LFRic2LFRic - realistic cases, and tidying rose stem

applications/lfric2lfric/source/initialisation/lfric2lfric_init_mesh.f90

@@ -328,29 +328,61 @@ subroutine init_mesh( config,                  &
     ! Read in all global meshes from input file
     !===========================================================
     if (mesh_file(dst) == mesh_file(src)) then
-      call load_global_mesh( mesh_file(dst), mesh_names )
+       call load_global_mesh( mesh_file(dst), mesh_names )
+
+      ! Partition the global meshes
+      !===========================================================
+      call create_local_mesh( mesh_names(dst:dst),           &
+                              local_rank, total_ranks,       &
+                              decomposition_dst,             &
+                              stencil_depths,                &
+                              generate_inner_halos(dst),     &
+                              partitioner_dst,               &
+                              enforce_constraints = .false. )
+      call create_local_mesh( mesh_names(src:src),           &
+                              local_rank, total_ranks,       &
+                              decomposition_src,             &
+                              stencil_depths,                &
+                              generate_inner_halos(src),     &
+                              partitioner_src,               &
+                              enforce_constraints = .false. )
+
     else
-      call load_global_mesh( mesh_file(dst), mesh_names(dst) )
+
+      !! SOURCE
       call load_global_mesh( mesh_file(src), mesh_names(src) )
-    endif
+      write( log_scratch_space, '(A)' )                                     &
+         'Loaded src'
+      call log_event(log_scratch_space, log_level_debug)
+
+      call create_local_mesh( mesh_names(src:src),           &
+                              local_rank, total_ranks,       &
+                              decomposition_src,             &
+                              stencil_depths,                &
+                              generate_inner_halos(src),     &
+                              partitioner_src,               &
+                              enforce_constraints = .false. )
+
+      call global_mesh_collection%clear()
+
+     !! DESTINATION
+      call load_global_mesh( mesh_file(dst), mesh_names(dst) )
+      write( log_scratch_space, '(A)' )                                     &
+         'Loaded dest'
+      call log_event(log_scratch_space, log_level_debug)
 
-    ! Partition the global meshes
-    !===========================================================
-    call create_local_mesh( mesh_names(dst:dst),           &
-                            local_rank, total_ranks,       &
-                            decomposition_dst,             &
-                            stencil_depths,                &
-                            generate_inner_halos(dst),     &
-                            partitioner_dst,               &
-                            enforce_constraints = .false. )
-
-    call create_local_mesh( mesh_names(src:src),           &
-                            local_rank, total_ranks,       &
-                            decomposition_src,             &
-                            stencil_depths,                &
-                            generate_inner_halos(src),     &
-                            partitioner_src,               &
-                            enforce_constraints = .false. )
+      call create_local_mesh( mesh_names(dst:dst),           &
+                              local_rank, total_ranks,       &
+                              decomposition_dst,             &
+                              stencil_depths,                &
+                              generate_inner_halos(dst),     &
+                              partitioner_dst,               &
+                              enforce_constraints = .false. )
+
+      call global_mesh_collection%clear()
+
+
+    endif
 
     ! Read in the global intergrid mesh mappings,
     ! then create the associated local mesh maps

