Update GABLS inputs, gold data, and SCM best practice

Docs/sphinx_doc/BestPractices.rst

@@ -74,9 +74,12 @@ Single-Column Model
 
   .. code-block:: python
 
-     geometry.prob_extent = 25  25  400
-     amr.n_cell           =  4   4   64
-     geometry.is_periodic =  1   1    0
+     geometry.prob_extent = 400  400  400
+     amr.n_cell           =   2    2   64
+     geometry.is_periodic =   1    1    0
+
+  When set up this way, the solution is not sensitive to horizontal problem
+  extent.
 
 * An SCM was successfully run with third-order advection in the horizontal and
   vertical.

Exec/ABL/inputs_GABLS1_mynn25

@@ -6,8 +6,8 @@ amrex.fpe_trap_invalid = 0
 fabarray.mfiter_tile_size = 1024 1024 1024
 
 # PROBLEM SIZE & GEOMETRY (Cuxart et al. 2006)
-geometry.prob_extent = 25  25  400
-amr.n_cell           =  4   4   64
+geometry.prob_extent = 400  400  400
+amr.n_cell           =   2    2   64
 
 geometry.is_periodic = 1 1 0
 

Tests/ERFGoldFiles/ABL_MYNN_PBL/Header

@@ -13,19 +13,16 @@ Khv
 100
 0
 0 0 0 
-25 25 400 
+400 400 400 
 
-((0,0,0) (3,3,63) (0,0,0)) 
+((0,0,0) (1,1,63) (0,0,0)) 
 100 
-6.25 6.25 6.25 
+200 200 6.25 
 0
 0
-0 2 100
+0 1 100
 100
-0 25
-0 12.5
 0 400
-0 25
-12.5 25
+0 400
 0 400
 Level_0/Cell

Tests/ERFGoldFiles/ABL_MYNN_PBL/Level_0/Cell_H

@@ -2,19 +2,15 @@
 1
 9
 0
-(2 0
-((0,0,0) (3,1,63) (0,0,0))
-((0,2,0) (3,3,63) (0,0,0))
+(1 0
+((0,0,0) (1,1,63) (0,0,0))
 )
-2
+1
 FabOnDisk: Cell_D_00000 0
-FabOnDisk: Cell_D_00001 0
 
-2,9
-1.2607004636439996e+00,9.9999999999999998e-13,3.4103449821444358e+00,-2.6773506172953551e-09,-8.8423079783204253e-07,2.6499848492940441e+02,9.5765513907325454e+04,4.9951600759531592e-12,1.5195287431764831e-12,
-1.2607004636439996e+00,9.9999999999999998e-13,3.4103449821444358e+00,-2.6773506172953551e-09,-8.8423079783204253e-07,2.6499848492940441e+02,9.5765513907325454e+04,4.9951600759531592e-12,1.5195287431764831e-12,
+1,9
+1.2607004783120845e+00,9.9999999999999998e-13,2.8950005153645018e+00,-2.5062307694356927e-09,-6.9571739827854739e-07,2.6499787728504919e+02,9.5765515467050223e+04,4.9951533518516673e-12,1.5195259100243211e-12,
 
-2,9
-1.3219702955572461e+00,7.2340449679826584e+00,8.0000002088658864e+00,3.0518417353730613e-02,3.4407652976844720e-06,2.6796875000487586e+02,1.0075944767732981e+05,1.6136077888832165e+00,3.1159644143346008e+00,
-1.3219702955572461e+00,7.2340449679826584e+00,8.0000002088658864e+00,3.0518417353730613e-02,3.4407652976844720e-06,2.6796875000487586e+02,1.0075944767732981e+05,1.6136077888832165e+00,3.1159644143346008e+00,
+1,9
+1.3219733393860191e+00,1.4773976822562200e+00,8.0000001693451086e+00,3.5277613553090698e-02,3.3743448278561294e-06,2.6796875000451178e+02,1.0075944901434385e+05,1.2129625489040476e+00,2.2687468576486003e+00,
 

