Preview of scalar as a simcomp

examples/scalar_mms/scalar_mms.case

@@ -34,16 +34,30 @@
         "absolute_tolerance": 1e-7,
         "max_iterations": 800
       },
-      "output_control": "nsamples",
-      "output_value": 1
+      "output_control": "never"
     },
-    "scalar": {
-      "enabled": true,
+    "simulation_components": [
+     {
+        "type": "probes",
+        "compute_control": "simulationtime",
+        "compute_value": 1,
+        "points_file": "probes.csv",
+        "output_file": "output.csv",
+        "fields": [
+            "s"
+        ],
+        "order" : 2
+     },
+     {
+      "type" : "scalar",
       "lambda": 0.01,
       "cp": 1,
       "initial_condition": {
         "type": "user"
       },
+      "output_filename" : "scalar",
+      "output_control" : "nsamples",
+      "output_value" : 1,
       "source_terms": [
         {
           "type": "user_vector"
@@ -54,19 +68,16 @@
             "1.0"
           ]
         }
-      ]
-    },
-    "simulation_components": [
-      {
-        "type": "probes",
-        "compute_control": "nsamples",
-        "compute_value": 1,
-        "points_file": "probes.csv",
-        "output_file": "output.csv",
-        "fields": [
-          "s"
-        ]
+      ],
+      "order": 1,
+      "solver": {
+        "type": "cg",
+        "preconditioner": "jacobi",
+        "projection_space_size": 0,
+        "absolute_tolerance": 1e-7,
+        "max_iterations": 800
       }
+    }
     ]
   }
-}
+}

