- Generated on Mon Apr 9 2018 20:02:25 for OpenCMISS-Iron Internal API Documentation by
1.8.11
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OpenCMISS-Iron Internal API Documentation
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This module handles all bioelectric domain equation routines. More...
Functions/Subroutines | |
| subroutine, public | biodomain_control_loop_post_loop (CONTROL_LOOP, ERR, ERROR,) |
| Runs after each control loop iteration. More... | |
| subroutine, public | biodomain_equationssetsetup (EQUATIONS_SET, EQUATIONS_SET_SETUP, ERR, ERROR,) |
| Sets up the bioelectric domain equation type of a bioelectric equations set class. More... | |
| subroutine, public | biodomain_equationssetsolutionmethodset (EQUATIONS_SET, SOLUTION_METHOD, ERR, ERROR,) |
| Sets/changes the solution method for a bioelectric domain equation type of an bioelectrics equations set class. More... | |
| subroutine, public | biodomain_equationssetspecificationset (equationsSet, specification, err, error,) |
| Sets the equation specification for a bioelectric domain equation type of a bioelectric equations set class. More... | |
| subroutine, public | biodomain_pre_solve (SOLVER, ERR, ERROR,) |
| Performs pre-solve actions for mono- and bi-domain problems. More... | |
| subroutine, public | biodomain_equation_problem_setup (PROBLEM, PROBLEM_SETUP, ERR, ERROR,) |
| Sets up the bioelectric domain problem. More... | |
| subroutine, public | biodomain_problemspecificationset (problem, problemSpecification, err, error,) |
| Sets the problem specification for a bioelectric domain problem class. More... | |
| subroutine, public | biodomain_equation_finite_element_calculate (EQUATIONS_SET, ELEMENT_NUMBER, ERR, ERROR,) |
| Calculates the element stiffness matrices and RHS for a bioelectric domain equation finite element equations set. More... | |
This module handles all bioelectric domain equation routines.
| subroutine, public biodomain_equation_routines::biodomain_control_loop_post_loop | ( | type(control_loop_type), pointer | CONTROL_LOOP, |
| integer(intg), intent(out) | ERR, | ||
| type(varying_string), intent(out) | ERROR | ||
| ) |
Runs after each control loop iteration.
| control_loop | A pointer to the control loop. | |
| [out] | err | The error code |
| [out] | error | The error string |
Definition at line 109 of file biodomain_equation_routines.f90.
References control_loop_routines::control_loop_progress_output, control_loop_routines::control_loop_solvers_get(), base_routines::enters(), base_routines::exits(), field_io_routines::field_io_nodes_export(), problem_constants::problem_control_fixed_loop_type, problem_constants::problem_control_load_increment_loop_type, problem_constants::problem_control_simple_type, problem_constants::problem_control_time_loop_type, problem_constants::problem_control_while_loop_type, and solver_routines::solvers_solver_get().
Referenced by bioelectric_routines::bioelectric_control_loop_post_loop(), and bioelectric_finite_elasticity_routines::bioelectricfiniteelasticity_controllooppostloop().
| subroutine, public biodomain_equation_routines::biodomain_equation_finite_element_calculate | ( | type(equations_set_type), pointer | EQUATIONS_SET, |
| integer(intg), intent(in) | ELEMENT_NUMBER, | ||
| integer(intg), intent(out) | ERR, | ||
| type(varying_string), intent(out) | ERROR | ||
| ) |
Calculates the element stiffness matrices and RHS for a bioelectric domain equation finite element equations set.
| equations_set | A pointer to the equations set to perform the finite element calculations on | |
| [in] | element_number | The element number to calculate |
| [out] | err | The error code |
| [out] | error | The error string |
Definition at line 2249 of file biodomain_equation_routines.f90.
References basis_routines::basis_default_quadrature_scheme, base_routines::enters(), equations_set_constants::equations_set_bidomain_equation_type, equations_set_constants::equations_set_first_bidomain_subtype, equations_set_constants::equations_set_monodomain_equation_type, equations_set_constants::equations_set_second_bidomain_subtype, base_routines::exits(), constants::first_part_deriv, constants::no_part_deriv, constants::partial_derivative_first_derivative_map, and constants::zero_tolerance.
