1. Satish Karra
  2. karra-pflotran-dev

Commits

Glenn Hammond  committed 410f27f

Updates to hydrogeophysics coupling.

  • Participants
  • Parent commits 6eef0ef
  • Branches default

Comments (0)

Files changed (4)

File src/pflotran/hydrogeophysics_factory.F90

View file
     call printErrMsg(option)
   endif
 
+#ifndef E4D
+  option%io_buffer = 'Must compile with E4D defined during preprocessing ' // &
+    'step in order to use HYDROGEOPHYSICS.'
+  call printErrMsg(option)
+#endif
+
   simulation => HydrogeophysicsCreate(option)
   
   num_subsurface_processes = 1

File src/pflotran/hydrogeophysics_wrapper.F90

View file
                    pflotran_solution_vec_mpi, pflotran_solution_vec_seq, &
                    pflotran_scatter
   use e4d_setup, only : setup_e4d
+  use e4d_run, only: run_e4D
 #endif
   
   implicit none
   VecScatter :: pflotran_scatter_
   PetscMPIInt :: pf_e4d_master_comm
   
-  call printMsg(option,'HydrogeophysicsWrapperInit()')
+!  call printMsg(option,'HydrogeophysicsWrapperInit()')
   
   ! from e4d_vars.F90
 #ifdef E4D
   pflotran_scatter = pflotran_scatter_
 
   call setup_e4d
+  call run_e4d
 #endif
   
 end subroutine HydrogeophysicsWrapperInit
 subroutine HydrogeophysicsWrapperStart(option)
   
   use Option_module
-#ifdef E4D
-  use e4d_run, only: run_e4D
-#endif
 
   implicit none
 
   type(option_type) :: option
   
-  call printMsg(option,'HydrogeophysicsWrapperStart()')
+!  call printMsg(option,'HydrogeophysicsWrapperStart()')
 
-#ifdef E4D
-  call run_e4d
-#endif
-  
 end subroutine HydrogeophysicsWrapperStart
 
 ! ************************************************************************** !
 ! date: 07/02/13
 !
 ! ************************************************************************** !
-subroutine HydrogeophysicsWrapperStep(sigma_mpi,sigma_seq,scatter,comm,option)
-  
+subroutine HydrogeophysicsWrapperStep(solution_mpi,solution_seq,scatter, &
+                                      comm,option)
   use Option_module
 
   implicit none
 #include "finclude/petscvec.h"
 #include "finclude/petscvec.h90"
 
-  Vec :: sigma_mpi
-  Vec :: sigma_seq
+  Vec :: solution_mpi
+  Vec :: solution_seq
   VecScatter :: scatter
   PetscMPIInt :: comm
   type(option_type) :: option
   
-  PetscReal, pointer :: vec_ptr(:)
   PetscErrorCode :: ierr
   
-  call printMsg(option,'HydrogeophysicsWrapperStep()')
+!  call printMsg(option,'HydrogeophysicsWrapperStep()')
   
-!  call VecGetArrayF90(sigma,vec_ptr,ierr)
-!  write(option%io_buffer,'(es13.6)') vec_ptr(365)
-!  call printMsg(option)
-!  call VecRestoreArrayF90(sigma,vec_ptr,ierr)
-  
+  ! Bcasting a 1 to E4D tells it to run a forward simulation 
   call MPI_Bcast(ONE_INTEGER_MPI,ONE_INTEGER_MPI,MPI_INTEGER, &
                  ZERO_INTEGER_MPI,comm,ierr)
-  call VecScatterBegin(scatter,sigma_mpi,sigma_seq, &
+  call VecScatterBegin(scatter,solution_mpi,solution_seq, &
                        INSERT_VALUES,SCATTER_FORWARD,ierr)
-  call VecScatterEnd(scatter,sigma_mpi,sigma_seq, &
+  call VecScatterEnd(scatter,solution_mpi,solution_seq, &
                      INSERT_VALUES,SCATTER_FORWARD,ierr)
   
 end subroutine HydrogeophysicsWrapperStep
   PetscMPIInt :: comm
   PetscErrorCode :: ierr
   
-  call printMsg(option,'HydrogeophysicsWrapperStop()')
+!  call printMsg(option,'HydrogeophysicsWrapperStop()')
   
+  ! Bcasting a 0 to E4D tells it to stop
   call MPI_Bcast(ZERO_INTEGER_MPI,ONE_INTEGER_MPI,MPI_INTEGER, &
                  ZERO_INTEGER_MPI,comm,ierr)
 
   
   type(option_type) :: option
   
-  call printMsg(option,'HydrogeophysicsWrapperDestroy()')
+!  call printMsg(option,'HydrogeophysicsWrapperDestroy()')
 
