStokes.{py, c, h} -> terms_navier_stokes.{py, c, h}
termsPiezo.{py, c, h} -> terms_piezo.{py, c, h}
termsPoint.py -> terms_point.py
termsSurface.{py, c, h} -> terms_surface.{py, c, h}
termsVolume.{py, c, h} -> terms_volume.{py, c, h}
termsHyperElasticity.{c, h} -> terms_hyperelastic.{c, h}
formSDCC.{c, h} -> form_sdcc.{c, h}
tests/testsBasic.py -> tests/tests_basic.py
docs:
fix gallery page title
new download page with the downloads counter
add debugging section to installation.rst
update development tab
fix and update description of defining material parameters by functions
delete findSurf.py related text
sync module index of developer guide with current sources
from 2013.3 to 2013.4¶
fix nodal polynomial spaces for orders >= 3:
merge branch ‘fix_nodal_basis’ - closes #205
fix get_facet_dof_permutations(), H1NodalMixin._setup_facet_orientations()
permutations should come from facet nodes in reference order
increase approximation orders of 3_4, 3_8 in tests/test_poly_spaces.py
prevent building ori_map for higher order elements in FESurface.__init__()
fields:
reimplement get_facet_dof_permutations() using simple iterators
update Field.from_conf() to set field kind from region kind
update surface field syntax in examples
simplify integrals - remove integral kind:
update transform_integrals() - remove/ignore integral kind
clean up sfepy/fem/integrals.py, add module docstring
remove kind attribute of Integral
remove Integral.get_key()
update Term for no integral kind, remove .get_integral_info()
remove PointTermBase
update sfepy.fem modules for no integral kind
allow ‘i’ as integral name in equations
update examples for no integral kind
update tests for no integral kind
docs: update users guide and tutorial for no integral kind
mesh, domain, regions:
add tdim argument to mesh_set_coors()
update CMesh to use max. topological dimension - new tdim attribute
update Region to use max. topological dimension - new tdim attribute
add tdim attribute to Domain.shape
update fields for max. topological dimension
start support of ‘plate’ integration/connectivity type
merge branch ‘plate_mapping’
update CMapping - new mtx_t attribute
update Approximation.describe_geometry() for plate integration
update get_physical_qps() - new map_kind argument
update Term.get_physical_qps() for plate integration
update get_shape_kind(), Term.iter_groups() for plate integration
update FieldVariable.get_data_shape(), .evaluate() for plate integration
update Approximation.get_connectivity() for plate integration
new transform_asm_vectors(), transform_asm_matrices()
update TLMembraneTerm.weak_function() - use transform functions
equation sequence solver:
new Variables.get_dual_names()
clean up sfepy/fem/equations.py, add module docstring
new Equations.get_variable_dependencies()
new sfepy/base/resolve_deps.py - functions for resolving dependencies
new get_nums(), solvable(), remove_known(), try_block(), resolve()
update tests/test_base.py: new test_resolve_deps()
new Equations.create_subequations()
new ProblemDefinition.create_subproblem()
new EquationSequenceSolver for stationary problems with an equation sequence
new examples/thermo_elasticity/thermo_elasticity_ess.py + test
scripts:
script/save_basis.py: fix mesh mode, make permutations directly from mesh
script/plot_mesh.py: fix help message
simple.py: –list option can list solvers, new print_solvers()
new script/plot_quadratures.py - closes #178
update QuadraturePoints.from_table() to store true order
new sfepy/postprocess/plot_quadrature.py
new script/show_terms_use.py
clean up script/eval_tl_forms.py, update for current sympy
clean up script/evalForms.py, update for current sympy
terms:
new ContactSphereTerm (dw_contact_sphere)
rename sfepy/mechanics/contact_planes.py -> sfepy/mechanics/contact_bodies.py
new ContactSphere - elastic contact sphere
new ContactPlaneTerm._get_force_pars(), update .get_fargs()
fix empty array condition in ContactPlaneTerm.smooth_f()
fix docstring of VolumeSurfaceTerm
remove Term.has_integral, .itype, .raw_itype attributes (unused)
fix form_tlcc_strainGreen_VS() - Green strain computation for post-processing - out-of diagonal entries are no more doubled
homogenization:
update AcousticMassTensor, AppliedLoadTensor zero division check, fix eye call
update MiniAppBase.init_solvers(): allow to use different solvers for the correctors
miscellaneous updates:
new sfepy/linalg/check_derivatives.py - check_fx(), check_vfvx()
update HypermeshAsciiMeshIO reader: support for quad4 and tri3 cells
update mesh reading/writing: print infromation about supported cell types
generalize dict_to_array() for nD arrays
fix type errors under Windows: in nm.take() cells
fix dict_to_array() for non-array sequences
update QuadraturePoints.from_table() to store true order
simplify ProblemDefinition.__init__() - re-implements #212
clean up sfepy/fem/parseEq.py
clean up sfepy/fem/variables.py, add module docstring
examples and tests:
new examples/linear_elasticity/elastic_contact_sphere.py + test
update docstrings of poisson.py, poisson_short_syntax.py examples
add mutual references, tutorial reference
remove comments in examples/diffusion/poisson.py as their text is in the tutorial
update docstring of poisson_periodic_boundary_condition.py example
update docstring of poisson_field_dependent_material.py example
new examples/diffusion/poisson_neumann.py + test - closes #195
docs:
fix issue, closes #236: move downloads from http://code.google.com/p/sfepy/ to sfepy.org/downloads
fix duplicated module index in html
remove link to GoogleWiki
add labels to tutorial
from 2013.2 to 2013.3¶
new implementation of Mesh topology data structures in C:
merge branch ‘cmesh’
rename mesh.pyx -> cmesh.pyx
new C mesh data structures:
new mesh.c, mesh.h
new MeshGeometry, MeshConnectivity, MeshTopology, Mesh, Region, Indices
mesh construction, printing
new MeshEntity, MeshEntityIterator + related functions
connectivity computation algorithms: mesh_transpose(), mesh_intersect(), mesh_build(), face and edge orientations
new CConnectivity, CMesh - cython wrappers of C mesh structures
new functions for getting entities incident to given entity: new Indices, me_get_incident(), me_get_incident2(), contains()
new functions for setting up local entities:
Mesh and CMesh: new .entities attribute, new LocalEntities struct
support DEBUG_MESH flag in sfepy/fem/extmods/
new debprintf(), use it in mesh connectivity setup functions
new tests/test_cmesh.py - test_cmesh_counts()
miscellaneous updates:
clean up common_python.c, common.h, fix size_t format specifiers
new mem_list_new(), mem_list_remove(), mem_check_ptr(), update mem_alloc_mem(), mem_free_mem()
new cmem_statistics() to access mem_statistics() from Python
new mem_get_cur_usage(), mem_get_max_usage(), get_cmem_usage() C functions
new get_cmem_usage()
new implementation of regions based on CMesh, CMesh improvements (w.r.t. above):
merge branch ‘regions’
Region (summary):
new attributes: kind, true_kind, entities, can, can_vertices, can_edges, can_faces, parent
removed attributes: true_cells, all_vertices
use CMesh
vertices, edges, faces, facets and cells are properties pointing to .entities attribute, automatically created when needed
refactor Region, part 1
use CMesh
new Region.setup_from_highest(), .setup_from_vertices()
vertices, edges, faces, facets and cells are properties pointing to .entities attribute, automatically created when needed
refactor Region, part 2 - update operators
remove old operators
new .eval_op_vertices(), .eval_op_edges(), .eval_op_faces(), .eval_op_facets(), .eval_op_cells()
simplify region_op()
refactor Region, part 3 - update special constructors
update .from_vertices(), update & rename .from_faces() -> .from_facets()
refactor Region, part 4 - group compatibility functions
new .igs property
update .update_shape(), .get_vertices_of_cells(), .get_vertices(), .get_edges(), .get_faces(), .get_surface_entities() -> .get_facets(), .get_cells()
remove .delete_zero_faces() body, .select_cells(), .select_cells_of_surface(), .has_cells_if_can()
update docstring
refactor Region, part 5 - all_vertices -> vertices
call region.update_shape() in Domain.create_region()
remove Region.select_cells_of_surface(), .setup_face_indices() calls
update FESurface.__init__()
update VolumeField._setup_geometry()
update Region.create_mapping(), .has_cells()
Region (other details):
new Region.__can, .__facet_kinds class attributes, add kind to .__init__() arguments
update Region.__init__() - new Region.set_kind()
replace Region.setup_face_indices() with new Region.get_facet_indices()
add group offset in Region.get_cells() by default
update Region.setup_mirror_region() - use parent region information, update term igs in Term.get_conn_info()
new Region.get_entities()
update Region: force creation of region entities to respect region kind
new Region._access()
warn about empty group indices in Region.igs()
update Region.iter_cells(), .get_charfun()
update Region.get_edge_graph()
C mesh:
new Mask struct
new mesh_select_complete() C function, new CMesh.get_complete()
new CMesh.get_surface_facets()
new mei_init_sub() C function - connectivity subset iterator
new CMesh.get_incident()- new mesh_count_incident(), mesh_get_incident() C functions
new CMesh.get_conn_as_graph()
new CMesh.get_from_cell_group(), .get_igs() adapter functions
for compatibility until new assembling is done
new CMesh.cell_groups attribute, update CMesh.from_mesh()
fix uninitialized memory error in mesh_build() - manifested on 32 bit platforms
update CMesh.get_incident() to optionally return offsets, update mesh_get_incident()
new mesh_get_local_ids() C function, CMesh.get_local_ids()
new CMesh.get_cell_coors(), mesh_get_cell_coors() C function
fix facet orientation computation in mesh_build()
fix array sizes in CMesh.setup_entities()
new CMesh.get_orientations()
improve debprintf() messages
new ind_print() C function
fix mei_init_conn(), conn_alloc() for no incident entities
check for zero length entities argument in CMesh - update .get_incident(), .get_local_ids(), .get_complete(), .get_igs()
fix facet orientation computation in mesh_build(), try 2: wrong last index
fix return type of CMesh.get_surface_facets()
Domain and Mesh:
rename sfepy/fem/parseReg.py -> sfepy/fem/parse_regions.py
update create_bnf() for new region selection operators
update Domain.create_region(), region_leaf(), region_op()
construct CMesh instance in Domain.__init__() - new Domain.cmesh attribute
remove old testing code in sfepy/fem/parse_regions.py
rename nodes -> vertices, elements -> cells in region selectors - update create_bnf(), region_leaf()
update transform_regions() - replace flags with kind, allow string only, update Domain.create_regions()
new Domain.get_cell_coors() - use in ‘cells by function’ region selector
remove Facets-related methods from Domain - remove .setup_facets(), .get_facets(), .surface_faces()
generalize mesh_get_cell_coors() -> mesh_get_centroids()
generalize CMesh.get_cell_coors() -> .get_centroids(), Domain.get_cell_coors() -> .get_centroids()
update transform_regions() for parent field, update Domain.create_region()
set region kind and definition in Domain.create_region()
call CMesh.setup_entities() in Domain.__init__()
remove Facets and most of sfepy/fem/facets.py contents, rename & update _build_orientation_map() -> build_orientation_map()
simplify FESurface.__init__() - use prepare_remap()
update FESurface.setup_mirror_connectivity() for CMesh, create .ori_map in .__init__()
new get_facet_dof_permutations(), permute_facets(), get_dof_orientation_maps() - updated and recombined code from removed Facets
remove for loop in FESurface.setup_mirror_connectivity()
update Domain.refine(), refine_2_3(), refine_2_4(), refine_3_4(), refine_3_8()
make FESurface.fis C-contiguous
update Mesh.from_region(), ._append_region_faces()
fields:
update H1NodalMixin._setup_facet_orientations()
update H1NodalMixin._setup_facet_dofs() - update ._setup_edge_dofs(), ._setup_face_dofs()
update Field._get_facet_dofs(), .get_dofs_in_region_group()
update H1HierarchicVolumeField._setup_facet_dofs() - update ._setup_edge_dofs(), ._setup_face_dofs()
remove unused facet_oris argument of H1NodalMixin._setup_facet_dofs()
terms:
adapt data types in ConnInfo.iter_igs(), Term.get_assembling_cells()
fix Term.get_physical_qps() for point integration
update NewTerm.integrate()
miscellaneous updates:
update define_box_regions()
update eval_in_els_and_qp()
update ConstantFunctionByRegion.get_constants()
new PhysicalQPs.__init__(), update get_physical_qps()
fix edit_filename() to use prefix
allow points and edges in MeditMeshIO, VTKMeshIO
fix Viewer.save_image() for file names with path
update smooth_mesh()
examples and tests:
update all examples and tests for new region syntax
update tests/test_poly_spaces.py
update tests/test_regions.py: add more selectors, number regions
update test_install.py
new examples/navier_stokes/stokes_slip_bc.py + test
scripts:
findSurf.py: update and clean up
new _get_facets(), get_surface_faces()
improve help message
script/gen_gallery.py:
fix figure paths in generate_images()
add custom view for stokes_slip_bc.py example
new script/plot_mesh.py - basic CMesh plotting
new sfepy/postprocess/plot_cmesh.py: new plot_wireframe()
new plot_entities(), label_global_entities(), label_local_entities()
configuration:
clean up sfepy/base/conf.py
fix key in transform_regions()
docs:
update primer and tutorial
update users guide
new MultiProblem solver: allows “conjugate” solution of subproblems
merge branch ‘subpb’ - closes #226
new example that uses MultiProblem solver:
new examples/acoustics/vibro_acoustic3d.py, examples/acoustics/vibro_acoustic3d_mid.py
new mesh files meshes/2d/acoustic_wg_mid.vtk, meshes/3d/acoustic_wg.vtk
new tests/test_input_vibro_acoustic3d.py
postprocessing and visualization:
update Viewer.build_mlab_pipeline() to display data in only_names order
new plot_points()
homogenization:
update CoefNN, CoefN and CoefSym (“smart” set_variables_default); new CoefExprPar
fix CoefSym and CopyData coefficients
terms:
fix SDLinearElasticTerm, new SDSufaceIntegrateTerm, remove SDSufaceNormalDotTerm
new dw_convect_v_grad_s (ConvectVGradSTerm, scalar gradient term with convective velocity)
update (adjoint) Navier-Stokes terms for 2D, update convect_build_vtg, convect_build_vtbg() for 2D
update LinearTractionTerm: material parameter is now optional (merge branch ‘ltr_opt_mat’ - closes #228)
clean up: remove PermeabilityRTerm
support ‘qp’ evaluation mode in HyperElasticBase - update .integrate(), .get_fargs(), .get_eval_shape()
