Merge pull request #65 from idaholab/PR_bc_sampp

Use SamApp for sam inputs

doc/content/pbfhr/reflector.md

@@ -619,11 +619,11 @@ in the graphite and steel.
 Next, the [MultiApps](https://mooseframework.inl.gov/syntax/MultiApps/index.html)
  and [Transfers](https://mooseframework.inl.gov/syntax/Transfers/index.html)
 blocks describe the interaction between Cardinal
-and MOOSE. The MOOSE heat conduction module is here run as the master application, with
+and MOOSE. The MOOSE heat conduction module is here run as the main application, with
 the nekRS wrapping run as the sub-application. We specify that MOOSE will run first on each
 time step. Allowing sub-cycling means that, if the MOOSE time step is 0.05 seconds, but
 the nekRS time step is 0.02 seconds, that for every MOOSE time step, nekRS will perform
-three time steps, of length 0.02, 0.02, and 0.01 seconds to "catch up" to the MOOSE master
+three time steps, of length 0.02, 0.02, and 0.01 seconds to "catch up" to the MOOSE main
 application. If sub-cycling is turned off, then the smallest time step among all the various
 applications is used.
 
@@ -762,7 +762,7 @@ The input consists of blocks and parameters. The `[GENERAL]` block describes the
 time stepping, simulation end control, and the polynomial order. Here, a time step
 of 0.025 (non-dimensional) is used; a nekRS output file is written every 100 time steps.
 Because nekRS is run as a sub-application to MOOSE, the `stopAt` and `numSteps`
-fields are actually ignored, so that the steady state tolerance in the MOOSE master
+fields are actually ignored, so that the steady state tolerance in the MOOSE main
 application dictates when a simulation terminates. Because the purpose of this
 simulation is only to obtain a reasonable initial condition, a low polynomial order
 of 2 is used.

doc/content/pbfhr/steady/griffin.md

@@ -1,6 +1,6 @@
 # Griffin steady state input
 
-We will first cover the input for the master application, Griffin, which tackles the neutronics
+We will first cover the input for the main application, Griffin, which tackles the neutronics
 problem. While the Griffin manual is ultimately the most complete reference on this input, we will
 try to provide enough details here for a complete comprehension of this input.
 
@@ -162,7 +162,7 @@ types:
   useful for easily importing then plotting the simulation results using Python or Matlab.
 
 - checkpoint files. [Checkpoint](https://mooseframework.inl.gov/source/outputs/Checkpoint.html) files are used solely for restarting simulations. Unlike Exodus files, they also
-  contain all the subapp information, so only the master app checkpoint files are necessary. Checkpoint files are
+  contain all the subapp information, so only the main app checkpoint files are necessary. Checkpoint files are
   output at a regular interval, specified by the `num_files` field.
 
 

htgr/mhtgr/tests

@@ -4,5 +4,6 @@
     input = 'MHTGR.i'
     check_input = True
     executable_pattern = 'sam*|blue_crab*'
+    cli_args = '--app SamApp'
   []
 []

htgr/pbmr400/steady/gold/oecd_pbmr400_ss0_rsnk_eigen_value_ix_dep.csv

@@ -0,0 +1,3 @@
+time,Decay_heat_tot,FRR_avg,Fiss_power_tot,NI_avg,NXe_avg,T_fuel_avg,T_mod_avg,T_ref_avg,Tt_pow,Tt_pow_check,eigenvalue,flux0_avg,flux1_avg,iodine_yield_avg,power_density_max,power_scaling,scaled_fast_flux_max,scaled_thermal_flux_max,xenon_yield_avg
+0,25704000,1.5245216104979e+17,374296000,0,0,900,700,700,400000000,400000000,1,9.0972125609476e+17,9.0972125609476e+17,0,0,2.9898536896588e+18,0,0,0
+1,25704000,1.5244890404514e+17,374296000,0.33228066245312,0.069961311140756,900,700,700,400000000,400000000,0.97812617654251,9.4869507187592e+17,9.1709749412722e+17,0.063862452014911,6307002.4191342,3.0283398832533e+18,1.2239880893765e+18,1.6641083271698e+18,0.0043609085076789

