From 240155e311cff56c4597b7452290dc476718306b Mon Sep 17 00:00:00 2001 From: ktbolt Date: Wed, 16 Oct 2024 17:05:10 +0000 Subject: [PATCH] deploy: f9fe6fe4b5025c54188aad4c1e0859d578230d70 --- _com_mod_8h_source.html | 2559 ++++++++-------- _fsils_linear_algebra_8h_source.html | 4 +- _linear_algebra_8h_source.html | 4 +- _parameters_8h_source.html | 1941 ++++++------- _petsc_linear_algebra_8h_source.html | 4 +- _simulation_8h_source.html | 6 +- _trilinos_linear_algebra_8h_source.html | 4 +- all__fun_8h_source.html | 8 +- baf__ini_8h_source.html | 6 +- bf_8h_source.html | 4 +- cep_8h_source.html | 4 +- ...constitutive_model_parameters-members.html | 53 +- class_constitutive_model_parameters.html | 13 +- classfib_strs_type-members.html | 7 +- classfib_strs_type.html | 3 + cmm_8h_source.html | 6 +- contact_8h_source.html | 2 +- distribute_8h_source.html | 14 +- eq__assem_8h_source.html | 6 +- fft_8h_source.html | 2 +- fluid_8h_source.html | 6 +- fs_8h_source.html | 6 +- fsi_8h_source.html | 4 +- heatf_8h_source.html | 4 +- heats_8h_source.html | 4 +- l__elas_8h_source.html | 4 +- lhsa_8h_source.html | 2 +- load__msh_8h_source.html | 6 +- ls_8h_source.html | 4 +- mat__fun__carray_8h_source.html | 221 +- mat__models_8h_source.html | 6 +- mat__models__carray_8h_source.html | 2571 +++++++++-------- mesh_8h_source.html | 4 +- nn_8h_source.html | 6 +- nn__elem__gip_8h_source.html | 4 +- nn__elem__gnn_8h_source.html | 4 +- nn__elem__nn__bnds_8h_source.html | 2 +- nn__elem__props_8h_source.html | 4 +- output_8h_source.html | 2 +- petsc__impl_8h_source.html | 2 +- post_8h_source.html | 2 +- read__files_8h_source.html | 20 +- read__msh_8h_source.html | 6 +- remesh_8h_source.html | 6 +- search/all_1.js | 4 +- search/all_2.js | 4 +- search/pages_0.js | 2 +- search/pages_1.js | 2 +- search/variables_1.js | 4 +- search/variables_10.js | 56 +- search/variables_11.js | 22 +- search/variables_12.js | 18 +- search/variables_13.js | 30 +- search/variables_14.js | 4 +- search/variables_15.js | 22 +- search/variables_16.js | 12 +- search/variables_17.js | 4 +- search/variables_2.js | 33 +- search/variables_3.js | 26 +- search/variables_4.js | 28 +- search/variables_5.js | 24 +- search/variables_6.js | 40 +- search/variables_7.js | 68 +- search/variables_8.js | 40 +- search/variables_9.js | 26 +- search/variables_a.js | 28 +- search/variables_b.js | 72 +- search/variables_c.js | 14 +- search/variables_d.js | 24 +- search/variables_e.js | 2 +- search/variables_f.js | 32 +- set__bc_8h_source.html | 6 +- set__equation__props_8h_source.html | 4 +- set__material__props_8h_source.html | 60 +- set__viscosity__props_8h_source.html | 6 +- shells_8h_source.html | 6 +- stokes_8h_source.html | 4 +- sv__struct_8h_source.html | 4 +- sv_zero_d__subroutines_8h_source.html | 2 +- todo.html | 4 +- trilinos__impl_8h_source.html | 2 +- txt_8h_source.html | 4 +- ustruct_8h_source.html | 4 +- vtk__xml_8h_source.html | 8 +- vtk__xml__parser_8h_source.html | 4 +- 85 files changed, 4283 insertions(+), 4026 deletions(-) diff --git a/_com_mod_8h_source.html b/_com_mod_8h_source.html index 25d6dc8e..d225ec14 100644 --- a/_com_mod_8h_source.html +++ b/_com_mod_8h_source.html @@ -405,1576 +405,1579 @@
333  // Constant steady value
334  double g = 0.0;
335 
-
336  // Unsteady time-dependent values
-
337  fcType gt;
-
338 };
-
339 
-
340 /// @brief Structural domain type
-
341 //
-
342 class stModelType
-
343 {
-
344  public:
-
345  // Type of constitutive model (volumetric) for struct/FSI
-
346  consts::ConstitutiveModelType volType = consts::ConstitutiveModelType::stIso_NA;
-
347 
-
348  // Penalty parameter
-
349  double Kpen = 0.0;
+
336  // Cross fiber stress parameter
+
337  double eta_s = 0.0;
+
338 
+
339  // Unsteady time-dependent values
+
340  fcType gt;
+
341 };
+
342 
+
343 /// @brief Structural domain type
+
344 //
+
345 class stModelType
+
346 {
+
347  public:
+
348  // Type of constitutive model (volumetric) for struct/FSI
+
349  consts::ConstitutiveModelType volType = consts::ConstitutiveModelType::stIso_NA;
350 
-
351  // Type of constitutive model (isochoric) for struct/FSI
-
352  consts::ConstitutiveModelType isoType = consts::ConstitutiveModelType::stIso_NA;
+
351  // Penalty parameter
+
352  double Kpen = 0.0;
353 
-
354  // Parameters specific to the constitutive model (isochoric)
-
355  // NeoHookean model (C10 = mu/2)
-
356  double C10 = 0.0;
-
357 
-
358  // Mooney-Rivlin model (C10, C01)
-
359  double C01 = 0.0;
+
354  // Type of constitutive model (isochoric) for struct/FSI
+
355  consts::ConstitutiveModelType isoType = consts::ConstitutiveModelType::stIso_NA;
+
356 
+
357  // Parameters specific to the constitutive model (isochoric)
+
358  // NeoHookean model (C10 = mu/2)
+
359  double C10 = 0.0;
360 
-
361  // Holzapfel model(a, b, aff, bff, ass, bss, afs, bfs, kap)
-
362  double a = 0.0;
-
363  double b = 0.0;
-
364  double aff = 0.0;
-
365  double bff = 0.0;
-
366  double ass = 0.0;
-
367  double bss = 0.0;
-
368  double afs = 0.0;
-
369  double bfs = 0.0;
-
370 
-
371  // Collagen fiber dispersion parameter (Holzapfel model)
-
372  double kap = 0.0;
+
361  // Mooney-Rivlin model (C10, C01)
+
362  double C01 = 0.0;
+
363 
+
364  // Holzapfel model(a, b, aff, bff, ass, bss, afs, bfs, kap)
+
365  double a = 0.0;
+
366  double b = 0.0;
+
367  double aff = 0.0;
+
368  double bff = 0.0;
+
369  double ass = 0.0;
+
370  double bss = 0.0;
+
371  double afs = 0.0;
+
372  double bfs = 0.0;
373 
-
374  // Heaviside function parameter (Holzapfel-Ogden model)
-
375  double khs = 100.0;
+
374  // Collagen fiber dispersion parameter (Holzapfel model)
+
375  double kap = 0.0;
376 
-
377  // Lee-Sacks model
-
378  double a0 = 0.0;
-
379  double b1 = 0.0;
-
380  double b2 = 0.0;
-
381  double mu0 = 0.0;
-
382 
-
383  // Fiber reinforcement stress
-
384  fibStrsType Tf;
-
385 };
-
386 
-
387 /// @brief Fluid viscosity model type
-
388 //
-
389 class fluidViscModelType
-
390 {
-
391  public:
-
392 
-
393  // Type of constitutive model for fluid viscosity
-
394  consts::FluidViscosityModelType viscType = consts::FluidViscosityModelType::viscType_NA;
+
377  // Heaviside function parameter (Holzapfel-Ogden model)
+
378  double khs = 100.0;
+
379 
+
380  // Lee-Sacks model
+
381  double a0 = 0.0;
+
382  double b1 = 0.0;
+
383  double b2 = 0.0;
+
384  double mu0 = 0.0;
+
385 
+
386  // Fiber reinforcement stress
+
387  fibStrsType Tf;
+
388 };
+
389 
+
390 /// @brief Fluid viscosity model type
+
391 //
+
392 class fluidViscModelType
+
393 {
+
394  public:
395 
-
396  // Limiting zero shear-rate viscosity value
-
397  double mu_o = 0.0;
+
396  // Type of constitutive model for fluid viscosity
+
397  consts::FluidViscosityModelType viscType = consts::FluidViscosityModelType::viscType_NA;
398 
-
399  // Limiting high shear-rate viscosity (asymptotic) value
-
400  double mu_i = 0.0;
+
399  // Limiting zero shear-rate viscosity value
+
400  double mu_o = 0.0;
401 
-
402  // Strain-rate tensor multiplier
-
403  double lam = 0.0;
+
402  // Limiting high shear-rate viscosity (asymptotic) value
+
403  double mu_i = 0.0;
404 
-
405  // Strain-rate tensor exponent
-
406  double a = 0.0;
+
405  // Strain-rate tensor multiplier
+
406  double lam = 0.0;
407 
-
408  // Power-law exponent
-
409  double n = 0.0;
-
410 };
-
411 
-
412 /// @brief Fluid viscosity model type
-
413 //
-
414 class solidViscModelType
-
415 {
-
416  public:
-
417 
-
418  // Type of constitutive model for fluid viscosity
-
419  consts::SolidViscosityModelType viscType = consts::SolidViscosityModelType::viscType_NA;
+
408  // Strain-rate tensor exponent
+
409  double a = 0.0;
+
410 
+
411  // Power-law exponent
+
412  double n = 0.0;
+
413 };
+
414 
+
415 /// @brief Fluid viscosity model type
+
416 //
+
417 class solidViscModelType
+
418 {
+
419  public:
420 
-
421  // Viscosity value
-
422  double mu = 0.0;
-
423 };
-
424 
-
425 /// @brief Domain type is to keep track with element belong to which domain
-
426 /// and also different physical quantities
-
427 //
-
428 class dmnType
-
429 {
-
430  public:
-
431  dmnType();
-
432  ~dmnType();
-
433 
-
434  // The domain ID. Default includes entire domain
-
435  int Id = -1;
+
421  // Type of constitutive model for fluid viscosity
+
422  consts::SolidViscosityModelType viscType = consts::SolidViscosityModelType::viscType_NA;
+
423 
+
424  // Viscosity value
+
425  double mu = 0.0;
+
426 };
+
427 
+
428 /// @brief Domain type is to keep track with element belong to which domain
+
429 /// and also different physical quantities
+
430 //
+
431 class dmnType
+
432 {
+
433  public:
+
434  dmnType();
+
435  ~dmnType();
436 
-
437  // Which physics must be solved in this domain
-
438  consts::EquationType phys = consts::EquationType::phys_NA;
+
437  // The domain ID. Default includes entire domain
+
438  int Id = -1;
439 
-
440  // The volume of this domain
-
441  double v = 0.0;
+
440  // Which physics must be solved in this domain
+
441  consts::EquationType phys = consts::EquationType::phys_NA;
442 
-
443  // General physical properties such as density, elastic modulus...
-
444  // FIX davep double prop[maxNProp] ;
-
445  std::map<consts::PhysicalProperyType,double> prop;
-
446  //double prop[consts::maxNProp];
-
447 
-
448  // Electrophysiology model
-
449  cepModelType cep;
+
443  // The volume of this domain
+
444  double v = 0.0;
+
445 
+
446  // General physical properties such as density, elastic modulus...
+
447  // FIX davep double prop[maxNProp] ;
+
448  std::map<consts::PhysicalProperyType,double> prop;
+
449  //double prop[consts::maxNProp];
450 
-
451  // Structure material model
-
452  stModelType stM;
+
451  // Electrophysiology model
+
452  cepModelType cep;
453 
-
454  // Viscosity model for fluids
-
455  fluidViscModelType fluid_visc;
+
454  // Structure material model
+
455  stModelType stM;
456 
-
457  // Viscosity model for solids
-
458  solidViscModelType solid_visc;
-
459 };
-
460 
-
461 /// @brief Mesh adjacency (neighboring element for each element)
-
462 //
-
463 class adjType
-
464 {
-
465  public:
-
466  void destroy();
-
467 
-
468  // No of non-zeros
-
469  int nnz = 0;
+
457  // Viscosity model for fluids
+
458  fluidViscModelType fluid_visc;
+
459 
+
460  // Viscosity model for solids
+
461  solidViscModelType solid_visc;
+
462 };
+
463 
+
464 /// @brief Mesh adjacency (neighboring element for each element)
+
465 //
+
466 class adjType
+
467 {
+
468  public:
+
469  void destroy();
470 
-
471  // Column pointer
-
472  Vector<int> pcol;
+
471  // No of non-zeros
+
472  int nnz = 0;
473 
-
474  // Row pointer
-
475  Vector<int> prow;
+
474  // Column pointer
+
475  Vector<int> pcol;
476 
-
477 };
-
478 
-
479 /// @brief Tracer type used for immersed boundaries. Identifies traces of
-
480 /// nodes and integration points on background mesh elements
-
481 //
-
482 class traceType
-
483 {
-
484  public:
-
485  // No. of non-zero nodal traces
-
486  int n = 0;
-
487 
-
488  // No. of non-zero integration point traces
-
489  int nG = 0;
+
477  // Row pointer
+
478  Vector<int> prow;
+
479 
+
480 };
+
481 
+
482 /// @brief Tracer type used for immersed boundaries. Identifies traces of
+
483 /// nodes and integration points on background mesh elements
+
484 //
+
485 class traceType
+
486 {
+
487  public:
+
488  // No. of non-zero nodal traces
+
489  int n = 0;
490 
-
491  // Local to global nodes maping nNo --> tnNo
-
492  Vector<int> gN;
+
491  // No. of non-zero integration point traces
+
492  int nG = 0;
493 
-
494  // Self pointer of each trace to the IB integration point and
-
495  // element ID
-
496  Array<int> gE;
-
497 
-
498  // Nodal trace pointer array stores two values for each trace.
-
499  // (1) background mesh element to which the trace points to,
-
500  // (2) mesh ID
-
501  Array<int> nptr;
-
502 
-
503  // Integration point tracer array stores two values for each trace
-
504  // (1) background mesh element to which the trace points to,
-
505  // (2) mesh ID
-
506  Array<int> gptr;
-
507 
-
508  // Parametric coordinate for each nodal trace
-
509  Array<double> xi;
+
494  // Local to global nodes maping nNo --> tnNo
+
495  Vector<int> gN;
+
496 
+
497  // Self pointer of each trace to the IB integration point and
+
498  // element ID
+
499  Array<int> gE;
+
500 
+
501  // Nodal trace pointer array stores two values for each trace.
+
502  // (1) background mesh element to which the trace points to,
+
503  // (2) mesh ID
+
504  Array<int> nptr;
+
505 
+
506  // Integration point tracer array stores two values for each trace
+
507  // (1) background mesh element to which the trace points to,
+
508  // (2) mesh ID
+
509  Array<int> gptr;
510 
-
511  // Parametric coordinate for each Gauss point trace
-
512  Array<double> xiG;
-
513 };
-
514 
-
515 /// @brief The face type containing mesh at boundary
-
516 //
-
517 class faceType
-
518 {
-
519  public:
-
520  faceType();
-
521  ~faceType();
-
522 
-
523  void destroy();
-
524 
-
525  //faceType& operator=(const faceType& rhs);
-
526 
-
527  // Parametric direction normal to this face (NURBS)
-
528  int d = 0;
+
511  // Parametric coordinate for each nodal trace
+
512  Array<double> xi;
+
513 
+
514  // Parametric coordinate for each Gauss point trace
+
515  Array<double> xiG;
+
516 };
+
517 
+
518 /// @brief The face type containing mesh at boundary
+
519 //
+
520 class faceType
+
521 {
+
522  public:
+
523  faceType();
+
524  ~faceType();
+
525 
+
526  void destroy();
+
527 
+
528  //faceType& operator=(const faceType& rhs);
529 
-
530  // Number of nodes (control points) in a single element
-
531  int eNoN = 0;
+
530  // Parametric direction normal to this face (NURBS)
+
531  int d = 0;
532 
-
533  // Element type
-
534  consts::ElementType eType = consts::ElementType::NA;
+
533  // Number of nodes (control points) in a single element
+
534  int eNoN = 0;
535 
-
536  // The mesh index that this face belongs to
-
537  int iM = 0;
+
536  // Element type
+
537  consts::ElementType eType = consts::ElementType::NA;
538 
-
539  // Number of elements
-
540  int nEl = 0;
+
539  // The mesh index that this face belongs to
+
540  int iM = 0;
541 
-
542  // Global number of elements
-
543  int gnEl = 0;
+
542  // Number of elements
+
543  int nEl = 0;
544 
-
545  // Number of function spaces
-
546  int nFs = 0;
+
545  // Global number of elements
+
546  int gnEl = 0;
547 
-
548  // Number of Gauss points for integration
-
549  int nG = 0;
+
548  // Number of function spaces
+
549  int nFs = 0;
550 
-
551  // Number of nodes
-
552  int nNo = 0;
+
551  // Number of Gauss points for integration
+
552  int nG = 0;
553 
-
554  // Global element Ids
-
555  Vector<int> gE;
+
554  // Number of nodes
+
555  int nNo = 0;
556 
-
557  // Global node Ids
-
558  Vector<int> gN;
+
557  // Global element Ids
+
558  Vector<int> gE;
559 
-
560  // Global to local maping tnNo --> nNo
-
561  Vector<int> lN;
+
560  // Global node Ids
+
561  Vector<int> gN;
562 
-
563  // Connectivity array
-
564  Array<int> IEN;
+
563  // Global to local maping tnNo --> nNo
+
564  Vector<int> lN;
565 
-
566  // EBC array (gE + gIEN)
-
567  Array<int> gebc;
+
566  // Connectivity array
+
567  Array<int> IEN;
568 
-
569  // Surface area
-
570  double area = 0.0;
+
569  // EBC array (gE + gIEN)
+
570  Array<int> gebc;
571 
-
572  // Gauss point weights
-
573  Vector<double> w;
+
572  // Surface area
+
573  double area = 0.0;
574 
-
575  // Position coordinates
-
576  Array<double> x;
+
575  // Gauss point weights
+
576  Vector<double> w;
577 
-
578  // Gauss points in parametric space
-
579  Array<double> xi;
+
578  // Position coordinates
+
579  Array<double> x;
580 
-
581  // Shape functions at Gauss points
-
582  Array<double> N;
+
581  // Gauss points in parametric space
+
582  Array<double> xi;
583 
-
584  // Normal vector to each nodal point
-
585  Array<double> nV;
+
584  // Shape functions at Gauss points
+
585  Array<double> N;
586 
-
587  // Shape functions derivative at Gauss points
-
588  // double Nx(:,:,:);
-
589  Array3<double> Nx;
-
590 
-
591  // Second derivatives of shape functions - for shells & IGA
-
592  // double Nxx(:,:,:);
-
593  Array3<double> Nxx;
-
594 
-
595  // Face name for flux files
-
596  std::string name;
+
587  // Normal vector to each nodal point
+
588  Array<double> nV;
+
589 
+
590  // Shape functions derivative at Gauss points
+
591  // double Nx(:,:,:);
+
592  Array3<double> Nx;
+
593 
+
594  // Second derivatives of shape functions - for shells & IGA
+
595  // double Nxx(:,:,:);
+
596  Array3<double> Nxx;
597 
-
598  // Face nodal adjacency
-
599  adjType nAdj;
+
598  // Face name for flux files
+
599  std::string name;
600 
-
601  // Face element adjacency
-
602  adjType eAdj;
+
601  // Face nodal adjacency
+
602  adjType nAdj;
603 
-
604  // Function spaces (basis)
-
605  std::vector<fsType> fs;
+
604  // Face element adjacency
+
605  adjType eAdj;
606 
-
607  // TRI3 quadrature modifier
-
608  double qmTRI3 = 2.0/3.0;
-
609 };
-
610 
-
611 /// @brief Declared type for outputed variables
-
612 //
-
613 class outputType
-
614 {
-
615  public:
-
616 
-
617  // Is this output suppose to be written into VTK, boundary, vol
-
618  std::vector<bool> wtn{false, false, false};
+
607  // Function spaces (basis)
+
608  std::vector<fsType> fs;
+
609 
+
610  // TRI3 quadrature modifier
+
611  double qmTRI3 = 2.0/3.0;
+
612 };
+
613 
+
614 /// @brief Declared type for outputed variables
+
615 //
+
616 class outputType
+
617 {
+
618  public:
619 
-
620  // The group that this belong to (one of outType_*)
-
621  consts::OutputType grp = consts::OutputType::outGrp_NA;
-
622  //int grp;
-
623 
-
624  // Length of the outputed variable
-
625  int l = 0;
+
620  // Is this output suppose to be written into VTK, boundary, vol
+
621  std::vector<bool> wtn{false, false, false};
+
622 
+
623  // The group that this belong to (one of outType_*)
+
624  consts::OutputType grp = consts::OutputType::outGrp_NA;
+
625  //int grp;
626 
-
627  // Offset from the first index
-
628  int o = 0;
+
627  // Length of the outputed variable
+
628  int l = 0;
629 
-
630  // The name to be used for the output and also in input file
-
631  std::string name;
-
632 };
-
633 
-
634 /// @brief Linear system of equations solver type
-
635 //
-
636 class lsType
-
637 {
-
638  public:
-
639 
-
640  /// @brief LS solver (IN)
-
641  consts::SolverType LS_type = consts::SolverType::lSolver_NA;
+
630  // Offset from the first index
+
631  int o = 0;
+
632 
+
633  // The name to be used for the output and also in input file
+
634  std::string name;
+
635 };
+
636 
+
637 /// @brief Linear system of equations solver type
+
638 //
+
639 class lsType
+
640 {
+
641  public:
642 
-
643  /// @brief Successful solving (OUT)
-
644  bool suc = false;
+
643  /// @brief LS solver (IN)
+
644  consts::SolverType LS_type = consts::SolverType::lSolver_NA;
645 
-
646  /// @brief Maximum iterations (IN)
-
647  int mItr = 1000;
+
646  /// @brief Successful solving (OUT)
+
647  bool suc = false;
648 
-
649  /// @brief Space dimension (IN)
-
650  int sD = 0;
+
649  /// @brief Maximum iterations (IN)
+
650  int mItr = 1000;
651 
-
652  /// @brief Number of iteration (OUT)
-
653  int itr = 0;
+
652  /// @brief Space dimension (IN)
+
653  int sD = 0;
654 
-
655  /// @brief Number of Ax multiple (OUT)
-
656  int cM = 0;
+
655  /// @brief Number of iteration (OUT)
+
656  int itr = 0;
657 
-
658  /// @brief Number of |x| norms (OUT)
-
659  int cN = 0;
+
658  /// @brief Number of Ax multiple (OUT)
+
659  int cM = 0;
660 
-
661  /// @brief Number of <x.y> dot products (OUT)
-
662  int cD = 0;
+
661  /// @brief Number of |x| norms (OUT)
+
662  int cN = 0;
663 
-
664  /// @brief Only for data alignment (-)
-
665  int reserve = 0;
+
664  /// @brief Number of <x.y> dot products (OUT)
+
665  int cD = 0;
666 
-
667  /// @brief Absolute tolerance (IN)
-
668  double absTol = 1e-08;
+
667  /// @brief Only for data alignment (-)
+
668  int reserve = 0;
669 
-
670  /// @brief Relative tolerance (IN)
-
671  double relTol = 0.0;
+
670  /// @brief Absolute tolerance (IN)
+
671  double absTol = 1e-08;
672 
-
673  /// @brief Initial norm of residual (OUT)
-
674  double iNorm = 0.0;
+
673  /// @brief Relative tolerance (IN)
+
674  double relTol = 0.0;
675 
-
676  /// @brief Final norm of residual (OUT)
-
677  double fNorm = 0.0;
+
676  /// @brief Initial norm of residual (OUT)
+
677  double iNorm = 0.0;
678 
-
679  /// @brief Res. rduction in last itr. (OUT)
-
680  double dB = 0.0;
+
679  /// @brief Final norm of residual (OUT)
+
680  double fNorm = 0.0;
681 
-
682  /// @brief Calling duration (OUT)
-
683  double callD = 0.0;
-
684 
-
685  //@brief Configuration file for linear solvers (Trilinos, PETSc)
-
686  std::string config;
-
687 };
-
688 
-
689 
-
690 /// @brief Contact model type
-
691 //
-
692 class cntctModelType
-
693 {
-
694  public:
-
695  // Contact model
-
696  consts::ContactModelType cType = consts::ContactModelType::cntctM_NA;
-
697 
-
698  // Penalty parameter
-
699  double k = 0.0;
+
682  /// @brief Res. rduction in last itr. (OUT)
+
683  double dB = 0.0;
+
684 
+
685  /// @brief Calling duration (OUT)
+
686  double callD = 0.0;
+
687 
+
688  //@brief Configuration file for linear solvers (Trilinos, PETSc)
+
689  std::string config;
+
690 };
+
691 
+
692 
+
693 /// @brief Contact model type
+
694 //
+
695 class cntctModelType
+
696 {
+
697  public:
+
698  // Contact model
+
699  consts::ContactModelType cType = consts::ContactModelType::cntctM_NA;
700 
-
701  // Min depth of penetration
-
702  double h = 0.0;
+
701  // Penalty parameter
+
702  double k = 0.0;
703 
-
704  // Max depth of penetration
-
705  double c = 0.0;
+
704  // Min depth of penetration
+
705  double h = 0.0;
706 
-
707  // Min norm of face normals in contact
-
708  double al = 0.0;
+
707  // Max depth of penetration
+
708  double c = 0.0;
709 
-
710  // Tolerance
-
711  double tol = 0.0;
-
712 };
-
713 
-
714 class cplFaceType
-
715 {
-
716  public:
-
717  // GenBC_Dir/GenBC_Neu
-
718  consts::CplBCType bGrp = consts::CplBCType::cplBC_NA;
-
719 
-
720  // Pointer to X
-
721  int Xptr = -1;
+
710  // Min norm of face normals in contact
+
711  double al = 0.0;
+
712 
+
713  // Tolerance
+
714  double tol = 0.0;
+
715 };
+
716 
+
717 class cplFaceType
+
718 {
+
719  public:
+
720  // GenBC_Dir/GenBC_Neu
+
721  consts::CplBCType bGrp = consts::CplBCType::cplBC_NA;
722 
-
723  // Internal genBC use
-
724  int eqv = 0;
+
723  // Pointer to X
+
724  int Xptr = -1;
725 
-
726  // Flow rates at t
-
727  double Qo = 0.0;
+
726  // Internal genBC use
+
727  int eqv = 0;
728 
-
729  // Flow rates at t+dt
-
730  double Qn = 0.0;
+
729  // Flow rates at t
+
730  double Qo = 0.0;
731 
-
732  // Pressures at t
-
733  double Po = 0.0;
+
732  // Flow rates at t+dt
+
733  double Qn = 0.0;
734 
-
735  // Pressures at t+dt
-
736  double Pn = 0.0;
+
735  // Pressures at t
+
736  double Po = 0.0;
737 
-
738  // Imposed flow/pressure
-
739  double y = 0.0;
+
738  // Pressures at t+dt
+
739  double Pn = 0.0;
740 
-
741  // Name of the face
-
742  std::string name;
+
741  // Imposed flow/pressure
+
742  double y = 0.0;
743 
-
744  // RCR type BC
-
745  rcrType RCR;
-
746 };
-
747 
-
748 /// @brief For coupled 0D-3D problems
-
749 //
-
750 class cplBCType
-
751 {
-
752  public:
-
753  cplBCType();
-
754  /// @brief Is multi-domain active
-
755  bool coupled = false;
-
756 
-
757  /// @brief Whether to use genBC
-
758  bool useGenBC = false;
-
759 
-
760  // Whether to use svZeroD
-
761  bool useSvZeroD = false;
+
744  // Name of the face
+
745  std::string name;
+
746 
+
747  // RCR type BC
+
748  rcrType RCR;
+
749 };
+
750 
+
751 /// @brief For coupled 0D-3D problems
+
752 //
+
753 class cplBCType
+
754 {
+
755  public:
+
756  cplBCType();
+
757  /// @brief Is multi-domain active
+
758  bool coupled = false;
+
759 
+
760  /// @brief Whether to use genBC
+
761  bool useGenBC = false;
762 
-
763  // Whether to initialize RCR from flow data
-
764  bool initRCR = false;
-
765 
-
766  /// @brief Number of coupled faces
-
767  int nFa = 0;
+
763  // Whether to use svZeroD
+
764  bool useSvZeroD = false;
+
765 
+
766  // Whether to initialize RCR from flow data
+
767  bool initRCR = false;
768 
-
769  /// @brief Number of unknowns in the 0D domain
-
770  int nX = 0;
+
769  /// @brief Number of coupled faces
+
770  int nFa = 0;
771 
-
772  /// @brief Number of output variables addition to nX
-
773  int nXp = 0;
+
772  /// @brief Number of unknowns in the 0D domain
+
773  int nX = 0;
774 
-
775  /// @brief Implicit/Explicit/Semi-implicit schemes
-
776  consts::CplBCType schm = consts::CplBCType::cplBC_NA;
-
777  //int schm = cplBC_NA;
-
778 
-
779  /// @brief Path to the 0D code binary file
-
780  std::string binPath;
+
775  /// @brief Number of output variables addition to nX
+
776  int nXp = 0;
+
777 
+
778  /// @brief Implicit/Explicit/Semi-implicit schemes
+
779  consts::CplBCType schm = consts::CplBCType::cplBC_NA;
+
780  //int schm = cplBC_NA;
781 
-
782  /// @brief File name for communication between 0D and 3D
-
783  std::string commuName;
-
784  //std::string commuName = ".CPLBC_0D_3D.tmp";
-
785 
-
786  /// @brief The name of history file containing "X"
-
787  std::string saveName;
-
788  //std::string(LEN=stdL) :: saveName = "LPN.dat";
-
789 
-
790  /// @brief New time step unknowns in the 0D domain
-
791  Vector<double> xn;
+
782  /// @brief Path to the 0D code binary file
+
783  std::string binPath;
+
784 
+
785  /// @brief File name for communication between 0D and 3D
+
786  std::string commuName;
+
787  //std::string commuName = ".CPLBC_0D_3D.tmp";
+
788 
+
789  /// @brief The name of history file containing "X"
+
790  std::string saveName;
+
791  //std::string(LEN=stdL) :: saveName = "LPN.dat";
792 
-
793  /// @brief Old time step unknowns in the 0D domain
-
794  Vector<double> xo;
+
793  /// @brief New time step unknowns in the 0D domain
+
794  Vector<double> xn;
795 
-
796  /// @brief Output variables to be printed
-
797  Vector<double> xp;
+
796  /// @brief Old time step unknowns in the 0D domain
+
797  Vector<double> xo;
798 
-
799  /// @brief Data structure used for communicating with 0D code
-
800  std::vector<cplFaceType> fa;
-
801 };
-
802 
-
803 /// @brief This is the container for a mesh or NURBS patch, those specific
-
804 /// to NURBS are noted
-
805 //
-
806 class mshType
-
807 {
-
808  public:
-
809  mshType();
-
810  std::string dname = "";
-
811 
-
812 /*
-
813  mshType(const mshType &other)
-
814  {
-
815  std::cout << "c c c c c mshType copy c c c c c" << std::endl;
-
816  }
-
817 
-
818  mshType& operator = (const mshType &other)
-
819  {
-
820  std::cout << "= = = = = mshType assignment = = = = =" << std::endl;
-
821  return *this;
-
822  }
-
823 */
-
824 
-
825  ~mshType()
-
826  {
-
827  //std::cout << "- - - - - mshType dtor - - - - - dname: " << dname << std::endl;
-
828  };
-
829 
-
830  /// @brief Whether the shape function is linear
-
831  bool lShpF = false;
+
799  /// @brief Output variables to be printed
+
800  Vector<double> xp;
+
801 
+
802  /// @brief Data structure used for communicating with 0D code
+
803  std::vector<cplFaceType> fa;
+
804 };
+
805 
+
806 /// @brief This is the container for a mesh or NURBS patch, those specific
+
807 /// to NURBS are noted
+
808 //
+
809 class mshType
+
810 {
+
811  public:
+
812  mshType();
+
813  std::string dname = "";
+
814 
+
815 /*
+
816  mshType(const mshType &other)
+
817  {
+
818  std::cout << "c c c c c mshType copy c c c c c" << std::endl;
+
819  }
+
820 
+
821  mshType& operator = (const mshType &other)
+
822  {
+
823  std::cout << "= = = = = mshType assignment = = = = =" << std::endl;
+
824  return *this;
+
825  }
+
826 */
+
827 
+
828  ~mshType()
+
829  {
+
830  //std::cout << "- - - - - mshType dtor - - - - - dname: " << dname << std::endl;
+
831  };
832 
-
833  /// @brief Whether the mesh is shell
-
834  bool lShl = false;
+
833  /// @brief Whether the shape function is linear
+
834  bool lShpF = false;
835 
-
836  /// @brief Whether the mesh is fibers (Purkinje)
-
837  bool lFib = false;
+
836  /// @brief Whether the mesh is shell
+
837  bool lShl = false;
838 
-
839  /// @brief Element type
-
840  consts::ElementType eType = consts::ElementType::NA;
-
841  //int eType = eType_NA
-
842 
-
843  /// @brief Number of nodes (control points) in a single element
-
844  int eNoN = 0;
+
839  /// @brief Whether the mesh is fibers (Purkinje)
+
840  bool lFib = false;
+
841 
+
842  /// @brief Element type
+
843  consts::ElementType eType = consts::ElementType::NA;
+
844  //int eType = eType_NA
845 
-
846  /// @brief Global number of elements (knot spans)
-
847  int gnEl = 0;
+
846  /// @brief Number of nodes (control points) in a single element
+
847  int eNoN = 0;
848 
-
849  /// @brief Global number of nodes (control points)
-
850  int gnNo = 0;
+
849  /// @brief Global number of elements (knot spans)
+
850  int gnEl = 0;
851 
-
852  /// @brief Number of element face. Used for reading Gambit mesh files
-
853  int nEf = 0;
+
852  /// @brief Global number of nodes (control points)
+
853  int gnNo = 0;
854 
-
855  /// @brief Number of elements (knot spans)
-
856  int nEl = 0;
+
855  /// @brief Number of element face. Used for reading Gambit mesh files
+
856  int nEf = 0;
857 
-
858  /// @brief Number of faces
-
859  int nFa = 0;
+
858  /// @brief Number of elements (knot spans)
+
859  int nEl = 0;
860 
-
861  /// @brief Number of function spaces
-
862  int nFs = 0;
+
861  /// @brief Number of faces
+
862  int nFa = 0;
863 
-
864  /// @brief Number of Gauss points for integration
-
865  int nG = 0;
+
864  /// @brief Number of function spaces
+
865  int nFs = 0;
866 
-
867  /// @brief Number of nodes (control points) for 2D elements?
-
868  int nNo = 0;
+
867  /// @brief Number of Gauss points for integration
+
868  int nG = 0;
869 
-
870  /// @brief Number of elements sample points to be outputs (NURBS)
-
871  int nSl = 0;
+
870  /// @brief Number of nodes (control points) for 2D elements?
+
871  int nNo = 0;
872 
-
873  /// @brief The element type recognized by VTK format
-
874  int vtkType = 0;
+
873  /// @brief Number of elements sample points to be outputs (NURBS)
+
874  int nSl = 0;
875 
-
876  /// @brief Number of fiber directions
-
877  int nFn = 0;
+
876  /// @brief The element type recognized by VTK format
+
877  int vtkType = 0;
878 
-
879  /// @brief Mesh scale factor
-
880  double scF = 0.0;
+
879  /// @brief Number of fiber directions
+
880  int nFn = 0;
881 
-
882  /// @brief IB: Mesh size parameter
-
883  double dx = 0.0;
+
882  /// @brief Mesh scale factor
+
883  double scF = 0.0;
884 
-
885  /// @breif ordering: node ordering for boundaries
-
886  std::vector<std::vector<int>> ordering;
+
885  /// @brief IB: Mesh size parameter
+
886  double dx = 0.0;
887 
-
888  /// @brief Element distribution between processors
-
889  Vector<int> eDist;
+
888  /// @breif ordering: node ordering for boundaries
+
889  std::vector<std::vector<int>> ordering;
890 
-
891  /// @brief Element domain ID number
-
892  Vector<int> eId;
+
891  /// @brief Element distribution between processors
+
892  Vector<int> eDist;
893 
-
894  /// @brief Global nodes maping nNo --> tnNo
-
895  Vector<int> gN;
+
894  /// @brief Element domain ID number
+
895  Vector<int> eId;
896 
-
897  /// @brief GLobal projected nodes mapping projected -> unprojected mapping
-
898  Vector<int> gpN;
+
897  /// @brief Global nodes maping nNo --> tnNo
+
898  Vector<int> gN;
899 
-
900  /// @brief Global connectivity array mappig eNoN,nEl --> gnNo
-
901  Array<int> gIEN;
+
900  /// @brief GLobal projected nodes mapping projected -> unprojected mapping
+
901  Vector<int> gpN;
902 
-
903  /// @brief The connectivity array mapping eNoN,nEl --> nNo
-
904  Array<int> IEN;
+
903  /// @brief Global connectivity array mappig eNoN,nEl --> gnNo
+
904  Array<int> gIEN;
905 
-
906  /// @brief gIEN mapper from old to new
-
907  Vector<int> otnIEN;
+
906  /// @brief The connectivity array mapping eNoN,nEl --> nNo
+
907  Array<int> IEN;
908 
-
909  /// @brief Local knot pointer (NURBS)
-
910  Array<int> INN;
+
909  /// @brief gIEN mapper from old to new
+
910  Vector<int> otnIEN;
911 
-
912  /// @brief Global to local maping tnNo --> nNo
-
913  Vector<int> lN;
+
912  /// @brief Local knot pointer (NURBS)
+
913  Array<int> INN;
914 
-
915  /// @brief Shells: extended IEN array with neighboring nodes
-
916  Array<int> eIEN;
+
915  /// @brief Global to local maping tnNo --> nNo
+
916  Vector<int> lN;
917 
-
918  /// @brief Shells: boundary condition variable
-
919  Array<int> sbc;
+
918  /// @brief Shells: extended IEN array with neighboring nodes
+
919  Array<int> eIEN;
920 
-
921  /// @brief IB: Whether a cell is a ghost cell or not
-
922  Vector<int> iGC;
+
921  /// @brief Shells: boundary condition variable
+
922  Array<int> sbc;
923 
-
924  /// @brief Control points weights (NURBS)
-
925  Vector<double> nW;
+
924  /// @brief IB: Whether a cell is a ghost cell or not
+
925  Vector<int> iGC;
926 
-
927  /// @brief Gauss weights
-
928  Vector<double> w;
+
927  /// @brief Control points weights (NURBS)
+
928  Vector<double> nW;
929 
-
930  /// @brief Gauss integration points in parametric space
-
931  Array<double> xi;
+
930  /// @brief Gauss weights
+
931  Vector<double> w;
932 
-
933  /// @brief Bounds on parameteric coordinates
-
934  Array<double> xib;
+
933  /// @brief Gauss integration points in parametric space
+
934  Array<double> xi;
935 
-
936  /// @brief Position coordinates
-
937  Array<double> x;
+
936  /// @brief Bounds on parameteric coordinates
+
937  Array<double> xib;
938 
-
939  /// @brief Parent shape function
-
940  Array<double> N;
+
939  /// @brief Position coordinates
+
940  Array<double> x;
941 
-
942  /// @brief Shape function bounds
-
943  Array<double> Nb;
+
942  /// @brief Parent shape function
+
943  Array<double> N;
944 
-
945  /// @brief Normal vector to each nodal point (for Shells)
-
946  Array<double> nV;
+
945  /// @brief Shape function bounds
+
946  Array<double> Nb;
947 
-
948  /// @brief Fiber orientations stored at the element level - used for
-
949  /// electrophysiology and solid mechanics
-
950  Array<double> fN;
-
951 
-
952  /// @brief Parent shape functions gradient
-
953  /// double Nx(:,:,:)
-
954  Array3<double> Nx;
-
955 
-
956  /// @brief Second derivatives of shape functions - used for shells & IGA
-
957  /// davep double Nxx(:,:,:)
-
958  Array3<double> Nxx;
-
959 
-
960  /// @brief Solution field (displacement, velocity, pressure, etc.) for a known, potentially
-
961  /// time-varying, quantity of interest across a mesh
-
962  Array3<double> Ys;
-
963 
-
964  /// @brief Mesh Name
-
965  std::string name;
+
948  /// @brief Normal vector to each nodal point (for Shells)
+
949  Array<double> nV;
+
950 
+
951  /// @brief Fiber orientations stored at the element level - used for
+
952  /// electrophysiology and solid mechanics
+
953  Array<double> fN;
+
954 
+
955  /// @brief Parent shape functions gradient
+
956  /// double Nx(:,:,:)
+
957  Array3<double> Nx;
+
958 
+
959  /// @brief Second derivatives of shape functions - used for shells & IGA
+
960  /// davep double Nxx(:,:,:)
+
961  Array3<double> Nxx;
+
962 
+
963  /// @brief Solution field (displacement, velocity, pressure, etc.) for a known, potentially
+
964  /// time-varying, quantity of interest across a mesh
+
965  Array3<double> Ys;
966 
-
967  /// @brief Mesh nodal adjacency
-
968  adjType nAdj;
+
967  /// @brief Mesh Name
+
968  std::string name;
969 
-
970  /// @brief Mesh element adjacency
-
971  adjType eAdj;
+
970  /// @brief Mesh nodal adjacency
+
971  adjType nAdj;
972 
-
973  /// @brief Function spaces (basis)
-
974  std::vector<fsType> fs;
+
973  /// @brief Mesh element adjacency
+
974  adjType eAdj;
975 
-
976  /// @brief BSpline in different directions (NURBS)
-
977  std::vector<bsType> bs;
+
976  /// @brief Function spaces (basis)
+
977  std::vector<fsType> fs;
978 
-
979  /// @brief Faces are stored in this variable
-
980  std::vector<faceType> fa;
+
979  /// @brief BSpline in different directions (NURBS)
+
980  std::vector<bsType> bs;
981 
-
982  /// @brief IB: tracers
-
983  traceType trc;
+
982  /// @brief Faces are stored in this variable
+
983  std::vector<faceType> fa;
984 
-
985  /// @brief TET4 quadrature modifier
-
986  double qmTET4 = (5.0+3.0*sqrt(5.0))/20.0;
-
987 
-
988  private:
-
989  //mshType(const mshType&);
-
990  //mshType& operator=(const mshType&);
-
991 
-
992 };
-
993 
-
994 /// @brief Equation type
-
995 //
-
996 class eqType
-
997 {
-
998  public:
-
999  eqType();
-
1000  ~eqType();
-
1001 
-
1002  /// @brief Should be satisfied in a coupled/uncoupled fashion
-
1003  bool coupled = false;
-
1004  //bool coupled = .TRUE.
-
1005 
-
1006  /// @brief Satisfied/not satisfied
-
1007  bool ok = false;
+
985  /// @brief IB: tracers
+
986  traceType trc;
+
987 
+
988  /// @brief TET4 quadrature modifier
+
989  double qmTET4 = (5.0+3.0*sqrt(5.0))/20.0;
+
990 
+
991  private:
+
992  //mshType(const mshType&);
+
993  //mshType& operator=(const mshType&);
+
994 
+
995 };
+
996 
+
997 /// @brief Equation type
+
998 //
+
999 class eqType
+
1000 {
+
1001  public:
+
1002  eqType();
+
1003  ~eqType();
+
1004 
+
1005  /// @brief Should be satisfied in a coupled/uncoupled fashion
+
1006  bool coupled = false;
+
1007  //bool coupled = .TRUE.
1008 
-
1009  /// @brief Use C++ Trilinos framework for the linear solvers
-
1010  bool useTLS = false;
+
1009  /// @brief Satisfied/not satisfied
+
1010  bool ok = false;
1011 
-
1012  /// @brief Use C++ Trilinos framework for assembly and for linear solvers
-
1013  bool assmTLS = false;
+
1012  /// @brief Use C++ Trilinos framework for the linear solvers
+
1013  bool useTLS = false;
1014 
-
1015  /// @brief Degrees of freedom
-
1016  int dof = 0;
+
1015  /// @brief Use C++ Trilinos framework for assembly and for linear solvers
+
1016  bool assmTLS = false;
1017 
-
1018  /// @brief Pointer to end of unknown Yo(:,s:e)
-
1019  int e = -1;
+
1018  /// @brief Degrees of freedom
+
1019  int dof = 0;
1020 
-
1021  /// @brief Pointer to start of unknown Yo(:,s:e)
-
1022  int s = -1;
+
1021  /// @brief Pointer to end of unknown Yo(:,s:e)
+
1022  int e = -1;
1023 
-
1024  /// @brief Number of performed iterations
-
1025  int itr = 0;
+
1024  /// @brief Pointer to start of unknown Yo(:,s:e)
+
1025  int s = -1;
1026 
-
1027  /// @brief Maximum iteration for this eq.
-
1028  int maxItr = 5;
+
1027  /// @brief Number of performed iterations
+
1028  int itr = 0;
1029 
-
1030  /// @brief Minimum iteration for this eq.
-
1031  int minItr = 1;
+
1030  /// @brief Maximum iteration for this eq.
+
1031  int maxItr = 5;
1032 
-
1033  /// @brief Number of possible outputs
-
1034  int nOutput = 0;
+
1033  /// @brief Minimum iteration for this eq.
+
1034  int minItr = 1;
1035 
-
1036  /// @brief IB: Number of possible outputs
-
1037  int nOutIB = 0;
+
1036  /// @brief Number of possible outputs
+
1037  int nOutput = 0;
1038 
-
1039  /// @brief Number of domains
-
1040  int nDmn = 0;
+
1039  /// @brief IB: Number of possible outputs
+
1040  int nOutIB = 0;
1041 
-
1042  /// @brief IB: Number of immersed domains
-
1043  int nDmnIB = 0;
+
1042  /// @brief Number of domains
+
1043  int nDmn = 0;
1044 
-
1045  /// @brief Number of BCs
-
1046  int nBc = 0;
+
1045  /// @brief IB: Number of immersed domains
+
1046  int nDmnIB = 0;
1047 
-
1048  /// @brief Number of BCs on immersed surfaces
-
1049  int nBcIB = 0;
+
1048  /// @brief Number of BCs
+
1049  int nBc = 0;
1050 
-
1051  /// @brief Number of BFs
-
1052  int nBf = 0;
+
1051  /// @brief Number of BCs on immersed surfaces
+
1052  int nBcIB = 0;
1053 
-
1054  /// @brief Type of equation fluid/heatF/heatS/lElas/FSI
-
1055  consts::EquationType phys = consts::EquationType::phys_NA;
-
1056 
-
1057  // Parameters used for the Generalized α− Method.
-
1058  //
-
1059  /// @brief \f$\alpha_f\f$
-
1060  double af = 0.0;
-
1061 
-
1062  /// @brief \f$\alpha_m\f$
-
1063  ///
-
1064  /// For second order equations: am = (2.0 - roInf) / (1.0 + roInf)
-
1065  /// First order equations: am = 0.5 * (3.0 - roInf) / (1.0 + roInf)
-
1066  //
-
1067  double am = 0.0;
-
1068 
-
1069  /// @brief \f$\beta\f$
-
1070  double beta = 0.0;
+
1054  /// @brief Number of BFs
+
1055  int nBf = 0;
+
1056 
+
1057  /// @brief Type of equation fluid/heatF/heatS/lElas/FSI
+
1058  consts::EquationType phys = consts::EquationType::phys_NA;
+
1059 
+
1060  // Parameters used for the Generalized α− Method.
+
1061  //
+
1062  /// @brief \f$\alpha_f\f$
+
1063  double af = 0.0;
+
1064 
+
1065  /// @brief \f$\alpha_m\f$
+
1066  ///
+
1067  /// For second order equations: am = (2.0 - roInf) / (1.0 + roInf)
+
1068  /// First order equations: am = 0.5 * (3.0 - roInf) / (1.0 + roInf)
+
1069  //
+
1070  double am = 0.0;
1071 
-
1072  /// @brief \f$\gamma\f$
-
1073  double gam = 0.0;
+
1072  /// @brief \f$\beta\f$
+
1073  double beta = 0.0;
1074 
-
1075  /// @brief Initial norm of residual
-
1076  double iNorm = 0.0;
+
1075  /// @brief \f$\gamma\f$
+
1076  double gam = 0.0;
1077 
-
1078  /// @brief First iteration norm
-
1079  double pNorm = 0.0;
+
1078  /// @brief Initial norm of residual
+
1079  double iNorm = 0.0;
1080 
-
1081  /// @brief \f$\rho_{infinity}\f$
-
1082  double roInf = 0.0;
+
1081  /// @brief First iteration norm
+
1082  double pNorm = 0.0;
1083 
-
1084  /// @brief Accepted relative tolerance
-
1085  double tol = 0.0;
+
1084  /// @brief \f$\rho_{infinity}\f$
+
1085  double roInf = 0.0;
1086 
-
1087  /// @brief Equation symbol
-
1088  std::string sym;
-
1089  //std::string(LEN=2) :: sym = "NA";
-
1090 
-
1091  /// @brief type of linear solver
-
1092  lsType ls;
+
1087  /// @brief Accepted relative tolerance
+
1088  double tol = 0.0;
+
1089 
+
1090  /// @brief Equation symbol
+
1091  std::string sym;
+
1092  //std::string(LEN=2) :: sym = "NA";
1093 
-
1094  /// @brief The type of interface to a numerical linear algebra library.
-
1095  consts::LinearAlgebraType linear_algebra_type;
+
1094  /// @brief type of linear solver
+
1095  lsType ls;
1096 
-
1097  /// @brief The type of assembly interface to a numerical linear algebra library.
-
1098  consts::LinearAlgebraType linear_algebra_assembly_type;
+
1097  /// @brief The type of interface to a numerical linear algebra library.