miscellaneous updates:
update Mesh.localize() to remove vertices not used in any cell
update Probe.probe() to report non-finite probe points
fix ProblemDefinition.set_equations_instance() for keep_solvers=True
check topological dimension of cells in VolumeField._check_region()
update ensure_path() to raise error on failure
update HypermeshAsciiMeshIO: use component id as material id
fix tiled_mesh1d()
new dets_fast()
update Region.igs to return parent igs if parent exists
update get_dependency_graph() to include parent region in dependencies
raise proper error when dependency is missing
examples and tests:
update poisson_functions.py example to use dw_convect_v_grad_s
new examples/navier_stokes/navier_stokes2d.py + test
update tests/test_poly_spaces.py for 2_3, 3_4 geometries, new 2_3_2z.mesh, 3_4_2z.mesh
new tests/test_mesh_smoothing.py - mesh smoothing test
clean up and update tests/test_parsing.py for new regions
scripts:
new script/gen_mesh_prev.py: generates mesh previews in a given directory
script/save_basis.py:
make sure that output directory exists
enable saving all geometry element permutations - new save_basis_on_mesh()
from 2013.1 to 2013.2¶
automatic testing of term calls:
merge branch ‘i154’ - closes #154
define arg_shapes attributes of terms
use new get_arg_kinds() in Term.classify_args() - simplify code
new Term._check_variables()
update Term.classify_args() to support ‘mode’ attribute
update Term to support arg_shapes and geometries attributes
fix SurfaceLaplaceLayerTerm, SurfaceCoupleLayerTerm
fix dw_ul_volume() - fixes VolumeULTerm, BulkPressureULTerm
docs: update developer guide - describe new Term attributes
fix and update DeformationGradientTerm
rename dq_def_grad -> ev_def_grad
remove DeformationGradientTerm.__call__(), new .function(), .get_fargs(), .get_eval_shape()
update dq_def_grad()
fix dw_v_dot_grad_s_sw() (VectorDotGradScalarTerm)
new fmf_mulATC()
fix ScalarDotGradIScalarTerm - add vector mode
fix docstrings of VectorDotGradScalarTerm, TLMembraneTerm
fix SufaceNormalDotTerm - make material shape (D, 1) to be compatible with SDSufaceNormalDotTerm
fix Term.call_function() to clear C errors properly
fix SDSufaceNormalDotTerm
update Term.get() to accept integration argument
fix NSOFSurfMinDPressDiffTerm, DiffusionTerm, DiffusionCoupling, PiezoCouplingTerm
fix docstrings of SDLinearElasticTerm, StokesTerm, GradTerm, DivTerm
new tests/test_term_call_modes.py to automatically test (almost) all terms, skips terms with an empty arg_shapes attribute
new elastic contact plane term:
new flag_points_in_polygon2d()
new ContactPlane - contact plane with polygonal boundary
new sfepy/mechanics/contact_planes.py
new plot_polygon(), plot_points()
new ContactPlaneTerm (dw_contact_plane)
add custom view for elastic_contact_planes.py example to script/gen_gallery.py
terms:
rename DotTermsDotProductSurfaceTerm functions:
dw_surface_dot_vectornormscalar -> dw_surface_s_v_dot_n
dw_surface_dot_scalarnormvector -> dw_surface_v_dot_n_s
update DotProductSurfaceTerm: new ‘scalar_norm_vector’ mode
postproc.py:
force re-read in VTKFileSource.set_filename()
add reload button to ViewerGUI, support watching of vtk files in Viewer
new ReloadSource
closes #217
fix default opacity in Viewer
input-output:
update VTKMeshIO.write() to mark unfinished write by ‘x’ in 1. byte
new HDF5MeshIO.read_bounding_box()
bases:
merge branch ‘cbases’
move low-level function from bases.pyx to new lagrange.c
new sfepy/fem/extmods/lagrange.[ch]
get_barycentric_coors(), get_xi_simplex(), get_xi_tensor(), eval_lagrange_simplex(), eval_lagrange_tensor_product() (‘_’ prefix from name removed) translated from Cython to C
update bases.pyx, use fmf_pretend_nc(), import FMField directly
rename & update script/gen_lobatto_pyx.py -> script/gen_lobatto1d_c.py
generate lobatto1d.c and lobatto1h.c
new lobatto1d_template.c, lobatto1d_template.h
split lobatto_template.pyx into lobatto_bases.pyx and lobatto.c, low level functions in lobatto.c, as in lagrange.c
miscellaneous updates:
clean up of many modules
new fmf_pretend_nc()
fix dependencies in sfepy/terms/extmods/setup.py - this fixes rebuilding terms.so even when an unrelated file was changed
fix Struct._str() for classes with overloaded .get() (e.g. Term)
fix Domain.save_regions_as_groups() for regions without true cells
fix iterative solvers for tolerances not given in conf - fix PyAMGSolver, PETScKrylovSolver, PETScParallelKrylovSolver
remove compatibility function sorted()
remove unused attribute of CharacteristicFunction
add f_tol tolerance option to ScipyBroyden nonlinear solver
add custom norms to RadialMesh
tests and examples:
new examples/homogenization/perfusion_micro.py + test
homogenization of a double-porous medium
new 3D mesh: matrix with two disconnected channels
new examples/linear_elasticity/elastic_contact_planes.py + test - demonstrating use of contact plane term
docs:
add development tab, new doc/development.rst
link wiki from development tab
add related projects section
new sections on term evaluation modes and postprocessing/probing
move description of term evaluation modes from developer to users guide
update users guide
closes #196
gallery:
improve gen_gallery.py
add captions, contents and section titles
move _gallery_template contents to new doc/gallery_template.html
fix script/gen_gallery.py for new time stepping
fix output suffix for time-dependent problems in generate_images()
update docstring of gen_gallery.py - describe docs regeneration steps
from 2012.4 to 2013.1¶
solvers:
move time stepping solvers to new sfepy/solvers/ts_solvers.py
redesign time stepping, unify use of stationary and evolutionary solvers:
new StationarySolver
update PDESolverApp.call()
update TimeSteppingSolver - change __init__(), __call__() arguments, remove .set_step_fun()
remove solve_stationary(), solve_evolutionary()
move prepare_matrix(), prepare_save_data(), make_implicit_step(), make_explicit_step() into sfepy/solvers/ts_solvers.py
new get_initial_state()
update SimpleTimeSteppingSolver.__call__() to implement fully the time stepping loop, new .solve_step()
update ExplicitTimeSteppingSolver, new .solve_step
new AdaptiveTimeSteppingSolver - implicit adaptive time stepping solver:
new get_min_dt(), adapt_time_step()
new VariableTimeStepper.from_conf(), .set_from_ts(), .set_n_digit_from_min_dt()
update VariableTimeStepper.set_step() to allow only step = 0
update VariableTimeStepper.__iter__() to include t1
input-output:
fix ANSYSCDBMeshIO.read(), guess it with .inp suffix:
new .guess()
for mixed element meshes and coordinates without “solid” keyword
allow quadratic elements in ANSYSCDBMeshIO.read(), strip extra nodes:
allow more format variants
add remap argument to mesh_from_groups()
add .dat suffix
update ANSYSCDBMeshIO.read() to support nodes of boundary conditions
support node sets (nodes of boundary conditions) in HDF5MeshIO.read(), .write()
fix omitting nodes of boundary conditions in Mesh.write()
add nodal_bcs argument to Mesh.from_data()
update HDF5MeshIO.read() for old meshes without node_sets group
mesh, domain, regions:
support mat_ids in merge_mesh()
new Mesh.__add__() to merge meshes
add verbose argument to gen_block_mesh(), gen_cylinder_mesh()
new gen_extended_block_mesh() mesh generator
fix smooth_mesh() - improve efficiency
support nodes and elements of set in create_bnf()
update region_leaf() and test for “nodes of set” selector:
prepare for “elements of set” selector
nodes of group support only int id
move bodies of functions for saving regions from ProblemDefinition to Domain:
new Domain.save_regions(), .save_regions_as_groups()
update ProblemDefinition.save_regions(), .save_regions_as_groups()
new Region.delete_zero_faces(), used in .complete_description()
use Region.get_cells() instead of direct access to cells
true cells are checked in Region.get_cells() if needed
true_cells attribute is properly initialized in Region.complete_description()
allow dot in set names in create_bnf()
allow dot in region names
fix Region.get_edge_graph() for degenerate edges
fields, variables:
update setting of variables data (use Variable.set_data())
rename/update Variables.non_state_data_from_state() -> .set_data_from_state()
rename/update Variable.data_from_any() -> .set_data()
rename FieldVariable.data_from_qp() -> .set_data_from_qp()
new Variable.is_finite()
new terms:
dw_tl_bulk_active (active bulk pressure term)
miscellaneous updates:
make view button to print view and roll as arguments of postproc.py
set ts directly in ProblemDefinition.update_time_stepper()
add verbose argument to MyBar progress bar
allow to run python shell from debugger
more grammar elements available in parse_conf.py
radial mesh - fixes, integrals and derivatives
new get_face_areas() + test
new global option ‘check_term_finiteness’
check finiteness in Term.evaluate()
fix compute_nodal_normals() for degenerate elements, check for zero normals
new configure_output()
remove many unused functions, code clean up
scripts:
script/save_basis.py: plot nodes of selected dofs, new plot_nodes()
script/convert_mesh.py: new –center option
examples and tests:
update linear_elastic_damping.py example to use adaptive time stepping
new tests/test_mesh_generators.py - test basic mesh generators
docs:
add support section to main page
from 2012.3 to 2012.4¶
initial implementation of elements with hierarchical basis:
merge hierarchic branch
fields and approximations:
split fields.py into fields_base.py, fields_nodal.py
new VolumeField, H1NodalMixin
new H1NodalVolumeField, H1DiscontinuousField, H1NodalSurfaceField
prepend underscore to non-API methods
new H1HierarchicVolumeField (fields_hierarchic.py)
move ._setup_esurface(), .create_mesh() into Field
new Field.from_args()
move setting DOFs from a function to a field method
new H1NodalMixin.set_dofs(), update EquationMap.map_equations()
add merge argument to Field.get_dofs_in_region_group()
new H1HierarchicVolumeField.set_dofs() - hack for constant values
define edge orientation (ap.ori) in H1HierarchicVolumeField
new code for face orientations
update H1HierarchicVolumeField._setup_facet_dofs()
new LobattoTensorProductPolySpace._get_counts(), ._get_face_axes_nodes()
update LobattoTensorProductPolySpace.__init__(), _define_nodes(), ._eval_base()
update Approximation for facet orientation, add ori attribute
new Approximation.clear_qp_base()
add iels argument to Approximation.get_base()
new Approximation.get_poly_space(), update .get_base()
bases and mappings:
update CVolumeMapping.describe() for basis per element
update VolumeMapping.get_mapping() for facet orientation argument
update PolySpace.eval_base() for facet orientation argument
support edge orientation in LobattoTensorProductPolySpace._eval_base()
add node_orders attribute to LobattoTensorProductPolySpace
add force_axis argument to PolySpace.eval_base()
use force_axis argument to fix Lagrange basis computations
fix gradient mode in eval_lobatto_tensor_product()
ensure c-contiguity in PolySpace.eval_base()
update PolySpace.any_from_args() for no simplex Lobatto class
raise error for surface mapping with hierarchical basis
facets and geometry elements:
new Facets.get_orientation()
fix axes orientation of 6th face of 3_8
new GeometryElement.get_grid()
new _get_grid_1_2(), _get_grid_2_3(), _get_grid_2_4(), _get_grid_3_4(), _get_grid_3_8()
linearization of higher order fields:
update linearizer.py for hierarchic basis
remove bf argument of DOF evaluation functions (use ps instead)
update get_eval_dofs() - add ps (poly. space) and ori (facet orientation) arguments
update create_output()
update Field.linearize(), eval_dofs() for updated linearizer.py
create linearized output for an expression
new create_expression_output()
new get_eval_expression(), eval_in_els_and_qp()
scripts:
update script/plot_condition_numbers.py
update script/save_basis.py for meshes (global basis)
new –lin-options, –dofs, –permutations, –plot-dofs options
support gradients in mesh mode
require output directory, print help by default
examples and tests:
new tests/test_normals.py - check surface normal orientations
new tests/test_poly_spaces.py - check hierarchic and nodal basis continuity
add two-element meshes
update examples/diffusion/sinbc.py to use hierarchical basis
miscellaneous updates:
new prepare_translate()
new GeometryElement.get_conn_permutations()
new make_h1_projection_data()
generalize sym2dim()
new sfepy/postprocess/plot_dofs.py
new _get_axes(), plot_mesh(), plot_global_dofs(), plot_local_dofs()
update filename attribute in UserMeshIO.read()
unify C/Cython structures for volume and surface mappings:
merge surfvol branch
rename geometry.[ch] -> refmaps.[ch]
merge VolumeGeometry and SurfaceGeometry into Mapping
merge CVolumeMapping and CSurfaceMapping into CMapping
update sfepy/fem/extmods/setup.py
update map_print(), small fixes in map_describe(), map_integrate()
update terms for Mapping
update VolumeMapping, SurfaceMapping for CMapping
miscellaneous updates for CMapping
remove eval_real_extra(), dq_grad_extra()
remove dw_surface_dot_vector(), dw_surface_dot_scalar()
update dw_volume_dot_vector(), dw_volume_dot_scalar(), DotProductVolumeTerm
update docstring of DotProductSurfaceTerm
remove remaining references to CMapping.area
new CauchyStrainSTerm (ev_cauchy_strain_s)
problem descriptions:
replace getattr() calls with ProblemConf.get_function()
fix for functions defined inside define() and not on the problem description module level
add allow_tuple, free_word arguments to create_bnf()
allow deferred setup of ProblemConf - add setup argument to .__init__()
update ProblemDefinition.setup_default_output() for missing options
data probing:
new Probe.set_n_point(), update .__init__()
allow extrapolation in probes
new Probe.set_options() - set close limit, update .__init__(), .probe()
probe.py: new –close-limit option, update generate_probes(), clean up
update generate_probes() to support multiple figures per probe hook
add size_hint to Probe.set_options(), fix refinement for multiple calls
new Probe.reset_refinement() - called in .probe()
new write_results(), read_results(), update generate_probes(), postprocess()
move read_header(), get_data_name() to sfepy/fem/probes.py, update
new dict_from_options(), update ProblemConf.from_file_and_options()
make dict_from_string a standalone function
generalize override in ProblemConf.__init__()
update generate_probes() to support -1 as last step
base:
new edit_tuple_strings(), add recur argument to edit_dict_strings()
