update SAM and tests

anshchaube · Jun 6, 2024 · 136d86d · 136d86d
1 parent 6496f7c
commit 136d86d
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Showing 9 changed files with 92 additions and 209 deletions.
diff --git a/Makefile b/Makefile
@@ -1,7 +1,6 @@
 # Optional environment variables:
 #
-# To control where various third-party dependencies are. You don't need to set
-# any of these unless you want to use non-submodule third-party dependencies.
+# To control where various third-party dependencies are.
 # NOTE: If you change any of these partway through a build, you will need to
 # clear out the build/ and install/ directories to be sure the proper build
 # flags are used.
@@ -53,6 +52,7 @@ OCCA_OPENCL_ENABLED=0
 # Whether to enable AMGX in Nek (only available for Nvidia GPU)
 AMGX_ENABLED=0
 
+# If user forgot to set OCCA_CUDA_ENABLED for AMGX, turn it on for them
 ifeq ($(AMGX_ENABLED),1)
   ifeq ($(OCCA_CUDA_ENABLED),0)
     $(info Turning on CUDA backend because AMGX was requested)
@@ -71,21 +71,10 @@ else
 	MOOSE_DIR        ?= $(shell dirname `pwd`)/moose
 endif
 
-NEKRS_DIR           ?= $(CONTRIB_DIR)/nekRS
-OPENMC_DIR          ?= $(CONTRIB_DIR)/openmc
-DAGMC_DIR           ?= $(CONTRIB_DIR)/DAGMC
-MOAB_DIR            ?= $(CONTRIB_DIR)/moab
 PETSC_DIR           ?= $(MOOSE_DIR)/petsc
 PETSC_ARCH          ?= arch-moose
 LIBMESH_DIR         ?= $(MOOSE_DIR)/libmesh/installed/
 CONTRIB_INSTALL_DIR ?= $(CARDINAL_DIR)/install
-GRIFFIN_DIR         ?= $(CONTRIB_DIR)/griffin
-BISON_DIR           ?= $(CONTRIB_DIR)/bison
-SAM_DIR             ?= $(CONTRIB_DIR)/SAM
-SOCKEYE_DIR         ?= $(CONTRIB_DIR)/sockeye
-SODIUM_DIR          ?= $(CONTRIB_DIR)/sodium
-POTASSIUM_DIR       ?= $(CONTRIB_DIR)/potassium
-IAPWS95_DIR         ?= $(CONTRIB_DIR)/iapws95
 
 # This is the Eigen3 location on CIVET. If you are using MOOSE's conda environment,
 # you don't need to set these variables, because conda sets them for you. The only
@@ -105,11 +94,6 @@ endif
 HDF5_INCLUDE_DIR    ?= $(HDF5_ROOT)/include
 HDF5_LIBDIR         ?= $(HDF5_ROOT)/lib
 
-# Check that NEKRS_HOME is set to the correct location
-ifeq ($(ENABLE_NEK), yes)
-  include config/check_nekrs.mk
-endif
-
 ALL_MODULES         := no
 
 # you may opt to enable additional modules by listing them here; any modules required
@@ -123,10 +107,11 @@ STOCHASTIC_TOOLS    := yes
 SOLID_MECHANICS     := yes
 THERMAL_HYDRAULICS  := yes
 
-# Perform various checks on the dependencies
+# Configure the optional dependencies (NekRS, OpenMC, submodules, etc.)
 include config/check_deps.mk
-include config/check_modules.mk
 
+# Report what MOOSE modules are being used
+include config/check_modules.mk
 
 # BUILD_TYPE will be passed to CMake via CMAKE_BUILD_TYPE
 ifeq ($(METHOD),dbg)
@@ -218,97 +203,11 @@ include $(FRAMEWORK_DIR)/moose.mk
 