+
1098  consts::LinearAlgebraType linear_algebra_type;
1099 
-
1100  /// @brief The type of preconditioner used by the interface to a numerical linear algebra library.
-
1101  consts::PreconditionerType linear_algebra_preconditioner = consts::PreconditionerType::PREC_FSILS;
+
1100  /// @brief The type of assembly interface to a numerical linear algebra library.
+
1101  consts::LinearAlgebraType linear_algebra_assembly_type;
1102 
-
1103  /// @brief Interface to a numerical linear algebra library.
-
1104  LinearAlgebra* linear_algebra = nullptr;
+
1103  /// @brief The type of preconditioner used by the interface to a numerical linear algebra library.
+
1104  consts::PreconditionerType linear_algebra_preconditioner = consts::PreconditionerType::PREC_FSILS;
1105 
-
1106  /// @brief FSILS type of linear solver
-
1107  fsi_linear_solver::FSILS_lsType FSILS;
+
1106  /// @brief Interface to a numerical linear algebra library.
+
1107  LinearAlgebra* linear_algebra = nullptr;
1108 
-
1109  /// @brief BCs associated with this equation;
-
1110  std::vector<bcType> bc;
+
1109  /// @brief FSILS type of linear solver
+
1110  fsi_linear_solver::FSILS_lsType FSILS;
1111 
-
1112  /// @brief IB: BCs associated with this equation on immersed surfaces
-
1113  std::vector<bcType> bcIB;
+
1112  /// @brief BCs associated with this equation;
+
1113  std::vector<bcType> bc;
1114 
-
1115  /// @brief domains that this equation must be solved
-
1116  std::vector<dmnType> dmn;
+
1115  /// @brief IB: BCs associated with this equation on immersed surfaces
+
1116  std::vector<bcType> bcIB;
1117 
-
1118  /// @brief IB: immersed domains that this equation must be solved
-
1119  std::vector<dmnType> dmnIB;
+
1118  /// @brief domains that this equation must be solved
+
1119  std::vector<dmnType> dmn;
1120 
-
1121  /// @brief Outputs
-
1122  std::vector<outputType> output;
+
1121  /// @brief IB: immersed domains that this equation must be solved
+
1122  std::vector<dmnType> dmnIB;
1123 
-
1124  /// @brief IB: Outputs
-
1125  std::vector<outputType> outIB;
+
1124  /// @brief Outputs
+
1125  std::vector<outputType> output;
1126 
-
1127  /// @brief Body force associated with this equation
-
1128  std::vector<bfType> bf;
-
1129 };
-
1130 
-
1131 /// @brief This type will be used to write data in the VTK files.
-
1132 //
-
1133 class dataType
-
1134 {
-
1135  public:
-
1136 
-
1137  // Element number of nodes
-
1138  int eNoN = 0;
+
1127  /// @brief IB: Outputs
+
1128  std::vector<outputType> outIB;
+
1129 
+
1130  /// @brief Body force associated with this equation
+
1131  std::vector<bfType> bf;
+
1132 };
+
1133 
+
1134 /// @brief This type will be used to write data in the VTK files.
+
1135 //
+
1136 class dataType
+
1137 {
+
1138  public:
1139 
-
1140  // Number of elements
-
1141  int nEl = 0;
+
1140  // Element number of nodes
+
1141  int eNoN = 0;
1142 
-
1143  // Number of nodes
-
1144  int nNo = 0;
+
1143  // Number of elements
+
1144  int nEl = 0;
1145 
-
1146  // vtk type
-
1147  int vtkType = 0;
+
1146  // Number of nodes
+
1147  int nNo = 0;
1148 
-
1149  // Connectivity array
-
1150  Array<int> IEN;
+
1149  // vtk type
+
1150  int vtkType = 0;
1151 
-
1152  // Element based variables to be written
-
1153  Array<double> xe;
+
1152  // Connectivity array
+
1153  Array<int> IEN;
1154 
-
1155  // All the variables after transformation to global format
-
1156  Array<double> gx;
+
1155  // Element based variables to be written
+
1156  Array<double> xe;
1157 
-
1158  // All the variables to be written (including position)
-
1159  Array<double> x;
-
1160 };
-
1161 
-
1162 
-
1163 class rmshType
-
1164 {
-
1165  public:
-
1166 
-
1167  rmshType();
-
1168 
-
1169  /// @brief Whether remesh is required for problem or not
-
1170  bool isReqd = false;
+
1158  // All the variables after transformation to global format
+
1159  Array<double> gx;
+
1160 
+
1161  // All the variables to be written (including position)
+
1162  Array<double> x;
+
1163 };
+
1164 
+
1165 
+
1166 class rmshType
+
1167 {
+
1168  public:
+
1169 
+
1170  rmshType();
1171 
-
1172  /// @brief Method for remeshing: 1-TetGen, 2-MeshSim
-
1173  consts::MeshGeneratorType method = consts::MeshGeneratorType::RMSH_TETGEN;
+
1172  /// @brief Whether remesh is required for problem or not
+
1173  bool isReqd = false;
1174 
-
1175  /// @brief Counter to track number of remesh done
-
1176  int cntr = 0;
+
1175  /// @brief Method for remeshing: 1-TetGen, 2-MeshSim
+
1176  consts::MeshGeneratorType method = consts::MeshGeneratorType::RMSH_TETGEN;
1177 
-
1178  /// @brief Time step from which remeshing is done
-
1179  int rTS = 0;
+
1178  /// @brief Counter to track number of remesh done
+
1179  int cntr = 0;
1180 
-
1181  /// @brief Time step freq for saving data
-
1182  int cpVar = 0;
+
1181  /// @brief Time step from which remeshing is done
+
1182  int rTS = 0;
1183 
-
1184  /// @brief Time step at which forced remeshing is done
-
1185  int fTS = 1000;
+
1184  /// @brief Time step freq for saving data
+
1185  int cpVar = 0;
1186 
-
1187  /// @brief Time step frequency for forced remeshing
-
1188  int freq = 1000;
+
1187  /// @brief Time step at which forced remeshing is done
+
1188  int fTS = 1000;
1189 
-
1190  /// @brief Time where remeshing starts
-
1191  double time = 0.0;
+
1190  /// @brief Time step frequency for forced remeshing
+
1191  int freq = 1000;
1192 
-
1193  /// @brief Mesh quality parameters
-
1194  double minDihedAng = 0.0;
-
1195  double maxRadRatio = 0.0;
-
1196 
-
1197  /// @brief Edge size of mesh
-
1198  Vector<double> maxEdgeSize;
+
1193  /// @brief Time where remeshing starts
+
1194  double time = 0.0;
+
1195 
+
1196  /// @brief Mesh quality parameters
+
1197  double minDihedAng = 0.0;
+
1198  double maxRadRatio = 0.0;
1199 
-
1200  /// @brief Initial norm of an equation
-
1201  Vector<double> iNorm;
+
1200  /// @brief Edge size of mesh
+
1201  Vector<double> maxEdgeSize;
1202 
-
1203  /// @brief Copy of solution variables where remeshing starts
-
1204  Array<double> A0;
-
1205  Array<double> Y0;
-
1206  Array<double> D0;
-
1207 
-
1208  /// @brief Flag is set if remeshing is required for each mesh
-
1209  std::vector<bool> flag;
-
1210 };
-
1211 
-
1212 class ibCommType
-
1213 {
-
1214  public:
-
1215  /// @brief Num traces (nodes) local to each process
-
1216  Vector<int> n;
-
1217 
-
1218  /// @brief Pointer to global trace (node num) stacked contiguously
-
1219  Vector<int> gN;
+
1203  /// @brief Initial norm of an equation
+
1204  Vector<double> iNorm;
+
1205 
+
1206  /// @brief Copy of solution variables where remeshing starts
+
1207  Array<double> A0;
+
1208  Array<double> Y0;
+
1209  Array<double> D0;
+
1210 
+
1211  /// @brief Flag is set if remeshing is required for each mesh
+
1212  std::vector<bool> flag;
+
1213 };
+
1214 
+
1215 class ibCommType
+
1216 {
+
1217  public:
+
1218  /// @brief Num traces (nodes) local to each process
+
1219  Vector<int> n;
1220 
-
1221  /// @brief Num traces (Gauss points) local to each process
-
1222  Vector<int> nG;
+
1221  /// @brief Pointer to global trace (node num) stacked contiguously
+
1222  Vector<int> gN;
1223 
-
1224  /// @brief Pointer to global trace (Gauss point) stacked contiguously
-
1225  Vector<int> gE;
-
1226 };
-
1227 
-
1228 
-
1229 /// @brief Immersed Boundary (IB) data type
-
1230 //
-
1231 class ibType
-
1232 {
-
1233  public:
-
1234 
-
1235  /// @brief Whether any file being saved
-
1236  bool savedOnce = false;
-
1237  //bool savedOnce = .FALSE.
-
1238 
-
1239  /// @brief IB method
-
1240  int mthd = 0;
-
1241  //int mthd = ibMthd_NA;
-
1242 
-
1243  /// @brief IB coupling
-
1244  int cpld = 0;
-
1245  //int cpld = ibCpld_NA;
-
1246 
-
1247  /// @brief IB interpolation method
-
1248  int intrp = 0;
-
1249  //int intrp = ibIntrp_NA;
-
1250 
-
1251  /// @brief Current IB domain ID
-
1252  int cDmn = 0;
+
1224  /// @brief Num traces (Gauss points) local to each process
+
1225  Vector<int> nG;
+
1226 
+
1227  /// @brief Pointer to global trace (Gauss point) stacked contiguously
+
1228  Vector<int> gE;
+
1229 };
+
1230 
+
1231 
+
1232 /// @brief Immersed Boundary (IB) data type
+
1233 //
+
1234 class ibType
+
1235 {
+
1236  public:
+
1237 
+
1238  /// @brief Whether any file being saved
+
1239  bool savedOnce = false;
+
1240  //bool savedOnce = .FALSE.
+
1241 
+
1242  /// @brief IB method
+
1243  int mthd = 0;
+
1244  //int mthd = ibMthd_NA;
+
1245 
+
1246  /// @brief IB coupling
+
1247  int cpld = 0;
+
1248  //int cpld = ibCpld_NA;
+
1249 
+
1250  /// @brief IB interpolation method
+
1251  int intrp = 0;
+
1252  //int intrp = ibIntrp_NA;
1253 
-
1254  /// @brief Current equation
-
1255  int cEq = 0;
+
1254  /// @brief Current IB domain ID
+
1255  int cDmn = 0;
1256 
-
1257  /// @brief Total number of IB nodes
-
1258  int tnNo = 0;
+
1257  /// @brief Current equation
+
1258  int cEq = 0;
1259 
-
1260  /// @brief Number of IB meshes
-
1261  int nMsh = 0;
+
1260  /// @brief Total number of IB nodes
+
1261  int tnNo = 0;
1262 
-
1263  /// @brief IB call duration (1: total time; 2: update; 3,4: communication)
-
1264  double callD[4] = {0.0, 0.0, 0.0, 0.0};
+
1263  /// @brief Number of IB meshes
+
1264  int nMsh = 0;
1265 
-
1266  /// @brief IB Domain ID
-
1267  Vector<int> dmnID;
+
1266  /// @brief IB call duration (1: total time; 2: update; 3,4: communication)
+
1267  double callD[4] = {0.0, 0.0, 0.0, 0.0};
1268 
-
1269  /// @brief Row pointer (for sparse LHS matrix storage)
-
1270  Vector<int> rowPtr;
+
1269  /// @brief IB Domain ID
+
1270  Vector<int> dmnID;
1271 
-
1272  /// @brief Column pointer (for sparse LHS matrix storage)
-
1273  Vector<int> colPtr;
+
1272  /// @brief Row pointer (for sparse LHS matrix storage)
+
1273  Vector<int> rowPtr;
1274 
-
1275  /// @brief IB position coordinates
-
1276  Array<double> x;
+
1275  /// @brief Column pointer (for sparse LHS matrix storage)
+
1276  Vector<int> colPtr;
1277 
-
1278  /// @brief Velocity (new)
-
1279  Array<double> Yb;
+
1278  /// @brief IB position coordinates
+
1279  Array<double> x;
1280 
-
1281  /// @brief Time derivative of displacement (old)
-
1282  Array<double> Auo;
+
1281  /// @brief Velocity (new)
+
1282  Array<double> Yb;
1283 
-
1284  /// @brief Time derivative of displacement (new)
-
1285  Array<double> Aun;
+
1284  /// @brief Time derivative of displacement (old)
+
1285  Array<double> Auo;
1286 
-
1287  /// @brief Time derivative of displacement (n+am)
-
1288  Array<double> Auk;
+
1287  /// @brief Time derivative of displacement (new)
+
1288  Array<double> Aun;
1289 
-
1290  /// @brief Displacement (old)
-
1291  Array<double> Ubo;
+
1290  /// @brief Time derivative of displacement (n+am)
+
1291  Array<double> Auk;
1292 
-
1293  /// @brief Displacement (new)
-
1294  Array<double> Ubn;
+
1293  /// @brief Displacement (old)
+
1294  Array<double> Ubo;
1295 
-
1296  /// @brief Displacement (n+af)
-
1297  Array<double> Ubk;
+
1296  /// @brief Displacement (new)
+
1297  Array<double> Ubn;
1298 
-
1299  /// @brief Displacement (projected on background mesh, old)
-
1300  Array<double> Uo;
+
1299  /// @brief Displacement (n+af)
+
1300  Array<double> Ubk;
1301 
-
1302  /// @brief Displacement (projected on background mesh, new, n+af)
-
1303  Array<double> Un;
+
1302  /// @brief Displacement (projected on background mesh, old)
+
1303  Array<double> Uo;
1304 
-
1305  /// @brief Residual (FSI force)
-
1306  Array<double> R;
+
1305  /// @brief Displacement (projected on background mesh, new, n+af)
+
1306  Array<double> Un;
1307 
-
1308  /// @brief Residual (displacement, background mesh)
-
1309  Array<double> Ru;
+
1308  /// @brief Residual (FSI force)
+
1309  Array<double> R;
1310 
-
1311  /// @brief Residual (displacement, IB mesh)
-
1312  Array<double> Rub;
+
1311  /// @brief Residual (displacement, background mesh)
+
1312  Array<double> Ru;
1313 
-
1314  /// @brief LHS tangent matrix for displacement
-
1315  Array<double> Ku;
+
1314  /// @brief Residual (displacement, IB mesh)
+
1315  Array<double> Rub;
1316 
-
1317  /// @brief DERIVED class VARIABLES IB meshes;
-
1318  std::vector<mshType> msh;
+
1317  /// @brief LHS tangent matrix for displacement
+
1318  Array<double> Ku;
1319 
-
1320  /// @brief IB communicator
-
1321  ibCommType cm;
-
1322 };
-
1323 
-
1324 /// @brief The ComMod class duplicates the data structures in the Fortran COMMOD module
-
1325 /// defined in MOD.f.
-
1326 ///
-
1327 /// The data members here are the global variables exposed by the COMMOD module.
-
1328 //
-
1329 class ComMod {
-
1330 
-
1331  public:
-
1332  ComMod();
-
1333  ~ComMod();
-
1334 
-
1335  //----- bool members -----//
-
1336 
-
1337  /// @brief Whether there is a requirement to update mesh and Dn-Do variables
-
1338  bool dFlag = false;
+
1320  /// @brief DERIVED class VARIABLES IB meshes;
+
1321  std::vector<mshType> msh;
+
1322 
+
1323  /// @brief IB communicator
+
1324  ibCommType cm;
+
1325 };
+
1326 
+
1327 /// @brief The ComMod class duplicates the data structures in the Fortran COMMOD module
+
1328 /// defined in MOD.f.
+
1329 ///
+
1330 /// The data members here are the global variables exposed by the COMMOD module.
+
1331 //
+
1332 class ComMod {
+
1333 
+
1334  public:
+
1335  ComMod();
+
1336  ~ComMod();
+
1337 
+
1338  //----- bool members -----//
1339 
-
1340  /// @brief Whether mesh is moving
-
1341  bool mvMsh = false;
+
1340  /// @brief Whether there is a requirement to update mesh and Dn-Do variables
+
1341  bool dFlag = false;
1342 
-
1343  /// @brief Whether to averaged results
-
1344  bool saveAve = false;
+
1343  /// @brief Whether mesh is moving
+
1344  bool mvMsh = false;
1345 
-
1346  /// @brief Whether to save to VTK files
-
1347  bool saveVTK = false;
+
1346  /// @brief Whether to averaged results
+
1347  bool saveAve = false;
1348 
-
1349  /// @brief Whether any file being saved
-
1350  bool savedOnce = false;
+
1349  /// @brief Whether to save to VTK files
+
1350  bool saveVTK = false;
1351 
-
1352  /// @brief Whether to use separator in output
-
1353  bool sepOutput = false;
+
1352  /// @brief Whether any file being saved
+
1353  bool savedOnce = false;
1354 
-
1355  /// @brief Whether start from beginning or from simulations
-
1356  bool stFileFlag = false;
+
1355  /// @brief Whether to use separator in output
+
1356  bool sepOutput = false;
1357 
-
1358  /// @brief Whether to overwrite restart file or not
-
1359  bool stFileRepl = false;
+
1358  /// @brief Whether start from beginning or from simulations
+
1359  bool stFileFlag = false;
1360 
-
1361  /// @brief Restart simulation after remeshing
-
1362  bool resetSim = false;
+
1361  /// @brief Whether to overwrite restart file or not
+
1362  bool stFileRepl = false;
1363 
-
1364  /// @brief Check IEN array for initial mesh
-
1365  bool ichckIEN = false;
+
1364  /// @brief Restart simulation after remeshing
+
1365  bool resetSim = false;
1366 
-
1367  /// @brief Reset averaging variables from zero
-
1368  bool zeroAve = false;
+
1367  /// @brief Check IEN array for initial mesh
+
1368  bool ichckIEN = false;
1369 
-
1370  /// @brief Whether CMM equation is initialized
-
1371  bool cmmInit = false;
+
1370  /// @brief Reset averaging variables from zero
+
1371  bool zeroAve = false;
1372 
-
1373  /// @brief Whether variable wall properties are used for CMM
-
1374  bool cmmVarWall = false;
+
1373  /// @brief Whether CMM equation is initialized
+
1374  bool cmmInit = false;
1375 
-
1376  /// @brief Whether shell equation is being solved
-
1377  bool shlEq = false;
+
1376  /// @brief Whether variable wall properties are used for CMM
+
1377  bool cmmVarWall = false;
1378 
-
1379  /// @brief Whether PRESTRESS is being solved
-
1380  bool pstEq = false;
+
1379  /// @brief Whether shell equation is being solved
+
1380  bool shlEq = false;
1381 
-
1382  /// @brief Whether velocity-pressure based structural dynamics solver is used
-
1383  bool sstEq = false;
+
1382  /// @brief Whether PRESTRESS is being solved
+
1383  bool pstEq = false;
1384 
-
1385  /// @brief Whether to detect and apply any contact model
-
1386  bool iCntct = false;
+
1385  /// @brief Whether velocity-pressure based structural dynamics solver is used
+
1386  bool sstEq = false;
1387 
-
1388  /// @brief Whether any Immersed Boundary (IB) treatment is required
-
1389  bool ibFlag = false;
+
1388  /// @brief Whether to detect and apply any contact model
+
1389  bool iCntct = false;
1390 
-
1391  /// @brief Postprocess step - convert bin to vtk
-
1392  bool bin2VTK = false;
+
1391  /// @brief Whether any Immersed Boundary (IB) treatment is required
+
1392  bool ibFlag = false;
1393 
-
1394  /// @brief Whether to use precomputed state-variable solutions
-
1395  bool usePrecomp = false;
-
1396  //----- int members -----//
-
1397 
-
1398  /// @brief Current domain
-
1399  int cDmn = 0;
+
1394  /// @brief Postprocess step - convert bin to vtk
+
1395  bool bin2VTK = false;
+
1396 
+
1397  /// @brief Whether to use precomputed state-variable solutions
+
1398  bool usePrecomp = false;
+
1399  //----- int members -----//
1400 
-
1401  /// @brief Current equation
-
1402  int cEq = 0;
+
1401  /// @brief Current domain
+
1402  int cDmn = 0;
1403 
-
1404  /// @brief Current time step
-
1405  int cTS = 0;
-
1406 
-
1407  std::array<double,3> timeP;
-
1408 
-
1409  /// @brief Starting time step
-
1410  int startTS = 0;
+
1404  /// @brief Current equation
+
1405  int cEq = 0;
+
1406 
+
1407  /// @brief Current time step
+
1408  int cTS = 0;
+
1409 
+
1410  std::array<double,3> timeP;
1411 
-
1412  /// @brief Current equation degrees of freedom
-
1413  int dof = 0;
+
1412  /// @brief Starting time step
+
1413  int startTS = 0;
1414 
-
1415  /// @brief Global total number of nodes, across all meshes (total) and all
-
1416  /// procs (global)
-
1417  int gtnNo = 0;
-
1418 
-
1419  /// @brief Number of equations
-
1420  int nEq = 0;
+
1415  /// @brief Current equation degrees of freedom
+
1416  int dof = 0;
+
1417 
+
1418  /// @brief Global total number of nodes, across all meshes (total) and all
+
1419  /// procs (global)
+
1420  int gtnNo = 0;
1421 
-
1422  /// @brief Number of faces in the LHS passed to FSILS
-
1423  int nFacesLS = 0;
+
1422  /// @brief Number of equations
+
1423  int nEq = 0;
1424 
-
1425  /// @brief Number of meshes
-
1426  int nMsh = 0;
+
1425  /// @brief Number of faces in the LHS passed to FSILS
+
1426  int nFacesLS = 0;
1427 
-
1428  /// @brief Number of spatial dimensions
-
1429  int nsd = 0;
+
1428  /// @brief Number of meshes
+
1429  int nMsh = 0;
1430 
-
1431  /// @brief Number of time steps
-
1432  int nTS = 0;
+
1431  /// @brief Number of spatial dimensions
+
1432  int nsd = 0;
1433 
-
1434  /// @brief Number of initialization time steps
-
1435  int nITs = 0;
+
1434  /// @brief Number of time steps
+
1435  int nTS = 0;
1436 
-
1437  /// @brief stFiles record length
-
1438  int recLn = 0;
+
1437  /// @brief Number of initialization time steps
+
1438  int nITs = 0;
1439 
-
1440  /// @brief Start saving after this number of time step
-
1441  int saveATS = 0;
+
1440  /// @brief stFiles record length
+
1441  int recLn = 0;
1442 
-
1443  /// @brief Increment in saving solutions
-
1444  int saveIncr = 0;
+
1443  /// @brief Start saving after this number of time step
+
1444  int saveATS = 0;
1445 
-
1446  /// @brief Stamp ID to make sure simulation is compatible with stFiles
-
1447  std::array<int,7> stamp;
+
1446  /// @brief Increment in saving solutions
+
1447  int saveIncr = 0;
1448 
-
1449  /// @brief Increment in saving restart file
-
1450  int stFileIncr = 0;
+
1449  /// @brief Stamp ID to make sure simulation is compatible with stFiles
+
1450  std::array<int,7> stamp;
1451 
-
1452  /// @brief Total number of degrees of freedom per node
-
1453  int tDof = 0;
+
1452  /// @brief Increment in saving restart file
+
1453  int stFileIncr = 0;
1454 
-
1455  /// @brief Total number of nodes (number of nodes on current proc across
-
1456  /// all meshes)
-
1457  int tnNo = 0;
-
1458 
-
1459  /// @brief Restart Time Step
-
1460  int rsTS = 0;
+
1455  /// @brief Total number of degrees of freedom per node
+
1456  int tDof = 0;
+
1457 
+
1458  /// @brief Total number of nodes (number of nodes on current proc across
+
1459  /// all meshes)
+
1460  int tnNo = 0;
1461 
-
1462  /// @brief Number of stress values to be stored
-
1463  int nsymd = 0;
-
1464 
-
1465 
-
1466  //----- double members -----//
-
1467 
-
1468  /// @brief Time step size
-
1469  double dt = 0.0;
+
1462  /// @brief Restart Time Step
+
1463  int rsTS = 0;
+
1464 
+
1465  /// @brief Number of stress values to be stored
+
1466  int nsymd = 0;
+
1467 
+
1468 
+
1469  //----- double members -----//
1470 
-
1471  /// @brief Time step size of the precomputed state-variables
-
1472  double precompDt = 0.0;
+
1471  /// @brief Time step size
+
1472  double dt = 0.0;
1473 
-
1474  /// @brief Time
-
1475  double time = 0.0;
-
1476 
-
1477 
-
1478  //----- string members -----//
-
1479 
-
1480  /// @brief Initialization file path
-
1481  std::string iniFilePath;
+
1474  /// @brief Time step size of the precomputed state-variables
+
1475  double precompDt = 0.0;
+
1476 
+
1477  /// @brief Time
+
1478  double time = 0.0;
+
1479 
+
1480 
+
1481  //----- string members -----//
1482 
-
1483  /// @brief Saved output file name
-
1484  std::string saveName;
+
1483  /// @brief Initialization file path
+
1484  std::string iniFilePath;
1485 
-
1486  /// @brief Restart file name
-
1487  std::string stFileName;
+
1486  /// @brief Saved output file name
+
1487  std::string saveName;
1488 
-
1489  /// @brief Stop_trigger file name
-
1490  std::string stopTrigName;
+
1489  /// @brief Restart file name
+
1490  std::string stFileName;
1491 
-
1492  /// @brief Precomputed state-variable file name
-
1493  std::string precompFileName;
+
1492  /// @brief Stop_trigger file name
+
1493  std::string stopTrigName;
1494 
-
1495  /// @brief Precomputed state-variable field name
-
1496  std::string precompFieldName;
-
1497  // ALLOCATABLE DATA
-
1498 
-
1499  /// @brief Column pointer (for sparse LHS matrix structure)
-
1500  /// Modified in: lhsa()
-
1501  Vector<int> colPtr;
-
1502 
-
1503  /// @brief Domain ID
-
1504  Vector<int> dmnId;
+
1495  /// @brief Precomputed state-variable file name
+
1496  std::string precompFileName;
+
1497 
+
1498  /// @brief Precomputed state-variable field name
+
1499  std::string precompFieldName;
+
1500  // ALLOCATABLE DATA
+
1501 
+
1502  /// @brief Column pointer (for sparse LHS matrix structure)
+
1503  /// Modified in: lhsa()
+
1504  Vector<int> colPtr;
1505 
-
1506  /// @brief Local to global pointer tnNo --> gtnNo
-
1507  Vector<int> ltg;
+
1506  /// @brief Domain ID
+
1507  Vector<int> dmnId;
1508 
-
1509  /// @brief Row pointer (for sparse LHS matrix structure)
-
1510  /// Modified in: lhsa()
-
1511  Vector<int> rowPtr;
-
1512 
-
1513  /// @brief Array that maps global node id to rowN in the matrix
-
1514  /// Modified in: lhsa()
-
1515  Vector<int> idMap;
-
1516 
-
1517  /// @brief Boundary nodes set for CMM initialization and for zeroing-out
-
1518  /// non-wall nodal displacements
-
1519  Vector<int> cmmBdry;
-
1520 
-
1521  /// @brief IB: iblank used for immersed boundaries (1 => solid, 0 => fluid)
-
1522  Vector<int> iblank;
+
1509  /// @brief Local to global pointer tnNo --> gtnNo
+
1510  Vector<int> ltg;
+
1511 
+
1512  /// @brief Row pointer (for sparse LHS matrix structure)
+
1513  /// Modified in: lhsa()
+
1514  Vector<int> rowPtr;
+
1515 
+
1516  /// @brief Array that maps global node id to rowN in the matrix
+
1517  /// Modified in: lhsa()
+
1518  Vector<int> idMap;
+
1519 
+
1520  /// @brief Boundary nodes set for CMM initialization and for zeroing-out
+
1521  /// non-wall nodal displacements
+
1522  Vector<int> cmmBdry;
1523 
-
1524  /// @brief Old time derivative of variables (acceleration)
-
1525  Array<double> Ao;
+
1524  /// @brief IB: iblank used for immersed boundaries (1 => solid, 0 => fluid)
+
1525  Vector<int> iblank;
1526 
-
1527  /// @brief New time derivative of variables
-
1528  Array<double> An;
+
1527  /// @brief Old time derivative of variables (acceleration)
+
1528  Array<double> Ao;
1529 
-
1530  /// @brief Old integrated variables (dissplacement)
-
1531  Array<double> Do;
+
1530  /// @brief New time derivative of variables
+
1531  Array<double> An;
1532 
-
1533  /// @brief New integrated variables
-
1534  Array<double> Dn;
+
1533  /// @brief Old integrated variables (dissplacement)
+
1534  Array<double> Do;
1535 
-
1536  /// @brief Residual vector
-
1537  Array<double> R;
+
1536  /// @brief New integrated variables
+
1537  Array<double> Dn;
1538 
-
1539  /// @brief LHS matrix
-
1540  Array<double> Val;
+
1539  /// @brief Residual vector
+
1540  Array<double> R;
1541 
-
1542  /// @brief Position vector of mesh nodes (in ref config)
-
1543  Array<double> x;
+
1542  /// @brief LHS matrix
+
1543  Array<double> Val;
1544 
-
1545  /// @brief Old variables (velocity)
-
1546  Array<double> Yo;
+
1545  /// @brief Position vector of mesh nodes (in ref config)
+
1546  Array<double> x;
1547 
-
1548  /// @brief New variables
-
1549  Array<double> Yn;
+
1548  /// @brief Old variables (velocity)
+
1549  Array<double> Yo;
1550 
-
1551  /// @brief Body force
-
1552  Array<double> Bf;
-
1553 
-
1554  //-----------------------------------------------------
-
1555  // Additional arrays for velocity-based formulation of
-
1556  // nonlinear solid mechanics.
+
1551  /// @brief New variables
+
1552  Array<double> Yn;
+
1553 
+
1554  /// @brief Body force
+
1555  Array<double> Bf;
+
1556 
1557  //-----------------------------------------------------
-
1558 
-
1559  /// @brief Time derivative of displacement
-
1560  Array<double> Ad;
+
1558  // Additional arrays for velocity-based formulation of
+
1559  // nonlinear solid mechanics.
+
1560  //-----------------------------------------------------
1561 
-
1562  /// @brief Residual of the displacement equation
-
1563  Array<double> Rd;
+
1562  /// @brief Time derivative of displacement
+
1563  Array<double> Ad;
1564 
-
1565  /// @brief LHS matrix for displacement equation
-
1566  Array<double> Kd;
+
1565  /// @brief Residual of the displacement equation
+
1566  Array<double> Rd;
1567 
-
1568  /// @brief Variables for prestress calculations
-
1569  Array<double> pS0;
-
1570  Array<double> pSn;
-
1571  Vector<double> pSa;
-
1572 
-
1573  /// @brief Temporary storage for initializing state variables
-
1574  Vector<double> Pinit;
-
1575  Array<double> Vinit;
-
1576  Array<double> Dinit;
-
1577 
-
1578  /// @brief CMM-variable wall properties: 1-thickness, 2-Elasticity modulus
-
1579  Array<double> varWallProps;
-
1580 
-
1581  //------------------------
-
1582  // DERIVED TYPE VARIABLES
-
1583  //------------------------
-
1584 
-
1585  /// @brief Coupled BCs structures used for multidomain simulations
-
1586  cplBCType cplBC;
+
1568  /// @brief LHS matrix for displacement equation
+
1569  Array<double> Kd;
+
1570 
+
1571  /// @brief Variables for prestress calculations
+
1572  Array<double> pS0;
+
1573  Array<double> pSn;
+
1574  Vector<double> pSa;
+
1575 
+
1576  /// @brief Temporary storage for initializing state variables
+
1577  Vector<double> Pinit;
+
1578  Array<double> Vinit;
+
1579  Array<double> Dinit;
+
1580 
+
1581  /// @brief CMM-variable wall properties: 1-thickness, 2-Elasticity modulus
+
1582  Array<double> varWallProps;
+
1583 
+
1584  //------------------------
+
1585  // DERIVED TYPE VARIABLES
+
1586  //------------------------
1587 
-
1588  /// @brief All data related to equations are stored in this container
-
1589  std::vector<eqType> eq;
+
1588  /// @brief Coupled BCs structures used for multidomain simulations
+
1589  cplBCType cplBC;
1590 
-
1591  /// @brief FSILS data structure to produce LHS sparse matrix
-
1592  fsi_linear_solver::FSILS_lhsType lhs;
+
1591  /// @brief All data related to equations are stored in this container
+
1592  std::vector<eqType> eq;
1593 
-
1594  /// @brief All the meshes are stored in this variable
-
1595  std::vector<mshType> msh;
+
1594  /// @brief FSILS data structure to produce LHS sparse matrix
+
1595  fsi_linear_solver::FSILS_lhsType lhs;
1596 
-
1597  /// @brief Input/output to the screen is handled by this structure
-
1598  chnlType std, err, wrn, dbg;
+
1597  /// @brief All the meshes are stored in this variable
+
1598  std::vector<mshType> msh;
1599 
-
1600  /// @brief To group above channels
-
1601  ioType io;
+
1600  /// @brief Input/output to the screen is handled by this structure
+
1601  chnlType std, err, wrn, dbg;
1602 
-
1603  /// @brief The general communicator
-
1604  cmType cm;
+
1603  /// @brief To group above channels
+
1604  ioType io;
1605 
-
1606  /// @brief Remesher type
-
1607  rmshType rmsh;
+
1606  /// @brief The general communicator
+
1607  cmType cm;
1608 
-
1609  /// @brief Contact model type
-
1610  cntctModelType cntctM;
+
1609  /// @brief Remesher type
+
1610  rmshType rmsh;
1611 
-
1612  /// @brief IB: Immersed boundary data structure
-
1613  ibType ib;
-
1614 
-
1615  bool debug_active = false;
-
1616 
-
1617  Timer timer;
-
1618 };
+
1612  /// @brief Contact model type
+
1613  cntctModelType cntctM;
+
1614 
+
1615  /// @brief IB: Immersed boundary data structure
+
1616  ibType ib;
+
1617 
+
1618  bool debug_active = false;
1619 
-
1620 #endif
-
1621 
+
1620  Timer timer;
+
1621 };
+
1622 
+
1623 #endif
+
1624 
Array3< double >
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
-
ComMod::stopTrigName
std::string stopTrigName
Stop_trigger file name.
Definition: ComMod.h:1490
-
ComMod::ib
ibType ib
IB: Immersed boundary data structure.
Definition: ComMod.h:1613
-
ComMod::stFileIncr
int stFileIncr
Increment in saving restart file.
Definition: ComMod.h:1450
-
ComMod::nITs
int nITs
Number of initialization time steps.
Definition: ComMod.h:1435
-
ComMod::ibFlag
bool ibFlag
Whether any Immersed Boundary (IB) treatment is required.
Definition: ComMod.h:1389
-
ComMod::colPtr
Vector< int > colPtr
Column pointer (for sparse LHS matrix structure) Modified in: lhsa()
Definition: ComMod.h:1501
-
ComMod::zeroAve
bool zeroAve
Reset averaging variables from zero.
Definition: ComMod.h:1368
-
ComMod::saveName
std::string saveName
Saved output file name.
Definition: ComMod.h:1484
-
ComMod::nMsh
int nMsh
Number of meshes.
Definition: ComMod.h:1426
-
ComMod::std
chnlType std
Input/output to the screen is handled by this structure.
Definition: ComMod.h:1598
-
ComMod::savedOnce
bool savedOnce
Whether any file being saved.
Definition: ComMod.h:1350
-
ComMod::stFileRepl
bool stFileRepl
Whether to overwrite restart file or not.
Definition: ComMod.h:1359
-
ComMod::varWallProps
Array< double > varWallProps
CMM-variable wall properties: 1-thickness, 2-Elasticity modulus.
Definition: ComMod.h:1579
-
ComMod::x
Array< double > x
Position vector of mesh nodes (in ref config)
Definition: ComMod.h:1543
-
ComMod::cmmVarWall
bool cmmVarWall
Whether variable wall properties are used for CMM.
Definition: ComMod.h:1374
-
ComMod::stamp
std::array< int, 7 > stamp
Stamp ID to make sure simulation is compatible with stFiles.
Definition: ComMod.h:1447
-
ComMod::Ad
Array< double > Ad
Time derivative of displacement.
Definition: ComMod.h:1560
-
ComMod::cTS
int cTS
Current time step.
Definition: ComMod.h:1405
-
ComMod::dof
int dof
Current equation degrees of freedom.
Definition: ComMod.h:1413
-
ComMod::gtnNo
int gtnNo
Global total number of nodes, across all meshes (total) and all procs (global)
Definition: ComMod.h:1417
-
ComMod::stFileName
std::string stFileName
Restart file name.
Definition: ComMod.h:1487
-
ComMod::tnNo
int tnNo
Total number of nodes (number of nodes on current proc across all meshes)
Definition: ComMod.h:1457
-
ComMod::nsd
int nsd
Number of spatial dimensions.
Definition: ComMod.h:1429
-
ComMod::nFacesLS
int nFacesLS
Number of faces in the LHS passed to FSILS.
Definition: ComMod.h:1423
-
ComMod::nsymd
int nsymd
Number of stress values to be stored.
Definition: ComMod.h:1463
-
ComMod::Yn
Array< double > Yn
New variables.
Definition: ComMod.h:1549
-
ComMod::ichckIEN
bool ichckIEN
Check IEN array for initial mesh.
Definition: ComMod.h:1365
-
ComMod::iniFilePath
std::string iniFilePath
Initialization file path.
Definition: ComMod.h:1481
-
ComMod::rowPtr
Vector< int > rowPtr
Row pointer (for sparse LHS matrix structure) Modified in: lhsa()
Definition: ComMod.h:1511
-
ComMod::precompFileName
std::string precompFileName
Precomputed state-variable file name.
Definition: ComMod.h:1493
-
ComMod::cEq
int cEq
Current equation.
Definition: ComMod.h:1402
-
ComMod::cmmBdry
Vector< int > cmmBdry
Boundary nodes set for CMM initialization and for zeroing-out non-wall nodal displacements.
Definition: ComMod.h:1519
-
ComMod::Val
Array< double > Val
LHS matrix.
Definition: ComMod.h:1540
-
ComMod::bin2VTK
bool bin2VTK
Postprocess step - convert bin to vtk.
Definition: ComMod.h:1392
-
ComMod::saveAve
bool saveAve
Whether to averaged results.
Definition: ComMod.h:1344
-
ComMod::saveVTK
bool saveVTK
Whether to save to VTK files.
Definition: ComMod.h:1347
-
ComMod::tDof
int tDof
Total number of degrees of freedom per node.
Definition: ComMod.h:1453
-
ComMod::precompFieldName
std::string precompFieldName
Precomputed state-variable field name.
Definition: ComMod.h:1496
-
ComMod::cmmInit
bool cmmInit
Whether CMM equation is initialized.
Definition: ComMod.h:1371
-
ComMod::Rd
Array< double > Rd
Residual of the displacement equation.
Definition: ComMod.h:1563
-
ComMod::cplBC
cplBCType cplBC
Coupled BCs structures used for multidomain simulations.
Definition: ComMod.h:1586
-
ComMod::time
double time
Time.
Definition: ComMod.h:1475
-
ComMod::Dn
Array< double > Dn
New integrated variables.
Definition: ComMod.h:1534
-
ComMod::pstEq
bool pstEq
Whether PRESTRESS is being solved.
Definition: ComMod.h:1380
-
ComMod::resetSim
bool resetSim
Restart simulation after remeshing.
Definition: ComMod.h:1362
-
ComMod::An
Array< double > An
New time derivative of variables.
Definition: ComMod.h:1528
-
ComMod::dt
double dt
Time step size.
Definition: ComMod.h:1469
-
ComMod::R
Array< double > R
Residual vector.
Definition: ComMod.h:1537
-
ComMod::rmsh
rmshType rmsh
Remesher type.
Definition: ComMod.h:1607
-
ComMod::saveIncr
int saveIncr
Increment in saving solutions.
Definition: ComMod.h:1444
-
ComMod::usePrecomp
bool usePrecomp
Whether to use precomputed state-variable solutions.
Definition: ComMod.h:1395
-
ComMod::io
ioType io
To group above channels.
Definition: ComMod.h:1601
-
ComMod::cntctM
cntctModelType cntctM
Contact model type.
Definition: ComMod.h:1610
-
ComMod::cm
cmType cm
The general communicator.
Definition: ComMod.h:1604
-
ComMod::startTS
int startTS
Starting time step.
Definition: ComMod.h:1410
-
ComMod::idMap
Vector< int > idMap
Array that maps global node id to rowN in the matrix Modified in: lhsa()
Definition: ComMod.h:1515
-
ComMod::stFileFlag
bool stFileFlag
Whether start from beginning or from simulations.
Definition: ComMod.h:1356
-
ComMod::sepOutput
bool sepOutput
Whether to use separator in output.
Definition: ComMod.h:1353
-
ComMod::shlEq
bool shlEq
Whether shell equation is being solved.
Definition: ComMod.h:1377
-
ComMod::eq
std::vector< eqType > eq
All data related to equations are stored in this container.
Definition: ComMod.h:1589
-
ComMod::iCntct
bool iCntct
Whether to detect and apply any contact model.
Definition: ComMod.h:1386
-
ComMod::precompDt
double precompDt
Time step size of the precomputed state-variables.
Definition: ComMod.h:1472
-
ComMod::Do
Array< double > Do
Old integrated variables (dissplacement)
Definition: ComMod.h:1531
-
ComMod::dFlag
bool dFlag
Whether there is a requirement to update mesh and Dn-Do variables.
Definition: ComMod.h:1338
-
ComMod::cDmn
int cDmn
Current domain.
Definition: ComMod.h:1399
-
ComMod::nTS
int nTS
Number of time steps.
Definition: ComMod.h:1432
-
ComMod::Ao
Array< double > Ao
Old time derivative of variables (acceleration)
Definition: ComMod.h:1525
-
ComMod::nEq
int nEq
Number of equations.
Definition: ComMod.h:1420
-
ComMod::iblank
Vector< int > iblank
IB: iblank used for immersed boundaries (1 => solid, 0 => fluid)
Definition: ComMod.h:1522
-
ComMod::Kd
Array< double > Kd
LHS matrix for displacement equation.
Definition: ComMod.h:1566
-
ComMod::msh
std::vector< mshType > msh
All the meshes are stored in this variable.
Definition: ComMod.h:1595
-
ComMod::recLn
int recLn
stFiles record length
Definition: ComMod.h:1438
-
ComMod::rsTS
int rsTS
Restart Time Step.
Definition: ComMod.h:1460
-
ComMod::mvMsh
bool mvMsh
Whether mesh is moving.
Definition: ComMod.h:1341
-
ComMod::Pinit
Vector< double > Pinit
Temporary storage for initializing state variables.
Definition: ComMod.h:1574
-
ComMod::ltg
Vector< int > ltg
Local to global pointer tnNo --> gtnNo.
Definition: ComMod.h:1507
-
ComMod::lhs
fsi_linear_solver::FSILS_lhsType lhs
FSILS data structure to produce LHS sparse matrix.
Definition: ComMod.h:1592
-
ComMod::Yo
Array< double > Yo
Old variables (velocity)
Definition: ComMod.h:1546
-
ComMod::Bf
Array< double > Bf
Body force.
Definition: ComMod.h:1552
-
ComMod::dmnId
Vector< int > dmnId
Domain ID.
Definition: ComMod.h:1504
-
ComMod::pS0
Array< double > pS0
Variables for prestress calculations.
Definition: ComMod.h:1569
-
ComMod::saveATS
int saveATS
Start saving after this number of time step.
Definition: ComMod.h:1441
-
ComMod::sstEq
bool sstEq
Whether velocity-pressure based structural dynamics solver is used.
Definition: ComMod.h:1383
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
+
ComMod::stopTrigName
std::string stopTrigName
Stop_trigger file name.
Definition: ComMod.h:1493
+
ComMod::ib
ibType ib
IB: Immersed boundary data structure.
Definition: ComMod.h:1616
+
ComMod::stFileIncr
int stFileIncr
Increment in saving restart file.
Definition: ComMod.h:1453
+
ComMod::nITs
int nITs
Number of initialization time steps.
Definition: ComMod.h:1438
+
ComMod::ibFlag
bool ibFlag
Whether any Immersed Boundary (IB) treatment is required.
Definition: ComMod.h:1392
+
ComMod::colPtr
Vector< int > colPtr
Column pointer (for sparse LHS matrix structure) Modified in: lhsa()
Definition: ComMod.h:1504
+
ComMod::zeroAve
bool zeroAve
Reset averaging variables from zero.
Definition: ComMod.h:1371
+
ComMod::saveName
std::string saveName
Saved output file name.
Definition: ComMod.h:1487
+
ComMod::nMsh
int nMsh
Number of meshes.
Definition: ComMod.h:1429
+
ComMod::std
chnlType std
Input/output to the screen is handled by this structure.
Definition: ComMod.h:1601
+
ComMod::savedOnce
bool savedOnce
Whether any file being saved.
Definition: ComMod.h:1353
+
ComMod::stFileRepl
bool stFileRepl
Whether to overwrite restart file or not.
Definition: ComMod.h:1362
+
ComMod::varWallProps
Array< double > varWallProps
CMM-variable wall properties: 1-thickness, 2-Elasticity modulus.
Definition: ComMod.h:1582
+
ComMod::x
Array< double > x
Position vector of mesh nodes (in ref config)
Definition: ComMod.h:1546
+
ComMod::cmmVarWall
bool cmmVarWall
Whether variable wall properties are used for CMM.
Definition: ComMod.h:1377
+
ComMod::stamp
std::array< int, 7 > stamp
Stamp ID to make sure simulation is compatible with stFiles.
Definition: ComMod.h:1450
+
ComMod::Ad
Array< double > Ad
Time derivative of displacement.
Definition: ComMod.h:1563
+
ComMod::cTS
int cTS
Current time step.
Definition: ComMod.h:1408
+
ComMod::dof
int dof
Current equation degrees of freedom.
Definition: ComMod.h:1416
+
ComMod::gtnNo
int gtnNo
Global total number of nodes, across all meshes (total) and all procs (global)
Definition: ComMod.h:1420
+
ComMod::stFileName
std::string stFileName
Restart file name.
Definition: ComMod.h:1490
+
ComMod::tnNo
int tnNo
Total number of nodes (number of nodes on current proc across all meshes)
Definition: ComMod.h:1460
+
ComMod::nsd
int nsd
Number of spatial dimensions.
Definition: ComMod.h:1432
+
ComMod::nFacesLS
int nFacesLS
Number of faces in the LHS passed to FSILS.
Definition: ComMod.h:1426
+
ComMod::nsymd
int nsymd
Number of stress values to be stored.
Definition: ComMod.h:1466
+
ComMod::Yn
Array< double > Yn
New variables.
Definition: ComMod.h:1552
+
ComMod::ichckIEN
bool ichckIEN
Check IEN array for initial mesh.
Definition: ComMod.h:1368
+
ComMod::iniFilePath
std::string iniFilePath
Initialization file path.
Definition: ComMod.h:1484
+
ComMod::rowPtr
Vector< int > rowPtr
Row pointer (for sparse LHS matrix structure) Modified in: lhsa()
Definition: ComMod.h:1514
+
ComMod::precompFileName
std::string precompFileName
Precomputed state-variable file name.
Definition: ComMod.h:1496
+
ComMod::cEq
int cEq
Current equation.
Definition: ComMod.h:1405
+
ComMod::cmmBdry
Vector< int > cmmBdry
Boundary nodes set for CMM initialization and for zeroing-out non-wall nodal displacements.
Definition: ComMod.h:1522
+
ComMod::Val
Array< double > Val
LHS matrix.
Definition: ComMod.h:1543
+
ComMod::bin2VTK
bool bin2VTK
Postprocess step - convert bin to vtk.
Definition: ComMod.h:1395
+
ComMod::saveAve
bool saveAve
Whether to averaged results.
Definition: ComMod.h:1347
+
ComMod::saveVTK
bool saveVTK
Whether to save to VTK files.
Definition: ComMod.h:1350
+
ComMod::tDof
int tDof
Total number of degrees of freedom per node.
Definition: ComMod.h:1456
+
ComMod::precompFieldName
std::string precompFieldName
Precomputed state-variable field name.
Definition: ComMod.h:1499
+
ComMod::cmmInit
bool cmmInit
Whether CMM equation is initialized.
Definition: ComMod.h:1374
+
ComMod::Rd
Array< double > Rd
Residual of the displacement equation.
Definition: ComMod.h:1566
+
ComMod::cplBC
cplBCType cplBC
Coupled BCs structures used for multidomain simulations.
Definition: ComMod.h:1589
+
ComMod::time
double time
Time.
Definition: ComMod.h:1478
+
ComMod::Dn
Array< double > Dn
New integrated variables.
Definition: ComMod.h:1537
+
ComMod::pstEq
bool pstEq
Whether PRESTRESS is being solved.
Definition: ComMod.h:1383
+
ComMod::resetSim
bool resetSim
Restart simulation after remeshing.
Definition: ComMod.h:1365
+
ComMod::An
Array< double > An
New time derivative of variables.
Definition: ComMod.h:1531
+
ComMod::dt
double dt
Time step size.
Definition: ComMod.h:1472
+
ComMod::R
Array< double > R
Residual vector.
Definition: ComMod.h:1540
+
ComMod::rmsh
rmshType rmsh
Remesher type.
Definition: ComMod.h:1610
+
ComMod::saveIncr
int saveIncr
Increment in saving solutions.
Definition: ComMod.h:1447
+
ComMod::usePrecomp
bool usePrecomp
Whether to use precomputed state-variable solutions.
Definition: ComMod.h:1398
+
ComMod::io
ioType io
To group above channels.
Definition: ComMod.h:1604
+
ComMod::cntctM
cntctModelType cntctM
Contact model type.
Definition: ComMod.h:1613
+
ComMod::cm
cmType cm
The general communicator.
Definition: ComMod.h:1607
+
ComMod::startTS
int startTS
Starting time step.
