Analysis symbol renaming

src/mumfim/macroscale/AnalysisIO.h

@@ -4,7 +4,7 @@
 #include <apf.h>
 namespace mumfim
 {
-  class NonlinearTissue;
+  class NonlinearTissueStep;
   /**
    * @brief for each model item in the range [bgn_mdl_itm,nd_mdl_itm),
    *  print the step, entity tag, and volume to the specified log
@@ -22,7 +22,7 @@ namespace mumfim
    *  step, entity tag, and loads in the i, j, and k directions.
    */
   template <typename I>
-    void logForces(I bgn, I end, amsi::Log log, int stp, NonlinearTissue * tssu);
+    void logForces(I bgn, I end, amsi::Log log, int stp, NonlinearTissueStep * tssu);
 }
 #include "AnalysisIO_impl.h"
 #endif

src/mumfim/macroscale/AnalysisIO_impl.h

@@ -1,6 +1,6 @@
 #include <apfMeasure.h>
 #include <apfWrapper.h>
-#include "NonlinearTissue.h"
+#include "NonlinearTissueStep.h"
 namespace mumfim
 {
   template <typename I>
@@ -71,7 +71,7 @@ namespace mumfim
     }
   }
   template <typename I>
-  void logForces(I bgn, I end, amsi::Log lg, int stp, NonlinearTissue * tssu)
+  void logForces(I bgn, I end, amsi::Log lg, int stp, NonlinearTissueStep * tssu)
   {
     int rnk = -1;
     MPI_Comm_rank(AMSI_COMM_SCALE, &rnk);

src/mumfim/macroscale/AnalysisStep.cc

@@ -0,0 +1 @@
+#include "AnalysisStep.h"

src/mumfim/macroscale/TissueBase.h → src/mumfim/macroscale/AnalysisStep.h

@@ -3,12 +3,13 @@
 #include <apfFEA.h>
 #include <memory>
 #include <unordered_map>
+#include "mumfim/exceptions.h"
 namespace mumfim
 {
-  class TissueBase : public amsi::apfFEA
+  class AnalysisStep : public amsi::apfFEA
   {
     protected:
-    TissueBase(apf::Mesh * mesh,
+    AnalysisStep(apf::Mesh * mesh,
                const mt::CategoryNode & analysis_case,
                std::vector<amsi::DirichletBCEntry> dbc,
                std::vector<amsi::NeumannBCEntry> nbc,
@@ -22,7 +23,7 @@ namespace mumfim
                        cm)
     {
     }
-    TissueBase(apf::Mesh * mesh,
+    AnalysisStep(apf::Mesh * mesh,
                const amsi::ModelDefinition & problem_definition,
                const amsi::ModelDefinition & solution_strategy,
                const amsi::ModelDefinition & output,
@@ -75,6 +76,17 @@ namespace mumfim
       }
       apf_mesh->end(it);
     }
+
+    public:
+    [[nodiscard]] virtual apf::Field * getUField()=0;
+    virtual void preRun (){};
+    virtual void step (){};
+    virtual void iter (){};
+    virtual void AcceptDOFs (){};
+    virtual void recoverSecondaryVariables(int){};
+    virtual void computeInitGuess(amsi::LAS* las){};
+
+
   };
 }  // namespace mumfim
 #endif  // MUMFIM_SRC_MUMFIM_MACROSCALE_MULTISCALETISSUE_CC_TISSUEBASE_H

src/mumfim/macroscale/CMakeLists.txt

@@ -1,13 +1,13 @@
 set(biotissue_src_files
         Analysis.cc
-        LinearTissue.cc
+        LinearTissueStep.cc
         MultiscaleTissue.cc
         ModelTraits.cc
-        NonlinearTissue.cc
+        NonlinearTissueStep.cc
         ReadStochasticField.cc
         RVECoupling.cc
         StiffnessVariation.cc
-        TissueAnalysis.cc
+        FEMAnalysis.cc
         MultiscaleTissueAnalysis.cc
         SinglescaleTissueAnalysis.cc
         VolumeConstraint.cc