htgr/pbmr400/steady/gold/oecd_pbmr400_ss1_phtn_flow_path.csv

@@ -0,0 +1,7 @@
+time,T_fluid_avg,T_fuel_avg,T_mod_avg,T_solid_avg,Tt_mfr_core_out,Tt_mfr_in,Tt_mfr_out,Tt_normalized_pow,Tt_pow,time_step_pp
+0,773.15,900,700,773.15,252.33485276416,-192.69977534233,123.11785397528,0,0,0
+0.01,773.15,900,700,773.15,86.611982323528,-173.4297978081,56.869583415037,0,0,0.01
+0.05,773.15,900,700,773.15,154.92155962714,-173.4297978081,99.771257151472,0,0,0.04
+0.21,773.15,900,700,773.15,187.21563454771,-173.4297978081,120.0497586682,0,0,0.16
+0.85,773.14999999554,900,700,773.1499999949,192.52245741576,-173.4297978081,123.38201449603,0,0,0.64
+3.41,773.1498033553,900,700,773.14978393211,192.76392310825,-173.4297978081,123.53362948339,0,0,2.56

htgr/pbmr400/steady/gold/oecd_pbmr400_ss2_mhtr_pebble_triso.csv

@@ -0,0 +1,4 @@
+time,fuel_average_temp,moderator_average_temp,pebble_core_average_temp,pebble_surface_temp
+0,0,0,0,0
+1e+15,0,0,0,0
+2e+15,0,0,0,0

htgr/pbmr400/steady/oecd_pbmr400_ss0_rsnk_eigen_value_ix_dep.i

@@ -1,6 +1,6 @@
 # ==============================================================================
 # PBMR-400 steady-state phase 1 exercise 3, NEA/NSC/DOC(2013)10.
-# MASTER0 Neutron kinetic model, T_fuel and T_mod feedback supplied by TH subapp.
+# MAIN0 Neutron kinetic model, T_fuel and T_mod feedback supplied by TH subapp.
 # FENIX input file
 # ------------------------------------------------------------------------------
 # Idaho Falls, INL, 02/22/2020
@@ -640,7 +640,7 @@ fis_fract            = ${fparse 1 - dh_fract} # Fission power fraction at t = 0.
     n_delay_groups = 6
     family = LAGRANGE
     order = FIRST
-    fission_source_as_material = true
+    fission_source_aux = true
     assemble_scattering_jacobian = true
     assemble_fission_jacobian = true
     diffusion_kernel_type = tensor
@@ -656,8 +656,8 @@ fis_fract            = ${fparse 1 - dh_fract} # Fission power fraction at t = 0.
 []
 
 [Executioner]
-  type = PicardEigen # Picard iteration to reach stable NK+TH solution.
-  solve_type = 'PJFNK'
+  type = Eigenvalue # Picard iteration to reach stable NK+TH solution.
+  solve_type = 'PJFNKMO'
   petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
   petsc_options_value = 'hypre boomeramg 50'
   line_search = none
@@ -677,10 +677,7 @@ fis_fract            = ${fparse 1 - dh_fract} # Fission power fraction at t = 0.
   []
 
   # Power iterations.
-  free_power_iterations = 2
-  extra_free_pi = 2
-  output_after_power_iterations = false
-  output_before_normalization = false
+  free_power_iterations = 4
 