Definition: ComMod.h:1413
+
ComMod::idMap
Vector< int > idMap
Array that maps global node id to rowN in the matrix Modified in: lhsa()
Definition: ComMod.h:1518
+
ComMod::stFileFlag
bool stFileFlag
Whether start from beginning or from simulations.
Definition: ComMod.h:1359
+
ComMod::sepOutput
bool sepOutput
Whether to use separator in output.
Definition: ComMod.h:1356
+
ComMod::shlEq
bool shlEq
Whether shell equation is being solved.
Definition: ComMod.h:1380
+
ComMod::eq
std::vector< eqType > eq
All data related to equations are stored in this container.
Definition: ComMod.h:1592
+
ComMod::iCntct
bool iCntct
Whether to detect and apply any contact model.
Definition: ComMod.h:1389
+
ComMod::precompDt
double precompDt
Time step size of the precomputed state-variables.
Definition: ComMod.h:1475
+
ComMod::Do
Array< double > Do
Old integrated variables (dissplacement)
Definition: ComMod.h:1534
+
ComMod::dFlag
bool dFlag
Whether there is a requirement to update mesh and Dn-Do variables.
Definition: ComMod.h:1341
+
ComMod::cDmn
int cDmn
Current domain.
Definition: ComMod.h:1402
+
ComMod::nTS
int nTS
Number of time steps.
Definition: ComMod.h:1435
+
ComMod::Ao
Array< double > Ao
Old time derivative of variables (acceleration)
Definition: ComMod.h:1528
+
ComMod::nEq
int nEq
Number of equations.
Definition: ComMod.h:1423
+
ComMod::iblank
Vector< int > iblank
IB: iblank used for immersed boundaries (1 => solid, 0 => fluid)
Definition: ComMod.h:1525
+
ComMod::Kd
Array< double > Kd
LHS matrix for displacement equation.
Definition: ComMod.h:1569
+
ComMod::msh
std::vector< mshType > msh
All the meshes are stored in this variable.
Definition: ComMod.h:1598
+
ComMod::recLn
int recLn
stFiles record length
Definition: ComMod.h:1441
+
ComMod::rsTS
int rsTS
Restart Time Step.
Definition: ComMod.h:1463
+
ComMod::mvMsh
bool mvMsh
Whether mesh is moving.
Definition: ComMod.h:1344
+
ComMod::Pinit
Vector< double > Pinit
Temporary storage for initializing state variables.
Definition: ComMod.h:1577
+
ComMod::ltg
Vector< int > ltg
Local to global pointer tnNo --> gtnNo.
Definition: ComMod.h:1510
+
ComMod::lhs
fsi_linear_solver::FSILS_lhsType lhs
FSILS data structure to produce LHS sparse matrix.
Definition: ComMod.h:1595
+
ComMod::Yo
Array< double > Yo
Old variables (velocity)
Definition: ComMod.h:1549
+
ComMod::Bf
Array< double > Bf
Body force.
Definition: ComMod.h:1555
+
ComMod::dmnId
Vector< int > dmnId
Domain ID.
Definition: ComMod.h:1507
+
ComMod::pS0
Array< double > pS0
Variables for prestress calculations.
Definition: ComMod.h:1572
+
ComMod::saveATS
int saveATS
Start saving after this number of time step.
Definition: ComMod.h:1444
+
ComMod::sstEq
bool sstEq
Whether velocity-pressure based structural dynamics solver is used.
Definition: ComMod.h:1386
LinearAlgebra
The LinearAlgebra class provides an abstract interface to linear algebra frameworks: FSILS,...
Definition: LinearAlgebra.h:40
MBType
Moving boundary data structure (used for general BC)
Definition: ComMod.h:100
Timer
Keep track of time.
Definition: Timer.h:40
Vector< double >
-
adjType
Mesh adjacency (neighboring element for each element)
Definition: ComMod.h:464
+
adjType
Mesh adjacency (neighboring element for each element)
Definition: ComMod.h:467
bcType
Boundary condition data type.
Definition: ComMod.h:144
bfType
Definition: ComMod.h:297
bsType
Class storing data for B-Splines.
Definition: ComMod.h:222
cepModelType
Cardiac electrophysiology model type.
Definition: CepMod.h:158
chnlType
Channel type, used in I/O.
Definition: ChnlMod.h:46
cmType
The cmType class stores data and defines methods used for mpi communication.
Definition: CmMod.h:82
-
cntctModelType
Contact model type.
Definition: ComMod.h:693
-
cplBCType
For coupled 0D-3D problems.
Definition: ComMod.h:751
-
cplBCType::schm
consts::CplBCType schm
Implicit/Explicit/Semi-implicit schemes.
Definition: ComMod.h:776
-
cplBCType::nX
int nX
Number of unknowns in the 0D domain.
Definition: ComMod.h:770
-
cplBCType::nFa
int nFa
Number of coupled faces.
Definition: ComMod.h:767
-
cplBCType::xo
Vector< double > xo
Old time step unknowns in the 0D domain.
Definition: ComMod.h:794
-
cplBCType::useGenBC
bool useGenBC
Whether to use genBC.
Definition: ComMod.h:758
-
cplBCType::binPath
std::string binPath
Path to the 0D code binary file.
Definition: ComMod.h:780
-
cplBCType::saveName
std::string saveName
The name of history file containing "X".
Definition: ComMod.h:787
-
cplBCType::commuName
std::string commuName
File name for communication between 0D and 3D.
Definition: ComMod.h:783
-
cplBCType::coupled
bool coupled
Is multi-domain active.
Definition: ComMod.h:755
-
cplBCType::fa
std::vector< cplFaceType > fa
Data structure used for communicating with 0D code.
Definition: ComMod.h:800
-
cplBCType::xp
Vector< double > xp
Output variables to be printed.
Definition: ComMod.h:797
-
cplBCType::xn
Vector< double > xn
New time step unknowns in the 0D domain.
Definition: ComMod.h:791
-
cplBCType::nXp
int nXp
Number of output variables addition to nX.
Definition: ComMod.h:773
-
cplFaceType
Definition: ComMod.h:715
-
dataType
This type will be used to write data in the VTK files.
Definition: ComMod.h:1134
-
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:429
-
eqType
Equation type.
Definition: ComMod.h:997
-
eqType::linear_algebra
LinearAlgebra * linear_algebra
Interface to a numerical linear algebra library.
Definition: ComMod.h:1104
-
eqType::roInf
double roInf
Definition: ComMod.h:1082
-
eqType::maxItr
int maxItr
Maximum iteration for this eq.
Definition: ComMod.h:1028
-
eqType::s
int s
Pointer to start of unknown Yo(:,s:e)
Definition: ComMod.h:1022
-
eqType::nDmnIB
int nDmnIB
IB: Number of immersed domains.
Definition: ComMod.h:1043
-
eqType::coupled
bool coupled
Should be satisfied in a coupled/uncoupled fashion.
Definition: ComMod.h:1003
-
eqType::ok
bool ok
Satisfied/not satisfied.
Definition: ComMod.h:1007
-
eqType::nBcIB
int nBcIB
Number of BCs on immersed surfaces.
Definition: ComMod.h:1049
-
eqType::sym
std::string sym
Equation symbol.
Definition: ComMod.h:1088
-
eqType::assmTLS
bool assmTLS
Use C++ Trilinos framework for assembly and for linear solvers.
Definition: ComMod.h:1013
-
eqType::ls
lsType ls
type of linear solver
Definition: ComMod.h:1092
-
eqType::outIB
std::vector< outputType > outIB
IB: Outputs.
Definition: ComMod.h:1125
-
eqType::tol
double tol
Accepted relative tolerance.
Definition: ComMod.h:1085
-
eqType::useTLS
bool useTLS
Use C++ Trilinos framework for the linear solvers.
Definition: ComMod.h:1010
-
eqType::itr
int itr
Number of performed iterations.
Definition: ComMod.h:1025
-
eqType::gam
double gam
Definition: ComMod.h:1073
-
eqType::nBc
int nBc
Number of BCs.
Definition: ComMod.h:1046
-
eqType::e
int e
Pointer to end of unknown Yo(:,s:e)
Definition: ComMod.h:1019
-
eqType::dmn
std::vector< dmnType > dmn
domains that this equation must be solved
Definition: ComMod.h:1116
-
eqType::linear_algebra_preconditioner
consts::PreconditionerType linear_algebra_preconditioner
The type of preconditioner used by the interface to a numerical linear algebra library.
Definition: ComMod.h:1101
-
eqType::nOutIB
int nOutIB
IB: Number of possible outputs.
Definition: ComMod.h:1037
-
eqType::am
double am
Definition: ComMod.h:1067
-
eqType::iNorm
double iNorm
Initial norm of residual.
Definition: ComMod.h:1076
-
eqType::linear_algebra_assembly_type
consts::LinearAlgebraType linear_algebra_assembly_type
The type of assembly interface to a numerical linear algebra library.
Definition: ComMod.h:1098
-
eqType::linear_algebra_type
consts::LinearAlgebraType linear_algebra_type
The type of interface to a numerical linear algebra library.
Definition: ComMod.h:1095
-
eqType::bf
std::vector< bfType > bf
Body force associated with this equation.
Definition: ComMod.h:1128
-
eqType::pNorm
double pNorm
First iteration norm.
Definition: ComMod.h:1079
-
eqType::af
double af
Definition: ComMod.h:1060
-
eqType::nBf
int nBf
Number of BFs.
Definition: ComMod.h:1052
-
eqType::nDmn
int nDmn
Number of domains.
Definition: ComMod.h:1040
-
eqType::nOutput
int nOutput
Number of possible outputs.
Definition: ComMod.h:1034
-
eqType::dmnIB
std::vector< dmnType > dmnIB
IB: immersed domains that this equation must be solved.
Definition: ComMod.h:1119
-
eqType::bc
std::vector< bcType > bc
BCs associated with this equation;.
Definition: ComMod.h:1110
-
eqType::bcIB
std::vector< bcType > bcIB
IB: BCs associated with this equation on immersed surfaces.
Definition: ComMod.h:1113
-
eqType::dof
int dof
Degrees of freedom.
Definition: ComMod.h:1016
-
eqType::FSILS
fsi_linear_solver::FSILS_lsType FSILS
FSILS type of linear solver.
Definition: ComMod.h:1107
-
eqType::phys
consts::EquationType phys
Type of equation fluid/heatF/heatS/lElas/FSI.
Definition: ComMod.h:1055
-
eqType::output
std::vector< outputType > output
Outputs.
Definition: ComMod.h:1122
-
eqType::beta
double beta
Definition: ComMod.h:1070
-
eqType::minItr
int minItr
Minimum iteration for this eq.
Definition: ComMod.h:1031
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
+
cntctModelType
Contact model type.
Definition: ComMod.h:696
+
cplBCType
For coupled 0D-3D problems.
Definition: ComMod.h:754
+
cplBCType::schm
consts::CplBCType schm
Implicit/Explicit/Semi-implicit schemes.
Definition: ComMod.h:779
+
cplBCType::nX
int nX
Number of unknowns in the 0D domain.
Definition: ComMod.h:773
+
cplBCType::nFa
int nFa
Number of coupled faces.
Definition: ComMod.h:770
+
cplBCType::xo
Vector< double > xo
Old time step unknowns in the 0D domain.
Definition: ComMod.h:797
+
cplBCType::useGenBC
bool useGenBC
Whether to use genBC.
Definition: ComMod.h:761
+
cplBCType::binPath
std::string binPath
Path to the 0D code binary file.
Definition: ComMod.h:783
+
cplBCType::saveName
std::string saveName
The name of history file containing "X".
Definition: ComMod.h:790
+
cplBCType::commuName
std::string commuName
File name for communication between 0D and 3D.
Definition: ComMod.h:786
+
cplBCType::coupled
bool coupled
Is multi-domain active.
Definition: ComMod.h:758
+
cplBCType::fa
std::vector< cplFaceType > fa
Data structure used for communicating with 0D code.
Definition: ComMod.h:803
+
cplBCType::xp
Vector< double > xp
Output variables to be printed.
Definition: ComMod.h:800
+
cplBCType::xn
Vector< double > xn
New time step unknowns in the 0D domain.
Definition: ComMod.h:794
+
cplBCType::nXp
int nXp
Number of output variables addition to nX.
Definition: ComMod.h:776
+
cplFaceType
Definition: ComMod.h:718
+
dataType
This type will be used to write data in the VTK files.
Definition: ComMod.h:1137
+
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:432
+
eqType
Equation type.
Definition: ComMod.h:1000
+
eqType::linear_algebra
LinearAlgebra * linear_algebra
Interface to a numerical linear algebra library.
Definition: ComMod.h:1107
+
eqType::roInf
double roInf
Definition: ComMod.h:1085
+
eqType::maxItr
int maxItr
Maximum iteration for this eq.
Definition: ComMod.h:1031
+
eqType::s
int s
Pointer to start of unknown Yo(:,s:e)
Definition: ComMod.h:1025
+
eqType::nDmnIB
int nDmnIB
IB: Number of immersed domains.
Definition: ComMod.h:1046
+
eqType::coupled
bool coupled
Should be satisfied in a coupled/uncoupled fashion.
Definition: ComMod.h:1006
+
eqType::ok
bool ok
Satisfied/not satisfied.
Definition: ComMod.h:1010
+
eqType::nBcIB
int nBcIB
Number of BCs on immersed surfaces.
Definition: ComMod.h:1052
+
eqType::sym
std::string sym
Equation symbol.
Definition: ComMod.h:1091
+
eqType::assmTLS
bool assmTLS
Use C++ Trilinos framework for assembly and for linear solvers.
Definition: ComMod.h:1016
+
eqType::ls
lsType ls
type of linear solver
Definition: ComMod.h:1095
+
eqType::outIB
std::vector< outputType > outIB
IB: Outputs.
Definition: ComMod.h:1128
+
eqType::tol
double tol
Accepted relative tolerance.
Definition: ComMod.h:1088
+
eqType::useTLS
bool useTLS
Use C++ Trilinos framework for the linear solvers.
Definition: ComMod.h:1013
+
eqType::itr
int itr
Number of performed iterations.
Definition: ComMod.h:1028
+
eqType::gam
double gam
Definition: ComMod.h:1076
+
eqType::nBc
int nBc
Number of BCs.
Definition: ComMod.h:1049
+
eqType::e
int e
Pointer to end of unknown Yo(:,s:e)
Definition: ComMod.h:1022
+
eqType::dmn
std::vector< dmnType > dmn
domains that this equation must be solved
Definition: ComMod.h:1119
+
eqType::linear_algebra_preconditioner
consts::PreconditionerType linear_algebra_preconditioner
The type of preconditioner used by the interface to a numerical linear algebra library.
Definition: ComMod.h:1104
+
eqType::nOutIB
int nOutIB
IB: Number of possible outputs.
Definition: ComMod.h:1040
+
eqType::am
double am
Definition: ComMod.h:1070
+
eqType::iNorm
double iNorm
Initial norm of residual.
Definition: ComMod.h:1079
+
eqType::linear_algebra_assembly_type
consts::LinearAlgebraType linear_algebra_assembly_type
The type of assembly interface to a numerical linear algebra library.
Definition: ComMod.h:1101
+
eqType::linear_algebra_type
consts::LinearAlgebraType linear_algebra_type
The type of interface to a numerical linear algebra library.
Definition: ComMod.h:1098
+
eqType::bf
std::vector< bfType > bf
Body force associated with this equation.
Definition: ComMod.h:1131
+
eqType::pNorm
double pNorm
First iteration norm.
Definition: ComMod.h:1082
+
eqType::af
double af
Definition: ComMod.h:1063
+
eqType::nBf
int nBf
Number of BFs.
Definition: ComMod.h:1055
+
eqType::nDmn
int nDmn
Number of domains.
Definition: ComMod.h:1043
+
eqType::nOutput
int nOutput
Number of possible outputs.
Definition: ComMod.h:1037
+
eqType::dmnIB
std::vector< dmnType > dmnIB
IB: immersed domains that this equation must be solved.
Definition: ComMod.h:1122
+
eqType::bc
std::vector< bcType > bc
BCs associated with this equation;.
Definition: ComMod.h:1113
+
eqType::bcIB
std::vector< bcType > bcIB
IB: BCs associated with this equation on immersed surfaces.
Definition: ComMod.h:1116
+
eqType::dof
int dof
Degrees of freedom.
Definition: ComMod.h:1019
+
eqType::FSILS
fsi_linear_solver::FSILS_lsType FSILS
FSILS type of linear solver.
Definition: ComMod.h:1110
+
eqType::phys
consts::EquationType phys
Type of equation fluid/heatF/heatS/lElas/FSI.
Definition: ComMod.h:1058
+
eqType::output
std::vector< outputType > output
Outputs.
Definition: ComMod.h:1125
+
eqType::beta
double beta
Definition: ComMod.h:1073
+
eqType::minItr
int minItr
Minimum iteration for this eq.
Definition: ComMod.h:1034
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
faceType::destroy
void destroy()
Free memory and reset some data members.
Definition: ComMod.cpp:138
fcType
Fourier coefficients that are used to specify unsteady BCs.
Definition: ComMod.h:64
fibStrsType
Definition: ComMod.h:327
-
fluidViscModelType
Fluid viscosity model type.
Definition: ComMod.h:390
+
fluidViscModelType
Fluid viscosity model type.
Definition: ComMod.h:393
fsType
Function spaces (basis) type.
Definition: ComMod.h:249
fsType::destroy
void destroy()
SUBROUTINE DESTROYFS(fs)
Definition: ComMod.cpp:175
-
ibCommType
Definition: ComMod.h:1213
-
ibCommType::nG
Vector< int > nG
Num traces (Gauss points) local to each process.
Definition: ComMod.h:1222
-
ibCommType::n
Vector< int > n
Num traces (nodes) local to each process.
Definition: ComMod.h:1216
-
ibCommType::gE
Vector< int > gE
Pointer to global trace (Gauss point) stacked contiguously.
Definition: ComMod.h:1225
-
ibCommType::gN
Vector< int > gN
Pointer to global trace (node num) stacked contiguously.
Definition: ComMod.h:1219
-
ibType
Immersed Boundary (IB) data type.
Definition: ComMod.h:1232
-
ibType::x
Array< double > x
IB position coordinates.
Definition: ComMod.h:1276
-
ibType::Aun
Array< double > Aun
Time derivative of displacement (new)
Definition: ComMod.h:1285
-
ibType::cpld
int cpld
IB coupling.
Definition: ComMod.h:1244
-
ibType::Ku
Array< double > Ku
LHS tangent matrix for displacement.
Definition: ComMod.h:1315
-
ibType::tnNo
int tnNo
Total number of IB nodes.
Definition: ComMod.h:1258
-
ibType::Un
Array< double > Un
Displacement (projected on background mesh, new, n+af)
Definition: ComMod.h:1303
-
ibType::cEq
int cEq
Current equation.
Definition: ComMod.h:1255
-
ibType::R
Array< double > R
Residual (FSI force)
Definition: ComMod.h:1306
-
ibType::intrp
int intrp
IB interpolation method.
Definition: ComMod.h:1248
-
ibType::Uo
Array< double > Uo
Displacement (projected on background mesh, old)
Definition: ComMod.h:1300
-
ibType::Yb
Array< double > Yb
Velocity (new)
Definition: ComMod.h:1279
-
ibType::Ubn
Array< double > Ubn
Displacement (new)
Definition: ComMod.h:1294
-
ibType::cDmn
int cDmn
Current IB domain ID.
Definition: ComMod.h:1252
-
ibType::callD
double callD[4]
IB call duration (1: total time; 2: update; 3,4: communication)
Definition: ComMod.h:1264
-
ibType::cm
ibCommType cm
IB communicator.
Definition: ComMod.h:1321
-
ibType::rowPtr
Vector< int > rowPtr
Row pointer (for sparse LHS matrix storage)
Definition: ComMod.h:1270
-
ibType::Rub
Array< double > Rub
Residual (displacement, IB mesh)
Definition: ComMod.h:1312
-
ibType::savedOnce
bool savedOnce
Whether any file being saved.
Definition: ComMod.h:1236
-
ibType::dmnID
Vector< int > dmnID
IB Domain ID.
Definition: ComMod.h:1267
-
ibType::Auo
Array< double > Auo
Time derivative of displacement (old)
Definition: ComMod.h:1282
-
ibType::Ubk
Array< double > Ubk
Displacement (n+af)
Definition: ComMod.h:1297
-
ibType::nMsh
int nMsh
Number of IB meshes.
Definition: ComMod.h:1261
-
ibType::mthd
int mthd
IB method.
Definition: ComMod.h:1240
-
ibType::msh
std::vector< mshType > msh
DERIVED class VARIABLES IB meshes;.
Definition: ComMod.h:1318
-
ibType::Ubo
Array< double > Ubo
Displacement (old)
Definition: ComMod.h:1291
-
ibType::colPtr
Vector< int > colPtr
Column pointer (for sparse LHS matrix storage)
Definition: ComMod.h:1273
-
ibType::Ru
Array< double > Ru
Residual (displacement, background mesh)
Definition: ComMod.h:1309
-
ibType::Auk
Array< double > Auk
Time derivative of displacement (n+am)
Definition: ComMod.h:1288
+
ibCommType
Definition: ComMod.h:1216
+
ibCommType::nG
Vector< int > nG
Num traces (Gauss points) local to each process.
Definition: ComMod.h:1225
+
ibCommType::n
Vector< int > n
Num traces (nodes) local to each process.
Definition: ComMod.h:1219
+
ibCommType::gE
Vector< int > gE
Pointer to global trace (Gauss point) stacked contiguously.
Definition: ComMod.h:1228
+
ibCommType::gN
Vector< int > gN
Pointer to global trace (node num) stacked contiguously.
Definition: ComMod.h:1222
+
ibType
Immersed Boundary (IB) data type.
Definition: ComMod.h:1235
+
ibType::x
Array< double > x
IB position coordinates.
Definition: ComMod.h:1279
+
ibType::Aun
Array< double > Aun
Time derivative of displacement (new)
Definition: ComMod.h:1288
+
ibType::cpld
int cpld
IB coupling.
Definition: ComMod.h:1247
+
ibType::Ku
Array< double > Ku
LHS tangent matrix for displacement.
Definition: ComMod.h:1318
+
ibType::tnNo
int tnNo
Total number of IB nodes.
Definition: ComMod.h:1261
+
ibType::Un
Array< double > Un
Displacement (projected on background mesh, new, n+af)
Definition: ComMod.h:1306
+
ibType::cEq
int cEq
Current equation.
Definition: ComMod.h:1258
+
ibType::R
Array< double > R
Residual (FSI force)
Definition: ComMod.h:1309
+
ibType::intrp
int intrp
IB interpolation method.
Definition: ComMod.h:1251
+
ibType::Uo
Array< double > Uo
Displacement (projected on background mesh, old)
Definition: ComMod.h:1303
+
ibType::Yb
Array< double > Yb
Velocity (new)
Definition: ComMod.h:1282
+
ibType::Ubn
Array< double > Ubn
Displacement (new)
Definition: ComMod.h:1297
+
ibType::cDmn
int cDmn
Current IB domain ID.
Definition: ComMod.h:1255
+
ibType::callD
double callD[4]
IB call duration (1: total time; 2: update; 3,4: communication)
Definition: ComMod.h:1267
+
ibType::cm
ibCommType cm
IB communicator.
Definition: ComMod.h:1324
+
ibType::rowPtr
Vector< int > rowPtr
Row pointer (for sparse LHS matrix storage)
Definition: ComMod.h:1273
+
ibType::Rub
Array< double > Rub
Residual (displacement, IB mesh)
Definition: ComMod.h:1315
+
ibType::savedOnce
bool savedOnce
Whether any file being saved.
Definition: ComMod.h:1239
+
ibType::dmnID
Vector< int > dmnID
IB Domain ID.
Definition: ComMod.h:1270
+
ibType::Auo
Array< double > Auo
Time derivative of displacement (old)
Definition: ComMod.h:1285
+
ibType::Ubk
Array< double > Ubk
Displacement (n+af)
Definition: ComMod.h:1300
+
ibType::nMsh
int nMsh
Number of IB meshes.
Definition: ComMod.h:1264
+
ibType::mthd
int mthd
IB method.
Definition: ComMod.h:1243
+
ibType::msh
std::vector< mshType > msh
DERIVED class VARIABLES IB meshes;.
Definition: ComMod.h:1321
+
ibType::Ubo
Array< double > Ubo
Displacement (old)
Definition: ComMod.h:1294
+
ibType::colPtr
Vector< int > colPtr
Column pointer (for sparse LHS matrix storage)
Definition: ComMod.h:1276
+
ibType::Ru
Array< double > Ru
Residual (displacement, background mesh)
Definition: ComMod.h:1312
+
ibType::Auk
Array< double > Auk
Time derivative of displacement (n+am)
Definition: ComMod.h:1291
ioType
Only to group four channels, in case I rather have them as one variable.
Definition: ChnlMod.h:77
-
lsType
Linear system of equations solver type.
Definition: ComMod.h:637
-
lsType::absTol
double absTol
Absolute tolerance (IN)
Definition: ComMod.h:668
-
lsType::cN
int cN
Number of |x| norms (OUT)
Definition: ComMod.h:659
-
lsType::cD
int cD
Number of <x.y> dot products (OUT)
Definition: ComMod.h:662
-
lsType::fNorm
double fNorm
Final norm of residual (OUT)
Definition: ComMod.h:677
-
lsType::callD
double callD
Calling duration (OUT)
Definition: ComMod.h:683
-
lsType::reserve
int reserve
Only for data alignment (-)
Definition: ComMod.h:665
-
lsType::suc
bool suc
Successful solving (OUT)
Definition: ComMod.h:644
-
lsType::mItr
int mItr
Maximum iterations (IN)
Definition: ComMod.h:647
-
lsType::LS_type
consts::SolverType LS_type
LS solver (IN)
Definition: ComMod.h:641
-
lsType::itr
int itr
Number of iteration (OUT)
Definition: ComMod.h:653
-
lsType::relTol
double relTol
Relative tolerance (IN)
Definition: ComMod.h:671
-
lsType::dB
double dB
Res. rduction in last itr. (OUT)
Definition: ComMod.h:680
-
lsType::sD
int sD
Space dimension (IN)
Definition: ComMod.h:650
-
lsType::cM
int cM
Number of Ax multiple (OUT)
Definition: ComMod.h:656
-
lsType::iNorm
double iNorm
Initial norm of residual (OUT)
Definition: ComMod.h:674
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
-
mshType::nNo
int nNo
Number of nodes (control points) for 2D elements?
Definition: ComMod.h:868
-
mshType::w
Vector< double > w
Gauss weights.
Definition: ComMod.h:928
-
mshType::ordering
std::vector< std::vector< int > > ordering
@breif ordering: node ordering for boundaries
Definition: ComMod.h:886
-
mshType::N
Array< double > N
Parent shape function.
Definition: ComMod.h:940
-
mshType::trc
traceType trc
IB: tracers.
Definition: ComMod.h:983
-
mshType::Ys
Array3< double > Ys
Solution field (displacement, velocity, pressure, etc.) for a known, potentially time-varying,...
Definition: ComMod.h:962
-
mshType::eDist
Vector< int > eDist
Element distribution between processors.
Definition: ComMod.h:889
-
mshType::iGC
Vector< int > iGC
IB: Whether a cell is a ghost cell or not.
Definition: ComMod.h:922
-
mshType::nAdj
adjType nAdj
Mesh nodal adjacency.
Definition: ComMod.h:968
-
mshType::xib
Array< double > xib
Bounds on parameteric coordinates.
Definition: ComMod.h:934
-
mshType::eAdj
adjType eAdj
Mesh element adjacency.
Definition: ComMod.h:971
-
mshType::nG
int nG
Number of Gauss points for integration.
Definition: ComMod.h:865
-
mshType::nFa
int nFa
Number of faces.
Definition: ComMod.h:859
-
mshType::x
Array< double > x
Position coordinates.
Definition: ComMod.h:937
-
mshType::fs
std::vector< fsType > fs
Function spaces (basis)
Definition: ComMod.h:974
-
mshType::Nxx
Array3< double > Nxx
Second derivatives of shape functions - used for shells & IGA davep double Nxx(:,:,...
Definition: ComMod.h:958
-
mshType::gnNo
int gnNo
Global number of nodes (control points)
Definition: ComMod.h:850
-
mshType::dx
double dx
IB: Mesh size parameter.
Definition: ComMod.h:883
-
mshType::lShpF
bool lShpF
Whether the shape function is linear.
Definition: ComMod.h:831
-
mshType::lN
Vector< int > lN
Global to local maping tnNo --> nNo.
Definition: ComMod.h:913
-
mshType::otnIEN
Vector< int > otnIEN
gIEN mapper from old to new
Definition: ComMod.h:907
-
mshType::nFn
int nFn
Number of fiber directions.
Definition: ComMod.h:877
-
mshType::eIEN
Array< int > eIEN
Shells: extended IEN array with neighboring nodes.
Definition: ComMod.h:916
-
mshType::gN
Vector< int > gN
Global nodes maping nNo --> tnNo.
Definition: ComMod.h:895
-
mshType::lFib
bool lFib
Whether the mesh is fibers (Purkinje)
Definition: ComMod.h:837
-
mshType::eNoN
int eNoN
Number of nodes (control points) in a single element.
Definition: ComMod.h:844
-
mshType::scF
double scF
Mesh scale factor.
Definition: ComMod.h:880
-
mshType::eId
Vector< int > eId
Element domain ID number.
Definition: ComMod.h:892
-
mshType::gnEl
int gnEl
Global number of elements (knot spans)
Definition: ComMod.h:847
-
mshType::nSl
int nSl
Number of elements sample points to be outputs (NURBS)
Definition: ComMod.h:871
-
mshType::xi
Array< double > xi
Gauss integration points in parametric space.
Definition: ComMod.h:931
-
mshType::fN
Array< double > fN
Fiber orientations stored at the element level - used for electrophysiology and solid mechanics.
Definition: ComMod.h:950
-
mshType::nFs
int nFs
Number of function spaces.
Definition: ComMod.h:862
-
mshType::sbc
Array< int > sbc
Shells: boundary condition variable.
Definition: ComMod.h:919
-
mshType::lShl
bool lShl
Whether the mesh is shell.
Definition: ComMod.h:834
-
mshType::Nb
Array< double > Nb
Shape function bounds.
Definition: ComMod.h:943
-
mshType::nV
Array< double > nV
Normal vector to each nodal point (for Shells)
Definition: ComMod.h:946
-
mshType::nW
Vector< double > nW
Control points weights (NURBS)
Definition: ComMod.h:925
-
mshType::Nx
Array3< double > Nx
Parent shape functions gradient double Nx(:,:,:)
Definition: ComMod.h:954
-
mshType::fa
std::vector< faceType > fa
Faces are stored in this variable.
Definition: ComMod.h:980
-
mshType::gpN
Vector< int > gpN
GLobal projected nodes mapping projected -> unprojected mapping.
Definition: ComMod.h:898
-
mshType::gIEN
Array< int > gIEN
Global connectivity array mappig eNoN,nEl --> gnNo.
Definition: ComMod.h:901
-
mshType::vtkType
int vtkType
The element type recognized by VTK format.
Definition: ComMod.h:874
-
mshType::nEl
int nEl
Number of elements (knot spans)
Definition: ComMod.h:856
-
mshType::eType
consts::ElementType eType
Element type.
Definition: ComMod.h:840
-
mshType::nEf
int nEf
Number of element face. Used for reading Gambit mesh files.
Definition: ComMod.h:853
-
mshType::name
std::string name
Mesh Name.
Definition: ComMod.h:965
-
mshType::bs
std::vector< bsType > bs
BSpline in different directions (NURBS)
Definition: ComMod.h:977
-
mshType::IEN
Array< int > IEN
The connectivity array mapping eNoN,nEl --> nNo.
Definition: ComMod.h:904
-
mshType::qmTET4
double qmTET4
TET4 quadrature modifier.
Definition: ComMod.h:986
-
mshType::INN
Array< int > INN
Local knot pointer (NURBS)
Definition: ComMod.h:910
-
outputType
Declared type for outputed variables.
Definition: ComMod.h:614
+
lsType
Linear system of equations solver type.
Definition: ComMod.h:640
+
lsType::absTol
double absTol
Absolute tolerance (IN)
Definition: ComMod.h:671
+
lsType::cN
int cN
Number of |x| norms (OUT)
Definition: ComMod.h:662
+
lsType::cD
int cD
Number of <x.y> dot products (OUT)
Definition: ComMod.h:665
+
lsType::fNorm
double fNorm
Final norm of residual (OUT)
Definition: ComMod.h:680
+
lsType::callD
double callD
Calling duration (OUT)
Definition: ComMod.h:686
+
lsType::reserve
int reserve
Only for data alignment (-)
Definition: ComMod.h:668
+
lsType::suc
bool suc
Successful solving (OUT)
Definition: ComMod.h:647
+
lsType::mItr
int mItr
Maximum iterations (IN)
Definition: ComMod.h:650
+
lsType::LS_type
consts::SolverType LS_type
LS solver (IN)
Definition: ComMod.h:644
+
lsType::itr
int itr
Number of iteration (OUT)
Definition: ComMod.h:656
+
lsType::relTol
double relTol
Relative tolerance (IN)
Definition: ComMod.h:674
+
lsType::dB
double dB
Res. rduction in last itr. (OUT)
Definition: ComMod.h:683
+
lsType::sD
int sD
Space dimension (IN)
Definition: ComMod.h:653
+
lsType::cM
int cM
Number of Ax multiple (OUT)
Definition: ComMod.h:659
+
lsType::iNorm
double iNorm
Initial norm of residual (OUT)
Definition: ComMod.h:677
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
+
mshType::nNo
int nNo
Number of nodes (control points) for 2D elements?
Definition: ComMod.h:871
+
mshType::w
Vector< double > w
Gauss weights.
Definition: ComMod.h:931
+
mshType::ordering
std::vector< std::vector< int > > ordering
@breif ordering: node ordering for boundaries
Definition: ComMod.h:889
+
mshType::N
Array< double > N
Parent shape function.
Definition: ComMod.h:943
+
mshType::trc
traceType trc
IB: tracers.
Definition: ComMod.h:986
+
mshType::Ys
Array3< double > Ys
Solution field (displacement, velocity, pressure, etc.) for a known, potentially time-varying,...
Definition: ComMod.h:965
+
mshType::eDist
Vector< int > eDist
Element distribution between processors.
Definition: ComMod.h:892
+
mshType::iGC
Vector< int > iGC
IB: Whether a cell is a ghost cell or not.
Definition: ComMod.h:925
+
mshType::nAdj
adjType nAdj
Mesh nodal adjacency.
Definition: ComMod.h:971
+
mshType::xib
Array< double > xib
Bounds on parameteric coordinates.
Definition: ComMod.h:937
+
mshType::eAdj
adjType eAdj
Mesh element adjacency.
Definition: ComMod.h:974
+
mshType::nG
int nG
Number of Gauss points for integration.
Definition: ComMod.h:868
+
mshType::nFa
int nFa
Number of faces.
Definition: ComMod.h:862
+
mshType::x
Array< double > x
Position coordinates.
Definition: ComMod.h:940
+
mshType::fs
std::vector< fsType > fs
Function spaces (basis)
Definition: ComMod.h:977
+
mshType::Nxx
Array3< double > Nxx
Second derivatives of shape functions - used for shells & IGA davep double Nxx(:,:,...
Definition: ComMod.h:961
+
mshType::gnNo
int gnNo
Global number of nodes (control points)
Definition: ComMod.h:853
+
mshType::dx
double dx
IB: Mesh size parameter.
Definition: ComMod.h:886
+
mshType::lShpF
bool lShpF
Whether the shape function is linear.
Definition: ComMod.h:834
+
mshType::lN
Vector< int > lN
Global to local maping tnNo --> nNo.
Definition: ComMod.h:916
+
mshType::otnIEN
Vector< int > otnIEN
gIEN mapper from old to new
Definition: ComMod.h:910
+
mshType::nFn
int nFn
Number of fiber directions.
Definition: ComMod.h:880
+
mshType::eIEN
Array< int > eIEN
Shells: extended IEN array with neighboring nodes.
Definition: ComMod.h:919
+
mshType::gN
Vector< int > gN
Global nodes maping nNo --> tnNo.
Definition: ComMod.h:898
+
mshType::lFib
bool lFib
Whether the mesh is fibers (Purkinje)
Definition: ComMod.h:840
+
mshType::eNoN
int eNoN
Number of nodes (control points) in a single element.
Definition: ComMod.h:847
+
mshType::scF
double scF
Mesh scale factor.
Definition: ComMod.h:883
+
mshType::eId
Vector< int > eId
Element domain ID number.
Definition: ComMod.h:895
+
mshType::gnEl
int gnEl
Global number of elements (knot spans)
Definition: ComMod.h:850
+
mshType::nSl
int nSl
Number of elements sample points to be outputs (NURBS)
Definition: ComMod.h:874
+
mshType::xi
Array< double > xi
Gauss integration points in parametric space.
Definition: ComMod.h:934
+
mshType::fN
Array< double > fN
Fiber orientations stored at the element level - used for electrophysiology and solid mechanics.
Definition: ComMod.h:953
+
mshType::nFs
int nFs
Number of function spaces.
Definition: ComMod.h:865
+
mshType::sbc
Array< int > sbc
Shells: boundary condition variable.
Definition: ComMod.h:922
+
mshType::lShl
bool lShl
Whether the mesh is shell.
Definition: ComMod.h:837
+
mshType::Nb
Array< double > Nb
Shape function bounds.
Definition: ComMod.h:946
+
mshType::nV
Array< double > nV
Normal vector to each nodal point (for Shells)
Definition: ComMod.h:949
+
mshType::nW
Vector< double > nW
Control points weights (NURBS)
Definition: ComMod.h:928
+
mshType::Nx
Array3< double > Nx
Parent shape functions gradient double Nx(:,:,:)
Definition: ComMod.h:957
+
mshType::fa
std::vector< faceType > fa
Faces are stored in this variable.
Definition: ComMod.h:983
+
mshType::gpN
Vector< int > gpN
GLobal projected nodes mapping projected -> unprojected mapping.
Definition: ComMod.h:901
+
mshType::gIEN
Array< int > gIEN
Global connectivity array mappig eNoN,nEl --> gnNo.
Definition: ComMod.h:904
+
mshType::vtkType
int vtkType
The element type recognized by VTK format.
Definition: ComMod.h:877
+
mshType::nEl
int nEl
Number of elements (knot spans)
Definition: ComMod.h:859
+
mshType::eType
consts::ElementType eType
Element type.
Definition: ComMod.h:843
+
mshType::nEf
int nEf
Number of element face. Used for reading Gambit mesh files.
Definition: ComMod.h:856
+
mshType::name
std::string name
Mesh Name.
Definition: ComMod.h:968
+
mshType::bs
std::vector< bsType > bs
BSpline in different directions (NURBS)
Definition: ComMod.h:980
+
mshType::IEN
Array< int > IEN
The connectivity array mapping eNoN,nEl --> nNo.
Definition: ComMod.h:907
+
mshType::qmTET4
double qmTET4
TET4 quadrature modifier.
Definition: ComMod.h:989
+
mshType::INN
Array< int > INN
Local knot pointer (NURBS)
Definition: ComMod.h:913
+
outputType
Declared type for outputed variables.
Definition: ComMod.h:617
rcrType
Definition: ComMod.h:122
-
rmshType
Definition: ComMod.h:1164
-
rmshType::iNorm
Vector< double > iNorm
Initial norm of an equation.
Definition: ComMod.h:1201
-
rmshType::rTS
int rTS
Time step from which remeshing is done.
Definition: ComMod.h:1179
-
rmshType::freq
int freq
Time step frequency for forced remeshing.
Definition: ComMod.h:1188
-
rmshType::cpVar
int cpVar
Time step freq for saving data.
Definition: ComMod.h:1182
-
rmshType::A0
Array< double > A0
Copy of solution variables where remeshing starts.
Definition: ComMod.h:1204
-
rmshType::cntr
int cntr
Counter to track number of remesh done.
Definition: ComMod.h:1176
-
rmshType::flag
std::vector< bool > flag
Flag is set if remeshing is required for each mesh.
Definition: ComMod.h:1209
-
rmshType::time
double time
Time where remeshing starts.
Definition: ComMod.h:1191
-
rmshType::method
consts::MeshGeneratorType method
Method for remeshing: 1-TetGen, 2-MeshSim.
Definition: ComMod.h:1173
-
rmshType::minDihedAng
double minDihedAng
Mesh quality parameters.
Definition: ComMod.h:1194
-
rmshType::fTS
int fTS
Time step at which forced remeshing is done.
Definition: ComMod.h:1185
-
rmshType::maxEdgeSize
Vector< double > maxEdgeSize
Edge size of mesh.
Definition: ComMod.h:1198
-
rmshType::isReqd
bool isReqd
Whether remesh is required for problem or not.
Definition: ComMod.h:1170
-
solidViscModelType
Fluid viscosity model type.
Definition: ComMod.h:415
-
stModelType
Structural domain type.
Definition: ComMod.h:343
-
traceType
Tracer type used for immersed boundaries. Identifies traces of nodes and integration points on backgr...
Definition: ComMod.h:483
+
rmshType
Definition: ComMod.h:1167
+
rmshType::iNorm
Vector< double > iNorm
Initial norm of an equation.
Definition: ComMod.h:1204
+
rmshType::rTS
int rTS
Time step from which remeshing is done.
Definition: ComMod.h:1182
+
rmshType::freq
int freq
Time step frequency for forced remeshing.
Definition: ComMod.h:1191
+
rmshType::cpVar
int cpVar
Time step freq for saving data.
Definition: ComMod.h:1185
+
rmshType::A0
Array< double > A0
Copy of solution variables where remeshing starts.
Definition: ComMod.h:1207
+
rmshType::cntr
int cntr
Counter to track number of remesh done.
Definition: ComMod.h:1179
+
rmshType::flag
std::vector< bool > flag
Flag is set if remeshing is required for each mesh.
Definition: ComMod.h:1212
+
rmshType::time
double time
Time where remeshing starts.
Definition: ComMod.h:1194
+
rmshType::method
consts::MeshGeneratorType method
Method for remeshing: 1-TetGen, 2-MeshSim.
Definition: ComMod.h:1176
+
rmshType::minDihedAng
double minDihedAng
Mesh quality parameters.
Definition: ComMod.h:1197
+
rmshType::fTS
int fTS
Time step at which forced remeshing is done.
Definition: ComMod.h:1188
+
rmshType::maxEdgeSize
Vector< double > maxEdgeSize
Edge size of mesh.
Definition: ComMod.h:1201
+
rmshType::isReqd
bool isReqd
Whether remesh is required for problem or not.
Definition: ComMod.h:1173
+
solidViscModelType
Fluid viscosity model type.
Definition: ComMod.h:418
+
stModelType
Structural domain type.
Definition: ComMod.h:346
+
traceType
Tracer type used for immersed boundaries. Identifies traces of nodes and integration points on backgr...
Definition: ComMod.h:486
diff --git a/_fsils_linear_algebra_8h_source.html b/_fsils_linear_algebra_8h_source.html index 970dbe74..763065a5 100644 --- a/_fsils_linear_algebra_8h_source.html +++ b/_fsils_linear_algebra_8h_source.html @@ -131,7 +131,7 @@
59 #endif
60 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
FsilsLinearAlgebra
The FsilsLinearAlgebra class implements the LinearAlgebra interface for the FSILS numerical linear al...
Definition: FsilsLinearAlgebra.h:39
FsilsLinearAlgebra::check_options
virtual void check_options(const consts::PreconditionerType prec_cond_type, const consts::LinearAlgebraType assembly_type)
Check the validity of the preconditioner and assembly types options.
Definition: FsilsLinearAlgebra.cpp:82
FsilsLinearAlgebra::set_preconditioner
virtual void set_preconditioner(consts::PreconditionerType prec_type)
Set the preconditioner.
Definition: FsilsLinearAlgebra.cpp:126
@@ -142,7 +142,7 @@
FsilsLinearAlgebra::initialize
virtual void initialize(ComMod &com_mod, eqType &lEq)
Initialize framework.
Definition: FsilsLinearAlgebra.cpp:104
LinearAlgebra
The LinearAlgebra class provides an abstract interface to linear algebra frameworks: FSILS,...
Definition: LinearAlgebra.h:40
-
eqType
Equation type.
Definition: ComMod.h:997
+
eqType
Equation type.
Definition: ComMod.h:1000
diff --git a/_linear_algebra_8h_source.html b/_linear_algebra_8h_source.html index 102412eb..54558db2 100644 --- a/_linear_algebra_8h_source.html +++ b/_linear_algebra_8h_source.html @@ -144,13 +144,13 @@
72 #endif
73 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
LinearAlgebraFactory
The LinearAlgebraFactory class provides a factory used to create objects derived from LinearAlgebra.
Definition: LinearAlgebra.h:66
LinearAlgebraFactory::create_interface
static LinearAlgebra * create_interface(consts::LinearAlgebraType interface_type)
Create objects derived from LinearAlgebra.
Definition: LinearAlgebra.cpp:72
LinearAlgebra
The LinearAlgebra class provides an abstract interface to linear algebra frameworks: FSILS,...
Definition: LinearAlgebra.h:40
LinearAlgebra::check_equation_compatibility
static void check_equation_compatibility(const consts::EquationType eq_phys, const consts::LinearAlgebraType lin_alg_type, const consts::LinearAlgebraType assembly_type)
Check that equation physics is compatible with LinearAlgebra type.
Definition: LinearAlgebra.cpp:52
-
eqType
Equation type.
Definition: ComMod.h:997
+
eqType
Equation type.
Definition: ComMod.h:1000
diff --git a/_parameters_8h_source.html b/_parameters_8h_source.html index 2227ef89..f4b1a42f 100644 --- a/_parameters_8h_source.html +++ b/_parameters_8h_source.html @@ -589,973 +589,974 @@
517  // Model types supported.
518  static const std::string GUCCIONE_MODEL;
519  static const std::string HGO_MODEL;
-
520  static const std::string HOLZAPFEL_MODEL;
-
521  static const std::string LEE_SACKS;
-
522  static const std::string NEOHOOKEAN_MODEL;
-
523  static const std::string STVENANT_KIRCHHOFF_MODEL;
-
524  static const std::map<std::string, std::string> constitutive_model_types;
-
525 
-
526  // Constitutive model type.
-
527  Parameter<std::string> type;
-
528 
-
529  GuccioneParameters guccione;
-
530  HolzapfelParameters holzapfel;
-
531  HolzapfelGasserOgdenParameters holzapfel_gasser_ogden;
-
532  LeeSacksParameters lee_sacks;
-
533  MooneyRivlinParameters mooney_rivlin;
-
534  NeoHookeanParameters neo_hookean;
-
535  StVenantKirchhoffParameters stvenant_kirchhoff;
-
536 
-
537  bool value_set = false;
-
538 };
-
539 
-
540 /// @brief Couple to reduced-order models.
-
541 class CoupleCplBCParameters : public ParameterLists
-
542 {
-
543  public:
-
544  CoupleCplBCParameters();
-
545 
-
546  static const std::string xml_element_name_;
-
547 
-
548  bool defined() const { return value_set; };
-
549  void set_values(tinyxml2::XMLElement* xml_elem);
-
550  void print_parameters();
-
551 
-
552  // attribute.
-
553  Parameter<std::string> type;
-
554 
-
555  Parameter<std::string> file_name_for_0D_3D_communication;
-
556  Parameter<std::string> file_name_for_saving_unknowns;
-
557  Parameter<int> number_of_unknowns;
-
558  Parameter<int> number_of_user_defined_outputs;
-
559  Parameter<std::string> unknowns_initialization_file_path;
-
560 
-
561  Parameter<std::string> zerod_code_file_path;
-
562 
-
563  bool value_set = false;
-
564 };
-
565 
-
566 /// @brief Coupling to GenBC.
-
567 class CoupleGenBCParameters : public ParameterLists
-
568 {
-
569  public:
-
570  CoupleGenBCParameters();
-
571 
-
572  static const std::string xml_element_name_;
-
573 
-
574  bool defined() const { return value_set; };
-
575  void set_values(tinyxml2::XMLElement* xml_elem);
-
576 
-
577  // attributes.
-
578  Parameter<std::string> type;
-
579 
-
580  // String parameters.
-
581  Parameter<std::string> zerod_code_file_path;
-
582 
-
583  bool value_set = false;
-
584 };
-
585 
-
586 //-----------------------
-
587 // CoupleSvZeroDParameters
-
588 //-----------------------
-
589 // Coupling to svZeroD.
-
590 //
-
591 class CoupleSvZeroDParameters : public ParameterLists
-
592 {
-
593  public:
-
594  CoupleSvZeroDParameters();
-
595 
-
596  static const std::string xml_element_name_;
-
597 
-
598  bool defined() const { return value_set; };
-
599  void set_values(tinyxml2::XMLElement* xml_elem);
-
600 
-
601  // attributes.
-
602  Parameter<std::string> type;
-
603 
-
604  bool value_set = false;
-
605 };
-
606 /// @brief Body force over a mesh using the "Add_BF" command.
-
607 ///
-
608 /// \code {.xml}
-
609 /// <Add_BF mesh="msh" >
-
610 /// <Type> volumetric </Type>
-
611 /// <Time_dependence> general </Time_dependence>
-
612 /// <Temporal_and_spatial_values_file_path> bforce.dat </Temporal_and_spatial_values_file_path>
-
613 /// </Add_BF>
-
614 /// \endcode
-
615 class BodyForceParameters : public ParameterLists
-
616 {
-
617  public:
-
618  BodyForceParameters();
-
619  void print_parameters();
-
620  void set_values(tinyxml2::XMLElement* xml_elem);
-
621  static const std::string xml_element_name_;
-
622 
-
623  // Attributes.
-
624  Parameter<std::string> mesh_name;
-
625 
-
626  // Boolean parameters.
-
627  Parameter<bool> ramp_function;
-
628 
-
629  // Double parameters.
-
630  Parameter<double> value;
-
631 
-
632  // String parameters.