update edit_dict_strings() for lists of replacements and tuple values
update assert_() for custom messages
add overwrite_by_none argument to update_dict_recursively()
remove sfepy/base/tasks.py
new edit_filename() utility function
new Struct._str(), .str_class(), update .__str__()
simplify dict-like methods of Struct
replace Struct.get_default_attr() with updated Struct.get()
rename .set_default_attr() -> set_default()
logging:
split sfepy/base/log.py - new sfepy/base/log_plotter.py, clean up
rename ProcessPlotter -> LogPlotter
implement reading and plotting of Log text output
new read_log(), plot_log()
add log_name argument to get_logging_conf(), update docstring
materials:
update Materials, Material for optional clearing of material data
improve updating of material parameters
update Materials.time_update() - force and clear arguments replaced by mode argument
update Material.__init__(), .update_special_data(), .update_special_constant_data(), .time_update()
phononic materials:
new get_log_freqs(), update detect_band_gaps()
new get_ranges(), update cut_freq_range(), BandGaps.__call__()
opts.eig_range is a slice now
update transform_plot_data() to work with nan values
linear combination boundary conditions:
rename _save_normals() -> _save_vectors(), update
new Region.get_edge_graph()
new get_edge_paths(), _get_edge_path()
new compute_nodal_edge_dirs()
new NormalDirectionOperator.get_vectors(), update .__init__()
new EdgeDirectionOperator, new ‘edge_direction’ LCBC
update LCBCOperators.add_from_bc()
fix and simplify LCBCOperator.treat_pbcs()
LCBCs combined with EPBCs in common nodes work correctly now, in particular for non-penetration conditions with general normals
scripts:
remove obsolete scripts:
mesh_to_vtk.py, hfm3_mesh.py, convert.py, edit_neu.py, make_spkg.py, spymatrix.py
new script/sync_module_docs.py
script/save_basis.py: fix –plot-dofs for no –permutations, update help
update script/gen_gallery.py for custom visualizations
script/plot_condition_numbers.py: report number of quadrature points
simple.py:
clean up, add docstring
new –save-ebc-nodes option, change meaning of –save-ebc
update solve_pde(), save_only(), PDESolverApp.call()
update generate_images(), test_hyperelastic_tlul.py, tests_basic.py
postproc.py:
group options, clean up, use docstring for help
allow negative time steps in Viewer.call_mlab()
Python-like indexing from the last step
check that step is in the range available
update step help message
solvers:
fix arguments in TimeStepper.from_conf()
fix ScipyFMinSolver.__call__() for old scipy (0.7.2)
add divergence tolerance option to PETSc solvers
miscellaneous updates:
fix examples in script/config.py
new sfepy/postprocess/plot_facets.py
new plot_geometry(), plot_edges(), plot_faces(), draw_arrow()
new get_perpendiculars()
move .setup_coors() to Field, fix vertex indices
new Region.get_vertices_of_cells(), update .update_vertices()
fix VolumeField._setup_vertex_dofs() for superfluous vertices
fix VolumeField.average_qp_to_vertices() for superfluous vertices
new RadialVector, ExplicitRadialMesh, update RadialHyperbolicMesh, RadialMesh
new H1NodalSurfaceField.interp_v_vals_to_n_vals() - initial stub
fix ProblemDefinition.save_ebc() for EBCs needing ProblemDefinition instance
report (initial) data ranges in Viewer.build_mlab_pipeline()
allow context variables in ProblemDefinition.evaluate()
add strip_variables argument to .evaluate(), .create_evaluable()
rename State.get_scaled_norm() -> get_weighted_norm()
fix weighting by state parts, add weights, return_weights arguments
fix EquationMap._init_empty() to initialize n_epbc
clean up sfepy/fem/dof_info.py
fix gen_mesh_from_voxels()
remove unused function: reorder_dofs_on_mirror
fix integration over mirror surface
treat separately real and imaginary fill value parts in Field.extend_dofs()
new get_min_value() - fill value is 0 for vectors, minimum for scalars
fix dw_jump term, use the (optional) material parameter as a multiplier
examples and tests:
update docstrings in examples/diffusion/poisson_functions.py
report number of failed tests in test_install.py
new example with field-dependent diffusion coefficient + test (examples/diffusion/poisson_field_dependent_material.py)
new diffusion example with periodic boundary conditions + test (examples/diffusion/poisson_periodic_boundary_condition.py)
new tests for field dependent and periodic diffusion examples
new acoustic 3d example (examples/acoustics/acoustics3d.py) + test
remove examples/diffusion/subdomains.py + test
docs:
include scripts in developer guide
sync module index of developer guide with current sources
from 2012.2 to 2012.3¶
terms:
fix BulkPressureULTerm and CompressibilityULTerm
move TLMembraneTerm.describe_membrane_geometry() into new describe_geometry()
fix TLMembraneTerm.eval_function() for updated transform_data()
new FibresActiveTLTerm.get_eval_shape()
update VolumeTLTerm.get_fargs() for ‘el_avg’ mode
fix term evaluation to clear properly the C error flag
new Term.call_get_fargs(), .call_function()
update Term.eval_real(), .eval_complex(), .evaluate()
new SurfaceNormalDotTerm (dw_surface_ndot)
new ScalarDotGradIScalarTerm (dw_s_dot_grad_i_s)
update DotProductSurfaceTerm: allow (vector * normal * scalar) product
new shape sensitivity terms: SDLinearElasticTerm (d_sd_lin_elastic), SDSufaceNormalDotTerm (d_sd_surface_ndot)
support ‘el’ mode in term evaluation:
update SurfaceFluxTerm for ‘el’ mode, update docstring
fix checking of term - integral compatibility
merge pull request #186 from vlukes/meshtiler:
new tiled_mesh() function
move mesh generating functions to sfepy/mesh/mesh_generators.py
update genPerMesh.py
update scripts cylindergen.py and blockgen.py
visualization:
postproc.py: allow finer control of opacity (closes Issue 194)
fix _get_scalars() for vectors
base:
move try_imports() into sfepy.base.base, fix error printing, add docstring
update invert_dict() - add unique argument, add docstring
fix find_subclasses() for no name attribute case
add name_attr argument to find_subclasses(), load_classes()
update Output to accept a file descriptor instead of a file name
update Output for global options, new test_verbose_output()
support global options (closes Issue 190) - new sfepy/base/goptions.py: - new ValidatedDict class, goptions instance - default_goptions with ‘verbose’ option
homogenization:
fix ‘return_all’ option in HomogenizationApp
fix CoefSymSym
fem:
new get_ref_coors(), update Field.evaluate_at()
new make_l2_projection_data(), update make_l2_projection()
support ‘space’ and ‘poly_space_base’ items in transform_fields()
fix Region.delete_groups() - update also all_vertices etc.
remove unused qp_indx field in PhysicalQPs
fix stiffness_from_lame_mixed()
material parameters can be defined per region using region names:
update linear homogenization examples using new material definition
fix Material.__init__() for special and keyword values
new SplineBox geometry parametrization
update extend_cell_data() for surface regions
allow different base function values per element:
add base function attribute (bf) to VolumeGeometry, SurfaceGeometry
make bf of CVolumeMapping, CSurfaceMapping point to the above bf
add flag argument to {CVolumeMapping, CSurfaceMapping}.__cinit__()
update Approximation.describe_geometry()
new FMF_SetCellX1() macro
update terms for base functions per element
define integrals by order instead of quadrature name:
update transform_integrals(), Integrals.from_conf(), Integral.__init__()
update tests and examples for new integral definition
input-output:
boundary condition id in Nastran format is used as the node group
update MeditMeshIO.read() to skip unsupported entities
solvers:
update imports in PysparseEigenvalueSolver.__call__() for new Pysparse
update ScipyIterative solver to allow preconditioning
check solver consistency in ProblemDefinition.set_solvers_instances()
fix preconditioner arguments for qmr method in ScipyIterative
update ScipyIterative solver for iteration callback
new standard_call() decorator for linear solvers, checks also data shapes
update docstring of Newton (configuration options, small fixes)
update docstring of Solver (common solver configuration options)
misc:
fix unique_rows() for non-contiguous arrays, add arguments of numpy.unique()
examples and tests:
update ULF hyperelastic examples, change error tolerance, number of iterations
update hyperelastic tests: test |TL - UL| and |UL - UL_mixed|
docs:
update for new integral definition
include special methods of nonlinear solvers
update User’s Guide (Problem description file/Materials)
add notes on solving PDEs by FEM in the tutorial part of the documentation
from 2012.1 to 2012.2¶
reimplement acoustic band gaps code using the homogenization engine:
merge band_gaps_he branch
rename eigen.py -> phonon.py
move AcousticBandGapsApp to new sfepy/homogenization/band_gaps_app.py
fix coding style in sfepy/homogenization/band_gaps_app.py
replace compute_density_volume_info() by DensityVolumeInfo
new MiniAppBase.process_options()
preserve order of requirements in HomogenizationEngine.call()
new SimpleEVP mini-application:
reimplement part of AcousticBandGapsApp.solve_eigen_problem() for ‘simple’ problems
rename sfepy/homogenization/phono.py -> …/coefs_phononic.py
new Eigenmomenta mini-application:
update compute_eigenmomenta()
remove prepare_eigenmomenta()
new CoefDummy
update AcousticBandGapsApp.process_options(), .process_options_pv() - options moved to corrector/coefficient classes
update AcousticBandGapsApp.call() - compute ingredients for band gap detection via HomogenizationEngine
update frequency-dependent tensors:
update AcousticMassTensor, AcousticMassLiquidTensor, AppliedLoadTensor
update Eigenmomenta
update band gaps functions, new BandGaps mini-application:
update cut_freq_range(), split_chunks(), detect_band_gaps(), get_callback(), find_zero(), describe_gaps()
remove setup_band_gaps()
update try_set_defaults() for one-level recurrence
move plotting functions: coefs_phononic.py -> band_gaps_app.py
split SimpleEVP.__call__():
new SimpleEVP.prepare_matrices(), .post_process()
new SchurEVP mini-application
remove obsolete code in AcousticBandGapsApp:
remove make_save_hook()
remove AcousticBandGapsApp.fix_eig_range(), .solve_eigen_problem(), .eval_homogenized_coefs()
update BandGaps for custom detection function and rhs matrix
set incident wave dir. in AcousticBandGapsApp.call()
new dispersion mini-applications:
new ChristoffelAcousticTensor, PolarizationAngles, PhaseVelocity mini-applications
new compute_cat_sym_sym(), compute_cat_dim_sym(), compute_cat_dim_dim(),
remove compute_cat(), compute_polarization_angles()
new AcousticBandGapsApp.plot_dispersion()
remove AcousticBandGapsApp.compute_cat(), .compute_phase_velocity()
remove report_iw_cat()
new HomogenizationEngine option ‘compute_only’:
unify handling of dependencies (requirements and coefficients)
remove _get_parents()
fix de-duplication of names in HomogenizationEngine.call()
inherit AcousticBandGapsApp from HomogenizationApp (common options)
update Coefficients._save_dict():
support custom ‘to_file_txt’ callable attribute of coefficients
ignore unknown types
update saving of figures in AcousticBandGapsApp
allow saving band gaps logs:
new BandGaps.to_file_txt(), .save_log()
new application option ‘log_save_name’
improve default plot resources
remove broken caching from AcousticBandGapsApp
update phononic examples for AcousticBandGapsApp:
new examples/phononic/band_gaps_conf.py
update examples/phononic/band_gaps.py, examples/phononic/band_gaps_rigid.py
remove coef_conf_elastic.py, gen_mesh.py, parametric.py, plot_gaps.py
update test_install.py
homogenization:
new homogenization corrector function OnesDim - unit vector in the directions
proper coding style in coefs_base.py
update float formatting capabilities of Coefficients.to_file_latex()
allow passing custom application options to HomogenizationEngine
new get_volume_from_options(), update HomogenizationApp.call()
allow to add some additional information to coefficients files
quadratures:
update table of 1_2 quadrature points
fix and update module docstring
update QuadraturePoints.__init__() - add symmetric argument
up to polynomial order 47
increase tolerance in test_quadratures()
create missing tensor product quadratures using 1_2 (line) quadratures: - order for tensor product geometries is given in terms of the 1D order - new QuadraturePoints.from_table(), _get_max_orders() - update QuadraturePoints.__init__() - update Integral.get_qp(), .integrate() - move & update Integral.get_actual_order() -> get_actual_order()
fix order in create_mass_matrix(), make_l2_projection()
test generated tensor product quadratures
cite PHAML in module docstring
update table of 2_3 quadrature points
fix polynomial order in get_poly()
report differences in test_weight_consistency(), test_quadratures()
create missing simplex (2_3, 3_4) quadratures
update QuadraturePoints.from_table()
new sfepy/fem/simplex_cubature.py
update test_quadratures()
solvers:
rewrite stabilization material handling
create_stabil_mat() -> StabilizationFunction
stabilization material uses now a “regular” material function
update Oseen solver for new stabilization material handling
fix eig() to obey options from keyword arguments
change num -> n_eigs
fix PysparseEigenvalueSolver.__call__() for no r.h.s. matrix
set default n_eigs, clean up
new SimpleTimeSteppingSolver.process_conf()
new TimeSteppingSolver.set_step_fun()
new ExplicitTimeSteppingSolver
new MassOperator
applications:
rename simple_app.py -> pde_solver_app.py
rename SimpleApp -> PDESolverApp
rename pde_solve() -> solve_pde(), add docstring
move it into sfepy/applications/pde_solver_app.py
remove sfepy/applications/top_level.py
clean up sfepy/applications/application.py
merge sfepy/solvers/generic.py with sfepy/applications/pde_solver_app.py
remove sfepy/solvers/generic.py
update solve_pde(), PDESolverApp.call()
rename solve_stationary_op() -> solve_stationary(), time_step_function() -> make_implicit_step(), solve_evolutionary_op() -> solve_evolutionary()
update PDESolverApp.call() for basic explicit time stepping
new make_explicit_step()
input-output:
update Mesh._set_shape_info() - add element group dimensions
update MeshIO classes to read elements of lower dimension
update VTKMeshIO, ComsolMeshIO, AVSUCDMeshIO, HypermeshAsciiMeshIO, AbaqusMeshIO, NEUMeshIO, ANSYSCDBMeshIO
merge mesh_from_tetra_hexa(), mesh_from_tri_quad() -> mesh_from_groups()
change default value of omit_facets to False (Mesh.from_file() etc.)
