Rename all GLS Navier Stokes files using Fluid Dynamics prefix (#1236)

Description This PR changes the name of the main class and the name of the files related to the lethe-fluid application. Is the sixth PR of a series of PRs that aim to rename all the Navier Stokes solvers of Lethe using the prefix FluidDynamics and removing GLS. Testing All the existent tests pass without any change.
chaos-polymtl · Aug 9, 2024 · aac4183 · aac4183
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,12 @@
 All notable changes to the Lethe project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
+## [Master] - 2024-08-09
+
+### Changed
+
+- MINOR Renamed the main file related to the `lethe-fluid` application: `gls_navier_stokes` to `fluid_dynamics_matrix_based`. The name of the `GLSNavierStokesSolver` class was changed to `FluidDynamicsMatrixBased`. [#1236](https://github.com/chaos-polymtl/lethe/pull/1236)
+
 ## [Master] - 2024-08-07
 
 ### Changed

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -104,7 +104,7 @@ because it
 but the `lethe-fluid` application
 [links only to `lethe-solvers`](applications/lethe-fluid/CMakeLists.txt)
 because it
-[includes only solvers headers](applications/lethe-fluid/gls_navier_stokes.cc),
+[includes only solvers headers](applications/lethe-fluid/fluid_dynamics_matrix_based.cc),
 and `lethe-core` is a transitive dependency of `lethe-solvers`.
 
 ## Dependencies between Lethe's libraries

diff --git a/applications/lethe-fluid/CMakeLists.txt b/applications/lethe-fluid/CMakeLists.txt
@@ -1,3 +1,3 @@
-add_executable(lethe-fluid gls_navier_stokes.cc)
+add_executable(lethe-fluid fluid_dynamics_matrix_based.cc)
 deal_ii_setup_target(lethe-fluid)
 target_link_libraries(lethe-fluid lethe-solvers)
diff --git a/...ications/lethe-fluid/gls_navier_stokes.cc → ...ethe-fluid/fluid_dynamics_matrix_based.cc b/...ications/lethe-fluid/gls_navier_stokes.cc → ...ethe-fluid/fluid_dynamics_matrix_based.cc
@@ -14,7 +14,7 @@
  * ---------------------------------------------------------------------
  */
 
-#include "solvers/gls_navier_stokes.h"
+#include "solvers/fluid_dynamics_matrix_based.h"
 
 int
 main(int argc, char *argv[])
@@ -48,7 +48,7 @@ main(int argc, char *argv[])
                                    "lethe-fluid",
                                    "lethe-fluid-nitsche"));
 
-          GLSNavierStokesSolver<2> problem(NSparam);
+          FluidDynamicsMatrixBased<2> problem(NSparam);
           problem.solve();
         }
 
@@ -66,7 +66,7 @@ main(int argc, char *argv[])
                                    "lethe-fluid",
                                    "lethe-fluid-nitsche"));
 
-          GLSNavierStokesSolver<3> problem(NSparam);
+          FluidDynamicsMatrixBased<3> problem(NSparam);
           problem.solve();
         }
       else

diff --git a/contrib/utilities/automatic_launch/launch_lethe.sh b/contrib/utilities/automatic_launch/launch_lethe.sh
@@ -8,4 +8,4 @@
 #SBATCH --output=%x-%j.out
 
 source $HOME/.dealii
-srun $HOME/lethe/inst/bin/gls_navier_stokes_2d cylinder.prm
+srun $HOME/lethe/inst/bin/lethe-fluid cylinder.prm
diff --git a/contrib/utilities/automatic_launch/launch_lethe_locally.py b/contrib/utilities/automatic_launch/launch_lethe_locally.py
@@ -9,7 +9,7 @@
 # User input
 CASE_PREFIX = 'cylinder_u_'
 PRM_FILE = 'cylinder.prm'
-LETHE_EXEC = 'gls_navier_stokes_2d'
+LETHE_EXEC = 'lethe-fluid'
 
 for root, directories, files in os.walk(PATH):
 

diff --git a/doc/doxygen/main.h b/doc/doxygen/main.h
@@ -23,7 +23,7 @@
       physics_solver:e -> navier_stokes_base:w [dir=back];
       physics_solver:e -> auxiliary_physics:w [dir=back];
 
