.. _sphinx_api: ############# |PROJECT| API ############# Common ====== config_software.py ------------------ .. automodule:: model_package.config_software :members: :show-inheritance: :synopsis: Configure software paths in a YAML file peta.py ------- .. automodule:: model_package.peta :members: :show-inheritance: :synopsis: Copy DNS results from the CU Peta library to the output directory xdmf_reader_tools.py -------------------- .. automodule:: model_package.xdmf_reader_tools :members: :show-inheritance: :synopsis: Functions for reading XDMF files DNS_Abaqus ========== build_dynamic_elastic_cylinder.py --------------------------------- .. automodule:: model_package.DNS_Abaqus.build_dynamic_elastic_cylinder :members: :show-inheritance: :synopsis: Create an Abaqus model of an elastic cylinder under dynamic compression build_elastic_cylinder.py ------------------------- .. automodule:: model_package.DNS_Abaqus.build_elastic_cylinder :members: :show-inheritance: :synopsis: Create an Abaqus model of an elastic cylinder under static compression convert_tess.py --------------- .. automodule:: model_package.DNS_Abaqus.convert_tess :members: :show-inheritance: :synopsis: Convert a tesselation file output by Neper to STL and create Abaqus mesh convert_tess_2d.py ------------------ .. automodule:: model_package.DNS_Abaqus.convert_tess_2d :members: :show-inheritance: :synopsis: Convert a 2D tesselation file output by Neper to STL and create an Abaqus mesh convert_tess_cylinder.py ------------------------ .. automodule:: model_package.DNS_Abaqus.convert_tess_cylinder :members: :show-inheritance: :synopsis: Convert a tesslation file output by Neper for a cylindrical geometry to STL and create Abaqus mesh dynamic_analytical_comparison.py -------------------------------- .. automodule:: model_package.DNS_Abaqus.dynamic_analytical_comparison :members: :show-inheritance: :synopsis: Plot dynamic Abaqus results against an analytical solution extract_frames.py ----------------- .. automodule:: model_package.DNS_Abaqus.extract_frames :members: :show-inheritance: :synopsis: Extracts 3D field output from a completed Abaqus simulation to save as 2D image extract_history.py ------------------ .. automodule:: model_package.DNS_Abaqus.extract_history :members: :show-inheritance: :synopsis: Plot Abaqus history output for force versus displacement modify_input.py --------------- .. automodule:: model_package.DNS_Abaqus.modify_input :members: :show-inheritance: :synopsis: Modify Abaqus input file to output 'COORD' at integration points ODBextract_to_XDMF.py --------------------- .. automodule:: model_package.DNS_Abaqus.ODBextract_to_XDMF :members: :show-inheritance: :synopsis: Convert Abaqus DNS results to XDMF format ODBextract_to_XDMF_neper.py --------------------------- .. automodule:: model_package.DNS_Abaqus.ODBextract_to_XDMF_neper :members: :show-inheritance: :synopsis: Convert Abaqus DNS results of 3D bonded grains to XDMF format ODBextract_to_XDMF_neper_2d.py ------------------------------ .. automodule:: model_package.DNS_Abaqus.ODBextract_to_XDMF_neper_2d :members: :show-inheritance: :synopsis: Convert Abaqus DNS results of 2D bonded grains to XDMF format parse_sets_from_inp.py ---------------------- .. automodule:: model_package.DNS_Abaqus.parse_sets_from_inp :members: :show-inheritance: :synopsis: Extract element IDs associated with element sets from Abaqus input file write_section_file.py --------------------- .. automodule:: model_package.DNS_Abaqus.write_section_file :members: :show-inheritance: :synopsis: Write an Abaqus input file for the section definition of grains" DNS_GEOS ======== plot_force_displacement.py -------------------------- .. automodule:: model_package.DNS_GEOS.plot_force_displacement :members: :show-inheritance: :synopsis: Process force-displacement from GEOS DNS results vtk_to_xdmf.py -------------- .. automodule:: model_package.DNS_GEOS.vtk_to_xdmf :members: :show-inheritance: :synopsis: Convert GEOS DNS results to XDMF format vtk_to_xdmf_fast.py ------------------- .. automodule:: model_package.DNS_GEOS.vtk_to_xdmf_fast :members: :show-inheritance: :synopsis: Convert GEOS DNS results to XDMF format using VTK utilities vtk_to_xdmf_fast_multi.py ------------------------- .. automodule:: model_package.DNS_GEOS.vtk_to_xdmf_fast_multi :members: :show-inheritance: :synopsis: Convert multiblock GEOS DNS results to XDMF format using VTK utilities DNS_RATEL ========= build_options_file.py --------------------- .. automodule:: model_package.DNS_Ratel.build_options_file :members: :show-inheritance: :synopsis: Write Ratel options file cgns_to_xdmf.py --------------- .. automodule:: model_package.DNS_Ratel.cgns_to_xdmf :members: :show-inheritance: :synopsis: Convert Ratel