   # Multiphysics coupling iterationa.
   fixed_point_abs_tol = 1e-7

htgr/pbmr400/steady/oecd_pbmr400_ss1_phtn_flow_path.i

@@ -1,12 +1,12 @@
 # ==============================================================================
 # PBMR-400 steady-state phase 1 exercise 3, NEA/NSC/DOC(2013)10.
-# SUBAPP1 MASTER1 thermal-hydraulics model, power supplied by NK MASTER0 app.
+# SUBAPP1 MAIN1 thermal-hydraulics model, power supplied by NK MAIN0 app.
 # FENIX input file
 # ------------------------------------------------------------------------------
 # Idaho Falls, Idaho National Laboratory, 02/03/2020
 # Author(s): Dr. Paolo Balestra, Dr. Sebastian Schunert
 # ==============================================================================
-# - ss1: Steady state simulation master app level 1
+# - ss1: Steady state simulation main app level 1
 # - phth: ProngHorn for thermal hydraulics
 # - lgcy: Legacy kernels
 # - supmix: Mixed superficial variables
@@ -904,7 +904,7 @@ riser_superficial_rho_v         = ${fparse reactor_total_mfr/riser_free_flow_are
   [barrel_to_rpv]
     type = GapHeatTransfer
     variable = T_solid
-    emissivity_master = ${global_emissivity}
+    emissivity_primary = ${global_emissivity}
     emissivity_secondary = ${global_emissivity}
     gap_geometry_type = CYLINDER
     primary = barrel_rpv_gap_outer

htgr/pbmr400/steady/oecd_pbmr400_ss2_mhtr_pebble_triso.i

@@ -1,7 +1,7 @@
 # ==============================================================================
 # PBMR-400 pebble/TRISO 1-D model, NEA/NSC/DOC(2013)10
 # SUBAPP2 Pebble/TRISO 1-D model, Pebble surface temp and power density supplied
-# by TH MASTER1 TH app.
+# by TH MAIN TH app.
 # FENIX input file
 # ------------------------------------------------------------------------------
 # Idaho Falls, INL, 01/20/2020
@@ -285,7 +285,7 @@ pebble_bed_porosity        = 0.39 # Pebble bed porosity (//)
   line_search = l2
 
   # Problem time parameters.
-  dt = 1e+15 # Let the master app control time steps.
+  dt = 1e+15 # Let the main app control time steps.
 
   # Linear/nonlinear iterations.
   nl_abs_tol = 1e-8
@@ -303,12 +303,12 @@ pebble_bed_porosity        = 0.39 # Pebble bed porosity (//)
     execute_on = 'LINEAR'
   []
 
-  # Feedbacks from the master.
+  # Feedbacks from the main app
   [pebble_surface_temp]
     type = Receiver
   []
 
-  # Feedbacks to the master.
+  # Feedbacks to the main app
   [moderator_average_temp]
     type = ElementAverageValue
     variable = T_pebble