update HDF5MeshIO.read_times() to return also time steps
update extract_times(), dump_to_vtk(), extractor.py for missing time steps
extraction now works with files where not all the time steps are saved
update VTKMeshIO.read() for pixels and voxels
domain:
update Domain: store group dimension
update Domain.fix_element_orientation() to skip facet groups
update Facets for empty facet groups
update Region.get_n_cells() for facet groups
scripts:
new script/plot_condition_numbers.py
update script/gen_lobatto_pyx.py to generate also derivatives
fix gen_lobatto() in script/gen_lobatto_pyx.py
new script/save_basis.py
clean up script/blockgen.py, new –2d option
clean up script/convert_mesh.py, new –refine option
visualization:
use new _get_scalars() in domain specific plot functions
new plot_warp_scalar() domain specific plot function
linearizer: update create_output() for custom evaluation functions
new get_eval_dofs(), get_eval_coors()
add coordinates argument to DOFs evaluation function in get_eval_dofs()
update create_output()
new LobattoTensorProductPolySpace - initial implementation of hierarchic basis
unify dot product and mass terms:
dw_mass, dw_mass_scalar, dw_surf_mass_scalar, dw_volume_wdot_scalar -> dw_volume_dot_vector, dw_surface_dot_vector, dw_volume_dot_scalar, dw_surface_dot_scalar
remove sfepy/terms/termsMass.py, sfepy/terms/extmods/termsMass.[ch]
remove MassVectorTerm, MassScalarTerm, MassScalarSurfaceTerm,
new sfepy/terms/terms_dot.py, sfepy/terms/extmods/terms_dot.[ch]
update examples
terms:
update AdjDivGradTerm, AdjConvect1Term, AdjConvect2Term for new term evaluation
update objective function terms for new term evaluation
update SUPGCAdjStabilizationTerm (fix name from AdjSUPGCtabilizationTerm)
update SUPGPAdj1StabilizationTerm, SUPGPAdj2StabilizationTerm
update adjoint Navier-Stokes stabilization terms for new term evaluation
merge NSOFMinGrad1Term, NSOFMinGrad2Term -> NSOFMinGradTerm
update NSOFSurfMinDPressTerm, NSOFSurfMinDPressDiffTerm
update Navier-Stokes shape derivative terms for new term evaluation
update SDDivTerm, SDDivGradTerm, SDConvectTerm
update SDDotScalarTerm for new term evaluation (was TestPQTerm)
update stabilized Navier-Stokes shape derivative terms for new term evaluation
update SDGradDivStabilizationTerm, SDSUPGCStabilizationTerm, SDPSPGCStabilizationTerm, SDPSPGPStabilizationTerm
fix their docstrings
make material argument of DivGradTerm optional, implement evaluation mode
update PermeabilityRTerm for new term evaluation
update SDDotVolumeTerm to support also vectors (was SDDotScalarTerm)
new VectorDotGradScalarTerm (dw_v_dot_grad_s)
update DotProductVolumeTerm for matrix coefficient
add optional material argument to NonPenetrationTerm
fix term_mode in d_sd_… terms - set default value to 1
examples:
update examples/navier_stokes/stabilized_navier_stokes.py
new examples/diffusion/time_poisson_explicit.py
shaper.py:
fix –direct, –adjoint options
update solve_stokes(), solve_navier_stokes(), solve_generic_direct(), solve_direct(), solve_adjoint() for State
fix main()
update and clean up
update vec -> state in shape optimization functions and ShapeOptimFlowCase
update ShapeOptimFlowCase: handling of materials, term evaluation mode
update update_mesh(), solve_problem_for_design() for current code
misc:
fix Equations.invalidate_term_caches() to invalidate all variables
further speed-up assemble.pyx by using pointer to iels, change int -> int32
major speed-up of some key functions
profiling using line_profiler -> use numpy.take() instead of fancy indexing
update Approximation.get_connectivity(), .describe_geometry() Field.setup_vertex_dofs(), .setup_coors(), Mapping.__init__(), create_adof_conn()
fix vg_getElementDiameters()
fix bf_actt_c1()
fix print_matrix_diff() for scipy with removed rowcol()
change default value of follow_epbc to False
update Equations.strip_state_vector(), State.get_reduced(), Variables.strip_state_vector(), FieldVariable.get_reduced()
new get_subdict()
new match_coors()
fix region comparison in Field.get_mapping()
fix package_check() for bogus versions
update Field.linearize()
new eval_lobatto_tensor_product()
make vertex_maps common, fix LagrangeTensorProductPolySpace._define_nodes()
update ProblemDefinition.get_integrals() - add names, kind arguments
remove unused MultiplierVariable, ConstantVariable
docs:
add archlinux installation requirements
fix numpy docstring standard links
add coding style section to developer guide
refer to web pages using new doc/links.inc
add NTC logo to main page
update developer guide to reflect the above updates
from 2011.4 to 2012.1¶
initial version of linearizer of higher order solutions:
merge linearizer branch
new Field.linearize()
clean up SimpleApp.process_options()
update output creation functions/methods
fix Field.get_true_order() for forced bubble DOFs
new Field.is_higher_order()
new application option ‘linearization’
new FieldVariable.linearize()
silence Domain.setup_facets()
HDF5:
do not linearize when saving to ‘h5’ format
update HDF5MeshIO.write() to save field name in ‘full’ mode
update HDF5MeshIO.read_data()
allow ‘strip’ mode for ‘h5’ in ProblemDefinition.setup_output()
fix HDF5MeshIO.read_time_stepper() to close file on exception
move output creation to Field, new Field.create_output()
remove FieldVariable.extend_dofs(), .remove_extra_dofs(), .linearize()
update recover_bones(), recover_paraflow()
extractor.py: new –linearization option
support linearization when dumping to VTK
new create_problem(), parse_linearization()
catch ValueError in dump_to_vtk()
new Struct.update()
add linearization options to examples/navier_stokes/navier_stokes.py, examples/diffusion/sinbc.py
new tests/test_linearization.py
docs: update developer guide, new linearizer.rst
solvers:
new PETScParallelKrylovSolver solver class, petsc_worker.py
add precond_side option to PETSc Krylov solvers
prevent unwanted importing of PETSc
allow changing properties of solvers via command line
fix PETSc Krylov solvers to obey nonzero initial guess
fix Newton, Oseen to pass current solution as initial guess to linear solver
add verbose option to Solver (base of all solvers)
use verbose option in Newton solver
new SchurGeneralized solver, update SchurComplement
new ScipyFMinSolver optimization solver
fix ScipyBroyden for non-array return value
postprocessing and visualization:
allow reusing viewer scene in make_animation()
build mlab.pipeline after scene is activated
reason: some VTK objects or properties require a scene with a camera and interaction to be open to work properly
new plot_velocity() domain specific plot function
force source update in Viewer.render_scene()
always use Viewer source change hack
fix error reporting in Viewer.call_mlab()
catch only ImportError in mayavi imports
fix Viewer.build_mlab_pipeline() for no point scalars
postproc.py: new –fgcolor, –bgcolor options
fix default colors in Viewer.call_mlab()
fix mayavi imports in postprocess.utils
homogenization:
new CopyData corrector
remove unused homog. coefficient functions
fix HomogenizationApp.call()
input-output:
support tensors in vertices in VTKMeshIO.write()
fix supported_capabilities (nastran supports write())
update read_array() for unknown number of columns
fix NEUMeshIO.read() - problem with boundary conditions
new MeshIO.for_format(), update MeshIO.any_from_filename() - update script/convert_mesh.py - move output_writable_meshes() to sfepy/fem/meshio.py
blockgen.py, cylindergen.py: new –format option
problem description:
allow extra arguments to define() in ProblemConf.from_file()
simple.py: new –define option
schroedinger:
remove specialized DFT code (move to a separate project)
move code to new sfepy/physics/schroedinger_app.py
add result names arguments to SchroedingerApp.save_results()
tests and examples:
update its2D_1.py example - use refine_mesh()
update Primer examples to use dw_point_load term
new examples/linear_elasticity/linear_viscoelastic.py + test
new examples/thermo_elasticity/thermo_elasticity.py + test
update examples/linear_elasticity/linear_viscoelastic.py
save in HDF5 format
new post_process() - compute strain, stresses
update linear_tension()
new main() - plot time histories
new examples/linear_elasticity/prestress_fibres.py + test
material coefficients:
fix bulk_modulus_lame()
clean up sfepy/mechanics/matcoefs.py, add/update docstrings
improve testing of material parameter conversion functions
rename test_tensors() -> test_elastic_constants()
new test_conversion_functions(), test_stiffness_tensors()
use better names for material parameter conversion functions
youngpoisson_to_lame() -> lame_from_youngpoisson()
stiffness_tensor_*() -> stiffness_from_*()
bulk_modulus_lame() -> bulk_from_lame()
bulk_modulus_youngpoisson() -> bulk_from_youngpoisson()
variable evaluation:
new find_ref_coors(), evaluate_in_rc() instead of evaluate_at()
update Field.evaluate_at() to use find_ref_coors(), evaluate_in_rc()
allow caching reference coordinates, add ret_ref_coors argument
change cache attribute ctree -> kdtree
print more detailed timings
update FieldVariable.evaluate_at()
term evaluation:
fix Term.evaluate() to pass diff_var argument to .eval_*()
add step, time_derivative arguments to Term.get()
support preserving evaluate caches in State and Variable
fix ProblemDefinition.solve() to preserve evaluate caches
rewrite variable and evaluate cache history handling
Variable.data attribute is now a deque with length given by history
history is given by integer >= 0, not string
evaluate cache is split by time steps (evaluate_cache(mode) -> step_cache(step) -> cache(key))
update examples for new history syntax
remove sfepy/terms/cache.py, sfepy/terms/cachesHistory.py
remove code related to term caches
allow preserving evaluate caches in ProblemDefinition.evaluate()
terms:
optional material parameter in LaplaceTerm
fix LaplaceTerm for test_msm_symbolic.py
fix arguments of dw_permeability_r()
new PointTermBase, update LinearPointSpringTerm
new concentrated point load term (dw_point_load)
fix acoustic terms
fix BulkPressureULTerm, DotProductVolumeTerm
new term assembling function mulATB_integrate()
update DiffusionCoupling term - simplify assembling
remove d_volume_dot term (subset of dw_volume_dot, same class name)
update DotProductVolumeTerm (dw_volume_dot)
fix TLMembraneTerm.describe_membrane_geometry()
fix parents of LinearElasticIsotropicTerm
update HyperElasticBase.get_family_data() for new evaluate cache handling
new THTerm, ETHTerm classes, support custom advance in Variable.advance()
update LinearElasticTHTerm, LinearElasticETHTerm for new term evaluation
fix and clean up compute_mean_decay()
update BiotTHTerm, BiotETHTerm for new term evaluation
update DotSProductVolumeOperatorWTHTerm, DotSProductVolumeOperatorWETHTerm for new term evaluation
update dw_volume_wdot_scalar()
update BiotStressTerm, BiotStressQTerm for new term evaluation
fix ConcentratedPointLoadTerm.check_shapes() for functions, update docstring
unify Cauchy strain, stress evaluation terms
dq_cauchy_strain, de_cauchy_strain -> ev_cauchy_strain
dq_cauchy_stress, de_cauchy_stress -> ev_cauchy_stress
unify Biot stress evaluation terms
de_biot_stress, dq_biot_stress -> ev_biot_stress
simplify Cauchy and Biot stress term evaluation in qp mode
unify diffusion velocity evaluation terms
de_diffusion_velocity, di_diffusion_integrate -> ev_diffusion_velocity
unify gradient and divergence evaluation terms
de_grad, dq_grad -> ev_grad
de_div, dq_div -> ev_div
rename di_surface_integrate -> ev_surface_integrate, update docstring
rename di_volume_integrate -> ev_volume_integrate, allow optional material
rename di_integrate_mat -> ev_integrate_mat, allow ‘qp’ mode
update CauchyStressTerm.function() for optional coefficient
new fading memory stress terms (ev_cauchy_stress_th, ev_cauchy_stress_eth)
simplify code of DiffusionVelocityTerm.function()
fix dw_volume_dot evaluation
update LinearPrestressTerm, LinearStrainFiberTerm for new term evaluation
remove obsolete sfepy/terms/terms_base.py, update docs
logging:
update Log.plot_vlines() to add line also to text log file
move plotting-related imports in log.py into ProcessPlotter and Log
update Log.__init__(), .plot_vlines() to allow better plot reconstruction
interactive:
move code from __init__.py to session.py in sfepy/interactive/
update isfepy for ipython 0.12 (adapted code from current isympy)
update isfepy docstring
setup: - install scripts, examples and tests along sources, do not install docs - update setup.py
misc:
new refine_mesh()
add conn attribute to GeometryElement
fix evaluate_at() for piecewise-constant approximations
speed-up assemble.pyx by using more pointer arithmetics
fix complex term evaluation
fix testing for string instances for Python 3
fix implicit function declaration warnings in generated terms.c
update test_install.py for updated its2D_3.py example
fix LagrangeNodes.append_tp_faces()
fix problem with connectivity in mirror surface
allow user defined base function in variable evaluation
add 2d von Mises stress calculation
update get_debug() for ipython 0.12
new get_mapping_data(), update get_jacobian(), new get_normals()
new mesh smoothing function smooth_mesh()
update Probe for ctree -> kdtree
update create_evaluable() to obey verbose argument in weak mode
add verbose argument to Variables.time_update(), Equations.time_update()
update ProblemDefinition.copy() to setup output of new problem
fix create_evaluable() to pass time stepper to terms
update Variable.init_data() to use .data_from_any()
remove unused evaluate()
cleanup in sfepy/geom, mesh and geometry tools moved to sfepy/mesh/
update term evaluation to use var_dict also with try_equations
update ProblemDefinition.create_evaluable()
fix section titles in docstrings
update formatting of term docstrings to remove sphinx warnings
many small docstring fixes to remove sphinx warnings
docs:
update script/gen_gallery.py:
omit __init__.py files, unify link names
skip missing images
update many docstrings (especially all docstrings of terms to remove sphinx warnings)
update nodal stress description in Primer, mention refinement
update ubuntu installation section
update Primer for dw_point_load term
update for missing/removed/renamed modules
update users guide for new postproc.py options
cleanup whitespace, add table of contents to users guide
add basic info about solvers to users guide
fix and update Primer
update gitwash, include it to developer guide table of contents
update variables section in users guide
move release notes to doc/, add sphinx section labels
add news and archived news
update main html page, add links
add google analytics support
update release tasks
update developer guide for ev_* terms
remove termsLinElasticity_full.rst from developer guide
process_terms(): insert term call signature before arguments lists
from 2011.3 to 2011.4¶
use cython instead of swig - merge cython branch:
wrap vxc() and vectorize it - new get_vxc():
update SchroedingerApp.iterate() to use get_vxc()
remove sfepy/physics/extmods/dft.i, update setup.py, __init__.py
new sfepy/fem/extmods/assemble.pyx:
new assemble_vector(), assemble_vector_complex()
new assemble_matrix(), assemble_matrix_complex()
use new assembling functions in Term.assemble_to()
remove old C assembling functions
update insert_sparse_to_csr() for assemble.pyx
remove unused functions in fem.c:
remove lagrange1*(), baseBiL*(), baseTriL*(), rezidual(), matrix(), inverse_element_mapping()
tests:
split tests/test_assembling.py
move test_eval_matrix(), test_vector_matrix(), test_surface_evaluate(), test_dq_de() into tests/test_term_consistency.py