 end subroutine HydrogeophysicsWrapperDestroy
 

File src/pflotran/makefile_hg

View file
+# $Id: makefile,v 1.3 2004/07/31 01:16:44 lichtner Exp $
+
+pflotran_src = ./
+common_src   = ./
+pflotran_test_dir = ../../regression_tests_refactor
+
+
+MYFLAGS = -I.
+MYFLAGS += -DPROCESS_MODEL
+MYFLAGS += -DSURFACE_FLOW
+MYFLAGS += -DE4D
+
+# if compiling pflotran_rxn or libpflotranchem.a, need to toggle 
+# PFLOTRAN_RXN_FLAG 
+ifneq (,$(filter libpflotranchem.a pflotran_rxn,$(MAKECMDGOALS)))
+  PFLOTRAN_RXN_FLAG := 1
+endif
+
+ifdef uo2
+  MYFLAGS += -DCOMPUTE_INTERNAL_MASS_FLUX
+endif
+
+ifdef glenn
+  MYFLAGS += -DXINGYUAN_BC
+endif
+
+ifdef solid_solution
+  MYFLAGS += -DSOLID_SOLUTION
+endif
+
+ifdef radioactive_decay
+  MYFLAGS += -DRADIOACTIVE_DECAY
+endif
+
+ifdef mualem_spline
+  MYFLAGS += -DMUALEM_SPLINE
+endif
+
+ifdef petsc_api_3_3
+  MYFLAGS += -DHAVE_PETSC_API_3_3
+endif
+
+ifdef have_petscpcmg_h
+	MYFLAGS += -DHAVE_PETSCPCMG_H
+endif
+
+ifdef dbl
+  MYFLAGS += -DDOUBLE_LAYER
+endif
+
+ifdef pcl
+  MYFLAGS += -DPCL -DMUALEM_SPLINE
+endif
+
+ifdef condnr
+  MYFLAGS += -DCONDNR
+endif
+
+ifdef perm
+  MYFLAGS += -DPERM
+endif
+
+ifdef tab
+  MYFLAGS += -DTABLE
+endif
+
+ifdef temp
+  MYFLAGS += -DTEMP_DEPENDENT_LOGK
+endif
+
+ifdef ice
+  MYFLAGS += -DICE
+endif
+
+ifdef remove_sat
+  MYFLAGS += -DREMOVE_SATURATION
+endif
+
+ifdef compressibility
+  MYFLAGS += -DUSE_COMPRESSIBILITY
+endif
+
+ifdef no_vapor_diffusion
+  MYFLAGS += -DNO_VAPOR_DIFFUSION
+endif
+
+ifdef scco2
+  MYFLAGS += -DCHUAN_CO2
+endif
+
+ifdef debug_gen
+  MYFLAGS += -DDEBUG_GENERAL
+endif 
+
+ifdef coll
+  MYFLAGS += -DCOLL
+endif
+
+ifdef dont_use_wateos
+  MYFLAGS += -DDONT_USE_WATEOS
+endif
+
+ifdef have_hdf5
+  MYFLAGS += -I$(HDF5_INCLUDE) -I$(HDF5_LIB) -DPETSC_HAVE_HDF5
+endif
+
+ifdef gpu
+  MYFLAGS += -DCHUNK
+endif
+
+ifdef mfd
+  MYFLAGS += -DDASVYAT
+endif
+
+ifdef dasvyat_debug
+  MYFLAGS += -DDASVYAT_DEBUG
+endif
+
+ifdef dasvyat_test_cut
+  MYFLAGS += -DDASVYAT_TEST_CUT
+endif
+
+ifdef ugrid_debug
+  MYFLAGS += -DUGRID_DEBUG
+endif
+
+ifdef surface_flow
+  MYFLAGS += -DSURFACE_FLOW -w -g
+endif
+
+ifdef amanzi_bgd
+  MYFLAGS += -DAMANZI_BGD
+endif
+
+ifdef store_flowrates
+  MYFLAGS += -DSTORE_FLOWRATES
+endif
+
+ifdef mfd_ugrid
+  MYFLAGS += -DMFD_UGRID
+endif
+
+CFLAGS   = 
+FFLAGS   =
+CPPFLAGS = ${MYFLAGS}
+FPPFLAGS = ${MYFLAGS}
+
+CLEANFILES       = pflotran pflotran_rxn libpflotranchem.a make.log
+
+include ${PETSC_DIR}/conf/variables
+include ${PETSC_DIR}/conf/rules
+
+ifdef have_hdf5
+LIBS +=  -L${HDF5_LIB} -lhdf5_fortran -lhdf5 -lz 
+endif
+
+# Set this accordingly on your platform
+# SCORPIO_DIR=${HOME}/soft/scorpio
+ifdef scorpio
+  LIBS += -L${SCORPIO_DIR}/lib -lscorpio
+  MYFLAGS += -DSCORPIO
+  MYFLAGS += -DSCORPIO_WRITE 
+  MYFLAGS += -I${SCORPIO_DIR}/include
+endif
+
+ifdef tau
+FC = /ccs/proj/geo002/tau/tau-2.19.1/craycnl/bin/tau_f90.sh -optCompInst -tau_makefile=$(TAU_MAKEFILE)
+FLINKER = /ccs/proj/geo002/tau/tau-2.19.1/craycnl/bin/tau_f90.sh -optCompInst -tau_makefile=$(TAU_MAKEFILE)
+endif
+
+# Begin Source Block
+
+util_obj  = \
+	${common_src}input.o \
+	${common_src}logging.o \
+	${common_src}matrix_block_aux.o \
+	${common_src}option.o \
+	${common_src}output_aux.o \
+	${common_src}string.o \
+	${common_src}units.o \
+	${common_src}utility.o \
+	${common_src}variables.o
+
+eos_obj = \
+	${common_src}co2eos.o \
+	${common_src}co2_sw.o \
+	${common_src}co2_sw_rtsafe.o \
+	${common_src}co2_span_wagner.o \
+	${common_src}co2_span_wagner_spline.o \
+	${common_src}gas_eos_mod.o \
+	${common_src}water_eos.o 
+
+mode_aux_obj = \
+	${common_src}auxiliary.o \
+	${common_src}flash2_aux.o \
+	${common_src}general_aux.o \
+	${common_src}immis_aux.o \
+	${common_src}miscible_aux.o \
+	${common_src}mphase_aux.o \
+        ${common_src}process_model_base.o \
+        ${common_src}process_model_richards.o \
+        ${common_src}process_model_rt.o \
+        ${common_src}process_model_surface_flow.o \
+        ${common_src}process_model_top.o \
+        ${common_src}process_model_th.o \
+        ${common_src}process_model_thc.o \
+	${common_src}richards_aux.o \
+	${common_src}th_aux.o \
+	${common_src}thc_aux.o \
+	${common_src}thmc_aux.o
+
+mode_obj = \
+	${common_src}flash2.o \
+	${common_src}general.o \
+	${common_src}global.o \
+	${common_src}immis.o \
+	${common_src}miscible.o \
+	${common_src}mphase.o \
+	${common_src}reactive_transport.o \
+	${common_src}richards.o \
+	${common_src}richards_common.o \
+	${common_src}richards_lsm.o \
+	${common_src}richards_mfd.o \
+	${common_src}th.o \
+	${common_src}thc.o \
+	${common_src}thmc.o 
+
+shared_mode_aux_obj = \
+	${common_src}global_aux.o \
+	${common_src}reactive_transport_aux.o 
+
+chem_obj = \
+	${common_src}constraint.o \
+	${common_src}database.o \
+	${common_src}database_aux.o \
+	${common_src}database_hpt.o \
+	${common_src}immobile.o \
+	${common_src}immobile_aux.o \
+	${common_src}microbial.o \
+	${common_src}microbial_aux.o \
+	${common_src}mineral.o \
+	${common_src}mineral_aux.o \
+	${common_src}reaction.o \
+	${common_src}reaction_aux.o \
+	${common_src}reaction_sandbox.o \
+	${common_src}reaction_sandbox_base.o \
+	${common_src}reaction_sandbox_clm_cn.o \
+	${common_src}reaction_sandbox_example.o \
+	${common_src}solid_solution.o \
+	${common_src}solid_solution_aux.o \
+	${common_src}surface_complexation.o \
+	${common_src}surface_complexation_aux.o 
+
+grid_obj = \
+	${common_src}connection.o \
+	${common_src}communicator_base.o \
+	${common_src}discretization.o \
+	${common_src}dm_kludge.o \
+	${common_src}general_grid.o \
+	${common_src}grid.o \
+	${common_src}mfd.o \
+	${common_src}mfd_aux.o \
+	${common_src}unstructured_cell.o \
+	${common_src}unstructured_communicator.o \
+	${common_src}unstructured_explicit.o \
+	${common_src}unstructured_grid_aux.o \
+	${common_src}unstructured_grid.o \
+	${common_src}structured_communicator.o \
+	${common_src}structured_grid.o 
+
+relations_obj = \
+	${common_src}saturation.o \
