Merge pull request #1366 from ExtremeFLOW/feature/field-initial-condi…

…tion

Initial condition from fld or chkp

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

@@ -215,6 +215,36 @@ file documentation.
    `base_value` keyword, and then assigned a zone value inside a point zone. The
    point zone is specified by the `name` keyword, and should be defined in the
    `case.point_zones` object. See more about point zones @ref point-zones.md.
+5. `field`, where the initial condition is retrieved from a field file.
+   The following keywords can be used:
+
+| Name             | Description                                                                                        | Admissible values            | Default value |
+| ---------------- | -------------------------------------------------------------------------------------------------- | ---------------------------- | ------------- |
+| `file_name`      | Name of the field file to use (e.g. `myfield0.f00034`).                                            | Strings ending with `f*****` | -             |
+| `interpolate`    | Whether to interpolate the velocity and pressure fields from the field file onto the current mesh. | `true` or `false`            | `false`       |
+| `tolerance`      | Tolerance for the point search.                                                                    | Positive real.               | `1e-6`        |
+| `mesh_file_name` | If interpolation is enabled, the name of the field file that contains the mesh coordinates.        | Strings ending with `f*****` | `file_name`   |
+
+   @attention Interpolating a field from the same mesh but different 
+   polynomial order is performed implicitly and does not require to enable
+   interpolation.
+
+   @note It is recommended to interpolate from `fld` files that were 
+   written in double precision. 
+   To check if your `fld` file was written in double precision, run
+   the command:
+   ~~~~~~~~~~~~~~~{.sh}
+   head -1 field0.f00000
+   ~~~~~~~~~~~~~~~
+   The output `#std 4 ...` indicates single precision, 
+   whereas `#std 8 ...` indicates double precision.
+   Neko write single precision `fld` files by default. To write your 
+   files in double precision, set `case.output_precision` to
+   `"double"`. 
+
+   @attention Neko does not detect wether interpolation is needed or not. 
+   Interpolation will always be performed if `"interpolate"` is set 
+   to `true` even if the field file matches with the current simulation. 
 
 ### Blasius profile
 The `blasius` object is used to specify the Blasius profile that can be used for the
@@ -467,8 +497,12 @@ that can be described concisely directly in the table.
 | `output_value`                          | The frequency of sampling in terms of `output_control`.                                           | Positive real or integer                         | -             |
 | `inflow_condition.type`                 | Velocity inflow condition type.                                                                   | `user`, `uniform`, `blasius`                     | -             |
 | `inflow_condition.value`                | Value of the inflow velocity.                                                                     | Vector of 3 reals                                | -             |
-| `initial_condition.type`                | Initial condition type.                                                                           | `user`, `uniform`, `blasius`                     | -             |
+| `initial_condition.type`                | Initial condition type.                                                                           | `user`, `uniform`, `blasius`, `field`            | -             |
 | `initial_condition.value`               | Value of the velocity initial condition.                                                          | Vector of 3 reals                                | -             |
+| `initial_condition.file_name`           | If `"type" = "field"`, the path to the field file to read from.                                   | String ending with `.fld`, `.chkp`, `.nek5000` or `f*****`.  | -             |
+| `initial_condition.sample_index`        | If `"type" = "field"`, and file type is `fld` or `nek5000`, the index of the file to sampled.     | Positive integer.                                | -1            |
+| `initial_condition.previous_mesh`       | If `"type" = "field"`, and file type is `chkp`, the previous mesh from which to interpolate.      | String ending with `.nmsh`.                      | -             |
+| `initial_condition.tolerance`           | If `"type" = "field"`, and file type is `chkp`, tolerance to use for mesh interpolation.          | Positive real.                                   | 1e-6          |
 | `blasius.delta`                         | Boundary layer thickness in the Blasius profile.                                                  | Positive real                                    | -             |
 | `blasius.freestream_velocity`           | Free-stream velocity in the Blasius profile.                                                      | Vector of 3 reals                                | -             |
 | `blasius.approximation`                 | Numerical approximation of the Blasius profile.                                                   | `linear`, `quadratic`, `cubic`, `quartic`, `sin` | -             |
@@ -544,7 +578,10 @@ file documentation.
    `base_value` keyword, and then assigned a zone value inside a point zone. The
    point zone is specified by the `name` keyword, and should be defined in the
    `case.point_zones` object. See more about point zones @ref point-zones.md.
-
+4. `field`, where the initial condition is retrieved from a field file. Works
+   in the same way as for the fluid. See the 
+   [fluid section](@ref case-file_fluid-ic) for detailed explanations.
+
 ### Source terms
 