src/mumfim/macroscale/TissueAnalysis.cc → src/mumfim/macroscale/FEMAnalysis.cc

@@ -1,4 +1,4 @@
-#include "mumfim/macroscale/TissueAnalysis.h"
+#include "mumfim/macroscale/FEMAnalysis.h"
 #include <amsiPETScLAS.h>
 #include <apf.h>
 #include <petscsnes.h>
@@ -11,7 +11,7 @@
 //  throw mumfim::petsc_error(petsc_error_code); }
 namespace mumfim
 {
-  TissueAnalysis::TissueAnalysis(apf::Mesh * mesh,
+  FEMAnalysis::FEMAnalysis(apf::Mesh * mesh,
                                  std::unique_ptr<const mt::CategoryNode> cs,
                                  MPI_Comm c,
                                  const amsi::Analysis & amsi_analysis)
@@ -22,7 +22,7 @@ namespace mumfim
       , dt(0.0)
       , stp(0)
       , mx_stp(1)
-      , tssu(nullptr)
+      , analysis_step_(nullptr)
       , itr()
       , itr_stps()
       , cvg()
@@ -68,7 +68,7 @@ namespace mumfim
                      << "   0,    0, 0.0, init\n";
 #endif
   }
-  void TissueAnalysis::addVolumeTracking(
+  void FEMAnalysis::addVolumeTracking(
       apf::Mesh * mesh,
       const mt::CategoryNode * solution_strategy)
   {
@@ -81,11 +81,11 @@ namespace mumfim
         std::vector<apf::ModelEntity *> model_entities;
         GetModelTraitNodeGeometry(mesh, &tracked_volume, model_entities);
         trkd_vols[tracked_volume.GetName()] = new VolCalc(
-            model_entities.begin(), model_entities.end(), tssu->getUField());
+            model_entities.begin(), model_entities.end(), analysis_step_->getUField());
       }
     }
   }
-  TissueAnalysis::~TissueAnalysis()
+  FEMAnalysis::~FEMAnalysis()
   {
     // since we know all of the iteration steps are allocated on the heap delete
     // them
@@ -103,25 +103,25 @@ namespace mumfim
       (*cvg_stp) = nullptr;
     }
     delete cvg;
-    delete tssu;
+    delete analysis_step_;
     delete las;
 #ifdef LOGRUN
     amsi::deleteLog(state);
 #endif
   }
-  void TissueAnalysis::run()
+  void FEMAnalysis::run()
   {
     try
     {
-      tssu->preRun();  // calls updateMicro for multiscale analysis
-      tssu->recoverSecondaryVariables(stp);
+      analysis_step_->preRun();  // calls updateMicro for multiscale analysis
+      analysis_step_->recoverSecondaryVariables(stp);
       checkpoint();
       // write the initial state of everything
       t += dt;
-      tssu->setSimulationTime(t);
+      analysis_step_->setSimulationTime(t);
       // logVolumes(vol_itms.begin(), vol_itms.end(), vols, stp,
-      // tssu->getUField());
-      tssu->computeInitGuess(las);
+      // analysis_step_->getUField());
+      analysis_step_->computeInitGuess(las);
       completed = false;
       SNES snes(cm);
       MumfimPetscCall(SNESSetFromOptions(snes));
@@ -147,7 +147,7 @@ namespace mumfim
                 // bit hacky...if the last finalized iteration is same as
                 // previous
                 static int num_calls = 0;
-                auto * an = static_cast<TissueAnalysis *>(ctx);
+                auto * an = static_cast<FEMAnalysis *>(ctx);
                 auto * petsc_las = dynamic_cast<amsi::PetscLAS *>(an->las);
                 try
                 {
@@ -173,23 +173,23 @@ namespace mumfim
                   // residuals
                   const double * sol;
                   VecGetArrayRead(displacement, &sol);
-                  an->tssu->UpdateDOFs(sol);
+                  an->analysis_step_->UpdateDOFs(sol);
                   VecRestoreArrayRead(displacement, &sol);
-                  an->tssu->ApplyBC_Dirichlet();
-                  an->tssu->RenumberDOFs();
+                  an->analysis_step_->ApplyBC_Dirichlet();
+                  an->analysis_step_->RenumberDOFs();
                   int gbl, lcl, off;
-                  an->tssu->GetDOFInfo(gbl, lcl, off);
+                  an->analysis_step_->GetDOFInfo(gbl, lcl, off);