+	${common_src}saturation_function.o \
+	${common_src}mphase_pckr_mod.o
+
+properties_obj = \
+	${common_src}fluid.o \
+	${common_src}material_aux.o \
+	${common_src}material.o 
+
+dataset_obj = \
+	${common_src}dataset_base.o \
+	${common_src}dataset_common_hdf5.o \
+	${common_src}dataset_global.o \
+	${common_src}dataset_map.o \
+	${common_src}dataset.o \
+	${common_src}dataset_xyz.o \
+	${common_src}time_series.o \
+	${common_src}time_storage.o 
+
+io_obj = \
+	${common_src}hdf5.o \
+	${common_src}hdf5_aux.o \
+	${common_src}output.o \
+	${common_src}output_common.o \
+	${common_src}output_hdf5.o \
+	${common_src}output_observation.o \
+	${common_src}output_surface.o \
+	${common_src}output_tecplot.o \
+	${common_src}output_vtk.o
+
+misc_obj = \
+	${common_src}block_solve.o \
+	${common_src}block_tridiag.o \
+	${common_src}checkpoint.o \
+	${common_src}condition.o \
+	${common_src}condition_control.o \
+	${common_src}convergence.o \
+	${common_src}coupler.o \
+	${common_src}debug.o \
+	${common_src}field.o \
+	${common_src}geometry.o \
+	${common_src}hydrogeophysics_factory.o \
+	${common_src}hydrogeophysics_simulation.o \
+	${common_src}hydrogeophysics_wrapper.o \
+	${common_src}hydrostatic.o \
+	${common_src}mat_inv.o \
+	${common_src}e4d_vars.o \
+	${common_src}e4d_setup.o \
+	${common_src}e4d_run.o \
+	${common_src}init.o \
+	${common_src}level.o \
+	${common_src}mass_transfer.o \
+	${common_src}matrix_buffer.o \
+	${common_src}observation.o \
+	${common_src}patch.o \
+	${common_src}pflotran_factory.o \
+	${common_src}pmc_base.o \
+	${common_src}pmc_hydrogeophysics.o \
+	${common_src}pmc_subsurface.o \
+	${common_src}realization.o \
+	${common_src}realization_base.o \
+	${common_src}region.o \
+	${common_src}regression.o \
+	${common_src}secondary_continuum_aux.o\
+	${common_src}secondary_continuum.o \
+	${common_src}simulation.o \
+	${common_src}simulation_base.o \
+	${common_src}subsurface_factory.o \
+	${common_src}subsurface_simulation.o \
+	${common_src}solver.o \
+	${common_src}spline.o \
+	${common_src}strata.o \
+	${common_src}timestepper.o \
+	${common_src}timestepper_base.o \
+	${common_src}transport.o \
+	${common_src}uniform_velocity.o \
+	${common_src}waypoint.o 
+#	${common_src}reaction_chunk.o\
+
+surface_obj = \
+	${common_src}pmc_surface.o \
+	${common_src}timestepper_surface.o \
+	${common_src}surface_auxiliary.o \
+	${common_src}surface_checkpoint.o \
+	${common_src}surface_factory.o \
+	${common_src}surfsubsurface_factory.o \
+	${common_src}surface_field.o \
+	${common_src}surface_flow.o \
+	${common_src}surface_flow_aux.o \
+	${common_src}surface_init.o \
+	${common_src}surface_global_aux.o \
+	${common_src}surface_global.o \
+	${common_src}surface_material.o \
+	${common_src}surface_realization.o \
+	${common_src}surface_simulation.o \
+	${common_src}surfsubsurface_simulation.o \
+	${common_src}surface_th_aux.o \
+	${common_src}surface_th.o
+
+# End Source Block
+
+pflotran_obj = $(util_obj) $(eos_obj) $(mode_aux_obj) $(mode_obj) \
+	$(shared_mode_aux_obj) $(chem_obj) $(grid_obj) \
+	$(relations_obj) $(properties_obj) $(dataset_obj) \
+	$(io_obj) $(misc_obj) $(surface_obj) ${pflotran_src}pflotran_new.o
+
+pflotran_rxn_obj = ${pflotran_src}pflotran_rxn.o
+
+pflotran : $(pflotran_obj)
+	${FLINKER} -o pflotran $(pflotran_obj) ${PETSC_LIB} ${LIBS} 
+
+libpflotranchem.a : $(util_obj) $(shared_mode_aux_obj) $(chem_obj)
+	$(AR) $(ARFLAGS) $@ $(util_obj) $(shared_mode_aux_obj) $(chem_obj)
+
+pflotran_rxn : libpflotranchem.a $(pflotran_rxn_obj)
+	${FLINKER} -o $@ $(pflotran_rxn_obj) -L. -lpflotranchem ${PETSC_LIB} ${LIBS} 
+
+ascii_to_hdf5: input.o hdf5_dataset.o ascii_to_hdf5.o 
+	${FLINKER} -o ascii_to_hdf5 ascii_to_hdf5.o hdf5_dataset.o input.o \
+	$(LIBS)
+
+# do these files exist anymore?
+#test: functions.o test.o
+#	${FLINKER} -o test test.o functions.o $(LIBS) $(PETSC_LIB)
+
+# Should add this to default PETSc targets as well?
+%.mod : %.F90
+	${FC} -c ${FC_FLAGS} ${FFLAGS} ${FCPPFLAGS} $<
+
+# Dependencies stemming from "use" statements.
+# These ensure that the module files are built in the correct order.
+auxiliary.o : flash2_aux.o general_aux.o global_aux.o immis_aux.o \
+              material_aux.o miscible_aux.o mphase_aux.o \
+              reactive_transport_aux.o richards_aux.o \
+              secondary_continuum_aux.o th_aux.o thc_aux.o thmc_aux.o
+block_solve.o :
+block_tridiag.o :
+checkpoint.o : discretization.o field.o flash2.o grid.o immis.o logging.o \
+               miscible.o mphase.o option.o output_aux.o reaction_aux.o \
+               reactive_transport.o realization.o realization_base.o \
+               variables.o
+co2_span_wagner.o : co2_sw_rtsafe.o option.o
+co2_span_wagner_spline.o : spline.o
+co2_sw.o : co2_span_wagner.o
+co2_sw_rtsafe.o :
+co2eos.o :
+communicator_base.o : dm_kludge.o option.o
+condition.o : constraint.o dataset_base.o dataset_common_hdf5.o dataset_map.o \
+              dataset_xyz.o general_aux.o global_aux.o hdf5_aux.o input.o \
+              logging.o option.o reaction_aux.o string.o time_series.o \
+              time_storage.o units.o utility.o
+condition_control.o : condition.o connection.o constraint.o coupler.o \
+                      dataset_base.o dataset_common_hdf5.o discretization.o \
+                      field.o general_aux.o global_aux.o grid.o hdf5.o level.o \
+                      mfd.o option.o patch.o reaction.o reaction_aux.o \
+                      reactive_transport_aux.o realization.o region.o \
+                      surface_field.o surface_global_aux.o \
+                      surface_realization.o surface_th_aux.o water_eos.o
+connection.o :
+ifdef PFLOTRAN_RXN_FLAG
+constraint.o : global_aux.o immobile_aux.o input.o mineral_aux.o option.o \
+               reaction_aux.o reactive_transport_aux.o string.o \
+               surface_complexation_aux.o units.o
+else
+constraint.o : global_aux.o immobile_aux.o input.o logging.o mineral_aux.o \