Referenced by bioelectric_routines::bioelectric_finite_element_calculate().
| subroutine, public biodomain_equation_routines::biodomain_equation_problem_setup | ( | type(problem_type), pointer | PROBLEM, |
| type(problem_setup_type), intent(inout) | PROBLEM_SETUP, | ||
| integer(intg), intent(out) | ERR, | ||
| type(varying_string), intent(out) | ERROR | ||
| ) |
Sets up the bioelectric domain problem.
| problem | A pointer to the problem set to setup a bioelectric domain equation on. | |
| [in,out] | problem_setup | The problem setup information |
| [out] | err | The error code |
| [out] | error | The error string |
Definition at line 1758 of file biodomain_equation_routines.f90.
References solver_routines::cellml_equations_create_finish(), solver_routines::cellml_equations_create_start(), control_loop_routines::control_loop_create_finish(), control_loop_routines::control_loop_create_start(), control_loop_routines::control_loop_node, control_loop_routines::control_loop_solvers_get(), control_loop_routines::control_loop_type_set(), base_routines::enters(), base_routines::exits(), problem_constants::problem_bidomain_equation_type, problem_constants::problem_bidomain_gudunov_split_subtype, problem_constants::problem_bidomain_strang_split_subtype, problem_constants::problem_control_time_loop_type, problem_constants::problem_monodomain_equation_type, problem_constants::problem_monodomain_gudunov_split_subtype, problem_constants::problem_monodomain_strang_split_subtype, problem_constants::problem_setup_cellml_equations_type, problem_constants::problem_setup_control_type, problem_constants::problem_setup_finish_action, problem_constants::problem_setup_initial_type, problem_constants::problem_setup_solver_equations_type, problem_constants::problem_setup_solvers_type, problem_constants::problem_setup_start_action, solver_routines::solver_cellml_equations_get(), solver_routines::solver_cmiss_library, solver_routines::solver_dae_type, solver_routines::solver_dynamic_crank_nicolson_scheme, solver_routines::solver_dynamic_degree_set(), solver_routines::solver_dynamic_first_degree, solver_routines::solver_dynamic_first_order, solver_routines::solver_dynamic_order_set(), solver_routines::solver_dynamic_restart_set(), solver_routines::solver_dynamic_scheme_set(), solver_routines::solver_dynamic_type, solver_routines::solver_equations_create_finish(), solver_routines::solver_equations_create_start(), problem_constants::solver_equations_first_order_dynamic, problem_constants::solver_equations_linear, solver_routines::solver_equations_linearity_type_set(), solver_routines::solver_equations_sparsity_type_set(), problem_constants::solver_equations_static, solver_routines::solver_equations_time_dependence_type_set(), solver_routines::solver_library_type_set(), solver_routines::solver_linear_type, solver_routines::solver_petsc_library, solver_routines::solver_solver_equations_get(), solver_routines::solver_sparse_matrices, solver_routines::solver_type_set(), solver_routines::solvers_create_finish(), solver_routines::solvers_create_start(), solver_routines::solvers_number_set(), and solver_routines::solvers_solver_get().
Referenced by bioelectric_routines::bioelectric_problem_setup().
| subroutine, public biodomain_equation_routines::biodomain_equationssetsetup | ( | type(equations_set_type), pointer | EQUATIONS_SET, |
| type(equations_set_setup_type), intent(inout) | EQUATIONS_SET_SETUP, | ||
| integer(intg), intent(out) | ERR, | ||
| type(varying_string), intent(out) | ERROR | ||
| ) |
Sets up the bioelectric domain equation type of a bioelectric equations set class.
| equations_set | A pointer to the equations set to setup a bioelectric domain equation on. | |
| [in,out] | equations_set_setup | The equations set setup information |
| [out] | err | The error code |
| [out] | error | The error string |
Definition at line 236 of file biodomain_equation_routines.f90.