Tests/ERFGoldFiles/ABL_MYNN_PBL/job_info

@@ -1,41 +1,41 @@
 ===============================================================================
  ERF Job Information
 ===============================================================================
-inputs file: /projects/erf/bperry/ERF/Build/build-tests/Tests/test_files/ABL_MYNN_PBL/ABL_MYNN_PBL.i
+inputs file: ABL_MYNN_PBL.i
 
-number of MPI processes: 2
+number of MPI processes: 1
 
-CPU time used since start of simulation (CPU-hours): 0.000220452
+CPU time used since start of simulation (CPU-hours): 6.79508e-05
 
 ===============================================================================
  Plotfile Information
 ===============================================================================
-output data / time: Mon Jul 15 14:19:52 2024
-output dir:         /kfs2/projects/erf/bperry/ERF/Build/build-tests/Tests/test_files/ABL_MYNN_PBL
+output data / time: Wed Aug 14 21:26:09 2024
+output dir:         /Users/equon/ERF/Tests/test_files/ABL_MYNN_PBL
 
 
 ===============================================================================
  Build Information
 ===============================================================================
-build date:    Jul 15 2024 14:15:38
-build machine: Linux x3000c0s25b0n0 4.18.0-477.10.1.el8_8.x86_64 #1 SMP Wed Apr 5 13:35:01 EDT 2023 x86_64
-build dir:     /projects/erf/bperry/ERF/Build/build-tests/Exec
-AMReX dir:     /projects/erf/bperry/ERF/Submodules/AMReX
+build date:    Aug 14 2024 16:39:05
+build machine: macOS equon-38562s 13.6.7 22G720 arm64
+build dir:     /Users/equon/ERF/MyBuild/Exec
+AMReX dir:     /Users/equon/ERF/Submodules/AMReX
 
-COMP:          GNU
-COMP version:  12.2.1
+COMP:          AppleClang
+COMP version:  15.0.0.15000100
 
 
-ERF       git hash: 24.06-69-gc09476bca82b-dirty
-AMReX       git hash: 24.03
+ERF       git hash: 24.04-205-g3d852cdf3168-dirty
+AMReX       git hash: 24.08
 
 
 ===============================================================================
  Grid Information
 ===============================================================================
  level: 0
-   number of boxes = 2
-   maximum zones   = 4 4 64 
+   number of boxes = 1
+   maximum zones   = 2 2 64 
 
