Continueing sundials merge

build/CMakeLists.txt

@@ -145,6 +145,7 @@ set(ENGINE_DIR ${F_MASTER}/build/source/engine)
 set(HOOKUP_DIR ${F_MASTER}/build/source/hookup)
 set(NETCDF_DIR ${F_MASTER}/build/source/netcdf)
 set(NOAHMP_DIR ${F_MASTER}/build/source/noah-mp)
+set(NUMREC_DIR ${F_MASTER}/build/source/numrec)
 
 #=========================================================================================
 # COMPILE PART 2: Assemble all of the SUMMA sub-routines

build/source/CMakeLists.txt

@@ -13,16 +13,16 @@ set(NOAHMP
 
 # Free versions of numerical recipes utilities for NOAH-MP modules
 set(NRUTIL
-    ${ENGINE_DIR}/f2008funcs.f90
-    ${ENGINE_DIR}/nr_utility.f90
-    ${ENGINE_DIR}/nrtype.f90
+    ${NUMREC_DIR}/f2008funcs.f90
+    ${NUMREC_DIR}/nr_utils.f90
+    ${NUMREC_DIR}/nr_type.f90
     CACHE INTERNAL "NRUTIL")
 
 # Free versions of numerical recipes procedures for SUMMA modules
 set(NRPROC
-    ${ENGINE_DIR}/expIntegral.f90
-    ${ENGINE_DIR}/spline_int.f90
-    ${ENGINE_DIR}/hyp_2F1.f90
+    ${NUMREC_DIR}/expIntegral.f90
+    ${NUMREC_DIR}/spline_int.f90
+    ${NUMREC_DIR}/hyp_2F1.f90
     CACHE INTERNAL "NRPROC")
 
 # Hook-up modules
@@ -34,7 +34,7 @@ set(HOOKUP
 # Data modules
 set(DATAMS
     ${DSHARE_DIR}/data_types.f90
-    ${DSHARE_DIR}/flxMapping.f90
+    ${DSHARE_DIR}/fluxMapping.f90
     ${DSHARE_DIR}/get_ixname.f90
     ${DSHARE_DIR}/globalData.f90
     ${DSHARE_DIR}/multiconst.f90
@@ -75,7 +75,7 @@ set(PRELIM
     ${ENGINE_DIR}/check_icond.f90
     ${ENGINE_DIR}/checkStruc.f90
     ${ENGINE_DIR}/childStruc.f90
-    ${ENGINE_DIR}/conv_funcs.f90
+    ${ENGINE_DIR}/convert_funcs.f90
     ${ENGINE_DIR}/ffile_info.f90
     ${ENGINE_DIR}/read_pinit.f90
     ${ENGINE_DIR}/read_attrb.f90
@@ -89,46 +89,44 @@ set(PRELIM
 set(MODRUN
     ${ENGINE_DIR}/canopySnow.f90
     ${ENGINE_DIR}/derivforce.f90
-    ${ENGINE_DIR}/enthalpyTemp.f90
+    ${ENGINE_DIR}/convertEnthalpyTemp.f90
     ${ENGINE_DIR}/getVectorz.f90
     ${ENGINE_DIR}/indexState.f90
     ${ENGINE_DIR}/layerMerge.f90
     ${ENGINE_DIR}/layerDivide.f90
     ${ENGINE_DIR}/qTimeDelay.f90
     ${ENGINE_DIR}/read_force.f90
     ${ENGINE_DIR}/snowAlbedo.f90
-    ${ENGINE_DIR}/snwCompact.f90
     ${ENGINE_DIR}/tempAdjust.f90
-    ${ENGINE_DIR}/updateVars.f90
+    ${ENGINE_DIR}/updatDiagn.f90
     ${ENGINE_DIR}/var_derive.f90
     ${ENGINE_DIR}/volicePack.f90
     CACHE INTERNAL "MODRUN")
 set(MODRUN_SUNDIALS
     ${ENGINE_DIR}/tol4ida.f90
-    ${ENGINE_DIR}/updateVarsWithPrime.f90
+    ${ENGINE_DIR}/updatDiagnWithPrime.f90
     CACHE INTERNAL "MODRUN_SUNDIALS")
 