move test_save_ebc() into new tests/test_ebcs.py
clean up and modernize
add new assembling tests to tests/test_assembling.py
new test_assemble_vector(), test_assemble_vector_complex(), test_assemble_matrix(), test_assemble_matrix_complex()
new sfepy/fem/extmods/bases.pyx:
new get_barycentric_coors(), _get_barycentric_coors()
new _eval_lagrange_simplex(), eval_lagrange_simplex()
new _eval_lagrange_tensor_product(), eval_lagrange_tensor_product()
new _get_xi_simplex(), _get_xi_tensor()
new evaluate_at()
update Field.evaluate_at() for new evaluate_at()
use new base evaluation functions:
update _eval_base() of LagrangeSimplexPolySpace, LagrangeSimplexBPolySpace, LagrangeTensorProductPolySpace
remove PolySpace.clear_c_errors()
new wrappers of orient_elements(), graph_components():
new sfepy/fem/extmods/mesh.pyx
add bases, mesh to __init__.py, remove meshutils
update Domain.fix_element_orientation()
update surface_components()
remove sfepy/fem/extmods/meshutils.i
new pyalloc(), pyfree() helper functions
move mesh_graph() and related functions to meshutils.c
remove raw_graph()
new create_mesh_graph()
define basic types in new types.pxd
new _fmfield.pyx, _fmfield.pxd - FMField-related wrappers:
new array2fmfield*()
remove fem module from setup.py
remove fem.c, fem.h, fem.i
remove geometry.i, update setup.py
new mappings.pyx:
new CVolumeMapping extension class
update setup.py for mappings.pyx, reuse _fmfield library
new mappings.pxd for mappings.pyx
new CSurfaceMapping extension class
use CVolumeMapping, CSurfaceMapping in VolumeMapping, SurfaceMapping
new Config.python_include()
use sfepy_common library for common C code
use sfepy_terms library for term C code
add ignore_errors argument to load_classes()
new array2pint2(), array2pint1() helper functions
simplify import of extmods.terms
new terms.pyx:
wrap dq_state_in_qp(), dq_grad(), dq_grad_extra(), dq_div_vector(), d_volume_surface(), di_surface_moment()
update eval_real(), eval_real_extra(), eval_complex()
wrap dq_finite_strain_tl(), dq_finite_strain_ul(), dq_tl_finite_strain_surface(), dq_tl_he_stress_bulk(), dq_ul_he_stress_bulk(), dq_tl_he_stress_neohook(), dq_ul_he_stress_neohook(), dq_tl_he_stress_mooney_rivlin(), dq_ul_he_stress_mooney_rivlin(), dq_tl_he_tan_mod_bulk(), dq_ul_he_tan_mod_bulk(), dq_tl_he_tan_mod_neohook(), dq_ul_he_tan_mod_neohook(), dq_tl_he_tan_mod_mooney_rivlin(), dq_ul_he_tan_mod_mooney_rivlin(), dw_he_rtm(), de_he_rtm(), dq_tl_stress_bulk_pressure(), dq_ul_stress_bulk_pressure(), dq_tl_tan_mod_bulk_pressure_u(), dq_ul_tan_mod_bulk_pressure_u(), dw_tl_volume(), dw_ul_volume(), dw_tl_diffusion(), dw_tl_surface_traction(), dq_def_grad(), he_residuum_from_mtx(), he_eval_from_mtx()
update hyperelastic term classes for terms.pyx:
update HyperElasticBase, HyperElastic{TL, UL}Base, SurfaceTractionTLTerm
wrap dw_volume_wdot_scalar(), dw_laplace(), d_laplace(), dw_diffusion(), d_diffusion(), dw_permeability_r(), dw_diffusion_coupling(), d_diffusion_coupling(), de_diffusion_velocity(), d_surface_flux()
wrap dw_lin_elastic_iso(), dw_lin_elastic(), d_lin_elastic(), dw_lin_prestress(), dw_lin_strain_fib(), de_cauchy_strain(), de_cauchy_stress(), dq_cauchy_strain(), dw_surface_ltr(), dw_volume_lvf(), dw_mass(), dw_mass_scalar(), d_mass_scalar(), dw_surf_mass_scalar()
wrap term_ns_asm_div_grad(), term_ns_asm_convect(), dw_lin_convect(), dw_div(), dw_grad(), dw_st_pspg_c(), dw_st_supg_p(), dw_st_supg_c(), dw_st_grad_div(), dw_biot_grad(), dw_biot_div(), d_biot_div(), dw_piezo_coupling(), d_piezo_coupling(), dw_electric_source()
wrap d_diffusion_sa(), dw_surf_laplace(), d_surf_laplace(), dw_surf_lcouple(), d_surf_lcouple()
add stubs for remaining functions
remove terms.i
new crcm.pyx:
rcm(), permute_in_place()
update setup.py and init files for crcm.pyx
remove rcm.i, array.i, common.i, fmfield.i
update .gitignore
update docs (swig -> cython)
fix script/gen_term_table.py for circular dependency
build:
update Clean.run() to remove cython-generated files
fix speed regression (numpy.distutils quirk)
make cython compulsory dependence in setup.py
set min. cython version to 0.14.1
make proper class for physical quadrature points:
new PhysicalQPs, .get_merged_values(), .get_shape()
update get_physical_qps()
update Material for PhysicalQPs
update PhysicalQPs.get_shape() - make ig optional, check shape compatibility
also allow any raveled shape length >= 1
update get_physical_qps(), add n_total attribute to PhysicalQPs
updated Lagrangian formulation:
fix evaluate.new_ulf_iteration()
update hyperelasticity (ULF) terms for new Term.evaluate()
remove cachesFiniteStrain.py:
functions moved to terms_hyperelastic_ul(tl).py
fix hyperelastic ULF terms: CompressibilityULTerm, VolumeULTerm
fix hyperelastic terms in ULF for mixed pressure-displacement formulation
terms:
update DiffusionIntegrateTerm, renamed: d_diff… –> di_diff…
new arg_type: ‘opt_material’ - optional material
remove “_mass_scalar_w” terms, use “_mass_scalar” instead
remove “_w” terms in termsBasic.py and termNavierStokes.py
fix Term.classify_args()
fix SurfaceMomentTerm.get_eval_shape()
fix dw_volume_dot, SurfaceTerm, SumNodalValuesTerm, DiffusionSATerm
update DiffusionIntegrateTerm, DiffusionVelocityTerm, DiffusionRTerm, disable PermeabilityRTerm
update acoustic and diffusion terms
problem description:
update ProblemConf.get_function() for passing functions directly
use ProblemConf.get_function() to get parametric hook
update ProblemConf.from_file() to accept define_args as tuple
tensors:
update transform_data() for fourth order tensors
check numbers of points in transform_data()
do not meddle with data shape implicitly
fix transform_data() (second order case)
add mode argument to prepare_cylindrical_transform()
fix docstring of transform_data()
polynomial spaces:
pass space, poly_space_base to Interpolant, SurfaceInterpolant:
update {SurfaceField, Field}.create_interpolant()
update PolySpace.eval_base() for array-like coors argument
new sfepy/fem/extmods/lobatto_template.pyx
new eval_lobatto()
update setup.py for lobatto.pyx
add generated sfepy/fem/extmods/lobatto.pyx to simplify building
mesh refinement:
new Mesh.get_element_coors()
new refine_3_8()
update Domain.refine() for hexahedral meshes
new gen_misc_mesh(), gen_mesh_from_string()
new ProblemDefinition.refine_uniformly()
new refine_2_3(), refine_2_4()
update Domain.refine() for 2D meshes
solvers:
simplify imports in ScipyIterative.__init__()
silence sparse efficiency warning
new linear solver - Schur complement
input-output:
update MeditMeshIO.read() - add omit_facets argument
update Mesh.from_file(), MeshIO.read() - add omit_facets argument
remove *args from MeshIO.read(), .write()
new BDFMeshIO.write() function (Nastran data format)
fix VTKMeshIO.read()
clean up ioutils.py (imports, whitespace, coding style)
update supported_capabilities dict - prepare for boundary conditions
update Mesh._set_data() - add nodal_bcs argument
update NEUMeshIO.read() to read nodes of boundary conditions
update Mesh.from_file() - allow passing Mesh instance in place of file name
fields, variables:
update Field.get_mapping() for initial time step
fix indx initialization in Variable.__init__()
update Field.setup_dof_conns() for string dc_type
report standalone vertices in evaluate_at()
check for standalone vertices in Field.evaluate_at()
scripts:
turn script/gen_term_table.py into sphinx extension
new script/gen_gallery.py:
generate documentation and gallery of sfepy examples
new script/gen_lobatto_pyx.py
postproc.py:
update parse_view(), –view help message
new –no-offscreen option
add script/show_authors.py
schroedinger:
more fixes for meshes with several element groups
new sfepy/physics/radial_mesh.py - RadialMesh, RadialHyperbolicMesh
fix for higher order approximations, clean up
update split of DFT and general options, update docstrings
add init_hook application option
add v_fun_name application option
update Potential for user arguments to evaluation function
new Potential.__len__()
rename –mesh option to -create-mesh
new –mesh, –mesh-dir options
use ensure_path(), allow only one of –mesh, –create-mesh
homogenization:
update recover_micro_hook(), new parameter ‘recovery_file_tag’
update homogenized coefficient classes for term_mode argument:
update MiniAppBase.__init__()
update {CoefSymSym, CoefFMSymSym, CoefDimSym, CoefNN, CoefN, CoefSym, CoefFMSym, CoefOne, CoefFMOne}.__call__()
new volume computation and selection
allow passing scalar volume to coefficient classes
new MiniAppBase._get_volume()
fix output key in CorrMiniApp.get_output()
update HomogenizationApp.process_options(), .call() - clean up
clean up Coefficients
tests and examples:
new test_hyperelastic_tlul.py - compare TLF and ULF solutions
remove tests/test_input_hyperelastic.py
test duplicated by test_hyperelastic_tlul.py
add basic docstrings with equations to examples in gallery
fix linear_elastic_probes.py example
update test_install.py to test linear_elastic_probes.py example
add test for refine_3_8():
new refine(), test_refine_hexa()
rename test_refine() -> test_refine_tetra()
add test for fourth order tensors support in transform_data():
new test_transform_data4()
test mesh interpolation invariance (FieldVariable.evaluate_at()):
new gen_datas(), test_invariance(), test_invariance_qp()
add __init__.py files to allow package imports in examples/
fix importing utils.py in Navier-Stokes examples:
wrong file (from pytables) got imported in Windows
improve testing of uniform mesh refinement
misc:
new get_jacobian() utility function
update set_mesh_coors() - add clear_all argument
fix argument types in gen_block_mesh(), gen_cylinder_mesh()
update FieldVariable.data_from_qp() for higher order approximations
fix test_install.py for windows
new ensure_path(), locate_files(), remove_files()
update Viewer.set_source_filename() - catch also AttributeError
fix syntax for python 2.5
remove FMField.stride (unused in cython wrappers)
update ‘nodes of group’ region selector for named groups
use NumPy C type definitions, fix pointer type and printf format warnings
remove unnecessary includes (fix _POSIX_C_SOURCE warnings)
remove unused vg_integrateChunk(), sg_integrateChunk()
remove caches attribute from Equations and Equation
improve getting default integrals in ProblemDefinition:
new ProblemDefinition.get_integrals()
fix common_python.c for 64bit systems
add reference element meshes
remove unused methods of GeometryElement:
remove .orient_edges(), .orient_faces3(), .orient_faces4()
remove sfepy/optimize/fluentutils.py
fix docstring of get_green_strain_sym3d() for LaTeX
fix centre argument in get_coors_in_tube()
build:
update Clean.run() to clean also examples/, script/, tests/
include *.pxd files and lobatto_template.pyx in distribution
do not install version.h.in
add lobatto_template.pyx, version.h.in to MANIFEST.in
documentation:
new examples.rst
update latex_preamble in doc/conf.py
add terms_constraints.rst to table of contents
new sfepy docs html layout
update region selection syntax in users guide
fix developer guide for renamed/deleted/new files
move installation docs into new doc/installation.rst, update
add remaining sfepy modules to developer guide
update script options in users guide
link examples, primer from index
add features to introduction
add applications to index
more on ebcs given by functions
from 2011.2 to 2011.3¶
major update of terms - merge easier_terms branch:
aim: easier usage and definition of terms while retaining original C functions
approximations and fields:
new Approximation.get_connectivity()
update Approximation.describe_geometry():
new return_mapping argument
make volume mappings local to given region
include used polynomial space in geometry object:
update Approximation.describe_geometry()
manage mappings in Field:
new Field.clear_mappings(), .save_mappings(), .create_mapping(), .get_mapping()
equations and variables:
evaluate and cache quantities in FieldVariable:
new FieldVariable.evaluate(), .clear_evaluate_cache()
update Variable.__call__() history behaviour for step 0
update Variable.advance() to advance evaluate cache
copy equations variables in ProblemDefinition.create_evaluable()
invalidate evaluate cache in Variable.data_from_any()
factor out variable evaluation to new evaluate_variable.py:
update FieldVariable.evaluate()
new eval_real(), eval_complex()
update Equations.invalidate_term_caches() for evaluate caches:
new FieldVariable.invalidate_evaluate_cache()
move NewTerm.get_shape_kind() to get_shape_kind()
update Term:
new Term.get(), .get_mapping(), .get_data_shape()
refactor Term.evaluate():
new Term.check_shapes(), .eval_real(), Term.eval_complex(), split_complex_args()
new Term.get_assembling_cells()
remove Term.needs_local_chunk()
update Term.assemble_to()
fix Term.iter_groups() for no cells in a group
update many terms for new Term.evaluate():
dw_laplace, dw_diffusion, de_diffusion_velocity, dw_biot, dw_lin_elastic, de_cauchy_strain, de_cauchy_stress:
update both Python and C code, lots of simplifications
dw_mass_scalar, dw_mass_scalar_w
dw_lin_elastic_iso, dq_cauchy_strain, dq_cauchy_stress, dw_mass_vector, dw_piezo_coupling, dw_surface_ltr
remove dw_mass
dw_div_grad, dw_convect, dw_lin_convect, dw_stokes, dw_stokes_w
merge dq_lin_convect with dw_lin_convect
dq_grad, de_grad, dq_div, de_div (was d_div)
dw_point_lspring, dw_volume_lvf
di_volume_integrate (merged with de_average_variable, dq_state_in_volume_qp)
di_surface_integrate (was d_surface_integrate, merged with dq_state_in_surface_qp)
di_surface_integrate_w (was d_surface_integrate_w)
dw_volume_integrate, dw_volume_integrate_w, dw_surface_integrate, dw_surface_integrate_w, d_volume_dot, d_surface_dot, d_surface_dot_w, d_volume, d_surface, d_volume_surface, di_surface_moment, d_sum_vals
dw_volume_dot_w, allow different approximation of the arguments
di_integrate_mat (was de_volume_average_mat + di_volume_integrate_mat)
dw_jump, remove dw_jump()
dw_non_penetration term
dw_st_pspg_c, dw_st_supg_p, dw_st_supg_c, dw_st_grad_div
dw_surface_mass_scalar, dw_surface_mass_scalar_w, dw_bc_newton
remove dw_mass_scalar_fine_coarse
d_surface_flux:
rename d_hdpm_surfdvel -> d_surface_flux
remove termsHDPM.* files, move functions to termsLaplace.*
dw_tl_membrane
dw_electric_source
update basic hyperelastic TL terms for new Term.evaluate()
new HyperElasticBase.get_family_data()
new HyperElasticTLBase.integrate(), .function(), .compute_family_data(), .compute_stress(), .compute_tan_mod(), .get_fargs(), .get_eval_shape()
dw_tl_he_neohook, dw_tl_he_mooney_rivlin, dw_tl_bulk_penalty
dw_tl_fib_a, dw_tl_surface_traction
update TL perfusion terms for new Term.evaluate()
dw_tl_bulk_pressure, dw_tl_volume, dw_tl_diffusion terms
update examples for new Term.evaluate():
examples/biot/biot_npbc.py
examples/navier_stokes/navier_stokes.py
examples/linear_elasticity/material_nonlinearity.py
examples/biot/biot_npbc_lagrange.py
examples/homogenization/linear_elastic_mM.py
update tests:
update test_surface_evaluate()
update test_laplace_unit_*.py for d_surface_flux
update Region.select_cells_of_surface() for passing to C
averaging mode in vg_integrate(), sg_integrate():
use vg.integrate() in de_grad, de_div terms
remove de_integrate()
fix regions, groups for argument traces
remove obsolete term caches:
remove sfepy/terms/cachesBasic.py
remove FiniteStrainTLDataCache, FiniteStrainSurfaceTLDataCache
new eval_real_extra(), dq_grad_extra()
update sfepy/homogenization/recovery.py
update FESurface for mirror connectivities:
start FESurface.setup_mirror_connectivity()
update FESurface.get_connectivity() - add is_trace argument