+               option.o reaction_aux.o reactive_transport_aux.o string.o \
+               surface_complexation_aux.o units.o
+endif
+convergence.o : grid.o option.o solver.o
+coupler.o : condition.o connection.o grid.o input.o mfd_aux.o option.o \
+            region.o string.o structured_grid.o unstructured_explicit.o \
+            unstructured_grid_aux.o
+database.o : database_aux.o immobile.o immobile_aux.o input.o microbial.o \
+             microbial_aux.o mineral.o mineral_aux.o option.o reaction.o \
+             reaction_aux.o reaction_sandbox.o solid_solution.o string.o \
+             surface_complexation_aux.o utility.o
+database_aux.o : input.o option.o string.o
+database_hpt.o : database.o database_aux.o input.o mineral_aux.o option.o \
+                 reaction.o reaction_aux.o string.o surface_complexation_aux.o \
+                 utility.o
+dataset.o : dataset_base.o dataset_common_hdf5.o dataset_global.o \
+            dataset_map.o dataset_xyz.o dm_kludge.o input.o option.o string.o
+dataset_base.o : option.o string.o time_storage.o utility.o
+dataset_common_hdf5.o : dataset_base.o hdf5_aux.o input.o logging.o option.o \
+                        string.o time_storage.o units.o utility.o
+dataset_global.o : dataset_base.o dataset_common_hdf5.o dm_kludge.o logging.o \
+                   option.o time_storage.o utility.o
+dataset_map.o : dataset_base.o dataset_common_hdf5.o input.o logging.o \
+                option.o string.o time_storage.o units.o utility.o
+dataset_xyz.o : dataset_base.o dataset_common_hdf5.o logging.o option.o \
+                string.o time_storage.o units.o utility.o
+debug.o : input.o option.o
+discretization.o : dm_kludge.o grid.o input.o mfd.o mfd_aux.o option.o \
+                   string.o structured_grid.o unstructured_explicit.o \
+                   unstructured_grid.o unstructured_grid_aux.o
+dm_kludge.o : unstructured_grid_aux.o
+e4d_run.o : e4d_vars.o
+e4d_setup.o : e4d_vars.o
+e4d_vars.o :
+field.o :
+flash2.o : co2_span_wagner.o co2_span_wagner_spline.o co2_sw.o co2eos.o \
+           connection.o coupler.o debug.o discretization.o field.o \
+           flash2_aux.o global_aux.o grid.o level.o logging.o material.o \
+           option.o output_aux.o patch.o realization.o variables.o water_eos.o
+flash2_aux.o : co2_span_wagner.o co2_span_wagner_spline.o co2_sw.o co2eos.o \
+               fluid.o gas_eos_mod.o global_aux.o mphase_pckr_mod.o option.o \
+               saturation_function.o water_eos.o
+fluid.o : input.o option.o string.o
+gas_eos_mod.o :
+general.o : connection.o coupler.o debug.o discretization.o field.o fluid.o \
+            general_aux.o global_aux.o grid.o level.o material.o \
+            material_aux.o option.o output_aux.o patch.o realization.o \
+            saturation_function.o variables.o water_eos.o
+general_aux.o : gas_eos_mod.o global_aux.o option.o saturation_function.o \
+                water_eos.o
+general_grid.o : connection.o discretization.o field.o grid.o hdf5.o \
+                 hdf5_aux.o logging.o option.o patch.o realization.o
+geometry.o : input.o option.o
+global.o : connection.o coupler.o discretization.o field.o global_aux.o grid.o \
+           option.o patch.o realization.o realization_base.o variables.o
+global_aux.o : option.o utility.o
+grid.o : connection.o logging.o mfd_aux.o option.o region.o structured_grid.o \
+         unstructured_cell.o unstructured_explicit.o unstructured_grid.o \
+         unstructured_grid_aux.o utility.o
+hdf5.o : discretization.o field.o grid.o hdf5_aux.o logging.o option.o patch.o \
+         realization.o realization_base.o region.o unstructured_cell.o \
+         utility.o
+hdf5_aux.o : logging.o option.o
+hydrogeophysics_factory.o : hydrogeophysics_simulation.o \
+                            hydrogeophysics_wrapper.o input.o option.o \
+                            pmc_hydrogeophysics.o simulation.o \
+                            simulation_base.o subsurface_factory.o
+hydrogeophysics_simulation.o : hydrogeophysics_wrapper.o option.o output.o \
+                               pmc_base.o pmc_hydrogeophysics.o \
+                               simulation_base.o subsurface_simulation.o
+hydrogeophysics_wrapper.o : e4d_run.o e4d_setup.o e4d_vars.o option.o
+hydrostatic.o : condition.o connection.o coupler.o dataset_xyz.o general_aux.o \
+                grid.o option.o region.o structured_grid.o utility.o \
+                water_eos.o
+immis.o : co2_span_wagner.o co2_span_wagner_spline.o co2_sw.o co2eos.o \
+          connection.o coupler.o debug.o discretization.o field.o global_aux.o \
+          grid.o immis_aux.o level.o material.o option.o output_aux.o patch.o \
+          realization.o variables.o water_eos.o
+immis_aux.o : co2_span_wagner.o co2_span_wagner_spline.o co2_sw.o co2eos.o \
+              fluid.o gas_eos_mod.o mphase_pckr_mod.o option.o \
+              saturation_function.o water_eos.o
+immobile.o : immobile_aux.o input.o option.o string.o utility.o
+immobile_aux.o : database_aux.o option.o string.o utility.o
+init.o : condition.o condition_control.o connection.o constraint.o \
+         convergence.o coupler.o database.o database_hpt.o dataset.o \
+         dataset_base.o dataset_common_hdf5.o debug.o discretization.o field.o \
+         flash2.o fluid.o general.o general_grid.o global.o grid.o hdf5.o \
+         immis.o input.o level.o logging.o mass_transfer.o material.o \
+         mineral.o miscible.o mphase.o observation.o option.o output.o \
+         output_aux.o output_tecplot.o patch.o reaction.o reaction_aux.o \
+         reactive_transport.o realization.o region.o regression.o richards.o \
+         richards_mfd.o saturation_function.o secondary_continuum.o \
+         simulation.o solid_solution.o solver.o strata.o string.o \
+         structured_grid.o surface_field.o surface_flow.o surface_global.o \
+         surface_init.o surface_realization.o surface_th.o th.o thc.o thmc.o \