rose-stem/app/lfric2lfric/file/iodef_diag_file.xml

@@ -0,0 +1,70 @@
+<!-- TODO : #325 Define fields to initialise for lfric2lfric miniapp -->
+<?xml version="1.0" encoding="UTF-8"?>
+<simulation>
+
+  <!-- File definition for LFRic checkpoint read  -->
+  <context id = "lfric2lfric_source">
+
+    <!-- Include axis definitions -->
+    <axis_definition src="./axis_def_main.xml"/>
+    <axis_definition src="./axis_def_urban1t.xml"/>
+
+    <!-- Include grid definitions -->
+    <grid_definition src="./grid_def_main.xml"/>
+
+    <!-- Local file definitions -->
+    <file_definition type="one_file" par_access="collective" time_counter="none">
+
+      <!-- File definition for LFRic checkpoint read -->
+      <file id="lfric_checkpoint_read" name="lfric_checkpoint_read" mode="read" output_freq="1ts" convention="UGRID" cyclic="true" enabled=".TRUE.">
+        <!-- Atmosphere fields -->
+        <field id="restart_theta" name="theta" long_name="air_potential_temperature" standard_name="air_potential_temperature" unit="K" grid_ref="full_level_face_grid" operation="once" />
+	<field id="restart_rho" name="rho" long_name="air_density" standard_name="air_density" unit="kg m-3" grid_ref="half_level_face_grid" operation="once" />
+      </file>
+    </file_definition>
+  </context>
+
+  <!-- File definition for LFRic checkpoint write -->
+  <context id = "lfric2lfric_destination">
+
+    <!-- Include axis definitions -->
+    <axis_definition src="./axis_def_main.xml"/>
+    <axis_definition src="./axis_def_urban1t.xml"/>
+
+    <!-- Include grid definitions -->
+    <grid_definition src="./grid_def_main.xml"/>
+
+    <!-- Local file definitions -->
+    <file_definition type="one_file" par_access="collective" time_counter="none">
+
+      <!-- File definition for LFRic checkpoint -->
+      <file id="lfric_checkpoint_write" name="lfric_checkpoint_write" mode="write" output_freq="1ts" convention="UGRID" enabled=".TRUE.">
+
+        <!-- Atmosphere fields -->
+        <field id="checkpoint_theta" name="theta" long_name="air_potential_temperature" standard_name="air_potential_temperature" unit="K" prec="8" domain_ref="checkpoint_Wtheta" operation="once" />
+        <field id="checkpoint_rho" name="rho" long_name="air_density" standard_name="air_density" unit="kg m-3" prec="8" domain_ref="checkpoint_W3" operation="once" />
+
+
+      </file>
+    </file_definition>
+
+  </context>
+
+  <context id = "xios">
+    <variable_definition>
+      <variable_group id = "buffer">
+        <variable id = "optimal_buffer_size" type = "string" >performance</variable>
+        <variable id = "buffer_size_factor" type = "double" >1.0</variable>
+      </variable_group>
+
+      <variable_group id = "parameters" >
+        <variable id = "using_server" type = "bool" >false</variable>
+        <variable id = "using_oasis" type = "bool">false</variable>
+        <variable id = "info_level" type = "int" >50</variable>
+        <variable id = "print_file" type="bool">true</variable>
+        <variable id = "oasis_codes_id" type="string" >lfric2lfric lfric2lfric</variable>
+      </variable_group>
+    </variable_definition>
+  </context>
+
+</simulation>

rose-stem/app/lfric2lfric/opt/rose-app-C24_C12.conf

@@ -1,3 +1,17 @@
+[file:lfric2lfric_clim_gal9_C12_MG.nc]
+source="$BIG_DATA_DIR/start_dumps/proto-ral/AppsTicket110/lfric_atm_clim_gal9_C12_dt-1800p0_intel_64-bit_fast-debug_000072.nc"
+
+[namelist:extrusion]
+domain_height=80000.0
+method='um_L70_50t_20s_80km'
+number_of_layers=70
+stretching_height=17507.0
+stretching_method='smooth'
+
+[namelist:files]
+checkpoint_stem_name='restart_lfric2lfric_clim_gal9_C12_MG'
+start_dump_filename='lfric2lfric_clim_gal9_C12_MG'
+
 [namelist:lfric2lfric]
 destination_mesh_name='C24'
 destination_meshfile_prefix='${MESH_DIR}/C24_C12/mesh_C24_C12'

rose-stem/app/lfric2lfric/opt/rose-app-destination-melbourne.conf

@@ -0,0 +1,13 @@
+[namelist:files]
+checkpoint_stem_name='restart_lfric2lfric_ral_seuk_MG'
+
+[namelist:lfric2lfric]
+target_domain='LAM'
+dst_ancil_directory='$BIG_DATA_DIR/ancils/proto-ral/Ticket255/Melbourne'
+destination_meshfile_prefix='${MESH_DIR}/melbourne_MG/mesh_melbourne_MG'
+destination_mesh_name='regional'
+dst_orography_mean_ancil_path='orography/gmted_ramp2/v2/qrparm.orog.ugrid'
+destination_topology='non_periodic'
+
+[namelist:partitioning(destination)]
+partitioner='planar'

rose-stem/app/lfric2lfric/opt/rose-app-destination-seuk.conf

@@ -0,0 +1,13 @@
+[namelist:files]
+checkpoint_stem_name='restart_lfric2lfric_ral_seuk_MG'
+
+[namelist:lfric2lfric]
+target_domain='LAM'
+dst_ancil_directory='$BIG_DATA_DIR/ancils/proto-ral/Ticket3510/seuk'
+destination_meshfile_prefix='${MESH_DIR}/seuk_MG/mesh_seuk_MG'
+destination_mesh_name='regional'
+dst_orography_mean_ancil_path='orography/gmted_ramp2/qrparm.orog.ugrid'
+destination_topology='non_periodic'
+
+[namelist:partitioning(destination)]
+partitioner='planar'

rose-stem/app/lfric2lfric/opt/rose-app-destination-ukv.conf

@@ -0,0 +1,13 @@
+[namelist:files]
+checkpoint_stem_name='restart_lfric2lfric_ral_ukv_MG'
+
+[namelist:lfric2lfric]
+target_domain='LAM'
+dst_ancil_directory=''
+destination_meshfile_prefix='${MESH_DIR}/ukv_MG/mesh_ukv_MG'
+destination_mesh_name='regional'
+dst_orography_mean_ancil_path=''
+destination_topology='non_periodic'
+
+[namelist:partitioning(destination)]
+partitioner='planar'

rose-stem/app/lfric2lfric/opt/rose-app-lbc.conf

@@ -9,10 +9,9 @@ mode=auto
 source=$BIG_DATA_DIR/lfric2lfric/lfric_gal_diagnostics.nc
 