update field and DOF connectivities for boundary traces:
is_trace is part of field DOF connectivity keys, active DOF connectivity keys and FieldVariable evaluate cache keys
update setup_dof_conns(), Field.setup_extra_data()
update Field.setup_surface_data(), .setup_dof_conns():
add is_trace argument
update Approximation.get_connectivity() - add is_trace argument
update Equations.get_graph_conns()
update FieldVariable.get_dof_conn(), .evaluate()
update Term.assemble_to()
update SurfaceField.setup_dof_conns() for is_trace argument
docs:
add Primer tutorial
installation: new Python(x,y) instructions with umfpackpy
dev guide: describe directory structure
add local table of contents at several places
fix term signature table generation in process_terms()
fix typeset_term_table() for multi-equation definitions
dev guide: rewrite section on implementing new terms
new terms_new.rst
make tutorial images smaller
update and link release tasks to developer guide
regions:
update define_box_regions() - add can_cells argument
add true_cells attribute to Region:
update Region.__init__(), .update_groups(), .set_faces(), .select_cells(), .select_cells_of_surface()
update Region.set_from_group(), .set_faces(), .complete_description()
update Region.get_n_cells() to return total count optionally
fix Region.set_faces()
fields:
check region passed to field constructor:
new Field.check_region(), SurfaceField.check_region()
new SurfaceField.average_qp_to_vertices()
fix Approximation.describe_geometry() for surface fields
fix default fill value in Field.extend_dofs() for scalars
fix Field.get_dofs_in_region_group() for surface regions (no true cells)
remove unused Field.update_geometry()
replace FieldVariable.describe_geometry() by new .get_mapping()
problem description:
update ProblemConf constructors - new override argument:
override given configuration items using override dict
new ProblemConf.dict_from_string()
new sfepy/base/parse_conf.py: create_bnf()
schroedinger.py: new –conf, –options options - allow override
simple.py: new –conf, –options options - allow override
new ProblemConf.get_function():
update assign_standard_hooks()
update schroedinger.py
remove obsolete ‘fe’ keyword
input-output:
fix reading mat_id in VTKMeshIO, read node_groups (if it exists)
set TetgenMeshIO.getnodes(), .getele() verbose default to False so that it does not interfere with runTests.py
update UserMeshIO.read() for functions returning new mesh
fix blockgen.py, cylindergen.py scripts
update gen_block_mesh(), gen_cylinder_mesh() for non-array arguments
fix SimpleApp.setup_output_info() for MeshIO instances as filename_mesh
implement geometrical surface groups in Domain:
new Domain.create_surface_group(), .clear_surface_groups()
update Approximation.describe_geometry() for surface groups
update Field.setup_extra_data()
integrals:
update Integrals.get() to accept int as quadrature name
new Integral.get_key()
remove unused dim attribute from Integral
terms:
fix Mooney-Rivlin stress term
remove VolumeDataCache, SurfaceDataCache:
simplify d_volume, d_surface terms
remove Term.describe_geometry(), use .get_mapping() instead
solvers:
update processing of solver options
use new make_get_conf()
options in ‘conf’ can be overridden using kwargs
remove LinearSolver.set_tolerance()
remove SymeigEigenvalueSolver, clean and fix sfepy/solvers/eigen.py
remove symeig reference
merge common code in eigensolvers to a decorator
fix PETScKrylovSolver for nonlinear problems
fix output indentation in PysparseEigenvalueSolver.__call__()
always compute initial residual in time_step_function()
schroedinger:
update schroedinger.py to follow style guide
schroedinger.py: new –save-restart, –load-restart options:
basic DFT restarting functionality
schroedinger.py: add save_dft_iterations application option
allow adding/subtracting zero to PotentialBase
make Potential iterable, numerical charge computation:
new Potential.__iter__(), .get_distance(), .get_charge()
update getvxc() to compute also energy
fix schroedinger.py for meshes with several element groups
schroedinger.py: move conf code to new ProblemConf.from_file_and_options()
scripts:
extractor.py: improve help message
remove sfepy_gui.py
update test_install.py to report success/failure in log of times
update test_install.py to test –config option
base:
new print_array_info(), update_dict_recursively(), edit_dict_strings()
misc:
new SimpleApp.save_dict(), .load_dict()
make PolySpace.node_coors C-contiguous
fix ElasticConstants for SymPy 0.7.0
remove unused Domain.get_orientation()
update evaluate_at() to be more robust for tensor product elements
update EquationMap.map_equations() for array values
fix mayavi imports for version 4.0.0
fix output shape in dot_sequences()
fix State.get_scaled_norm() for zero scaling norm
fix set_mesh_coors(), ProblemDefinition.set_mesh_coors()
remove geometries and geometries0 attributes
implement updated Lagrangian formulation for finite strain elasticity
example
setup reference state for nonlinear homogenization
fix and add terms, support for nonlinear homogenization
updating reference geometry
new “ulf” options, setup iter_hook
setup actual and initial coordinates
fix computation of the deformation gradient
new example hyperelastic_ul_up.py - ULF, displacement-pressure formulation
new dw_ul_volume and dw_ul_compressible terms
new terms:
dw_div_w (weighted divergence term of a test function)
examples:
new examples/standalone/thermal_electric/thermal_electric.py:
update test_install.py to test it
new examples/linear_elasticity/its2D_1.py
new examples/linear_elasticity/its2D_2.py
new examples/linear_elasticity/its2D_3.py
update test_install.py to test it
new examples/linear_elasticity/its2D_4.py
setup:
fix setup.py files to correctly define DEBUG_FMF flag
allow calling “python setup.py” via Makefile
update site_cfg_template.py
fix matplotlib version for ubuntu 10.04
update package_check() for alternative names
update mayavi version check
from 2011.1 to 2011.2¶
experimental implementation of terms - merge new_terms branch:
aim: easier usage and definition of terms
new NewTerm class, to coexist with Term for some time
update FieldVariable:
new .set_current_group(), .clear_current_group()
new .val(), .val_qp(), .grad(), .grad_qp(), .iter_dofs()
new .assign_geometries(), .clear_bases(), .setup_bases()
new .get_element_zeros(), .get_component_indices()
add spatial dimension attribute
cache base functions and geometries
new get_range_indices()
new examples:
examples/miscellaneous/compare_scalar_terms.py
examples/miscellaneous/compare_vector_terms.py
new new terms:
dw_new_diffusion
dw_new_mass_scalar
dw_new_mass
dw_new_lin_elastic
implement basic membrane elements - merge tl_membrane_term branch:
new dw_tl_membrane (Mooney-Rivlin membrane term)
update build system to use exclusively setup.py:
update setup.py to check dependencies, prepare for using Cython
update setup.py clean to remove files generated by in-place build
new setup.py options: htmldocs, pdfdocs, doxygendocs
remove all Makefiles
new MANIFEST.in for excluding paths/files from distribution
site configuration:
update options in site_cfg_template.py, update Config
remove archlib, numpy_include
rename opt_flags -> compile_flags
set options for building extension modules via Config
update and clean up setup.py files
docs:
update for no Makefiles, add sympy as dependency
add sphinx build file for windows
fix doc/doxygen.config to exclude generated files
update tutorial:
add long, short syntax sections, add TOC
add basic notions, sneak peek sections
boundary condition:
allow switching boundary conditions on/off depending on time:
update boundary conditions to have times attribute
update Conditions, EssentialBC, PeriodicBC, LinearCombinationBC
use new is_active_bc(), update matrix graph as needed
pass problem definition to user EBC functions:
update tests and examples
postprocessing and visualization:
fix Viewer and add_subdomains_surface() for animations:
new FileSource.setup_mat_id(), set mat_id in .create_source()
update ViewerGUI - ‘make snapshots’ button
fix animation view setting in Viewer, ViewerGUI:
use all view components including distance and focal point
postproc.py:
new –opacity option
new –domain-specific option
new parse_domain_specific()
new sfepy/postprocess/domain_specific.py
new DomainSpecificPlot class, plot_displacements()
linalg:
prevent nans in cg_eigs()
fix cg_eigs() for array input
new normalize_vectors()
update dot_sequences() to use numpy.core.umath_tests.matrix_multiply():
more than ten times faster, if available!
input-output:
extractor.py: new –times option
support for variable time steps:
new extract_times()
new MeshIO.read_times(), HDF5MeshIO.read_times()
update VTKMeshIO, HDF5MeshIO to save true time step data
solvers:
update Newton:
new ‘give_up_warp’ configuration option
return number of iterations in status
support iter_hook
improve bad linear solver convergence report
allow linear solver precision relative to residual norm:
new ‘lin_precision’ solver option
new VariableTimeStepper - time stepper with a variable time step
update ProblemDefinition for nonlinear solver iter_hook
improve convergence reporting of ScipyIterative, PETScKrylovSolver
add tolerance arguments to linear solvers
homogenization:
new CorrSetBCS corrector - “zero” state with applied boundary conditions
misc:
new invert_remap()
new Region.from_faces(), .set_faces()
new guess_time_units()
add test_install.py
new terms:
dw_lin_strain_fib (linear prestrain term - defined by direct. fibers)
removed terms:
remove d_surf_diffusion_integrate term (same as d_hdpm_surfdvel)
examples:
new examples/diffusion/poisson_short_syntax.py
rearrange examples/diffusion/poisson.py
many bug fixes =:)
from 2010.4 to 2011.1¶
implement discontinuous fields - merge ‘discontinuous’ branch
use mesh connectivity to construct reference maps
independently from approximations of variables (fields)
always P1 or Q1, based on element geometry
update Approximation.describe_geometry() and related functions
new DiscontinuousField, DiscontinuousApproximation classes
use DiscontinuousField for P0, Q0 approximations
new eval_nodal_coors()
update Approximation.eval_extra_coor()
new Field.average_qp_to_vertices(), .interp_to_qp()
update surface fields:
new SurfaceApproximation class, used by SurfaceField
new SurfaceInterpolant class, used by SurfaceField
fields:
new Field.get_true_order(), .get_vertices()
new Field.evaluate_at()
allows different behaviour for Field subclasses
new Field.get_output_approx_order() - correct output order
remove Approximations class, move its functionality to Field
simplification to remove a layer of code that was not needed
Field.aps is an ordinary dict
methods using is_surface split between Field and SurfaceField
state, variables, degrees of freedom:
new DofInfo.get_n_dof_total()
new Linear Combination BC operator: IntegralMeanValueOperator
new EquationMap.get_operator()
new State.from_variables(), .set_parts()
add force argument to State.set_full()
new Variables.check_vector_size(), use it to check DOF vectors
fix Variables.state_to_output() for saving by parts
fix Variable.advance() - prevent history modification
new FieldVariable.apply_ebc(), .apply_ic()
update Variables.apply_ebc(), .apply_ic()
new FieldVariable.get_full()
update Variables.make_full_vec(), remove var_name argument
new FieldVariable.get_reduced()
update Variables.strip_state_vector(), fix for non-first variables
remove Variable.get_indx(), update State accordingly
the indx attribute of a variable is local only, it does not index the state vector - dangerous to expose it
materials: rewrite updating of material parameters
allow material nonlinearity, i.e. parameters dependent on state
ProblemDefinition instance needs to be passed into Materials.time_update() and related functions
material user function syntax changed
takes ts, coors, mode, equations, term, problem and group_indx
the coors argument are the QP coordinates for all element groups merged
equations and evaluation:
split Equations.time_update() - new Equations.time_update_materials()
fix term evaluation with complex variables
update Equations.eval_tangent_matrices() - names argument
fix Equations.eval_tangent_matrices() for multi-variate terms
clear the matrix there, not in BasicEvaluator.eval_tangent_matrix()
update Equations.eval_residuals() - by_blocks, names arguments
new Equations.print_terms()
add regions argument to create_evaluable()
terms:
new register_term()
ensure that each Term instance has caches attribute
ensure that all terms in equations share the same DataCaches instance
new Equations.setup_caches()
update Term.get_arg_name() - add docstring, join argument
fix Term.assign_caches(), .get_cache() for material arguments
update cachesBasic for complex values
mesh, domain, regions:
generate meshes using: 2D - triangle, 3D - tetgen
speed-up mesh reading by using numpy.fromfile()
update read_array()
update VTKMeshIO, ComsolMeshIO, VTKMeshIO, MeditMeshIO
update skip_read_line(), read_token()
coordinate transformation matrix can be defined in options
allows translation in coordinate transformation
new Domain.refine() - uniform tetrahedral mesh refinement
new sfepy/fem/refine.py: refine_3_4()
new Region.from_vertices()
new Region.update_shape(), update Region.complete_description()
new Facets.get_complete_facets()
problem definition:
new ProblemDefinition.setup_hooks()
fix ProblemDefinition.solve() for LCBCs
new ProblemDefinition.set_output_dir(), .set_solvers_instances()
update ProblemDefinition.init_solvers() to report presolve time
new ProblemDefinition.set_equations_instance()
solvers:
fix time_step_function() to allow presolve if possible
fix Newton, SemismoothNewton exception handling (define ok)
update/fix TimeStepper construction arguments
new pre_process_hook - called in solve_direct
fix TimeStepper, get_print_info() for n_step set to 1
fix time stepping solver for quasistatic linear problems
new prepare_matrix()
sfepy.linalg:
new get_coors_in_ball()
new assemble1d(), unique_rows(), infinity_norm()
new insert_strided_axis()
update cg_eigs(), sym_tri_eigen(), allow eigenvalue selection
fix and update dot_sequences() - general mode argument
large deformation:
fix HyperElasticBase for several element groups
fix HyperElasticBase for matrix-only assembling
compute stress in matrix mode if no previous residual mode call
fix BulkPressureTLTerm (dw_tl_bulk_pressure) for several element groups
update VolumeTLTerm to work in initial step
fix error handling in hyperelastic term caches
new sfepy/mechanics/membranes.py: functions for membranes
new describe_deformation(), get_tangent_stress_matrix(), create_transformation_matrix(), create_mapping(), get_invariants()
schroedinger: update and clean up
update for recent changes (on the fly geometries, Materials under Equations, for material nonlinearity, …)
add iter_hook_final application option
fix getting parametric hook for inputs with define()
homogenization:
update plotPerfusionCoefs.py
new CorrEqPar - parametrized equation via ‘eq_pars’
update TCorrectorsViaPressureEVP for Variable.get_full()
allow complex coefficients
fix CorrectorsPermeability
update PressureEigenvalueProblem
remove obsolete fading memory coefficients
remove ViscousFMCoef, BiotFMCoef, BiotFM2Coef, FMRBiotModulus
update fading memory coefficients CoefFMSymSym, CoefFMSym, CoefFMOne
fading corrector file names obtained by set_variables()
update time dependent pressure eigenvalue problem based correctors
update TCorrectorsViaPressureEVP
update TCorrectorsRSViaPressureEVP, TCorrectorsPressureViaPressureEVP