+         timestepper.o uniform_velocity.o units.o unstructured_grid.o \
+         unstructured_grid_aux.o variables.o water_eos.o waypoint.o
+input.o : option.o string.o
+level.o : patch.o
+logging.o :
+mass_transfer.o : dataset_common_hdf5.o dataset_global.o discretization.o \
+                  grid.o input.o option.o string.o
+mat_inv.o :
+material.o : dataset_common_hdf5.o input.o option.o string.o
+material_aux.o : option.o
+matrix_block_aux.o : option.o
+matrix_buffer.o : grid.o structured_grid.o
+mfd.o : connection.o field.o global_aux.o grid.o mfd_aux.o option.o patch.o \
+        richards_aux.o unstructured_cell.o unstructured_grid_aux.o water_eos.o
+mfd_aux.o : connection.o option.o
+microbial.o : global_aux.o immobile_aux.o input.o microbial_aux.o option.o \
+              reaction_aux.o reactive_transport_aux.o string.o utility.o
+microbial_aux.o : database_aux.o utility.o
+mineral.o : database_aux.o global_aux.o input.o mineral_aux.o option.o \
+            reaction_aux.o reactive_transport_aux.o solid_solution_aux.o \
+            string.o units.o utility.o
+mineral_aux.o : database_aux.o option.o string.o utility.o
+miscible.o : co2_span_wagner.o co2_span_wagner_spline.o co2_sw.o co2eos.o \
+             connection.o coupler.o debug.o discretization.o field.o \
+             global_aux.o grid.o level.o logging.o material.o miscible_aux.o \
+             option.o output_aux.o patch.o realization.o variables.o \
+             water_eos.o
+miscible_aux.o : fluid.o global_aux.o option.o water_eos.o
+mphase.o : co2_span_wagner.o co2_span_wagner_spline.o co2_sw.o co2eos.o \
+           connection.o coupler.o debug.o discretization.o field.o \
+           gas_eos_mod.o global_aux.o grid.o level.o material.o mphase_aux.o \
+           option.o output_aux.o patch.o realization.o secondary_continuum.o \
+           secondary_continuum_aux.o variables.o water_eos.o
+mphase_aux.o : co2_span_wagner.o co2_span_wagner_spline.o co2_sw.o co2eos.o \
+               fluid.o gas_eos_mod.o global_aux.o mphase_pckr_mod.o option.o \
+               saturation_function.o water_eos.o
+mphase_pckr_mod.o : material.o option.o saturation_function.o
+observation.o : connection.o input.o option.o region.o string.o
+option.o : logging.o
+output.o : connection.o coupler.o debug.o discretization.o field.o grid.o \
+           hdf5.o input.o level.o logging.o option.o output_aux.o \
+           output_common.o output_hdf5.o output_observation.o output_tecplot.o \
+           output_vtk.o patch.o reaction_aux.o realization_base.o variables.o
+output_aux.o : input.o option.o string.o variables.o
+output_common.o : connection.o coupler.o field.o grid.o hdf5.o hdf5_aux.o \
+                  logging.o option.o output_aux.o patch.o realization_base.o \
+                  unstructured_cell.o unstructured_grid_aux.o variables.o
+output_hdf5.o : connection.o coupler.o discretization.o field.o grid.o hdf5.o \
+                hdf5_aux.o logging.o option.o output_aux.o output_common.o \
+                patch.o reaction_aux.o realization_base.o string.o \
+                unstructured_cell.o unstructured_grid_aux.o variables.o
+output_observation.o : connection.o coupler.o discretization.o field.o \
+                       general.o global_aux.o grid.o immis.o logging.o \
+                       miscible.o mphase.o observation.o option.o output_aux.o \
+                       output_common.o patch.o reaction_aux.o \
+                       reactive_transport.o reactive_transport_aux.o \
+                       realization.o realization_base.o region.o richards.o \
+                       structured_grid.o th.o thc.o thmc.o utility.o \
+                       variables.o
+output_surface.o : connection.o coupler.o discretization.o field.o grid.o \
+                   hdf5.o hdf5_aux.o input.o logging.o option.o output_aux.o \
+                   output_common.o output_hdf5.o output_tecplot.o patch.o \
+                   reaction_aux.o realization.o string.o surface_field.o \
+                   surface_realization.o unstructured_cell.o \
+                   unstructured_grid_aux.o utility.o variables.o
+output_tecplot.o : connection.o discretization.o field.o grid.o logging.o \
+                   observation.o option.o output_aux.o output_common.o patch.o \
+                   reaction_aux.o realization_base.o region.o \
+                   secondary_continuum_aux.o structured_grid.o \
+                   unstructured_cell.o unstructured_grid_aux.o utility.o \
+                   variables.o
+output_vtk.o : discretization.o field.o grid.o logging.o option.o output_aux.o \
+               output_common.o patch.o reaction_aux.o realization_base.o \
+               string.o structured_grid.o variables.o
+patch.o : auxiliary.o condition.o connection.o constraint.o coupler.o \
+          dataset_base.o dataset_common_hdf5.o dataset_map.o field.o \
+          general_aux.o global_aux.o grid.o hydrostatic.o immis_aux.o \
+          material.o mineral.o mineral_aux.o miscible_aux.o mphase_aux.o \
+          observation.o option.o output_aux.o reaction.o reaction_aux.o \
+          reactive_transport_aux.o region.o richards_aux.o saturation.o \
+          saturation_function.o strata.o surface_auxiliary.o \
+          surface_complexation_aux.o surface_field.o surface_material.o \
+          th_aux.o thc_aux.o thmc_aux.o utility.o variables.o water_eos.o
+pflotran_factory.o : init.o input.o logging.o option.o regression.o \
+                     simulation.o string.o timestepper.o
+pflotran_new.o : hydrogeophysics_factory.o option.o pflotran_factory.o \
+                 simulation_base.o subsurface_factory.o surface_factory.o \
+                 surfsubsurface_factory.o
+pmc_base.o : option.o output.o output_aux.o process_model_base.o \
+             process_model_top.o timestepper_base.o utility.o waypoint.o
+pmc_hydrogeophysics.o : hydrogeophysics_wrapper.o option.o pmc_base.o \
+                        realization.o realization_base.o utility.o variables.o