src/.depends

@@ -166,7 +166,7 @@ common/bcknd/sx/rhs_maker_sx.o : common/bcknd/sx/rhs_maker_sx.f90 field/scratch_
 common/bcknd/device/rhs_maker_device.o : common/bcknd/device/rhs_maker_device.F90 config/num_types.o field/field.o field/field_series.o common/utils.o device/device.o common/rhs_maker.o 
 common/material_properties.o : common/material_properties.f90 comm/comm.o common/utils.o common/user_intf.o common/log.o common/json_utils.o config/num_types.o 
 config/neko_config.o : config/neko_config.f90 
-case.o : case.f90 common/material_properties.o mesh/point_zone_registry.o field/scratch_registry.o common/json_utils.o scalar/scalar_pnpn.o common/user_intf.o common/jobctrl.o common/log.o time_schemes/time_scheme_controller.o comm/comm.o mesh/mesh.o common/utils.o io/file.o common/statistics.o scalar/scalar_ic.o fluid/flow_ic.o common/sampler.o comm/redist.o comm/parmetis.o field/mesh_field.o io/fluid_stats_output.o io/mean_flow_output.o io/mean_sqr_flow_output.o io/chkp_output.o io/fluid_output.o fluid/fluid_fctry.o config/num_types.o 
+case.o : case.f90 common/material_properties.o mesh/point_zone_registry.o field/scratch_registry.o common/json_utils.o common/user_intf.o common/jobctrl.o common/log.o time_schemes/time_scheme_controller.o comm/comm.o mesh/mesh.o common/utils.o io/file.o common/statistics.o fluid/flow_ic.o common/sampler.o comm/redist.o comm/parmetis.o field/mesh_field.o io/fluid_stats_output.o io/mean_flow_output.o io/mean_sqr_flow_output.o io/chkp_output.o io/fluid_output.o fluid/fluid_fctry.o config/num_types.o 
 common/user_intf.o : common/user_intf.f90 common/utils.o config/num_types.o bc/usr_scalar.o bc/usr_inflow.o mesh/mesh.o sem/coef.o scalar/scalar_user_source_term.o fluid/fluid_user_source_term.o field/field.o 
 fluid/fluid_scheme.o : fluid/fluid_scheme.f90 common/material_properties.o common/utils.o common/user_intf.o field/scratch_registry.o common/json_utils.o field/field_registry.o common/log.o math/operators.o math/mathops.o time_schemes/time_scheme_controller.o math/math.o mesh/mesh.o bc/bc.o fluid/fluid_stats.o krylov/precon_fctry.o krylov/krylov_fctry.o bc/non_normal.o bc/symmetry.o bc/dong_outflow.o bc/dirichlet.o bc/blasius.o bc/usr_inflow.o bc/inflow.o bc/wall.o sem/coef.o krylov/krylov.o sem/dofmap.o sem/space.o field/field.o field/field_list.o fluid/fluid_source_term.o fluid/fluid_user_source_term.o config/num_types.o fluid/mean_flow.o common/checkpoint.o config/neko_config.o fluid/mean_sqr_flow.o gs/gather_scatter.o 
 fluid/fluid_aux.o : fluid/fluid_aux.f90 krylov/krylov.o config/num_types.o common/log.o 
@@ -235,8 +235,9 @@ simulation_components/simulation_component.o : simulation_components/simulation_
 simulation_components/simcomp_executor.o : simulation_components/simcomp_executor.f90 case.o common/json_utils.o simulation_components/simulation_component_factory.o simulation_components/simulation_component.o config/num_types.o 
 simulation_components/vorticity.o : simulation_components/vorticity.f90 common/json_utils.o io/fld_file_output.o case.o math/operators.o field/field.o field/field_registry.o simulation_components/simulation_component.o config/num_types.o 
 simulation_components/lambda2.o : simulation_components/lambda2.f90 device/device.o case.o math/operators.o field/field.o field/field_registry.o simulation_components/simulation_component.o config/num_types.o 
+simulation_components/scalar.o : simulation_components/scalar.f90 common/json_utils.o scalar/scalar_ic.o common/log.o scalar/scalar_pnpn.o case.o math/operators.o field/field.o field/field_registry.o simulation_components/simulation_component.o config/num_types.o 
 simulation_components/les_simcomp.o : simulation_components/les_simcomp.f90 common/json_utils.o les/les_model_fctry.o les/les_model.o case.o math/operators.o field/field.o field/field_registry.o simulation_components/simulation_component.o config/num_types.o 
-simulation_components/simulation_component_factory.o : simulation_components/simulation_component_factory.f90 common/log.o common/json_utils.o case.o simulation_components/les_simcomp.o simulation_components/probes.o simulation_components/lambda2.o simulation_components/vorticity.o simulation_components/simulation_component.o 