raise original exception in MiniAppBase.init_solvers()
update recover_bones()
fix variable names in CorrMiniApp.get_output() for no components
genPerMesh.py:
new –repeat option
split and move functionality into sfepy.fem
move fix_double_nodes(), get_min_edge_size(), get_min_vertex_distance(), get_min_vertex_distance_naive() into sfepy/fem/mesh.py
new compose_periodic_mesh()
remove broken –test option
new terms:
d_sum_vals (sum nodal values, for use in postprocessing)
d_diffusion_integrate (diffusion integral term)
d_surf_diffusion_integrate (diffusion surface integral term)
dw_diffusion_coupling (diffusion copupling term)
new d_div term (evaluate divergence term)
d_surface_integrate_w (integrate a variable over a surface)
d_surface_dot_w (surface dot product for both scalar and vector fields)
clean up in acoustic terms
some of them replaced by more general diffusion terms
simplify acoustic/diffusion sensitivity terms
d_llaplace_p_sa1, d_llaplace_p_sa2, d_llaplace_t_sa2 -> d_diffusion_sa
dw_surface_llaplace -> dw_surface_laplace
remove obsolete code, clean up:
BasicEvaluator.strip_state_vector(), LCBCEvaluator.strip_state_vector()
remove obsolete function and code (_fix_scalar_dc())
remove Field.get_extra_nodes_as_simplices(), .write_mesh()
simple.py: remove –save-region-field-meshes option
remove code depending on removed Field.get_extra_nodes_as_simplices()
Mesh.from_region_and_field()
ProblemDefinition.save_region_field_meshes()
remove Field.interp_c_vals_to_n_vals()
remove parameter ‘shape’ from term di_volume_integrate_mat
remove read_tuple()
docs:
new projections.rst, fields.rst, variables.rst
misc:
remove star imports
fix Output.__init__() arguments
new Container.extend()
allow construction of OneTypeList from sequence
fix acoustic band gaps code
new Interpolant.get_geom_poly_space()
new make_l2_projection() for scalar field variables
add tetrahedron quadratures of order 4 and 6
update get_physical_qps() - use slices for efficiency
update Viewer - plot scalar cell data as cell data if possible
isfepy: update startup message
tests and examples:
tests/test_projections.py: new test_projection_tri_quad()
new examples/linear_elasticity/material_nonlinearity.py + test
fix, update examples/diffusion/poisson_parametric_study.py
update tests/test_tensors.py
new test_transform_data(), test_stress_transform()
new tests/test_linalg.py - test dot_sequences(), insert_strided_axis()
update tests/test_linalg.py - new test_unique_rows(), test_assemble1d()
new tests/test_domain.py - very basic tests of facets and refinement
many bug fixes
from 2010.3 to 2010.4¶
base:
better printing formatting for basic data types
docs:
use viewcode Sphinx extension
add gitwash tutorial (adapted from Numpy)
sfepy.linalg:
new insert_sparse_to_csr() - insert a sparse matrix into a CSR matrix
new compose_sparse()
improve structuring:
move some functions from sfepy.linalg.utils to sfepy.linalg.geometry
remove unneeded functions
simplify importing:
import all its contents into sfepy.linalg namespace
new sfepy/linalg/eigen.py - eigenvalues utility functions
new sfepy/linalg/geometry.py - barycentic coordinates and simplex utilities
conditions:
make active LCBC-constrained DOF information always defined
update make_global_lcbc_operator() to preserve matrix blocks
also create and return global active LCBC-constrained DOF information
new NormalDirectionOperator class
solvers:
solvers: provide default name and kind for any type of conf
allow (re)setting data of an existing TimeStepper instance
use a single time stepper instance in ProblemDefinition
pass the instance to .set_equations() as user data to satisfy time-dependent term arguments
update Newton, SemismoothNewton - raise original residual/matrix exceptions
update SemismoothNewton to use compose_sparse()
the Jacobian needs no longer to have the non-smooth part preallocated
refactoring of geometries (reference mappings) - merge ‘geo’ branch
create geometries as needed on the fly, similarly to term caches
equations only assign container for geometries to terms
geometries no longer stored in Approximations instances
greatly simplify Approximations.describe_geometry()
new sfepy/fem/mappings.py:
handle reference element mappings by new Mapping, VolumeMapping, SurfaceMapping classes
update Equations to create, hold and update Materials:
only materials actually present in equations are updated during ProblemDefinition.time_update() call now
update materials in ProblemDefinition to be created on demand
similar to creating variables
DOF vector synchronization with variables - merge ‘state’ branch
new sfepy/fem/state.py
new State class for handling state Variables
Domain and Mesh:
new Facets class for handling edges and faces
remove C code superseded by Facets
remove unused code superseded by scipy.spatial
new Mesh.explode_groups()
update Field:
simplify Field, Approximations - assume single base and region
new SurfaceField - subclass of Field
enrich the field region syntax - allow (region, ‘surface’) tuple
add is_surface attribute to Approximations, Approximation
update Mesh.from_region() for surface field regions
useful for saving SurfaceField variables with file_per_var option
simplify setting Field approximation order and Interpolant construction
move code for getting DOFs in a region to Field
move DOF manipulation functions to Field
update Equations:
allow passing additional connectivities to Equations.create_matrix_graph()
allow passing single Term to Equation.__init__()
update Equations.eval_tangent_matrices() - block assembling mode
update Variables:
set _variables attribute in Variables.__setitem__() so that any Variable has it once it is added to Variables
new MultiplierVariable - subclass of FieldVariable
update Terms:
allow different Term integration per call mode
simplify setting of term geometry and connectivity types:
new Term.integration attribute
new Term.setup_integration() to determine geometry and connectivity types according to the integration attribute
remove Volume, Surface, Edge, Point, SurfaceExtra constants
geometry types lower-cased
expression evaluation:
pass integral instances instead of integral names where applicable
pass Term instance to .init_data() of DataCache subclasses
update all affected terms and term caches
enable calling user functions on tangent matrix in evaluators
check argument names consistency in ProblemDefinition.create_evaluable()
implement higher order elements - merge ‘ori’ branch:
new NodeDescription class
prepare all possible facet DOF permutations
update Facets to store raw orientation
reimplement Approximations.setup_global_base():
for any polynomial degrees (including extra face DOFs), no C
update computation of extra node coordinates, no C
remove obsolete/unused methods and C functions
prepare remap vectors and DOF indices for all DOF kinds
new sfepy/fem/projections.py
start projections between FE spaces
homogenization:
remove unused (obsolete) correctors and coefficients
remove ‘auxiliary’ coefficients
new sfepy/mechanics/friction.py, DualMesh class
problem description file:
allow optional arguments to define()
update field keywords to match Field constructor arguments
new ANSYS CDB file reader
output:
new FieldVariable.create_output(), simplify Variables.state_to_output()
update Variables.state_to_output() - allow skipping variables
new terms:
dw_non_penetration (non-penetration condition term)
dw_surface_lcouple (acoustic term - derivatives in surface directions)
dw_surface_llaplace (acoustic term - derivatives in surface directions)
dq_div (new divergence in QP term)
scripts:
new friction_slip.py (work in progress)
compare_elastic_materials.py: new –no-plot option
postproc.py:
new –subdomains option
update Viewer - new vector cut plane plotting mode
tests and examples:
new examples/biot/biot_npbc_lagrange.py + test
uses dw_non_penetration term
update tests/test_volume.py to report volumes
update examples/navier_stokes/navier_stokes.py
check divergence-free solution
new tests/test_sparse.py - test compose_sparse()
new ‘linear_elastic_up.py’ example + test
linear elasticity, mixed formulation
new test_eval_matrix()
tests/test_meshio.py: new _compare_meshes(), test_write_read_meshes()
new tests/test_projections.py
many bug fixes
from 2010.2 to 2010.3¶
refactor for interactive use, making things simpler:
redesign term evaluation: non-assembling modes, hierarchy of calls:
hierarchy: ProblemDefinition.evaluate() - evaluate() - Equation.evaluate() - Term.evaluate()
each level can be used by itself
‘eval’, ‘el_avg’, ‘qp’ and ‘weak’ modes
split call_mode into (call_)mode and new term_mode
split evaluate() into create_evaluable() and eval_equations()
new Domain methods to access underlying mesh
refactor Field, remove Fields:
update Field construction (remove bases)
move DOF connectivity setup to fields
refactor construction of Variables
move field-specific methods into FieldVariable
refactor Materials, Material:
remove regions from Material definition:
a Material instance is now really just a collection of values
region is given by a term using the particular Material
split material update code into several functions
allow mixing special constants with parameters given by user-defined function by passing mode=’special_constant’ to the function
refactor construction of Equations, Equation:
Equation.__init__() accepts Terms instance directly
make parse_definition() a regular function
update Equations to create and hold Variables
variables collected from individual terms
Equations now hold geometries instead of ProblemDefinition
remove term prefixes (namespaces) from description of equations
move setup of equations from ProblemDefinition to Equations
move mirror region handling to Region
move creation of ConnInfo into Term
move assembling to Equations (and Term)
refactor Terms, Term:
allow override of term arguments in Term.get_args()
new Term.new() factory constructor
simplified equation parser (full argument parsing now in create_arg_parser())
support basic arithmetics
set term integral at time of term construction
new basic boundary condition classes: BoundaryConditions, BoundaryCondition, EssentialBC, PeriodicBC, LinearCombinationBC
allow Function instances in conditions
refactor linear combination BC
new LCBCOperator, RigidOperator, NoPenetrationOperator, LCBCOperators, make_global_lcbc_operator()
refactor DofInfo into proper class (and module)
refactor equation mapping into EquationMap class
implement simplified integral specification in equations
the integral can either be a string representation of a non-negative integer (the integral order) or ‘a’ (automatic order) or a string beginning with ‘i’ (existing custom integral name)
integrals are created on demand
ConnInfo now stores directly variables instead of their names
update ProblemDefinition for interactive use:
evaluators do not hold the tangent matrix
split and update ProblemDefinition.time_update()
remove unnecessary arguments from evaluators and generic solvers
remove historical cruft, obsolete code
update all examples
update applications for new term evaluation:
schroedinger.py
shaper.py
simplify interactive construction of solvers:
when a non-abstract class is used, name and kind are inferred automatically
improve tests of examples:
update TestInput to call hook functions and to use solve_direct()
simplify TestInputEvolutionary
check nonlinear solver stopping conditions also for evolutionary problems
homogenization:
new CoefSum and CorrSum
new CoefEval - evaluate expression (e.g. ‘c.A/2 + c.B*c.C’)
update for new evaluation code
simplify saving/dumping of correctors by new CorrSolution class
correctors stored by variables, not as the whole state vector
user should provide set_variables() functions for all required correctors/coefficients
pass only the direct dependencies to coefficient and corrector mini_apps
mesh readers:
add support for 2d abaqus quad and tri elements
add full read and write support for comsol mesh format for sfepy supported types
examples:
update examples/quantum:
unify 2D and 3D versions
remove broken DFT examples
new example + test (linear_elastic_tractions.py):
employs simplified integral definition
new examples/standalone/interactive/linear_elasticity.py
tests:
new tests/test_high_level.py
documentation:
improve docstrings:
add argument description for all terms
prepend term call signature(s) into term docstrings
new tutorial “Interactive Example: Linear Elasticity”
many bug fixes
base:
update Container class to be more dict-like
new AUTHORS file
from 2010.1 to 2010.2¶
new mesh readers:
MED (Salome, PythonOCC) format
Gambit NEU mesh format
UserMeshIO class:
creating, writing meshes by user-supplied functions
mechanics:
ElasticConstants class - conversion formulas for elastic constants
StressTransform class to convert various stress tensors
basic tensor transformations
updated documentation:
new sections in developer guide
updated tutorial
many new docstrings
solvers:
semi-smooth Newton method
allow registering custom solvers
examples:
usage of functions to define various parameter
usage of probes
scripts:
simple.py: new –log, –quiet options
postproc.py: new –wireframe, –group-names options
extractor.py: new –same-dir, –to, –step options
split homogen.py:
HomogenizationApp moved to sfepy/homogenization/homogen_app.py
new tests:
test region construction
test quadratures using symbolic integration
test semi-smooth Newton solver
miscellaneous updates:
automatic order of variables
refactor integrals and quadratures
improve printing of Struct instances
IPython-enabled debug()
fixed probes in 2D
split Material.time_update() to allow easier setting of data
region selection of several nodes or elements by their ids
update dump_to_vtk() for stationary results (no time stepper)
update import_file(), load_classes() for package namespaces
update all terms for the new Term constructor
refactor dof connectivity setup, info, active dof info
refactor term argument checking
update equations and terms construction
update HomogenizationEngine to allow inter-coefficient dependencies
update term and cache table generation
run tests in alphabetical order
fix paths to meshes and other data in system-wide installation
new get_lattice_volume()
many small bug fixes
new terms:
dw_stokes_w (Stokes term weighted by scalar function)
dq_biot_stress (Biot stress term in QP)
dq_cauchy_strain (Cauchy strain term in QP)
dq_cauchy_stress (Cauchy stress term in QP)
dq_def_grad (deformation gradient term)
dw_lin_prestress (linear prestress term)
dw_surface_mass_scalar_w (weighted surface scalar mass term)
de_biot_stress (averaged Biot stress term)
di_surface_moment (surface moment term)
from 2009.4 to 2010.1¶
new sphinx-based documentation
major branches merged:
‘interp’ branch: interpolation between different meshes
‘shape’ branch: shape optimization in optimal flow problems
fast evaluation (in C) of Lagrange base functions:
new sfepy/fem/poly_spaces.py, tests/test_fem.py
new GeometryElement class:
tensor product geometry now in [0, 1] instead of [-1, 1]
remove sfepy/eldesc/*
clean-up of examples and meshes
examples:
perfusion in the total Lagrangian (TL) formulation
active fibres in the TL formulation
homogenization:
new examples:
linear elasticity, micro-macro coupling + test, micro-recovery
updated homogenization engine:
support for coefficients summing
improved saving of correctors
new acoustic and perfusion homogenized coefficients
data probing:
automatic refinement of probe points
speed-up:
point caching, use cKDTree for speed
generate_probes() can reuse problem, probes, etc.