htgr/pbmr400/steady/tests

@@ -1,44 +1,135 @@
 [Tests]
-  [multiphysics]
+  # Individual steady syntax checks
+  [neutronics_syntax_only]
     type = RunApp
     input = 'oecd_pbmr400_ss0_rsnk_eigen_value_ix_dep.i'
-    executable_pattern = 'blue_crab*|fenix*'
-    cli_args = 'Executioner/fixed_point_max_its=1'
+    check_input = True
+    executable_pattern = 'griffin*|blue_crab*|dire_wolf*|fenix*'
+    cli_args = "MultiApps/active='' Transfers/active=''"
     method = 'opt' # see Griffin #230
-    min_parallel = 4
   []
-  [neutronics]
+  [fluid_flow_syntax_only]
     type = RunApp
+    input = 'oecd_pbmr400_ss1_phtn_flow_path.i'
+    check_input = True
+    executable_pattern = 'pronghorn*|blue_crab*|fenix*'
+    cli_args = "MultiApps/active='' Transfers/active=''"
+  []
+  [fuel_performance_syntax_only]
+    type = RunApp
+    input = 'oecd_pbmr400_ss2_mhtr_pebble_triso.i'
+    check_input = True
+    executable_pattern = 'pronghorn*|blue_crab*|fenix*'
+    cli_args = 'Executioner/num_steps=1'
+  []
+
+  # Steady regression tests
+  # Run these before so they dont overwrite the good checkpoint file for transients
+  [neutronics_only]
+    type = CSVDiff
     input = 'oecd_pbmr400_ss0_rsnk_eigen_value_ix_dep.i'
+    csvdiff = 'oecd_pbmr400_ss0_rsnk_eigen_value_ix_dep.csv'
+    executable_pattern = 'griffin*|blue_crab*|dire_wolf*|fenix*'
+    cli_args = "MultiApps/active='' Transfers/active='' Executioner/nl_abs_tol=0.1"
+    method = 'opt' # see Griffin #230
+  []
+  [fluid_flow_only]
+    type = CSVDiff
+    input = 'oecd_pbmr400_ss1_phtn_flow_path.i'
+    csvdiff = 'oecd_pbmr400_ss1_phtn_flow_path.csv'
+    executable_pattern = 'pronghorn*|blue_crab*|fenix*'
+    cli_args = "MultiApps/active='' Transfers/active='' Executioner/num_steps=5"
+  []
+  [fuel_performance_only]
+    type = CSVDiff
+    input = 'oecd_pbmr400_ss2_mhtr_pebble_triso.i'
+    csvdiff = 'oecd_pbmr400_ss2_mhtr_pebble_triso.csv'
+    executable_pattern = 'pronghorn*|blue_crab*|fenix*'
+    cli_args = 'Executioner/num_steps=2 Outputs/csv=true'
+  []
+
+  # Individual transient syntax checks
+  [transient_neutronics_syntax_only]
+    type = RunApp
+    working_directory = '../transient'
+    input = 'oecd_pbmr400_tr0_pplofc_rsnk_keff_calc.i'
     check_input = True
     executable_pattern = 'griffin*|blue_crab*|dire_wolf*|fenix*'
     cli_args = "MultiApps/active='' Transfers/active=''"
+    prereq = 'neutronics_only'
     method = 'opt' # see Griffin #230
   []
-  [fluid_flow]
+  [transient_fluid_flow_syntax_only]
     type = RunApp
-    input = 'oecd_pbmr400_ss1_phtn_flow_path.i'
+    working_directory = '../transient'
+    input = 'oecd_pbmr400_tr1_pplofc_phtn_flow_path.i'
     check_input = True
     executable_pattern = 'pronghorn*|blue_crab*|fenix*'