-
633  Parameter<std::string> fourier_coefficients_file_path;
-
634  Parameter<std::string> spatial_values_file_path;
-
635  Parameter<std::string> temporal_and_spatial_values_file_path;
-
636  Parameter<std::string> temporal_values_file_path;
-
637  Parameter<std::string> time_dependence;
-
638  Parameter<std::string> type;
-
639 };
-
640 
-
641 /// @brief RCR values for Neumann BC type.
-
642 ///
-
643 /// \code {.xml}
-
644 /// <RCR_values>
-
645 /// <Proximal_resistance> 121.0 </Proximal_resistance>
-
646 /// <Capacitance> 1.5e-5 </Capacitance>
-
647 /// <Distal_resistance> 1212.0 </Distal_resistance>
-
648 /// </RCR_values>
-
649 /// \endcode
-
650 class BoundaryConditionRCRParameters : public ParameterLists
-
651 {
-
652  public:
-
653  BoundaryConditionRCRParameters();
-
654 
-
655  static const std::string xml_element_name_;
-
656 
-
657  void set_values(tinyxml2::XMLElement* xml_elem);
-
658  void print_parameters();
-
659 
-
660  Parameter<double> capacitance;
-
661  Parameter<double> distal_pressure;
-
662  Parameter<double> distal_resistance;
-
663  Parameter<double> initial_pressure;
-
664  Parameter<double> proximal_resistance;
-
665 
-
666  bool value_set = false;
-
667 };
-
668 
-
669 /// @brief The BoundaryConditionParameters stores paramaters for various
-
670 /// type of boundary conditions under the Add_BC XML element.
-
671 class BoundaryConditionParameters : public ParameterLists
-
672 {
-
673  public:
-
674  BoundaryConditionParameters();
-
675  void print_parameters();
-
676  void set_values(tinyxml2::XMLElement* bc_params);
-
677  static const std::string xml_element_name_;
-
678 
-
679  // RCR parameters sub-element.
-
680  BoundaryConditionRCRParameters rcr;
-
681 
-
682  // Add_BC name= attribute.
-
683  Parameter<std::string> name;
-
684 
-
685  // Add_BC XML elements.
-
686  //
-
687  Parameter<bool> apply_along_normal_direction;
-
688  Parameter<std::string> bct_file_path;
-
689 
-
690  Parameter<double> damping;
-
691  Parameter<double> distal_pressure;
-
692  VectorParameter<int> effective_direction;
-
693  Parameter<bool> follower_pressure_load;
-
694  Parameter<std::string> fourier_coefficients_file_path;
-
695 
-
696  Parameter<bool> impose_flux;
-
697  Parameter<bool> impose_on_state_variable_integral;
-
698  Parameter<std::string> initial_displacements_file_path;
-
699 
-
700  Parameter<double> penalty_parameter;
-
701  Parameter<double> penalty_parameter_normal;
-
702  Parameter<double> penalty_parameter_tangential;
-
703  Parameter<std::string> prestress_file_path;
-
704  Parameter<std::string> profile;
-
705  Parameter<bool> ramp_function;
-
706 
-
707  Parameter<std::string> cst_shell_bc_type;
-
708  Parameter<std::string> spatial_profile_file_path;
-
709  Parameter<std::string> spatial_values_file_path;
-
710  Parameter<double> stiffness;
-
711 
-
712  Parameter<std::string> temporal_and_spatial_values_file_path;
-
713  Parameter<std::string> temporal_values_file_path;
-
714  Parameter<std::string> time_dependence;
-
715  Parameter<std::string> traction_values_file_path;
-
716  Parameter<double> traction_multiplier;
-
717  Parameter<std::string> type;
-
718 
-
719  Parameter<bool> undeforming_neu_face;
-
720  Parameter<double> value;
-
721  Parameter<bool> weakly_applied;
-
722  Parameter<bool> zero_out_perimeter;
-
723 };
-
724 
-
725 /// @brief The OutputParameters class stores parameters for the
-
726 /// Output XML element under Add_equation.
-
727 ///
-
728 /// \code {.xml}
-
729 /// <Output type="Volume_integral" >
-
730 /// <Temperature> true </Temperature>
-
731 /// </Output>
-
732 /// \endcode
-
733 class OutputParameters : public ParameterLists
-
734 {
-
735  public:
-
736  OutputParameters();
-
737 
-
738  static const std::string xml_element_name_;
-
739 
-
740  void print_parameters();
-
741  void set_values(tinyxml2::XMLElement* xml_elem);
-
742  bool get_output_value(const std::string& name);
-
743  std::string get_alias_value(const std::string& name);
-
744 
-
745  Parameter<std::string> type;
-
746 
-
747  // List of output names.
-
748  std::vector<Parameter<bool>> output_list;
-
749 
-
750  // List of alias output names.
-
751  std::vector<Parameter<std::string>> alias_list;
-
752 };
-
753 
-
754 /// @brief The ProjectionParameters class stores parameters for the
-
755 /// 'Add_projection' XML element used for fluid-structure interaction
-
756 /// simulations.
-
757 /// \code {.xml}
-
758 /// <Add_projection name="wall_inner" >
-
759 /// <Project_from_face> lumen_wall </Project_from_face>
-
760 /// </Add_projection>
-
761 /// \endcode
-
762 class ProjectionParameters : public ParameterLists
-
763 {
-
764  public:
-
765  ProjectionParameters();
-
766 
-
767  void set_values(tinyxml2::XMLElement* xml_elem);
-
768 
-
769  static const std::string xml_element_name_;
-
770 
-
771  Parameter<std::string> name;
-
772 
-
773  Parameter<std::string> project_from_face;
-
774  Parameter<double> projection_tolerance;
-
775 };
-
776 
-
777 /// @brief The VariableWallPropsParameters class stores parameters for
-
778 /// variable wall properties for the CMM equation.
-
779 class VariableWallPropsParameters : public ParameterLists
-
780 {
-
781  public:
-
782  VariableWallPropsParameters();
-
783  static const std::string xml_element_name_;
-
784  bool defined() const { return value_set; };
-
785  void set_values(tinyxml2::XMLElement* xml_elemnt);
-
786 
-
787  Parameter<std::string> mesh_name;
-
788  Parameter<std::string> wall_properties_file_path;
-
789  bool value_set = false;
-
790 };
-
791 
-
792 
-
793 //////////////////////////////////////////////////////////
-
794 // FluidViscosity //
-
795 //////////////////////////////////////////////////////////
-
796 
-
797 // The following classes are used to store parameters for
-
798 // various fluid viscosity models.
-
799 
-
800 class FluidViscosityNewtonianParameters : public ParameterLists
-
801 {
-
802  public:
-
803  FluidViscosityNewtonianParameters();
-
804  void print_parameters();
-
805  void set_values(tinyxml2::XMLElement* equation_params);
-
806  Parameter<double> constant_value;
-
807 };
-
808 
-
809 class FluidViscosityCarreauYasudaParameters : public ParameterLists
-
810 {
-
811  public:
-
812  FluidViscosityCarreauYasudaParameters();
-
813  void print_parameters();
-
814  void set_values(tinyxml2::XMLElement* xml_elem);
-
815 
-
816  Parameter<double> limiting_high_shear_rate_viscosity;
-
817  Parameter<double> limiting_low_shear_rate_viscosity;
-
818  Parameter<double> power_law_index;
-
819  Parameter<double> shear_rate_tensor_multipler;
-
820  Parameter<double> shear_rate_tensor_exponent;
-
821 };
-
822 
-
823 class FluidViscosityCassonsParameters : public ParameterLists
-
824 {
-
825  public:
-
826  FluidViscosityCassonsParameters();
-
827  void print_parameters();
-
828  void set_values(tinyxml2::XMLElement* xml_elem);
-
829  Parameter<double> asymptotic_viscosity;
-
830  Parameter<double> yield_stress;
-
831  Parameter<double> low_shear_rate_threshold;
-
832 };
-
833 
-
834 class FluidViscosityParameters : public ParameterLists
-
835 {
-
836  public:
-
837  FluidViscosityParameters();
-
838 
-
839  static const std::string xml_element_name_;
-
840 
-
841  static const std::string CONSTANT_MODEL;
-
842  static const std::string CARREAU_YASUDA_MODEL;
-
843  static const std::string CASSONS_MODEL;
-
844  static const std::set<std::string> model_names;
-
845 
-
846  void print_parameters();
-
847  void set_values(tinyxml2::XMLElement* xml_elem);
-
848 
-
849  Parameter<std::string> model;
-
850 
-
851  FluidViscosityNewtonianParameters newtonian_model;
-
852  FluidViscosityCarreauYasudaParameters carreau_yasuda_model;
-
853  FluidViscosityCassonsParameters cassons_model;
-
854 };
-
855 
-
856 //////////////////////////////////////////////////////////
-
857 // SolidViscosity //
-
858 //////////////////////////////////////////////////////////
-
859 
-
860 // The following classes are used to store parameters for
-
861 // various solid viscosity models.
-
862 
-
863 class SolidViscosityNewtonianParameters : public ParameterLists
-
864 {
-
865  public:
-
866  SolidViscosityNewtonianParameters();
-
867  void print_parameters();
-
868  void set_values(tinyxml2::XMLElement* equation_params);
-
869  Parameter<double> constant_value;
-
870 };
-
871 
-
872 class SolidViscosityPotentialParameters : public ParameterLists
-
873 {
-
874  public:
-
875  SolidViscosityPotentialParameters();
-
876  void print_parameters();
-
877  void set_values(tinyxml2::XMLElement* equation_params);
-
878  Parameter<double> constant_value;
-
879 };
-
880 
-
881 class SolidViscosityParameters : public ParameterLists
-
882 {
-
883  public:
-
884  SolidViscosityParameters();
-
885 
-
886  static const std::string xml_element_name_;
-
887 
-
888  static const std::string NEWTONIAN_MODEL;
-
889  static const std::string POTENTIAL_MODEL;
-
890  static const std::set<std::string> model_names;
-
891 
-
892  void print_parameters();
-
893  void set_values(tinyxml2::XMLElement* xml_elem);
-
894 
-
895  Parameter<std::string> model;
-
896 
-
897  SolidViscosityNewtonianParameters newtonian_model;
-
898  SolidViscosityPotentialParameters potential_model;
-
899 };
-
900 
-
901 
-
902 /// @brief The LinearAlgebraParameters class stores parameters for
-
903 /// the 'Linear_algebra' XML element.
-
904 class LinearAlgebraParameters : public ParameterLists
-
905 {
-
906  public:
-
907  static const std::string xml_element_name_;
-
908  LinearAlgebraParameters();
-
909  void check_input_parameters();
-
910  void print_parameters();
-
911  void set_values(tinyxml2::XMLElement* fsi_file);
-
912  bool defined() const { return values_set_; };
-
913 
-
914  bool values_set_ = false;
-
915  Parameter<std::string> type;
-
916 
-
917  Parameter<std::string> assembly;
-
918  Parameter<std::string> configuration_file;
-
919  Parameter<std::string> preconditioner;
-
920 };
-
921 
-
922 /// @brief The LinearSolverParameters class stores parameters for
-
923 /// the 'LS' XML element.
-
924 class LinearSolverParameters : public ParameterLists
-
925 {
-
926  public:
-
927  LinearSolverParameters();
-
928 
-
929  void print_parameters();
-
930  void set_values(tinyxml2::XMLElement* fsi_file);
-
931 
-
932  static const std::string xml_element_name_;
-
933 
-
934  Parameter<std::string> type;
-
935 
-
936  Parameter<double> absolute_tolerance;
-
937  Parameter<int> krylov_space_dimension;
-
938 
-
939  Parameter<int> max_iterations;
-
940  Parameter<int> ns_cg_max_iterations;
-
941  Parameter<double> ns_cg_tolerance;
-
942  Parameter<int> ns_gm_max_iterations;
-
943  Parameter<double> ns_gm_tolerance;
-
944 
-
945  //Parameter<std::string> preconditioner;
-
946 
-
947  Parameter<double> tolerance;
-
948 
-
949  LinearAlgebraParameters linear_algebra;
-
950 };
-
951 
-
952 /// @brief The StimulusParameters class stores parameters for
-
953 /// 'Stimulus' XML element used to parameters for
-
954 /// pacemaker cells.
-
955 ///
-
956 /// \code {.xml}
-
957 /// <Stimulus type="Istim" >
-
958 /// <Amplitude> -52.0 </Amplitude>
-
959 /// <Start_time> 0.0 </Start_time>
-
960 /// <Duration> 1.0 </Duration>
-
961 /// <Cycle_length> 10000.0 </Cycle_length>
-
962 /// </Stimulus>
-
963 /// \endcode
-
964 class StimulusParameters : public ParameterLists
-
965 {
-
966  public:
-
967  StimulusParameters();
-
968 
-
969  static const std::string xml_element_name_;
-
970 
-
971  bool defined() const { return value_set; };
-
972  void print_parameters();
-
973  void set_values(tinyxml2::XMLElement* xml_elem);
-
974 
-
975  Parameter<std::string> type;
-
976 
-
977  Parameter<double> amplitude;
-
978  Parameter<double> cycle_length;
-
979  Parameter<double> duration;
-
980  Parameter<double> start_time;
-
981 
-
982  bool value_set = false;
-
983 };
-
984 
-
985 class ECGLeadsParameters : public ParameterLists
-
986 {
-
987  public:
-
988  ECGLeadsParameters();
-
989 
-
990  static const std::string xml_element_name_;
-
991 
-
992  bool defined() const { return value_set; };
-
993  void print_parameters();
-
994  void set_values(tinyxml2::XMLElement* xml_elem);
-
995 
-
996  Parameter<std::string> x_coords_file_path;
-
997  Parameter<std::string> y_coords_file_path;
-
998  Parameter<std::string> z_coords_file_path;
-
999 
-
1000  bool value_set = false;
-
1001 };
-
1002 
-
1003 /// @brief The FiberReinforcementStressParameters class stores fiber
-
1004 /// reinforcement stress parameters for the 'Fiber_reinforcement_stress`
-
1005 /// XML element.
-
1006 ///
-
1007 /// \code {.xml}
-
1008 /// <Fiber_reinforcement_stress type="Unsteady" >
-
1009 /// <Temporal_values_file_path> fib_stress.dat </Temporal_values_file_path>
-
1010 /// <Ramp_function> true </Ramp_function>
-
1011 /// </Fiber_reinforcement_stress>
-
1012 /// \endcode
-
1013 class FiberReinforcementStressParameters : public ParameterLists
-
1014 {
-
1015  public:
-
1016  FiberReinforcementStressParameters();
-
1017 
-
1018  static const std::string xml_element_name_;
-
1019 
-
1020  bool defined() const { return value_set; };
-
1021  void print_parameters();
-
1022  void set_values(tinyxml2::XMLElement* xml_elem);
-
1023 
-
1024  Parameter<std::string> type;
-
1025 
-
1026  Parameter<bool> ramp_function;
-
1027  Parameter<std::string> temporal_values_file_path;
-
1028  Parameter<double> value;
-
1029 
-
1030  bool value_set = false;
-
1031 };
-
1032 
-
1033 /// @brief The DomainParameters class stores parameters for the XML
-
1034 /// 'Domain' element to specify properties for solving equations.
-
1035 ///
-
1036 /// \code {.xml}
-
1037 /// <Domain id="1" >
-
1038 /// <Equation> fluid </Equation>
-
1039 /// <Density> 1.06 </Density>
-
1040 /// <Viscosity model="Constant" >
-
1041 /// <Value> 0.04 </Value>
-
1042 /// </Viscosity>
-
1043 /// <Backflow_stabilization_coefficient> 0.2 </Backflow_stabilization_coefficient>
-
1044 /// </Domain>
-
1045 /// \endcode
-
1046 class DomainParameters : public ParameterLists
-
1047 {
-
1048  public:
-
1049  DomainParameters();
-
1050 
-
1051  static const std::string xml_element_name_;
-
1052 
-
1053  void print_parameters();
-
1054  void set_values(tinyxml2::XMLElement* xml_elem);
-
1055 
-
1056  // Parameters for sub-elements under the Domain element.
-
1057  ConstitutiveModelParameters constitutive_model;
-
1058  FiberReinforcementStressParameters fiber_reinforcement_stress;
-
1059  StimulusParameters stimulus;
-
1060  FluidViscosityParameters fluid_viscosity;
-
1061  SolidViscosityParameters solid_viscosity;
-
1062 
-
1063  // Attributes.
-
1064  Parameter<std::string> id;
-
1065 
-
1066  Parameter<double> absolute_tolerance;
-
1067  VectorParameter<double> anisotropic_conductivity;
-
1068  Parameter<double> backflow_stabilization_coefficient;
-
1069 
-
1070  Parameter<double> conductivity;
-
1071  //Parameter<std::string> constitutive_model_name;
-
1072  Parameter<double> continuity_stabilization_coefficient;
-
1073 
-
1074  Parameter<double> density;
-
1075  Parameter<std::string> dilational_penalty_model;
-
1076 
-
1077  Parameter<std::string> equation;
-
1078  Parameter<double> elasticity_modulus;
-
1079  Parameter<std::string> electrophysiology_model;
-
1080 
-
1081  Parameter<double> feedback_parameter_for_stretch_activated_currents;
-
1082  Parameter<double> fluid_density;
-
1083  Parameter<double> force_x;
-
1084  Parameter<double> force_y;
-
1085  Parameter<double> force_z;
-
1086 
-
1087  Parameter<double> isotropic_conductivity;
-
1088 
-
1089  Parameter<double> mass_damping;
-
1090  Parameter<int> maximum_iterations;
-
1091  Parameter<double> momentum_stabilization_coefficient;
-
1092  Parameter<std::string> myocardial_zone;
-
1093 
-
1094  Parameter<double> G_Na;
-
1095  Parameter<double> G_CaL;
-
1096  Parameter<double> G_Kr;
-
1097  Parameter<double> G_Ks;
-
1098  Parameter<double> G_to;
-
1099 
-
1100  Parameter<double> tau_fi;
-
1101  Parameter<double> tau_si;
-
1102 
-
1103  Parameter<std::string> ode_solver;
-
1104  Parameter<double> penalty_parameter;
-
1105  Parameter<double> poisson_ratio;
-
1106  Parameter<double> relative_tolerance;
-
1107 
-
1108  Parameter<double> shell_thickness;
-
1109  Parameter<double> solid_density;
-
1110  Parameter<double> source_term;
-
1111  Parameter<double> time_step_for_integration;
-
1112 };
-
1113 
-
1114 /// @brief The RemesherParameters class stores parameters for the
-
1115 /// 'Remesher' XML element used for remeshing.
-
1116 ///
-
1117 /// \code {.xml}
-
1118 /// <Remesher type="Tetgen" >
-
1119 /// <Max_edge_size name="lumen" value="0.7"> </Max_edge_size>
-
1120 /// <Max_edge_size name="wall" value="0.5"> </Max_edge_size>
-
1121 /// <Min_dihedral_angle> 10.0 </Min_dihedral_angle>
-
1122 /// <Max_radius_ratio> 1.1 </Max_radius_ratio>
-
1123 /// <Remesh_frequency> 1000 </Remesh_frequency>
-
1124 /// <Frequency_for_copying_data> 1 </Frequency_for_copying_data>
-
1125 /// </Remesher>
-
1126 /// \endcode
-
1127 class RemesherParameters : public ParameterLists
-
1128 {
-
1129  public:
-
1130  RemesherParameters();
-
1131 
-
1132  static const std::string xml_element_name_;
-
1133  bool values_set_ = false;
-
1134 
-
1135  bool defined() const { return values_set_; };
-
1136  void print_parameters();
-
1137  double get_edge_size(const std::string& name) const { return max_edge_sizes_.at(name); }
-
1138  bool has_edge_size(const std::string& name) const { return max_edge_sizes_.count(name) == 1; }
-
1139  void set_values(tinyxml2::XMLElement* mesh_elem);
-
1140 
-
1141  // Values given in the 'Max_edge_size' element.
-
1142  std::map<std::string, double> max_edge_sizes_;
-
1143 
-
1144  Parameter<std::string> type;
-
1145  Parameter<double> min_dihedral_angle;
-
1146  Parameter<double> max_radius_ratio;
-
1147  Parameter<int> remesh_frequency;
-
1148  Parameter<int> frequency_for_copying_data;
-
1149 };
-
1150 
-
1151 /// @brief The ContactParameters class stores parameters for the 'Contact''
-
1152 /// XML element used to specify parameter values for contact
-
1153 /// computations.
-
1154 class ContactParameters : public ParameterLists
-
1155 {
-
1156  public:
-
1157  ContactParameters();
-
1158 
-
1159  static const std::string xml_element_name_;
-
1160 
-
1161  void print_parameters();
-
1162  void set_values(tinyxml2::XMLElement* xml_elem);
-
1163 
-
1164  Parameter<double> closest_gap_to_activate_penalty;
-
1165 
-
1166  Parameter<double> desired_separation;
-
1167 
-
1168  Parameter<double> min_norm_of_face_normals;
-
1169 
-
1170  Parameter<std::string> model;
-
1171 
-
1172  Parameter<double> penalty_constant;
-
1173 };
-
1174 
-
1175 /// @brief The EquationParameters class stores parameters for the 'Add_equation'
-
1176 /// XML element used to specify an equation to be solved (e.g. fluid).
-
1177 ///
-
1178 /// \code {.xml}
-
1179 /// <Add_equation type="FSI" >
-
1180 /// <Coupled> true </Coupled>
-
1181 /// <Min_iterations> 1 </Min_iterations>
-
1182 /// <Max_iterations> 1 </Max_iterations>
-
1183 /// .
+
520  static const std::string HOLZAPFEL_OGDEN_MODEL;
+
521  static const std::string HOLZAPFEL_OGDEN_MA_MODEL;
+
522  static const std::string LEE_SACKS;
+
523  static const std::string NEOHOOKEAN_MODEL;
+
524  static const std::string STVENANT_KIRCHHOFF_MODEL;
+
525  static const std::map<std::string, std::string> constitutive_model_types;
+
526 
+
527  // Constitutive model type.
+
528  Parameter<std::string> type;
+
529 
+
530  GuccioneParameters guccione;
+
531  HolzapfelParameters holzapfel;
+
532  HolzapfelGasserOgdenParameters holzapfel_gasser_ogden;
+
533  LeeSacksParameters lee_sacks;
+
534  MooneyRivlinParameters mooney_rivlin;
+
535  NeoHookeanParameters neo_hookean;
+
536  StVenantKirchhoffParameters stvenant_kirchhoff;
+
537 
+
538  bool value_set = false;
+
539 };
+
540 
+
541 /// @brief Couple to reduced-order models.
+
542 class CoupleCplBCParameters : public ParameterLists
+
543 {
+
544  public:
+
545  CoupleCplBCParameters();
+
546 
+
547  static const std::string xml_element_name_;
+
548 
+
549  bool defined() const { return value_set; };
+
550  void set_values(tinyxml2::XMLElement* xml_elem);
+
551  void print_parameters();
+
552 
+
553  // attribute.
+
554  Parameter<std::string> type;
+
555 
+
556  Parameter<std::string> file_name_for_0D_3D_communication;
+
557  Parameter<std::string> file_name_for_saving_unknowns;
+
558  Parameter<int> number_of_unknowns;
+
559  Parameter<int> number_of_user_defined_outputs;
+
560  Parameter<std::string> unknowns_initialization_file_path;
+
561 
+
562  Parameter<std::string> zerod_code_file_path;
+
563 
+
564  bool value_set = false;
+
565 };
+
566 
+
567 /// @brief Coupling to GenBC.
+
568 class CoupleGenBCParameters : public ParameterLists
+
569 {
+
570  public:
+
571  CoupleGenBCParameters();
+
572 
+
573  static const std::string xml_element_name_;
+
574 
+
575  bool defined() const { return value_set; };
+
576  void set_values(tinyxml2::XMLElement* xml_elem);
+
577 
+
578  // attributes.
+
579  Parameter<std::string> type;
+
580 
+
581  // String parameters.
+
582  Parameter<std::string> zerod_code_file_path;
+
583 
+
584  bool value_set = false;
+
585 };
+
586 
+
587 //-----------------------
+
588 // CoupleSvZeroDParameters
+
589 //-----------------------
+
590 // Coupling to svZeroD.
+
591 //
+
592 class CoupleSvZeroDParameters : public ParameterLists
+
593 {
+
594  public:
+
595  CoupleSvZeroDParameters();
+
596 
+
597  static const std::string xml_element_name_;
+
598 
+
599  bool defined() const { return value_set; };
+
600  void set_values(tinyxml2::XMLElement* xml_elem);
+
601 
+
602  // attributes.
+
603  Parameter<std::string> type;
+
604 
+
605  bool value_set = false;
+
606 };
+
607 /// @brief Body force over a mesh using the "Add_BF" command.
+
608 ///
+
609 /// \code {.xml}
+
610 /// <Add_BF mesh="msh" >
+
611 /// <Type> volumetric </Type>
+
612 /// <Time_dependence> general </Time_dependence>
+
613 /// <Temporal_and_spatial_values_file_path> bforce.dat </Temporal_and_spatial_values_file_path>
+
614 /// </Add_BF>
+
615 /// \endcode
+
616 class BodyForceParameters : public ParameterLists
+
617 {
+
618  public:
+
619  BodyForceParameters();
+
620  void print_parameters();
+
621  void set_values(tinyxml2::XMLElement* xml_elem);
+
622  static const std::string xml_element_name_;
+
623 
+
624  // Attributes.
+
625  Parameter<std::string> mesh_name;
+
626 
+
627  // Boolean parameters.
+
628  Parameter<bool> ramp_function;
+
629 
+
630  // Double parameters.
+
631  Parameter<double> value;
+
632 
+
633  // String parameters.
+
634  Parameter<std::string> fourier_coefficients_file_path;
+
635  Parameter<std::string> spatial_values_file_path;
+
636  Parameter<std::string> temporal_and_spatial_values_file_path;
+
637  Parameter<std::string> temporal_values_file_path;
+
638  Parameter<std::string> time_dependence;
+
639  Parameter<std::string> type;
+
640 };
+
641 
+
642 /// @brief RCR values for Neumann BC type.
+
643 ///
+
644 /// \code {.xml}
+
645 /// <RCR_values>
+
646 /// <Proximal_resistance> 121.0 </Proximal_resistance>
+
647 /// <Capacitance> 1.5e-5 </Capacitance>
+
648 /// <Distal_resistance> 1212.0 </Distal_resistance>
+
649 /// </RCR_values>
+
650 /// \endcode
+
651 class BoundaryConditionRCRParameters : public ParameterLists
+
652 {
+
653  public:
+
654  BoundaryConditionRCRParameters();
+
655 
+
656  static const std::string xml_element_name_;
+
657 
+
658  void set_values(tinyxml2::XMLElement* xml_elem);
+
659  void print_parameters();
+
660 
+
661  Parameter<double> capacitance;
+
662  Parameter<double> distal_pressure;
+
663  Parameter<double> distal_resistance;
+
664  Parameter<double> initial_pressure;
+
665  Parameter<double> proximal_resistance;
+
666 
+
667  bool value_set = false;
+
668 };
+
669 
+
670 /// @brief The BoundaryConditionParameters stores paramaters for various
+
671 /// type of boundary conditions under the Add_BC XML element.
+
672 class BoundaryConditionParameters : public ParameterLists
+
673 {
+
674  public:
+
675  BoundaryConditionParameters();
+
676  void print_parameters();
+
677  void set_values(tinyxml2::XMLElement* bc_params);
+
678  static const std::string xml_element_name_;
+
679 
+
680  // RCR parameters sub-element.
+
681  BoundaryConditionRCRParameters rcr;
+
682 
+
683  // Add_BC name= attribute.
+
684  Parameter<std::string> name;
+
685 
+
686  // Add_BC XML elements.
+
687  //
+
688  Parameter<bool> apply_along_normal_direction;
+
689  Parameter<std::string> bct_file_path;
+
690 
+
691  Parameter<double> damping;
+
692  Parameter<double> distal_pressure;
+
693  VectorParameter<int> effective_direction;
+
694  Parameter<bool> follower_pressure_load;
+
695  Parameter<std::string> fourier_coefficients_file_path;
+
696 
+
697  Parameter<bool> impose_flux;
+
698  Parameter<bool> impose_on_state_variable_integral;
+
699  Parameter<std::string> initial_displacements_file_path;
+
700 
+
701  Parameter<double> penalty_parameter;
+
702  Parameter<double> penalty_parameter_normal;
+
703  Parameter<double> penalty_parameter_tangential;
+
704  Parameter<std::string> prestress_file_path;
+
705  Parameter<std::string> profile;
+
706  Parameter<bool> ramp_function;
+
707 
+
708  Parameter<std::string> cst_shell_bc_type;
+
709  Parameter<std::string> spatial_profile_file_path;
+
710  Parameter<std::string> spatial_values_file_path;
+
711  Parameter<double> stiffness;
+
712 
+
713  Parameter<std::string> temporal_and_spatial_values_file_path;
+
714  Parameter<std::string> temporal_values_file_path;
+
715  Parameter<std::string> time_dependence;
+
716  Parameter<std::string> traction_values_file_path;
+
717  Parameter<double> traction_multiplier;
+
718  Parameter<std::string> type;
+
719 
+
720  Parameter<bool> undeforming_neu_face;
+
721  Parameter<double> value;
+
722  Parameter<bool> weakly_applied;
+
723  Parameter<bool> zero_out_perimeter;
+
724 };
+
725 
+
726 /// @brief The OutputParameters class stores parameters for the
+
727 /// Output XML element under Add_equation.
+
728 ///
+
729 /// \code {.xml}
+
730 /// <Output type="Volume_integral" >
+
731 /// <Temperature> true </Temperature>
+
732 /// </Output>
+
733 /// \endcode
+
734 class OutputParameters : public ParameterLists
+
735 {
+
736  public:
+
737  OutputParameters();
+
738 
+
739  static const std::string xml_element_name_;
+
740 
+
741  void print_parameters();
+
742  void set_values(tinyxml2::XMLElement* xml_elem);
+
743  bool get_output_value(const std::string& name);
+
744  std::string get_alias_value(const std::string& name);
+
745 
+
746  Parameter<std::string> type;
+
747 
+
748  // List of output names.
+
749  std::vector<Parameter<bool>> output_list;
+
750 
+
751  // List of alias output names.
+
752  std::vector<Parameter<std::string>> alias_list;
+
753 };
+
754 
+
755 /// @brief The ProjectionParameters class stores parameters for the
+
756 /// 'Add_projection' XML element used for fluid-structure interaction
+
757 /// simulations.
+
758 /// \code {.xml}
+
759 /// <Add_projection name="wall_inner" >
+
760 /// <Project_from_face> lumen_wall </Project_from_face>
+
761 /// </Add_projection>
+
762 /// \endcode
+
763 class ProjectionParameters : public ParameterLists
+
764 {
+
765  public:
+
766  ProjectionParameters();
+
767 
+
768  void set_values(tinyxml2::XMLElement* xml_elem);
+
769 
+
770  static const std::string xml_element_name_;
+
771 
+
772  Parameter<std::string> name;
+
773 
+
774  Parameter<std::string> project_from_face;
+
775  Parameter<double> projection_tolerance;
+
776 };
+
777 
+
778 /// @brief The VariableWallPropsParameters class stores parameters for
+
779 /// variable wall properties for the CMM equation.
+
780 class VariableWallPropsParameters : public ParameterLists
+
781 {
+
782  public:
+
783  VariableWallPropsParameters();
+
784  static const std::string xml_element_name_;
+
785  bool defined() const { return value_set; };
+
786  void set_values(tinyxml2::XMLElement* xml_elemnt);
+
787 
+
788  Parameter<std::string> mesh_name;
+
789  Parameter<std::string> wall_properties_file_path;
+
790  bool value_set = false;
+
791 };
+
792 
+
793 
+
794 //////////////////////////////////////////////////////////
+
795 // FluidViscosity //
+
796 //////////////////////////////////////////////////////////
+
797 
+
798 // The following classes are used to store parameters for
+
799 // various fluid viscosity models.
+
800 
+
801 class FluidViscosityNewtonianParameters : public ParameterLists
+
802 {
+
803  public:
+
804  FluidViscosityNewtonianParameters();
+
805  void print_parameters();
+
806  void set_values(tinyxml2::XMLElement* equation_params);
+
807  Parameter<double> constant_value;
+
808 };
+
809 
+
810 class FluidViscosityCarreauYasudaParameters : public ParameterLists
+
811 {
+
812  public:
+
813  FluidViscosityCarreauYasudaParameters();
+
814  void print_parameters();
+
815  void set_values(tinyxml2::XMLElement* xml_elem);
+
816 
+
817  Parameter<double> limiting_high_shear_rate_viscosity;
+
818  Parameter<double> limiting_low_shear_rate_viscosity;
+
819  Parameter<double> power_law_index;
+
820  Parameter<double> shear_rate_tensor_multipler;
+
821  Parameter<double> shear_rate_tensor_exponent;
+
822 };
+
823 
+
824 class FluidViscosityCassonsParameters : public ParameterLists
+
825 {
+
826  public:
+
827  FluidViscosityCassonsParameters();
+
828  void print_parameters();
+
829  void set_values(tinyxml2::XMLElement* xml_elem);
+
830  Parameter<double> asymptotic_viscosity;
+
831  Parameter<double> yield_stress;
+
832  Parameter<double> low_shear_rate_threshold;
+
833 };
+
834 
+
835 class FluidViscosityParameters : public ParameterLists
+
836 {
+
837  public:
+
838  FluidViscosityParameters();
+
839 
+
840  static const std::string xml_element_name_;
+
841 
+
842  static const std::string CONSTANT_MODEL;
+
843  static const std::string CARREAU_YASUDA_MODEL;
+
844  static const std::string CASSONS_MODEL;
+
845  static const std::set<std::string> model_names;
+
846 
+
847  void print_parameters();
+
848  void set_values(tinyxml2::XMLElement* xml_elem);
+
849 
+
850  Parameter<std::string> model;
+
851 
+
852  FluidViscosityNewtonianParameters newtonian_model;
+
853  FluidViscosityCarreauYasudaParameters carreau_yasuda_model;
+
854  FluidViscosityCassonsParameters cassons_model;
+
855 };
+
856 
+
857 //////////////////////////////////////////////////////////
+
858 // SolidViscosity //
+
859 //////////////////////////////////////////////////////////
+
860 
+
861 // The following classes are used to store parameters for
+
862 // various solid viscosity models.
+
863 
+
864 class SolidViscosityNewtonianParameters : public ParameterLists
+
865 {
+
866  public:
+
867  SolidViscosityNewtonianParameters();
+
868  void print_parameters();
+
869  void set_values(tinyxml2::XMLElement* equation_params);
+
870  Parameter<double> constant_value;
+
871 };
+
872 
+
873 class SolidViscosityPotentialParameters : public ParameterLists
+
874 {
+
875  public:
+
876  SolidViscosityPotentialParameters();
+
877  void print_parameters();
+
878  void set_values(tinyxml2::XMLElement* equation_params);
+
879  Parameter<double> constant_value;
+
880 };
+
881 
+
882 class SolidViscosityParameters : public ParameterLists
+
883 {
+
884  public:
+
885  SolidViscosityParameters();
+
886 
+
887  static const std::string xml_element_name_;
+
888 
+
889  static const std::string NEWTONIAN_MODEL;
+
890  static const std::string POTENTIAL_MODEL;
+
891  static const std::set<std::string> model_names;
+
892 
+
893  void print_parameters();
+
894  void set_values(tinyxml2::XMLElement* xml_elem);
+
895 
+
896  Parameter<std::string> model;
+
897 
+
898  SolidViscosityNewtonianParameters newtonian_model;
+
899  SolidViscosityPotentialParameters potential_model;
+
900 };
+
901 
+
902 
+
903 /// @brief The LinearAlgebraParameters class stores parameters for
+
904 /// the 'Linear_algebra' XML element.
+
905 class LinearAlgebraParameters : public ParameterLists
+
906 {
+
907  public:
+
908  static const std::string xml_element_name_;
+
909  LinearAlgebraParameters();
+
910  void check_input_parameters();
+
911  void print_parameters();
+
912  void set_values(tinyxml2::XMLElement* fsi_file);
+
913  bool defined() const { return values_set_; };
+
914 
+
915  bool values_set_ = false;
+
916  Parameter<std::string> type;
+
917 
+
918  Parameter<std::string> assembly;
+
919  Parameter<std::string> configuration_file;
+
920  Parameter<std::string> preconditioner;
+
921 };
+
922 
+
923 /// @brief The LinearSolverParameters class stores parameters for
+
924 /// the 'LS' XML element.
+
925 class LinearSolverParameters : public ParameterLists
+
926 {
+
927  public:
+
928  LinearSolverParameters();
+
929 
+
930  void print_parameters();
+
931  void set_values(tinyxml2::XMLElement* fsi_file);
+
932 
+
933  static const std::string xml_element_name_;
+
934 
+
935  Parameter<std::string> type;
+
936 
+
937  Parameter<double> absolute_tolerance;
+
938  Parameter<int> krylov_space_dimension;
+
939 
+
940  Parameter<int> max_iterations;
+
941  Parameter<int> ns_cg_max_iterations;
+
942  Parameter<double> ns_cg_tolerance;
+
943  Parameter<int> ns_gm_max_iterations;
+
944  Parameter<double> ns_gm_tolerance;
+
945 
+
946  //Parameter<std::string> preconditioner;
+
947 
+
948  Parameter<double> tolerance;
+
949 
+
950  LinearAlgebraParameters linear_algebra;
+
951 };
+
952 
+
953 /// @brief The StimulusParameters class stores parameters for
+
954 /// 'Stimulus' XML element used to parameters for
+
955 /// pacemaker cells.
+
956 ///
+
957 /// \code {.xml}
+
958 /// <Stimulus type="Istim" >
+
959 /// <Amplitude> -52.0 </Amplitude>
+
960 /// <Start_time> 0.0 </Start_time>
+
961 /// <Duration> 1.0 </Duration>
+
962 /// <Cycle_length> 10000.0 </Cycle_length>
+
963 /// </Stimulus>
+
964 /// \endcode
+
965 class StimulusParameters : public ParameterLists
+
966 {
+
967  public:
+
968  StimulusParameters();
+
969 
+
970  static const std::string xml_element_name_;
+
971 
+
972  bool defined() const { return value_set; };
+
973  void print_parameters();
+
974  void set_values(tinyxml2::XMLElement* xml_elem);
+
975 
+
976  Parameter<std::string> type;
+
977 
+
978  Parameter<double> amplitude;
+
979  Parameter<double> cycle_length;
+
980  Parameter<double> duration;
+
981  Parameter<double> start_time;
+
982 
+
983  bool value_set = false;
+
984 };
+
985 
+
986 class ECGLeadsParameters : public ParameterLists
+
987 {
+
988  public:
+
989  ECGLeadsParameters();
+
990 
+
991  static const std::string xml_element_name_;
+
992 
+
993  bool defined() const { return value_set; };
+
994  void print_parameters();
+
995  void set_values(tinyxml2::XMLElement* xml_elem);
+
996 
+
997  Parameter<std::string> x_coords_file_path;
+
998  Parameter<std::string> y_coords_file_path;
+
999  Parameter<std::string> z_coords_file_path;
+
1000 
+
1001  bool value_set = false;
+
1002 };
+
1003 
+
1004 /// @brief The FiberReinforcementStressParameters class stores fiber
+
1005 /// reinforcement stress parameters for the 'Fiber_reinforcement_stress`
+
1006 /// XML element.
+
1007 ///
+
1008 /// \code {.xml}
+
1009 /// <Fiber_reinforcement_stress type="Unsteady" >
+
1010 /// <Temporal_values_file_path> fib_stress.dat </Temporal_values_file_path>
+
1011 /// <Ramp_function> true </Ramp_function>
+
1012 /// </Fiber_reinforcement_stress>
+
1013 /// \endcode
+
1014 class FiberReinforcementStressParameters : public ParameterLists
+
1015 {
+
1016  public:
+
1017  FiberReinforcementStressParameters();
+
1018 
+
1019  static const std::string xml_element_name_;
+
1020 
+
1021  bool defined() const { return value_set; };
+
1022  void print_parameters();
+
1023  void set_values(tinyxml2::XMLElement* xml_elem);
+
1024 
+
1025  Parameter<std::string> type;
+
1026 
+
1027  Parameter<bool> ramp_function;
+
1028  Parameter<std::string> temporal_values_file_path;
+
1029  Parameter<double> value;
+
1030 
+
1031  bool value_set = false;
+
1032 };
+
1033 
+
1034 /// @brief The DomainParameters class stores parameters for the XML
+
1035 /// 'Domain' element to specify properties for solving equations.
+
1036 ///
+
1037 /// \code {.xml}
+
1038 /// <Domain id="1" >
+
1039 /// <Equation> fluid </Equation>
+
1040 /// <Density> 1.06 </Density>
+
1041 /// <Viscosity model="Constant" >
+
1042 /// <Value> 0.04 </Value>
+
1043 /// </Viscosity>
+
1044 /// <Backflow_stabilization_coefficient> 0.2 </Backflow_stabilization_coefficient>
+
1045 /// </Domain>
+
1046 /// \endcode
+
1047 class DomainParameters : public ParameterLists
+
1048 {
+
1049  public:
+
1050  DomainParameters();
+
1051 
+
1052  static const std::string xml_element_name_;
+
1053 
+
1054  void print_parameters();
+
1055  void set_values(tinyxml2::XMLElement* xml_elem);
+
1056 
+
1057  // Parameters for sub-elements under the Domain element.
+
1058  ConstitutiveModelParameters constitutive_model;
+
1059  FiberReinforcementStressParameters fiber_reinforcement_stress;
+
1060  StimulusParameters stimulus;
+
1061  FluidViscosityParameters fluid_viscosity;
+
1062  SolidViscosityParameters solid_viscosity;
+
1063 
+
1064  // Attributes.
+
1065  Parameter<std::string> id;
+
1066 
+
1067  Parameter<double> absolute_tolerance;
+
1068  VectorParameter<double> anisotropic_conductivity;
+
1069  Parameter<double> backflow_stabilization_coefficient;
+
1070 
+
1071  Parameter<double> conductivity;
+
1072  //Parameter<std::string> constitutive_model_name;
+
1073  Parameter<double> continuity_stabilization_coefficient;
+
1074 
+
1075  Parameter<double> density;
+
1076  Parameter<std::string> dilational_penalty_model;
+
1077 
+
1078  Parameter<std::string> equation;
+
1079  Parameter<double> elasticity_modulus;
+
1080  Parameter<std::string> electrophysiology_model;
+
1081 
+
1082  Parameter<double> feedback_parameter_for_stretch_activated_currents;
+
1083  Parameter<double> fluid_density;
+
1084  Parameter<double> force_x;
+
1085  Parameter<double> force_y;
+
1086  Parameter<double> force_z;
+
1087 
+
1088  Parameter<double> isotropic_conductivity;
+
1089 
+
1090  Parameter<double> mass_damping;
+
1091  Parameter<int> maximum_iterations;
+
1092  Parameter<double> momentum_stabilization_coefficient;
+
1093  Parameter<std::string> myocardial_zone;
+
1094 
+
1095  Parameter<double> G_Na;
+
1096  Parameter<double> G_CaL;
+
1097  Parameter<double> G_Kr;
+
1098  Parameter<double> G_Ks;
+
1099  Parameter<double> G_to;
+
1100 
+
1101  Parameter<double> tau_fi;
+
1102  Parameter<double> tau_si;
+
1103 
+
1104  Parameter<std::string> ode_solver;
+
1105  Parameter<double> penalty_parameter;
+
1106  Parameter<double> poisson_ratio;
+
1107  Parameter<double> relative_tolerance;
+
1108 
+
1109  Parameter<double> shell_thickness;
+
1110  Parameter<double> solid_density;
+
1111  Parameter<double> source_term;
+
1112  Parameter<double> time_step_for_integration;
+
1113 };
+
1114 
+
1115 /// @brief The RemesherParameters class stores parameters for the
+
1116 /// 'Remesher' XML element used for remeshing.
+
1117 ///
+
1118 /// \code {.xml}
+
1119 /// <Remesher type="Tetgen" >
+
1120 /// <Max_edge_size name="lumen" value="0.7"> </Max_edge_size>
+
1121 /// <Max_edge_size name="wall" value="0.5"> </Max_edge_size>
+
1122 /// <Min_dihedral_angle> 10.0 </Min_dihedral_angle>
+
1123 /// <Max_radius_ratio> 1.1 </Max_radius_ratio>
+
1124 /// <Remesh_frequency> 1000 </Remesh_frequency>
+
1125 /// <Frequency_for_copying_data> 1 </Frequency_for_copying_data>
+
1126 /// </Remesher>
+
1127 /// \endcode
+
1128 class RemesherParameters : public ParameterLists
+
1129 {
+
1130  public:
+
1131  RemesherParameters();
+
1132 
+
1133  static const std::string xml_element_name_;
+
1134  bool values_set_ = false;
+
1135 
+
1136  bool defined() const { return values_set_; };
+
1137  void print_parameters();
+
1138  double get_edge_size(const std::string& name) const { return max_edge_sizes_.at(name); }
+
1139  bool has_edge_size(const std::string& name) const { return max_edge_sizes_.count(name) == 1; }
+
1140  void set_values(tinyxml2::XMLElement* mesh_elem);
+
1141 
+
1142  // Values given in the 'Max_edge_size' element.
+
1143  std::map<std::string, double> max_edge_sizes_;
+
1144 
+
1145  Parameter<std::string> type;
+
1146  Parameter<double> min_dihedral_angle;
+
1147  Parameter<double> max_radius_ratio;
+
1148  Parameter<int> remesh_frequency;
+
1149  Parameter<int> frequency_for_copying_data;
+
1150 };
+
1151 
+
1152 /// @brief The ContactParameters class stores parameters for the 'Contact''
+
1153 /// XML element used to specify parameter values for contact
+
1154 /// computations.
+
1155 class ContactParameters : public ParameterLists
+
1156 {
+
1157  public:
+
1158  ContactParameters();
+
1159 
+
1160  static const std::string xml_element_name_;
+
1161 
+
1162  void print_parameters();
+
1163  void set_values(tinyxml2::XMLElement* xml_elem);
+
1164 
+
1165  Parameter<double> closest_gap_to_activate_penalty;
+
1166 
+
1167  Parameter<double> desired_separation;
+
1168 
+
1169  Parameter<double> min_norm_of_face_normals;
+
1170 
+
1171  Parameter<std::string> model;
+
1172 
+
1173  Parameter<double> penalty_constant;
+
1174 };
+
1175 
+
1176 /// @brief The EquationParameters class stores parameters for the 'Add_equation'
+
1177 /// XML element used to specify an equation to be solved (e.g. fluid).
+
1178 ///
+
1179 /// \code {.xml}
+
1180 /// <Add_equation type="FSI" >
+
1181 /// <Coupled> true </Coupled>
+
1182 /// <Min_iterations> 1 </Min_iterations>
+
1183 /// <Max_iterations> 1 </Max_iterations>
1184 /// .
1185 /// .
-
1186 /// </Add_equation>
-
1187 /// \endcode
-
1188 class EquationParameters : public ParameterLists
-
1189 {
-
1190  public:
-
1191  EquationParameters();
-
1192 
-
1193  static const std::string xml_element_name_;
-
1194 
-
1195  void print_parameters();
-
1196  void set_values(tinyxml2::XMLElement* xml_elem);
-
1197 
-
1198  Parameter<double> backflow_stabilization_coefficient;
-
1199 
-
1200  Parameter<double> conductivity;
-
1201  Parameter<double> continuity_stabilization_coefficient;
-
1202  Parameter<bool> coupled;
-
1203 
-
1204  Parameter<double> density;
-
1205  Parameter<std::string> dilational_penalty_model;
-
1206 
-
1207  Parameter<double> elasticity_modulus;
-
1208 
-
1209  Parameter<std::string> initialize;
-
1210  Parameter<bool> initialize_rcr_from_flow;
-
1211 
-
1212  Parameter<int> max_iterations;
-
1213  Parameter<int> min_iterations;
-
1214  Parameter<double> momentum_stabilization_coefficient;
-
1215 
-
1216  Parameter<double> penalty_parameter;
-
1217  Parameter<double> poisson_ratio;
-
1218  Parameter<bool> prestress;
-
1219 
-
1220  Parameter<double> source_term;
-
1221  Parameter<double> tolerance;
-
1222 
-
1223  Parameter<std::string> type;
-
1224  Parameter<bool> use_taylor_hood_type_basis;
-
1225 
-
1226  // Sub-element parameters.
-
1227  //
-
1228  std::vector<BodyForceParameters*> body_forces;
-
1229 
-
1230  std::vector<BoundaryConditionParameters*> boundary_conditions;
-
1231 
-
1232  CoupleCplBCParameters couple_to_cplBC;
-
1233  CoupleGenBCParameters couple_to_genBC;
-
1234  CoupleSvZeroDParameters couple_to_svZeroD;
-
1235 
-
1236  DomainParameters* default_domain = nullptr;
-
1237 
-
1238  std::vector<DomainParameters*> domains;
-
1239 
-
1240  LinearSolverParameters linear_solver;
-
1241 
-
1242  std::vector<OutputParameters*> outputs;
-
1243 
-
1244  RemesherParameters remesher;
-
1245 
-
1246  VariableWallPropsParameters variable_wall_properties;
-
1247 
-
1248  FluidViscosityParameters fluid_viscosity;
-
1249 
-
1250  SolidViscosityParameters solid_viscosity;
-
1251 
-
1252  ECGLeadsParameters ecg_leads;
-
1253 };
-
1254 
-
1255 /// @brief The GeneralSimulationParameters class stores paramaters for the
-
1256 /// 'GeneralSimulationParameters' XML element.