+pmc_subsurface.o : option.o pmc_base.o realization.o utility.o
+pmc_surface.o : option.o output.o pmc_base.o process_model_base.o \
+                process_model_surface_flow.o realization.o surface_flow.o \
+                surface_realization.o timestepper_base.o timestepper_surface.o \
+                utility.o
+process_model_base.o : option.o output_aux.o realization_base.o
+process_model_richards.o : communicator_base.o condition.o discretization.o \
+                           global.o grid.o option.o process_model_base.o \
+                           realization.o richards.o structured_communicator.o \
+                           unstructured_communicator.o
+process_model_rt.o : communicator_base.o condition.o discretization.o global.o \
+                     grid.o mass_transfer.o option.o process_model_base.o \
+                     reaction_aux.o reactive_transport.o realization.o \
+                     structured_communicator.o unstructured_communicator.o
+process_model_surface_flow.o : communicator_base.o condition.o \
+                               discretization.o grid.o option.o \
+                               process_model_base.o realization.o \
+                               surface_field.o surface_flow.o \
+                               surface_realization.o \
+                               unstructured_communicator.o
+process_model_th.o : communicator_base.o condition.o discretization.o global.o \
+                     grid.o option.o process_model_base.o realization.o \
+                     structured_communicator.o th.o \
+                     unstructured_communicator.o
+process_model_thc.o : communicator_base.o condition.o discretization.o \
+                      global.o grid.o option.o process_model_base.o \
+                      realization.o structured_communicator.o thc.o \
+                      unstructured_communicator.o
+process_model_top.o : option.o process_model_base.o process_model_richards.o \
+                      process_model_rt.o realization.o richards.o
+ifdef PFLOTRAN_RXN_FLAG
+reaction.o : constraint.o global_aux.o immobile.o immobile_aux.o input.o \
+             microbial.o microbial_aux.o mineral.o mineral_aux.o option.o \
+             reaction_aux.o reaction_sandbox.o reactive_transport_aux.o \
+             solid_solution.o solid_solution_aux.o string.o \
+             surface_complexation.o surface_complexation_aux.o utility.o \
+             variables.o
+else
+reaction.o : co2_span_wagner.o co2eos.o constraint.o global_aux.o immobile.o \
+             immobile_aux.o input.o microbial.o microbial_aux.o mineral.o \
+             mineral_aux.o option.o reaction_aux.o reaction_sandbox.o \
+             reactive_transport_aux.o solid_solution.o solid_solution_aux.o \
+             string.o surface_complexation.o surface_complexation_aux.o \
+             utility.o variables.o water_eos.o
+endif
+reaction_aux.o : database_aux.o immobile_aux.o microbial_aux.o mineral_aux.o \
+                 option.o solid_solution_aux.o string.o \
+                 surface_complexation_aux.o utility.o
+reaction_chunk.o : co2eos.o global_aux.o option.o reaction_aux.o \
+                   reactive_transport_aux.o utility.o water_eos.o
+reaction_sandbox.o : global_aux.o input.o option.o reaction_aux.o \
+                     reaction_sandbox_base.o reaction_sandbox_clm_cn.o \
+                     reaction_sandbox_example.o reactive_transport_aux.o \
+                     string.o utility.o
+reaction_sandbox_base.o : global_aux.o input.o option.o reaction_aux.o \
+                          reactive_transport_aux.o
+reaction_sandbox_clm_cn.o : global_aux.o immobile_aux.o input.o option.o \
+                            reaction_aux.o reaction_sandbox_base.o \
+                            reactive_transport_aux.o string.o units.o \
+                            utility.o
+reaction_sandbox_example.o : global_aux.o input.o option.o reaction_aux.o \
+                             reaction_sandbox_base.o reactive_transport_aux.o \
+                             string.o units.o
+reactive_transport.o : condition.o connection.o constraint.o coupler.o debug.o \
+                       discretization.o field.o fluid.o global.o global_aux.o \
+                       grid.o logging.o mass_transfer.o material.o option.o \
+                       output_aux.o output_tecplot.o patch.o reaction.o \
+                       reaction_aux.o reactive_transport_aux.o realization.o \
+                       region.o secondary_continuum.o \
+                       secondary_continuum_aux.o transport.o variables.o
+reactive_transport_aux.o : matrix_block_aux.o option.o reaction_aux.o \
+                           surface_complexation_aux.o utility.o
+realization.o : condition.o connection.o constraint.o coupler.o dataset.o \
+                dataset_base.o dataset_common_hdf5.o debug.o discretization.o \
+                dm_kludge.o field.o fluid.o grid.o input.o level.o \
+                mass_transfer.o material.o mfd.o mfd_aux.o observation.o \
+                option.o output_aux.o patch.o reaction.o reaction_aux.o \
+                reactive_transport_aux.o realization_base.o region.o \
+                saturation_function.o strata.o string.o structured_grid.o \
+                uniform_velocity.o unstructured_cell.o unstructured_grid.o \
+                unstructured_grid_aux.o waypoint.o
+realization_base.o : debug.o discretization.o field.o input.o level.o \
+                     mass_transfer.o option.o output_aux.o patch.o \
+                     reaction_aux.o
+region.o : geometry.o input.o logging.o option.o string.o structured_grid.o \
+           unstructured_cell.o utility.o
+regression.o : discretization.o grid.o input.o option.o output.o output_aux.o \
+               output_common.o realization.o string.o timestepper.o \
+               timestepper_base.o utility.o
+richards.o : connection.o coupler.o debug.o discretization.o field.o \