 The configuration of source terms is the same as for the fluid. A demonstration

src/.depends

@@ -113,7 +113,7 @@ io/map_file.o : io/map_file.f90 io/format/map.o comm/comm.o common/utils.o io/ge
 io/re2_file.o : io/re2_file.f90 common/log.o adt/htable.o io/map_file.o io/format/map.o io/format/re2.o common/datadist.o comm/mpi_types.o comm/comm.o mesh/point.o mesh/mesh.o common/utils.o config/num_types.o io/generic_file.o 
 io/rea_file.o : io/rea_file.f90 common/log.o adt/htable.o common/datadist.o comm/comm.o io/map_file.o io/re2_file.o io/format/rea.o io/format/map.o mesh/point.o mesh/mesh.o common/utils.o config/num_types.o io/generic_file.o 
 io/fld_file.o : io/fld_file.f90 comm/mpi_types.o math/math.o common/datadist.o comm/comm.o common/utils.o mesh/mesh.o fluid/mean_sqr_flow.o fluid/mean_flow.o io/fld_file_data.o math/vector.o common/structs.o sem/space.o sem/dofmap.o field/field_list.o field/field.o io/generic_file.o config/num_types.o 
-io/fld_file_data.o : io/fld_file_data.f90 math/vector.o math/math.o config/num_types.o 
+io/fld_file_data.o : io/fld_file_data.f90 mesh/mesh.o common/utils.o common/global_interpolation.o sem/space.o sem/dofmap.o field/field.o math/vector.o math/math.o config/num_types.o 
 io/vtk_file.o : io/vtk_file.f90 comm/comm.o common/log.o mesh/tri_mesh.o mesh/tet_mesh.o field/mesh_field.o sem/dofmap.o field/field.o mesh/mesh.o common/utils.o io/generic_file.o config/num_types.o 
 io/stl_file.o : io/stl_file.f90 io/format/stl.o comm/comm.o common/utils.o comm/mpi_types.o mesh/point.o common/log.o mesh/tri_mesh.o io/generic_file.o config/num_types.o 
 io/nmsh_file.o : io/nmsh_file.f90 common/log.o comm/mpi_types.o common/datadist.o mesh/element.o io/format/nmsh.o adt/tuple.o mesh/point.o common/utils.o mesh/mesh.o config/num_types.o comm/comm.o io/generic_file.o 
@@ -130,7 +130,7 @@ io/fluid_stats_output.o : io/fluid_stats_output.f90 math/matrix.o io/output.o de
 io/mean_sqr_flow_output.o : io/mean_sqr_flow_output.f90 io/output.o config/num_types.o fluid/mean_sqr_flow.o 
 io/data_streamer.o : io/data_streamer.F90 config/neko_config.o comm/mpi_types.o comm/comm.o device/device.o common/utils.o sem/coef.o field/field.o config/num_types.o 
 common/sampler.o : common/sampler.f90 common/time_based_controller.o config/num_types.o common/profiler.o common/utils.o common/log.o comm/comm.o io/fld_file.o io/output.o 
-common/global_interpolation.o : common/global_interpolation.F90 comm/mpi_types.o math/math.o comm/comm.o sem/local_interpolation.o common/utils.o common/log.o mesh/mesh.o sem/dofmap.o sem/space.o config/num_types.o 
+common/global_interpolation.o : common/global_interpolation.F90 common/structs.o comm/mpi_types.o math/math.o comm/comm.o sem/local_interpolation.o common/utils.o common/log.o mesh/mesh.o sem/dofmap.o sem/space.o config/num_types.o 
 common/profiler.o : common/profiler.F90 common/runtime_statistics.o common/craypat.o device/hip/roctx.o device/cuda/nvtx.o device/device.o config/neko_config.o 
 common/craypat.o : common/craypat.F90 
 bc/bc.o : bc/bc.f90 common/utils.o adt/tuple.o adt/stack.o mesh/facet_zone.o mesh/mesh.o sem/space.o sem/coef.o sem/dofmap.o device/device.o config/num_types.o config/neko_config.o 
@@ -208,7 +208,7 @@ fluid/mean_flow.o : fluid/mean_flow.f90 field/field.o field/mean_field.o
 fluid/fluid_stats.o : fluid/fluid_stats.f90 common/utils.o config/neko_config.o device/device.o common/stats_quant.o field/field_list.o field/field.o sem/coef.o math/operators.o math/math.o config/num_types.o math/bcknd/device/device_math.o field/mean_field.o 