DNS results to XDMF format plot_force_displacement.py -------------------------- .. automodule:: model_package.DNS_Ratel.plot_force_displacement :members: :show-inheritance: :synopsis: Process force-displacement from Ratel DNS results vtk_to_xdmf.py -------------- .. automodule:: model_package.DNS_Ratel.vtk_to_xdmf :members: :show-inheritance: :synopsis: Convert Ratel DNS results to XDMF format Filter ====== bounds_from_DNS.py ------------------ .. automodule:: model_package.Filter.bounds_from_DNS :members: :show-inheritance: :synopsis: Create a csv containing the extents of a DNS file build_filter_config.py ---------------------- .. automodule:: model_package.Filter.build_filter_config :members: :show-inheritance: :synopsis: Write the configuration file for the Micromorphic Filter collect_multi_domain_errors.py ------------------------------ .. automodule:: model_package.Filter.collect_multi_domain_errors :members: :show-inheritance: :synopsis: Collect balance equation errors across filter domain studies collect_multi_domain_stats.py ----------------------------- .. automodule:: model_package.Filter.collect_multi_domain_stats :members: :show-inheritance: :synopsis: Collect statistics of a homogenized micromorphic quantity across filter domain studies force_bounds.py --------------- .. automodule:: model_package.Filter.force_bounds :members: :show-inheritance: :synopsis: Create a csv file containing information for a bounding box encompassing all DNS points parse_balance_errors.py ----------------------- .. automodule:: model_package.Filter.parse_balance_errors :members: :show-inheritance: :synopsis: Parse balance equation errors from Micromorphic Filter standard output run_micromorphic_filter.py -------------------------- .. automodule:: model_package.Filter.run_micromorphic_filter :members: :show-inheritance: :synopsis: Run the Micromorphic Filter single_macroscale.py -------------------- .. automodule:: model_package.Filter.single_macroscale :members: :show-inheritance: :synopsis: Write a single macroscale domain file for the Micromorphic Filter visualize_results.py -------------------- .. automodule:: model_package.Filter.visualize_results :members: :show-inheritance: :synopsis: Post-process Micromorphic Filter output xdmf_3d_calculations.py ----------------------- .. automodule:: model_package.Filter.xdmf_3d_calculations :members: :show-inheritance: :synopsis: Create an XDMF file containing a variety of derived quantities xdmf_local_paths.py ------------------- .. automodule:: model_package.Filter.xdmf_local_paths :members: :show-inheritance: :synopsis: Create a copy of an XDMF file with absolute H5 paths replaced with relative paths xdmf_tomfoolery.py ------------------ .. automodule:: model_package.Filter.xdmf_tomfoolery :members: :show-inheritance: :synopsis: Modify an XDMF file by combining elements from separate 'blocks' Calibrate ========= build_calibration_map.py ------------------------ .. automodule:: model_package.Calibrate.build_calibration_map :members: :show-inheritance: :synopsis: Create a file mapping calibration results for each macroscale element calibrate_element.py -------------------- .. automodule:: model_package.Calibrate.calibrate_element :members: :show-inheritance: :synopsis: Calibrate micromorphic linear elasticity for a single filter element (i.e. macroscale element) calibrate_element_plastic.py ---------------------------- .. automodule:: model_package.Calibrate.calibrate_element_plastic :members: :show-inheritance: :synopsis: Calibrate micromorphic elastoplasticity on a single filter domain (i.e. macroscale element) calibrate_qp.py --------------- .. automodule:: model_package.Calibrate.calibrate_qp :members: :show-inheritance: :synopsis: Calibrate micromorphic linear elasticity on a single filter domain (i.e. macroscale element) and quadrature point calibration_tools.py -------------------- .. automodule:: model_package.Calibrate.calibration_tools :members: :show-inheritance: :synopsis: Collection of utilities for calibration elastic_map_to_material_card.py ------------------------------- .. automodule:: model_package.Calibrate.elastic_map_to_material_card :members: :show-inheritance: :synopsis: Unpack a csv file of elastic parameters and call function to write elastic yaml file identify_z_boundary_elements.py ------------------------------- .. automodule:: model_package.Calibrate.identify_z_boundary_elements :members: :show-inheritance: :synopsis: Read in macroscale XDMF file of a cylindrical geometry and identify element found on the z-boundary joint_probability_distributions.py ---------------------------------- .. automodule:: model_package.Calibrate.joint_probability_distributions :members: :show-inheritance: :synopsis: Create a