Add Pipe Drain Evaluator

src/executables/CMakeLists.txt

@@ -30,6 +30,7 @@ include_directories(${DBG_SOURCE_DIR})
 include_directories(${TRANSPORT_SOURCE_DIR})
 get_property(CHEM_INCLUDES_DIR GLOBAL PROPERTY CHEM_INCLUDES_DIR)
 include_directories(${CHEM_INCLUDES_DIR})
+include_directories(${SHALLOW_WATER_SOURCE_DIR})
 
 include_directories(${ATS_SOURCE_DIR}/src/constitutive_relations)
 include_directories(${ATS_SOURCE_DIR}/src/constitutive_relations/eos)
@@ -97,6 +98,7 @@ set(amanzi_link_libs
   mesh_logical
   chemistry_pk
   #mpc_tree
+  shallow_water
   transport
   )
 

src/executables/main.cc

@@ -34,6 +34,7 @@
 
 // registration files
 #include "ats_registration_files.hh"
+#include "pks_shallow_water_registration.hh"
 
 int
 main(int argc, char* argv[])

src/pks/flow/constitutive_relations/CMakeLists.txt

@@ -1,54 +1,185 @@
 # -*- mode: cmake -*-
+
+# # Need this define. Errors from MSTK include files 
+# # about MPI_COMM_WORLD. --lpritch
+# add_definitions("-DMSTK_HAVE_MPI")
+# add_definitions("-DDISABLE_PHYSICS")
+
+# if (WITH_MSTK_2_20rc1_OR_NEWER)
+#   add_definitions("-DMSTK_2_20rc1_OR_NEWER")
+# endif ()
+
+# if (WITH_MSTK_2_21rc1_OR_NEWER)
+#   add_definitions("-DMSTK_2_21rc1_OR_NEWER")
+# endif ()
+
+project(EXECUTABLE)
+
 #
 #  ATS
-#    Constitutive relations for flow
+#    Executable
 #
+include_directories(${GEOCHEM_SOURCE_DIR})
+include_directories(${MESH_FACTORY_SOURCE_DIR})
+include_directories(${MESH_LOGICAL_SOURCE_DIR})
+include_directories(${MESH_EXTRACTED_SOURCE_DIR})
+include_directories(${MESH_MSTK_SOURCE_DIR})
+include_directories(${CHEMPK_SOURCE_DIR})
+include_directories(${MPC_TREE_SOURCE_DIR})
+include_directories(${DBG_SOURCE_DIR})
+include_directories(${TRANSPORT_SOURCE_DIR})
+get_property(CHEM_INCLUDES_DIR GLOBAL PROPERTY CHEM_INCLUDES_DIR)
+include_directories(${CHEM_INCLUDES_DIR})
+include_directories(${SHALLOW_WATER_SOURCE_DIR})
 
+include_directories(${ATS_SOURCE_DIR}/src/constitutive_relations)
+include_directories(${ATS_SOURCE_DIR}/src/constitutive_relations/eos)
+include_directories(${ATS_SOURCE_DIR}/src/constitutive_relations/surface_subsurface_fluxes)
+include_directories(${ATS_SOURCE_DIR}/src/constitutive_relations/generic_evaluators)
+include_directories(${ATS_SOURCE_DIR}/src/constitutive_relations/column_integrators)
+include_directories(${ATS_SOURCE_DIR}/src/pks)
+include_directories(${ATS_SOURCE_DIR}/src/pks/mpc)
+include_directories(${ATS_SOURCE_DIR}/src/pks/energy)
+include_directories(${ATS_SOURCE_DIR}/src/pks/flow)
+include_directories(${ATS_SOURCE_DIR}/src/pks/deformation)
+include_directories(${ATS_SOURCE_DIR}/src/pks/transport)
+include_directories(${ATS_SOURCE_DIR}/src/operators/upwinding)
+include_directories(${ATS_SOURCE_DIR}/src/operators/advection)
+include_directories(${ATS_SOURCE_DIR}/src/operators/deformation)
 
-# collect all sources
-
-list(APPEND subdirs elevation overland_conductivity porosity sources water_content wrm)
+include_directories(${AMANZI_BINARY_DIR}) # required to pick up amanzi_version.hh
+include_directories(${ATS_BINARY_DIR})
 
-set(ats_flow_relations_src_files "")
-set(ats_flow_relations_inc_files "")
+include_evaluators_directories(LISTNAME REGISTER_AMANZI_STATE_EVALUATORS_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_RELATIONS_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_TRANSPORT_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_ENERGY_PKS_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_ENERGY_RELATIONS_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_FLOW_PKS_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_FLOW_RELATIONS_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_DEFORMATION_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_SURFACE_BALANCE_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_BGC_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_MPC_REG_INCLUDES)
+include_evaluators_directories(LISTNAME SED_TRANSPORT_REG_INCLUDES)
 
-foreach(lcv IN LISTS subdirs)
-  include_directories(${ATS_SOURCE_DIR}/src/pks/flow/constitutive_relations/${lcv})
-
-  file(GLOB subdir_sources "./${lcv}/*.cc")
-  set(ats_flow_relations_src_files ${ats_flow_relations_src_files} ${subdir_sources})
+set(ats_src_files
+  ats_mesh_factory.cc
+  coordinator.cc
+  ats_driver.cc
+  )
 