 include $(MOOSE_DIR)/modules/modules.mk
 
-# Griffin submodule
-ifneq ($(GRIFFIN_CONTENT),)
- libmesh_CXXFLAGS    += -DENABLE_GRIFFIN_COUPLING
-
- APPLICATION_DIR    := $(GRIFFIN_DIR)/isoxml
- APPLICATION_NAME   := isoxml
- include            $(FRAMEWORK_DIR)/app.mk
- #ADDITIONAL_DEPEND_LIBS += $(CURDIR)/isoxml/lib/libisoxml-$(METHOD).la
-
- APPLICATION_DIR    := $(GRIFFIN_DIR)/xs_generation
- APPLICATION_NAME   := mcc3
- include            $(APPLICATION_DIR)/mcc3.dep
- include            $(FRAMEWORK_DIR)/app.mk
-
- APPLICATION_DIR    := $(GRIFFIN_DIR)/radiation_transport
- APPLICATION_NAME   := radiation_transport
- include            $(FRAMEWORK_DIR)/app.mk
-
- APPLICATION_DIR     := $(GRIFFIN_DIR)
- APPLICATION_NAME    := griffin
- include             $(FRAMEWORK_DIR)/app.mk
-endif
-
-# Bison submodule
-ifneq ($(BISON_CONTENT),)
-  libmesh_CXXFLAGS    += -DENABLE_BISON_COUPLING
-  APPLICATION_DIR     := $(BISON_DIR)
-  APPLICATION_NAME    := bison
-  include             $(FRAMEWORK_DIR)/app.mk
-endif
-
-# SAM submodule
-ifneq ($(SAM_CONTENT),)
-  libmesh_CXXFLAGS    += -DENABLE_SAM_COUPLING
-  APPLICATION_DIR     := $(SAM_DIR)
-  APPLICATION_NAME    := sam
-  SOLID_MECHANICS     := yes
-  include             $(FRAMEWORK_DIR)/app.mk
-endif
-
-# Sockeye submodule
-ifneq ($(SOCKEYE_CONTENT),)
-  libmesh_CXXFLAGS    += -DENABLE_SOCKEYE_COUPLING
-  APPLICATION_DIR     := $(SOCKEYE_DIR)
-  APPLICATION_NAME    := sockeye
-  include             $(FRAMEWORK_DIR)/app.mk
-endif
-
-# sodium submodule
-ifneq ($(SODIUM_CONTENT),)
-  libmesh_CXXFLAGS    += -DENABLE_SODIUM
-  APPLICATION_DIR     := $(SODIUM_DIR)
-  APPLICATION_NAME    := sodium
-  include             $(FRAMEWORK_DIR)/app.mk
-  include             $(SODIUM_DIR)/libSodiumProperties.mk
-endif
-
-# potassium submodule
-ifneq ($(POTASSIUM_CONTENT),)
-  libmesh_CXXFLAGS    += -DENABLE_POTASSIUM
-  APPLICATION_DIR     := $(POTASSIUM_DIR)
-  APPLICATION_NAME    := potassium
-  include             $(FRAMEWORK_DIR)/app.mk
-  include             $(POTASSIUM_DIR)/libPotassiumProperties.mk
-endif
-
-# iapws95 submodule
-ifneq ($(IAPWS95_CONTENT),)
-  libmesh_CXXFLAGS    += -DENABLE_IAPWS95
-  APPLICATION_DIR     := $(IAPWS95_DIR)
-  APPLICATION_NAME    := iapws95
-  include             $(FRAMEWORK_DIR)/app.mk
-  include             $(IAPWS95_DIR)/libSBTL.mk
-endif
-
-ifeq ($(ENABLE_NEK), yes)
-  ADDITIONAL_CPPFLAGS += $(NEKRS_INCLUDES)
-  libmesh_CXXFLAGS    += -DENABLE_NEK_COUPLING
-endif
-
-ifeq ($(ENABLE_OPENMC), yes)
-  ADDITIONAL_CPPFLAGS += $(HDF5_INCLUDES) $(OPENMC_INCLUDES)
-  libmesh_CXXFLAGS    += -DENABLE_OPENMC_COUPLING
-endif
-
-ifeq ($(ENABLE_DAGMC), yes)
-  libmesh_CXXFLAGS    += -DENABLE_DAGMC
+# ======================================================================================
+# Third-Party Dependencies
+# ======================================================================================
 
-  # this flag is used in OpenMC
-  libmesh_CXXFLAGS    += -DDAGMC
-endif
+include config/add_flags.mk
 
 # ======================================================================================
 # External apps
@@ -395,7 +294,7 @@ ifeq ($(ENABLE_OPENMC), yes)
   ADDITIONAL_LIBS += $(CC_LINKER_SLFLAG)$(OPENMC_LIBDIR)
 endif
 
-# Determin if we need libpng and where using pkg-config (if available)
+# Determine if we need libpng and where using pkg-config (if available)
 LIBPNG_FLAGS ?= $(shell pkg-config --libs libpng 2>/dev/null)
 ifneq (,$(findstring -lpng, $(LIBPNG_FLAGS)))
   ADDITIONAL_LIBS += $(LIBPNG_FLAGS)
@@ -427,7 +326,7 @@ ifeq ($(ENABLE_OPENMC), yes)
   CARDINAL_EXTERNAL_FLAGS += $(CC_LINKER_SLFLAG)$(OPENMC_LIBDIR) \
 	                           $(CC_LINKER_SLFLAG)$(HDF5_LIBDIR)
 endif
-#
+
 # EXTERNAL_FLAGS are for rules in app.mk
 $(app_LIB): EXTERNAL_FLAGS := $(CARDINAL_EXTERNAL_FLAGS)
 $(app_test_LIB): EXTERNAL_FLAGS := $(CARDINAL_EXTERNAL_FLAGS)

