Feature/write mesh control (#2281)

Added an option to print out the mesh every time.

I am having problems on deciding how to do this. Generally I would like
that one can control what is written when the write method is called,
but that is not the way we do things in Neko, so for the moment it is
just like this.

I guess if one creates a file_t in the user file, it is possible to
control if the mesh is written by directly modifying the attribute in
the object, so at least that's something.

This is based on what @arash-mp will also add in #2244.

---------

Co-authored-by: Timofey Mukha <timofey.mukha@protonmail.com>
Co-authored-by: Victor Baconnet <baconnet@kth.se>

Author: 3 people

CHANGELOG.md

@@ -1,6 +1,7 @@
 # Changelog
 
 ## Develop
+- Added an option for writing the mesh in every output field file.
 - *BREAKING* All simcomps now have a `name` keyword in the case file. A default
   name is assigned, but all `name`s must be unique. If you have two or more
   simcomps of the same `type`, you must manually provide each a unique `name`.

doc/pages/user-guide/case-file.md

@@ -1160,6 +1160,7 @@ concisely directly in the table.
 | `nut_field`                             | The name of the turbulent viscosity field.                                                        | String                                                      | -             |
 | `output_control`                        | Defines the interpretation of `output_value` to define the frequency of writing checkpoint files. | `nsamples`, `simulationtime`, `tsteps`, `never`             | -             |
 | `output_value`                          | The frequency of sampling in terms of `output_control`.                                           | Positive real or integer                                    | -             |
+| `output_mesh_in_all_files`              | Indicates if the mesh should be written in every output fld file.                                | `true` or `false`                                           | `false`       |
 | `output_filename`                       | The output filename.                                                                              | String                                                      | `field`       |
 | `inflow_condition.type`                 | Velocity inflow condition type.                                                                   | `user`, `uniform`, `blasius`                                | -             |
 | `inflow_condition.value`                | Value of the inflow velocity.                                                                     | Vector of 3 reals                                           | -             |

src/.depends

@@ -146,7 +146,7 @@ io/csv_file.lo : io/csv_file.f90 comm/comm.lo common/log.lo config/num_types.lo
 io/hdf5_file.lo : io/hdf5_file.F90 comm/comm.lo common/log.lo sem/dofmap.lo field/field_series.lo field/field_list.lo field/field.lo mesh/mesh.lo common/utils.lo common/checkpoint.lo io/generic_file.lo config/num_types.lo 
 io/file.lo : io/file.f90 io/hdf5_file.lo io/csv_file.lo io/stl_file.lo io/vtk_file.lo io/fld_file_data.lo io/fld_file.lo io/bp_file.lo io/re2_file.lo io/rea_file.lo io/map_file.lo io/chkp_file.lo io/nmsh_file.lo io/generic_file.lo config/num_types.lo common/utils.lo 
 io/output.lo : io/output.f90 io/file.lo config/num_types.lo 
-io/fluid_output.lo : io/fluid_output.f90 field/field.lo registries/registry.lo scalar/scalars.lo io/output.lo device/device.lo config/neko_config.lo field/field_list.lo scalar/scalar_scheme.lo fluid/fluid_scheme_base.lo fluid/fluid_scheme_compressible.lo fluid/fluid_scheme_incompressible.lo config/num_types.lo 
+io/fluid_output.lo : io/fluid_output.f90 io/fld_file.lo field/field.lo registries/registry.lo scalar/scalars.lo io/output.lo device/device.lo config/neko_config.lo field/field_list.lo scalar/scalar_scheme.lo fluid/fluid_scheme_base.lo fluid/fluid_scheme_compressible.lo fluid/fluid_scheme_incompressible.lo config/num_types.lo 
 io/fld_file_output.lo : io/fld_file_output.f90 io/output.lo device/device.lo config/neko_config.lo field/field_list.lo config/num_types.lo 
 io/chkp_output.lo : io/chkp_output.f90 config/num_types.lo io/output.lo common/checkpoint.lo 
 io/fluid_stats_output.lo : io/fluid_stats_output.f90 math/matrix.lo io/output.lo device/device.lo io/fld_file_data.lo sem/map_2d.lo sem/map_1d.lo config/num_types.lo config/neko_config.lo fluid/fluid_stats.lo 