 fluid/mean_sqr_flow.o : fluid/mean_sqr_flow.f90 field/field.o field/mean_sqr_field.o 
 fluid/flow_profile.o : fluid/flow_profile.f90 config/num_types.o 
-fluid/flow_ic.o : fluid/flow_ic.f90 mesh/point_zone_registry.o mesh/point_zone.o common/json_utils.o common/user_intf.o math/bcknd/device/device_math.o math/math.o sem/coef.o common/utils.o field/field.o device/device.o fluid/flow_profile.o config/neko_config.o gs/gather_scatter.o config/num_types.o 
+fluid/flow_ic.o : fluid/flow_ic.f90 sem/space.o sem/interpolation.o common/global_interpolation.o io/file.o io/fld_file.o io/fld_file_data.o mesh/point_zone_registry.o mesh/point_zone.o common/json_utils.o common/user_intf.o math/bcknd/device/device_math.o math/math.o sem/coef.o common/utils.o field/field.o device/device.o fluid/flow_profile.o config/neko_config.o gs/gather_scatter.o common/log.o config/num_types.o 
 fluid/advection.o : fluid/advection.f90 time_schemes/time_scheme_controller.o field/field_series.o sem/coef.o field/field.o sem/space.o config/num_types.o 
 fluid/advection_fctry.o : fluid/advection_fctry.f90 fluid/bcknd/advection/adv_oifs.o fluid/bcknd/advection/adv_no_dealias.o fluid/bcknd/advection/adv_dealias.o common/json_utils.o fluid/advection.o 
 fluid/bcknd/advection/adv_dealias.o : fluid/bcknd/advection/adv_dealias.f90 device/device.o sem/interpolation.o math/operators.o config/neko_config.o math/bcknd/device/device_math.o sem/coef.o field/field.o sem/space.o math/math.o config/num_types.o fluid/advection.o 
@@ -268,7 +268,7 @@ scalar/scalar_pnpn.o : scalar/scalar_pnpn.f90 field/scratch_registry.o common/ti
 scalar/scalar_aux.o : scalar/scalar_aux.f90 krylov/krylov.o config/num_types.o common/log.o 
 scalar/scalar_residual.o : scalar/scalar_residual.f90 config/num_types.o mesh/mesh.o sem/space.o bc/facet_normal.o scalar/source_scalar.o sem/coef.o field/field.o math/ax.o gs/gather_scatter.o 
 scalar/scalar_residual_fctry.o : scalar/scalar_residual_fctry.f90 scalar/bcknd/sx/scalar_residual_sx.o scalar/bcknd/cpu/scalar_residual_cpu.o scalar/bcknd/device/scalar_residual_device.o config/neko_config.o scalar/scalar_residual.o 
-scalar/scalar_ic.o : scalar/scalar_ic.f90 mesh/point_zone_registry.o mesh/point_zone.o common/json_utils.o common/user_intf.o math/math.o sem/coef.o common/utils.o field/field.o device/device.o math/bcknd/device/device_math.o config/num_types.o config/neko_config.o gs/gather_scatter.o 
+scalar/scalar_ic.o : scalar/scalar_ic.f90 sem/space.o sem/interpolation.o common/global_interpolation.o io/file.o common/checkpoint.o io/fld_file.o io/fld_file_data.o common/log.o field/field_registry.o mesh/point_zone_registry.o mesh/point_zone.o common/json_utils.o common/user_intf.o math/math.o sem/coef.o common/utils.o field/field.o device/device.o math/bcknd/device/device_math.o config/num_types.o config/neko_config.o gs/gather_scatter.o 
 scalar/scalar_source_term.o : scalar/scalar_source_term.f90 common/user_intf.o sem/coef.o field/field_list.o field/field.o source_terms/source_term_handler.o source_terms/source_term.o scalar/scalar_user_source_term.o 
 scalar/scalar_user_source_term.o : scalar/scalar_user_source_term.f90 sem/dofmap.o math/math.o math/bcknd/device/device_math.o device/device.o sem/coef.o field/field_list.o source_terms/source_term.o common/utils.o config/num_types.o config/neko_config.o 
 scalar/bcknd/cpu/scalar_residual_cpu.o : scalar/bcknd/cpu/scalar_residual_cpu.f90 math/math.o config/num_types.o mesh/mesh.o sem/space.o sem/coef.o field/field.o math/ax.o scalar/scalar_residual.o 