-
1257 ///
-
1258 /// \code {.xml}
-
1259 /// <GeneralSimulationParameters>
-
1260 /// <Continue_previous_simulation> 0 </Continue_previous_simulation>
-
1261 /// <Number_of_spatial_dimensions> 3 </Number_of_spatial_dimensions>
-
1262 /// <Number_of_time_steps> 1 </Number_of_time_steps>
-
1263 /// <Time_step_size> 1e-4 </Time_step_size>
-
1264 /// <Spectral_radius_of_infinite_time_step> 0.50 </Spectral_radius_of_infinite_time_step>
-
1265 /// <Searched_file_name_to_trigger_stop> STOP_SIM </Searched_file_name_to_trigger_stop>
-
1266 /// <Save_results_to_VTK_format> true </Save_results_to_VTK_format>
-
1267 /// <Name_prefix_of_saved_VTK_files> result </Name_prefix_of_saved_VTK_files>
-
1268 /// <Increment_in_saving_VTK_files> 1 </Increment_in_saving_VTK_files>
-
1269 /// <Start_saving_after_time_step> 1 </Start_saving_after_time_step>
-
1270 /// <Increment_in_saving_restart_files> 1 </Increment_in_saving_restart_files>
-
1271 /// <Convert_BIN_to_VTK_format> 0 </Convert_BIN_to_VTK_format>
-
1272 /// <Verbose> 1 </Verbose>
-
1273 /// <Warning> 0 </Warning>
-
1274 /// <Debug> 0 </Debug>
-
1275 /// <Simulation_requires_remeshing> true </Simulation_requires_remeshing>
-
1276 /// </GeneralSimulationParameters>
-
1277 /// \endcode
-
1278 class GeneralSimulationParameters : public ParameterLists
-
1279 {
-
1280  public:
-
1281  GeneralSimulationParameters();
-
1282 
-
1283  void print_parameters();
-
1284  void set_values(tinyxml2::XMLElement* xml_element);
-
1285 
-
1286  std::string xml_element_name;
-
1287 
-
1288  Parameter<bool> check_ien_order;
-
1289  Parameter<bool> continue_previous_simulation;
-
1290  Parameter<bool> convert_bin_to_vtk_format;
-
1291  Parameter<bool> debug;
-
1292  Parameter<bool> overwrite_restart_file;
-
1293  Parameter<bool> save_averaged_results;
-
1294  Parameter<bool> save_results_to_vtk_format;
-
1295  Parameter<bool> simulation_requires_remeshing;
-
1296  Parameter<bool> start_averaging_from_zero;
-
1297  Parameter<bool> verbose;
-
1298  Parameter<bool> warning;
-
1299  Parameter<bool> use_precomputed_solution;
-
1300 
-
1301  Parameter<double> spectral_radius_of_infinite_time_step;
-
1302  Parameter<double> time_step_size;
-
1303  Parameter<double> precomputed_time_step_size;
-
1304 
-
1305  Parameter<int> increment_in_saving_restart_files;
-
1306  Parameter<int> increment_in_saving_vtk_files;
-
1307  Parameter<int> number_of_spatial_dimensions;
-
1308  Parameter<int> number_of_initialization_time_steps;
-
1309  Parameter<int> start_saving_after_time_step;
-
1310  Parameter<int> starting_time_step;
-
1311  Parameter<int> number_of_time_steps;
-
1312 
-
1313  Parameter<std::string> name_prefix_of_saved_vtk_files;
-
1314  Parameter<std::string> restart_file_name;
-
1315  Parameter<std::string> searched_file_name_to_trigger_stop;
-
1316  Parameter<std::string> save_results_in_folder;
-
1317  Parameter<std::string> simulation_initialization_file_path;
-
1318  Parameter<std::string> precomputed_solution_file_path;
-
1319  Parameter<std::string> precomputed_solution_field_name;
-
1320 };
-
1321 
-
1322 /// @brief The FaceParameters class is used to store parameters for the
-
1323 /// 'Add_face' XML element.
-
1324 class FaceParameters : public ParameterLists
-
1325 {
-
1326  public:
-
1327  FaceParameters();
-
1328 
-
1329  void print_parameters();
-
1330  void set_values(tinyxml2::XMLElement* xml_elem);
-
1331 
-
1332  static const std::string xml_element_name_;
-
1333 
-
1334  Parameter<std::string> end_nodes_face_file_path;
-
1335  Parameter<std::string> face_file_path;
-
1336  Parameter<std::string> name;
-
1337 
-
1338  Parameter<double> quadrature_modifier_TRI3;
-
1339 };
-
1340 
-
1341 /// @brief The MeshParameters class is used to store paramaters for the
-
1342 /// 'Add_mesh' XML element.
-
1343 ///
-
1344 /// \code {.xml}
-
1345 /// <Add_mesh name="lumen" >
-
1346 /// <Mesh_file_path> mesh/lumen/mesh-complete.mesh.vtu </Mesh_file_path>
-
1347 ///
-
1348 /// <Add_face name="lumen_inlet">
-
1349 /// <Face_file_path> mesh/lumen/mesh-surfaces/lumen_inlet.vtp </Face_file_path>
-
1350 /// </Add_face>
-
1351 ///
-
1352 /// <Add_face name="lumen_outlet">
-
1353 /// <Face_file_path> mesh/lumen/mesh-surfaces/lumen_outlet.vtp </Face_file_path>
-
1354 /// </Add_face>
-
1355 ///
-
1356 /// <Add_face name="lumen_wall">
-
1357 /// <Face_file_path> mesh/lumen/mesh-surfaces/lumen_wall.vtp </Face_file_path>
-
1358 /// </Add_face>
-
1359 ///
-
1360 /// <Domain> 0 </Domain>
-
1361 ///
-
1362 /// </Add_mesh>
-
1363 /// \endcode
-
1364 class MeshParameters : public ParameterLists
-
1365 {
-
1366  public:
-
1367  MeshParameters();
-
1368 
-
1369  static const std::string xml_element_name_;
-
1370 
-
1371  void print_parameters();
-
1372  void set_values(tinyxml2::XMLElement* mesh_elem);
-
1373  std::string get_name() const { return name.value(); };
-
1374  std::string get_path() const { return mesh_file_path.value(); };
-
1375 
-
1376  std::vector<FaceParameters*> face_parameters;
-
1377 
-
1378  // Add_mesh name=
-
1379  Parameter<std::string> name;
-
1380 
-
1381  // Parameters under Add_mesh
-
1382  //
-
1383  Parameter<int> domain_id;
-
1384  Parameter<std::string> domain_file_path;
-
1385 
-
1386  VectorParameter<std::string> fiber_direction_file_paths;
-
1387  //Parameter<std::string> fiber_direction_file_path;
-
1388  std::vector<VectorParameter<double>> fiber_directions;
-
1389  //VectorParameter<double> fiber_direction;
-
1390 
-
1391  Parameter<std::string> initial_displacements_file_path;
-
1392  Parameter<std::string> initial_pressures_file_path;
-
1393  Parameter<bool> initialize_rcr_from_flow;
-
1394  Parameter<std::string> initial_velocities_file_path;
-
1395 
-
1396  Parameter<std::string> mesh_file_path;
-
1397  Parameter<double> mesh_scale_factor;
-
1398  Parameter<std::string> prestress_file_path;
-
1399 
-
1400  Parameter<bool> set_mesh_as_fibers;
-
1401  Parameter<bool> set_mesh_as_shell;
-
1402 
-
1403  Parameter<double> quadrature_modifier_TET4;
-
1404 };
-
1405 
-
1406 /// @brief The Parameters class stores parameter values read in from a solver input file.
-
1407 class Parameters {
-
1408 
-
1409  public:
-
1410  Parameters();
-
1411 
-
1412  static const std::set<std::string> constitutive_model_names;
-
1413  static const std::set<std::string> equation_names;
-
1414  static const std::string FSI_FILE;
-
1415 
-
1416  void get_logging_levels(int& verbose, int& warning, int& debug);
-
1417  void print_parameters();
-
1418  void read_xml(std::string file_name);
-
1419 
-
1420  void set_contact_values(tinyxml2::XMLElement* root_element);
-
1421  void set_equation_values(tinyxml2::XMLElement* root_element);
-
1422  void set_mesh_values(tinyxml2::XMLElement* root_element);
-
1423  void set_projection_values(tinyxml2::XMLElement* root_element);
-
1424 
-
1425  // Objects representing each parameter section of XML file.
-
1426  ContactParameters contact_parameters;
-
1427  GeneralSimulationParameters general_simulation_parameters;
-
1428  std::vector<MeshParameters*> mesh_parameters;
-
1429  std::vector<EquationParameters*> equation_parameters;
-
1430  std::vector<ProjectionParameters*> projection_parameters;
-
1431 };
-
1432 
-
1433 #endif
-
1434 
-
BodyForceParameters
Body force over a mesh using the "Add_BF" command.
Definition: Parameters.h:616
-
BodyForceParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for boundary condition parameters.
Definition: Parameters.h:621
-
BoundaryConditionParameters
The BoundaryConditionParameters stores paramaters for various type of boundary conditions under the A...
Definition: Parameters.h:672
-
BoundaryConditionParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation boundary condition parameters.
Definition: Parameters.h:677
-
BoundaryConditionRCRParameters
RCR values for Neumann BC type.
Definition: Parameters.h:651
+
1186 /// .
+
1187 /// </Add_equation>
+
1188 /// \endcode
+
1189 class EquationParameters : public ParameterLists
+
1190 {
+
1191  public:
+
1192  EquationParameters();
+
1193 
+
1194  static const std::string xml_element_name_;
+
1195 
+
1196  void print_parameters();
+
1197  void set_values(tinyxml2::XMLElement* xml_elem);
+
1198 
+
1199  Parameter<double> backflow_stabilization_coefficient;
+
1200 
+
1201  Parameter<double> conductivity;
+
1202  Parameter<double> continuity_stabilization_coefficient;
+
1203  Parameter<bool> coupled;
+
1204 
+
1205  Parameter<double> density;
+
1206  Parameter<std::string> dilational_penalty_model;
+
1207 
+
1208  Parameter<double> elasticity_modulus;
+
1209 
+
1210  Parameter<std::string> initialize;
+
1211  Parameter<bool> initialize_rcr_from_flow;
+
1212 
+
1213  Parameter<int> max_iterations;
+
1214  Parameter<int> min_iterations;
+
1215  Parameter<double> momentum_stabilization_coefficient;
+
1216 
+
1217  Parameter<double> penalty_parameter;
+
1218  Parameter<double> poisson_ratio;
+
1219  Parameter<bool> prestress;
+
1220 
+
1221  Parameter<double> source_term;
+
1222  Parameter<double> tolerance;
+
1223 
+
1224  Parameter<std::string> type;
+
1225  Parameter<bool> use_taylor_hood_type_basis;
+
1226 
+
1227  // Sub-element parameters.
+
1228  //
+
1229  std::vector<BodyForceParameters*> body_forces;
+
1230 
+
1231  std::vector<BoundaryConditionParameters*> boundary_conditions;
+
1232 
+
1233  CoupleCplBCParameters couple_to_cplBC;
+
1234  CoupleGenBCParameters couple_to_genBC;
+
1235  CoupleSvZeroDParameters couple_to_svZeroD;
+
1236 
+
1237  DomainParameters* default_domain = nullptr;
+
1238 
+
1239  std::vector<DomainParameters*> domains;
+
1240 
+
1241  LinearSolverParameters linear_solver;
+
1242 
+
1243  std::vector<OutputParameters*> outputs;
+
1244 
+
1245  RemesherParameters remesher;
+
1246 
+
1247  VariableWallPropsParameters variable_wall_properties;
+
1248 
+
1249  FluidViscosityParameters fluid_viscosity;
+
1250 
+
1251  SolidViscosityParameters solid_viscosity;
+
1252 
+
1253  ECGLeadsParameters ecg_leads;
+
1254 };
+
1255 
+
1256 /// @brief The GeneralSimulationParameters class stores paramaters for the
+
1257 /// 'GeneralSimulationParameters' XML element.
+
1258 ///
+
1259 /// \code {.xml}
+
1260 /// <GeneralSimulationParameters>
+
1261 /// <Continue_previous_simulation> 0 </Continue_previous_simulation>
+
1262 /// <Number_of_spatial_dimensions> 3 </Number_of_spatial_dimensions>
+
1263 /// <Number_of_time_steps> 1 </Number_of_time_steps>
+
1264 /// <Time_step_size> 1e-4 </Time_step_size>
+
1265 /// <Spectral_radius_of_infinite_time_step> 0.50 </Spectral_radius_of_infinite_time_step>
+
1266 /// <Searched_file_name_to_trigger_stop> STOP_SIM </Searched_file_name_to_trigger_stop>
+
1267 /// <Save_results_to_VTK_format> true </Save_results_to_VTK_format>
+
1268 /// <Name_prefix_of_saved_VTK_files> result </Name_prefix_of_saved_VTK_files>
+
1269 /// <Increment_in_saving_VTK_files> 1 </Increment_in_saving_VTK_files>
+
1270 /// <Start_saving_after_time_step> 1 </Start_saving_after_time_step>
+
1271 /// <Increment_in_saving_restart_files> 1 </Increment_in_saving_restart_files>
+
1272 /// <Convert_BIN_to_VTK_format> 0 </Convert_BIN_to_VTK_format>
+
1273 /// <Verbose> 1 </Verbose>
+
1274 /// <Warning> 0 </Warning>
+
1275 /// <Debug> 0 </Debug>
+
1276 /// <Simulation_requires_remeshing> true </Simulation_requires_remeshing>
+
1277 /// </GeneralSimulationParameters>
+
1278 /// \endcode
+
1279 class GeneralSimulationParameters : public ParameterLists
+
1280 {
+
1281  public:
+
1282  GeneralSimulationParameters();
+
1283 
+
1284  void print_parameters();
+
1285  void set_values(tinyxml2::XMLElement* xml_element);
+
1286 
+
1287  std::string xml_element_name;
+
1288 
+
1289  Parameter<bool> check_ien_order;
+
1290  Parameter<bool> continue_previous_simulation;
+
1291  Parameter<bool> convert_bin_to_vtk_format;
+
1292  Parameter<bool> debug;
+
1293  Parameter<bool> overwrite_restart_file;
+
1294  Parameter<bool> save_averaged_results;
+
1295  Parameter<bool> save_results_to_vtk_format;
+
1296  Parameter<bool> simulation_requires_remeshing;
+
1297  Parameter<bool> start_averaging_from_zero;
+
1298  Parameter<bool> verbose;
+
1299  Parameter<bool> warning;
+
1300  Parameter<bool> use_precomputed_solution;
+
1301 
+
1302  Parameter<double> spectral_radius_of_infinite_time_step;
+
1303  Parameter<double> time_step_size;
+
1304  Parameter<double> precomputed_time_step_size;
+
1305 
+
1306  Parameter<int> increment_in_saving_restart_files;
+
1307  Parameter<int> increment_in_saving_vtk_files;
+
1308  Parameter<int> number_of_spatial_dimensions;
+
1309  Parameter<int> number_of_initialization_time_steps;
+
1310  Parameter<int> start_saving_after_time_step;
+
1311  Parameter<int> starting_time_step;
+
1312  Parameter<int> number_of_time_steps;
+
1313 
+
1314  Parameter<std::string> name_prefix_of_saved_vtk_files;
+
1315  Parameter<std::string> restart_file_name;
+
1316  Parameter<std::string> searched_file_name_to_trigger_stop;
+
1317  Parameter<std::string> save_results_in_folder;
+
1318  Parameter<std::string> simulation_initialization_file_path;
+
1319  Parameter<std::string> precomputed_solution_file_path;
+
1320  Parameter<std::string> precomputed_solution_field_name;
+
1321 };
+
1322 
+
1323 /// @brief The FaceParameters class is used to store parameters for the
+
1324 /// 'Add_face' XML element.
+
1325 class FaceParameters : public ParameterLists
+
1326 {
+
1327  public:
+
1328  FaceParameters();
+
1329 
+
1330  void print_parameters();
+
1331  void set_values(tinyxml2::XMLElement* xml_elem);
+
1332 
+
1333  static const std::string xml_element_name_;
+
1334 
+
1335  Parameter<std::string> end_nodes_face_file_path;
+
1336  Parameter<std::string> face_file_path;
+
1337  Parameter<std::string> name;
+
1338 
+
1339  Parameter<double> quadrature_modifier_TRI3;
+
1340 };
+
1341 
+
1342 /// @brief The MeshParameters class is used to store paramaters for the
+
1343 /// 'Add_mesh' XML element.
+
1344 ///
+
1345 /// \code {.xml}
+
1346 /// <Add_mesh name="lumen" >
+
1347 /// <Mesh_file_path> mesh/lumen/mesh-complete.mesh.vtu </Mesh_file_path>
+
1348 ///
+
1349 /// <Add_face name="lumen_inlet">
+
1350 /// <Face_file_path> mesh/lumen/mesh-surfaces/lumen_inlet.vtp </Face_file_path>
+
1351 /// </Add_face>
+
1352 ///
+
1353 /// <Add_face name="lumen_outlet">
+
1354 /// <Face_file_path> mesh/lumen/mesh-surfaces/lumen_outlet.vtp </Face_file_path>
+
1355 /// </Add_face>
+
1356 ///
+
1357 /// <Add_face name="lumen_wall">
+
1358 /// <Face_file_path> mesh/lumen/mesh-surfaces/lumen_wall.vtp </Face_file_path>
+
1359 /// </Add_face>
+
1360 ///
+
1361 /// <Domain> 0 </Domain>
+
1362 ///
+
1363 /// </Add_mesh>
+
1364 /// \endcode
+
1365 class MeshParameters : public ParameterLists
+
1366 {
+
1367  public:
+
1368  MeshParameters();
+
1369 
+
1370  static const std::string xml_element_name_;
+
1371 
+
1372  void print_parameters();
+
1373  void set_values(tinyxml2::XMLElement* mesh_elem);
+
1374  std::string get_name() const { return name.value(); };
+
1375  std::string get_path() const { return mesh_file_path.value(); };
+
1376 
+
1377  std::vector<FaceParameters*> face_parameters;
+
1378 
+
1379  // Add_mesh name=
+
1380  Parameter<std::string> name;
+
1381 
+
1382  // Parameters under Add_mesh
+
1383  //
+
1384  Parameter<int> domain_id;
+
1385  Parameter<std::string> domain_file_path;
+
1386 
+
1387  VectorParameter<std::string> fiber_direction_file_paths;
+
1388  //Parameter<std::string> fiber_direction_file_path;
+
1389  std::vector<VectorParameter<double>> fiber_directions;
+
1390  //VectorParameter<double> fiber_direction;
+
1391 
+
1392  Parameter<std::string> initial_displacements_file_path;
+
1393  Parameter<std::string> initial_pressures_file_path;
+
1394  Parameter<bool> initialize_rcr_from_flow;
+
1395  Parameter<std::string> initial_velocities_file_path;
+
1396 
+
1397  Parameter<std::string> mesh_file_path;
+
1398  Parameter<double> mesh_scale_factor;
+
1399  Parameter<std::string> prestress_file_path;
+
1400 
+
1401  Parameter<bool> set_mesh_as_fibers;
+
1402  Parameter<bool> set_mesh_as_shell;
+
1403 
+
1404  Parameter<double> quadrature_modifier_TET4;
+
1405 };
+
1406 
+
1407 /// @brief The Parameters class stores parameter values read in from a solver input file.
+
1408 class Parameters {
+
1409 
+
1410  public:
+
1411  Parameters();
+
1412 
+
1413  static const std::set<std::string> constitutive_model_names;
+
1414  static const std::set<std::string> equation_names;
+
1415  static const std::string FSI_FILE;
+
1416 
+
1417  void get_logging_levels(int& verbose, int& warning, int& debug);
+
1418  void print_parameters();
+
1419  void read_xml(std::string file_name);
+
1420 
+
1421  void set_contact_values(tinyxml2::XMLElement* root_element);
+
1422  void set_equation_values(tinyxml2::XMLElement* root_element);
+
1423  void set_mesh_values(tinyxml2::XMLElement* root_element);
+
1424  void set_projection_values(tinyxml2::XMLElement* root_element);
+
1425 
+
1426  // Objects representing each parameter section of XML file.
+
1427  ContactParameters contact_parameters;
+
1428  GeneralSimulationParameters general_simulation_parameters;
+
1429  std::vector<MeshParameters*> mesh_parameters;
+
1430  std::vector<EquationParameters*> equation_parameters;
+
1431  std::vector<ProjectionParameters*> projection_parameters;
+
1432 };
+
1433 
+
1434 #endif
+
1435 
+
BodyForceParameters
Body force over a mesh using the "Add_BF" command.
Definition: Parameters.h:617
+
BodyForceParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for boundary condition parameters.
Definition: Parameters.h:622
+
BoundaryConditionParameters
The BoundaryConditionParameters stores paramaters for various type of boundary conditions under the A...
Definition: Parameters.h:673
+
BoundaryConditionParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation boundary condition parameters.
Definition: Parameters.h:678
+
BoundaryConditionRCRParameters
RCR values for Neumann BC type.
Definition: Parameters.h:652
BoundaryConditionRCRParameters::BoundaryConditionRCRParameters
BoundaryConditionRCRParameters()
RCR values for Neumann BC type.
Definition: Parameters.cpp:315
ConstitutiveModelParameters
The ConstitutiveModelParameters class store parameters for various constitutive models.
Definition: Parameters.h:509
-
ConstitutiveModelParameters::constitutive_model_types
static const std::map< std::string, std::string > constitutive_model_types
Supported constitutive model types and their aliases.
Definition: Parameters.h:524
+
ConstitutiveModelParameters::constitutive_model_types
static const std::map< std::string, std::string > constitutive_model_types
Supported constitutive model types and their aliases.
Definition: Parameters.h:525
ConstitutiveModelParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for various constitutive models.
Definition: Parameters.h:515
-
ContactParameters
The ContactParameters class stores parameters for the 'Contact'' XML element used to specify paramete...
Definition: Parameters.h:1155
-
ContactParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for the 'Contact' XML element used to specify parameters for contact computation.
Definition: Parameters.h:1159
-
CoupleCplBCParameters
Couple to reduced-order models.
Definition: Parameters.h:542
-
CoupleCplBCParameters::xml_element_name_
static const std::string xml_element_name_
Couple to reduced-order models.
Definition: Parameters.h:546
-
CoupleGenBCParameters
Coupling to GenBC.
Definition: Parameters.h:568
-
CoupleGenBCParameters::xml_element_name_
static const std::string xml_element_name_
Coupling to GenBC.
Definition: Parameters.h:572
-
CoupleSvZeroDParameters
Definition: Parameters.h:592
-
DomainParameters
The DomainParameters class stores parameters for the XML 'Domain' element to specify properties for s...
Definition: Parameters.h:1047
-
DomainParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for domain parameters.
Definition: Parameters.h:1051
-
ECGLeadsParameters
Definition: Parameters.h:986
-
ECGLeadsParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for ECG leads parameters.
Definition: Parameters.h:990
-
EquationParameters
The EquationParameters class stores parameters for the 'Add_equation' XML element used to specify an ...
Definition: Parameters.h:1189
-
EquationParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation parameters.
Definition: Parameters.h:1193
-
FaceParameters
The FaceParameters class is used to store parameters for the 'Add_face' XML element.
Definition: Parameters.h:1325
-
FaceParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for the 'Add_face' XML element.
Definition: Parameters.h:1332
-
FiberReinforcementStressParameters
The FiberReinforcementStressParameters class stores fiber reinforcement stress parameters for the 'Fi...
Definition: Parameters.h:1014
-
FiberReinforcementStressParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for fiber reinforcement stress parameters.
Definition: Parameters.h:1018
-
FluidViscosityCarreauYasudaParameters
Definition: Parameters.h:810
-
FluidViscosityCassonsParameters
Definition: Parameters.h:824
-
FluidViscosityNewtonianParameters
Definition: Parameters.h:801
-
FluidViscosityParameters
Definition: Parameters.h:835
-
FluidViscosityParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for various fluid viscosity models.
Definition: Parameters.h:839
-
GeneralSimulationParameters
The GeneralSimulationParameters class stores paramaters for the 'GeneralSimulationParameters' XML ele...
Definition: Parameters.h:1279
-
GeneralSimulationParameters::GeneralSimulationParameters
GeneralSimulationParameters()
Process paramaters for the 'GeneralSimulationParameters' XML element.
Definition: Parameters.cpp:1958
-
GeneralSimulationParameters::set_values
void set_values(tinyxml2::XMLElement *xml_element)
Set general parameters values from XML.
Definition: Parameters.cpp:2021
+
ContactParameters
The ContactParameters class stores parameters for the 'Contact'' XML element used to specify paramete...
Definition: Parameters.h:1156
+
ContactParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for the 'Contact' XML element used to specify parameters for contact computation.
Definition: Parameters.h:1160
+
CoupleCplBCParameters
Couple to reduced-order models.
Definition: Parameters.h:543
+
CoupleCplBCParameters::xml_element_name_
static const std::string xml_element_name_
Couple to reduced-order models.
Definition: Parameters.h:547
+
CoupleGenBCParameters
Coupling to GenBC.
Definition: Parameters.h:569
+
CoupleGenBCParameters::xml_element_name_
static const std::string xml_element_name_
Coupling to GenBC.
Definition: Parameters.h:573
+
CoupleSvZeroDParameters
Definition: Parameters.h:593
+
DomainParameters
The DomainParameters class stores parameters for the XML 'Domain' element to specify properties for s...
Definition: Parameters.h:1048
+
DomainParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for domain parameters.
Definition: Parameters.h:1052
+
ECGLeadsParameters
Definition: Parameters.h:987
+
ECGLeadsParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for ECG leads parameters.
Definition: Parameters.h:991
+
EquationParameters
The EquationParameters class stores parameters for the 'Add_equation' XML element used to specify an ...
Definition: Parameters.h:1190
+
EquationParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation parameters.
Definition: Parameters.h:1194
+
FaceParameters
The FaceParameters class is used to store parameters for the 'Add_face' XML element.
Definition: Parameters.h:1326
+
FaceParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for the 'Add_face' XML element.
Definition: Parameters.h:1333
+
FiberReinforcementStressParameters
The FiberReinforcementStressParameters class stores fiber reinforcement stress parameters for the 'Fi...
Definition: Parameters.h:1015
+
FiberReinforcementStressParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for fiber reinforcement stress parameters.
Definition: Parameters.h:1019
+
FluidViscosityCarreauYasudaParameters
Definition: Parameters.h:811
+
FluidViscosityCassonsParameters
Definition: Parameters.h:825
+
FluidViscosityNewtonianParameters
Definition: Parameters.h:802
+
FluidViscosityParameters
Definition: Parameters.h:836
+
FluidViscosityParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for various fluid viscosity models.
Definition: Parameters.h:840
+
GeneralSimulationParameters
The GeneralSimulationParameters class stores paramaters for the 'GeneralSimulationParameters' XML ele...
Definition: Parameters.h:1280
+
GeneralSimulationParameters::GeneralSimulationParameters
GeneralSimulationParameters()
Process paramaters for the 'GeneralSimulationParameters' XML element.
Definition: Parameters.cpp:1964
+
GeneralSimulationParameters::set_values
void set_values(tinyxml2::XMLElement *xml_element)
Set general parameters values from XML.
Definition: Parameters.cpp:2027
GuccioneParameters
Definition: Parameters.h:424
HolzapfelGasserOgdenParameters
Definition: Parameters.h:462
HolzapfelParameters
Definition: Parameters.h:441
LeeSacksParameters
Definition: Parameters.h:409
-
LinearAlgebraParameters
The LinearAlgebraParameters class stores parameters for the 'Linear_algebra' XML element.
Definition: Parameters.h:905
-
LinearAlgebraParameters::check_input_parameters
void check_input_parameters()
Check the validity of the input parameters.
Definition: Parameters.cpp:2430
-
LinearAlgebraParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation output parameters.
Definition: Parameters.h:907
-
LinearSolverParameters
The LinearSolverParameters class stores parameters for the 'LS' XML element.
Definition: Parameters.h:925
-
LinearSolverParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation output parameters.
Definition: Parameters.h:932
-
MeshParameters
The MeshParameters class is used to store paramaters for the 'Add_mesh' XML element.
Definition: Parameters.h:1365
-
MeshParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for mesh parameters.
Definition: Parameters.h:1369
+
LinearAlgebraParameters
The LinearAlgebraParameters class stores parameters for the 'Linear_algebra' XML element.
Definition: Parameters.h:906
+
LinearAlgebraParameters::check_input_parameters
void check_input_parameters()
Check the validity of the input parameters.
Definition: Parameters.cpp:2436
+
LinearAlgebraParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation output parameters.
Definition: Parameters.h:908
+
LinearSolverParameters
The LinearSolverParameters class stores parameters for the 'LS' XML element.
Definition: Parameters.h:926
+
LinearSolverParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation output parameters.
Definition: Parameters.h:933
+
MeshParameters
The MeshParameters class is used to store paramaters for the 'Add_mesh' XML element.
Definition: Parameters.h:1366
+
MeshParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for mesh parameters.
Definition: Parameters.h:1370
MooneyRivlinParameters
Definition: Parameters.h:477
NeoHookeanParameters
Definition: Parameters.h:489
-
NeoHookeanParameters::NeoHookeanParameters
NeoHookeanParameters()
There are no parameters associated with a Neohookean model.
Definition: Parameters.cpp:704
-
OutputParameters
The OutputParameters class stores parameters for the Output XML element under Add_equation.
Definition: Parameters.h:734
-
OutputParameters::get_alias_value
std::string get_alias_value(const std::string &name)
Get the value of an alias by name.
Definition: Parameters.cpp:1003
-
OutputParameters::get_output_value
bool get_output_value(const std::string &name)
Get the value of an output by name.
Definition: Parameters.cpp:1015
-
OutputParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation output parameters.
Definition: Parameters.h:738
+
NeoHookeanParameters::NeoHookeanParameters
NeoHookeanParameters()
There are no parameters associated with a Neohookean model.
Definition: Parameters.cpp:710
+
OutputParameters
The OutputParameters class stores parameters for the Output XML element under Add_equation.
Definition: Parameters.h:735
+
OutputParameters::get_alias_value
std::string get_alias_value(const std::string &name)
Get the value of an alias by name.
Definition: Parameters.cpp:1009
+
OutputParameters::get_output_value
bool get_output_value(const std::string &name)
Get the value of an output by name.
Definition: Parameters.cpp:1021
+
OutputParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation output parameters.
Definition: Parameters.h:739
Parameter
The Parameter class template is used to store a named paramater and its scalar value as a basic type:...
Definition: Parameters.h:113
Parameter::set
void set(const std::string &name, bool required, T value)
Set the parameter name and value, and if it is required.
Definition: Parameters.h:144
Parameter::set
void set(const std::string &str_value)
Set the parameter value from a string.
Definition: Parameters.h:151
@@ -1567,22 +1568,22 @@
ParameterLists::params_map
std::map< std::string, std::variant< Parameter< bool > *, Parameter< double > *, Parameter< int > *, Parameter< std::string > *, VectorParameter< double > *, VectorParameter< int > *, VectorParameter< std::string > * > > params_map
Map used for storing parameters by name / Parameter template union.
Definition: Parameters.h:396
ParameterLists::get_parameter_list
std::map< std::string, std::string > get_parameter_list()
Get the defined parameters as a map of strings.
Definition: Parameters.h:368
ParameterLists::print_parameter_list
void print_parameter_list()
Print the parameters.
Definition: Parameters.h:382
-
Parameters
The Parameters class stores parameter values read in from a solver input file.
Definition: Parameters.h:1407
+
Parameters
The Parameters class stores parameter values read in from a solver input file.
Definition: Parameters.h:1408
Parameters::read_xml
void read_xml(std::string file_name)
Set the simulation parameter values given in an XML format file.
Definition: Parameters.cpp:147
-
ProjectionParameters
The ProjectionParameters class stores parameters for the 'Add_projection' XML element used for fluid-...
Definition: Parameters.h:763
-
ProjectionParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for mesh parameters.
Definition: Parameters.h:769
-
RemesherParameters
The RemesherParameters class stores parameters for the 'Remesher' XML element used for remeshing.
Definition: Parameters.h:1128
-
RemesherParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for mesh parameters.
Definition: Parameters.h:1132
-
SolidViscosityNewtonianParameters
Definition: Parameters.h:864
-
SolidViscosityParameters
Definition: Parameters.h:882
-
SolidViscosityParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for various solid viscosity models.
Definition: Parameters.h:886
-
SolidViscosityPotentialParameters
Definition: Parameters.h:873
+
ProjectionParameters
The ProjectionParameters class stores parameters for the 'Add_projection' XML element used for fluid-...
Definition: Parameters.h:764
+
ProjectionParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for mesh parameters.
Definition: Parameters.h:770
+
RemesherParameters
The RemesherParameters class stores parameters for the 'Remesher' XML element used for remeshing.
Definition: Parameters.h:1129
+
RemesherParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for mesh parameters.
Definition: Parameters.h:1133
+
SolidViscosityNewtonianParameters
Definition: Parameters.h:865
+
SolidViscosityParameters
Definition: Parameters.h:883
+
SolidViscosityParameters::xml_element_name_
static const std::string xml_element_name_
Process parameters for various solid viscosity models.
Definition: Parameters.h:887
+
SolidViscosityPotentialParameters
Definition: Parameters.h:874
StVenantKirchhoffParameters
Definition: Parameters.h:498
-
StVenantKirchhoffParameters::StVenantKirchhoffParameters
StVenantKirchhoffParameters()
There are no parameters associated with a StVenantKirchhoff model.
Definition: Parameters.cpp:718
-
StimulusParameters
The StimulusParameters class stores parameters for 'Stimulus' XML element used to parameters for pace...
Definition: Parameters.h:965
-
StimulusParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation output parameters.
Definition: Parameters.h:969
-
VariableWallPropsParameters
The VariableWallPropsParameters class stores parameters for variable wall properties for the CMM equa...
Definition: Parameters.h:780
-
VariableWallPropsParameters::xml_element_name_
static const std::string xml_element_name_
The VariableWallPropsParameters class stores parameters for variable wall properties for the CMM equa...
Definition: Parameters.h:783
+
StVenantKirchhoffParameters::StVenantKirchhoffParameters
StVenantKirchhoffParameters()
There are no parameters associated with a StVenantKirchhoff model.
Definition: Parameters.cpp:724
+
StimulusParameters
The StimulusParameters class stores parameters for 'Stimulus' XML element used to parameters for pace...
Definition: Parameters.h:966
+
StimulusParameters::xml_element_name_
static const std::string xml_element_name_
Define the XML element name for equation output parameters.
Definition: Parameters.h:970
+
VariableWallPropsParameters
The VariableWallPropsParameters class stores parameters for variable wall properties for the CMM equa...
Definition: Parameters.h:781
+
VariableWallPropsParameters::xml_element_name_
static const std::string xml_element_name_
The VariableWallPropsParameters class stores parameters for variable wall properties for the CMM equa...
Definition: Parameters.h:784
VectorParameter
The VectorParameter class template is used to store a named paramater and its vector of values as a b...
Definition: Parameters.h:192
VectorParameter::set
void set(const std::string &str_value)
Set the parameter value from a string.
Definition: Parameters.h:246
VectorParameter::set
void set(const std::string &name, bool required, const std::vector< T > &value)
Set the parameter name and value, and if it is required.
Definition: Parameters.h:238
diff --git a/_petsc_linear_algebra_8h_source.html b/_petsc_linear_algebra_8h_source.html index e1511dbc..2cabeff1 100644 --- a/_petsc_linear_algebra_8h_source.html +++ b/_petsc_linear_algebra_8h_source.html @@ -136,7 +136,7 @@
64 #endif
65 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
LinearAlgebra
The LinearAlgebra class provides an abstract interface to linear algebra frameworks: FSILS,...
Definition: LinearAlgebra.h:40
PetscLinearAlgebra::PetscImpl
Definition: petsc_impl.cpp:933
PetscLinearAlgebra
The PetscLinearAlgebra class implements the LinearAlgebra interface for the PETSc numerical linear al...
Definition: PetscLinearAlgebra.h:39
@@ -148,7 +148,7 @@
PetscLinearAlgebra::check_options
virtual void check_options(const consts::PreconditionerType prec_cond_type, const consts::LinearAlgebraType assembly_type)
Check the validity of the precondition and assembly types options.
Definition: PetscLinearAlgebra.cpp:92
PetscLinearAlgebra::alloc
virtual void alloc(ComMod &com_mod, eqType &lEq)
Allocate data arrays.
Definition: PetscLinearAlgebra.cpp:79
-
eqType
Equation type.
Definition: ComMod.h:997
+
eqType
Equation type.
Definition: ComMod.h:1000
diff --git a/_simulation_8h_source.html b/_simulation_8h_source.html index e079f155..a8589bee 100644 --- a/_simulation_8h_source.html +++ b/_simulation_8h_source.html @@ -167,14 +167,14 @@
CepMod
Definition: CepMod.h:220
ChnlMod
Definition: ChnlMod.h:101
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
LinearAlgebra
The LinearAlgebra class provides an abstract interface to linear algebra frameworks: FSILS,...
Definition: LinearAlgebra.h:40
-
Parameters
The Parameters class stores parameter values read in from a solver input file.
Definition: Parameters.h:1407
+
Parameters
The Parameters class stores parameter values read in from a solver input file.
Definition: Parameters.h:1408
Simulation
Definition: Simulation.h:41
Simulation::set_module_parameters
void set_module_parameters()
Set the simulation and module member data.
Definition: Simulation.cpp:74
Simulation::read_parameters
void read_parameters(const std::string &fileName)
Read solver parameters.
Definition: Simulation.cpp:63
SimulationLogger
The SimulationLogger class is used to write information to a text file and optionally to cout.
Definition: SimulationLogger.h:40
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/_trilinos_linear_algebra_8h_source.html b/_trilinos_linear_algebra_8h_source.html index 27823c52..896cc4b2 100644 --- a/_trilinos_linear_algebra_8h_source.html +++ b/_trilinos_linear_algebra_8h_source.html @@ -137,7 +137,7 @@
65 #endif
66 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
LinearAlgebra
The LinearAlgebra class provides an abstract interface to linear algebra frameworks: FSILS,...
Definition: LinearAlgebra.h:40
TrilinosLinearAlgebra::TrilinosImpl
Definition: trilinos_impl.cpp:1088
TrilinosLinearAlgebra
The TrilinosLinearAlgebra class implements the LinearAlgebra interface for the Trilinos numerical lin...
Definition: TrilinosLinearAlgebra.h:39
@@ -149,7 +149,7 @@
TrilinosLinearAlgebra::check_options
virtual void check_options(const consts::PreconditionerType prec_cond_type, const consts::LinearAlgebraType assembly_type)
Check the validity of the precondition and assembly options.
Definition: TrilinosLinearAlgebra.cpp:115
TrilinosLinearAlgebra::alloc
virtual void alloc(ComMod &com_mod, eqType &lEq)
Allocate data arrays.
Definition: TrilinosLinearAlgebra.cpp:86
-
eqType
Equation type.
Definition: ComMod.h:997
+
eqType
Equation type.
Definition: ComMod.h:1000
diff --git a/all__fun_8h_source.html b/all__fun_8h_source.html index 1390b3e6..368c2485 100644 --- a/all__fun_8h_source.html +++ b/all__fun_8h_source.html @@ -167,12 +167,12 @@
95 
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
cmType
The cmType class stores data and defines methods used for mpi communication.
Definition: CmMod.h:82
-
eqType
Equation type.
Definition: ComMod.h:997
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
eqType
Equation type.
Definition: ComMod.h:1000
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/baf__ini_8h_source.html b/baf__ini_8h_source.html index 58b2440d..de8931f7 100644 --- a/baf__ini_8h_source.html +++ b/baf__ini_8h_source.html @@ -127,11 +127,11 @@
55 #endif
56 
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
bcType
Boundary condition data type.
Definition: ComMod.h:144
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/bf_8h_source.html b/bf_8h_source.html index 0ed852ab..b309f46e 100644 --- a/bf_8h_source.html +++ b/bf_8h_source.html @@ -119,10 +119,10 @@
47 
48 #endif
49 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
bfType
Definition: ComMod.h:297
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/cep_8h_source.html b/cep_8h_source.html index c9303b37..716ed49f 100644 --- a/cep_8h_source.html +++ b/cep_8h_source.html @@ -130,9 +130,9 @@
58 
CepMod
Definition: CepMod.h:220
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/class_constitutive_model_parameters-members.html b/class_constitutive_model_parameters-members.html index 511b347c..a5299512 100644 --- a/class_constitutive_model_parameters-members.html +++ b/class_constitutive_model_parameters-members.html @@ -79,32 +79,33 @@ HGO_MODEL (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic holzapfel (defined in ConstitutiveModelParameters)ConstitutiveModelParameters holzapfel_gasser_ogden (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - HOLZAPFEL_MODEL (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic - LEE_SACKS (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic - lee_sacks (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - mooney_rivlin (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - neo_hookean (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - NEOHOOKEAN_MODEL (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic - ParameterLists() (defined in ParameterLists)ParameterListsinline - params_mapParameterLists - print_parameter_list()ParameterListsinline - print_parameters() (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - set_parameter(const std::string &name, const bool value, bool required, Parameter< bool > &param)ParameterListsinline - set_parameter(const std::string &name, const double value, bool required, Parameter< double > &param) (defined in ParameterLists)ParameterListsinline - set_parameter(const std::string &name, std::initializer_list< double > value, bool required, VectorParameter< double > &param) (defined in ParameterLists)ParameterListsinline - set_parameter(const std::string &name, std::initializer_list< int > value, bool required, VectorParameter< int > &param) (defined in ParameterLists)ParameterListsinline - set_parameter(const std::string &name, std::initializer_list< std::string > value, bool required, VectorParameter< std::string > &param) (defined in ParameterLists)ParameterListsinline - set_parameter(const std::string &name, const int value, bool required, Parameter< int > &param, std::vector< int > range={}) (defined in ParameterLists)ParameterListsinline - set_parameter(const std::string &name, const std::string &value, bool required, Parameter< std::string > &param) (defined in ParameterLists)ParameterListsinline - set_parameter_value(const std::string &name, const std::string &value)ParameterListsinline - set_values(tinyxml2::XMLElement *modl_params) (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - set_xml_element_name(const std::string &name) (defined in ParameterLists)ParameterListsinline - stvenant_kirchhoff (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - STVENANT_KIRCHHOFF_MODEL (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic - type (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - value_set (defined in ConstitutiveModelParameters)ConstitutiveModelParameters - xml_element_name (defined in ParameterLists)ParameterLists - xml_element_name_ConstitutiveModelParametersstatic + HOLZAPFEL_OGDEN_MA_MODEL (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic + HOLZAPFEL_OGDEN_MODEL (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic + LEE_SACKS (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic + lee_sacks (defined in ConstitutiveModelParameters)ConstitutiveModelParameters + mooney_rivlin (defined in ConstitutiveModelParameters)ConstitutiveModelParameters + neo_hookean (defined in ConstitutiveModelParameters)ConstitutiveModelParameters + NEOHOOKEAN_MODEL (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic + ParameterLists() (defined in ParameterLists)ParameterListsinline + params_mapParameterLists + print_parameter_list()ParameterListsinline + print_parameters() (defined in ConstitutiveModelParameters)ConstitutiveModelParameters + set_parameter(const std::string &name, const bool value, bool required, Parameter< bool > &param)ParameterListsinline + set_parameter(const std::string &name, const double value, bool required, Parameter< double > &param) (defined in ParameterLists)ParameterListsinline + set_parameter(const std::string &name, std::initializer_list< double > value, bool required, VectorParameter< double > &param) (defined in ParameterLists)ParameterListsinline + set_parameter(const std::string &name, std::initializer_list< int > value, bool required, VectorParameter< int > &param) (defined in ParameterLists)ParameterListsinline + set_parameter(const std::string &name, std::initializer_list< std::string > value, bool required, VectorParameter< std::string > &param) (defined in ParameterLists)ParameterListsinline + set_parameter(const std::string &name, const int value, bool required, Parameter< int > &param, std::vector< int > range={}) (defined in ParameterLists)ParameterListsinline + set_parameter(const std::string &name, const std::string &value, bool required, Parameter< std::string > &param) (defined in ParameterLists)ParameterListsinline + set_parameter_value(const std::string &name, const std::string &value)ParameterListsinline + set_values(tinyxml2::XMLElement *modl_params) (defined in ConstitutiveModelParameters)ConstitutiveModelParameters + set_xml_element_name(const std::string &name) (defined in ParameterLists)ParameterListsinline + stvenant_kirchhoff (defined in ConstitutiveModelParameters)ConstitutiveModelParameters + STVENANT_KIRCHHOFF_MODEL (defined in ConstitutiveModelParameters)ConstitutiveModelParametersstatic + type (defined in ConstitutiveModelParameters)ConstitutiveModelParameters + value_set (defined in ConstitutiveModelParameters)ConstitutiveModelParameters + xml_element_name (defined in ParameterLists)ParameterLists + xml_element_name_ConstitutiveModelParametersstatic
diff --git a/class_constitutive_model_parameters.html b/class_constitutive_model_parameters.html index 5909d763..2f96d501 100644 --- a/class_constitutive_model_parameters.html +++ b/class_constitutive_model_parameters.html @@ -180,9 +180,12 @@ static const std::string HGO_MODEL = "HGO"   - -static const std::string HOLZAPFEL_MODEL = "Holzapfel" -  + +static const std::string HOLZAPFEL_OGDEN_MODEL = "HolzapfelOgden" +  + +static const std::string HOLZAPFEL_OGDEN_MA_MODEL = "HolzapfelOgden-ModifiedAnisotropy" +  static const std::string LEE_SACKS = "Lee-Sacks"   @@ -224,7 +227,9 @@

{ConstitutiveModelParameters::HGO_MODEL, ConstitutiveModelParameters::HGO_MODEL},
-
{ConstitutiveModelParameters::HOLZAPFEL_MODEL, ConstitutiveModelParameters::HOLZAPFEL_MODEL},
+
{ConstitutiveModelParameters::HOLZAPFEL_OGDEN_MODEL, ConstitutiveModelParameters::HOLZAPFEL_OGDEN_MODEL},
+
+
{ConstitutiveModelParameters::HOLZAPFEL_OGDEN_MA_MODEL, ConstitutiveModelParameters::HOLZAPFEL_OGDEN_MA_MODEL},
{ConstitutiveModelParameters::LEE_SACKS, ConstitutiveModelParameters::LEE_SACKS},
diff --git a/classfib_strs_type-members.html b/classfib_strs_type-members.html index 294f7220..d9c4715f 100644 --- a/classfib_strs_type-members.html +++ b/classfib_strs_type-members.html @@ -69,9 +69,10 @@

This is the complete list of members for fibStrsType, including all inherited members.

- - - + + + +
fType (defined in fibStrsType)fibStrsType
g (defined in fibStrsType)fibStrsType
gt (defined in fibStrsType)fibStrsType
eta_s (defined in fibStrsType)fibStrsType
fType (defined in fibStrsType)fibStrsType
g (defined in fibStrsType)fibStrsType
gt (defined in fibStrsType)fibStrsType
diff --git a/classfib_strs_type.html b/classfib_strs_type.html index d5c2c50b..05aadfb8 100644 --- a/classfib_strs_type.html +++ b/classfib_strs_type.html @@ -78,6 +78,9 @@ double g = 0.0   + +double eta_s = 0.0 +  fcType gt   diff --git a/cmm_8h_source.html b/cmm_8h_source.html index c395c3fc..a073ddbd 100644 --- a/cmm_8h_source.html +++ b/cmm_8h_source.html @@ -136,10 +136,10 @@
64 #endif
65 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
cmm
These subroutines implement the Coupled Momentum Method (CMM).
Definition: cmm.cpp:43
cmm::cmmi
void cmmi(ComMod &com_mod, const mshType &lM, const Array< double > &al, const Array< double > &dl, const Array< double > &xl, const Array< double > &bfl, const Vector< double > &pS0l, const Vector< double > &vwp, const Vector< int > &ptr)
CMM initialization (interior).
Definition: cmm.cpp:378
cmm::construct_cmm
void construct_cmm(ComMod &com_mod, const mshType &lM, const Array< double > &Ag, const Array< double > &Yg, const Array< double > &Dg)
Reproduces Fortran 'CONSTRUCT_CMM'.
Definition: cmm.cpp:782
diff --git a/contact_8h_source.html b/contact_8h_source.html index c9c0d6b0..6c6bbbd3 100644 --- a/contact_8h_source.html +++ b/contact_8h_source.html @@ -114,7 +114,7 @@
42 #endif
43 
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
diff --git a/distribute_8h_source.html b/distribute_8h_source.html index 60956569..44a0212e 100644 --- a/distribute_8h_source.html +++ b/distribute_8h_source.html @@ -129,18 +129,18 @@
57 
CepMod
Definition: CepMod.h:220
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
bcType
Boundary condition data type.
Definition: ComMod.h:144
bfType
Definition: ComMod.h:297
cmType
The cmType class stores data and defines methods used for mpi communication.
Definition: CmMod.h:82
-
eqType
Equation type.
Definition: ComMod.h:997
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
fluidViscModelType
Fluid viscosity model type.
Definition: ComMod.h:390
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
-
solidViscModelType
Fluid viscosity model type.
Definition: ComMod.h:415
-
stModelType
Structural domain type.
Definition: ComMod.h:343
+
eqType
Equation type.
Definition: ComMod.h:1000
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
fluidViscModelType
Fluid viscosity model type.
Definition: ComMod.h:393
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
+
solidViscModelType
Fluid viscosity model type.
Definition: ComMod.h:418
+
stModelType
Structural domain type.
Definition: ComMod.h:346
diff --git a/eq__assem_8h_source.html b/eq__assem_8h_source.html index 1300a474..4826b74e 100644 --- a/eq__assem_8h_source.html +++ b/eq__assem_8h_source.html @@ -121,11 +121,11 @@
49 #endif
50 
CepMod
Definition: CepMod.h:220
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
bcType
Boundary condition data type.
Definition: ComMod.h:144
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/fft_8h_source.html b/fft_8h_source.html index 570096cc..f6d004f0 100644 --- a/fft_8h_source.html +++ b/fft_8h_source.html @@ -115,7 +115,7 @@
43 
44 #endif
45 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
MBType
Moving boundary data structure (used for general BC)
Definition: ComMod.h:100
fcType
Fourier coefficients that are used to specify unsteady BCs.
