Rename all GLS Navier Stokes files using Fluid Dynamics prefix (chaos…

…-polymtl#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.
M-Badri · 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