# created: 20.07.2007 (-1)
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()
- update active DOF connectivities only when needed in Equations.time_update()
- 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
- update ProblemDefinition to provide and store default nls_status
- 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
- new ContactSphereTerm (dw_contact_sphere)
- 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()
- findSurf.py: update and clean up
- 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
- rename DotTermsDotProductSurfaceTerm functions:
- 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
- new examples/homogenization/perfusion_micro.py + test
- 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
- improve gen_gallery.py
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
- fix ANSYSCDBMeshIO.read(), guess it with .inp suffix:
- 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()
- update linearizer.py for hierarchic basis
- 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
- replace getattr() calls with ProblemConf.get_function()
- 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
- split sfepy/base/log.py - new sfepy/base/log_plotter.py, clean up
- 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
- remove obsolete scripts:
- 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()
- update table of 1_2 quadrature points
- 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
- rewrite stabilization material handling
- 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
- update Domain: store group dimension
- 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
- update script/gen_gallery.py:
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()
- split tests/test_assembling.py
- 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
- wrap vxc() and vectorize it - new get_vxc():
- 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
- pass space, poly_space_base to Interpolant, SurfaceInterpolant:
- 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()
- evaluate and cache quantities in FieldVariable:
- 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
- dw_laplace, dw_diffusion, de_diffusion_velocity, dw_biot,
dw_lin_elastic, de_cauchy_strain, de_cauchy_stress:
- 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()
- check region passed to field constructor:
- 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
- update ProblemConf constructors - new override argument:
- 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
- new examples/standalone/thermal_electric/thermal_electric.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
- allow switching boundary conditions on/off depending on time:
- 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()
- fix Viewer and add_subdomains_surface() for animations:
- 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
- update Newton:
- 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()
- use mesh connectivity to construct reference maps
- 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()
- pass integral instances instead of integral names where applicable
- 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
- new examples/biot/biot_npbc_lagrange.py + test
- 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
- remove regions from Material definition:
- 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
- redesign term evaluation: non-assembling modes, hierarchy of calls:
- 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
- update examples/quantum:
- 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”
- improve docstrings:
- 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
- new examples:
- 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
- using FileSource class abstracts the particular format for storing results:
- 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
- added probe.py - a script to probe and plot results saved in result files
- 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
- homogenization:
- 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
- phononic materials:
- scripts:
- convert_mesh.py:
- –scale option, support different scaling for each axis
- convert_mesh.py:
- 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
- terms, caches now imported dynamically by load_classes()
- 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