-  file(GLOB subdir_incs "./${lcv}/*.hh")
-  set(ats_flow_relations_inc_files ${ats_flow_relations_inc_files} ${subdir_incs})
+set(ats_inc_files
+  ats_mesh_factory.hh
+  coordinator.hh
+  ats_driver.hh
+  )
 
-  file(GLOB registrations "./${lcv}/*_reg.hh" )
-  foreach(reg_lcv IN LISTS registrations)
-    register_abs_evaluator_with_factory(HEADERFILE ${reg_lcv} LISTNAME ATS_FLOW_RELATIONS_REG)
-  endforeach(reg_lcv)
+set(amanzi_link_libs
+  operators
+  pks
+  geochemrxns
+  geochembase
+  geochemutil
+  geochemsolvers
+  state
+  whetstone
+  time_integration
+  solvers
+  dbg       
+  data_structures
+  mesh
+  mesh_functions
+  functions
+  geometry
+  mesh_factory
+  output
+  mesh_mstk
+  mesh_logical
+  chemistry_pk
+  #mpc_tree
+  shallow_water
+  transport
+  )
+
+set(ats_link_libs
+  ats_operators
+  ats_generic_evals
+  ats_column_integrator
+  ats_surf_subsurf
+  ats_eos
+  ats_pks
+  ats_transport
+  #ats_sed_transport  
+  ats_energy
+  ats_energy_relations
+  ats_flow
+  ats_flow_relations
+  ats_deform
+  ats_bgc
+  ats_surface_balance
+  ats_mpc
+  ats_mpc_relations
+  )
 
-endforeach(lcv)
 
-set(ats_flow_relations_link_libs
+# note, we can be inclusive here, because if they aren't enabled,
+# these won't be defined and will result in empty strings.
+set(tpl_link_libs
+  ${ALQUIMIA_LIBRARIES}
+  ${PFLOTRAN_LIBRARIES}
   ${Teuchos_LIBRARIES}
   ${Epetra_LIBRARIES}
-  error_handling
-  atk
-  mesh
-  data_structures
-  whetstone
-  solvers
-  state
+  ${Boost_LIBRARIES}
+  ${PETSC_LIBRARIES}
+  ${MSTK_LIBRARIES}
+  ${SILO_LIBRARIES}
+  ${HYPRE_LIBRARIES}
+  ${HDF5_LIBRARIES}
+  ${CLM_LIBRARIES}
   )
 
-# make the library
-add_amanzi_library(ats_flow_relations
-                   SOURCE ${ats_flow_relations_src_files}
-                   HEADERS ${ats_flow_relations_inc_files}
-		   LINK_LIBS ${ats_flow_relations_link_libs})
-
-generate_evaluators_registration_header(
-    HEADERFILE ats_flow_relations_registration.hh
-    LISTNAME   ATS_FLOW_RELATIONS_REG
-    INSTALL    True
-    )
-
+add_amanzi_library(ats_executable
+  SOURCE ${ats_src_files}
+  HEADERS ${ats_inc_files}
+  LINK_LIBS ${amanzi_link_libs} ${tpl_link_libs})
+if (APPLE AND BUILD_SHARED_LIBS)
+  set_target_properties(ats_executable PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
+endif()			  
+
+if (BUILD_TESTS) 
+
+  # Add UnitTest includes
+  include_directories(${UnitTest_INCLUDE_DIRS})
+  include_directories(${EXECUTABLE_SOURCE_DIR})
+
+  # Copy test subdirectory for out of source builds
+  if (NOT ("${EXECUTABLE_SOURCE_DIR}" STREQUAL "${EXECUTABLE_BINARY_DIR}"))
+    file(GLOB DataFiles "${EXECUTABLE_SOURCE_DIR}/test/*.xml"
+      "${EXECUTABLE_SOURCE_DIR}/test/*.exo"
+      "${EXECUTABLE_SOURCE_DIR}/test/*.h5"
+      "${EXECUTABLE_SOURCE_DIR}/test/*.bin")
+    file(COPY ${DataFiles} DESTINATION ${EXECUTABLE_BINARY_DIR}/test/)
+  endif()
+
+  # test for ats mesh factory
+  add_amanzi_test(executable_mesh_factory executable_mesh_factory
+           KIND int
+           SOURCE test/Main.cc test/executable_mesh_factory.cc
+           LINK_LIBS ats_executable ${ats_link_libs} ${UnitTest_LIBRARIES} ${NOX_LIBRARIES} ${HDF5_LIBRARIES})
+  add_amanzi_test(executable_mesh_factory_np2 executable_mesh_factory NPROCS 2 KIND uint)
+  add_amanzi_test(executable_mesh_factory_np4 executable_mesh_factory NPROCS 4 KIND uint)
+
+  # test for coupled water preconditioners
+  add_amanzi_test(executable_coupled_water executable_coupled_water
+    KIND int
+    SOURCE test/Main.cc test/executable_coupled_water.cc
+    LINK_LIBS ats_executable ${ats_link_libs} ${UnitTest_LIBRARIES} ${NOX_LIBRARIES} ${HDF5_LIBRARIES})
+
+endif()
+
+add_amanzi_executable(ats
+  SOURCE main.cc
+  LINK_LIBS ats_executable ${fates_link_libs} ${tpl_link_libs} ${ats_link_libs} ${amanzi_link_libs} 
+  OUTPUT_NAME ats
+  OUTPUT_DIRECTORY ${ATS_BINARY_DIR})