                   an->las->Reinitialize(gbl, lcl, off);
                   an->las->Zero();
                   // assembles into Mat/vec
-                  an->tssu->Assemble(an->las);
+                  an->analysis_step_->Assemble(an->las);
                   VecAssemblyBegin(petsc_las->GetVector());
                   VecAssemblyEnd(petsc_las->GetVector());
                   MatAssemblyBegin(petsc_las->GetMatrix(), MAT_FINAL_ASSEMBLY);
                   MatAssemblyEnd(petsc_las->GetMatrix(), MAT_FINAL_ASSEMBLY);
-                  an->tssu->iter();
+                  an->analysis_step_->iter();
                   VecCopy(petsc_las->GetVector(), residual);
-                  //an->tssu->AcceptDOFs();
+                  //an->analysis_step_->AcceptDOFs();
                 }
                 catch (mumfim_error & e)
                 {
@@ -219,7 +219,7 @@ namespace mumfim
           [](::SNES snes, Vec displacement, Mat Amat, Mat Pmat,
              void * ctx) -> PetscErrorCode
           {
-            auto * an = static_cast<TissueAnalysis *>(ctx);
+            auto * an = static_cast<FEMAnalysis *>(ctx);
             auto * petsc_las = dynamic_cast<amsi::PetscLAS *>(an->las);
             MatCopy(petsc_las->GetMatrix(), Amat, SAME_NONZERO_PATTERN);
             MatScale(Amat, -1);
@@ -232,7 +232,7 @@ namespace mumfim
              PetscReal f, SNESConvergedReason * reason,
              void * ctx) -> PetscErrorCode
           {
-            auto * an = static_cast<TissueAnalysis *>(ctx);
+            auto * an = static_cast<FEMAnalysis *>(ctx);
             auto error =
                 SNESConvergedDefault(snes, it, xnorm, gnorm, f, reason, ctx);
             bool converged =
@@ -242,7 +242,7 @@ namespace mumfim
             // done the microscale knows that a value of 0 means step is
             // accepted but not converged
             an->finalizeIteration(accepted);
-            an->tssu->AcceptDOFs();
+            an->analysis_step_->AcceptDOFs();
             // HACK set this to zero so we don't finalize iteration
             // in form function
             an->iteration = 0;
@@ -297,14 +297,14 @@ namespace mumfim
         std::cout << "checkpointing (macro)" << std::endl;
         std::cout << "Rewriting at end of load step to include orientation data"
                   << std::endl;
-        tssu->recoverSecondaryVariables(stp);
+        analysis_step_->recoverSecondaryVariables(stp);
         checkpoint();
         // reset the iteration from the numerical solve after checkpointing
         // which records iteration information
         itr->reset();
         stp++;
         t += dt;
-        tssu->setSimulationTime(t);
+        analysis_step_->setSimulationTime(t);
         // Warning! this function has a potentially blocking MPI CALL!
         finalizeStep();
       }
@@ -313,7 +313,7 @@ namespace mumfim
     {
       stp = -4;
       // Write out the failed state
-      // tssu->recoverSecondaryVariables(stp);
+      // analysis_step_->recoverSecondaryVariables(stp);
       checkpoint();
       PetscViewer viewer;
       auto * petsc_las = dynamic_cast<amsi::PetscLAS *>(this->las);
@@ -333,9 +333,9 @@ namespace mumfim
       throw;
     }
   }
-  void TissueAnalysis::finalizeStep(){};
-  void TissueAnalysis::finalizeIteration(int){};
-  void TissueAnalysis::checkpoint()
+  void FEMAnalysis::finalizeStep(){};
+  void FEMAnalysis::finalizeIteration(int){};
+  void FEMAnalysis::checkpoint()
   {
 #ifdef LOGRUN
     std::ofstream st_fs(state_fn.c_str(), std::ios::out | std::ios::app);
@@ -352,6 +352,6 @@ namespace mumfim
     cnvrt << iteration;
     apf::writeVtkFiles(
         std::string(amsi::fs->getResultsDir() + "/" + cnvrt.str()).c_str(),
-        tssu->getMesh());
+        analysis_step_->getMesh());
   }
 }  // namespace mumfim