Definition: ComMod.h:64
diff --git a/fluid_8h_source.html b/fluid_8h_source.html index f8be6dde..1b9df7e2 100644 --- a/fluid_8h_source.html +++ b/fluid_8h_source.html @@ -149,10 +149,10 @@
77 #endif
78 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:429
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:432
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/fs_8h_source.html b/fs_8h_source.html index 20d8e215..695ae278 100644 --- a/fs_8h_source.html +++ b/fs_8h_source.html @@ -128,10 +128,10 @@
56 
57 #endif
58 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
fsType
Function spaces (basis) type.
Definition: ComMod.h:249
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/fsi_8h_source.html b/fsi_8h_source.html index 82a70b23..426fab14 100644 --- a/fsi_8h_source.html +++ b/fsi_8h_source.html @@ -116,8 +116,8 @@
44 #endif
45 
CepMod
Definition: CepMod.h:220
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/heatf_8h_source.html b/heatf_8h_source.html index 7dc84145..4232308a 100644 --- a/heatf_8h_source.html +++ b/heatf_8h_source.html @@ -123,9 +123,9 @@
51 #endif
52 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/heats_8h_source.html b/heats_8h_source.html index bf33244e..7a60e351 100644 --- a/heats_8h_source.html +++ b/heats_8h_source.html @@ -122,9 +122,9 @@
50 #endif
51 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/l__elas_8h_source.html b/l__elas_8h_source.html index 0971c319..ab67688b 100644 --- a/l__elas_8h_source.html +++ b/l__elas_8h_source.html @@ -125,9 +125,9 @@
53 #endif
54 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/lhsa_8h_source.html b/lhsa_8h_source.html index 439505c6..02f5c79a 100644 --- a/lhsa_8h_source.html +++ b/lhsa_8h_source.html @@ -121,7 +121,7 @@
49 #endif
50 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
diff --git a/load__msh_8h_source.html b/load__msh_8h_source.html index b58f1e25..40c177c4 100644 --- a/load__msh_8h_source.html +++ b/load__msh_8h_source.html @@ -121,10 +121,10 @@
49 
50 #endif
51 
-
MeshParameters
The MeshParameters class is used to store paramaters for the 'Add_mesh' XML element.
Definition: Parameters.h:1365
+
MeshParameters
The MeshParameters class is used to store paramaters for the 'Add_mesh' XML element.
Definition: Parameters.h:1366
Simulation
Definition: Simulation.h:41
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/ls_8h_source.html b/ls_8h_source.html index ebdd8973..0279a87d 100644 --- a/ls_8h_source.html +++ b/ls_8h_source.html @@ -120,9 +120,9 @@
48 
49 #endif
50 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
eqType
Equation type.
Definition: ComMod.h:997
+
eqType
Equation type.
Definition: ComMod.h:1000
diff --git a/mat__fun__carray_8h_source.html b/mat__fun__carray_8h_source.html index cee7055c..08212eb1 100644 --- a/mat__fun__carray_8h_source.html +++ b/mat__fun__carray_8h_source.html @@ -531,118 +531,119 @@
459 }
460 
461 
-
462 template <size_t N>
-
463 void mat_symm(const double A[N][N], double S[N][N])
-
464 {
-
465  for (int i = 0; i < N; i++) {
-
466  for (int j = 0; j < N; j++) {
-
467  S[i][j] = 0.5 * (A[i][j] + A[j][i]);
-
468  }
-
469  }
-
470 }
-
471 
-
472 template <size_t N>
-
473 void mat_dev(const double A[N][N], double dev[N][N])
-
474 {
-
475  double trA = mat_trace<N>(A);
-
476  double id[N][N];
-
477  mat_id<N>(id);
-
478 
-
479  for (int i = 0; i < N; i++) {
-
480  for (int j = 0; j < N; j++) {
-
481  dev[i][j] = A[i][j] - (trA / static_cast<double>(N)) * id[i][j];
-
482  }
-
483  }
-
484 }
-
485 
+
462 
+
463 template <size_t N>
+
464 void mat_symm(const double A[N][N], double S[N][N])
+
465 {
+
466  for (int i = 0; i < N; i++) {
+
467  for (int j = 0; j < N; j++) {
+
468  S[i][j] = 0.5 * (A[i][j] + A[j][i]);
+
469  }
+
470  }
+
471 }
+
472 
+
473 template <size_t N>
+
474 void mat_dev(const double A[N][N], double dev[N][N])
+
475 {
+
476  double trA = mat_trace<N>(A);
+
477  double id[N][N];
+
478  mat_id<N>(id);
+
479 
+
480  for (int i = 0; i < N; i++) {
+
481  for (int j = 0; j < N; j++) {
+
482  dev[i][j] = A[i][j] - (trA / static_cast<double>(N)) * id[i][j];
+
483  }
+
484  }
+
485 }
486 
-
487 template <size_t N>
-
488 void ten_ddot_3424(const double A[N][N][N][N], const double B[N][N][N][N], double C[N][N][N][N])
-
489 {
-
490  int nn = pow(N,4);
-
491  ten_zero(C);
-
492 
-
493  if (N == 2) {
-
494  for (int ii = 0; ii < nn; ii++) {
-
495  int i = t_ind(0,ii);
-
496  int j = t_ind(1,ii);
-
497  int k = t_ind(2,ii);
-
498  int l = t_ind(3,ii);
-
499 
-
500  C[i][j][k][l] += A[i][j][0][0]*B[k][0][l][0] +
-
501  A[i][j][0][1]*B[k][0][l][1] +
-
502  A[i][j][1][0]*B[k][1][l][0] +
-
503  A[i][j][1][1]*B[k][1][l][1];
-
504  }
-
505 
-
506  } else {
-
507 
-
508  for (int ii = 0; ii < nn; ii++) {
-
509  int i = t_ind(0,ii);
-
510  int j = t_ind(1,ii);
-
511  int k = t_ind(2,ii);
-
512  int l = t_ind(3,ii);
-
513 
-
514  C[i][j][k][l] += A[i][j][0][0]*B[k][0][l][0] +
-
515  A[i][j][0][1]*B[k][0][l][1] +
-
516  A[i][j][0][2]*B[k][0][l][2] +
-
517  A[i][j][1][0]*B[k][1][l][0] +
-
518  A[i][j][1][1]*B[k][1][l][1] +
-
519  A[i][j][1][2]*B[k][1][l][2] +
-
520  A[i][j][2][0]*B[k][2][l][0] +
-
521  A[i][j][2][1]*B[k][2][l][1] +
-
522  A[i][j][2][2]*B[k][2][l][2];
-
523 
-
524  }
-
525  }
-
526 }
-
527 
-
528 template <size_t N>
-
529 void ten_ddot_2412(const double A[N][N][N][N], const double B[N][N][N][N], double C[N][N][N][N])
-
530 {
-
531  int nn = pow(N,4);
-
532  ten_zero(C);
-
533 
-
534  if (N == 2) {
-
535  for (int ii = 0; ii < nn; ii++) {
-
536  int i = t_ind(0,ii);
-
537  int j = t_ind(1,ii);
-
538  int k = t_ind(2,ii);
-
539  int l = t_ind(3,ii);
-
540 
-
541  C[i][j][k][l] += A[i][0][j][0]*B[0][0][k][l] +
-
542  A[i][0][j][1]*B[0][1][k][l] +
-
543  A[i][1][j][0]*B[1][0][k][l] +
-
544  A[i][1][j][1]*B[1][1][k][l];
-
545 
-
546  }
-
547 
-
548  } else {
-
549 
-
550  for (int ii = 0; ii < nn; ii++) {
-
551  int i = t_ind(0,ii);
-
552  int j = t_ind(1,ii);
-
553  int k = t_ind(2,ii);
-
554  int l = t_ind(3,ii);
-
555 
-
556  C[i][j][k][l] += A[i][0][j][0]*B[0][0][k][l] +
-
557  A[i][0][j][1]*B[0][1][k][l] +
-
558  A[i][0][j][2]*B[0][2][k][l] +
-
559  A[i][1][j][0]*B[1][0][k][l] +
-
560  A[i][1][j][1]*B[1][1][k][l] +
-
561  A[i][1][j][2]*B[1][2][k][l] +
-
562  A[i][2][j][0]*B[2][0][k][l] +
-
563  A[i][2][j][1]*B[2][1][k][l] +
-
564  A[i][2][j][2]*B[2][2][k][l];
-
565  }
-
566  }
-
567 }
-
568 
+
487 
+
488 template <size_t N>
+
489 void ten_ddot_3424(const double A[N][N][N][N], const double B[N][N][N][N], double C[N][N][N][N])
+
490 {
+
491  int nn = pow(N,4);
+
492  ten_zero(C);
+
493 
+
494  if (N == 2) {
+
495  for (int ii = 0; ii < nn; ii++) {
+
496  int i = t_ind(0,ii);
+
497  int j = t_ind(1,ii);
+
498  int k = t_ind(2,ii);
+
499  int l = t_ind(3,ii);
+
500 
+
501  C[i][j][k][l] += A[i][j][0][0]*B[k][0][l][0] +
+
502  A[i][j][0][1]*B[k][0][l][1] +
+
503  A[i][j][1][0]*B[k][1][l][0] +
+
504  A[i][j][1][1]*B[k][1][l][1];
+
505  }
+
506 
+
507  } else {
+
508 
+
509  for (int ii = 0; ii < nn; ii++) {
+
510  int i = t_ind(0,ii);
+
511  int j = t_ind(1,ii);
+
512  int k = t_ind(2,ii);
+
513  int l = t_ind(3,ii);
+
514 
+
515  C[i][j][k][l] += A[i][j][0][0]*B[k][0][l][0] +
+
516  A[i][j][0][1]*B[k][0][l][1] +
+
517  A[i][j][0][2]*B[k][0][l][2] +
+
518  A[i][j][1][0]*B[k][1][l][0] +
+
519  A[i][j][1][1]*B[k][1][l][1] +
+
520  A[i][j][1][2]*B[k][1][l][2] +
+
521  A[i][j][2][0]*B[k][2][l][0] +
+
522  A[i][j][2][1]*B[k][2][l][1] +
+
523  A[i][j][2][2]*B[k][2][l][2];
+
524 
+
525  }
+
526  }
+
527 }
+
528 
+
529 template <size_t N>
+
530 void ten_ddot_2412(const double A[N][N][N][N], const double B[N][N][N][N], double C[N][N][N][N])
+
531 {
+
532  int nn = pow(N,4);
+
533  ten_zero(C);
+
534 
+
535  if (N == 2) {
+
536  for (int ii = 0; ii < nn; ii++) {
+
537  int i = t_ind(0,ii);
+
538  int j = t_ind(1,ii);
+
539  int k = t_ind(2,ii);
+
540  int l = t_ind(3,ii);
+
541 
+
542  C[i][j][k][l] += A[i][0][j][0]*B[0][0][k][l] +
+
543  A[i][0][j][1]*B[0][1][k][l] +
+
544  A[i][1][j][0]*B[1][0][k][l] +
+
545  A[i][1][j][1]*B[1][1][k][l];
+
546 
+
547  }
+
548 
+
549  } else {
+
550 
+
551  for (int ii = 0; ii < nn; ii++) {
+
552  int i = t_ind(0,ii);
+
553  int j = t_ind(1,ii);
+
554  int k = t_ind(2,ii);
+
555  int l = t_ind(3,ii);
+
556 
+
557  C[i][j][k][l] += A[i][0][j][0]*B[0][0][k][l] +
+
558  A[i][0][j][1]*B[0][1][k][l] +
+
559  A[i][0][j][2]*B[0][2][k][l] +
+
560  A[i][1][j][0]*B[1][0][k][l] +
+
561  A[i][1][j][1]*B[1][1][k][l] +
+
562  A[i][1][j][2]*B[1][2][k][l] +
+
563  A[i][2][j][0]*B[2][0][k][l] +
+
564  A[i][2][j][1]*B[2][1][k][l] +
+
565  A[i][2][j][2]*B[2][2][k][l];
+
566  }
+
567  }
+
568 }
569 
-
570 };
-
571 
-
572 #endif
-
573 
+
570 
+
571 };
+
572 
+
573 #endif
+
574 
mat_fun::ten_init
void ten_init(const int nd)
Initialize tensor index pointer.
Definition: mat_fun.cpp:791
mat_fun::ten_symm_prod
Tensor4< double > ten_symm_prod(const Array< double > &A, const Array< double > &B, const int nd)
Create a 4th order tensor from symmetric outer product of two matrices.
Definition: mat_fun.cpp:883
diff --git a/mat__models_8h_source.html b/mat__models_8h_source.html index f58e5a11..a8fe8354 100644 --- a/mat__models_8h_source.html +++ b/mat__models_8h_source.html @@ -144,12 +144,12 @@
72 #endif
73 
CepMod
Definition: CepMod.h:220
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Tensor4
The Tensor4 template class implements a simple interface to 4th order tensors.
Definition: Tensor4.h:45
-
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:429
+
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:432
fibStrsType
Definition: ComMod.h:327
-
stModelType
Structural domain type.
Definition: ComMod.h:343
+
stModelType
Structural domain type.
Definition: ComMod.h:346
diff --git a/mat__models__carray_8h_source.html b/mat__models__carray_8h_source.html index 6e49ca0e..4227cfbf 100644 --- a/mat__models__carray_8h_source.html +++ b/mat__models__carray_8h_source.html @@ -294,1204 +294,1427 @@
222  // Fiber-reinforced stress
223  double Tfa = 0.0;
224  mat_models::get_fib_stress(com_mod, cep_mod, stM.Tf, Tfa);
-
225 
-
226  // Electromechanics coupling - active stress
-
227  if (cep_mod.cem.aStress) {
-
228  Tfa = Tfa + ya;
-
229  }
-
230 
-
231  // Electromechanics coupling - active strain
-
232  double Fe[N][N];
-
233  for (int i = 0; i < N; i++) {
-
234  for (int j = 0; j < N; j++) {
-
235  Fe[i][j] = F[i][j];
-
236  }
-
237  }
-
238 
-
239  double Fa[N][N];
-
240  mat_fun_carray::mat_zero(Fa);
-
241  double Fai[N][N];
-
242  mat_fun_carray::mat_zero(Fai);
-
243 
-
244  for (int i = 0; i < N; i++) {
-
245  for (int j = 0; j < N; j++) {
-
246  if (i == j) {
-
247  Fa[i][j] = 1.0;
-
248  Fai[i][j] = 1.0;
-
249  }
-
250  }
-
251  }
-
252 
-
253  double J = mat_fun_carray::mat_det<N>(Fe);
-
254  double J2d = pow(J, (-2.0/nd));
-
255  double J4d = J2d*J2d;
-
256 
-
257  double Idm[N][N];
-
258  mat_fun_carray::mat_id<N>(Idm);
-
259 
-
260  double Fe_t[N][N];
-
261  mat_fun_carray::transpose<N>(Fe, Fe_t);
-
262 
-
263  double C[N][N];
-
264  mat_fun_carray::mat_mul<N>(Fe_t, Fe, C);
-
265 
-
266  double E[N][N];
-
267  for (int i = 0; i < nsd; i++) {
-
268  for (int j = 0; j < nsd; j++) {
-
269  E[i][j] = 0.50 * (C[i][j] - Idm[i][j]);
-
270  }
-
271  }
-
272 
-
273  double Ci[N][N];
-
274  mat_fun_carray::mat_inv<N>(C, Ci);
-
275 
-
276  double Cprod[N][N];
-
277  mat_fun_carray::mat_mul<N>(C,C,Cprod);
-
278  double trE = mat_fun_carray::mat_trace<N>(E);
-
279  double Inv1 = J2d * mat_fun_carray::mat_trace<N>(C);
-
280  double Inv2 = 0.50 * (Inv1*Inv1 - J4d * mat_fun_carray::mat_trace<N>(Cprod));
-
281 
-
282  // Contribution of dilational penalty terms to S and CC
-
283  double p = 0.0;
-
284  double pl = 0.0;
-
285 
-
286  if (!utils::is_zero(Kp)) {
-
287  mat_models::get_svol_p(com_mod, cep_mod, stM, J, p, pl);
-
288  }
-
289 
-
290  // Now, compute isochoric and total stress, elasticity tensors
-
291  //
-
292  double CC[N][N][N][N];
-
293  double Idm_prod[N][N][N][N];
-
294  double Ids[N][N][N][N];
-
295  mat_fun_carray::ten_ids<N>(Ids);
-
296 
-
297  switch (stM.isoType) {
-
298  case ConstitutiveModelType::stIso_lin: {
-
299  double g1 = stM.C10; // mu
-
300  for (int i = 0; i < nsd; i++) {
-
301  for (int j = 0; j < nsd; j++) {
-
302  S[i][j] = g1 * Idm[i][j];
-
303  }
-
304  }
-
305  return;
-
306  } break;
-
307 
-
308  // St.Venant-Kirchhoff
-
309  //
-
310  case ConstitutiveModelType::stIso_StVK: {
-
311  double g1 = stM.C10; // lambda
-
312  double g2 = stM.C01 * 2.0; // 2*mu
-
313 
-
314  for (int i = 0; i < N; i++) {
-
315  for (int j = 0; j < N; j++) {
-
316  S[i][j] = g1 * trE * Idm[i][j] + g2 * E[i][j];
-
317  }
-
318  }
-
319 
-
320  mat_fun_carray::ten_dyad_prod<N>(Idm, Idm, Idm_prod);
-
321  mat_fun_carray::ten_ids<N>(Ids);
-
322 
-
323  for (int i = 0; i < N; i++) {
-
324  for (int j = 0; j < N; j++) {
-
325  for (int k = 0; k < N; k++) {
-
326  for (int l = 0; l < N; l++) {
-
327  CC[i][j][k][l] = g1 * Idm_prod[i][j][k][l] + g2 * Ids[i][j][k][l];
-
328  }
-
329  }
-
330  }
-
331  }
-
332  } break;
-
333 
-
334  // modified St.Venant-Kirchhoff
-
335  //
-
336  case ConstitutiveModelType::stIso_mStVK: {
-
337  double g1 = stM.C10; // kappa
-
338  double g2 = stM.C01; // mu
-
339 
-
340  for (int i = 0; i < nsd; i++) {
-
341  for (int j = 0; j < nsd; j++) {
-
342  S[i][j] = g1 * log(J) * Ci[i][j] + g2 * (C[i][j] - Idm[i][j]);
-
343  }
-
344  }
-
345 
-
346  mat_fun_carray::ten_ids<N>(Ids);
-
347 
-
348  double Ci_Ci_prod[N][N][N][N];
-
349  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
-
350 
-
351  double Ci_Ci_symm_prod[N][N][N][N];
-
352  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_Ci_symm_prod);
-
353 
-
354  for (int i = 0; i < N; i++) {
-
355  for (int j = 0; j < N; j++) {
-
356  for (int k = 0; k < N; k++) {
-
357  for (int l = 0; l < N; l++) {
-
358  CC[i][j][k][l] = g1 * ( -2.0 * log(J) * Ci_Ci_symm_prod[i][j][k][l] + Ci_Ci_prod[i][j][k][l] ) +
-
359  2.0 * g2 * Ids[i][j][k][l];
-
360  }
-
361  }
-
362  }
-
363  }
-
364 
-
365  } break;
-
366 
-
367  // NeoHookean model
-
368  //
-
369  case ConstitutiveModelType::stIso_nHook: {
-
370  double g1 = 2.0 * stM.C10;
-
371 
-
372  double Sb[N][N];
-
373  for (int i = 0; i < nsd; i++) {
-
374  for (int j = 0; j < nsd; j++) {
-
375  Sb[i][j] = g1*Idm[i][j];
-
376  }
-
377  }
-
378 
-
379  // Fiber reinforcement/active stress
-
380  double prod[N][N];
-
381  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), prod);
-
382 
-
383  for (int i = 0; i < nsd; i++) {
-
384  for (int j = 0; j < nsd; j++) {
-
385  Sb[i][j] += Tfa * prod[i][j];
-
386  }
-
387  }
-
388 
-
389  double r1 = g1 * Inv1 / nd;
-
390  for (int j = 0; j < N; j++) {
-
391  for (int i = 0; i < N; i++) {
-
392  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
-
393  }
-
394  }
-
395 
-
396  double Ci_S_prod[N][N][N][N];
-
397  double S_Ci_prod[N][N][N][N];
-
398  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
-
399  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
-
400 
-
401  for (int j = 0; j < N; j++) {
-
402  for (int i = 0; i < N; i++) {
-
403  S[i][j] += p * J * Ci[i][j];
-
404  }
-
405  }
-
406 
-
407  for (int i = 0; i < nsd; i++) {
-
408  for (int j = 0; j < nsd; j++) {
-
409  for (int k = 0; k < nsd; k++) {
-
410  for (int l = 0; l < nsd; l++) {
-
411  CC[i][j][k][l] = (-2.0/nd) * (Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
-
412  }
-
413  }
-
414  }
-
415  }
-
416 
-
417  double Ci_sym_prod[N][N][N][N];
-
418  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
-
419 
-
420  double Ci_Ci_prod[N][N][N][N];
-
421  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
-
422 
-
423  for (int i = 0; i < nsd; i++) {
-
424  for (int j = 0; j < nsd; j++) {
-
425  for (int k = 0; k < nsd; k++) {
-
426  for (int l = 0; l < nsd; l++) {
-
427  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
-
428  }
-
429  }
-
430  }
-
431  }
-
432 
-
433  } break;
-
434 
-
435  // Mooney-Rivlin model
-
436  //
-
437  case ConstitutiveModelType::stIso_MR: {
-
438  double g1 = 2.0 * (stM.C10 + Inv1*stM.C01);
-
439  double g2 = -2.0 * stM.C01;
-
440 
-
441  double Sb[N][N];
-
442  for (int i = 0; i < nsd; i++) {
-
443  for (int j = 0; j < nsd; j++) {
-
444  Sb[i][j] = g1*Idm[i][j] + g2*J2d*C[i][j];
-
445  }
-
446  }
-
447 
-
448  // Fiber reinforcement/active stress
-
449  double prod[N][N];
-
450  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), prod);
-
451 
-
452  for (int i = 0; i < nsd; i++) {
-
453  for (int j = 0; j < nsd; j++) {
-
454  Sb[i][j] += Tfa*prod[i][j];
-
455  }
-
456  }
-
457 
-
458  g1 = 4.0 * J4d * stM.C01;
-
459 
-
460  double CCb[N][N][N][N];
-
461  mat_fun_carray::ten_dyad_prod<N>(Idm, Idm, Idm_prod);
-
462 
-
463  for (int i = 0; i < nsd; i++) {
-
464  for (int j = 0; j < nsd; j++) {
-
465  for (int k = 0; k < nsd; k++) {
-
466  for (int l = 0; l < nsd; l++) {
-
467  CCb[i][j][k][l] = g1 * (Idm_prod[i][j][k][l] - Ids[i][j][k][l]);
-
468  }
-
469  }
-
470  }
-
471  }
-
472 
-
473  double r1 = J2d * mat_fun_carray::mat_ddot<N>(C, Sb) / nd;
-
474  for (int i = 0; i < nsd; i++) {
-
475  for (int j = 0; j < nsd; j++) {
-
476  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
-
477  }
-
478  }
-
479 
-
480  double Ci_Ci_prod[N][N][N][N];
-
481  double Ci_C_prod[N][N][N][N];
-
482  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
-
483  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
-
484 
-
485  double PP[N][N][N][N];
-
486 
-
487  for (int i = 0; i < nsd; i++) {
-
488  for (int j = 0; j < nsd; j++) {
-
489  for (int k = 0; k < nsd; k++) {
-
490  for (int l = 0; l < nsd; l++) {
-
491  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
-
492  }
-
493  }
-
494  }
-
495  }
-
496 
-
497  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
-
498 
-
499  double CC_t[N][N][N][N];
-
500  mat_fun_carray::ten_transpose<N>(CC, CC_t);
-
501 
-
502  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
-
503 
-
504  double Ci_S_prod[N][N][N][N];
-
505  double S_Ci_prod[N][N][N][N];
-
506  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
-
507  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
-
508 
-
509  for (int i = 0; i < nsd; i++) {
-
510  for (int j = 0; j < nsd; j++) {
-
511  for (int k = 0; k < nsd; k++) {
-
512  for (int l = 0; l < nsd; l++) {
-
513  CC[i][j][k][l] -= (2.0/nd) * ( Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
-
514  }
-
515  }
-
516  }
-
517  }
-
518 
-
519  for (int i = 0; i < nsd; i++) {
-
520  for (int j = 0; j < nsd; j++) {
-
521  S[i][j] += p * J * Ci[i][j];
-
522  }
-
523  }
-
524 
-
525  double Ci_sym_prod[N][N][N][N];
-
526  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
-
527 
-
528  for (int i = 0; i < nsd; i++) {
-
529  for (int j = 0; j < nsd; j++) {
-
530  for (int k = 0; k < nsd; k++) {
-
531  for (int l = 0; l < nsd; l++) {
-
532  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
-
533  }
-
534  }
-
535  }
-
536  }
-
537 
-
538  } break;
-
539 
-
540  // HGO (Holzapfel-Gasser-Ogden) model with additive splitting of
-
541  // the anisotropic fiber-based strain-energy terms
-
542  //
-
543  case ConstitutiveModelType::stIso_HGO: {
-
544  if (nfd != 2) {
-
545  //err = "Min fiber directions not defined for HGO material model (2)"
-
546  }
-
547  double kap = stM.kap;
-
548 
-
549  double C_fl[N];
-
550  mat_fun_carray::mat_mul(C, fl.rcol(0), C_fl);
-
551  double Inv4 = J2d * mat_fun_carray::norm<N>(fl.rcol(0), C_fl);
-
552 
-
553  mat_fun_carray::mat_mul(C, fl.rcol(1), C_fl);
-
554  double Inv6 = J2d * mat_fun_carray::norm<N>(fl.rcol(1), C_fl);
-
555 
-
556  double Eff = kap*Inv1 + (1.0-3.0*kap)*Inv4 - 1.0;
-
557  double Ess = kap*Inv1 + (1.0-3.0*kap)*Inv6 - 1.0;
-
558 
-
559  double Hff[N][N];
-
560  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), Hff);
-
561 
-
562  for (int i = 0; i < N; i++) {
-
563  for (int j = 0; j < N; j++) {
-
564  Hff[i][j] = kap*Idm[i][j] + (1.0-3.0*kap)*Hff[i][j];
-
565  }
-
566  }
-
567 
-
568  double Hss[N][N];
-
569  mat_fun_carray::mat_dyad_prod<N>(fl.col(1), fl.col(1), Hss);
-
570 
-
571  for (int i = 0; i < N; i++) {
-
572  for (int j = 0; j < N; j++) {
-
573  Hss[i][j] = kap*Idm[i][j] + (1.0-3.0*kap)*Hss[i][j];
-
574  }
-
575  }
-
576 
-
577  double g1 = stM.C10;
-
578  double g2 = stM.aff * Eff * exp(stM.bff*Eff*Eff);
-
579  double g3 = stM.ass * Ess * exp(stM.bss*Ess*Ess);
-
580 
-
581  double Sb[N][N];
-
582  for (int i = 0; i < N; i++) {
-
583  for (int j = 0; j < N; j++) {
-
584  Sb[i][j] = 2.0 * (g1*Idm[i][j] + g2*Hff[i][j] + g3*Hss[i][j]);
-
585  }
-
586  }
-
587 
-
588  // Fiber reinforcement/active stress
-
589  double prod[N][N];
-
590  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), prod);
-
591 
-
592  for (int i = 0; i < N; i++) {
-
593  for (int j = 0; j < N; j++) {
-
594  Sb[i][j] += Tfa*prod[i][j];
-
595  }
-
596  }
-
597 
-
598  g1 = stM.aff*(1.0 + 2.0*stM.bff*Eff*Eff)*exp(stM.bff*Eff*Eff);
-
599  g2 = stM.ass*(1.0 + 2.0*stM.bss*Ess*Ess)*exp(stM.bss*Ess*Ess);
-
600  g1 = 4.0*J4d*g1;
-
601  g2 = 4.0*J4d*g2;
-
602 
-
603  double CCb_hff[N][N][N][N];
-
604  mat_fun_carray::ten_dyad_prod<N>(Hff, Hff, CCb_hff);
-
605 
-
606  double CCb_hss[N][N][N][N];
-
607  mat_fun_carray::ten_dyad_prod<N>(Hss, Hss, CCb_hss);
-
608 
-
609  double CCb[N][N][N][N];
-
610 
-
611  for (int i = 0; i < N; i++) {
-
612  for (int j = 0; j < N; j++) {
-
613  for (int k = 0; k < N; k++) {
-
614  for (int l = 0; l < N; l++) {
-
615  CCb[i][j][k][l] = g1 * CCb_hff[i][j][k][l] + g2 * CCb_hss[i][j][k][l];
-
616  }
-
617  }
-
618  }
-
619  }
-
620 
-
621  double r1 = J2d * mat_fun_carray::mat_ddot<N>(C, Sb) / nd;
-
622 
-
623  for (int i = 0; i < N; i++) {
-
624  for (int j = 0; j < N; j++) {
-
625  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
-
626  }
-
627  }
-
628 
-
629  double Ci_C_prod[N][N][N][N];
-
630  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
-
631  double PP[N][N][N][N];
-
632 
-
633  for (int i = 0; i < N; i++) {
-
634  for (int j = 0; j < N; j++) {
-
635  for (int k = 0; k < N; k++) {
-
636  for (int l = 0; l < N; l++) {
-
637  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
-
638  }
-
639  }
-
640  }
-
641  }
-
642 
-
643  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
-
644 
-
645  double CC_t[N][N][N][N];
-
646  mat_fun_carray::ten_transpose<N>(CC, CC_t);
-
647 
-
648  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
-
649 
-
650  double Ci_S_prod[N][N][N][N];
-
651  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
-
652 
-
653  double S_Ci_prod[N][N][N][N];
-
654  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
-
655 
-
656  for (int i = 0; i < N; i++) {
-
657  for (int j = 0; j < N; j++) {
-
658  for (int k = 0; k < N; k++) {
-
659  for (int l = 0; l < N; l++) {
-
660  CC[i][j][k][l] -= (2.0/nd) * ( Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
-
661  }
-
662  }
-
663  }
-
664  }
-
665 
-
666  for (int i = 0; i < nsd; i++) {
-
667  for (int j = 0; j < nsd; j++) {
-
668  S[i][j] += p * J * Ci[i][j];
-
669  }
-
670  }
-
671 
-
672  double Ci_sym_prod[N][N][N][N];
-
673  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
-
674 
-
675  double Ci_Ci_prod[N][N][N][N];
-
676  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
-
677 
-
678  for (int i = 0; i < nsd; i++) {
-
679  for (int j = 0; j < nsd; j++) {
-
680  for (int k = 0; k < nsd; k++) {
-
681  for (int l = 0; l < nsd; l++) {
-
682  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
-
683  }
-
684  }
-
685  }
-
686  }
-
687 
-
688  } break;
-
689 
-
690  // Guccione (1995) transversely isotropic model
-
691  //
-
692  case ConstitutiveModelType::stIso_Gucci: {
-
693  #ifdef debug_get_pk2cc
-
694  std::cout << msg_prefix << "stIso_Gucci" << std::endl;
-
695  #endif
-
696  if (nfd != 2) {
-
697  //err = "Min fiber directions not defined for Guccione material model (2)"
-
698  }
-
699 
-
700  // Compute isochoric component of E
-
701  double E[N][N];
-
702  for (int i = 0; i < N; i++) {
-
703  for (int j = 0; j < N; j++) {
-
704  E[i][j] = 0.50 * (J2d*C[i][j] - Idm[i][j]);
-
705  }
-
706  }
-
707 
-
708  // Transform into local orthogonal coordinate system
-
709  //
-
710  double Rm[N][N];
-
711  auto fl_0 = fl.col(0);
-
712  auto fl_1 = fl.col(1);
-
713  auto fl_cross = cross(fl);
-
714 
-
715  for (int i = 0; i < N; i++) {
-
716  Rm[i][0] = fl_0[i];
-
717  Rm[i][1] = fl_1[i];
-
718  Rm[i][2] = fl_cross[i];
-
719  }
-
720 
-
721  // Project E to local orthogocal coordinate system
-
722  //
-
723  double Es_1[N][N];
-
724  mat_fun_carray::mat_mul(E, Rm, Es_1);
-
725 
-
726  double Rm_t[N][N];
-
727  mat_fun_carray::transpose<N>(Rm, Rm_t);
-
728 
-
729  double Es[N][N];
-
730  mat_fun_carray::mat_mul(Rm_t, Es_1, Es);
-
731 
-
732  double g1 = stM.bff;
-
733  double g2 = stM.bss;
-
734  double g3 = stM.bfs;
-
735 
-
736  double QQ = g1 * Es[0][0]*Es[0][0] +
-
737  g2 * (Es[1][1]*Es[1][1] + Es[2][2]*Es[2][2] + Es[1][2]*Es[1][2] + Es[2][1]*Es[2][1]) +
-
738  g3 * (Es[0][1]*Es[0][1] + Es[1][0]*Es[1][0] + Es[0][2]*Es[0][2] + Es[2][0]*Es[2][0]);
-
739 
-
740  double r2 = stM.C10 * exp(QQ);
-
741 
-
742  // Fiber stiffness contribution := (dE*_ab / dE_IJ)
-
743  //
-
744  // Use Array in the following since it is a bit tricky.
-
745  //
-
746  Array<double> Rm_a(N,N);
-
747  for (int i = 0; i < N; i++) {
-
748  for (int j = 0; j < N; j++) {
-
749  Rm_a(i,j) = Rm[i][j];
-
750  }
-
751  }
-
752 
-
753  Array3<double> RmRm(N,N,6);
-
754 
-
755  RmRm.set_slice(0, mat_dyad_prod(Rm_a.col(0), Rm_a.col(0), nsd));
-
756  RmRm.set_slice(1, mat_dyad_prod(Rm_a.col(1), Rm_a.col(1), nsd));
-
757  RmRm.set_slice(2, mat_dyad_prod(Rm_a.col(2), Rm_a.col(2), nsd));
-
758 
-
759  RmRm.set_slice(3, mat_symm_prod(Rm_a.col(0), Rm_a.col(1), nsd));
-
760  RmRm.set_slice(4, mat_symm_prod(Rm_a.col(1), Rm_a.col(2), nsd));
-
761  RmRm.set_slice(5, mat_symm_prod(Rm_a.col(2), Rm_a.col(0), nsd));
-
762 
-
763  double Sb[N][N];
-
764 
-
765  for (int i = 0; i < N; i++) {
-
766  for (int j = 0; j < N; j++) {
-
767  Sb[i][j] = g1 * Es[0][0] * RmRm.rslice(0)(i,j) +
-
768  g2 * (Es[1][1] * RmRm.rslice(1)(i,j) + Es[2][2]*RmRm.rslice(2)(i,j) +
-
769  2.0*Es[1][2]*RmRm.rslice(4)(i,j)) +
-
770  2.0 * g3 * (Es[0][1] * RmRm.rslice(3)(i,j) + Es[0][2]*RmRm.rslice(5)(i,j));
-
771 
-
772  }
-
773  }
-
774 
-
775  double Sb_prod[N][N][N][N];
-
776  mat_fun_carray::ten_dyad_prod<N>(Sb, Sb, Sb_prod);
-
777  double CCb[N][N][N][N];
-
778 
-
779  for (int i = 0; i < N; i++) {
-
780  for (int j = 0; j < N; j++) {
-
781  for (int k = 0; k < N; k++) {
-
782  for (int l = 0; l < N; l++) {
-
783  CCb[i][j][k][l] = 2.0 * Sb_prod[i][j][k][l];
-
784  }
-
785  }
-
786  }
-
787  }
-
788 
-
789  for (int i = 0; i < N; i++) {
-
790  for (int j = 0; j < N; j++) {
-
791  Sb[i][j] = Sb[i][j] * r2;
-
792  }
-
793  }
-
794 
-
795  // Fiber reinforcement/active stress
-
796  //
-
797  double prod[N][N];
-
798  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), prod);
-
799 
-
800  for (int i = 0; i < N; i++) {
-
801  for (int j = 0; j < N; j++) {
-
802  Sb[i][j] += Tfa * prod[i][j];
-
803  }
-
804  }
-
805 
-
806  double r1 = J2d * mat_fun_carray::mat_ddot<N>(C, Sb) / nd;
-
807 
-
808  for (int i = 0; i < nsd; i++) {
-
809  for (int j = 0; j < nsd; j++) {
-
810  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
-
811  }
-
812  }
-
813 
-
814  CArray4 prod_0;
-
815  CArray4 prod_1;
-
816  CArray4 prod_2;
-
817  CArray4 prod_3;
-
818  CArray4 prod_4;
-
819  CArray4 prod_5;
-
820 
-
821  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(0), RmRm.slice(0), prod_0);
-
822  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(1), RmRm.slice(1), prod_1);
-
823  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(2), RmRm.slice(2), prod_2);
-
824  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(3), RmRm.slice(3), prod_3);
-
825  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(4), RmRm.slice(4), prod_4);
-
826  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(5), RmRm.slice(5), prod_5);
-
827 
-
828  r2 = r2 * J4d;
-
829 
-
830  for (int i = 0; i < N; i++) {
-
831  for (int j = 0; j < N; j++) {
-
832  for (int k = 0; k < N; k++) {
-
833  for (int l = 0; l < N; l++) {
-
834  CCb[i][j][k][l] = r2 * (CCb[i][j][k][l] + g1 * prod_0[i][j][k][l] +
-
835  g2 * ( prod_1[i][j][k][l] + prod_2[i][j][k][l] + 2.0*prod_4[i][j][k][l] ) +
-
836  2.0 * g3 * (prod_3[i][j][k][l] + prod_5[i][j][k][l] ));
-
837  }
-
838  }
-
839  }
-
840  }
-
841 
-
842  double Ci_C_prod[N][N][N][N];
-
843  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
-
844  CArray4 PP;
-
845 
-
846  for (int i = 0; i < N; i++) {
-
847  for (int j = 0; j < N; j++) {
-
848  for (int k = 0; k < N; k++) {
-
849  for (int l = 0; l < N; l++) {
-
850  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
-
851  }
-
852  }
-
853  }
-
854  }
-
855 
-
856  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
-
857 
-
858  double CC_t[N][N][N][N];
-
859  mat_fun_carray::ten_transpose<N>(CC, CC_t);
-
860 
-
861  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
-
862 
-
863  CArray4 Ci_S_prod;
-
864  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
-
865 
-
866  CArray4 S_Ci_prod;
-
867  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
-
868 
-
869  for (int i = 0; i < N; i++) {
-
870  for (int j = 0; j < N; j++) {
-
871  for (int k = 0; k < N; k++) {
-
872  for (int l = 0; l < N; l++) {
-
873  CC[i][j][k][l] -= (2.0/nd) * ( Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
-
874  }
-
875  }
-
876  }
-
877  }
-
878 
-
879  for (int i = 0; i < nsd; i++) {
-
880  for (int j = 0; j < nsd; j++) {
-
881  S[i][j] += p * J * Ci[i][j];
-
882  }
-
883  }
-
884 
-
885  CArray4 Ci_sym_prod;
-
886  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
-
887 
-
888  CArray4 Ci_Ci_prod;
-
889  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
-
890 
-
891  for (int i = 0; i < nsd; i++) {
-
892  for (int j = 0; j < nsd; j++) {
-
893  for (int k = 0; k < nsd; k++) {
-
894  for (int l = 0; l < nsd; l++) {
-
895  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
-
896  }
-
897  }
-
898  }
-
899  }
-
900 
-
901  } break;
-
902 
-
903  // HO (Holzapfel-Ogden) model for myocardium (2009)
-
904  case ConstitutiveModelType::stIso_HO: {
-
905  if (nfd != 2) {
-
906  //err = "Min fiber directions not defined for Holzapfel material model (2)"
-
907  }
-
908 
-
909  double C_fl[N];
-
910  mat_fun_carray::mat_mul(C, fl.rcol(0), C_fl);
-
911  double Inv4 = J2d * mat_fun_carray::norm<N>(fl.rcol(0), C_fl);
-
912  //double Inv4 = J2d*utils::norm(fl.col(0), mat_mul(C, fl.col(0)));
-
913 
-
914  mat_fun_carray::mat_mul(C, fl.rcol(1), C_fl);
-
915  double Inv6 = J2d * mat_fun_carray::norm<N>(fl.rcol(1), C_fl);
-
916  //double Inv6 = J2d*utils::norm(fl.col(1), mat_mul(C, fl.col(1)));
+
225  double Tsa = Tfa*stM.Tf.eta_s;
+
226 
+
227  // Electromechanics coupling - active stress
+
228  if (cep_mod.cem.aStress) {
+
229  Tfa = Tfa + ya;
+
230  }
+
231 
+
232  // Electromechanics coupling - active strain
+
233  double Fe[N][N];
+
234  for (int i = 0; i < N; i++) {
+
235  for (int j = 0; j < N; j++) {
+
236  Fe[i][j] = F[i][j];
+
237  }
+
238  }
+
239 
+
240  double Fa[N][N];
+
241  mat_fun_carray::mat_zero(Fa);
+
242  double Fai[N][N];
+
243  mat_fun_carray::mat_zero(Fai);
+
244 
+
245  for (int i = 0; i < N; i++) {
+
246  for (int j = 0; j < N; j++) {
+
247  if (i == j) {
+
248  Fa[i][j] = 1.0;
+
249  Fai[i][j] = 1.0;
+
250  }
+
251  }
+
252  }
+
253 
+
254  double J = mat_fun_carray::mat_det<N>(Fe);
+
255  double J2d = pow(J, (-2.0/nd));
+
256  double J4d = J2d*J2d;
+
257 
+
258  double Idm[N][N];
+
259  mat_fun_carray::mat_id<N>(Idm);
+
260 
+
261  double Fe_t[N][N];
+
262  mat_fun_carray::transpose<N>(Fe, Fe_t);
+
263 
+
264  double C[N][N];
+
265  mat_fun_carray::mat_mul<N>(Fe_t, Fe, C);
+
266 
+
267  double E[N][N];
+
268  for (int i = 0; i < nsd; i++) {
+
269  for (int j = 0; j < nsd; j++) {
+
270  E[i][j] = 0.50 * (C[i][j] - Idm[i][j]);
+
271  }
+
272  }
+
273 
+
274  double Ci[N][N];
+
275  mat_fun_carray::mat_inv<N>(C, Ci);
+
276 
+
277  double Cprod[N][N];
+
278  mat_fun_carray::mat_mul<N>(C,C,Cprod);
+
279  double trE = mat_fun_carray::mat_trace<N>(E);
+
280  double Inv1 = J2d * mat_fun_carray::mat_trace<N>(C);
+
281  double Inv2 = 0.50 * (Inv1*Inv1 - J4d * mat_fun_carray::mat_trace<N>(Cprod));
+
282 
+
283  // Contribution of dilational penalty terms to S and CC
+
284  double p = 0.0;
+
285  double pl = 0.0;
+
286 
+
287  if (!utils::is_zero(Kp)) {
+
288  mat_models::get_svol_p(com_mod, cep_mod, stM, J, p, pl);
+
289  }
+
290 
+
291  // Now, compute isochoric and total stress, elasticity tensors
+
292  //
+
293  double CC[N][N][N][N];
+
294  double Idm_prod[N][N][N][N];
+
295  double Ids[N][N][N][N];
+
296  mat_fun_carray::ten_ids<N>(Ids);
+
297 
+
298  switch (stM.isoType) {
+
299  case ConstitutiveModelType::stIso_lin: {
+
300  double g1 = stM.C10; // mu
+
301  for (int i = 0; i < nsd; i++) {
+
302  for (int j = 0; j < nsd; j++) {
+
303  S[i][j] = g1 * Idm[i][j];
+
304  }
+
305  }
+
306  return;
+
307  } break;
+
308 
+
309  // St.Venant-Kirchhoff
+
310  //
+
311  case ConstitutiveModelType::stIso_StVK: {
+
312  double g1 = stM.C10; // lambda
+
313  double g2 = stM.C01 * 2.0; // 2*mu
+
314 
+
315  for (int i = 0; i < N; i++) {
+
316  for (int j = 0; j < N; j++) {
+
317  S[i][j] = g1 * trE * Idm[i][j] + g2 * E[i][j];
+
318  }
+
319  }
+
320 
+
321  mat_fun_carray::ten_dyad_prod<N>(Idm, Idm, Idm_prod);
+
322  mat_fun_carray::ten_ids<N>(Ids);
+
323 
+
324  for (int i = 0; i < N; i++) {
+
325  for (int j = 0; j < N; j++) {
+
326  for (int k = 0; k < N; k++) {
+
327  for (int l = 0; l < N; l++) {
+
328  CC[i][j][k][l] = g1 * Idm_prod[i][j][k][l] + g2 * Ids[i][j][k][l];
+
329  }
+
330  }
+
331  }
+
332  }
+
333  } break;
+
334 
+
335  // modified St.Venant-Kirchhoff
+
336  //
+
337  case ConstitutiveModelType::stIso_mStVK: {
+
338  double g1 = stM.C10; // kappa
+
339  double g2 = stM.C01; // mu
+
340 
+
341  for (int i = 0; i < nsd; i++) {
+
342  for (int j = 0; j < nsd; j++) {
+
343  S[i][j] = g1 * log(J) * Ci[i][j] + g2 * (C[i][j] - Idm[i][j]);
+
344  }
+
345  }
+
346 
+
347  mat_fun_carray::ten_ids<N>(Ids);
+
348 
+
349  double Ci_Ci_prod[N][N][N][N];
+
350  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
+
351 
+
352  double Ci_Ci_symm_prod[N][N][N][N];
+
353  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_Ci_symm_prod);
+
354 
+
355  for (int i = 0; i < N; i++) {
+
356  for (int j = 0; j < N; j++) {
+
357  for (int k = 0; k < N; k++) {
+
358  for (int l = 0; l < N; l++) {
+
359  CC[i][j][k][l] = g1 * ( -2.0 * log(J) * Ci_Ci_symm_prod[i][j][k][l] + Ci_Ci_prod[i][j][k][l] ) +
+
360  2.0 * g2 * Ids[i][j][k][l];
+
361  }
+
362  }
+
363  }
+
364  }
+
365 
+
366  } break;
+
367 
+
368  // NeoHookean model
+
369  //
+
370  case ConstitutiveModelType::stIso_nHook: {
+
371  double g1 = 2.0 * stM.C10;
+
372 
+
373  double Sb[N][N];
+
374  for (int i = 0; i < nsd; i++) {
+
375  for (int j = 0; j < nsd; j++) {
+
376  Sb[i][j] = g1*Idm[i][j];
+
377  }
+
378  }
+
379 
+
380  // Fiber reinforcement/active stress
+
381  double prod[N][N];
+
382  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), prod);
+
383 
+
384  for (int i = 0; i < nsd; i++) {
+
385  for (int j = 0; j < nsd; j++) {
+
386  Sb[i][j] += Tfa * prod[i][j];
+
387  }
+
388  }
+
389 
+
390  double r1 = g1 * Inv1 / nd;
+
391  for (int j = 0; j < N; j++) {
+
392  for (int i = 0; i < N; i++) {
+
393  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
+
394  }
+
395  }
+
396 
+
397  double Ci_S_prod[N][N][N][N];
+
398  double S_Ci_prod[N][N][N][N];
+
399  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
+
400  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
+
401 
+
402  for (int j = 0; j < N; j++) {
+
403  for (int i = 0; i < N; i++) {
+
404  S[i][j] += p * J * Ci[i][j];
+
405  }
+
406  }
+
407 
+
408  for (int i = 0; i < nsd; i++) {
+
409  for (int j = 0; j < nsd; j++) {
+
410  for (int k = 0; k < nsd; k++) {
+
411  for (int l = 0; l < nsd; l++) {
+
412  CC[i][j][k][l] = (-2.0/nd) * (Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
+
413  }
+
414  }
+
415  }
+
416  }
+
417 
+
418  double Ci_sym_prod[N][N][N][N];
+
419  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
+
420 
+
421  double Ci_Ci_prod[N][N][N][N];
+
422  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
+
423 
+
424  for (int i = 0; i < nsd; i++) {
+
425  for (int j = 0; j < nsd; j++) {
+
426  for (int k = 0; k < nsd; k++) {
+
427  for (int l = 0; l < nsd; l++) {
+
428  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
+
429  }
+
430  }
+
431  }
+
432  }
+
433 
+
434  } break;
+
435 
+
436  // Mooney-Rivlin model
+
437  //
+
438  case ConstitutiveModelType::stIso_MR: {
+
439  double g1 = 2.0 * (stM.C10 + Inv1*stM.C01);
+
440  double g2 = -2.0 * stM.C01;
+
441 
+
442  double Sb[N][N];
+
443  for (int i = 0; i < nsd; i++) {
+
444  for (int j = 0; j < nsd; j++) {
+
445  Sb[i][j] = g1*Idm[i][j] + g2*J2d*C[i][j];
+
446  }
+
447  }
+
448 
+
449  // Fiber reinforcement/active stress
+
450  double prod[N][N];
+
451  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), prod);
+
452 
+
453  for (int i = 0; i < nsd; i++) {
+
454  for (int j = 0; j < nsd; j++) {
+
455  Sb[i][j] += Tfa*prod[i][j];
+
456  }
+
457  }
+
458 
+
459  g1 = 4.0 * J4d * stM.C01;
+
460 
+
461  double CCb[N][N][N][N];
+
462  mat_fun_carray::ten_dyad_prod<N>(Idm, Idm, Idm_prod);
+
463 
+
464  for (int i = 0; i < nsd; i++) {
+
465  for (int j = 0; j < nsd; j++) {
+
466  for (int k = 0; k < nsd; k++) {
+
467  for (int l = 0; l < nsd; l++) {
+
468  CCb[i][j][k][l] = g1 * (Idm_prod[i][j][k][l] - Ids[i][j][k][l]);
+
469  }
+
470  }
+
471  }
+
472  }
+
473 
+
474  double r1 = J2d * mat_fun_carray::mat_ddot<N>(C, Sb) / nd;
+
475  for (int i = 0; i < nsd; i++) {
+
476  for (int j = 0; j < nsd; j++) {
+
477  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
+
478  }
+
479  }
+
480 
+
481  double Ci_Ci_prod[N][N][N][N];
+
482  double Ci_C_prod[N][N][N][N];
+
483  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
+
484  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
+
485 
+
486  double PP[N][N][N][N];
+
487 
+
488  for (int i = 0; i < nsd; i++) {
+
489  for (int j = 0; j < nsd; j++) {
+
490  for (int k = 0; k < nsd; k++) {
+
491  for (int l = 0; l < nsd; l++) {
+
492  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
+
493  }
+
494  }
+
495  }
+
496  }
+
497 
+
498  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
+
499 
+
500  double CC_t[N][N][N][N];
+
501  mat_fun_carray::ten_transpose<N>(CC, CC_t);
+
502 
+
503  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
+
504 
+
505  double Ci_S_prod[N][N][N][N];
+
506  double S_Ci_prod[N][N][N][N];
+
507  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
+
508  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
+
509 
+
510  for (int i = 0; i < nsd; i++) {
+
511  for (int j = 0; j < nsd; j++) {
+
512  for (int k = 0; k < nsd; k++) {
+
513  for (int l = 0; l < nsd; l++) {
+
514  CC[i][j][k][l] -= (2.0/nd) * ( Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
+
515  }
+
516  }
+
517  }
+
518  }
+
519 
+
520  for (int i = 0; i < nsd; i++) {
+
521  for (int j = 0; j < nsd; j++) {
+
522  S[i][j] += p * J * Ci[i][j];
+
523  }
+
524  }
+
525 
+
526  double Ci_sym_prod[N][N][N][N];
+
527  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
+
528 
+
529  for (int i = 0; i < nsd; i++) {
+
530  for (int j = 0; j < nsd; j++) {
+
531  for (int k = 0; k < nsd; k++) {
+
532  for (int l = 0; l < nsd; l++) {
+
533  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
+
534  }
+
535  }
+
536  }
+
537  }
+
538 
+
539  } break;
+
540 
+
541  // HGO (Holzapfel-Gasser-Ogden) model with additive splitting of
+
542  // the anisotropic fiber-based strain-energy terms
+
543  //
+
544  case ConstitutiveModelType::stIso_HGO: {
+
545  if (nfd != 2) {
+
546  //err = "Min fiber directions not defined for HGO material model (2)"
+
547  }
+
548  double kap = stM.kap;
+
549 
+
550  double C_fl[N];
+
551  mat_fun_carray::mat_mul(C, fl.rcol(0), C_fl);
+
552  double Inv4 = J2d * mat_fun_carray::norm<N>(fl.rcol(0), C_fl);
+
553 
+
554  mat_fun_carray::mat_mul(C, fl.rcol(1), C_fl);
+
555  double Inv6 = J2d * mat_fun_carray::norm<N>(fl.rcol(1), C_fl);
+
556 
+
557  double Eff = kap*Inv1 + (1.0-3.0*kap)*Inv4 - 1.0;
+
558  double Ess = kap*Inv1 + (1.0-3.0*kap)*Inv6 - 1.0;
+
559 
+
560  double Hff[N][N];
+
561  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), Hff);
+
562 
+
563  for (int i = 0; i < N; i++) {
+
564  for (int j = 0; j < N; j++) {
+
565  Hff[i][j] = kap*Idm[i][j] + (1.0-3.0*kap)*Hff[i][j];
+
566  }
+
567  }
+
568 
+
569  double Hss[N][N];
+
570  mat_fun_carray::mat_dyad_prod<N>(fl.col(1), fl.col(1), Hss);
+
571 
+
572  for (int i = 0; i < N; i++) {
+
573  for (int j = 0; j < N; j++) {
+
574  Hss[i][j] = kap*Idm[i][j] + (1.0-3.0*kap)*Hss[i][j];
+
575  }
+
576  }
+
577 
+
578  double g1 = stM.C10;
+
579  double g2 = stM.aff * Eff * exp(stM.bff*Eff*Eff);
+
580  double g3 = stM.ass * Ess * exp(stM.bss*Ess*Ess);
+
581 
+
582  double Sb[N][N];
+
583  for (int i = 0; i < N; i++) {
+
584  for (int j = 0; j < N; j++) {
+
585  Sb[i][j] = 2.0 * (g1*Idm[i][j] + g2*Hff[i][j] + g3*Hss[i][j]);
+
586  }
+
587  }
+
588 
+
589  // Fiber reinforcement/active stress
+
590  double prod[N][N];
+
591  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), prod);
+
592 
+
593  for (int i = 0; i < N; i++) {
+
594  for (int j = 0; j < N; j++) {
+
595  Sb[i][j] += Tfa*prod[i][j];
+
596  }
+
597  }
+
598 
+
599  g1 = stM.aff*(1.0 + 2.0*stM.bff*Eff*Eff)*exp(stM.bff*Eff*Eff);
+
600  g2 = stM.ass*(1.0 + 2.0*stM.bss*Ess*Ess)*exp(stM.bss*Ess*Ess);
+
601  g1 = 4.0*J4d*g1;
+
602  g2 = 4.0*J4d*g2;
+
603 
+
604  double CCb_hff[N][N][N][N];
+
605  mat_fun_carray::ten_dyad_prod<N>(Hff, Hff, CCb_hff);
+
606 
+
607  double CCb_hss[N][N][N][N];
+
608  mat_fun_carray::ten_dyad_prod<N>(Hss, Hss, CCb_hss);
+
609 
+
610  double CCb[N][N][N][N];
+
611 
+
612  for (int i = 0; i < N; i++) {
+
613  for (int j = 0; j < N; j++) {
+
614  for (int k = 0; k < N; k++) {
+
615  for (int l = 0; l < N; l++) {
+
616  CCb[i][j][k][l] = g1 * CCb_hff[i][j][k][l] + g2 * CCb_hss[i][j][k][l];
+
617  }
+
618  }
+
619  }
+
620  }
+
621 
+
622  double r1 = J2d * mat_fun_carray::mat_ddot<N>(C, Sb) / nd;
+
623 
+
624  for (int i = 0; i < N; i++) {
+
625  for (int j = 0; j < N; j++) {
+
626  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
+
627  }
+
628  }
+
629 
+
630  double Ci_C_prod[N][N][N][N];
+
631  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
+
632  double PP[N][N][N][N];
+
633 
+
634  for (int i = 0; i < N; i++) {
+
635  for (int j = 0; j < N; j++) {
+
636  for (int k = 0; k < N; k++) {
+
637  for (int l = 0; l < N; l++) {
+
638  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
+
639  }
+
640  }
+
641  }
+
642  }
+
643 
+
644  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
+
645 
+
646  double CC_t[N][N][N][N];
+
647  mat_fun_carray::ten_transpose<N>(CC, CC_t);
+
648 
+
649  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
+
650 
+
651  double Ci_S_prod[N][N][N][N];
+
652  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
+
653 
+
654  double S_Ci_prod[N][N][N][N];
+
655  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
+
656 
+
657  for (int i = 0; i < N; i++) {
+
658  for (int j = 0; j < N; j++) {
+
659  for (int k = 0; k < N; k++) {
+
660  for (int l = 0; l < N; l++) {
+
661  CC[i][j][k][l] -= (2.0/nd) * ( Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
+
662  }
+
663  }
+
664  }
+
665  }
+
666 
+
667  for (int i = 0; i < nsd; i++) {
+
668  for (int j = 0; j < nsd; j++) {
+
669  S[i][j] += p * J * Ci[i][j];
+
670  }
+
671  }
+
672 
+
673  double Ci_sym_prod[N][N][N][N];
+
674  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
+
675 
+
676  double Ci_Ci_prod[N][N][N][N];
+
677  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
+
678 
+
679  for (int i = 0; i < nsd; i++) {
+
680  for (int j = 0; j < nsd; j++) {
+
681  for (int k = 0; k < nsd; k++) {
+
682  for (int l = 0; l < nsd; l++) {
+
683  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
+
684  }
+
685  }
+
686  }
+
687  }
+
688 
+
689  } break;
+
690 
+
691  // Guccione (1995) transversely isotropic model
+
692  //
+
693  case ConstitutiveModelType::stIso_Gucci: {
+
694  #ifdef debug_get_pk2cc
+
695  std::cout << msg_prefix << "stIso_Gucci" << std::endl;
+
696  #endif
+
697  if (nfd != 2) {
+
698  //err = "Min fiber directions not defined for Guccione material model (2)"
+
699  }
+
700 
+
701  // Compute isochoric component of E
+
702  double E[N][N];
+
703  for (int i = 0; i < N; i++) {
+
704  for (int j = 0; j < N; j++) {
+
705  E[i][j] = 0.50 * (J2d*C[i][j] - Idm[i][j]);
+
706  }
+
707  }
+
708 
+
709  // Transform into local orthogonal coordinate system
+
710  //
+
711  double Rm[N][N];
+
712  auto fl_0 = fl.col(0);
+
713  auto fl_1 = fl.col(1);
+
714  auto fl_cross = cross(fl);
+
715 
+
716  for (int i = 0; i < N; i++) {
+
717  Rm[i][0] = fl_0[i];
+
718  Rm[i][1] = fl_1[i];
+
719  Rm[i][2] = fl_cross[i];
+
720  }
+
721 
+
722  // Project E to local orthogocal coordinate system
+
723  //
+
724  double Es_1[N][N];
+
725  mat_fun_carray::mat_mul(E, Rm, Es_1);
+
726 
+
727  double Rm_t[N][N];
+
728  mat_fun_carray::transpose<N>(Rm, Rm_t);
+
729 
+
730  double Es[N][N];
+
731  mat_fun_carray::mat_mul(Rm_t, Es_1, Es);
+
732 
+
733  double g1 = stM.bff;
+
734  double g2 = stM.bss;
+
735  double g3 = stM.bfs;
+
736 
+
737  double QQ = g1 * Es[0][0]*Es[0][0] +
+
738  g2 * (Es[1][1]*Es[1][1] + Es[2][2]*Es[2][2] + Es[1][2]*Es[1][2] + Es[2][1]*Es[2][1]) +
+
739  g3 * (Es[0][1]*Es[0][1] + Es[1][0]*Es[1][0] + Es[0][2]*Es[0][2] + Es[2][0]*Es[2][0]);
+
740 
+
741  double r2 = stM.C10 * exp(QQ);
+
742 
+
743  // Fiber stiffness contribution := (dE*_ab / dE_IJ)
+
744  //
+
745  // Use Array in the following since it is a bit tricky.