-      navier_stokes_base_1 [label=<<B>GLSNavierStokesSolver</B> <br/>(lethe-fluid)>,href="https://chaos-polymtl.github.io/lethe/doxygen/classGLSNavierStokesSolver.html", tooltip="GLSNavierStokesSolver"];
+      navier_stokes_base_1 [label=<<B>FluidDynamicsMatrixBased</B> <br/>(lethe-fluid)>,href="https://chaos-polymtl.github.io/lethe/doxygen/classFluidDynamicsMatrixBased.html", tooltip="FluidDynamicsMatrixBased"];
       navier_stokes_base_2 [label=<<B>FluidDynamicsBlock</B> <br/> (lethe-fluid-block)>,href="https://chaos-polymtl.github.io/lethe/doxygen/classFluidDynamicsBlock.html", tooltip="FluidDynamicsBlock"];
       navier_stokes_base_3 [label=<<B>FluidDynamicsMatrixFree</B> <br/> (lethe-fluid-matrix-free)>,href="https://chaos-polymtl.github.io/lethe/doxygen/classFluidDynamicsMatrixFree.html", tooltip="FluidDynamicsMatrixFree"];
 

diff --git a/include/fem-dem/fluid_dynamics_sharp.h b/include/fem-dem/fluid_dynamics_sharp.h
@@ -20,7 +20,7 @@
 #include <core/shape.h>
 #include <core/vector.h>
 
-#include <solvers/gls_navier_stokes.h>
+#include <solvers/fluid_dynamics_matrix_based.h>
 
 #include <fem-dem/cfd_dem_simulation_parameters.h>
 #include <fem-dem/ib_particles_dem.h>
@@ -43,7 +43,7 @@ using namespace dealii;
  */
 
 template <int dim>
-class FluidDynamicsSharp : public GLSNavierStokesSolver<dim>
+class FluidDynamicsSharp : public FluidDynamicsMatrixBased<dim>
 {
 public:
   FluidDynamicsSharp(CFDDEMSimulationParameters<dim> &nsparam);
@@ -157,7 +157,7 @@ class FluidDynamicsSharp : public GLSNavierStokesSolver<dim>
   /*
    Modified version of assemble_matrix_and_rhs to include the presence of
    extra steps. For more detail see the same function in the
-   gls_navier_stokes.h solver.
+   fluid_dynamics_matrix_based.h solver.
    */
 
   virtual void
@@ -183,7 +183,7 @@ class FluidDynamicsSharp : public GLSNavierStokesSolver<dim>
         else
           generate_cut_cells_map();
       }
-    this->GLSNavierStokesSolver<dim>::assemble_system_matrix();
+    this->FluidDynamicsMatrixBased<dim>::assemble_system_matrix();
 
     sharp_edge();
   }
@@ -197,12 +197,12 @@ class FluidDynamicsSharp : public GLSNavierStokesSolver<dim>
    *
    * Modified version of assemble_matrix_and_rhs to include the presence of
    * extra steps. For more detail see the same function in the
-   * gls_navier_stokes.h solver.
+   * fluid_dynamics_matrix_based.h solver.
    */
   virtual void
   assemble_rhs()
   {
-    this->GLSNavierStokesSolver<dim>::assemble_system_rhs();
+    this->FluidDynamicsMatrixBased<dim>::assemble_system_rhs();
   }
 
   /**

diff --git a/include/fem-dem/fluid_dynamics_vans.h b/include/fem-dem/fluid_dynamics_vans.h
@@ -22,7 +22,7 @@
 #include <core/parameters.h>
 #include <core/time_integration_utilities.h>
 
-#include <solvers/gls_navier_stokes.h>
+#include <solvers/fluid_dynamics_matrix_based.h>
 #include <solvers/postprocessing_cfd.h>
 