src/mumfim/macroscale/TissueAnalysis.h → src/mumfim/macroscale/FEMAnalysis.h

@@ -1,7 +1,7 @@
 #ifndef MUMFIM_TISSUE_ANALYSIS_H_
 #define MUMFIM_TISSUE_ANALYSIS_H_
 #include <amsiNonlinearAnalysis.h>
-#include "NonlinearTissue.h"
+#include "NonlinearTissueStep.h"
 #include "VolumeConvergence.h"
 #include <model_traits/CategoryNode.h>
 namespace mumfim
@@ -34,14 +34,14 @@ namespace mumfim
       apf::Field * u,
       I vl_tks,
       O out);
-  class TissueAnalysis
+  class FEMAnalysis
   {
     public:
-    TissueAnalysis(apf::Mesh * mesh,
+    FEMAnalysis(apf::Mesh * mesh,
                    std::unique_ptr<const mt::CategoryNode> cs,
                    MPI_Comm c,
                    const amsi::Analysis & amsi_analysis);
-    virtual ~TissueAnalysis();
+    virtual ~FEMAnalysis();
     virtual void run();
     virtual void checkpoint();
     virtual void finalizeStep();
@@ -58,7 +58,7 @@ namespace mumfim
     int stp;
     int mx_stp;
     int iteration{0};
-    NonlinearTissue * tssu;
+    AnalysisStep * analysis_step_;
     // this is actually a MultiIteration
     amsi::MultiIteration * itr;
     std::vector<amsi::Iteration *> itr_stps;
@@ -80,11 +80,11 @@ namespace mumfim
   class TissueIteration : public amsi::Iteration
   {
     protected:
-    NonlinearTissue * tssu;
+    AnalysisStep * tssu;
     amsi::LAS * las;
 
     public:
-    TissueIteration(NonlinearTissue * t, amsi::LAS * l) : tssu(t), las(l) {}
+    TissueIteration(AnalysisStep * t, amsi::LAS * l) : tssu(t), las(l) {}
     virtual void iterate()
     {
       // Note this is same as FEMLinearIteration
@@ -99,10 +99,10 @@ namespace mumfim
   class TissueCheckpointIteration : public amsi::Iteration
   {
     protected:
-    TissueAnalysis * tssu;
+    FEMAnalysis * tssu;
 
     public:
-    TissueCheckpointIteration(TissueAnalysis * t) : tssu(t) {}
+    TissueCheckpointIteration(FEMAnalysis * t) : tssu(t) {}
     virtual void iterate()
     {
       std::cout << "Checkpointing iteration: " << this->iteration()

src/mumfim/macroscale/HolmesMowIntegrator.h

@@ -1,6 +1,6 @@
 #ifndef MUMFIM_HOLMESMOW_INTEGRATOR_H_
 #define MUMFIM_HOLMESMOW_INTEGRATOR_H_
-#include "NonlinearTissue.h"
+#include "NonlinearTissueStep.h"
 #include <ElementalSystem.h>
 #include <apfShape.h>
 #include <cstring>
@@ -12,7 +12,7 @@ namespace mumfim
   class HolmesMowIntegrator : public amsi::ElementalSystem
   {
   public:
-  HolmesMowIntegrator(NonlinearTissue * n,
+  HolmesMowIntegrator(NonlinearTissueStep * n,
                       apf::Field * field,
                       double shear_modulus,
                       double poisson_ratio,
@@ -296,7 +296,7 @@ namespace mumfim
     }
     int current_integration_point;
   private:
-    NonlinearTissue * analysis;
+    NonlinearTissueStep * analysis;
     int dim;
     apf::FieldShape * fs;
     apf::EntityShape * es;