+             global_aux.o grid.o logging.o material.o matrix_buffer.o option.o \
+             output_aux.o patch.o realization.o realization_base.o \
+             richards_aux.o richards_common.o richards_lsm.o richards_mfd.o \
+             saturation_function.o variables.o water_eos.o
+richards_aux.o : global_aux.o matrix_buffer.o option.o saturation_function.o \
+                 water_eos.o
+richards_common.o : global_aux.o option.o richards_aux.o saturation_function.o \
+                    water_eos.o
+richards_lsm.o : connection.o coupler.o field.o global_aux.o grid.o logging.o \
+                 material.o option.o patch.o realization.o richards_aux.o \
+                 richards_common.o saturation_function.o
+richards_mfd.o : connection.o coupler.o debug.o discretization.o field.o \
+                 global_aux.o grid.o logging.o material.o matrix_buffer.o \
+                 mfd.o mfd_aux.o option.o patch.o realization.o richards_aux.o \
+                 richards_common.o water_eos.o
+saturation.o : condition.o connection.o coupler.o grid.o option.o region.o \
+               saturation_function.o water_eos.o
+saturation_function.o : input.o option.o string.o utility.o
+secondary_continuum.o : block_solve.o block_tridiag.o condition.o constraint.o \
+                        coupler.o global_aux.o grid.o material.o mphase_aux.o \
+                        option.o reaction.o reaction_aux.o \
+                        reactive_transport_aux.o realization.o \
+                        secondary_continuum_aux.o string.o utility.o \
+                        water_eos.o
+secondary_continuum_aux.o : option.o reactive_transport_aux.o utility.o
+simulation.o : general.o option.o reactive_transport.o realization.o \
+               regression.o richards.o solver.o surface_realization.o \
+               timestepper.o
+simulation_base.o : logging.o option.o output.o output_aux.o pmc_base.o \
+                    waypoint.o
+solid_solution.o : input.o mineral.o mineral_aux.o option.o reaction_aux.o \
+                   solid_solution_aux.o string.o utility.o
+solid_solution_aux.o : mineral_aux.o
+solver.o : input.o option.o string.o
+spline.o :
+strata.o : input.o material.o option.o region.o string.o surface_material.o
+string.o :
+structured_communicator.o : communicator_base.o dm_kludge.o structured_grid.o
+structured_grid.o : connection.o input.o option.o string.o
+subsurface_factory.o : checkpoint.o condition_control.o flash2.o general.o \
+                       immis.o init.o input.o logging.o miscible.o mphase.o \
+                       option.o output.o output_aux.o pmc_base.o \
+                       pmc_subsurface.o process_model_base.o \
+                       process_model_richards.o process_model_rt.o \
+                       process_model_th.o process_model_thc.o \
+                       process_model_top.o reactive_transport.o realization.o \
+                       richards.o simulation.o simulation_base.o \
+                       subsurface_simulation.o th.o thc.o thmc.o timestepper.o \
+                       timestepper_base.o waypoint.o
+subsurface_simulation.o : logging.o option.o output.o pmc_base.o \
+                          pmc_subsurface.o realization.o regression.o \
+                          simulation_base.o timestepper_base.o
+surface_auxiliary.o : surface_global_aux.o surface_th_aux.o
+surface_checkpoint.o : discretization.o grid.o option.o output_aux.o \
+                       surface_field.o surface_realization.o
+surface_complexation.o : global_aux.o input.o matrix_block_aux.o option.o \
+                         reaction_aux.o reactive_transport_aux.o string.o \
+                         surface_complexation_aux.o utility.o
+surface_complexation_aux.o : database_aux.o option.o utility.o
+surface_factory.o : condition_control.o init.o input.o logging.o option.o \
+                    output.o output_aux.o output_surface.o pmc_base.o \
+                    pmc_surface.o process_model_base.o \
+                    process_model_surface_flow.o process_model_top.o \
+                    simulation.o simulation_base.o surface_checkpoint.o \
+                    surface_realization.o surface_simulation.o timestepper.o \
+                    timestepper_base.o timestepper_surface.o
+surface_field.o :
+surface_flow.o : condition.o connection.o coupler.o debug.o discretization.o \
+                 dm_kludge.o field.o global_aux.o grid.o level.o logging.o \
+                 option.o output_aux.o patch.o realization.o \
+                 realization_base.o region.o saturation_function.o string.o \
+                 surface_field.o surface_global_aux.o surface_material.o \
+                 surface_realization.o unstructured_cell.o unstructured_grid.o \
+                 unstructured_grid_aux.o variables.o water_eos.o
+surface_flow_aux.o :
+surface_global.o : connection.o coupler.o discretization.o grid.o level.o \
+                   option.o patch.o surface_field.o surface_global_aux.o \
+                   surface_realization.o variables.o
+surface_global_aux.o : option.o utility.o
+surface_init.o : condition.o coupler.o dataset.o dataset_base.o \
+                 dataset_common_hdf5.o debug.o discretization.o field.o grid.o \
+                 hdf5.o input.o level.o material.o option.o output_aux.o \
+                 output_surface.o output_tecplot.o patch.o region.o solver.o \
+                 strata.o string.o structured_grid.o surface_auxiliary.o \
+                 surface_field.o surface_material.o surface_realization.o \
+                 units.o unstructured_grid.o unstructured_grid_aux.o \
+                 waypoint.o
+surface_material.o : input.o option.o string.o
+surface_realization.o : condition.o coupler.o dataset.o dataset_base.o debug.o \
+                        discretization.o dm_kludge.o field.o grid.o input.o \
+                        level.o option.o output_aux.o patch.o reaction_aux.o \