src/case.f90

@@ -103,7 +103,7 @@ subroutine case_init_from_file(C, case_file)
     end if
 
     call MPI_Bcast(integer_val, 1, MPI_INTEGER, 0, NEKO_COMM, ierr)
-    if (pe_rank .ne. 0) allocate(character(len=integer_val)::json_buffer)
+    if (pe_rank .ne. 0) allocate(character(len = integer_val) :: json_buffer)
     call MPI_Bcast(json_buffer, integer_val, MPI_CHARACTER, 0, NEKO_COMM, ierr)
     call C%params%load_from_string(json_buffer)
 
@@ -137,7 +137,7 @@ subroutine case_init_common(C)
     logical :: found, logical_val
     integer :: integer_val
     real(kind=rp) :: real_val
-    character(len=:), allocatable :: string_val
+    character(len = :), allocatable :: string_val
     real(kind=rp) :: stats_start_time, stats_output_val
     integer :: stats_sampling_interval
     integer :: output_dir_len
@@ -270,6 +270,9 @@ subroutine case_init_common(C)
     !
     call json_get(C%params, 'case.fluid.initial_condition.type',&
                   string_val)
+
+    call neko_log%section("Fluid initial condition ")
+
     if (trim(string_val) .ne. 'user') then
        call set_flow_ic(C%fluid%u, C%fluid%v, C%fluid%w, C%fluid%p, &
             C%fluid%c_Xh, C%fluid%gs_Xh, string_val, C%params)
@@ -278,15 +281,24 @@ subroutine case_init_common(C)
             C%fluid%c_Xh, C%fluid%gs_Xh, C%usr%fluid_user_ic, C%params)
     end if
 
+    call neko_log%end_section()
+
     if (scalar) then
+
        call json_get(C%params, 'case.scalar.initial_condition.type', string_val)
+
+       call neko_log%section("Scalar initial condition ")
+
        if (trim(string_val) .ne. 'user') then
           call set_scalar_ic(C%scalar%s, &
             C%scalar%c_Xh, C%scalar%gs_Xh, string_val, C%params)
        else
           call set_scalar_ic(C%scalar%s, &
             C%scalar%c_Xh, C%scalar%gs_Xh, C%usr%scalar_user_ic, C%params)
        end if
+
+       call neko_log%end_section()
+
     end if
 
     ! Add initial conditions to BDF scheme (if present)