Add regtest for MYNN PBL scheme to CI (erf-model#1688)

* begin adding mynn test

* working mynn test case

Tests/CTestList.cmake

@@ -29,7 +29,7 @@ macro(setup_test)
 
     # Set some default runtime options for all tests in this category
     # set(RUNTIME_OPTIONS "time.max_step=10 amr.plot_file=plt time.plot_interval=10 amrex.throw_exception=1 amrex.signal_handling=0")
-    # set(RUNTIME_OPTIONS "max_step=10 amr.plot_file=plt amr.checkpoint_files_output=0 amr.plot_files_output=1 amrex.signal_handling=0")    
+    # set(RUNTIME_OPTIONS "max_step=10 amr.plot_file=plt amr.checkpoint_files_output=0 amr.plot_files_output=1 amrex.signal_handling=0")
 
 endmacro(setup_test)
 
@@ -110,8 +110,9 @@ add_test_r(TaylorGreenAdvectingDiffusing     "RegTests/TaylorGreenVortex/*/erf_t
 add_test_r(MSF_NoSub_IsentropicVortexAdv     "RegTests/IsentropicVortex/*/erf_isentropic_vortex.exe" "plt00010")
 add_test_r(MSF_Sub_IsentropicVortexAdv       "RegTests/IsentropicVortex/*/erf_isentropic_vortex.exe" "plt00010")
 add_test_r(ABL_MOST                          "ABL/*/erf_abl.exe" "plt00010")
+add_test_r(ABL_MYNN_PBL                      "ABL/*/erf_abl.exe" "plt00100")
 add_test_r(MoistBubble                       "RegTests/Bubble/*/erf_bubble.exe" "plt00010")
-    
+
 add_test_0(Deardorff_stationary              "ABL/*/erf_abl.exe" "plt00010")
 
 else()
@@ -148,6 +149,7 @@ add_test_r(TaylorGreenAdvectingDiffusing     "RegTests/TaylorGreenVortex/erf_tay
 add_test_r(MSF_NoSub_IsentropicVortexAdv     "RegTests/IsentropicVortex/erf_isentropic_vortex" "plt00010")
 add_test_r(MSF_Sub_IsentropicVortexAdv       "RegTests/IsentropicVortex/erf_isentropic_vortex" "plt00010")
 add_test_r(ABL_MOST                          "ABL/erf_abl" "plt00010")
+add_test_r(ABL_MYNN_PBL                      "ABL/erf_abl" "plt00100")
 add_test_r(MoistBubble                       "RegTests/Bubble/erf_bubble" "plt00010")
 
 add_test_0(InitSoundingIdeal_stationary      "ABL/erf_abl" "plt00010")
@@ -156,4 +158,3 @@ endif()
 #=============================================================================
 # Performance tests
 #=============================================================================
-

Tests/ERFGoldFiles/ABL_MYNN_PBL/Header

@@ -0,0 +1,31 @@
+HyperCLaw-V1.1
+9
+density
+rhoQKE
+x_velocity
+y_velocity
+z_velocity
+theta
+pressure
+Kmv
+Khv
+3
+100
+0
+0 0 0 
+25 25 400 
+
+((0,0,0) (3,3,63) (0,0,0)) 
+100 
+6.25 6.25 6.25 
+0
+0
+0 2 100
+100
+0 25
+0 12.5
+0 400
+0 25
+12.5 25
+0 400
+Level_0/Cell

Tests/ERFGoldFiles/ABL_MYNN_PBL/Level_0/Cell_H

@@ -0,0 +1,20 @@
+1
+1
+9
+0
+(2 0
+((0,0,0) (3,1,63) (0,0,0))
+((0,2,0) (3,3,63) (0,0,0))
+)
+2
+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,
+
+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,
+