  Boundary conditions
    -x: Periodic
@@ -49,112 +49,114 @@ AMReX       git hash: 24.03
 ===============================================================================
  Inputs File Parameters
 ===============================================================================
-stop_time = 32400.0
-max_step = 100
-amrex.fpe_trap_invalid = 0
-fabarray.mfiter_tile_size = 1024 1024 1024
-geometry.prob_extent = 25 25 400
-amr.n_cell = 4 4 64
-geometry.is_periodic = 1 1 0
-zlo.type = Most
-erf.most.z0 = 0.1
-erf.most.surf_temp = 265.0
-erf.most.surf_heating_rate = -0.25
-zhi.type = SlipWall
-zhi.theta_grad = 0.01
-erf.init_type = input_sounding
-erf.init_sounding_ideal = 1
-erf.input_sounding_file = input_sounding_GABLS1
-erf.fixed_dt = 1.0
-erf.fixed_mri_dt_ratio = 6
-erf.sum_interval = 1
-erf.v = 1
-amr.v = 1
+DistributionMapping.efficiency = 0.90000000000000002
+DistributionMapping.node_size = 0
+DistributionMapping.sfc_threshold = 0
+DistributionMapping.v = 0
+DistributionMapping.verbose = 0
+DistributionMapping.verbose_mapper = 0
+amr.blocking_factor = 1
+amr.check_input = 1
+amr.grid_eff = 0.69999999999999996
+amr.max_grid_size = 2048
 amr.max_level = 0
-erf.check_file = chk
-erf.check_int = -1
-erf.plot_file_1 = plt
-erf.plot_int_1 = 300
-erf.plot_vars_1 = density x_velocity y_velocity z_velocity pressure theta rhoQKE Kmv Khv
-erf.dycore_vert_adv_type = Upwind_3rd
-erf.dryscal_vert_adv_type = Upwind_3rd
-erf.molec_diff_type = None
-erf.use_gravity = true
-erf.use_coriolis = true
-erf.latitude = 73.0
-erf.rotational_time_period = 86455.2516813368
-erf.abl_driver_type = GeostrophicWind
-erf.abl_geo_wind = 8.0 0.0 0.0
-erf.les_type = None
-erf.pbl_type = MYNN2.5
-prob.KE_0 = 0.4
-prob.KE_decay_height = 250.
-prob.KE_decay_order = 1
+amr.n_cell = 2 2 64
+amr.n_error_buf = 0
+amr.n_proper = 2
+amr.refine_grid_layout = 1
 amr.refine_grid_layout_x = 1
 amr.refine_grid_layout_y = 1
 amr.refine_grid_layout_z = 0
-amr.n_proper = 2
-amr.max_grid_size = 2048
-amr.blocking_factor = 1
-amr.n_error_buf = 0
-amrex.v = 1
-amrex.verbose = 1
-amrex.regtest_reduction = 0
-amrex.signal_handling = 1
-amrex.throw_exception = 0
-amrex.call_addr2line = 1
+amr.v = 1
+amrex.abort_on_out_of_gpu_memory = 0
 amrex.abort_on_unused_inputs = 0
-amrex.handle_sigsegv = 1
-amrex.handle_sigterm = 0
-amrex.handle_sigint = 1
+amrex.async_out = 0
+amrex.async_out_nfiles = 64
+amrex.call_addr2line = 1
+amrex.fpe_trap_invalid = 0
+amrex.fpe_trap_overflow = 0
+amrex.fpe_trap_zero = 0
 amrex.handle_sigabrt = 1
 amrex.handle_sigfpe = 1
 amrex.handle_sigill = 1
-amrex.fpe_trap_zero = 0
-amrex.fpe_trap_overflow = 0
-amrex.use_gpu_aware_mpi = 0
+amrex.handle_sigint = 1
+amrex.handle_sigsegv = 1
+amrex.handle_sigterm = 0
+amrex.init_snan = 0
+amrex.mf.alloc_single_chunk = 0
+amrex.regtest_reduction = 0
+amrex.signal_handling = 1
 amrex.the_arena_init_size = 0
-amrex.the_device_arena_init_size = 8388608
-amrex.the_managed_arena_init_size = 8388608
-amrex.the_pinned_arena_init_size = 8388608
-amrex.the_comms_arena_init_size = 8388608
+amrex.the_arena_is_managed = 0
 amrex.the_arena_release_threshold = 9223372036854775807
+amrex.the_async_arena_release_threshold = 9223372036854775807
+amrex.the_comms_arena_init_size = 8388608
+amrex.the_comms_arena_release_threshold = 9223372036854775807