References biodomain_equationssetsolutionmethodset(), distributed_matrix_vector::distributed_matrix_block_storage_type, distributed_matrix_vector::distributed_matrix_compressed_row_storage_type, distributed_matrix_vector::distributed_matrix_diagonal_storage_type, base_routines::enters(), equations_routines::equations_create_finish(), equations_routines::equations_create_start(), equations_set_constants::equations_first_order_dynamic, equations_set_constants::equations_linear, equations_routines::equations_linearity_type_set(), equations_routines::equations_lumped_matrices, equations_mapping_routines::equations_mapping_create_finish(), equations_mapping_routines::equations_mapping_create_start(), equations_mapping_routines::equations_mapping_dynamic_variable_type_set(), equations_mapping_routines::equations_mapping_rhs_variable_type_set(), equations_matrices_routines::equations_matrices_create_finish(), equations_matrices_routines::equations_matrices_create_start(), equations_matrices_routines::equations_matrices_dynamic_lumping_type_set(), equations_matrices_routines::equations_matrices_dynamic_storage_type_set(), equations_matrices_routines::equations_matrices_full_matrices, equations_matrices_routines::equations_matrices_linear_storage_type_set(), equations_matrices_routines::equations_matrices_sparse_matrices, equations_matrices_routines::equations_matrix_diagonal_structure, equations_matrices_routines::equations_matrix_fem_structure, equations_matrices_routines::equations_matrix_lumped, equations_matrices_routines::equations_matrix_unlumped, equations_set_constants::equations_set_1d3d_monodomain_active_strain_subtype, equations_set_constants::equations_set_1d3d_monodomain_elasticity_subtype, equations_set_constants::equations_set_bem_solution_method, equations_set_constants::equations_set_bidomain_equation_type, equations_routines::equations_set_equations_get(), equations_set_constants::equations_set_fd_solution_method, equations_set_constants::equations_set_fem_solution_method, equations_set_constants::equations_set_first_bidomain_subtype, equations_set_constants::equations_set_fv_solution_method, equations_set_constants::equations_set_gfem_solution_method, equations_set_constants::equations_set_gfv_solution_method, equations_set_constants::equations_set_monodomain_elasticity_velocity_subtype, equations_set_constants::equations_set_monodomain_elasticity_w_titin_subtype, equations_set_constants::equations_set_monodomain_equation_type, equations_set_constants::equations_set_monodomain_strang_splitting_equation_type, equations_set_constants::equations_set_no_subtype, equations_set_constants::equations_set_second_bidomain_subtype, equations_set_constants::equations_set_setup_analytic_type, equations_set_constants::equations_set_setup_dependent_type, equations_set_constants::equations_set_setup_equations_type, equations_set_constants::equations_set_setup_finish_action, equations_set_constants::equations_set_setup_geometry_type, equations_set_constants::equations_set_setup_independent_type, equations_set_constants::equations_set_setup_initial_type, equations_set_constants::equations_set_setup_materials_type, equations_set_constants::equations_set_setup_source_type, equations_set_constants::equations_set_setup_start_action, equations_set_constants::equations_static, equations_routines::equations_time_dependence_type_set(), equations_mapping_routines::equationsmapping_linearmatricesnumberset(), equations_mapping_routines::equationsmapping_linearmatricesvariabletypesset(), equations_matrices_routines::equationsmatrices_dynamicstructuretypeset(), equations_matrices_routines::equationsmatrices_linearstructuretypeset(), base_routines::exits(), matrix_vector::matrix_block_storage_type, and matrix_vector::matrix_compressed_row_storage_type.
Referenced by bioelectric_routines::bioelectric_equations_set_setup().
| subroutine, public biodomain_equation_routines::biodomain_equationssetsolutionmethodset | ( | type(equations_set_type), pointer | EQUATIONS_SET, |
| integer(intg), intent(in) | SOLUTION_METHOD, | ||
| integer(intg), intent(out) | ERR, | ||
| type(varying_string), intent(out) | ERROR | ||
| ) |
Sets/changes the solution method for a bioelectric domain equation type of an bioelectrics equations set class.
| equations_set | A pointer to the equations set to set the solution method for | |
| [in] | solution_method | The solution method to set |
| [out] | err | The error code |
| [out] | error | The error string |
Definition at line 1421 of file biodomain_equation_routines.f90.
References base_routines::enters(), equations_set_constants::equations_set_1d3d_monodomain_active_strain_subtype, equations_set_constants::equations_set_1d3d_monodomain_elasticity_subtype, equations_set_constants::equations_set_bem_solution_method, equations_set_constants::equations_set_bidomain_equation_type, equations_set_constants::equations_set_fd_solution_method, equations_set_constants::equations_set_fem_solution_method, equations_set_constants::equations_set_first_bidomain_subtype, equations_set_constants::equations_set_fv_solution_method, equations_set_constants::equations_set_gfem_solution_method, equations_set_constants::equations_set_gfv_solution_method, equations_set_constants::equations_set_monodomain_elasticity_velocity_subtype, equations_set_constants::equations_set_monodomain_elasticity_w_titin_subtype, equations_set_constants::equations_set_monodomain_equation_type, equations_set_constants::equations_set_no_subtype, equations_set_constants::equations_set_second_bidomain_subtype, base_routines::errors(), and base_routines::exits().