 # Solver main modules
 set(SOLVER
     ${ENGINE_DIR}/bigAquifer.f90
     ${ENGINE_DIR}/computFlux.f90
-    ${ENGINE_DIR}/computHeatCap.f90
+    ${ENGINE_DIR}/heat_Cp_Cm.f90
     ${ENGINE_DIR}/computJacob.f90
     ${ENGINE_DIR}/computResid.f90
-    ${ENGINE_DIR}/computSnowDepth.f90
-    ${ENGINE_DIR}/computThermConduct.f90
+    ${ENGINE_DIR}/snowDepth.f90
+    ${ENGINE_DIR}/thermConductivity.f90
     ${ENGINE_DIR}/coupled_em.f90
-    ${ENGINE_DIR}/diagn_evar.f90
     ${ENGINE_DIR}/eval8summa.f90
     ${ENGINE_DIR}/groundwatr.f90
     ${ENGINE_DIR}/opSplittin.f90
     ${ENGINE_DIR}/run_oneGRU.f90
     ${ENGINE_DIR}/run_oneHRU.f90
-    ${ENGINE_DIR}/snowLiqFlx.f90
-    ${ENGINE_DIR}/soilLiqFlx.f90
-    ${ENGINE_DIR}/ssdNrgFlux.f90
+    ${ENGINE_DIR}/snowLiqFlux.f90
+    ${ENGINE_DIR}/soilLiqFlux.f90
+    ${ENGINE_DIR}/snowSoilNrgFlux.f90
     ${ENGINE_DIR}/stomResist.f90
-    ${ENGINE_DIR}/summaSolve4homegrown.f90
+    ${ENGINE_DIR}/summaSolv4homegrown.f90
     ${ENGINE_DIR}/systemSolv.f90
     ${ENGINE_DIR}/varSubstep.f90
     ${ENGINE_DIR}/vegLiqFlux.f90
@@ -140,8 +138,8 @@ set(SOLVER_SUNDIALS
     ${ENGINE_DIR}/computJacobWithPrime.f90
     ${ENGINE_DIR}/computResidWithPrime.f90
     ${ENGINE_DIR}/eval8summaWithPrime.f90
-    ${ENGINE_DIR}/summaSolve4ida.f90
-    ${ENGINE_DIR}/summaSolve4kinsol.f90
+    ${ENGINE_DIR}/summaSolv4ida.f90
+    ${ENGINE_DIR}/summaSolv4kinsol.f90
     CACHE INTERNAL "SOLVER_SUNDIALS")
 
 # Driver support modules

build/source/driver/summa_alarms.f90

@@ -21,6 +21,9 @@
 module summa_alarms
 ! used to set alarms to write model output
 
+! named variables for time information
+USE globalData, only: numtim                  ! number of model time steps
+
 ! named variables to define new output files
 USE globalData, only: noNewFiles              ! no new output files
 USE globalData, only: newFileEveryOct1        ! create a new file on Oct 1 every year (start of the USA water year)
@@ -53,19 +56,21 @@ module summa_alarms
 contains
 
 ! used to set alarms to write model output
-subroutine summa_setWriteAlarms(oldTime, newTime, endTime,     &   ! time vectors
-                              newOutputFile, defNewOutputFile, &   ! flag to define new output file
-                              ixRestart,     printRestart,     &   ! flag to print the restart file
-                              ixProgress,    printProgress,    &   ! flag to print simulation progress
-                              resetStats,    finalizeStats,    &   ! flags to reset and finalize stats
-                              statCounter,                     &   ! statistics counter
-                              err,message)                         ! error control
+subroutine summa_setWriteAlarms(modelTimeStep,                   &   ! time index
+                                oldTime, newTime, endTime,       &   ! time vectors
+                                newOutputFile, defNewOutputFile, &   ! flag to define new output file
+                                ixRestart,     printRestart,     &   ! flag to print the restart file
+                                ixProgress,    printProgress,    &   ! flag to print simulation progress
+                                resetStats,    finalizeStats,    &   ! flags to reset and finalize stats
+                                statCounter,                     &   ! statistics counter
+                                err,message)                         ! error control
   ! ---------------------------------------------------------------------------------------
   ! data types
-  USE nrtype                                                  ! variable types, etc.
+  USE nr_type                                                 ! variable types, etc.
   ! ---------------------------------------------------------------------------------------
   implicit none
   ! dummy variables: time vectors
+  integer(i4b),intent(in)               :: modelTimeStep      ! index of model time step
   integer(i4b),intent(in)               :: oldTime(:)         ! time vector from the previous time step
   integer(i4b),intent(in)               :: newTime(:)         ! time vector from the current time step
   integer(i4b),intent(in)               :: endTime(:)         ! time vector at the end of the simulation
@@ -111,6 +116,12 @@ subroutine summa_setWriteAlarms(oldTime, newTime, endTime,     &   ! time vector
 
   end select
 
+  ! check that we do not have multiple files for the buffered write
+  if(defNewOutputFile .and. modelTimeStep>1)then
+   err=10
+   message=trim(message)//'cannot have multiple output files when using the buffered write decision (check the -n option)'; return
+  endif
+
   ! *****************************************************************************
   ! *** define the need to create a restart file
   ! *****************************************************************************
@@ -145,7 +156,7 @@ subroutine summa_setWriteAlarms(oldTime, newTime, endTime,     &   ! time vector
   ! *****************************************************************************
 
   ! reset output counters/flags
-  do iFreq=1,maxVarFreq  ! loop through output frequencies
+  do iFreq=1,maxvarFreq  ! loop through output frequencies
 
     ! define the need to finalize statistics
     ! NOTE: time vector is configured so that ih=0 at the start of the day, hence day in oldTime and timeStruct%var differ
@@ -157,11 +168,14 @@ subroutine summa_setWriteAlarms(oldTime, newTime, endTime,     &   ! time vector
       case default; err=20; message=trim(message)//'unable to identify output frequency'; return
     end select
 