     cli_args = "MultiApps/active='' Transfers/active=''"
+    prereq = 'fluid_flow_only'
   []
-  [fuel_performance]
+  [transient_fuel_performance_syntax_only]
     type = RunApp
-    input = 'oecd_pbmr400_ss2_mhtr_pebble_triso.i'
+    working_directory = '../transient'
+    input = 'oecd_pbmr400_tr2_pplofc_mhtr_pebble_triso.i'
     check_input = True
     executable_pattern = 'pronghorn*|blue_crab*|fenix*'
     cli_args = 'Executioner/num_steps=1'
   []
+
+  # Run simulation, no results checking
+  [steady_multiphysics]
+    type = RunApp
+    input = 'oecd_pbmr400_ss0_rsnk_eigen_value_ix_dep.i'
+    executable_pattern = 'blue_crab*|fenix*'
+    cli_args = 'Executioner/fixed_point_max_its=1'
+    method = 'opt' # see Griffin #230
+    min_parallel = 8
+    # require the others so the restart files dont get overwritten
+    prereq = 'transient_neutronics_only transient_fluid_flow_only'
+  []
+
   # This will fail until:
   # - griffin can load restart binary files from another folder
   # - the issue with cross sections (tensor diffusion coef) is fixed
   [transient_multiphysics]
     type = RunApp
+    working_directory = '../transient'
     input = 'oecd_pbmr400_tr0_pplofc_rsnk_keff_calc.i'
     executable_pattern = 'blue_crab*|fenix*'
+    cli_args = 'Executioner/fixed_point_max_its=2 Executioner/num_steps=1 MultiApps/th_sub/cli_args=Executioner/end_time=800'
+    method = 'opt' # see Griffin #230
+    # Checkpoint file must have been generated with same number of ranks
+    prereq = 'steady_multiphysics'
+    min_parallel = 8
+  []
+
+  # Transient regression tests
+  [transient_neutronics_only]
+    type = CSVDiff
     working_directory = '../transient'
-    cli_args = 'Executioner/num_steps=1'
-    prereq = 'multiphysics'
+    input = 'oecd_pbmr400_tr0_pplofc_rsnk_keff_calc.i'
+    csvdiff = 'oecd_pbmr400_tr0_pplofc_rsnk_keff_calc.csv'
+    executable_pattern = 'griffin*|blue_crab*|dire_wolf*|fenix*'
+    cli_args = "MultiApps/active='' Transfers/active='' Executioner/num_steps=2"
     method = 'opt' # see Griffin #230
+    prereq = 'neutronics_only'
+  []
+  [transient_fluid_flow_only]
+    type = CSVDiff
+    working_directory = '../transient'
+    input = 'oecd_pbmr400_tr1_pplofc_phtn_flow_path.i'
+    csvdiff = 'oecd_pbmr400_tr1_pplofc_phtn_flow_path.csv'
+    executable_pattern = 'pronghorn*|blue_crab*|fenix*'
+    cli_args = "MultiApps/active='' Transfers/active='' Executioner/num_steps=5"
+    prereq = 'fluid_flow_only'
+  []
+  [transient_fuel_performance_only]
+    type = CSVDiff
+    working_directory = '../transient'
+    input = 'oecd_pbmr400_tr2_pplofc_mhtr_pebble_triso.i'
+    csvdiff = 'oecd_pbmr400_tr2_lf40_mhtr_pebble_triso.csv'
+    executable_pattern = 'pronghorn*|blue_crab*|fenix*'
+    cli_args = 'Executioner/num_steps=2 Outputs/csv=true'
   []
 []

