Ustruct and volumetric material tests

Code/Source/svFSI/mat_models.cpp

@@ -142,6 +142,18 @@ void get_fib_stress(const ComMod& com_mod, const CepMod& cep_mod, const fibStrsT
 ///
 /// Reproduces the Fortran 'GETPK2CC' subroutine.
 //
+// ARGS:
+// - com_mod: Object containing global common variables.
+// - cep_mod: Object containing electrophysiology-specific common variables.
+// - lDmn: Domain object
+// - F: Deformation gradient tensor
+// - nfd: Number of fiber directions
+// - fl: Fiber directions
+// - ya: Electrophysiology active stress
+// - S: 2nd Piola-Kirchhoff stress tensor
+// - Dm: Material stiffness tensor
+//
+// RETURNS: None, but modifies S and Dm in place.
 void get_pk2cc(const ComMod& com_mod, const CepMod& cep_mod, const dmnType& lDmn, const Array<double>& F, const int nfd,
  const Array<double>& fl, const double ya, Array<double>& S, Array<double>& Dm)
 {
@@ -483,6 +495,19 @@ void get_pk2cc(const ComMod& com_mod, const CepMod& cep_mod, const dmnType& lDmn
 ///
 /// Reproduces 'SUBROUTINE GETPK2CCdev(lDmn, F, nfd, fl, ya, S, Dm, Ja)'. 
 //
+// ARGS:
+// - com_mod: Object containing global common variables.
+// - cep_mod: Object containing electrophysiology-specific common variables.
+// - lDmn: Domain object
+// - F: Deformation gradient tensor
+// - nfd: Number of fiber directions
+// - fl: Fiber directions
+// - ya: Electrophysiology active stress
+// - S: 2nd Piola-Kirchhoff stress tensor (isochoric part)
+// - Dm: Material stiffness tensor (isochoric part)
+// - Ja: Jacobian for active strain
+//
+// RETURNS: None, but modifies S, Dm, and Ja in place.
 void get_pk2cc_dev(const ComMod& com_mod, const CepMod& cep_mod, const dmnType& lDmn, const Array<double>& F, const int nfd, 
  const Array<double>& fl, const double ya, Array<double>& S, Array<double>& Dm, double& Ja)
 {
@@ -765,7 +790,7 @@ void get_pk2cc_dev(const ComMod& com_mod, const CepMod& cep_mod, const dmnType&
  }
 
  double r1 = J2d*mat_ddot(C, Sb, nsd) / nd;
- auto S = J2d*Sb - r1*Ci;
+ S = J2d*Sb - r1*Ci;
 
  auto PP = ten_ids(nsd) - (1.0/nd) * ten_dyad_prod(Ci, C, nsd);
  CC = ten_ddot(CCb, PP, nsd);
@@ -1409,6 +1434,21 @@ void get_tau(const ComMod& com_mod, const dmnType& lDmn, const double detF, cons
  tauC = ctC * (he*c) * (rho0/detF);
 }
 
+/// @brief Compute rho, beta, drho/dp, dbeta/dp for volumetric penalty terms in 
+/// the ustruct formulation.
+/// See ustruct paper (https://doi.org/10.1016/j.cma.2018.03.045) Section 2.4
+//
+// ARGS:
+// com_mod: ComMod object
+// lDmn: dmnType object
+// p: pressure
+// ro: Solid density, rho
+// bt: Isothermal compressibility coefficient, beta
+// dro: Derivative of rho w.r.t. p
+// dbt: Derivative of beta w.r.t. p
+// Ja: Active strain Jacobian
+//
+// RETURNS: None, but updates ro, bt, dro, dbt
 void g_vol_pen(const ComMod& com_mod, const dmnType& lDmn, const double p, 
  double& ro, double& bt, double& dro, double& dbt, const double Ja)
 {

Code/Source/svFSI/mat_models_carray.h

@@ -164,6 +164,23 @@ void voigt_to_cc_carray(const double Dm[2*N][2*N], double CC[N][N][N][N]) {
 // get_pk2cc
 //-----------
 //
+/// @brief Compute 2nd Piola-Kirchhoff stress and material stiffness tensors
+/// including both dilational and isochoric components.
+///
+/// Reproduces the Fortran 'GETPK2CC' subroutine.
+//
+// ARGS:
+// - com_mod: Object containing global common variables.
+// - cep_mod: Object containing electrophysiology-specific common variables.
+// - lDmn: Domain object
+// - F: Deformation gradient tensor
+// - nfd: Number of fiber directions
+// - fl: Fiber directions
+// - ya: Electrophysiology active stress
+// - S: 2nd Piola-Kirchhoff stress tensor
+// - Dm: Material stiffness tensor
+//
+// RETURNS: None, but modifies S and Dm in place
 template <size_t N>
 void get_pk2cc(const ComMod& com_mod, const CepMod& cep_mod, const dmnType& lDmn, const double F[N][N], const int nfd,
  const Array<double>& fl, const double ya, double S[N][N], double Dm[2*N][2*N])

Code/Source/svFSI/ustruct.cpp

@@ -28,6 +28,23 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+/* 
+This structural mechanics implementation is based on the following reference:
+
+Ju Liu, Alison L. Marsden,
+A unified continuum and variational multiscale formulation for fluids, solids, and fluid–structure interaction,
+Computer Methods in Applied Mechanics and Engineering,
+Volume 337,
+2018,
+Pages 549-597,
+ISSN 0045-7825,
+https://doi.org/10.1016/j.cma.2018.03.045.
+
+This paper describes a unified framework for fluid, solids, and FSI. The code
+in this file is based on the solid mechanics portion of the paper, which can be
+found in Section 4
+*/
+
 #include "ustruct.h"
 
 #include "all_fun.h"