+                        realization.o realization_base.o region.o strata.o \
+                        string.o surface_field.o surface_material.o \
+                        unstructured_cell.o unstructured_grid.o \
+                        unstructured_grid_aux.o waypoint.o
+surface_simulation.o : logging.o option.o output.o pmc_base.o pmc_surface.o \
+                       regression.o simulation_base.o surface_realization.o \
+                       timestepper_base.o
+surface_th.o : condition.o connection.o coupler.o debug.o discretization.o \
+               dm_kludge.o field.o fluid.o grid.o level.o option.o \
+               output_aux.o patch.o realization.o realization_base.o region.o \
+               saturation_function.o string.o surface_field.o \
+               surface_global_aux.o surface_material.o surface_realization.o \
+               surface_th_aux.o unstructured_cell.o unstructured_grid.o \
+               unstructured_grid_aux.o variables.o water_eos.o
+surface_th_aux.o : option.o saturation_function.o surface_global_aux.o \
+                   water_eos.o
+surfsubsurface_factory.o : init.o input.o option.o simulation.o \
+                           simulation_base.o subsurface_factory.o \
+                           subsurface_simulation.o surface_factory.o \
+                           surface_simulation.o surfsubsurface_simulation.o \
+                           timestepper_base.o
+surfsubsurface_simulation.o : logging.o option.o output.o pmc_base.o \
+                              pmc_subsurface.o pmc_surface.o realization.o \
+                              regression.o simulation_base.o \
+                              subsurface_simulation.o surface_realization.o \
+                              surface_simulation.o timestepper_base.o
+th.o : connection.o coupler.o debug.o discretization.o field.o fluid.o \
+       global_aux.o grid.o level.o material.o option.o output_aux.o patch.o \
+       realization.o region.o saturation_function.o secondary_continuum.o \
+       secondary_continuum_aux.o th_aux.o utility.o variables.o water_eos.o
+th_aux.o : global_aux.o option.o saturation_function.o water_eos.o
+thc.o : connection.o coupler.o debug.o discretization.o field.o fluid.o \
+        global_aux.o grid.o level.o material.o option.o output_aux.o patch.o \
+        realization.o region.o saturation_function.o secondary_continuum.o \
+        secondary_continuum_aux.o thc_aux.o utility.o variables.o water_eos.o
+thc_aux.o : global_aux.o option.o saturation_function.o water_eos.o
+thmc.o : connection.o coupler.o debug.o discretization.o field.o fluid.o \
+         global_aux.o grid.o level.o material.o option.o patch.o realization.o \
+         region.o saturation_function.o thmc_aux.o utility.o water_eos.o
+thmc_aux.o : global_aux.o option.o saturation_function.o water_eos.o
+time_series.o : option.o
+time_storage.o : option.o
+timestepper.o : checkpoint.o condition_control.o convergence.o \
+                discretization.o field.o flash2.o general.o global.o \
+                global_aux.o grid.o immis.o input.o level.o logging.o \
+                miscible.o mphase.o option.o output.o output_aux.o \
+                output_surface.o patch.o reaction.o reaction_aux.o \
+                reactive_transport.o reactive_transport_aux.o realization.o \
+                richards.o secondary_continuum_aux.o solver.o string.o \
+                surface_checkpoint.o surface_field.o surface_flow.o \
+                surface_realization.o surface_th.o th.o thc.o thmc.o utility.o \
+                waypoint.o
+timestepper_base.o : convergence.o input.o option.o output.o \
+                     process_model_base.o solver.o string.o utility.o \
+                     waypoint.o
+timestepper_surface.o : option.o output.o process_model_base.o \
+                        process_model_surface_flow.o solver.o surface_flow.o \
+                        timestepper_base.o waypoint.o
+transport.o : global_aux.o matrix_block_aux.o option.o \
+              reactive_transport_aux.o
+uniform_velocity.o : input.o logging.o option.o string.o units.o utility.o
+units.o : option.o
+unstructured_cell.o : option.o utility.o
+unstructured_communicator.o : communicator_base.o dm_kludge.o \
+                              unstructured_explicit.o unstructured_grid.o \
+                              unstructured_grid_aux.o
+unstructured_explicit.o : connection.o geometry.o input.o option.o string.o \
+                          unstructured_grid_aux.o utility.o
+unstructured_grid.o : connection.o geometry.o hdf5_aux.o input.o option.o \
+                      string.o unstructured_cell.o unstructured_grid_aux.o \
+                      utility.o
+unstructured_grid_aux.o : geometry.o option.o unstructured_cell.o utility.o
+utility.o : input.o option.o string.o
+variables.o :
+water_eos.o :
+waypoint.o : option.o output_aux.o utility.o
+
+# developer level regression testing
+test : FORCE
+	@if [ -d $(pflotran_test_dir) ]; then \
+		$(MAKE) --directory=$(pflotran_test_dir) $(MAKECMDGOALS); \
+	fi
+
+clean-tests : FORCE
+	@if [ -d $(pflotran_test_dir) ]; then \
+		$(MAKE) --directory=$(pflotran_test_dir) $(MAKECMDGOALS); \
+	fi
+
+# user lever tests to verify pflotran is built correctly
+check : FORCE
+	@if [ -d $(pflotran_test_dir) ]; then \
+		$(MAKE) --directory=$(pflotran_test_dir) $(MAKECMDGOALS); \
+	fi
+
+# null rule to force things to happen
+FORCE :
+

File src/pflotran/pmc_hydrogeophysics.F90

View file
 ! ************************************************************************** !
 recursive subroutine PMCHydrogeophysicsInitializeRun(this)
 
-  use Hydrogeophysics_Wrapper_module, only : HydrogeophysicsWrapperStart
-
   implicit none
   
   class(pmc_hydrogeophysics_type) :: this
   
   call printMsg(this%option,'PMCHydrogeophysics%InitializeRun()')
   
-  call HydrogeophysicsWrapperStart(this%option)
-  
   if (associated(this%below)) then
     call this%below%InitializeRun()
   endif