+simulation_components/simulation_component_factory.o : simulation_components/simulation_component_factory.f90 common/log.o common/json_utils.o case.o simulation_components/les_simcomp.o simulation_components/probes.o simulation_components/scalar.o simulation_components/lambda2.o simulation_components/vorticity.o simulation_components/simulation_component.o 
 source_terms/source_term.o : source_terms/source_term.f90 field/field_list.o sem/coef.o config/num_types.o config/neko_config.o 
 source_terms/const_source_term.o : source_terms/const_source_term.f90 source_terms/bcknd/device/const_source_term_device.o source_terms/bcknd/cpu/const_source_term_cpu.o common/utils.o config/neko_config.o sem/coef.o source_terms/source_term.o common/json_utils.o field/field_list.o config/num_types.o 
 source_terms/bcknd/cpu/const_source_term_cpu.o : source_terms/bcknd/cpu/const_source_term_cpu.f90 math/math.o field/field_list.o config/num_types.o 
@@ -246,5 +247,5 @@ les/les_model.o : les/les_model.f90 device/device.o config/neko_config.o gs/gs_o
 les/les_model_fctry.o : les/les_model_fctry.f90 sem/coef.o sem/dofmap.o les/vreman.o les/les_model.o 
 les/vreman.o : les/vreman.f90 sem/coef.o les/bcknd/cpu/vreman_cpu.o config/neko_config.o common/utils.o common/json_utils.o sem/dofmap.o les/les_model.o field/field.o config/num_types.o 
 les/bcknd/cpu/vreman_cpu.o : les/bcknd/cpu/vreman_cpu.f90 sem/coef.o math/operators.o field/field.o field/field_registry.o field/scratch_registry.o math/math.o field/field_list.o config/num_types.o 
-neko.o : neko.f90 mesh/point_zone_registry.o mesh/point_zones/sphere_point_zone.o mesh/point_zones/box_point_zone.o mesh/point_zone.o sem/point_interpolator.o common/time_interpolator.o io/data_streamer.o simulation_components/simcomp_executor.o field/scratch_registry.o field/field_registry.o common/system.o sem/spectral_error_indicator.o simulation_components/probes.o simulation_components/simulation_component.o math/tensor.o math/vector.o fluid/fluid_user_source_term.o field/field_list.o fluid/fluid_stats.o sem/cpr.o math/bcknd/device/device_math.o device/device.o common/jobctrl.o common/signal.o comm/parmetis.o common/user_intf.o common/projection.o math/mathops.o math/operators.o simulation.o io/output.o common/sampler.o case.o config/neko_config.o math/ax.o math/ax_helm_fctry.o krylov/precon_fctry.o krylov/krylov_fctry.o bc/dirichlet.o bc/wall.o bc/bc.o sem/coef.o gs/gather_scatter.o comm/mpi_types.o field/field.o io/file.o common/global_interpolation.o math/mxm_wrapper.o io/format/map.o field/mesh_field.o mesh/point.o mesh/mesh.o adt/tuple.o adt/stack.o adt/uset.o adt/htable.o sem/space.o sem/dofmap.o sem/speclib.o math/math.o common/log.o common/utils.o comm/comm.o config/num_types.o 
+neko.o : neko.f90 mesh/point_zone_registry.o mesh/point_zones/sphere_point_zone.o mesh/point_zones/box_point_zone.o mesh/point_zone.o sem/point_interpolator.o common/time_interpolator.o io/data_streamer.o simulation_components/simcomp_executor.o field/scratch_registry.o field/field_registry.o common/system.o sem/spectral_error_indicator.o simulation_components/probes.o simulation_components/simulation_component.o math/tensor.o math/vector.o scalar/scalar_user_source_term.o fluid/fluid_user_source_term.o field/field_list.o fluid/fluid_stats.o sem/cpr.o math/bcknd/device/device_math.o device/device.o common/jobctrl.o common/signal.o comm/parmetis.o common/user_intf.o common/projection.o math/mathops.o math/operators.o simulation.o io/output.o common/sampler.o case.o config/neko_config.o math/ax.o math/ax_helm_fctry.o krylov/precon_fctry.o krylov/krylov_fctry.o bc/dirichlet.o bc/wall.o bc/bc.o sem/coef.o gs/gather_scatter.o comm/mpi_types.o field/field.o io/file.o common/global_interpolation.o math/mxm_wrapper.o io/format/map.o field/mesh_field.o mesh/point.o mesh/mesh.o adt/tuple.o adt/stack.o adt/uset.o adt/htable.o sem/space.o sem/dofmap.o sem/speclib.o math/math.o common/log.o common/utils.o comm/comm.o config/num_types.o 
 driver.o : driver.f90 neko.o 