 #include <dem/dem.h>
@@ -112,7 +112,7 @@ particle_sphere_intersection_3d(double r_particle,
  */
 
 template <int dim>
-class FluidDynamicsVANS : public GLSNavierStokesSolver<dim>
+class FluidDynamicsVANS : public FluidDynamicsMatrixBased<dim>
 {
 public:
   FluidDynamicsVANS(CFDDEMSimulationParameters<dim> &nsparam);

diff --git a/include/solvers/gls_navier_stokes.h → ...ude/solvers/fluid_dynamics_matrix_based.h b/include/solvers/gls_navier_stokes.h → ...ude/solvers/fluid_dynamics_matrix_based.h
@@ -13,8 +13,8 @@
  *
  * ---------------------------------------------------------------------*/
 
-#ifndef lethe_gls_navier_stokes_h
-#define lethe_gls_navier_stokes_h
+#ifndef lethe_fluid_dynamics_matrix_based_h
+#define lethe_fluid_dynamics_matrix_based_h
 
 #include <core/exceptions.h>
 #include <core/vector.h>
@@ -41,12 +41,12 @@ using namespace dealii;
  */
 
 template <int dim>
-class GLSNavierStokesSolver
+class FluidDynamicsMatrixBased
   : public NavierStokesBase<dim, GlobalVectorType, IndexSet>
 {
 public:
-  GLSNavierStokesSolver(SimulationParameters<dim> &nsparam);
-  ~GLSNavierStokesSolver();
+  FluidDynamicsMatrixBased(SimulationParameters<dim> &nsparam);
+  ~FluidDynamicsMatrixBased();
 
   /**
    * @brief solve Solves the Navier-Stokes problem
@@ -130,7 +130,7 @@ class GLSNavierStokesSolver
    * @brief Define the zero constraints used to solved the problem that change
    * with other physics' solutions.
    *
-   * It differs from GLSNavierStokesSolver::define_zero_constraints as it
+   * It differs from FluidDynamicsMatrixBased::define_zero_constraints as it
    * changes in time depending on the physics' solutions. Currently, it is only
    * used to constraint solid with the temperature's evolution.
    */

diff --git a/include/solvers/fluid_dynamics_nitsche.h b/include/solvers/fluid_dynamics_nitsche.h
@@ -20,7 +20,7 @@
 #include <core/exceptions.h>
 #include <core/solid_base.h>
 
-#include <solvers/gls_navier_stokes.h>
+#include <solvers/fluid_dynamics_matrix_based.h>
 
 #include <deal.II/lac/trilinos_vector.h>
 
@@ -38,7 +38,7 @@ using namespace dealii;
  */
 
 template <int dim, int spacedim = dim>
-class FluidDynamicsNitsche : public GLSNavierStokesSolver<spacedim>
+class FluidDynamicsNitsche : public FluidDynamicsMatrixBased<spacedim>
 {
 public:
   FluidDynamicsNitsche(SimulationParameters<spacedim> &nsparam);
@@ -112,7 +112,7 @@ class FluidDynamicsNitsche : public GLSNavierStokesSolver<spacedim>
   }
 
   /**
-   * @brief Same as in gls_navier_stokes, but calls assemble_nitsche_restriction() when global matrix and rhs are assembled
+   * @brief Same as in fluid_dynamics_matrix_based, but calls assemble_nitsche_restriction() when global matrix and rhs are assembled
    *
    * @deprecated This function is to be deprecated when the new assembly mechanism
    * is integrated to this solver
@@ -121,7 +121,7 @@ class FluidDynamicsNitsche : public GLSNavierStokesSolver<spacedim>
   assemble_matrix_and_rhs();
 
   /**
-   * @brief Same as in gls_navier_stokes, but calls assemble_nitsche_restriction() when rhs is assembled
+   * @brief Same as in fluid_dynamics_matrix_based, but calls assemble_nitsche_restriction() when rhs is assembled
    *
    * @deprecated This function is to be deprecated when the new assembly mechanism
    * is integrated to this solver

diff --git a/source/fem-dem/cfd_dem_coupling.cc b/source/fem-dem/cfd_dem_coupling.cc
@@ -1023,7 +1023,7 @@ CFDDEMSolver<dim>::postprocess_fd(bool first_iteration)
     << "---------------------------------------------------------------"
     << std::endl;
 
-  this->GLSNavierStokesSolver<dim>::postprocess_fd(first_iteration);
+  this->FluidDynamicsMatrixBased<dim>::postprocess_fd(first_iteration);
 