diff --git a/config/check_deps.mk b/config/check_deps.mk
@@ -3,7 +3,21 @@ define n
 
 endef
 
-# First, we can find which optional dependencies we have been pulled in
+# Set default values for all third party dependencies
+NEKRS_DIR           ?= $(CONTRIB_DIR)/nekRS
+OPENMC_DIR          ?= $(CONTRIB_DIR)/openmc
+DAGMC_DIR           ?= $(CONTRIB_DIR)/DAGMC
+MOAB_DIR            ?= $(CONTRIB_DIR)/moab
+GRIFFIN_DIR         ?= $(CONTRIB_DIR)/griffin
+BISON_DIR           ?= $(CONTRIB_DIR)/bison
+SAM_DIR             ?= $(CONTRIB_DIR)/SAM
+SOCKEYE_DIR         ?= $(CONTRIB_DIR)/sockeye
+SODIUM_DIR          ?= $(CONTRIB_DIR)/sodium
+POTASSIUM_DIR       ?= $(CONTRIB_DIR)/potassium
+IAPWS95_DIR         ?= $(CONTRIB_DIR)/iapws95
+
+# Then, we can find which optional dependencies we have been pulled in
+# by seeing if those directories are empty or not
 MOOSE_CONTENT     := $(shell ls $(MOOSE_DIR) 2> /dev/null)
 NEKRS_CONTENT     := $(shell ls $(NEKRS_DIR) 2> /dev/null)
 OPENMC_CONTENT    := $(shell ls $(OPENMC_DIR) 2> /dev/null)
@@ -17,11 +31,6 @@ SODIUM_CONTENT    := $(shell ls $(SODIUM_DIR) 2> /dev/null)
 POTASSIUM_CONTENT := $(shell ls $(POTASSIUM_DIR) 2> /dev/null)
 IAPWS95_CONTENT   := $(shell ls $(IAPWS95_DIR) 2> /dev/null)
 
-ifeq ($(ENABLE_OPENMC), yes)
-  # HDF5 is only needed to be linked if using OpenMC
-  $(info Cardinal is using HDF5 from      $(HDF5_ROOT))
-endif
-
 # convert ENABLE_NEK, ENABLE_OPENMC, and ENABLE_DAGMC to consistent truthy value
 ifeq ($(ENABLE_OPENMC),$(filter $(ENABLE_OPENMC), true yes on 1 TRUE YES ON))
   ENABLE_OPENMC := yes
@@ -33,16 +42,21 @@ ifeq ($(ENABLE_DAGMC),$(filter $(ENABLE_DAGMC), true yes on 1 TRUE YES ON))
   ENABLE_DAGMC := yes
 endif
 
+# Check that NEKRS_HOME is set to the correct location
+ifeq ($(ENABLE_NEK), yes)
+  include config/check_nekrs.mk
+endif
+
 ifeq ($(ENABLE_OPENMC), yes)
+  # HDF5 is only needed to be linked if using OpenMC
+  $(info Cardinal is using HDF5 from      $(HDF5_ROOT))
 else
   ifeq ($(ENABLE_DAGMC), yes)
     $(info Ignoring ENABLE_DAGMC because OpenMC is not enabled.)
     ENABLE_DAGMC := no
   endif
 endif
 
-
-
 ifeq ($(MOOSE_CONTENT),)
   $(error $n"MOOSE framework does not seem to be available. Make sure that either the submodule is checked out$nor that MOOSE_DIR points to a location with the MOOSE source.$n$nTo fetch the MOOSE submodule, use ./scripts/get-dependencies.sh")
 else
@@ -103,8 +117,6 @@ ifeq ($(ENABLE_DAGMC), yes)
   endif
 endif
 
-
-
 ifneq ($(SAM_CONTENT),)
   $(info Cardinal is using SAM from       $(SAM_DIR))
 endif
@@ -124,6 +136,18 @@ ifneq ($(BISON_CONTENT),)
   SOLID_MECHANICS    := yes
   THERMAL_HYDRAULICS := yes
   XFEM               := yes
+
+  # We can check that if it looks like we're going to build Bison, that
+  # all of its dependencies are there
+  ifeq ($(IAPWS95_CONTENT),)
+    $(error $n"IAPWS95 dependency for Bison does not seem to be available. Make sure that either the submodule is checked out$nor that IAPWS95_DIR points to a location with the IAPWS95 source.$n$nTo fetch the IAPWS95 submodule, use 'git submodule update --init contrib/iapws95'")
+  else
+    ifeq ($(SOCKEYE_CONTENT),)
+      # don't print location info for IAPWS twice, if we are building with both
+      # Sockeye and Bison (since both require IAPWS)
+      $(info Cardinal is using water from     $(IAPWS95_DIR))
+    endif
+  endif
 endif
 
 ifneq ($(GRIFFIN_CONTENT),)
@@ -155,13 +179,9 @@ ifneq ($(SOCKEYE_CONTENT),)
   SOLID_PROPERTIES   := yes
   STOCHASTIC_TOOLS   := yes
   THERMAL_HYDRAULICS := yes
-endif
 