Referenced by biodomain_equationssetsetup(), and bioelectric_routines::bioelectric_equationssetsolutionmethodset().
| subroutine, public biodomain_equation_routines::biodomain_equationssetspecificationset | ( | type(equations_set_type), pointer | equationsSet, |
| integer(intg), dimension(:), intent(in) | specification, | ||
| integer(intg), intent(out) | err, | ||
| type(varying_string), intent(out) | error | ||
| ) |
Sets the equation specification for a bioelectric domain equation type of a bioelectric equations set class.
| equationsset | A pointer to the equations set to set the specification for | |
| [in] | specification | The equations set specification to set |
| [out] | err | The error code |
| [out] | error | The error string |
Definition at line 1535 of file biodomain_equation_routines.f90.
References base_routines::enters(), equations_set_constants::equations_set_1d3d_monodomain_active_strain_subtype, equations_set_constants::equations_set_1d3d_monodomain_elasticity_subtype, equations_set_constants::equations_set_bidomain_equation_type, equations_set_constants::equations_set_bioelectrics_class, equations_set_constants::equations_set_first_bidomain_subtype, equations_set_constants::equations_set_monodomain_elasticity_velocity_subtype, equations_set_constants::equations_set_monodomain_elasticity_w_titin_subtype, equations_set_constants::equations_set_monodomain_equation_type, equations_set_constants::equations_set_no_subtype, equations_set_constants::equations_set_second_bidomain_subtype, base_routines::errors(), and base_routines::exits().
Referenced by bioelectric_routines::bioelectric_equationssetspecificationset().
| subroutine, public biodomain_equation_routines::biodomain_pre_solve | ( | type(solver_type), pointer | SOLVER, |
| integer(intg), intent(out) | ERR, | ||
| type(varying_string), intent(out) | ERROR | ||
| ) |
Performs pre-solve actions for mono- and bi-domain problems.
| solver | A pointer to the solver to perform the pre-solve actions for. | |
| [out] | err | The error code |
| [out] | error | The error string |
Definition at line 1611 of file biodomain_equation_routines.f90.
References control_loop_routines::control_loop_current_times_get(), base_routines::enters(), equations_set_constants::equations_set_monodomain_elasticity_velocity_subtype, base_routines::exits(), problem_constants::problem_bidomain_equation_type, problem_constants::problem_bidomain_gudunov_split_subtype, problem_constants::problem_bidomain_strang_split_subtype, problem_constants::problem_bioelectric_finite_elasticity_type, problem_constants::problem_gudunov_monodomain_1d3d_elasticity_subtype, problem_constants::problem_gudunov_monodomain_simple_elasticity_subtype, problem_constants::problem_monodomain_1d3d_active_strain_subtype, problem_constants::problem_monodomain_elasticity_w_titin_subtype, problem_constants::problem_monodomain_equation_type, problem_constants::problem_monodomain_gudunov_split_subtype, problem_constants::problem_monodomain_strang_split_subtype, and solver_routines::solver_dae_times_set().
Referenced by bioelectric_finite_elasticity_routines::bioelectric_finite_elasticity_pre_solve(), and bioelectric_routines::bioelectric_pre_solve().
| subroutine, public biodomain_equation_routines::biodomain_problemspecificationset | ( | type(problem_type), intent(in), pointer | problem, |
| integer(intg), dimension(:), intent(in) | problemSpecification, | ||
| integer(intg), intent(out) | err, | ||
| type(varying_string), intent(out) | error | ||
| ) |
Sets the problem specification for a bioelectric domain problem class.
| [in] | problem | A pointer to the problem to set the specification for |
| [in] | problemspecification | The problem specification to set |
| [out] | err | The error code |
| [out] | error | The error string |
Definition at line 2178 of file biodomain_equation_routines.f90.
References base_routines::enters(), base_routines::errors(), base_routines::exits(), problem_constants::problem_bidomain_equation_type, problem_constants::problem_bidomain_gudunov_split_subtype, problem_constants::problem_bidomain_strang_split_subtype, problem_constants::problem_bioelectrics_class, problem_constants::problem_monodomain_equation_type, problem_constants::problem_monodomain_gudunov_split_subtype, and problem_constants::problem_monodomain_strang_split_subtype.
Referenced by bioelectric_routines::bioelectric_problemspecificationset().
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