   // Visualization
   if (this->simulation_control->is_output_iteration())

diff --git a/source/fem-dem/fluid_dynamics_sharp.cc b/source/fem-dem/fluid_dynamics_sharp.cc
@@ -21,11 +21,11 @@
 
 #include <deal.II/lac/full_matrix.h>
 
-// Constructor for class GLSNavierStokesSolver
+// Constructor for class FluidDynamicsSharp
 template <int dim>
 FluidDynamicsSharp<dim>::FluidDynamicsSharp(
   CFDDEMSimulationParameters<dim> &p_nsparam)
-  : GLSNavierStokesSolver<dim>(p_nsparam.cfd_parameters)
+  : FluidDynamicsMatrixBased<dim>(p_nsparam.cfd_parameters)
   , cfd_dem_parameters(p_nsparam)
   , all_spheres(true)
   , combined_shapes()
@@ -4171,7 +4171,7 @@ template <int dim>
 void
 FluidDynamicsSharp<dim>::write_checkpoint()
 {
-  this->GLSNavierStokesSolver<dim>::write_checkpoint();
+  this->FluidDynamicsMatrixBased<dim>::write_checkpoint();
 
 
   // Write a table with all the relevant properties of the particle in a table.
@@ -4314,7 +4314,7 @@ template <int dim>
 void
 FluidDynamicsSharp<dim>::read_checkpoint()
 {
-  this->GLSNavierStokesSolver<dim>::read_checkpoint();
+  this->FluidDynamicsMatrixBased<dim>::read_checkpoint();
 
   TimerOutput::Scope t(this->computing_timer,
                        "Reset Sharp-Edge particle information");

diff --git a/source/fem-dem/fluid_dynamics_vans.cc b/source/fem-dem/fluid_dynamics_vans.cc
@@ -12,7 +12,7 @@
 template <int dim>
 FluidDynamicsVANS<dim>::FluidDynamicsVANS(
   CFDDEMSimulationParameters<dim> &nsparam)
-  : GLSNavierStokesSolver<dim>(nsparam.cfd_parameters)
+  : FluidDynamicsMatrixBased<dim>(nsparam.cfd_parameters)
   , cfd_dem_simulation_parameters(nsparam)
   , void_fraction_dof_handler(*this->triangulation)
   , fe_void_fraction(nsparam.cfd_parameters.fem_parameters.void_fraction_order)
@@ -57,7 +57,7 @@ template <int dim>
 void
 FluidDynamicsVANS<dim>::setup_dofs()
 {
-  GLSNavierStokesSolver<dim>::setup_dofs();
+  FluidDynamicsMatrixBased<dim>::setup_dofs();
 
   void_fraction_dof_handler.distribute_dofs(fe_void_fraction);
   locally_owned_dofs_voidfraction =
@@ -172,7 +172,7 @@ FluidDynamicsVANS<dim>::finish_time_step_fd()
   // ensure that the checkpointed information is correct
   percolate_void_fraction();
 
-  GLSNavierStokesSolver<dim>::finish_time_step();
+  FluidDynamicsMatrixBased<dim>::finish_time_step();
 }
 
 template <int dim>

diff --git a/source/solvers/CMakeLists.txt b/source/solvers/CMakeLists.txt
@@ -8,7 +8,7 @@ add_library(lethe-solvers
   cahn_hilliard_scratch_data.cc
   flow_control.cc
   fluid_dynamics_block.cc
-  gls_navier_stokes.cc
+  fluid_dynamics_matrix_based.cc
   fluid_dynamics_nitsche.cc
   heat_transfer.cc
   heat_transfer_assemblers.cc
@@ -48,7 +48,7 @@ add_library(lethe-solvers
   ../../include/solvers/copy_data.h
   ../../include/solvers/flow_control.h
   ../../include/solvers/fluid_dynamics_block.h
-  ../../include/solvers/gls_navier_stokes.h
+  ../../include/solvers/fluid_dynamics_matrix_based.h
   ../../include/solvers/fluid_dynamics_nitsche.h
   ../../include/solvers/heat_transfer.h
   ../../include/solvers/heat_transfer_assemblers.h