src/case.f90

@@ -494,15 +494,20 @@ subroutine case_init_common(this)
          name, "field")
     call json_get_or_default(this%params, 'case.fluid.output_format', &
          file_format, 'fld')
+    call json_get_or_default(this%params, &
+                             'case.fluid.output_mesh_in_all_files', &
+                             logical_val, .false.)
     call this%output_controller%init(this%time%end_time)
     if (scalar) then
        call this%f_out%init(precision, this%fluid, this%scalars, name = name, &
             path = trim(this%output_directory), &
-            fmt = trim(file_format), layout = layout)
+            fmt = trim(file_format), layout = layout, &
+            always_write_mesh = logical_val)
     else
        call this%f_out%init(precision, this%fluid, name = name, &
             path = trim(this%output_directory), &
-            fmt = trim(file_format), layout = layout)
+            fmt = trim(file_format), layout = layout, &
+            always_write_mesh = logical_val)
     end if
 
     call json_get_or_default(this%params, 'case.fluid.output_control',&

src/io/fld_file.f90

@@ -63,6 +63,7 @@ module fld_file
   !> Interface for NEKTON fld files
   type, public, extends(generic_file_t) :: fld_file_t
      logical :: dp_precision = .false. !< Precision of output data
+     logical :: write_mesh = .false. !< Whether to write the mesh
    contains
      procedure :: read => fld_file_read
      procedure :: write => fld_file_write
@@ -281,7 +282,12 @@ subroutine fld_file_write(this, data, t)
     !
 
     call this%increment_counter()
-    write_mesh = (this%get_counter() .eq. this%get_start_counter())
+    ! Check if I should write the mesh. Always override at the start counters
+    if (.not. this%write_mesh) then
+       write_mesh = (this%get_counter() .eq. this%get_start_counter())
+    else
+       write_mesh = this%write_mesh
+    end if
     call MPI_Allreduce(MPI_IN_PLACE, write_mesh, 1, &
          MPI_LOGICAL, MPI_LOR, NEKO_COMM)
     call MPI_Allreduce(MPI_IN_PLACE, write_velocity, 1, &

src/io/fluid_output.f90

@@ -44,12 +44,14 @@ module fluid_output
   use scalars, only : scalars_t
   use registry, only : neko_registry
   use field, only : field_t
+  use fld_file, only : fld_file_t
   implicit none
   private
 
   !> Fluid output
   type, public, extends(output_t) :: fluid_output_t
      type(field_list_t) :: fluid
+     logical :: always_write_mesh = .false.
    contains
      procedure, pass(this) :: init => fluid_output_init
      procedure, pass(this) :: sample => fluid_output_sample
@@ -59,14 +61,15 @@ module fluid_output
 contains
 
   subroutine fluid_output_init(this, precision, fluid, scalar_fields, name, &
-       path, fmt, layout)
+       path, fmt, layout, always_write_mesh)
     class(fluid_output_t), intent(inout) :: this
     integer, intent(inout) :: precision
     class(fluid_scheme_base_t), intent(in), target :: fluid
     class(scalars_t), intent(in), optional, target :: scalar_fields
     character(len=*), intent(in), optional :: name
     character(len=*), intent(in), optional :: path
     character(len=*), intent(in), optional :: fmt
+    logical, intent(in), optional :: always_write_mesh
     integer, intent(in), optional :: layout
     character(len=1024) :: fname
     integer :: i, j, n_scalars
@@ -81,6 +84,10 @@ subroutine fluid_output_init(this, precision, fluid, scalar_fields, name, &
        end if
     end if
 
+    if (present(always_write_mesh)) then
+       this%always_write_mesh = always_write_mesh
+    end if
+
     if (present(name) .and. present(path)) then
        fname = trim(path) // trim(name) // trim(suffix)
     else if (present(name)) then
@@ -188,7 +195,14 @@ subroutine fluid_output_sample(this, t)
 
     end if
 
-    call this%file_%write(this%fluid, t)
+    select type (ft => this%file_%file_type)
+       ! Only fld files have the option to write the mesh at command
+    type is (fld_file_t)
+       ft%write_mesh = this%always_write_mesh
+       call ft%write(this%fluid, t)
+    class default
+       call ft%write(this%fluid, t)
+    end select
 
   end subroutine fluid_output_sample