+
746  //
+
747  Array<double> Rm_a(N,N);
+
748  for (int i = 0; i < N; i++) {
+
749  for (int j = 0; j < N; j++) {
+
750  Rm_a(i,j) = Rm[i][j];
+
751  }
+
752  }
+
753 
+
754  Array3<double> RmRm(N,N,6);
+
755 
+
756  RmRm.set_slice(0, mat_dyad_prod(Rm_a.col(0), Rm_a.col(0), nsd));
+
757  RmRm.set_slice(1, mat_dyad_prod(Rm_a.col(1), Rm_a.col(1), nsd));
+
758  RmRm.set_slice(2, mat_dyad_prod(Rm_a.col(2), Rm_a.col(2), nsd));
+
759 
+
760  RmRm.set_slice(3, mat_symm_prod(Rm_a.col(0), Rm_a.col(1), nsd));
+
761  RmRm.set_slice(4, mat_symm_prod(Rm_a.col(1), Rm_a.col(2), nsd));
+
762  RmRm.set_slice(5, mat_symm_prod(Rm_a.col(2), Rm_a.col(0), nsd));
+
763 
+
764  double Sb[N][N];
+
765 
+
766  for (int i = 0; i < N; i++) {
+
767  for (int j = 0; j < N; j++) {
+
768  Sb[i][j] = g1 * Es[0][0] * RmRm.rslice(0)(i,j) +
+
769  g2 * (Es[1][1] * RmRm.rslice(1)(i,j) + Es[2][2]*RmRm.rslice(2)(i,j) +
+
770  2.0*Es[1][2]*RmRm.rslice(4)(i,j)) +
+
771  2.0 * g3 * (Es[0][1] * RmRm.rslice(3)(i,j) + Es[0][2]*RmRm.rslice(5)(i,j));
+
772 
+
773  }
+
774  }
+
775 
+
776  double Sb_prod[N][N][N][N];
+
777  mat_fun_carray::ten_dyad_prod<N>(Sb, Sb, Sb_prod);
+
778  double CCb[N][N][N][N];
+
779 
+
780  for (int i = 0; i < N; i++) {
+
781  for (int j = 0; j < N; j++) {
+
782  for (int k = 0; k < N; k++) {
+
783  for (int l = 0; l < N; l++) {
+
784  CCb[i][j][k][l] = 2.0 * Sb_prod[i][j][k][l];
+
785  }
+
786  }
+
787  }
+
788  }
+
789 
+
790  for (int i = 0; i < N; i++) {
+
791  for (int j = 0; j < N; j++) {
+
792  Sb[i][j] = Sb[i][j] * r2;
+
793  }
+
794  }
+
795 
+
796  // Fiber reinforcement/active stress
+
797  //
+
798  double prod[N][N];
+
799  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), prod);
+
800 
+
801  for (int i = 0; i < N; i++) {
+
802  for (int j = 0; j < N; j++) {
+
803  Sb[i][j] += Tfa * prod[i][j];
+
804  }
+
805  }
+
806 
+
807  double r1 = J2d * mat_fun_carray::mat_ddot<N>(C, Sb) / nd;
+
808 
+
809  for (int i = 0; i < nsd; i++) {
+
810  for (int j = 0; j < nsd; j++) {
+
811  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
+
812  }
+
813  }
+
814 
+
815  CArray4 prod_0;
+
816  CArray4 prod_1;
+
817  CArray4 prod_2;
+
818  CArray4 prod_3;
+
819  CArray4 prod_4;
+
820  CArray4 prod_5;
+
821 
+
822  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(0), RmRm.slice(0), prod_0);
+
823  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(1), RmRm.slice(1), prod_1);
+
824  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(2), RmRm.slice(2), prod_2);
+
825  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(3), RmRm.slice(3), prod_3);
+
826  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(4), RmRm.slice(4), prod_4);
+
827  mat_fun_carray::ten_dyad_prod<N>(RmRm.slice(5), RmRm.slice(5), prod_5);
+
828 
+
829  r2 = r2 * J4d;
+
830 
+
831  for (int i = 0; i < N; i++) {
+
832  for (int j = 0; j < N; j++) {
+
833  for (int k = 0; k < N; k++) {
+
834  for (int l = 0; l < N; l++) {
+
835  CCb[i][j][k][l] = r2 * (CCb[i][j][k][l] + g1 * prod_0[i][j][k][l] +
+
836  g2 * ( prod_1[i][j][k][l] + prod_2[i][j][k][l] + 2.0*prod_4[i][j][k][l] ) +
+
837  2.0 * g3 * (prod_3[i][j][k][l] + prod_5[i][j][k][l] ));
+
838  }
+
839  }
+
840  }
+
841  }
+
842 
+
843  double Ci_C_prod[N][N][N][N];
+
844  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
+
845  CArray4 PP;
+
846 
+
847  for (int i = 0; i < N; i++) {
+
848  for (int j = 0; j < N; j++) {
+
849  for (int k = 0; k < N; k++) {
+
850  for (int l = 0; l < N; l++) {
+
851  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
+
852  }
+
853  }
+
854  }
+
855  }
+
856 
+
857  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
+
858 
+
859  double CC_t[N][N][N][N];
+
860  mat_fun_carray::ten_transpose<N>(CC, CC_t);
+
861 
+
862  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
+
863 
+
864  CArray4 Ci_S_prod;
+
865  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
+
866 
+
867  CArray4 S_Ci_prod;
+
868  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
+
869 
+
870  for (int i = 0; i < N; i++) {
+
871  for (int j = 0; j < N; j++) {
+
872  for (int k = 0; k < N; k++) {
+
873  for (int l = 0; l < N; l++) {
+
874  CC[i][j][k][l] -= (2.0/nd) * ( Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
+
875  }
+
876  }
+
877  }
+
878  }
+
879 
+
880  for (int i = 0; i < nsd; i++) {
+
881  for (int j = 0; j < nsd; j++) {
+
882  S[i][j] += p * J * Ci[i][j];
+
883  }
+
884  }
+
885 
+
886  CArray4 Ci_sym_prod;
+
887  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
+
888 
+
889  CArray4 Ci_Ci_prod;
+
890  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
+
891 
+
892  for (int i = 0; i < nsd; i++) {
+
893  for (int j = 0; j < nsd; j++) {
+
894  for (int k = 0; k < nsd; k++) {
+
895  for (int l = 0; l < nsd; l++) {
+
896  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
+
897  }
+
898  }
+
899  }
+
900  }
+
901 
+
902  } break;
+
903 
+
904  // HO (Holzapfel-Ogden) model for myocardium (2009)
+
905  case ConstitutiveModelType::stIso_HO: {
+
906  if (nfd != 2) {
+
907  //err = "Min fiber directions not defined for Holzapfel material model (2)"
+
908  }
+
909 
+
910  // Compute fiber-based isochoric invariants
+
911  double C_fl[N];
+
912  mat_fun_carray::mat_mul(C, fl.rcol(0), C_fl);
+
913  double Inv4 = J2d * mat_fun_carray::norm<N>(fl.rcol(0), C_fl);
+
914 
+
915  mat_fun_carray::mat_mul(C, fl.rcol(1), C_fl);
+
916  double Inv6 = J2d * mat_fun_carray::norm<N>(fl.rcol(1), C_fl);
917 
-
918  mat_fun_carray::mat_mul(C, fl.rcol(0), C_fl);
-
919  double Inv8 = J2d * mat_fun_carray::norm<N>(fl.rcol(1), C_fl);
-
920  //double Inv8 = J2d*utils::norm(fl.col(0), mat_mul(C, fl.col(1)));
-
921 
-
922  double Eff = Inv4 - 1.0;
-
923  double Ess = Inv6 - 1.0;
-
924  double Efs = Inv8;
-
925 
-
926  double g1 = stM.a * exp(stM.b*(Inv1-3.0));
-
927  double g2 = 2.0 * stM.afs * Efs * exp(stM.bfs*Efs*Efs);
-
928 
-
929  double Hfs[N][N];
-
930  mat_fun_carray::mat_symm_prod<N>(fl.rcol(0), fl.rcol(1), Hfs);
-
931  //auto Hfs = mat_symm_prod(fl.col(0), fl.col(1), nsd);
-
932 
-
933  double Sb[N][N];
-
934  for (int i = 0; i < N; i++) {
-
935  for (int j = 0; j < N; j++) {
-
936  Sb[i][j] = g1*Idm[i][j] + g2*Hfs[i][j];
-
937  }
-
938  }
-
939  //auto Sb = g1*Idm + g2*Hfs;
-
940 
-
941  Efs = Efs * Efs;
-
942  g1 = 2.0*J4d*stM.b*g1;
-
943  g2 = 4.0*J4d*stM.afs*(1.0 + 2.0*stM.bfs*Efs)* exp(stM.bfs*Efs);
-
944 
-
945  CArray4 Idm_prod;
-
946  mat_fun_carray::ten_dyad_prod<N>(Idm, Idm, Idm_prod);
+
918  mat_fun_carray::mat_mul(C, fl.rcol(1), C_fl);
+
919  double Inv8 = J2d * mat_fun_carray::norm<N>(fl.rcol(0), C_fl);
+
920 
+
921  double Eff = Inv4 - 1.0;
+
922  double Ess = Inv6 - 1.0;
+
923  double Efs = Inv8;
+
924 
+
925  // Smoothed Heaviside function: 1 / (1 + exp(-kx)) = 1 - 1 / (1 + exp(kx))
+
926  double k = stM.khs;
+
927  double one_over_exp_plus_one_f = 1.0 / (exp(k * Eff) + 1.0);
+
928  double one_over_exp_plus_one_s = 1.0 / (exp(k * Ess) + 1.0);
+
929  double c4f = 1.0 - one_over_exp_plus_one_f;
+
930  double c4s = 1.0 - one_over_exp_plus_one_s;
+
931 
+
932  // Approx. derivative of smoothed heaviside function
+
933  // double dc4f = 0.25*stM.khs*exp(-stM.khs*abs(Eff));
+
934  // double dc4s = 0.25*stM.khs*exp(-stM.khs*abs(Ess));
+
935 
+
936  // Exact first derivative of smoothed heaviside function (from Wolfram Alpha)
+
937  double dc4f = k * (one_over_exp_plus_one_f - pow(one_over_exp_plus_one_f,2));
+
938  double dc4s = k * (one_over_exp_plus_one_s - pow(one_over_exp_plus_one_s,2));
+
939 
+
940  // Exact second derivative of smoothed heaviside function (from Wolfram Alpha)
+
941  double ddc4f = pow(k,2) * (-one_over_exp_plus_one_f + 3.0*pow(one_over_exp_plus_one_f,2) - 2.0*pow(one_over_exp_plus_one_f,3));
+
942  double ddc4s = pow(k,2) * (-one_over_exp_plus_one_s + 3.0*pow(one_over_exp_plus_one_s,2) - 2.0*pow(one_over_exp_plus_one_s,3));
+
943 
+
944  // Isotropic + fiber-sheet interaction stress
+
945  double g1 = stM.a * exp(stM.b*(Inv1-3.0));
+
946  double g2 = 2.0 * stM.afs * exp(stM.bfs*Efs*Efs);
947 
-
948  CArray4 Hfs_prod;
-
949  mat_fun_carray::ten_dyad_prod<N>(Hfs, Hfs, Hfs_prod);
+
948  double Hfs[N][N];
+
949  mat_fun_carray::mat_symm_prod<N>(fl.rcol(0), fl.rcol(1), Hfs);
950 
-
951  CArray4 CCb;
-
952 
-
953  for (int i = 0; i < N; i++) {
-
954  for (int j = 0; j < N; j++) {
-
955  for (int k = 0; k < N; k++) {
-
956  for (int l = 0; l < N; l++) {
-
957  CCb[i][j][k][l] = g1 * Idm_prod[i][j][k][l] + g2 * Hfs_prod[i][j][k][l];
-
958  }
-
959  }
-
960  }
-
961  }
-
962  //auto CCb = g1 * ten_dyad_prod(Idm, Idm, nsd) + g2 * ten_dyad_prod(Hfs, Hfs, nsd);
-
963 
-
964  // Fiber reinforcement/active stress
-
965  if (Eff > 0.0) {
-
966  g1 = Tfa;
-
967  g1 = g1 + 2.0 * stM.aff * Eff * exp(stM.bff*Eff*Eff);
-
968 
-
969  double Hff[N][N];
-
970  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), Hff);
-
971  //auto Hff = mat_dyad_prod(fl.col(0), fl.col(0), nsd);
-
972 
-
973  for (int i = 0; i < N; i++) {
-
974  for (int j = 0; j < N; j++) {
-
975  Sb[i][j] += g1 * Hff[i][j];
+
951  double Sb[N][N];
+
952  for (int i = 0; i < N; i++) {
+
953  for (int j = 0; j < N; j++) {
+
954  Sb[i][j] = g1*Idm[i][j] + g2*Efs*Hfs[i][j];
+
955  }
+
956  }
+
957 
+
958  // Isotropic + fiber-sheet interaction stiffness
+
959  g1 = g1 * 2.0 * J4d * stM.b;
+
960  g2 = g2 * 2.0 * J4d * (1.0 + 2.0*stM.bfs*Efs*Efs);
+
961 
+
962  CArray4 Idm_prod;
+
963  mat_fun_carray::ten_dyad_prod<N>(Idm, Idm, Idm_prod);
+
964 
+
965  CArray4 Hfs_prod;
+
966  mat_fun_carray::ten_dyad_prod<N>(Hfs, Hfs, Hfs_prod);
+
967 
+
968  CArray4 CCb;
+
969 
+
970  for (int i = 0; i < N; i++) {
+
971  for (int j = 0; j < N; j++) {
+
972  for (int k = 0; k < N; k++) {
+
973  for (int l = 0; l < N; l++) {
+
974  CCb[i][j][k][l] = g1 * Idm_prod[i][j][k][l] + g2 * Hfs_prod[i][j][k][l];
+
975  }
976  }
977  }
-
978  //Sb = Sb + g1*Hff;
+
978  }
979 
-
980  Eff = Eff * Eff;
-
981  g1 = 4.0*J4d*stM.aff*(1.0 + 2.0*stM.bff*Eff)*exp(stM.bff*Eff);
-
982 
-
983  CArray4 Hff_prod;
-
984  mat_fun_carray::ten_dyad_prod<N>(Hff, Hff, Hff_prod);
-
985 
-
986  for (int i = 0; i < N; i++) {
-
987  for (int j = 0; j < N; j++) {
-
988  for (int k = 0; k < N; k++) {
-
989  for (int l = 0; l < N; l++) {
-
990  CCb[i][j][k][l] += g1 * Hff_prod[i][j][k][l];
-
991  }
-
992  }
-
993  }
-
994  }
-
995  //CCb = CCb + g1*ten_dyad_prod(Hff, Hff, nsd);
-
996  }
-
997 
-
998  if (Ess > 0.0) {
-
999  g2 = 2.0 * stM.ass * Ess * exp(stM.bss*Ess*Ess);
+
980  // Fiber-fiber interaction stress + additional reinforcement (Tfa)
+
981  double rexp = exp(stM.bff*Eff*Eff);
+
982  g1 = c4f * Eff * rexp;
+
983  g1 = g1 + (0.5*dc4f/stM.bff) * (rexp - 1.0);
+
984  g1 = 2.0 * stM.aff * g1 + Tfa;
+
985  double Hff[N][N];
+
986  mat_fun_carray::mat_dyad_prod<N>(fl.col(0), fl.col(0), Hff);
+
987  for (int i = 0; i < N; i++) {
+
988  for (int j = 0; j < N; j++) {
+
989  Sb[i][j] += g1 * Hff[i][j];
+
990  }
+
991  }
+
992 
+
993  // Fiber-fiber interaction stiffness
+
994  g1 = c4f * (1.0 + 2.0*stM.bff*Eff*Eff);
+
995  g1 = (g1 + 2.0*dc4f*Eff) * rexp;
+
996  g1 = g1 + (0.5*ddc4f/stM.bff)*(rexp - 1.0);
+
997  g1 = 4.0 * J4d * stM.aff * g1;
+
998  CArray4 Hff_prod;
+
999  mat_fun_carray::ten_dyad_prod<N>(Hff, Hff, Hff_prod);
1000 
-
1001  double Hss[N][N];
-
1002  mat_fun_carray::mat_dyad_prod<N>(fl.col(1), fl.col(1), Hss);
-
1003  //auto Hss = mat_dyad_prod(fl.col(1), fl.col(1), nsd);
-
1004 
-
1005  for (int i = 0; i < N; i++) {
-
1006  for (int j = 0; j < N; j++) {
-
1007  Sb[i][j] += g2 * Hss[i][j];
-
1008  }
-
1009  }
-
1010  //Sb = Sb + g2*Hss;
-
1011 
-
1012  Ess = Ess * Ess;
-
1013  g2 = 4.0 * J4d * stM.ass * (1.0 + 2.0*stM.bss*Ess) * exp(stM.bss * Ess);
-
1014 
-
1015  CArray4 Hss_prod;
-
1016  mat_fun_carray::ten_dyad_prod<N>(Hss, Hss, Hss_prod);
-
1017 
-
1018  for (int i = 0; i < N; i++) {
-
1019  for (int j = 0; j < N; j++) {
-
1020  for (int k = 0; k < N; k++) {
-
1021  for (int l = 0; l < N; l++) {
-
1022  CCb[i][j][k][l] += g2 * Hss_prod[i][j][k][l];
-
1023  }
-
1024  }
-
1025  }
-
1026  }
-
1027  //CCb = CCb + g2*ten_dyad_prod(Hss, Hss, nsd);
-
1028 
-
1029  }
+
1001  for (int i = 0; i < N; i++) {
+
1002  for (int j = 0; j < N; j++) {
+
1003  for (int k = 0; k < N; k++) {
+
1004  for (int l = 0; l < N; l++) {
+
1005  CCb[i][j][k][l] += g1 * Hff_prod[i][j][k][l];
+
1006  }
+
1007  }
+
1008  }
+
1009  }
+
1010 
+
1011  // Sheet-sheet interaction stress + additional cross-fiber stress
+
1012  rexp = exp(stM.bss*Ess*Ess);
+
1013  g2 = c4s * Ess * rexp;
+
1014  g2 = g2 + (0.5*dc4s/stM.bss) * (rexp - 1.0);
+
1015  g2 = 2.0 * stM.ass * g2 + Tsa;
+
1016  double Hss[N][N];
+
1017  mat_fun_carray::mat_dyad_prod<N>(fl.col(1), fl.col(1), Hss);
+
1018 
+
1019  for (int i = 0; i < N; i++) {
+
1020  for (int j = 0; j < N; j++) {
+
1021  Sb[i][j] += g2 * Hss[i][j];
+
1022  }
+
1023  }
+
1024 
+
1025  // Sheet-sheet interaction stiffness
+
1026  g2 = c4s * (1.0 + 2.0 * stM.bss * Ess * Ess);
+
1027  g2 = (g2 + 2.0*dc4s*Ess) * rexp;
+
1028  g2 = g2 + (0.5*ddc4s/stM.bss)*(rexp - 1.0);
+
1029  g2 = 4.0 * J4d * stM.ass * g2;
1030 
-
1031  double r1 = J2d * mat_fun_carray::mat_ddot<N>(C, Sb) / nd;
-
1032  //double r1 = J2d*mat_ddot(C, Sb, nsd) / nd;
+
1031  CArray4 Hss_prod;
+
1032  mat_fun_carray::ten_dyad_prod<N>(Hss, Hss, Hss_prod);
1033 
-
1034  for (int i = 0; i < nsd; i++) {
-
1035  for (int j = 0; j < nsd; j++) {
-
1036  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
-
1037  }
-
1038  }
-
1039  //S = J2d*Sb - r1*Ci;
-
1040 
-
1041  CArray4 Ci_C_prod;
-
1042  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
-
1043  double PP[N][N][N][N];
-
1044 
-
1045  for (int i = 0; i < N; i++) {
-
1046  for (int j = 0; j < N; j++) {
-
1047  for (int k = 0; k < N; k++) {
-
1048  for (int l = 0; l < N; l++) {
-
1049  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
-
1050  }
-
1051  }
-
1052  }
-
1053  }
-
1054  //auto PP = ten_ids(nsd) - (1.0/nd) * ten_dyad_prod(Ci, C, nsd);
-
1055 
-
1056  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
-
1057  //CC = ten_ddot(CCb, PP, nsd);
-
1058 
-
1059  CArray4 CC_t;
-
1060  mat_fun_carray::ten_transpose<N>(CC, CC_t);
-
1061  //CC = ten_transpose(CC, nsd);
-
1062 
-
1063  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
-
1064  //CC = ten_ddot(PP, CC, nsd);
-
1065 
-
1066  CArray4 Ci_S_prod;
-
1067  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
+
1034  for (int i = 0; i < N; i++) {
+
1035  for (int j = 0; j < N; j++) {
+
1036  for (int k = 0; k < N; k++) {
+
1037  for (int l = 0; l < N; l++) {
+
1038  CCb[i][j][k][l] += g2 * Hss_prod[i][j][k][l];
+
1039  }
+
1040  }
+
1041  }
+
1042  }
+
1043 
+
1044  // Isochoric 2nd-Piola-Kirchhoff stress and stiffness tensors
+
1045  double r1 = J2d * mat_fun_carray::mat_ddot<N>(C, Sb) / nd;
+
1046 
+
1047  for (int i = 0; i < nsd; i++) {
+
1048  for (int j = 0; j < nsd; j++) {
+
1049  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
+
1050  }
+
1051  }
+
1052 
+
1053  CArray4 Ci_C_prod;
+
1054  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
+
1055  double PP[N][N][N][N];
+
1056 
+
1057  for (int i = 0; i < N; i++) {
+
1058  for (int j = 0; j < N; j++) {
+
1059  for (int k = 0; k < N; k++) {
+
1060  for (int l = 0; l < N; l++) {
+
1061  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
+
1062  }
+
1063  }
+
1064  }
+
1065  }
+
1066 
+
1067  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
1068 
-
1069  CArray4 S_Ci_prod;
-
1070  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
+
1069  CArray4 CC_t;
+
1070  mat_fun_carray::ten_transpose<N>(CC, CC_t);
1071 
-
1072  for (int i = 0; i < N; i++) {
-
1073  for (int j = 0; j < N; j++) {
-
1074  for (int k = 0; k < N; k++) {
-
1075  for (int l = 0; l < N; l++) {
-
1076  CC[i][j][k][l] -= (2.0/nd) * (Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
-
1077  }
-
1078  }
-
1079  }
-
1080  }
-
1081  // CC = CC - (2.0/nd) * ( ten_dyad_prod(Ci, S, nsd) + ten_dyad_prod(S, Ci, nsd) );
-
1082 
-
1083  for (int i = 0; i < nsd; i++) {
-
1084  for (int j = 0; j < nsd; j++) {
-
1085  S[i][j] += p * J * Ci[i][j];
-
1086  }
-
1087  }
-
1088  //S = S + p*J*Ci;
+
1072  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
+
1073 
+
1074  CArray4 Ci_S_prod;
+
1075  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
+
1076 
+
1077  CArray4 S_Ci_prod;
+
1078  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
+
1079 
+
1080  for (int i = 0; i < N; i++) {
+
1081  for (int j = 0; j < N; j++) {
+
1082  for (int k = 0; k < N; k++) {
+
1083  for (int l = 0; l < N; l++) {
+
1084  CC[i][j][k][l] -= (2.0/nd) * (Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
+
1085  }
+
1086  }
+
1087  }
+
1088  }
1089 
-
1090  CArray4 Ci_sym_prod;
-
1091  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
-
1092 
-
1093  CArray4 Ci_Ci_prod;
-
1094  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
-
1095 
-
1096  for (int i = 0; i < nsd; i++) {
-
1097  for (int j = 0; j < nsd; j++) {
-
1098  for (int k = 0; k < nsd; k++) {
-
1099  for (int l = 0; l < nsd; l++) {
-
1100  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
-
1101  }
-
1102  }
-
1103  }
-
1104  }
-
1105  //CC = CC + 2.0*(r1 - p*J) * ten_symm_prod(Ci, Ci, nsd) + (pl*J - 2.0*r1/nd) * ten_dyad_prod(Ci, Ci, nsd);
-
1106 
-
1107  if (cep_mod.cem.aStrain) {
-
1108  double S_prod[N][N];
-
1109  mat_fun_carray::mat_mul<N>(Fai, S, S_prod);
-
1110  //S = mat_mul(Fai, S);
-
1111 
-
1112  double Fai_t[N][N];
-
1113  mat_fun_carray::transpose<N>(Fai, Fai_t);
-
1114  mat_fun_carray::mat_mul<N>(S_prod, Fai_t, S);
-
1115  //S = mat_mul(S, transpose(Fai));
-
1116 
-
1117  mat_fun_carray::ten_dyad_prod<N>(Fai, Fai, CCb);
-
1118  //CCb = ten_dyad_prod(Fai, Fai, nsd);
-
1119 
-
1120  CArray4 CC_dot;
-
1121  mat_fun_carray::ten_ddot_3424<N>(CC, CCb, CC_dot);
-
1122  //CC = ten_ddot_3424(CC, CCb, nsd);
-
1123 
-
1124  mat_fun_carray::ten_ddot_2412<N>(CCb, CC_dot, CC);
-
1125  //CC = ten_ddot_2412(CCb, CC, nsd);
-
1126  }
-
1127 
-
1128  } break;
+
1090  // Add pressure contribution
+
1091  for (int i = 0; i < nsd; i++) {
+
1092  for (int j = 0; j < nsd; j++) {
+
1093  S[i][j] += p * J * Ci[i][j];
+
1094  }
+
1095  }
+
1096 
+
1097  CArray4 Ci_sym_prod;
+
1098  mat_fun_carray::ten_symm_prod<N>(Ci, Ci, Ci_sym_prod);
+
1099 
+
1100  CArray4 Ci_Ci_prod;
+
1101  mat_fun_carray::ten_dyad_prod<N>(Ci, Ci, Ci_Ci_prod);
+
1102 
+
1103  for (int i = 0; i < nsd; i++) {
+
1104  for (int j = 0; j < nsd; j++) {
+
1105  for (int k = 0; k < nsd; k++) {
+
1106  for (int l = 0; l < nsd; l++) {
+
1107  CC[i][j][k][l] += 2.0*(r1 - p*J) * Ci_sym_prod[i][j][k][l] + (pl*J - 2.0*r1/nd) * Ci_Ci_prod[i][j][k][l];
+
1108  }
+
1109  }
+
1110  }
+
1111  }
+
1112 
+
1113  if (cep_mod.cem.aStrain) {
+
1114  double S_prod[N][N];
+
1115  mat_fun_carray::mat_mul<N>(Fai, S, S_prod);
+
1116  //S = mat_mul(Fai, S);
+
1117 
+
1118  double Fai_t[N][N];
+
1119  mat_fun_carray::transpose<N>(Fai, Fai_t);
+
1120  mat_fun_carray::mat_mul<N>(S_prod, Fai_t, S);
+
1121  //S = mat_mul(S, transpose(Fai));
+
1122 
+
1123  mat_fun_carray::ten_dyad_prod<N>(Fai, Fai, CCb);
+
1124  //CCb = ten_dyad_prod(Fai, Fai, nsd);
+
1125 
+
1126  CArray4 CC_dot;
+
1127  mat_fun_carray::ten_ddot_3424<N>(CC, CCb, CC_dot);
+
1128  //CC = ten_ddot_3424(CC, CCb, nsd);
1129 
-
1130  default:
-
1131  throw std::runtime_error("Undefined material constitutive model.");
-
1132  }
+
1130  mat_fun_carray::ten_ddot_2412<N>(CCb, CC_dot, CC);
+
1131  //CC = ten_ddot_2412(CCb, CC, nsd);
+
1132  }
1133 
-
1134  // Convert to Voigt Notation
-
1135  cc_to_voigt_carray<N>(CC, Dm);
-
1136 }
-
1137 
-
1138 
-
1139 /**
-
1140  * @brief Get the viscous PK2 stress and corresponding tangent matrix contributions for a solid
-
1141  * with a viscous pseudo-potential model.
-
1142  * This is defined by a viscous pseuo-potential
-
1143  * Psi = mu/2 * tr(E_dot^2)
-
1144  * The viscous 2nd Piola-Kirchhoff stress is given by
-
1145  * Svis = dPsi/dE_dot
-
1146  * = mu * E_dot
-
1147  * = mu * 1/2 * F^T * (grad(v) + grad(v)^T) * F
-
1148  * = mu * 1/2 * ( (F^T * Grad(v)) + (F^T * Grad(v))^T )
-
1149  *
-
1150  * @tparam nsd Number of spatial dimensions
-
1151  * @param mu Solid viscosity parameter
-
1152  * @param eNoN Number of nodes in an element
-
1153  * @param Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX)
-
1154  * @param vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX)
-
1155  * @param F Deformation gradient matrix
-
1156  * @param Svis Viscous 2nd Piola-Kirchhoff stress matrix
-
1157  * @param Kvis_u Viscous tangent matrix contribution due to displacement
-
1158  * @param Kvis_v Visous tangent matrix contribution due to velocity
-
1159  */
-
1160 template <size_t nsd>
-
1161 void get_visc_stress_pot(const double mu, const int eNoN, const Array<double>& Nx, const double vx[nsd][nsd], const double F[nsd][nsd],
-
1162  Array<double>& Svis, Array3<double>& Kvis_u, Array3<double>& Kvis_v) {
-
1163 
-
1164 
-
1165  // Initialize Svis, Kvis_u, Kvis_v to zero
-
1166  for (int i = 0; i < nsd; i++) {
-
1167  for (int j = 0; j < nsd; j++) {
-
1168  Svis(i,j) = 0.0;
-
1169  for (int a = 0; a < eNoN; a++) {
-
1170  for (int b = 0; b < eNoN; b++) {
-
1171  Kvis_u(i*nsd+j,a,b) = 0.0;
-
1172  Kvis_v(i*nsd+j,a,b) = 0.0;
-
1173  }
-
1174  }
-
1175  }
-
1176  }
-
1177 
+
1134  } break;
+
1135 
+
1136 // HO (Holzapfel-Ogden)-MA model for myocardium with full invariants for the anisotropy terms (modified-anisotropy)
+
1137  case ConstitutiveModelType::stIso_HO_ma: {
+
1138  if (nfd != 2) {
+
1139  //err = "Min fiber directions not defined for Holzapfel material model (2)"
+
1140  }
+
1141 
+
1142  // Compute fiber-based full invariants (not isochoric)
+
1143  double C_fl[N];
+
1144  mat_fun_carray::mat_mul(C, fl.rcol(0), C_fl);
+
1145  double Inv4 = mat_fun_carray::norm<N>(fl.rcol(0), C_fl);
+
1146 
+
1147  mat_fun_carray::mat_mul(C, fl.rcol(1), C_fl);
+
1148  double Inv6 = mat_fun_carray::norm<N>(fl.rcol(1), C_fl);
+
1149 
+
1150  mat_fun_carray::mat_mul(C, fl.rcol(1), C_fl);
+
1151  double Inv8 = mat_fun_carray::norm<N>(fl.rcol(0), C_fl);
+
1152 
+
1153  double Eff = Inv4 - 1.0;
+
1154  double Ess = Inv6 - 1.0;
+
1155  double Efs = Inv8;
+
1156 
+
1157  // Smoothed Heaviside function: 1 / (1 + exp(-kx)) = 1 - 1 / (1 + exp(kx))
+
1158  double k = stM.khs;
+
1159  double one_over_exp_plus_one_f = 1.0 / (exp(k * Eff) + 1.0);
+
1160  double one_over_exp_plus_one_s = 1.0 / (exp(k * Ess) + 1.0);
+
1161  double c4f = 1.0 - one_over_exp_plus_one_f;
+
1162  double c4s = 1.0 - one_over_exp_plus_one_s;
+
1163 
+
1164  // Approx. derivative of smoothed heaviside function
+
1165  // double dc4f = 0.25*stM.khs*exp(-stM.khs*abs(Eff));
+
1166  // double dc4s = 0.25*stM.khs*exp(-stM.khs*abs(Ess));
+
1167 
+
1168  // Exact first derivative of smoothed heaviside function (from Wolfram Alpha)
+
1169  double dc4f = k * (one_over_exp_plus_one_f - pow(one_over_exp_plus_one_f,2));
+
1170  double dc4s = k * (one_over_exp_plus_one_s - pow(one_over_exp_plus_one_s,2));
+
1171 
+
1172  // Exact second derivative of smoothed heaviside function (from Wolfram Alpha)
+
1173  double ddc4f = pow(k,2) * (-one_over_exp_plus_one_f + 3.0*pow(one_over_exp_plus_one_f,2) - 2.0*pow(one_over_exp_plus_one_f,3));
+
1174  double ddc4s = pow(k,2) * (-one_over_exp_plus_one_s + 3.0*pow(one_over_exp_plus_one_s,2) - 2.0*pow(one_over_exp_plus_one_s,3));
+
1175 
+
1176  // Isochoric stress and stiffness
+
1177  double g1 = stM.a * exp(stM.b*(Inv1-3.0));
1178 
-
1179  // Required intermediate terms for stress and tangent
-
1180  double Ft[nsd][nsd] = {0}, vxt[nsd][nsd] = {0}, F_Ft[nsd][nsd] = {0}, Ft_vx[nsd][nsd] = {0}, F_vxt[nsd][nsd] = {0};
-
1181  mat_fun_carray::transpose<nsd>(F, Ft);
-
1182  mat_fun_carray::mat_mul<nsd>(F, Ft, F_Ft);
-
1183  mat_fun_carray::mat_mul<nsd>(Ft, vx, Ft_vx);
-
1184  mat_fun_carray::transpose<nsd>(vx, vxt);
-
1185  mat_fun_carray::mat_mul<nsd>(F, vxt, F_vxt);
-
1186 
-
1187  //double F_Nx[nsd][eNoN] = {0}, vx_Nx[nsd][eNoN] = {0};
-
1188  Array<double> F_Nx(nsd,eNoN), vx_Nx(nsd,eNoN);
-
1189 
-
1190  for (int a = 0; a < eNoN; ++a) {
-
1191  for (int i = 0; i < nsd; ++i) {
-
1192  for (int j = 0; j < nsd; ++j) {
-
1193  F_Nx(i,a) += F[i][j] * Nx(j,a);
-
1194  vx_Nx(i,a) += vx[i][j] * Nx(j,a);
-
1195  }
-
1196  }
-
1197  }
-
1198 
-
1199  // 2nd Piola-Kirchhoff stress due to viscosity
-
1200  // Svis = mu * 1/2 * ( (F^T * dv/dX) + (F^T * dv/dX)^T )
-
1201  double Ft_vx_symm[nsd][nsd] = {0};
-
1202  mat_fun_carray::mat_symm<nsd>(Ft_vx, Ft_vx_symm);
-
1203  for (int i = 0; i < nsd; i++) {
-
1204  for (int j = 0; j < nsd; j++) {
-
1205  Svis(i,j) = mu * Ft_vx_symm[i][j];
+
1179  double Sb[N][N];
+
1180  for (int i = 0; i < N; i++) {
+
1181  for (int j = 0; j < N; j++) {
+
1182  Sb[i][j] = g1*Idm[i][j];
+
1183  }
+
1184  }
+
1185  double r1 = J2d/nd*mat_fun_carray::mat_ddot(C,Sb);
+
1186  g1 = g1*2.0*J4d*stM.b;
+
1187 
+
1188  CArray4 Idm_prod;
+
1189  mat_fun_carray::ten_dyad_prod<N>(Idm, Idm, Idm_prod);
+
1190 
+
1191  CArray4 CCb;
+
1192  for (int i = 0; i < N; i++) {
+
1193  for (int j = 0; j < N; j++) {
+
1194  for (int k = 0; k < N; k++) {
+
1195  for (int l = 0; l < N; l++) {
+
1196  CCb[i][j][k][l] = g1 * Idm_prod[i][j][k][l];
+
1197  }
+
1198  }
+
1199  }
+
1200  }
+
1201 
+
1202  // Add isochoric stress and stiffness contribution
+
1203  for (int i = 0; i < N; i++) {
+
1204  for (int j = 0; j < N; j++) {
+
1205  S[i][j] = J2d*Sb[i][j] - r1*Ci[i][j];
1206  }
-
1207  }
-
1208 
-
1209  // Tangent matrix contributions due to viscosity
-
1210  for (int b = 0; b < eNoN; ++b) {
-
1211  for (int a = 0; a < eNoN; ++a) {
-
1212  double Nx_Nx = 0.0;
-
1213  for (int i = 0; i < nsd; ++i) {
-
1214  Nx_Nx += Nx(i,a) * Nx(i,b);
-
1215  }
-
1216 
-
1217  for (int i = 0; i < nsd; ++i) {
-
1218  for (int j = 0; j < nsd; ++j) {
-
1219  int ii = i * nsd + j;
-
1220  Kvis_u(ii,a,b) = 0.5 * mu * (F_Nx(i,b) * vx_Nx(j,a) + Nx_Nx * F_vxt[i][j]);
-
1221  Kvis_v(ii,a,b) = 0.5 * mu * (Nx_Nx * F_Ft[i][j] + F_Nx(i,b) * F_Nx(j,a));
-
1222  }
-
1223  }
-
1224  }
-
1225  }
-
1226 }
-
1227 
-
1228 /**
-
1229  * @brief Get the viscous PK2 stress and corresponding tangent matrix contributions for a solid
-
1230  * with a Newtonian fluid-like viscosity model.