+amrex.the_device_arena_init_size = 8388608
 amrex.the_device_arena_release_threshold = 9223372036854775807
+amrex.the_managed_arena_init_size = 8388608
 amrex.the_managed_arena_release_threshold = 9223372036854775807
+amrex.the_pinned_arena_init_size = 8388608
 amrex.the_pinned_arena_release_threshold = 9223372036854775807
-amrex.the_comms_arena_release_threshold = 9223372036854775807
-amrex.the_async_arena_release_threshold = 9223372036854775807
-amrex.the_arena_is_managed = 0
-amrex.abort_on_out_of_gpu_memory = 0
+amrex.throw_exception = 0
+amrex.use_gpu_aware_mpi = 0
+amrex.v = 1
+amrex.vector_growth_factor = 1.5
+amrex.verbose = 1
+erf.abl_driver_type = GeostrophicWind
+erf.abl_geo_wind = 8.0 0.0 0.0
+erf.check_file = chk
+erf.check_int = -1
+erf.dryscal_vert_adv_type = Upwind_3rd
+erf.dycore_vert_adv_type = Upwind_3rd
+erf.fixed_dt = 1.0
+erf.fixed_mri_dt_ratio = 6
+erf.init_sounding_ideal = 1
+erf.init_type = input_sounding
+erf.input_sounding_file = input_sounding_GABLS1
+erf.latitude = 73.0
+erf.les_type = None
+erf.molec_diff_type = None
+erf.most.surf_heating_rate = -0.25
+erf.most.surf_temp = 265.0
+erf.most.z0 = 0.1
+erf.pbl_type = MYNN2.5
+erf.plot_file_1 = plt
+erf.plot_int_1 = 300
+erf.plot_vars_1 = density x_velocity y_velocity z_velocity pressure theta rhoQKE Kmv Khv
+erf.rotational_time_period = 86455.2516813368
+erf.sum_interval = 1
+erf.use_coriolis = true
+erf.use_gravity = true
+erf.v = 1
+fab.do_initval = 0
 fab.init_snan = 0
-DistributionMapping.v = 0
-DistributionMapping.verbose = 0
-DistributionMapping.efficiency = 0.90000000000000002
-DistributionMapping.sfc_threshold = 0
-DistributionMapping.node_size = 0
-DistributionMapping.verbose_mapper = 0
 fab.initval = nan
-fab.do_initval = 0
 fabarray.maxcomp = 25
-vismf.v = 0
-vismf.headerversion = 1
+fabarray.mfiter_tile_size = 1024 1024 1024
+geometry.coord_sys = 0
+geometry.is_periodic = 1 1 0
+geometry.prob_extent = 400 400 400
+geometry.prob_lo = 0 0 0
+machine.verbose = 0
+machine.very_verbose = 0
+max_step = 100
+prob.KE_0 = 0.4
+prob.KE_decay_height = 250.
+prob.KE_decay_order = 1
+stop_time = 32400.0
+vismf.allowsparsewrites = 1
+vismf.checkfilepositions = 0
 vismf.groupsets = 0
+vismf.headerversion = 1
+vismf.iobuffersize = 2097152
 vismf.setbuf = 1
+vismf.usedynamicsetselection = 1
+vismf.usepersistentifstreams = 0
 vismf.usesingleread = 0
 vismf.usesinglewrite = 0
-vismf.checkfilepositions = 0
-vismf.usepersistentifstreams = 0
 vismf.usesynchronousreads = 0
-vismf.usedynamicsetselection = 1
-vismf.iobuffersize = 2097152
-vismf.allowsparsewrites = 1
-amrex.async_out = 0
-amrex.async_out_nfiles = 64
-amrex.vector_growth_factor = 1.5
-machine.verbose = 0
-machine.very_verbose = 0
-geometry.coord_sys = 0
-geometry.prob_lo = 0 0 0
-amr.grid_eff = 0.69999999999999996
-amr.refine_grid_layout = 1
-amr.check_input = 1
+vismf.v = 0
+zhi.theta_grad = 0.01
+zhi.type = SlipWall
+zlo.type = Most

Tests/test_files/ABL_MYNN_PBL/ABL_MYNN_PBL.i

@@ -7,8 +7,8 @@ amrex.fpe_trap_invalid = 0
 fabarray.mfiter_tile_size = 1024 1024 1024
 
 # PROBLEM SIZE & GEOMETRY (Cuxart et al. 2006)
-geometry.prob_extent = 25  25  400
-amr.n_cell           =  4   4   64
+geometry.prob_extent = 400  400  400
+amr.n_cell           =   2    2   64
 
 geometry.is_periodic = 1 1 0