new PointsProbe data probe
update generate_probes() for multiple probe hooks
postprocessing and visualization:
VTK source construction for any format supported by MeshIO classes
HDF5FileSource -> GenericFileSource
new GenericSequenceFileSource
graphical logging:
support logging to a text file, vertical line plot (see live_plot.py)
update Log and ProcessPlotter for several Log instances
Log class: wait until figure save is acknowledged
convergence log support in Newton and Oseen solvers
schroedinger: components of V evaluated point-wise in QPs
miscellaneous updates:
new –save-regions-as-groups option in simple.py
move and update functions from extractor.py into time_history.py
Oseen solver: leave setup of stabilization parameters to user
allow also ‘dq’, ‘de’ call modes in InstantaneousBase._call()
split termsHyperElasticity.py to base, TL and UL parts
utilities for work with units of physical quantities:
new sfepy/mechanics/units.py
functions to compute tensor-related quantities usual in continuum mechanics:
new sfepy/mechanics/tensors.py
many bug fixes
new terms:
d_surface (surface of a subdomain)
dw_volume_integrate_variable (volume integration a variable coefficient)
dw_diffusion_r (diffusion-like term)
TL formulation terms:
dw_tl_fib_a (hyperelastic active fibres)
dw_tl_bulk_pressure (hyperelastic bulk pressure)
dw_tl_volume (volume)
dw_tl_diffusion (diffusion with deformation-dependent permeability)
dw_tl_surface_traction (surface traction)
acoustic terms:
dw_acoustic (acoustic term)
d_acoustic_surface (acoustic surface term (in-plane directions))
d_acoustic_alpha (evaluation of acoustic term (in-plane directions))
dw_acoustic_integrate (integration of acoustic term (in-plane directions))
terms for sensitivity analysis:
d_sa_acoustic_alpha, d_sa_acoustic_alpha2, d_sa_acoustic_z, d_sa_acoustic_z2
from 2009.3 to 2009.4¶
major branches merged:
‘ulf’ branch: updated Lagrangian (UL) formulation
‘functions’ branch:
unified passing extra arguments to boundary condition, material, and region functions
physical quadrature point generation
unified/improved handling of material parameters in terms:
all material parameters defined in physical quadrature points
all terms updated, some terms were coalesced into one
‘porous’ branch: homogenized porous media
input file keywords:
new ‘functions’ keyword
simplifications & unifications:
results of all time steps of an evolutionary problem can be saved to a single HDF5 file
enable passing variables data to ProblemDefinition.solve()
runTests.py: allow multiple test files as command line arguments
Viewer.call_mlab() split and refactored
short syntax for periodic boundary conditions
simplified input file syntax of materials
postprocessing and visualization:
using FileSource class abstracts the particular format for storing results:
VTK, HDF5 supported now
support for file sequences (evolutionary simulations)
time step selection for HDF5 (single) and VTK (sequence) files
animations (using ffmpeg)
minimalistic ViewerGUI
show scalar bars
various vector plotting modes
watch results file (HDF5) and add time steps as they are saved
listing data ranges works offscreen, summary for file sequence
sfepy_gui.py: Mayavi2-based GUI to launch simulations
changes aimed at interactive work:
Domain, Region, Field creation refactoring
data probing - postprocessing mode:
read a previously probed data from the probe text file, re-plot them, and integrate them along the probe
graphical logging:
dynamic adding of data groups (new axes) to Log and ProcessPlotter
many bug fixes, namely:
fix import_file() for multiple imports
fix saving results with piece-wise constant (Q0) approximation
miscellaneous updates:
quasistatic time stepping
new zero-order elements: 3_4_P0, 3_8_Q0
more elastic tensor construction functions:
elastic tensor from Young’s modulus and Poisson’s ratio
elastic tensors for use in mixed formulation
setting of parameter variables by a user-defined function
gen_block_mesh() can generate also 2D meshes
reversed Cuthill-McKee permutation algorithm, graph in-place permutation
new terms:
dw_volume_wdot_scalar_eth (exponential decay dot product convolution term)
dw_biot_eth (exponential decay Biot convolution term)
dw_lin_elastic_eth (exponential decay elastic convolution term)
updated Lagrangian (UL) formulation terms:
dw_ul_bulk_penalty, dw_ul_he_neohook, dw_ul_he_mooney_rivlin
from 2009.2 to 2009.3¶
basic support for Windows installation via numpy distutils (finally!):
installation using standard “python setup.py install”…
postproc.py:
quite usable now for fast first glance at the results
plots point, cell data of all kinds (scalar, vector, tensor)
draw iso-surface in 3D mode
fixed filename in Viewer for femhub notebook
new options: –scalar-mode, –list-names, –only-names, –rel-text-width, –no-show, –roll, –view, –all, –layout, -o
cylindergen.py:
cylindrical mesh generator
probe.py:
can probe selected quantities only
new options: –only-names, –auto-dir, –same-dir
isfepy:
new options: –no-wx, –no-viewer
phono: basic support for liquid inclusions
support for inner band gaps detection (brute force) and plotting
homogenization: added new-style piezo-elastic corrector and coefficient classes
schroedinger: fixed charge density computation
solvers:
added SciPy direct sparse solvers (ls.scipy_direct) - unified umfpack, superlu
new terms:
de_grad (element average of gradient)
d_volume_surface (compute volume using surface integral)
dw_bc_newton (Newton boundary condition)
dq_state_in_volume_qp, dq_state_in_surface_qp (interpolating state into quadrature points)
dw_surface_integrate_variable (weak surface term with variable coefficient)
from 2009.1 to 2009.2:¶
scripts:
added probe.py - a script to probe and plot results saved in result files
data probes along geometrical objects (e.g. lines, rays) intersecting the mesh
added postproc.py - a script to visualize results saved in result files
added Viewer class - 3D plots using mayavi2
rudimentary automatic mode only
added isfepy (interactive sfepy) IPython shell
uses new pde_solve(), pre-imports mayavi2 based Viewer
short input syntax for LCBC conditions, fields, integrals, materials and solvers
automatic html documentation generation via doxygen
new mesh readers:
Nastran (.bdf) format
Abaqus ascii (.inp)
new example problems:
subdomains.py + test - test dw_jump interface term
stabilized_navier_stokes.py input + test - test Oseen solver
acoustics.py + test - compute complex acoustic pressure
solvers:
changed API of nonlinear solvers so that scipy solvers can be used
added Broyden and Anderson nonlinear solvers (SciPy implementation)
updated Oseen solver
major rewrite of handling of dof connectivities, matrix graph and term geometries:
lots of dof connectivity related code was simplified/removed
extra connectivity data (surface, point) computed on demand in Variables.setup_dof_conns()
support for terms with traces of variables on interface regions
surface data computation for terms of volume dof_conn and Surface geometry
extended syntax of equations to allow boundary traces of variables:
to use when a field value at an interface boundary is needed from the neighbouring subdomain side and the field is not defined there
example: dw_jump.isurf.Gamma12_1( jump1.val, q1, p1, tr(p2) )
refactored linear combination boundary conditions (LCBC) code:
fixed rigid LCBC for multi-field problems
added no penetration LCBC
major speed-up (several orders) of LCBC operator construction
assembled via the coo_matrix instead of the lil_matrix
fixed check_tangent_matrix() for LCBC
applications:
homogenization:
prefactorize the matrix for linear corrector problems - major speed-up
phononic materials:
plot also middle eigenvalues in 3D, fixed plot labels, polarization angles
caching of eigenvalue problem solution and Christoffel acoustic tensor
schroedinger.py:
choose and call DFT solver via solver interface
general:
fixed boundary quadrature points for multi-field problems
fixed complex assembling
fixed live plotting (ProcessPlotter) for multi-core machines
improved Output class, simplified its usage
Struct.__str__() prints in alphabetical order
unified version information by introducing sfepy.__version__
polished MeshIO class
implemented region selection by node groups
refactored Mesh nodes, lots of simplifications
many small fixes and updates
new terms:
dw_jump (scalar interface jump term)
dw_surface_mass_scalar (scalar mass on a surface boundary)
from 2008.4 to 2009.1:¶
new solvers:
simple backtracking steepest descent optimization solver
PETSc Krylov solvers via petsc4py, sequential mode
LOBPCG eigenvalue solver (SciPy implementation)
new mesh readers:
mesh3d (hermes3d)
AVS UCD ascii mesh
Hypermesh ascii mesh
homogenization:
MiniAppBase base class for “mini-applications”: micro-problem correctors, homogenized coefficients
unified approach to resolve data dependencies: HomogenizationEngine class
applications:
phononic materials:
dispersion analysis, phase velocity computation for phononic materials
homogenized coefficients computed via the HomogenizationEngine
caching of coefficients to speed up parametric runs
schroedinger.py:
all functionality moved into SchroedingerApp class
inherits from SimpleApp -> can be parametrized
fixed DFT iterations, iteration plot saving
basic smearing around Fermi limit
scripts:
convert_mesh.py:
–scale option, support different scaling for each axis
general:
terms, caches now imported dynamically by load_classes()
to add a new term/cache module just put it into sfepy/terms/
better setup of Application options
automatic option update in parametric studies
default configuration options for the linear, nonlinear and eigen- solvers
various 64bit fixes
allow empty output prefix, combined output to file and terminal
new terms:
dw_electric_source (electric source term)
from 00.50.00 to 2008.4:¶
framework for running parametric studies
allow time derivatives of variables as term arguments
example (transient diffusion): “””dw_mass_scalar.i1.Omega( s, dT/dt ) + dw_laplace.i1.Omega( coef.val, s, T ) = 0”””
initial conditions via ics, ic_<number> keywords
enhanced acoustic band gaps code
dispersion analysis (polarization angle calculation)
applied load tensor computation
phase velocity computation for periodic perforated media with empty holes
term base classes
actual term code reduced significantly
adding new terms is even easier now
type of term arguments determined fully at run-time
live plotting using multiprocessing module
assumes GTKAgg matplotlib backend
support for setting x axis values and labels and y labels
figure saving
printing messages: Output class
homogenized coefficients classes prototypes
improved schroedinger.py
plotting DFT iterations
created sfepy/mechanics
conversions of elastic constants and transformations to plane
float format used for saving results can be set by the ‘float_format’ option
new terms:
dw_piezo_coupling (piezo-electric coupling term)
dw_biot (Biot coupling term, former dw_biot_div, dw_biot_grad, …)
dw_stokes (Stokes coupling term, former dw_div, dw_grad, …)
dw_lin_elastic_th (linear elasticity fading memory, former dw_lin_viscous_th)
dw_biot_th (Biot fading memory terms unified)
from 00.46.02 to 00.50.00:¶
finite strain elasticity: neo-Hookean, Mooney-Rivlin materials
total Lagrangian (TL) formulation
geometric data via finite_strain_tl DataCache
solving problems in complex numbers
generalized equations to allow linear combination of terms
example: “””2 * aterm.i1.Omega( v, u ) = - 3.0 * bterm.i1.Omega2( v, u )”””
run-time type of state term arguments
removed all *_r terms, now useless
‘elements by function( domain )’ region selector
refactoring to follow Python coding style guidelines
history support in variables
MeshIO.read_dimension() to quickly get dimension in an input file
improved site_cfg_template.py
improved schroedinger.py
new terms:
de_average_variable (average a variable in elements)
dw_surface_integrate (integrate over surface operator)
dw_tl_bulk_penalty (bulk penalty in TL formulation)
dw_tl_he_neohook (neo-Hooekan term in TL formulation)
dw_tl_he_mooney_rivlin (Mooney-Rivlin term in TL formulation)
from 00.41.03 to 00.46.02:¶
alternative short syntax for specifying essential boundary conditions, variables and regions
saving results per variable (useful when variables defined in different subdomains)
manufactured solutions tests:
SymPy support
new eigenvalue solvers:
removed symeig dependence
linear solvers based on PyAMG
simple block mesh generator
unified HDF5 mesh/solution reading/writing
site configuration now via script/config.py + site_cfg.py
example: computing homogenized elastic coefficients
new terms and lots of reorganization:
Biot terms
some fading memory terms
from 00.35.01 to 00.41.03:¶
works on 64 bits
support for various mesh formats:
medit: .mesh
text VTK: .vtk
tetgen: .node + .ele
comsol: .txt
Schroedinger equation solver
run via ‘schroedinger.py’
input files:
new syntax for variables and boundary conditions
improved handling of degrees of freedom
more descriptive (and less) test and simulation messages
new handling of approximations (-> lots of thing simplified)
material parameters can be defined in mesh vertices
simple.py: allow user-specified postProcessHook function
documentation generation via prettydoc
new solvers:
generic time-dependent problem solver
pysparse, symeig, scipy-based eigenproblem solvers
scipy-based iterative solvers
new terms:
dw_volume_integrate (volume integral operator)
dw_mass_scalar_r (rhs for time-dependent Poisson problem)
di_volume_integrate_mat (integrate material parameters)
dw_volume_wdot and related terms (weighted dot product)
dw_mass_scalar_variable (scalar mass term with variable coefficients)
dw_lin_elastic and related terms (anisotropic linear elasticity)
dw_lin_viscous (linear viscosity)
de_cauchy_stress (element-averaged Cauchy stress)
from 00.31.06 to 00.35.01:¶
per term integration, major rewrite of sfe.fem and related:
term.integral.domain( arguments ) syntax
‘integral_*’ keyword for input files
each term can use its own quadrature points
‘field’ keyword syntax changed
minor:
genDocs.py: PDF term documentation generator
from 00.26.01 to 00.31.06:¶
acoustic band gaps determination:
zones of frequencies where elastic waves do not propagate
based on homogenization of material made of small inclusions periodically embedded in an elastic matrix
run via ‘eigen.py’
general linear combination boundary conditions - ‘lcbc’ keyword:
rigid body motion constraint imposed on regions
new Solver classes, solver reorganization:
all solvers now configured in a uniform way (‘solver_[0-9]+’ keywords)
specify solvers using ‘options’ keyword
new terms:
dot product in a volume or on a surface region
vector field mass term
scalar field “mass”, fine-coarse scalar “mass” terms:
used for coarse mesh -> fine mesh interpolation of scalar fields
minor:
added updated findSurf.py into distribution - extract surface from a mesh
script/kill_*
script/writeMesh2D.m
script/writeSparseMatrixHDF5.m
from 00.22.02 to 00.26.01:¶
testing framework (in the spirit of unit tests):
particularly tests that standard input files work
runTests.py: output filtering
linear spring term (kind of a relaxed Dirichlet BC on node displacements)
volume term
Laplace term in 2D
chained periodic boundary conditions resolving
new options for simple.py: –save-field-meshes, –solve-not
periodic mesh merger (genPerMesh.py)
minor:
improved region saving
growing term data cache
sparse matrix saving into HDF5
point dof connectivity and geometry
region handling improvements (canCells flag)
nonlinear solver status reporting
distribution: test and example meshes included in the release tarball