 [namelist:lfric2lfric]
-destination_mesh_name='dynamics'
+destination_mesh_name='regional'
 mode='lbc'
 source_file_lbc='source_file_lbc'
-source_mesh_name='C12'
 
 [namelist:time]
 timestep_end='2'

rose-stem/app/lfric2lfric/opt/rose-app-ral3_seuk.conf

@@ -1,3 +1,38 @@
+[file:iodef.xml]
+source=$ROSE_SUITE_DIR/app/lfric2lfric/file/iodef_ral3.xml
+
+[file:lfric2lfric_ral3_seuk.nc]
+source="$BIG_DATA_DIR/start_dumps/proto-ral/Ticket3510/seuk/checkpoint_um2lfric_000001.nc"
+
+[namelist:extrusion]
+domain_height=40000.0
+method='um_L70_61t_9s_40km'
+number_of_layers=70
+stretching_height=16641.984
+stretching_method='smooth'
+
+[namelist:files]
+checkpoint_stem_name='restart_lfric2lfric_ral3_seuk'
+!!lbc_directory='$BIG_DATA_DIR/lbcs/proto-ral/Ticket3510/seuk'
+!!lbc_filename='checkpoint_um2lfric_000001_fixedtime_date'
+start_dump_filename='lfric2lfric_ral3_seuk'
+
+[namelist:finite_element]
+coord_order=2
+coord_order_nonprime=2
+
 [namelist:lfric2lfric]
 destination_meshfile_prefix='${MESH_DIR}/ral3_seuk/mesh_ral3_seuk'
+destination_mesh_name='regional'
+destination_topology='non_periodic'
+origin_domain='LAM'
 source_meshfile_prefix='${MESH_DIR}/ral3_seuk/mesh_ral3_seuk'
+source_mesh_name='multigrid_l1'
+source_topology='non_periodic'
+target_domain='LAM'
+
+[namelist:partitioning(destination)]
+partitioner='planar'
+
+[namelist:partitioning(source)]
+partitioner='planar'

rose-stem/app/lfric2lfric/opt/rose-app-ral_seuk.conf

@@ -24,3 +24,12 @@ destination_topology='non_periodic'
 origin_domain='LAM'
 source_topology='non_periodic'
 target_domain='LAM'
+destination_meshfile_prefix='${MESH_DIR}/seuk_MG/mesh_seuk_MG'
+source_meshfile_prefix='${MESH_DIR}/seuk_MG/mesh_seuk_MG'
+source_mesh_name='regional'
+
+[namelist:partitioning(destination)]
+partitioner='planar'
+
+[namelist:partitioning(source)]
+partitioner='planar'

rose-stem/app/lfric2lfric/opt/rose-app-clim_gal9_ral_seuk.conf → rose-stem/app/lfric2lfric/opt/rose-app-source-C12.conf

@@ -1,3 +1,9 @@
+[file:iodef.xml]
+source=$ROSE_SUITE_DIR/app/lfric2lfric/file/iodef_orography.xml
+
+[namelist:files]
+orography_mean_ancil_path=''
+
 [file:lfric2lfric_clim_gal9_C12_MG.nc]
 source="$BIG_DATA_DIR/start_dumps/proto-ral/AppsTicket110/lfric_atm_clim_gal9_C12_dt-1800p0_intel_64-bit_fast-debug_000072.nc"
 
@@ -15,6 +21,11 @@ start_dump_filename='lfric2lfric_clim_gal9_C12_MG'
 [namelist:lfric2lfric]
 destination_topology='non_periodic'
 target_domain='LAM'
+source_mesh_name='dynamics'
+source_meshfile_prefix='${MESH_DIR}/C12_MG/mesh_C12_MG'
+src_ancil_directory='$BIG_DATA_DIR/ancils/basic-gagl/Puku/C12/n96e'
+src_orography_mean_ancil_path='orography/globe30/qrparm.orog.ugrid'
+
+[namelist:orography]
+orog_init_option='none'
 
-[namelist:partitioning(destination)]
-partitioner='planar'