htgr/pbmr400/transient/gold/oecd_pbmr400_tr0_pplofc_rsnk_keff_calc.csv

@@ -0,0 +1,3 @@
+time,Decay_heat_tot,FRR_avg,Fiss_power_tot,NI_avg,NXe_avg,T_fuel_avg,T_fuel_max,T_fuel_max_kernel,T_mod_avg,Transient_decay_heat_tot,Tt_pow,decay_heat_scaling_factor,flux0_avg,flux1_avg,power_scaling,reactor_total_power_check,time_step_pp
+0,25704000,1.5244890404514e+17,374296000,0.33228066245312,0.069961311140756,900,900,0,700,25704000,400000000,1,9.4869507187592e+17,9.1709749412722e+17,3.2394800939706e+19,400000000,0
+180000,25704000,6409553311.883,15.735388296098,0.052952307182353,0.072892712857253,900,900,0,700,1658411.7984,16.815983388652,0.0645196,42311929996.041,37836922204.61,3.2394800939706e+19,1658427.5337883,180000

htgr/pbmr400/transient/gold/oecd_pbmr400_tr1_pplofc_phtn_flow_path.csv

@@ -0,0 +1,7 @@
+time,T_fluid_avg,T_fuel_avg,T_mod_avg,T_solid_avg,Tt_pow,courant_condition,he_mass_tt,he_temp_avg,he_vol_tt,min_courant_num,pressure_avg,switch,time_step_pp,timestep_pp,trip_valve
+0,773.1498033553,900,700,773.14978393211,0,0,836.50797263881,773.14984879563,149.30377617162,0,9123075.3591948,0,2.56,0,0
+0.01,773.1498027685,900,700,773.14978393061,0,15.711136829381,836.41363257775,773.14984830227,149.30377617162,0.00063649117874777,9122032.367246,598.23363415754,0.01,0.99930769230769,0
+0.03,773.14980201063,900,700,773.14978392579,0,31.432365530089,836.11986334573,773.14984757067,149.30377617162,0.00063628682291999,9118784.2577271,598.23363415754,0.02,0.99792307692308,0
+0.07,773.14980125397,900,700,773.14978391241,0,62.819249715482,835.36053328338,773.14984668849,149.30377617162,0.00063674749668559,9110388.341142,598.23363415754,0.04,0.99515384615385,0
+0.15,773.14980066824,900,700,773.14978387987,0,125.227342945,833.6547602585,773.1498458941,149.30377617162,0.00063883811728828,9091528.0226786,598.23363415754,0.08,0.98961538461538,0
+0.31,773.14980021172,900,700,773.14978380665,0,248.50089688814,830.12409596089,773.14984534562,149.30377617162,0.00064386085524683,9052493.5251907,598.23363415754,0.16,0.97853846153846,0

htgr/pbmr400/transient/gold/oecd_pbmr400_tr2_lf40_mhtr_pebble_triso.csv

@@ -0,0 +1,4 @@
+time,fuel_average_temp,moderator_average_temp,pebble_core_average_temp,pebble_core_center_temp,pebble_surface_temp
+0,0,0,0,0,0
+1e+15,0,0,0,0,0
+2e+15,0,0,0,0,0

htgr/pbmr400/transient/oecd_pbmr400_tr0_pplofc_rsnk_keff_calc.i

@@ -1,6 +1,6 @@
 # ==============================================================================
 # PBMR-400 steady-state phase 1 exercise 3, NEA/NSC/DOC(2013)10.
-# MASTER0 Neutron kinetic model, T_fuel and T_mod feedback supplied by TH subapp.
+# MAIN0 Neutron kinetic model, T_fuel and T_mod feedback supplied by TH subapp.
 # FENIX input file
 # ------------------------------------------------------------------------------
 # Idaho Falls, INL, 02/22/2020
@@ -141,11 +141,11 @@ fis_fract            = ${fparse 1 - dh_fract} # Fission power fraction at t = 0.
                      133 133 133 133 155 116 113 113 113 113 113 135 164 144 144 152 152 152 189 190 '
   []
   [cartesian_mesh_ids]
-    type = SubdomainElementIDs
+    type = SubdomainExtraElementIDGenerator
     input = cartesian_mesh
-    subdomains   = ${all_bloks}
-    equivalence_ids = ${all_bloks}
-    material_ids = ${material_ids}
+    subdomains = ${all_bloks}
+    extra_element_id_names = 'material_id equivalence_id'
+    extra_element_ids = '${material_ids}; ${all_bloks}'
   []
   uniform_refine = 0
 []
@@ -673,7 +673,7 @@ fis_fract            = ${fparse 1 - dh_fract} # Fission power fraction at t = 0.
     n_delay_groups = 6
     family = LAGRANGE
     order = FIRST
-    fission_source_as_material = true
+    fission_source_aux = true
     assemble_scattering_jacobian = true
     assemble_fission_jacobian = true
     diffusion_kernel_type = tensor
@@ -695,7 +695,7 @@ fis_fract            = ${fparse 1 - dh_fract} # Fission power fraction at t = 0.
 
   # end_time = 6000.0
   end_time = 180000.0
-  dt = 1e+15 # Let the master app control time steps.
+  dt = 1e+15 # Let the fluid control time steps.
 
   l_tol = 1e-4
   nl_rel_tol = 1e-7
@@ -724,10 +724,9 @@ fis_fract            = ${fparse 1 - dh_fract} # Fission power fraction at t = 0.
 [MultiApps]
   [th_sub]
     type = TransientMultiApp
-    app_type = FenixApp
     input_files = 'oecd_pbmr400_tr1_pplofc_phtn_flow_path.i'
     positions = '0.0 -2.8500 0.0' # Vertical offset between the two meshes.
-    # sub_cycling = true
+    sub_cycling = true
   []
 []