-
-
-# We can check that if it looks like we're going to build Sockeye, that
-# all of its dependencies are there
-ifneq ($(SOCKEYE_CONTENT),)
+  # We can check that if it looks like we're going to build Sockeye, that
+  # all of its dependencies are there
   ifeq ($(SODIUM_CONTENT),)
     $(error $n"Sodium dependency for Sockeye does not seem to be available. Make sure that either the submodule is checked out$nor that SODIUM_DIR points to a location with the sodium source.$n$nTo fetch the sodium submodule, use 'git submodule update --init contrib/sodium'")
   else
@@ -179,20 +199,6 @@ ifneq ($(SOCKEYE_CONTENT),)
   endif
 endif
 
-# We can check that if it looks like we're going to build Bison, that
-# all of its dependencies are there
-ifneq ($(BISON_CONTENT),)
-  ifeq ($(IAPWS95_CONTENT),)
-    $(error $n"IAPWS95 dependency for Bison does not seem to be available. Make sure that either the submodule is checked out$nor that IAPWS95_DIR points to a location with the IAPWS95 source.$n$nTo fetch the IAPWS95 submodule, use 'git submodule update --init contrib/iapws95'")
-  else
-    ifeq ($(SOCKEYE_CONTENT),)
-      # don't print location info for IAPWS twice, if we are building with both
-      # Sockeye and Bison (since both require IAPWS)
-      $(info Cardinal is using water from     $(IAPWS95_DIR))
-    endif
-  endif
-endif
-
 # Cannot currently build with both SAM and Sockeye due to a conflict in THM.
 # Someone might just build with THM (and not Sockeye), so we check both to be explicit.
 ifneq ($(SOCKEYE_CONTENT),)

diff --git a/contrib/SAM b/contrib/SAM
diff --git a/test/tests/sam_coupling/sam_master/cardinal_sub.i b/test/tests/sam_coupling/sam_master/cardinal_sub.i
@@ -1,46 +1,33 @@
 [Mesh]
-  type = GeneratedMesh
-  dim = 2
-  nx = 3
-  ny = 3
+  [sphere]
+    type = FileMeshGenerator
+    file = ../../neutronics/meshes/sphere.e
+  []
 []
 
-[Variables]
-  [./u]
-  [../]
+[Problem]
+  type = FEProblem
+  solve = false
 []
 
-[Kernels]
-  [./diff]
-    type = Diffusion
-    variable = u
-  [../]
+[AuxVariables]
+  [g]
+    family = MONOMIAL
+    order = CONSTANT
+  []
 []
 
-[BCs]
-  [./left]
-    type = DirichletBC
-    variable = u
-    boundary = 'left'
-    value = 0
-  [../]
-  [./right]
-    type = DirichletBC
-    variable = u
-    boundary = 'right'
-    value = 1
-  [../]
+[AuxKernels]
+  [grid]
+    type = CartesianGrid
+    variable = g
+    nx = 4
+    ny = 4
+    nz = 4
+  []
 []
 
 [Executioner]
   type = Transient
-  num_steps = 1
-  petsc_options_iname = '-pc_type -pc_hypre_type'
-  petsc_options_value = 'hypre boomeramg'
-  nl_abs_tol = 1e-10
+  num_steps = 2
 []
-
-[Outputs]
-  exodus = true
-[]
-
diff --git a/test/tests/sam_coupling/sam_master/sam_master.i b/test/tests/sam_coupling/sam_master/sam_master.i
@@ -42,7 +42,7 @@
   [../]
 
   [./outlet]
-    type = PressureOutlet
+    type = PBTDV
     input = 'pipe1(out) '              # Name of the connected components and the end type
     eos = eos                          # The equation-of-state
     p_bc = '1.0e5'                     # Pressure boundary condition
@@ -99,8 +99,8 @@
   l_max_its = 100                     # Number of linear iterations for each Krylov solve
 
   start_time = 0.0                    # Physical time at the beginning of the simulation
-  num_steps = 20                      # Max. simulation time steps
-  end_time = 10.                      # Max. physical time at the end of the simulation
+  num_steps = 20                     # Max. simulation time steps
+  end_time = 10.                     # Max. physical time at the end of the simulation
 
   [./Quadrature]
     type = TRAP                       # Using trapezoid integration rule