src/Makefile.am

@@ -238,6 +238,7 @@ neko_fortran_SOURCES = \
 	simulation_components/simcomp_executor.f90\
 	simulation_components/vorticity.f90\
 	simulation_components/lambda2.f90\
+	simulation_components/scalar.f90\
 	simulation_components/les_simcomp.f90\
 	simulation_components/simulation_component_factory.f90\
 	source_terms/source_term.f90\

src/case.f90

@@ -45,7 +45,6 @@ module case
   use redist
   use sampler
   use flow_ic
-  use scalar_ic, only : set_scalar_ic
   use stats
   use file
   use utils
@@ -55,7 +54,6 @@ module case
   use logger
   use jobctrl
   use user_intf
-  use scalar_pnpn ! todo directly load the pnpn? can we have other
   use json_module, only : json_file, json_core, json_value
   use json_utils, only : json_get, json_get_or_default
   use scratch_registry, only : scratch_registry_t, neko_scratch_registry
@@ -80,7 +78,6 @@ module case
      type(stats_t) :: q
      type(user_t) :: usr
      class(fluid_scheme_t), allocatable :: fluid
-     type(scalar_pnpn_t), allocatable :: scalar
      type(material_properties_t):: material_properties
   end type case_t
 
@@ -139,7 +136,6 @@ subroutine case_init_common(C)
     type(case_t), target, intent(inout) :: C
     character(len=:), allocatable :: output_directory
     integer :: lx = 0
-    logical :: scalar = .false.
     type(file_t) :: msh_file, bdry_file, part_file
     type(mesh_fld_t) :: msh_part, parts
     logical :: found, logical_val
@@ -227,25 +223,6 @@ subroutine case_init_common(C)
     !
     call neko_point_zone_registry%init(C%params, C%fluid%u%dof)
 
-    !
-    ! Setup scalar scheme
-    !
-    ! @todo no scalar factory for now, probably not needed
-    if (C%params%valid_path('case.scalar')) then
-       call json_get_or_default(C%params, 'case.scalar.enabled', scalar,&
-                                .true.)
-    end if
-
-    if (scalar) then
-       allocate(C%scalar)
-       call C%scalar%init(C%msh, C%fluid%c_Xh, C%fluid%gs_Xh, C%params, C%usr,&
-                          C%material_properties)
-       call C%fluid%chkp%add_scalar(C%scalar%s)
-       C%fluid%chkp%abs1 => C%scalar%abx1
-       C%fluid%chkp%abs2 => C%scalar%abx2
-       C%fluid%chkp%slag => C%scalar%slag
-    end if
-
     !
     ! Setup user defined conditions
     !
@@ -257,11 +234,6 @@ subroutine case_init_common(C)
        end if
     end if
 
-    ! Setup user boundary conditions for the scalar.
-    if (scalar) then
-       call C%scalar%set_user_bc(C%usr%scalar_user_bc)
-    end if
-
     !
     ! Setup initial conditions
     !
@@ -275,17 +247,6 @@ subroutine case_init_common(C)
             C%fluid%c_Xh, C%fluid%gs_Xh, C%usr%fluid_user_ic, C%params)
     end if
 
-    if (scalar) then
-       call json_get(C%params, 'case.scalar.initial_condition.type', string_val)
-       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
-    end if
-
     ! Add initial conditions to BDF scheme (if present)
     select type(f => C%fluid)
     type is(fluid_pnpn_t)
@@ -300,11 +261,6 @@ subroutine case_init_common(C)
     !
     call C%fluid%validate
 
-    if (scalar) then
-       call C%scalar%slag%set(C%scalar%s)
-       call C%scalar%validate
-    end if
-
     !
     ! Set order of timestepper
     !
@@ -363,16 +319,10 @@ subroutine case_init_common(C)
     end if
 
     !
-    ! Setup sampler
+    ! Setup sampler and add fluid output
     !
     call C%s%init(C%end_time)
-    if (scalar) then
-       C%f_out = fluid_output_t(precision, C%fluid, C%scalar, &
-            path=trim(output_directory))
-    else
-       C%f_out = fluid_output_t(precision, C%fluid, &
-            path=trim(output_directory))
-    end if
+    C%f_out = fluid_output_t(precision, C%fluid, path=trim(output_directory))
 
     call json_get_or_default(C%params, 'case.fluid.output_control',&
                              string_val, 'org')
@@ -485,11 +435,6 @@ subroutine case_free(C)
        deallocate(C%fluid)
     end if
 
-    if (allocated(C%scalar)) then
-       call C%scalar%free()
-       deallocate(C%scalar)
-    end if
-
     call C%msh%free()
 
     call C%s%free()

src/common/json_utils.f90

@@ -38,7 +38,7 @@ module json_utils
   implicit none
   private
 
-  public :: json_get, json_get_or_default
+  public :: json_get, json_get_or_default, json_extract_subdict
 
