Add new material models and excitation-contraction coupling from svFSI

[ktbolt]

The Fortran svFSI code has several changes to material models that we need to add to svFSIplus

• HGO-decoupled
• HGO-modified
• HO-decoupled
• HO-modified

I think HGO-modified and HO-modified are new.

HGO-decoupled and HO-decoupled seem to be HGO and HO renamed. I will still need to figure out if these have been modified.

[ktbolt]

I'm going to also add the new excitation-contraction coupling implementation here since the material models need this.

[ktbolt]

I've converted the updated material models, updated a bunch of functions and added new material types (enums)

• update consts.h
• update consts.cpp
• update ComMod.h
• update read_mat_model()
• update get_pk2cc()
• update get_pk2cc()
• add ActiveStrainType enum
• add eccModelType class
• add get_actv_def_grad()
• update tpost()
• update struct_2d()
• update struct_3d()
• update construct_fsi()
• update get_pk2cc_dev()
• update ustruct_2d_m()
• update ustruct_3d_m()

I see a lot of code duplication in the material models code. I will need to think about how to better organize material models in the Stage 2 code.

[ktbolt]

I've updated and converted more code for excitation-contraction coupling

• modify construct_cep()
• modify cep_3d()
• modify cep_2d()
• modify cep_init_l()
• modify cep_init()
• modify cep_integ()
• modify cep_integ_l()
• add CepModAp::actv_strs_be()
• add CepModAp::actv_strs_fe()
• add CepModAp::actv_strs_rk()
• add CepModBo::actv_strs_fe()
• add CepModBo::actv_strs_fb()
• add CepModBo::actv_strs_rk()
• add CepModTtp::actv_strs_be()
• add CepModTtp::actv_strs_fe()
• add CepModTtp::actv_strs_rk()
• add CepModTtp::actv_strn_fe()
• add CepModTtp::actv_strn_rk()
• add CepModTtp::actv_strn_be()
• add CepModAp::astrs_getf()
• add CepModBo::astrs_getf()
• add CepModBo::astrn_getj()
• add CepModBo::astrs_getf()
• add CepModTtp::astrn_getf()
• add CepModTtp::astrn_getj()
• add CepModTtp::astrs_getf()
• modify dist_eq()
• add dist_ec_model()
• modify part_msh()

[ktbolt]

I've updated and converted more code for excitation-contraction coupling

• add EcMod class to reproduce code in ECMOD_DCPLD.f and PARAMS_EC_DCPLD.f
  • add EcMod::actv_strs_fe()
  • add EcMod::actv_strs_be()
  • add EcMod::actv_strs_rk()
  • add EcMod::astrs_getf()
  • add EcMod::actv_strn_sin2()
  • add ec_dcpld.{n,cpp}
  • add ec_dcpld::init()
  • add ec_dcpld::get_y()
  • modify initialize.cpp
  • modify picp()
  • modify cep_2d()
  • modify cep_3d()
  • modify cep_integ()
  • modify cep_integ_l()
  • modify dist_eq()
  • modify write_restart()
  • modify read_cep_domain()

There appears to be a new file type that stores parameters for excitation-contraction coupling. This is used to overwrite default excitation-contraction coupling parameters. The parameters seem to be stored like

<NAME>: <VALUE>

Is this correct @vvedula22

There is also a new parameter section called Excitation-contraction coupling defined for the solver input file. @vvedula22 The excitation-contraction coupling parameters are not documented in the svFSI_master.inp file, please update it.

[vvedula22]

@ktbolt Yes, that is correct. Will update svFSI_master.inp on the usage soon and also couple of test cases to the examples repository.

[ktbolt]

@vvedula22 Thanks!

[ktbolt]

I've added more excitation-contraction code

modified:   CepMod.h
modified:   ComMod.h
modified:   Simulation.h
modified:   cep.cpp
modified:   cep_ion.cpp
modified:   distribute.cpp
modified:   fsi.cpp
modified:   initialize.cpp
modified:   mat_models.cpp
modified:   mesh.cpp
modified:   output.cpp
modified:   pic.cpp
modified:   read_files.cpp
modified:   read_files.h
modified:   set_equation_props.h
added: EcMod.cpp
added: EcMod.h
added: ec_dcpld.cpp
added: ec_dcpld.h

Adding new Fortran code from svFSI is truly a nightmare trying to figure out what to add/modify in the C++ code.

[ktbolt]

@vvedula22 I am now stalled on the conversion. I need 1) updated svFSI_master.inp with the new excitation-contraction parameters 2) Format of the excitation-contraction parameter files 3) svFSI-Tests examples

[vvedula22]

@ktbolt Will do. Just wanted to make sure the mechanics model is properly validated before uploading it to svFSI-Tests.

[aabrown100-git]

@vvedula22 @ktbolt What's the status of this issue? I'd like to test @vvedula22 's cardiac benchmark simulation in svFSIplus, but it seems the excitation-contraction coupling is not fully implemented yet.

[ktbolt]

@aabrown100-git I've added the new material models but there are no tests to check the C++ implementation so I have not checked-in the changes.

[ktbolt]

Recent changes to the svFSI material models makes the changes I made obsolete, better to just start over.