Tests/ERFGoldFiles/ABL_MYNN_PBL/job_info

@@ -0,0 +1,160 @@
+===============================================================================
+ ERF Job Information
+===============================================================================
+inputs file: /projects/erf/bperry/ERF/Build/build-tests/Tests/test_files/ABL_MYNN_PBL/ABL_MYNN_PBL.i
+
+number of MPI processes: 2
+
+CPU time used since start of simulation (CPU-hours): 0.000220452
+
+===============================================================================
+ 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
+
+
+===============================================================================
+ 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
+
+COMP:          GNU
+COMP version:  12.2.1
+
+
+ERF       git hash: 24.06-69-gc09476bca82b-dirty
+AMReX       git hash: 24.03
+
+
+===============================================================================
+ Grid Information
+===============================================================================
+ level: 0
+   number of boxes = 2
+   maximum zones   = 4 4 64 
+
+ Boundary conditions
+   -x: Periodic
+   +x: Periodic
+   -y: Periodic
+   +y: Periodic
+   -z: MOST
+   +z: SlipWall
+
+
+===============================================================================
+ 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
+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.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
+amrex.abort_on_unused_inputs = 0
+amrex.handle_sigsegv = 1
+amrex.handle_sigterm = 0
+amrex.handle_sigint = 1
+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.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_release_threshold = 9223372036854775807
+amrex.the_device_arena_release_threshold = 9223372036854775807
+amrex.the_managed_arena_release_threshold = 9223372036854775807
+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
+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
+vismf.groupsets = 0
+vismf.setbuf = 1
+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

Tests/test_files/ABL_MYNN_PBL/ABL_MYNN_PBL.i

@@ -0,0 +1,80 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+stop_time = 32400.0  # 540 min = 9 h (Cuxart et al. 2006)
+max_step = 100
+  
+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.is_periodic = 1 1 0
+
+# MOST BOUNDARY (DEFAULT IS ADIABATIC FOR THETA)
+zlo.type                    = "Most"
+erf.most.z0                 = 0.1  # from Cuxart et al. 2006
+erf.most.surf_temp          = 265.0 # initial value, should match input_sounding
+erf.most.surf_heating_rate  = -0.25 # [K/h] from Cuxart et al. 2006
+
+zhi.type        = "SlipWall"
+zhi.theta_grad  = 0.01  # [K/m] to match the input sounding
+
+# INITIALIZATION (Cuxart et al. 2006)
+erf.init_type           = "input_sounding"
+erf.init_sounding_ideal = 1
+erf.input_sounding_file = "input_sounding_GABLS1"
+
+# TIME STEP CONTROL
+erf.fixed_dt        = 1.0  # largest stable low Mach dt
+erf.fixed_mri_dt_ratio = 6
+
+# DIAGNOSTICS & VERBOSITY
+erf.sum_interval    = 1       # timesteps between computing mass
+erf.v               = 1       # verbosity in ERF.cpp
+amr.v               = 1       # verbosity in Amr.cpp
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 0       # maximum level number allowed
+
+# CHECKPOINT FILES
+erf.check_file      = chk        # root name of checkpoint file
+erf.check_int       = -1         # number of timesteps between checkpoints
+
+# PLOTFILES
+erf.plot_file_1     = plt       # prefix of plotfile name
+erf.plot_int_1      = 300        # number of timesteps between plotfiles
+erf.plot_vars_1     = density x_velocity y_velocity z_velocity pressure theta rhoQKE Kmv Khv
+
+
+# SOLVER CHOICE
+erf.dycore_vert_adv_type   = "Upwind_3rd"
+erf.dryscal_vert_adv_type  = "Upwind_3rd"
+
+erf.molec_diff_type = "None"
+
+erf.use_gravity = true
+
+# Coriolis parameter f = 1.39e-4 s^-1 (Cuxart et al. 2006)
+erf.use_coriolis = true
+erf.latitude = 73.0
+erf.rotational_time_period = 86455.2516813368
+
+# Geostrophic wind (Cuxart et al. 2006)
+erf.abl_driver_type = "GeostrophicWind"
+erf.abl_geo_wind = 8.0 0.0 0.0
+
+# Turbulence closure
+erf.les_type        = "None"
+
+# NOT USED
+#erf.rho0_trans      = 1.3223 # from Cuxart et al. 2006
+#erf.theta_ref       = 263.5 # from Cuxart et al. 2006
+
+erf.pbl_type    = "MYNN2.5"
+
+# Initial conditions from Beare et al. 2006
+prob.KE_0            = 0.4 # [m2/s2]
+prob.KE_decay_height = 250. # [m]
+prob.KE_decay_order  = 1

Tests/test_files/ABL_MYNN_PBL/input_sounding_GABLS1

@@ -0,0 +1,4 @@
+1008.0 265.0 0.0
+   0.0 265.0 0.0 8.0 0.0
+ 100.0 265.0 0.0 8.0 0.0
+ 400.0 268.0 0.0 8.0 0.0