joint probability distribution plot to summarize calibration results return_minimum_smith_constraint.py ---------------------------------- .. automodule:: model_package.Calibrate.return_minimum_smith_constraint :members: :show-inheritance: :synopsis: Evaluate the 13 Smith constraints for micromorphic linear elasticity and return the minimum value summarize_calibration_results.py -------------------------------- .. automodule:: model_package.Calibrate.summarize_calibration_results :members: :show-inheritance: :synopsis: Summarize results of parameter calibration summarize_calibration_results_from_csv.py ----------------------------------------- .. automodule:: model_package.Calibrate.summarize_calibration_results_from_csv :members: :show-inheritance: :synopsis: Summarize results of parameter calibration from a calibration map csv summarize_calibration_results_ignore_boundary.py ------------------------------------------------ .. automodule:: model_package.Calibrate.summarize_calibration_results_ignore_boundary :members: :show-inheritance: :synopsis: Summarize results of parameter calibration while ignoring elements on the z-boundary" Tardigrade_MOOSE ================ add_element_blocks_to_mesh.py ----------------------------- .. automodule:: model_package.Tardigrade_MOOSE.add_element_blocks_to_mesh :members: :show-inheritance: :synopsis: Take an existing exodus mesh, add element blocks for each element, save with new name annulus_from_bounds.py ---------------------- .. automodule:: model_package.Tardigrade_MOOSE.annulus_from_bounds :members: :show-inheritance: :synopsis: Create an annular mesh from the bounds of a DNS file brazilian_disk_apparatus.py --------------------------- .. automodule:: model_package.Tardigrade_MOOSE.brazilian_disk_apparatus :members: :show-inheritance: :synopsis: Create a Brazilian Disk specimen and loading apparatus brazilian_disk_apparatus_symmetry.py ------------------------------------ .. automodule:: model_package.Tardigrade_MOOSE.brazilian_disk_apparatus_symmetry :members: :show-inheritance: :synopsis: Create a Brazilian Disk specimen and loading apparatus using 1/8th symmetry Brazil_disk_normalized_force_vs_displacements.py ------------------------------------------------ .. automodule:: model_package.Tardigrade_MOOSE.Brazil_disk_normalized_force_vs_displacements :members: :show-inheritance: :synopsis: Process force-displacement from Tardigrade-MOOSE results build_dynamic_Tardigrade_input_deck.py -------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_dynamic_Tardigrade_input_deck :members: :show-inheritance: :synopsis: Write a Tardigrade-MOOSE input file for dynamic simulation build_elastic_MOOSE_input_deck_brazil_disk_platens.py ----------------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_elastic_MOOSE_input_deck_brazil_disk_platens :members: :show-inheritance: :synopsis: Write MOOSE input file for eighth symmetry Brazilian disk simulation with platens build_elastic_MOOSE_input_deck_brazil_disk_platens_symmetry.py -------------------------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_elastic_MOOSE_input_deck_brazil_disk_platens_symmetry :members: :show-inheritance: :synopsis: Write MOOSE input file for symmetric Brazilian disk simulation with platens build_elastic_MOOSE_input_deck_brazil_disk_rigid_platens.py ----------------------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_elastic_MOOSE_input_deck_brazil_disk_rigid_platens :members: :show-inheritance: :synopsis: Write MOOSE input file for Brazilian disk simulation with rigid platens build_GED_Tardigrade_input_deck_from_csv.py ------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_GED_Tardigrade_input_deck_from_csv :members: :show-inheritance: :synopsis: Write Tardigrade-MOOSE input file for a gradient-enhanced damage plasticity simulation build_plastic_Tardigrade_input_deck.py -------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_plastic_Tardigrade_input_deck :members: :show-inheritance: :synopsis: Write Tardigrade-MOOSE input file for a plastic simulation build_plastic_Tardigrade_input_deck_brazil_disk_platens.py ---------------------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_plastic_Tardigrade_input_deck_brazil_disk_platens :members: :show-inheritance: :synopsis: Write Tardigrade-MOOSE input file for Brazilian disk simulation with platens build_plastic_Tardigrade_input_deck_brazil_disk_platens_symmetry.py ------------------------------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_plastic_Tardigrade_input_deck_brazil_disk_platens_symmetry :members: :show-inheritance: :synopsis: Write Tardigrade-MOOSE input file for eighth symmetry Brazilian disk simulation with platens build_plastic_Tardigrade_input_deck_platens.py ---------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_plastic_Tardigrade_input_deck_platens :members: :show-inheritance: :synopsis: Write Tardigrade-MOOSE input file for a plastic simulation with platens build_Tardigrade_input_deck.py ------------------------------ .. automodule:: model_package.Tardigrade_MOOSE.build_Tardigrade_input_deck :members: :show-inheritance: :synopsis: Write Tardigrade-MOOSE input file build_Tardigrade_input_deck_brazil_disk_kernel_platens.py --------------------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_Tardigrade_input_deck_brazil_disk_kernel_platens :members: :show-inheritance: :synopsis: Write MOOSE input file for Brazilian disk simulation with nodal kernel contact build_Tardigrade_input_deck_brazil_disk_rigid_platens.py -------------------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.build_Tardigrade_input_deck_brazil_disk_rigid_platens :members: :show-inheritance: :synopsis: Write MOOSE input file for Brazilian disk simulation with rigid contact platens cube_mesh.py ------------ .. automodule:: model_package.Tardigrade_MOOSE.cube_mesh :members: :show-inheritance: :synopsis: Create a cube mesh cylinder_from_bounds.py ----------------------- .. automodule:: model_package.Tardigrade_MOOSE.cylinder_from_bounds :members: :show-inheritance: :synopsis: Create a cylinder mesh from the bounds of a DNS file cylinder_from_bounds_with_platens.py ------------------------------------ .. automodule:: model_package.Tardigrade_MOOSE.cylinder_from_bounds_with_platens :members: :show-inheritance: :synopsis: Create a cylinder mesh from the bounds of a DNS file with platens extract_exodus_data.py ---------------------- .. automodule:: model_package.Tardigrade_MOOSE.extract_exodus_data :members: :show-inheritance: :synopsis: Process results from a MOOSE exodus simulation results file finite_stVK_calculation.py -------------------------- .. automodule:: model_package.Tardigrade_MOOSE.finite_stVK_calculation :members: :show-inheritance: :synopsis: Solution for uniaxial stress of a cylinder for finite deformation using the St. Venant-Kirchhoff elasticity model MOOSE_input_deck_tools.py -------------------------- .. automodule:: model_package.Tardigrade_MOOSE.MOOSE_input_deck_tools :members: :show-inheritance: :synopsis: Utility script containing functions for writing common MOOSE input deck blocks plot_dynamic_displacement.py ---------------------------- .. automodule:: model_package.Tardigrade_MOOSE.plot_dynamic_displacement :members: :show-inheritance: :synopsis: Process displacement vs time from Tardigrade-MOOSE results plot_force_displacement.py -------------------------- .. automodule:: model_package.Tardigrade_MOOSE.plot_force_displacement :members: :show-inheritance: :synopsis: Process force-displacement from Tardigrade-MOOSE results plot_lateral_displacement.py ---------------------------- .. automodule:: model_package.Tardigrade_MOOSE.plot_lateral_displacement :members: :show-inheritance: :synopsis: Process lateral displacement from Tardigrade-MOOSE results process_calibration_map_to_parameter_csv.py ------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.process_calibration_map_to_parameter_csv :members: :show-inheritance: :synopsis: Process a calibration map file to a parameter csv for Tardigrade-MOOSE summarize_dynamic_displacements.py ---------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.summarize_dynamic_displacements :members: :show-inheritance: :synopsis: Plot mutliple dynamic displacement plots against each other summarize_micro_macro_force_displacements.py -------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.summarize_micro_macro_force_displacements :members: :show-inheritance: :synopsis: Process force-displacement from Tardigrade-MOOSE results summarize_micro_macro_lateral_displacements.py ---------------------------------------------- .. automodule:: model_package.Tardigrade_MOOSE.summarize_micro_macro_lateral_displacements :members: :show-inheritance: :synopsis: Plot mutliple lateral displacement plots against each other uniformly_refine_mesh.py ------------------------ .. automodule:: model_package.Tardigrade_MOOSE.uniformly_refine_mesh :members: :show-inheritance: :synopsis: Uniformly refine an exodus mesh and update a calibration map with new element IDs write_elastic_material_card.py ------------------------------ .. automodule:: model_package.Tardigrade_MOOSE.write_elastic_material_card :members: :show-inheritance: :synopsis: Write elastic Tardigrade-MOOSE input card (.yml) write_plastic_material_card.py ------------------------------ .. automodule:: model_package.Tardigrade_MOOSE.write_plastic_material_card :members: :show-inheritance: :synopsis: Write elastoplastic Tardigrade-MOOSE input card