-
1231  * The viscous deviatoric Cauchy stress is given by
-
1232  * sigma_vis_dev = 2 * mu * d_dev
-
1233  * where d_dev = 1/2 * (grad(v) + grad(v)^T) - 1/3 * (div(v)) * I
-
1234  * The viscous 2nd Piola-Kirchhoff stress is given by a pull-back operation
-
1235  * Svis = 2 * mu * J * F^-1 * d_dev * F^-T
-
1236  *
-
1237  * Note, there is likely an error/bug in the tangent contributions that leads to suboptimal nonlinear convergence
-
1238  *
-
1239  * @tparam nsd Number of spatial dimensions
-
1240  * @param mu Solid viscosity parameter
-
1241  * @param eNoN Number of nodes in an element
-
1242  * @param Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX)
-
1243  * @param vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX)
-
1244  * @param F Deformation gradient matrix
-
1245  * @param Svis Viscous 2nd Piola-Kirchhoff stress matrix
-
1246  * @param Kvis_u Viscous tangent matrix contribution due to displacement
-
1247  * @param Kvis_v Visous tangent matrix contribution due to velocity
-
1248  */
-
1249 template <size_t nsd>
-
1250 void get_visc_stress_newt(const double mu, const int eNoN, const Array<double>& Nx, const double vx[nsd][nsd], const double F[nsd][nsd],
-
1251  Array<double>& Svis, Array3<double>& Kvis_u, Array3<double>& Kvis_v) {
-
1252 
-
1253 
-
1254  // Initialize Svis, Kvis_u, Kvis_v to zero
-
1255  for (int i = 0; i < nsd; i++) {
-
1256  for (int j = 0; j < nsd; j++) {
-
1257  Svis(i,j) = 0.0;
-
1258  for (int a = 0; a < eNoN; a++) {
-
1259  for (int b = 0; b < eNoN; b++) {
-
1260  Kvis_u(i*nsd+j,a,b) = 0.0;
-
1261  Kvis_v(i*nsd+j,a,b) = 0.0;
-
1262  }
-
1263  }
+
1207  }
+
1208  CArray4 Ci_C_prod;
+
1209  mat_fun_carray::ten_dyad_prod<N>(Ci, C, Ci_C_prod);
+
1210  double PP[N][N][N][N];
+
1211 
+
1212  for (int i = 0; i < N; i++) {
+
1213  for (int j = 0; j < N; j++) {
+
1214  for (int k = 0; k < N; k++) {
+
1215  for (int l = 0; l < N; l++) {
+
1216  PP[i][j][k][l] = Ids[i][j][k][l] - (1.0/nd) * Ci_C_prod[i][j][k][l];
+
1217  }
+
1218  }
+
1219  }
+
1220  }
+
1221 
+
1222  mat_fun_carray::ten_ddot<N>(CCb, PP, CC);
+
1223 
+
1224  CArray4 CC_t;
+
1225  mat_fun_carray::ten_transpose<N>(CC, CC_t);
+
1226 
+
1227  mat_fun_carray::ten_ddot<N>(PP, CC_t, CC);
+
1228 
+
1229  CArray4 Ci_S_prod;
+
1230  mat_fun_carray::ten_dyad_prod<N>(Ci, S, Ci_S_prod);
+
1231 
+
1232  CArray4 S_Ci_prod;
+
1233  mat_fun_carray::ten_dyad_prod<N>(S, Ci, S_Ci_prod);
+
1234 
+
1235  for (int i = 0; i < N; i++) {
+
1236  for (int j = 0; j < N; j++) {
+
1237  for (int k = 0; k < N; k++) {
+
1238  for (int l = 0; l < N; l++) {
+
1239  CC[i][j][k][l] -= (2.0/nd) * (Ci_S_prod[i][j][k][l] + S_Ci_prod[i][j][k][l]);
+
1240  }
+
1241  }
+
1242  }
+
1243  }
+
1244 
+
1245  // Add pressure contribution to stress and stiffness
+
1246  for (int i = 0; i < N; i++) {
+
1247  for (int j = 0; j < N; j++) {
+
1248  S[i][j] += p*J*Ci[i][j];
+
1249  }
+
1250  }
+
1251 
+
1252  CArray4 Ci_Ci_prod;
+
1253  mat_fun_carray::ten_dyad_prod(Ci, Ci, Ci_Ci_prod);
+
1254  CArray4 Ci_Ci_symprod;
+
1255  mat_fun_carray::ten_symm_prod(Ci, Ci, Ci_Ci_symprod);
+
1256  for (int i = 0; i < N; i++) {
+
1257  for (int j = 0; j < N; j++) {
+
1258  for (int k = 0; k < N; k++) {
+
1259  for (int l = 0; l < N; l++) {
+
1260  CC[i][j][k][l] += 2.0*(r1 - p*J)*Ci_Ci_symprod[i][j][k][l] + (pl*J - 2.0*r1/nd)*Ci_Ci_prod[i][j][k][l];
+
1261  }
+
1262  }
+
1263  }
1264  }
-
1265  }
-
1266 
-
1267  // Get identity matrix, Jacobian, and F^-1
-
1268  double Idm[nsd][nsd] = {0};
-
1269  mat_fun_carray::mat_id<nsd>(Idm);
-
1270  double J = mat_fun_carray::mat_det<nsd>(F);
-
1271  double Fi[nsd][nsd] = {0};
-
1272  mat_fun_carray::mat_inv<nsd>(F, Fi);
-
1273 
-
1274  // Required intermediate terms for stress and tangent
-
1275  double vx_Fi[nsd][nsd] = {0}, vx_Fi_symm[nsd][nsd] = {0}, ddev[nsd][nsd] = {0};
-
1276  // vx_Fi: Velocity gradient in current configuration
-
1277  mat_fun_carray::mat_mul<nsd>(vx, Fi, vx_Fi);
-
1278  mat_fun_carray::mat_symm<nsd>(vx_Fi, vx_Fi_symm);
-
1279  // ddev: Deviatoric part of rate of strain tensor
-
1280  mat_fun_carray::mat_dev<nsd>(vx_Fi_symm, ddev);
-
1281  //double Nx_Fi[nsd][eNoN] = {0}, ddev_Nx_Fi[nsd][eNoN] = {0}, vx_Fi_Nx_Fi[nsd][eNoN] = {0};
-
1282  Array<double> Nx_Fi(nsd,eNoN), ddev_Nx_Fi(nsd,eNoN), vx_Fi_Nx_Fi(nsd,eNoN);
-
1283  for (int a = 0; a < eNoN; ++a) {
-
1284  for (int i = 0; i < nsd; ++i) {
-
1285  for (int j = 0; j < nsd; ++j) {
-
1286  Nx_Fi(i,a) += Nx(j,a) * Fi[j][i];
-
1287  }
-
1288  }
-
1289  for (int i = 0; i < nsd; ++i) {
-
1290  for (int j = 0; j < nsd; ++j) {
-
1291  ddev_Nx_Fi(i,a) += ddev[i][j] * Nx_Fi(j,a);
-
1292  vx_Fi_Nx_Fi(i,a) += vx_Fi[j][i] * Nx_Fi(j,a);
-
1293  }
-
1294  }
-
1295  }
-
1296 
-
1297  // 2nd Piola-Kirchhoff stress due to viscosity
-
1298  // Svis = 2 * mu * J * F^-1 * d_dev * F^-T
-
1299  double Fit[nsd][nsd] = {0};
-
1300  mat_fun_carray::transpose<nsd>(Fi, Fit);
-
1301  double ddev_Fit[nsd][nsd] = {0};
-
1302  mat_fun_carray::mat_mul<nsd>(ddev, Fit, ddev_Fit);
-
1303  double Fi_ddev_Fit[nsd][nsd] = {0};
-
1304  mat_fun_carray::mat_mul<nsd>(Fi, ddev_Fit, Fi_ddev_Fit);
-
1305  for (int i = 0; i < nsd; i++) {
-
1306  for (int j = 0; j < nsd; j++) {
-
1307  Svis(i,j) = 2.0 * mu * J * Fi_ddev_Fit[i][j];
-
1308  }
-
1309  }
-
1310 
-
1311  // Tangent matrix contributions due to viscosity
-
1312  double r2d = 2.0 / nsd;
-
1313  for (int b = 0; b < eNoN; ++b) {
-
1314  for (int a = 0; a < eNoN; ++a) {
-
1315  double Nx_Fi_Nx_Fi = 0.0;
-
1316  for (int i = 0; i < nsd; ++i) {
-
1317  Nx_Fi_Nx_Fi += Nx_Fi(i,a) * Nx_Fi(i,b);
+
1265 
+
1266  // Now that both isochoric and volumetric components were added, anisotropic components need to be added
+
1267 
+
1268  // Fiber-sheet interaction terms
+
1269  g1 = 2.0 * stM.afs * exp(stM.bfs*Efs*Efs);
+
1270  double Hfs[N][N];
+
1271  mat_fun_carray::mat_symm_prod<N>(fl.rcol(0), fl.rcol(1), Hfs);
+
1272  for (int i = 0; i < N; i++) {
+
1273  for (int j = 0; j < N; j++) {
+
1274  S[i][j] += g1*Efs*Hfs[i][j];
+
1275  }
+
1276  }
+
1277 
+
1278  g1 = g1 * 2.0*(1.0 + 2.0*stM.bfs*Efs*Efs);
+
1279 
+
1280  CArray4 Hfs_Hfs_prod;
+
1281  mat_fun_carray::ten_dyad_prod(Hfs, Hfs, Hfs_Hfs_prod);
+
1282  for (int i = 0; i < N; i++) {
+
1283  for (int j = 0; j < N; j++) {
+
1284  for (int k = 0; k < N; k++) {
+
1285  for (int l = 0; l < N; l++) {
+
1286  CC[i][j][k][l] += g1*Hfs_Hfs_prod[i][j][k][l];
+
1287  }
+
1288  }
+
1289  }
+
1290  }
+
1291 
+
1292  // Fiber-fiber interaction stress + additional reinforcement (Tfa)
+
1293  double rexp = exp(stM.bff * Eff * Eff);
+
1294  g1 = c4f*Eff*rexp;
+
1295  g1 = g1 + (0.5*dc4f/stM.bff)*(rexp - 1.0);
+
1296  g1 = (2.0*stM.aff*g1) + Tfa;
+
1297  double Hff[N][N];
+
1298  mat_fun_carray::mat_dyad_prod<N>(fl.rcol(0), fl.rcol(0), Hff);
+
1299  for (int i = 0; i < N; i++) {
+
1300  for (int j = 0; j < N; j++) {
+
1301  S[i][j] += g1*Hff[i][j];
+
1302  }
+
1303  }
+
1304 
+
1305  // Fiber-fiber interaction stiffness
+
1306  g1 = c4f*(1.0 + (2.0*stM.bff*Eff*Eff));
+
1307  g1 = (g1 + (2.0*dc4f*Eff))*rexp;
+
1308  g1 = g1 + (0.5*ddc4f/stM.bff)*(rexp - 1.0);
+
1309  g1 = 4.0*stM.aff*g1;
+
1310  CArray4 Hff_Hff_prod;
+
1311  mat_fun_carray::ten_dyad_prod(Hff, Hff, Hff_Hff_prod);
+
1312  for (int i = 0; i < N; i++) {
+
1313  for (int j = 0; j < N; j++) {
+
1314  for (int k = 0; k < N; k++) {
+
1315  for (int l = 0; l < N; l++) {
+
1316  CC[i][j][k][l] += g1*Hff_Hff_prod[i][j][k][l];
+
1317  }
1318  }
-
1319 
-
1320  for (int i = 0; i < nsd; ++i) {
-
1321  for (int j = 0; j < nsd; ++j) {
-
1322  int ii = i * nsd + j;
-
1323 
-
1324  // Derivative of the residual w.r.t displacement
-
1325  Kvis_u(ii,a,b) = mu * J * (2.0 *
-
1326  (ddev_Nx_Fi(i,a) * Nx_Fi(j,b) - ddev_Nx_Fi(i,b) * Nx_Fi(j,a)) -
-
1327  (Nx_Fi_Nx_Fi * vx_Fi[i][j] + Nx_Fi(i,b) * vx_Fi_Nx_Fi(j,a) -
-
1328  r2d * Nx_Fi(i,a) * vx_Fi_Nx_Fi(j,b)));
-
1329 
-
1330  // Derivative of the residual w.r.t velocity
-
1331  Kvis_v(ii,a,b) = mu * J * (Nx_Fi_Nx_Fi * Idm[i][j] +
-
1332  Nx_Fi(i,b) * Nx_Fi(j,a) - r2d * Nx_Fi(i,a) * Nx_Fi(j,b));
-
1333  }
-
1334  }
-
1335  }
-
1336  }
-
1337 }
-
1338 
-
1339 
-
1340 /**
-
1341  * @brief Get the solid viscous PK2 stress and corresponding tangent matrix contributions
-
1342  * Calls the appropriate function based on the viscosity type, either viscous
-
1343  * pseudo-potential or Newtonian viscosity model.
-
1344  *
-
1345  * @tparam nsd Number of spatial dimensions
-
1346  * @param[in] lDmn Domain object
-
1347  * @param[in] eNoN Number of nodes in an element
-
1348  * @param[in] Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX)
-
1349  * @param[in] vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX)
-
1350  * @param[in] F Deformation gradient matrix
-
1351  * @param[out] Svis Viscous 2nd Piola-Kirchhoff stress matrix
-
1352  * @param[out] Kvis_u Viscous tangent matrix contribution due to displacement
-
1353  * @param[out] Kvis_v Viscous tangent matrix contribution due to velocity
-
1354  */
-
1355 template <size_t nsd>
-
1356 void get_visc_stress_and_tangent(const dmnType& lDmn, const int eNoN, const Array<double>& Nx, const double vx[nsd][nsd], const double F[nsd][nsd],
-
1357  Array<double>& Svis, Array3<double>& Kvis_u, Array3<double>& Kvis_v) {
-
1358 
-
1359  switch (lDmn.solid_visc.viscType) {
-
1360  case consts::SolidViscosityModelType::viscType_Newtonian:
-
1361  get_visc_stress_newt<nsd>(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v);
-
1362  break;
-
1363 
-
1364  case consts::SolidViscosityModelType::viscType_Potential:
-
1365  get_visc_stress_pot<nsd>(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v);
-
1366  break;
-
1367  }
-
1368 }
-
1369 
-
1370 /**
-
1371  * @brief Get the solid viscous PK2 stress and corresponding tangent matrix contributions
-
1372  * Calls the appropriate function based on the viscosity type, either viscous
-
1373  * pseudo-potential or Newtonian viscosity model.
-
1374  *
-
1375  * Same as above, except takes vx and F as Array objects instead of C-style arrays.
-
1376  *
-
1377  * @tparam nsd Number of spatial dimensions
-
1378  * @param[in] lDmn Domain object
-
1379  * @param[in] eNoN Number of nodes in an element
-
1380  * @param[in] Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX)
-
1381  * @param[in] vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX)
-
1382  * @param[in] F Deformation gradient matrix
-
1383  * @param[out] Svis Viscous 2nd Piola-Kirchhoff stress matrix
-
1384  * @param[out] Kvis_u Viscous tangent matrix contribution due to displacement
-
1385  * @param[out] Kvis_v Viscous tangent matrix contribution due to velocity
-
1386  */
-
1387 template <size_t nsd>
-
1388 void get_visc_stress_and_tangent(const dmnType& lDmn, const int eNoN, const Array<double>& Nx, Array<double>& vx_Array, Array<double>& F_Array,
-
1389  Array<double>& Svis, Array3<double>& Kvis_u, Array3<double>& Kvis_v) {
-
1390 
-
1391  // Convert vx_Array and F_Array to C-style arrays
-
1392  double vx[nsd][nsd], F[nsd][nsd];
-
1393  for (int i = 0; i < nsd; i++) {
-
1394  for (int j = 0; j < nsd; j++) {
-
1395  vx[i][j] = vx_Array(i,j);
-
1396  F[i][j] = F_Array(i,j);
-
1397  }
-
1398  }
-
1399  switch (lDmn.solid_visc.viscType) {
-
1400  case consts::SolidViscosityModelType::viscType_Newtonian:
-
1401  get_visc_stress_newt<nsd>(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v);
-
1402  break;
-
1403 
-
1404  case consts::SolidViscosityModelType::viscType_Potential:
-
1405  get_visc_stress_pot<nsd>(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v);
-
1406  break;
-
1407  }
-
1408 }
+
1319  }
+
1320  }
+
1321 
+
1322  // Sheet-sheet interaction stress + additional cross-fiber stress
+
1323  rexp = exp(stM.bss * Ess * Ess);
+
1324  double g2 = c4s*Ess*rexp;
+
1325  g2 = g2 + (0.5*dc4s/stM.bss)*(rexp - 1.0);
+
1326  g2 = 2.0*stM.ass*g2 + Tsa;
+
1327  double Hss[N][N];
+
1328  mat_fun_carray::mat_dyad_prod<N>(fl.rcol(1), fl.rcol(1), Hss);
+
1329  for (int i = 0; i < N; i++) {
+
1330  for (int j = 0; j < N; j++) {
+
1331  S[i][j] += g2*Hss[i][j];
+
1332  }
+
1333  }
+
1334 
+
1335  // Sheet-sheet interaction stiffness
+
1336  g2 = c4s*(1.0 + (2.0*stM.bss*Ess*Ess));
+
1337  g2 = (g2 + (2.0*dc4s*Ess))*rexp;
+
1338  g2 = g2 + (0.5*ddc4s/stM.bss)*(rexp - 1.0);
+
1339  g2 = 4.0*stM.ass*g2;
+
1340  CArray4 Hss_Hss_prod;
+
1341  mat_fun_carray::ten_dyad_prod(Hss,Hss,Hss_Hss_prod);
+
1342  for (int i = 0; i < N; i++) {
+
1343  for (int j = 0; j < N; j++) {
+
1344  for (int k = 0; k < N; k++) {
+
1345  for (int l = 0; l < N; l++) {
+
1346  CC[i][j][k][l] += g2*Hss_Hss_prod[i][j][k][l];
+
1347  }
+
1348  }
+
1349  }
+
1350  }
+
1351  } break;
+
1352 
+
1353  default:
+
1354  throw std::runtime_error("Undefined material constitutive model.");
+
1355  }
+
1356 
+
1357  // Convert to Voigt Notation
+
1358  cc_to_voigt_carray<N>(CC, Dm);
+
1359 }
+
1360 
+
1361 
+
1362 /**
+
1363  * @brief Get the viscous PK2 stress and corresponding tangent matrix contributions for a solid
+
1364  * with a viscous pseudo-potential model.
+
1365  * This is defined by a viscous pseuo-potential
+
1366  * Psi = mu/2 * tr(E_dot^2)
+
1367  * The viscous 2nd Piola-Kirchhoff stress is given by
+
1368  * Svis = dPsi/dE_dot
+
1369  * = mu * E_dot
+
1370  * = mu * 1/2 * F^T * (grad(v) + grad(v)^T) * F
+
1371  * = mu * 1/2 * ( (F^T * Grad(v)) + (F^T * Grad(v))^T )
+
1372  *
+
1373  * @tparam nsd Number of spatial dimensions
+
1374  * @param mu Solid viscosity parameter
+
1375  * @param eNoN Number of nodes in an element
+
1376  * @param Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX)
+
1377  * @param vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX)
+
1378  * @param F Deformation gradient matrix
+
1379  * @param Svis Viscous 2nd Piola-Kirchhoff stress matrix
+
1380  * @param Kvis_u Viscous tangent matrix contribution due to displacement
+
1381  * @param Kvis_v Visous tangent matrix contribution due to velocity
+
1382  */
+
1383 template <size_t nsd>
+
1384 void get_visc_stress_pot(const double mu, const int eNoN, const Array<double>& Nx, const double vx[nsd][nsd], const double F[nsd][nsd],
+
1385  Array<double>& Svis, Array3<double>& Kvis_u, Array3<double>& Kvis_v) {
+
1386 
+
1387 
+
1388  // Initialize Svis, Kvis_u, Kvis_v to zero
+
1389  for (int i = 0; i < nsd; i++) {
+
1390  for (int j = 0; j < nsd; j++) {
+
1391  Svis(i,j) = 0.0;
+
1392  for (int a = 0; a < eNoN; a++) {
+
1393  for (int b = 0; b < eNoN; b++) {
+
1394  Kvis_u(i*nsd+j,a,b) = 0.0;
+
1395  Kvis_v(i*nsd+j,a,b) = 0.0;
+
1396  }
+
1397  }
+
1398  }
+
1399  }
+
1400 
+
1401 
+
1402  // Required intermediate terms for stress and tangent
+
1403  double Ft[nsd][nsd] = {0}, vxt[nsd][nsd] = {0}, F_Ft[nsd][nsd] = {0}, Ft_vx[nsd][nsd] = {0}, F_vxt[nsd][nsd] = {0};
+
1404  mat_fun_carray::transpose<nsd>(F, Ft);
+
1405  mat_fun_carray::mat_mul<nsd>(F, Ft, F_Ft);
+
1406  mat_fun_carray::mat_mul<nsd>(Ft, vx, Ft_vx);
+
1407  mat_fun_carray::transpose<nsd>(vx, vxt);
+
1408  mat_fun_carray::mat_mul<nsd>(F, vxt, F_vxt);
1409 
-
1410 };
-
1411 
-
1412 #endif
-
1413 
+
1410  //double F_Nx[nsd][eNoN] = {0}, vx_Nx[nsd][eNoN] = {0};
+
1411  Array<double> F_Nx(nsd,eNoN), vx_Nx(nsd,eNoN);
+
1412 
+
1413  for (int a = 0; a < eNoN; ++a) {
+
1414  for (int i = 0; i < nsd; ++i) {
+
1415  for (int j = 0; j < nsd; ++j) {
+
1416  F_Nx(i,a) += F[i][j] * Nx(j,a);
+
1417  vx_Nx(i,a) += vx[i][j] * Nx(j,a);
+
1418  }
+
1419  }
+
1420  }
+
1421 
+
1422  // 2nd Piola-Kirchhoff stress due to viscosity
+
1423  // Svis = mu * 1/2 * ( (F^T * dv/dX) + (F^T * dv/dX)^T )
+
1424  double Ft_vx_symm[nsd][nsd] = {0};
+
1425  mat_fun_carray::mat_symm<nsd>(Ft_vx, Ft_vx_symm);
+
1426  for (int i = 0; i < nsd; i++) {
+
1427  for (int j = 0; j < nsd; j++) {
+
1428  Svis(i,j) = mu * Ft_vx_symm[i][j];
+
1429  }
+
1430  }
+
1431 
+
1432  // Tangent matrix contributions due to viscosity
+
1433  for (int b = 0; b < eNoN; ++b) {
+
1434  for (int a = 0; a < eNoN; ++a) {
+
1435  double Nx_Nx = 0.0;
+
1436  for (int i = 0; i < nsd; ++i) {
+
1437  Nx_Nx += Nx(i,a) * Nx(i,b);
+
1438  }
+
1439 
+
1440  for (int i = 0; i < nsd; ++i) {
+
1441  for (int j = 0; j < nsd; ++j) {
+
1442  int ii = i * nsd + j;
+
1443  Kvis_u(ii,a,b) = 0.5 * mu * (F_Nx(i,b) * vx_Nx(j,a) + Nx_Nx * F_vxt[i][j]);
+
1444  Kvis_v(ii,a,b) = 0.5 * mu * (Nx_Nx * F_Ft[i][j] + F_Nx(i,b) * F_Nx(j,a));
+
1445  }
+
1446  }
+
1447  }
+
1448  }
+
1449 }
+
1450 
+
1451 /**
+
1452  * @brief Get the viscous PK2 stress and corresponding tangent matrix contributions for a solid
+
1453  * with a Newtonian fluid-like viscosity model.
+
1454  * The viscous deviatoric Cauchy stress is given by
+
1455  * sigma_vis_dev = 2 * mu * d_dev
+
1456  * where d_dev = 1/2 * (grad(v) + grad(v)^T) - 1/3 * (div(v)) * I
+
1457  * The viscous 2nd Piola-Kirchhoff stress is given by a pull-back operation
+
1458  * Svis = 2 * mu * J * F^-1 * d_dev * F^-T
+
1459  *
+
1460  * Note, there is likely an error/bug in the tangent contributions that leads to suboptimal nonlinear convergence
+
1461  *
+
1462  * @tparam nsd Number of spatial dimensions
+
1463  * @param mu Solid viscosity parameter
+
1464  * @param eNoN Number of nodes in an element
+
1465  * @param Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX)
+
1466  * @param vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX)
+
1467  * @param F Deformation gradient matrix
+
1468  * @param Svis Viscous 2nd Piola-Kirchhoff stress matrix
+
1469  * @param Kvis_u Viscous tangent matrix contribution due to displacement
+
1470  * @param Kvis_v Visous tangent matrix contribution due to velocity
+
1471  */
+
1472 template <size_t nsd>
+
1473 void get_visc_stress_newt(const double mu, const int eNoN, const Array<double>& Nx, const double vx[nsd][nsd], const double F[nsd][nsd],
+
1474  Array<double>& Svis, Array3<double>& Kvis_u, Array3<double>& Kvis_v) {
+
1475 
+
1476 
+
1477  // Initialize Svis, Kvis_u, Kvis_v to zero
+
1478  for (int i = 0; i < nsd; i++) {
+
1479  for (int j = 0; j < nsd; j++) {
+
1480  Svis(i,j) = 0.0;
+
1481  for (int a = 0; a < eNoN; a++) {
+
1482  for (int b = 0; b < eNoN; b++) {
+
1483  Kvis_u(i*nsd+j,a,b) = 0.0;
+
1484  Kvis_v(i*nsd+j,a,b) = 0.0;
+
1485  }
+
1486  }
+
1487  }
+
1488  }
+
1489 
+
1490  // Get identity matrix, Jacobian, and F^-1
+
1491  double Idm[nsd][nsd] = {0};
+
1492  mat_fun_carray::mat_id<nsd>(Idm);
+
1493  double J = mat_fun_carray::mat_det<nsd>(F);
+
1494  double Fi[nsd][nsd] = {0};
+
1495  mat_fun_carray::mat_inv<nsd>(F, Fi);
+
1496 
+
1497  // Required intermediate terms for stress and tangent
+
1498  double vx_Fi[nsd][nsd] = {0}, vx_Fi_symm[nsd][nsd] = {0}, ddev[nsd][nsd] = {0};
+
1499  // vx_Fi: Velocity gradient in current configuration
+
1500  mat_fun_carray::mat_mul<nsd>(vx, Fi, vx_Fi);
+
1501  mat_fun_carray::mat_symm<nsd>(vx_Fi, vx_Fi_symm);
+
1502  // ddev: Deviatoric part of rate of strain tensor
+
1503  mat_fun_carray::mat_dev<nsd>(vx_Fi_symm, ddev);
+
1504  //double Nx_Fi[nsd][eNoN] = {0}, ddev_Nx_Fi[nsd][eNoN] = {0}, vx_Fi_Nx_Fi[nsd][eNoN] = {0};
+
1505  Array<double> Nx_Fi(nsd,eNoN), ddev_Nx_Fi(nsd,eNoN), vx_Fi_Nx_Fi(nsd,eNoN);
+
1506  for (int a = 0; a < eNoN; ++a) {
+
1507  for (int i = 0; i < nsd; ++i) {
+
1508  for (int j = 0; j < nsd; ++j) {
+
1509  Nx_Fi(i,a) += Nx(j,a) * Fi[j][i];
+
1510  }
+
1511  }
+
1512  for (int i = 0; i < nsd; ++i) {
+
1513  for (int j = 0; j < nsd; ++j) {
+
1514  ddev_Nx_Fi(i,a) += ddev[i][j] * Nx_Fi(j,a);
+
1515  vx_Fi_Nx_Fi(i,a) += vx_Fi[j][i] * Nx_Fi(j,a);
+
1516  }
+
1517  }
+
1518  }
+
1519 
+
1520  // 2nd Piola-Kirchhoff stress due to viscosity
+
1521  // Svis = 2 * mu * J * F^-1 * d_dev * F^-T
+
1522  double Fit[nsd][nsd] = {0};
+
1523  mat_fun_carray::transpose<nsd>(Fi, Fit);
+
1524  double ddev_Fit[nsd][nsd] = {0};
+
1525  mat_fun_carray::mat_mul<nsd>(ddev, Fit, ddev_Fit);
+
1526  double Fi_ddev_Fit[nsd][nsd] = {0};
+
1527  mat_fun_carray::mat_mul<nsd>(Fi, ddev_Fit, Fi_ddev_Fit);
+
1528  for (int i = 0; i < nsd; i++) {
+
1529  for (int j = 0; j < nsd; j++) {
+
1530  Svis(i,j) = 2.0 * mu * J * Fi_ddev_Fit[i][j];
+
1531  }
+
1532  }
+
1533 
+
1534  // Tangent matrix contributions due to viscosity
+
1535  double r2d = 2.0 / nsd;
+
1536  for (int b = 0; b < eNoN; ++b) {
+
1537  for (int a = 0; a < eNoN; ++a) {
+
1538  double Nx_Fi_Nx_Fi = 0.0;
+
1539  for (int i = 0; i < nsd; ++i) {
+
1540  Nx_Fi_Nx_Fi += Nx_Fi(i,a) * Nx_Fi(i,b);
+
1541  }
+
1542 
+
1543  for (int i = 0; i < nsd; ++i) {
+
1544  for (int j = 0; j < nsd; ++j) {
+
1545  int ii = i * nsd + j;
+
1546 
+
1547  // Derivative of the residual w.r.t displacement
+
1548  Kvis_u(ii,a,b) = mu * J * (2.0 *
+
1549  (ddev_Nx_Fi(i,a) * Nx_Fi(j,b) - ddev_Nx_Fi(i,b) * Nx_Fi(j,a)) -
+
1550  (Nx_Fi_Nx_Fi * vx_Fi[i][j] + Nx_Fi(i,b) * vx_Fi_Nx_Fi(j,a) -
+
1551  r2d * Nx_Fi(i,a) * vx_Fi_Nx_Fi(j,b)));
+
1552 
+
1553  // Derivative of the residual w.r.t velocity
+
1554  Kvis_v(ii,a,b) = mu * J * (Nx_Fi_Nx_Fi * Idm[i][j] +
+
1555  Nx_Fi(i,b) * Nx_Fi(j,a) - r2d * Nx_Fi(i,a) * Nx_Fi(j,b));
+
1556  }
+
1557  }
+
1558  }
+
1559  }
+
1560 }
+
1561 
+
1562 
+
1563 /**
+
1564  * @brief Get the solid viscous PK2 stress and corresponding tangent matrix contributions
+
1565  * Calls the appropriate function based on the viscosity type, either viscous
+
1566  * pseudo-potential or Newtonian viscosity model.
+
1567  *
+
1568  * @tparam nsd Number of spatial dimensions
+
1569  * @param[in] lDmn Domain object
+
1570  * @param[in] eNoN Number of nodes in an element
+
1571  * @param[in] Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX)
+
1572  * @param[in] vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX)
+
1573  * @param[in] F Deformation gradient matrix
+
1574  * @param[out] Svis Viscous 2nd Piola-Kirchhoff stress matrix
+
1575  * @param[out] Kvis_u Viscous tangent matrix contribution due to displacement
+
1576  * @param[out] Kvis_v Viscous tangent matrix contribution due to velocity
+
1577  */
+
1578 template <size_t nsd>
+
1579 void get_visc_stress_and_tangent(const dmnType& lDmn, const int eNoN, const Array<double>& Nx, const double vx[nsd][nsd], const double F[nsd][nsd],
+
1580  Array<double>& Svis, Array3<double>& Kvis_u, Array3<double>& Kvis_v) {
+
1581 
+
1582  switch (lDmn.solid_visc.viscType) {
+
1583  case consts::SolidViscosityModelType::viscType_Newtonian:
+
1584  get_visc_stress_newt<nsd>(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v);
+
1585  break;
+
1586 
+
1587  case consts::SolidViscosityModelType::viscType_Potential:
+
1588  get_visc_stress_pot<nsd>(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v);
+
1589  break;
+
1590  }
+
1591 }
+
1592 
+
1593 /**
+
1594  * @brief Get the solid viscous PK2 stress and corresponding tangent matrix contributions
+
1595  * Calls the appropriate function based on the viscosity type, either viscous
+
1596  * pseudo-potential or Newtonian viscosity model.
+
1597  *
+
1598  * Same as above, except takes vx and F as Array objects instead of C-style arrays.
+
1599  *
+
1600  * @tparam nsd Number of spatial dimensions
+
1601  * @param[in] lDmn Domain object
+
1602  * @param[in] eNoN Number of nodes in an element
+
1603  * @param[in] Nx Shape function gradient w.r.t. reference configuration coordinates (dN/dX)
+
1604  * @param[in] vx Velocity gradient matrix w.r.t reference configuration coordinates (dv/dX)
+
1605  * @param[in] F Deformation gradient matrix
+
1606  * @param[out] Svis Viscous 2nd Piola-Kirchhoff stress matrix
+
1607  * @param[out] Kvis_u Viscous tangent matrix contribution due to displacement
+
1608  * @param[out] Kvis_v Viscous tangent matrix contribution due to velocity
+
1609  */
+
1610 template <size_t nsd>
+
1611 void get_visc_stress_and_tangent(const dmnType& lDmn, const int eNoN, const Array<double>& Nx, Array<double>& vx_Array, Array<double>& F_Array,
+
1612  Array<double>& Svis, Array3<double>& Kvis_u, Array3<double>& Kvis_v) {
+
1613 
+
1614  // Convert vx_Array and F_Array to C-style arrays
+
1615  double vx[nsd][nsd], F[nsd][nsd];
+
1616  for (int i = 0; i < nsd; i++) {
+
1617  for (int j = 0; j < nsd; j++) {
+
1618  vx[i][j] = vx_Array(i,j);
+
1619  F[i][j] = F_Array(i,j);
+
1620  }
+
1621  }
+
1622  switch (lDmn.solid_visc.viscType) {
+
1623  case consts::SolidViscosityModelType::viscType_Newtonian:
+
1624  get_visc_stress_newt<nsd>(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v);
+
1625  break;
+
1626 
+
1627  case consts::SolidViscosityModelType::viscType_Potential:
+
1628  get_visc_stress_pot<nsd>(lDmn.solid_visc.mu, eNoN, Nx, vx, F, Svis, Kvis_u, Kvis_v);
+
1629  break;
+
1630  }
+
1631 }
+
1632 
+
1633 };
+
1634 
+
1635 #endif
+
1636 
CepMod
Definition: CepMod.h:220
CepMod::cem
cemModelType cem
Cardiac electromechanics type.
Definition: CepMod.h:233
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
-
ComMod::nsd
int nsd
Number of spatial dimensions.
Definition: ComMod.h:1429
-
ComMod::cm
cmType cm
The general communicator.
Definition: ComMod.h:1604
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
+
ComMod::nsd
int nsd
Number of spatial dimensions.
Definition: ComMod.h:1432
+
ComMod::cm
cmType cm
The general communicator.
Definition: ComMod.h:1607
cemModelType::aStress
bool aStress
Whether active stress formulation is employed.
Definition: CepMod.h:206
cemModelType::aStrain
bool aStrain
Whether active strain formulation is employed.
Definition: CepMod.h:210
-
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:429
+
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:432
mat_fun
The classes defined here duplicate the data structures in the Fortran MATFUN module defined in MATFUN...
Definition: mat_fun.cpp:45
mat_fun::mat_symm_prod
Array< double > mat_symm_prod(const Vector< double > &u, const Vector< double > &v, const int nd)
Create a matrix from symmetric product of two vectors.
Definition: mat_fun.cpp:603
mat_fun::mat_dyad_prod
Array< double > mat_dyad_prod(const Vector< double > &u, const Vector< double > &v, const int nd)
Create a matrix from outer product of two vectors.
Definition: mat_fun.cpp:112
diff --git a/mesh_8h_source.html b/mesh_8h_source.html index 78d4c730..be28e072 100644 --- a/mesh_8h_source.html +++ b/mesh_8h_source.html @@ -116,8 +116,8 @@
44 #endif
45 
CepMod
Definition: CepMod.h:220
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/nn_8h_source.html b/nn_8h_source.html index 3002f1d9..73ef6308 100644 --- a/nn_8h_source.html +++ b/nn_8h_source.html @@ -154,11 +154,11 @@
82 #endif
83 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/nn__elem__gip_8h_source.html b/nn__elem__gip_8h_source.html index 57e02e1c..de321d11 100644 --- a/nn__elem__gip_8h_source.html +++ b/nn__elem__gip_8h_source.html @@ -850,8 +850,8 @@
778 
779 };
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/nn__elem__gnn_8h_source.html b/nn__elem__gnn_8h_source.html index 0fd5cde1..ff755b20 100644 --- a/nn__elem__gnn_8h_source.html +++ b/nn__elem__gnn_8h_source.html @@ -1684,8 +1684,8 @@
1612 
1613 };
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/nn__elem__nn__bnds_8h_source.html b/nn__elem__nn__bnds_8h_source.html index d1b86d9c..2c7e915c 100644 --- a/nn__elem__nn__bnds_8h_source.html +++ b/nn__elem__nn__bnds_8h_source.html @@ -149,7 +149,7 @@
77 
78 };
79 
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/nn__elem__props_8h_source.html b/nn__elem__props_8h_source.html index 600afd07..7d1b23fe 100644 --- a/nn__elem__props_8h_source.html +++ b/nn__elem__props_8h_source.html @@ -335,8 +335,8 @@
263 
264 };
265 
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/output_8h_source.html b/output_8h_source.html index 5d35761f..39e1fd66 100644 --- a/output_8h_source.html +++ b/output_8h_source.html @@ -124,7 +124,7 @@
52 
53 #endif
54 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
diff --git a/petsc__impl_8h_source.html b/petsc__impl_8h_source.html index f42e61ac..d4365301 100644 --- a/petsc__impl_8h_source.html +++ b/petsc__impl_8h_source.html @@ -202,7 +202,7 @@
130 PetscErrorCode petsc_debug_save_mat(const char *, Mat);
131 
132 #endif
-
lsType
Linear system of equations solver type.
Definition: ComMod.h:637
+
lsType
Linear system of equations solver type.
Definition: ComMod.h:640
LHSCtx
Definition: petsc_impl.h:48
LSCtx
Definition: petsc_impl.h:66
diff --git a/post_8h_source.html b/post_8h_source.html index 3a01b9da..43117c51 100644 --- a/post_8h_source.html +++ b/post_8h_source.html @@ -139,7 +139,7 @@
67 
Simulation
Definition: Simulation.h:41
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/read__files_8h_source.html b/read__files_8h_source.html index 67018f83..e053ce3e 100644 --- a/read__files_8h_source.html +++ b/read__files_8h_source.html @@ -174,21 +174,21 @@
102 
103 #endif
104 
-
BodyForceParameters
Body force over a mesh using the "Add_BF" command.
Definition: Parameters.h:616
-
BoundaryConditionParameters
The BoundaryConditionParameters stores paramaters for various type of boundary conditions under the A...
Definition: Parameters.h:672
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
-
DomainParameters
The DomainParameters class stores parameters for the XML 'Domain' element to specify properties for s...
Definition: Parameters.h:1047
-
EquationParameters
The EquationParameters class stores parameters for the 'Add_equation' XML element used to specify an ...
Definition: Parameters.h:1189
+
BodyForceParameters
Body force over a mesh using the "Add_BF" command.
Definition: Parameters.h:617
+
BoundaryConditionParameters
The BoundaryConditionParameters stores paramaters for various type of boundary conditions under the A...
Definition: Parameters.h:673
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
+
DomainParameters
The DomainParameters class stores parameters for the XML 'Domain' element to specify properties for s...
Definition: Parameters.h:1048
+
EquationParameters
The EquationParameters class stores parameters for the 'Add_equation' XML element used to specify an ...
Definition: Parameters.h:1190
MBType
Moving boundary data structure (used for general BC)
Definition: ComMod.h:100
Simulation
Definition: Simulation.h:41
bcType
Boundary condition data type.
Definition: ComMod.h:144
bfType
Definition: ComMod.h:297
-
cplBCType
For coupled 0D-3D problems.
Definition: ComMod.h:751
-
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:429
-
eqType
Equation type.
Definition: ComMod.h:997
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
cplBCType
For coupled 0D-3D problems.
Definition: ComMod.h:754
+
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:432
+
eqType
Equation type.
Definition: ComMod.h:1000
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
read_files_ns
Define some types used to pass data to functions.
Definition: read_files.cpp:54
read_files_ns::face_match
void face_match(ComMod &com_mod, faceType &lFa, faceType &gFa, Vector< int > &ptr)
Match two faces?
Definition: read_files.cpp:65
diff --git a/read__msh_8h_source.html b/read__msh_8h_source.html index ce857198..c81130cc 100644 --- a/read__msh_8h_source.html +++ b/read__msh_8h_source.html @@ -158,11 +158,11 @@
86 #endif
87 
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
read_msh_ns::blkType
Definition: read_msh.h:45
utils::stackType
Definition: utils.h:39
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44 #endif
45 
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
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['rts_1088',['rTS',['../classrmsh_type.html#a65ce23495ee818b526301eaab320514f',1,'rmshType']]], + ['ru_1089',['Ru',['../classib_type.html#af8be6c215991200c6d2008f3447331cf',1,'ibType']]], + ['rub_1090',['Rub',['../classib_type.html#a972bd5ae1f2b9862f6425610e1837d32',1,'ibType']]] ]; diff --git a/set__bc_8h_source.html b/set__bc_8h_source.html index cf5f1507..8e3221e6 100644 --- a/set__bc_8h_source.html +++ b/set__bc_8h_source.html @@ -147,10 +147,10 @@
75 #endif
76 
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
bcType
Boundary condition data type.
Definition: ComMod.h:144
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/set__equation__props_8h_source.html b/set__equation__props_8h_source.html index 68823f30..0ee6d6c4 100644 --- a/set__equation__props_8h_source.html +++ b/set__equation__props_8h_source.html @@ -717,9 +717,9 @@
645 } },
646 };
647 
-
EquationParameters
The EquationParameters class stores parameters for the 'Add_equation' XML element used to specify an ...
Definition: Parameters.h:1189
+
EquationParameters
The EquationParameters class stores parameters for the 'Add_equation' XML element used to specify an ...
Definition: Parameters.h:1190
Simulation
Definition: Simulation.h:41
-
eqType
Equation type.
Definition: ComMod.h:997
+
eqType
Equation type.
Definition: ComMod.h:1000
diff --git a/set__material__props_8h_source.html b/set__material__props_8h_source.html index 78ce9434..7c3f0551 100644 --- a/set__material__props_8h_source.html +++ b/set__material__props_8h_source.html @@ -228,27 +228,47 @@
156 } },
157 
158 //---------------------------//
-
159 // stIso_LS //
+
159 // stIso_HO_ma //
160 //---------------------------//
-
161 // Lee-Sacks material model.
-
162 //
-
163 {consts::ConstitutiveModelType::stIso_LS, [](DomainParameters* domain_params, double mu, double kap, double lam,
-
164  dmnType& lDmn) -> void
-
165 {
-
166  lDmn.stM.isoType = consts::ConstitutiveModelType::stIso_LS;
-
167  auto& params = domain_params->constitutive_model.lee_sacks;
-
168 
-
169  lDmn.stM.a = params.a.value();
-
170  lDmn.stM.a0 = params.a0.value();
-
171  lDmn.stM.b1 = params.b1.value();
-
172  lDmn.stM.b2 = params.b2.value();
-
173  lDmn.stM.mu0 = params.mu0.value();
-
174 
-
175 } },
-
176 
-
177 };
-
DomainParameters
The DomainParameters class stores parameters for the XML 'Domain' element to specify properties for s...
Definition: Parameters.h:1047
-
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:429
+
161 //
+
162 {consts::ConstitutiveModelType::stIso_HO_ma, [](DomainParameters* domain_params, double mu, double kap, double lam,
+
163  dmnType& lDmn) -> void
+
164 {
+
165  lDmn.stM.isoType = consts::ConstitutiveModelType::stIso_HO_ma;
+
166  auto& params = domain_params->constitutive_model.holzapfel;
+
167  lDmn.stM.a = params.a.value();
+
168  lDmn.stM.b = params.b.value();
+
169  lDmn.stM.aff = params.a4f.value();
+
170  lDmn.stM.bff = params.b4f.value();
+
171  lDmn.stM.ass = params.a4s.value();
+
172  lDmn.stM.bss = params.b4s.value();
+
173  lDmn.stM.afs = params.afs.value();
+
174  lDmn.stM.bfs = params.bfs.value();
+
175  lDmn.stM.khs = params.k.value();
+
176 } },
+
177 
+
178 //---------------------------//
+
179 // stIso_LS //
+
180 //---------------------------//
+
181 // Lee-Sacks material model.
+
182 //
+
183 {consts::ConstitutiveModelType::stIso_LS, [](DomainParameters* domain_params, double mu, double kap, double lam,
+
184  dmnType& lDmn) -> void
+
185 {
+
186  lDmn.stM.isoType = consts::ConstitutiveModelType::stIso_LS;
+
187  auto& params = domain_params->constitutive_model.lee_sacks;
+
188 
+
189  lDmn.stM.a = params.a.value();
+
190  lDmn.stM.a0 = params.a0.value();
+
191  lDmn.stM.b1 = params.b1.value();
+
192  lDmn.stM.b2 = params.b2.value();
+
193  lDmn.stM.mu0 = params.mu0.value();
+
194 
+
195 } },
+
196 
+
197 };
+
DomainParameters
The DomainParameters class stores parameters for the XML 'Domain' element to specify properties for s...
Definition: Parameters.h:1048
+
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:432
diff --git a/set__viscosity__props_8h_source.html b/set__viscosity__props_8h_source.html index c0b21192..224585ae 100644 --- a/set__viscosity__props_8h_source.html +++ b/set__viscosity__props_8h_source.html @@ -215,10 +215,10 @@
143 };
144 
145 
-
FluidViscosityParameters
Definition: Parameters.h:835
+
FluidViscosityParameters
Definition: Parameters.h:836
Simulation
Definition: Simulation.h:41
-
SolidViscosityParameters
Definition: Parameters.h:882
-
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:429
+
SolidViscosityParameters
Definition: Parameters.h:883
+
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:432
diff --git a/shells_8h_source.html b/shells_8h_source.html index acfc69a1..3d4d1392 100644 --- a/shells_8h_source.html +++ b/shells_8h_source.html @@ -139,10 +139,10 @@
67 #endif
68 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:429
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
dmnType
Domain type is to keep track with element belong to which domain and also different physical quantiti...
Definition: ComMod.h:432
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/stokes_8h_source.html b/stokes_8h_source.html index 2e917c27..f65e64d3 100644 --- a/stokes_8h_source.html +++ b/stokes_8h_source.html @@ -135,9 +135,9 @@
63 #endif
64 
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/sv__struct_8h_source.html b/sv__struct_8h_source.html index 1115ce63..178a4134 100644 --- a/sv__struct_8h_source.html +++ b/sv__struct_8h_source.html @@ -139,9 +139,9 @@
67 
CepMod
Definition: CepMod.h:220
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/sv_zero_d__subroutines_8h_source.html b/sv_zero_d__subroutines_8h_source.html index 2f6987c3..38ad5893 100644 --- a/sv_zero_d__subroutines_8h_source.html +++ b/sv_zero_d__subroutines_8h_source.html @@ -124,7 +124,7 @@
52 
53 #endif
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
diff --git a/todo.html b/todo.html index 79776aa8..56559f4c 100644 --- a/todo.html +++ b/todo.html @@ -71,10 +71,10 @@
[TODO:DaveP] these guys should be maps map<int,double>.
Namespace mat_fun
[TODO:DaveP] this should just be a namespace?
-
Member mat_fun::mat_inv_ge_orig (const Array< double > &A, const int nd, bool debug)
-
[TODO:DaveP] The original version sometimes produced NaNs.
Namespace read_files_ns
[TODO:DaveP] maxOutput=5 is is defined in consts but in the Fortran READEQ subroutine is defined as maxOutput=22.
+
Member mat_fun::mat_inv_ge_orig (const Array< double > &A, const int nd, bool debug)
+
[TODO:DaveP] The original version sometimes produced NaNs.
Member read_files_ns::face_match (ComMod &com_mod, faceType &lFa, faceType &gFa, Vector< int > &ptr)
[TODO:DaveP] this has not been tested.
diff --git a/trilinos__impl_8h_source.html b/trilinos__impl_8h_source.html index 19a0698d..9f385377 100644 --- a/trilinos__impl_8h_source.html +++ b/trilinos__impl_8h_source.html @@ -326,7 +326,7 @@
TrilinosMatVec::NormInf
double NormInf() const
Infinity norm for global stiffness does not add in the boundary term.
Definition: trilinos_impl.h:139
TrilinosMatVec::SetUseTranspose
int SetUseTranspose(bool use_transpose)
Definition: trilinos_impl.h:127
TrilinosMatVec::UseTranspose
bool UseTranspose() const
Returns current UseTranspose setting.
Definition: trilinos_impl.h:151
-
lsType
Linear system of equations solver type.
Definition: ComMod.h:637
+
lsType
Linear system of equations solver type.
Definition: ComMod.h:640
Trilinos
Initialize all Epetra types we need separate from Fortran.
Definition: trilinos_impl.h:95
Trilinos::ghostX
static Epetra_Vector * ghostX
Solution vector with nodes owned by processor followed by its ghost nodes.
Definition: trilinos_impl.h:100
Trilinos::Importer
static Epetra_Import * Importer
Import ghostMap into blockMap to create ghost map.
Definition: trilinos_impl.h:101
diff --git a/txt_8h_source.html b/txt_8h_source.html index 169ade3e..22b0dac7 100644 --- a/txt_8h_source.html +++ b/txt_8h_source.html @@ -123,9 +123,9 @@
51 #endif
52 
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
-
eqType
Equation type.
Definition: ComMod.h:997
+
eqType
Equation type.
Definition: ComMod.h:1000
diff --git a/ustruct_8h_source.html b/ustruct_8h_source.html index f59a3818..0ae12101 100644 --- a/ustruct_8h_source.html +++ b/ustruct_8h_source.html @@ -155,9 +155,9 @@
83 
CepMod
Definition: CepMod.h:220
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
ustruct::ustruct_2d_c
void ustruct_2d_c(ComMod &com_mod, CepMod &cep_mod, const bool vmsFlag, const int eNoNw, const int eNoNq, const double w, const double Je, const Vector< double > &Nw, const Vector< double > &Nq, const Array< double > &Nwx, const Array< double > &Nqx, const Array< double > &al, const Array< double > &yl, const Array< double > &dl, const Array< double > &bfl, Array< double > &lR, Array3< double > &lK, Array3< double > &lKd)
Reproduces Fortran USTRUCT2D_C.
Definition: ustruct.cpp:428
ustruct::construct_usolid
void construct_usolid(ComMod &com_mod, CepMod &cep_mod, const mshType &lM, const Array< double > &Ag, const Array< double > &Yg, const Array< double > &Dg)
Reproduces Fortran CONSTRUCT_uSOLID.
Definition: ustruct.cpp:216
ustruct::ustruct_r
void ustruct_r(ComMod &com_mod, const Array< double > &Yg)
Definition: ustruct.cpp:1726
diff --git a/vtk__xml_8h_source.html b/vtk__xml_8h_source.html index d10ef5db..ca6b368a 100644 --- a/vtk__xml_8h_source.html +++ b/vtk__xml_8h_source.html @@ -139,11 +139,11 @@
67 
68 
CmMod
The CmMod class duplicates the data structures in the Fortran CMMOD module defined in COMU....
Definition: CmMod.h:62
-
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1329
+
ComMod
The ComMod class duplicates the data structures in the Fortran COMMOD module defined in MOD....
Definition: ComMod.h:1332
Simulation
Definition: Simulation.h:41
-
dataType
This type will be used to write data in the VTK files.
Definition: ComMod.h:1134
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
dataType
This type will be used to write data in the VTK files.
Definition: ComMod.h:1137
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
diff --git a/vtk__xml__parser_8h_source.html b/vtk__xml__parser_8h_source.html index 2439eb20..3f84b6ea 100644 --- a/vtk__xml__parser_8h_source.html +++ b/vtk__xml__parser_8h_source.html @@ -136,8 +136,8 @@
64 #endif
65 
66 
-
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:518
-
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:807
+
faceType
The face type containing mesh at boundary.
Definition: ComMod.h:521
+
mshType
This is the container for a mesh or NURBS patch, those specific to NURBS are noted.
Definition: ComMod.h:810
vtk_xml_parser::VtkFileExtentions
Definition: vtk_xml_parser.h:43