   !> Retrieves a parameter by name or throws an error
   interface json_get
@@ -296,4 +296,24 @@ subroutine json_get_or_default_string(json, name, value, default)
     end if
   end subroutine json_get_or_default_string
 
+  !> Extract `i`th json object from a json array.
+  !! @param core JSON core object.
+  !! @param parent The parent JSON object with the array.
+  !! @param i The index of the object to extract.
+  !! @param subdict JSON object object to be filled with the subdict.
+  subroutine json_extract_subdict(core, parent, i, subdict)
+    type(json_core), intent(inout) :: core
+    type(json_value), pointer, intent(in) :: parent
+    integer, intent(in) :: i
+    type(json_file), intent(inout) :: subdict
+    type(json_value), pointer :: ptr
+    logical :: found
+    character(len=:), allocatable :: buffer
+
+    call core%get_child(parent, i, ptr, found)
+    call core%print_to_string(ptr, buffer)
+    call subdict%load_from_string(buffer)
+
+  end subroutine json_extract_subdict
+
 end module json_utils

src/common/material_properties.f90

@@ -126,56 +126,13 @@ subroutine material_properties_init(this, params, user)
        end if
 
        !
-       ! Scalar
+       ! Scalar dummy values
        !
-       if (.not. params%valid_path('case.scalar')) then
-          ! Set dummy values
-          this%cp = 1.0_rp
-          this%lambda = 1.0_rp
-          call this%write_to_log(.false.)
-          return
-       end if
-
-       ! Incorrect user input
-       if (nondimensional .and. &
-           (params%valid_path('case.scalar.lambda') .or. &
-            params%valid_path('case.scalar.cp'))) then
-          call neko_error("For non-dimensional setup set the Pe number for&
-          & the scalar")
-       else if (.not. nondimensional .and. &
-                params%valid_path('case.scalar.Pe')) then
-          call neko_error("Dimensional material properties input detected,&
-          & because you set rho and mu for the fluid. &
-          & Please set cp and lambda for the scalar.")
-
-          ! Non-dimensional case
-       else if (nondimensional) then
-          write(log_buf, '(A)') 'Non-dimensional scalar material properties &
-          & input.'
-          call neko_log%message(log_buf, lvl=NEKO_LOG_VERBOSE)
-          write(log_buf, '(A)') 'Specific heat capacity will be set to 1, &
-          & conductivity to 1/Pe.'
-          call neko_log%message(log_buf, lvl=NEKO_LOG_VERBOSE)
-
-          ! Read Pe into lambda for further manipulation.
-          call json_get(params, 'case.scalar.Pe', this%lambda)
-          write(log_buf, '(A,ES13.6)') 'Pe         :',  this%lambda
-          call neko_log%message(log_buf)
-
-          ! Set cp and rho to 1 since the setup is non-dimensional.
-          this%cp = 1.0_rp
-          this%rho = 1.0_rp
-          ! Invert the Pe to get conductivity
-          this%lambda = 1.0_rp/this%lambda
-          ! Dimensional case
-       else
-          call json_get(params, 'case.scalar.lambda', this%lambda)
-          call json_get(params, 'case.scalar.cp', this%cp)
-       end if
+       this%cp = 1.0_rp
+       this%lambda = 1.0_rp
+       call this%write_to_log(.false.)
+       return
     end if
-
-    call this%write_to_log(.true.)
-
   end subroutine material_properties_init
 
   !> Write final dimensional values to the log.

src/io/fld_file_output.f90

@@ -78,7 +78,7 @@ subroutine fld_file_output_init(this, precision, name, nfields, path)
        deallocate(this%fields%fields)
     end if
 
-    allocate(this%fields%fields(3))
+    allocate(this%fields%fields(nfields))
 
    end subroutine fld_file_output_init