+    ! force finalize the stats if the last model time step
+    if(modelTimeStep == numtim) finalizeStats(iFreq)=.true.
+
     ! reset ouput timestep
     if(resetStats(iFreq)) statCounter(iFreq)=1
 
   end do ! looping through output frequencies
 
 end subroutine summa_setWriteAlarms
 
-end module summa_alarms
+end module summa_alarms

build/source/driver/summa_bmi.f90

@@ -25,7 +25,7 @@ module summabmi
   ! *****************************************************************************
   ! data types
   USE,intrinsic :: iso_c_binding, only: c_ptr, c_loc, c_f_pointer
-  USE nrtype                                                  ! variable types, etc.
+  USE nr_type                                                 ! variable types, etc.
 ! NGEN_ACTIVE is to be set when running in the Nextgen framework
 ! https://github.com/NOAA-OWP/ngen
 #ifdef NGEN_ACTIVE
@@ -66,7 +66,7 @@ module summabmi
   USE globalData, only: fileout, output_fileSuffix            ! output filename and suffix
   USE globalData, only: outFreq                               ! output frequency flags
   USE globalData, only: ncid                                  ! netcdf output file id
-  USE globalData, only: maxLayers, maxSnowLayers              ! maximum number of layers and snow layers
+  USE globalData, only: maxLayers,maxSnowLayers,maxSoilLayers ! maximum number of layers and snow soil layers
   USE globalData, only: ixProgress                            ! define frequency to write progress
   USE globalData, only: ixRestart                             ! define frequency to write restart files
   USE globalData, only: newOutputFile                         ! define option for new output files
@@ -112,7 +112,7 @@ module summabmi
      character(len=256)                 :: fileout, output_fileSuffix        ! output filename and suffix
      logical(lgt),dimension(maxvarFreq) :: outFreq                           ! true if the output frequency is desired
      integer(i4b),dimension(maxvarFreq) :: ncid                              ! netcdf output file id
-     integer(i4b)                       :: maxLayers, maxSnowLayers          ! maximum number of layers and snow layers, could be different for different GRUs
+     integer(i4b)                       :: maxLayers,maxSnowLayers,maxSoilLayers ! maximum number of layers and snow soil layers, could be different for different GRUs
      integer(i4b)                       :: ixProgress                        ! define frequency to write progress
      integer(i4b)                       :: ixRestart                         ! define frequency to write restart files
      integer(i4b)                       :: newOutputFile                     ! define option for new output files
@@ -317,6 +317,7 @@ function summa_bmi_initialize(this, config_file) result (bmi_status)
      this%model%output_fileSuffix = output_fileSuffix
      this%model%maxLayers = maxLayers
      this%model%maxSnowLayers = maxSnowLayers
+     this%model%maxSoilLayers = maxSoilLayers
      this%model%urbanVegCategory = urbanVegCategory
      this%model%ixProgress = ixProgress
      this%model%ixRestart = ixRestart
@@ -359,6 +360,7 @@ function summa_update(this) result (bmi_status)
      outFreq = this%model%outFreq
      maxLayers = this%model%maxLayers
      maxSnowLayers = this%model%maxSnowLayers
+     maxSoilLayers = this%model%maxSoilLayers
      urbanVegCategory = this%model%urbanVegCategory
      ixProgress = this%model%ixProgress
      ixRestart = this%model%ixRestart

build/source/driver/summa_defineOutput.f90

@@ -20,10 +20,6 @@
 
 module summa_defineOutput                     ! used to define model output files
 
-! access missing values
-USE globalData,only:integerMissing            ! missing integer
-USE globalData,only:realMissing               ! missing real number
-
 ! named variables to define new output files
 USE globalData, only: noNewFiles              ! no new output files
 USE globalData, only: newFileEveryOct1        ! create a new file on Oct 1 every year (start of the USA water year)
@@ -36,7 +32,6 @@ module summa_defineOutput                     ! used to define model output file
 USE globalData,only:bpar_meta                 ! basin parameter metadata structure
 
 ! named variables
-USE var_lookup,only:maxvarFreq                ! maximum number of output files
 USE var_lookup,only:iLookTIME                 ! named variables for time data structure
 USE var_lookup,only:iLookFREQ                 ! named variables for the frequency structure
 
@@ -47,16 +42,16 @@ module summa_defineOutput                     ! used to define model output file
 contains
 
  ! used to define model output files
- subroutine summa_defineOutputFiles(modelTimeStep, summa1_struc, err, message)
+ subroutine summa_defineOutputFiles(modelTimeStep, using_buffer, summa1_struc, err, message)
  ! ---------------------------------------------------------------------------------------
  ! * desired modules
  ! ---------------------------------------------------------------------------------------
  ! data types
- USE nrtype                                                  ! variable types, etc.
+ USE nr_type                                                 ! variable types, etc.
  USE summa_type, only:summa1_type_dec                        ! master summa data type
  ! functions and subroutines
  USE def_output_module,only:def_output                       ! module to define model output
- USE modelwrite_module,only:writeParm                        ! module to write model parameters
+ USE modelwrite_module,only:writeParam                       ! module to write model parameters
  ! global data structures
  USE globalData,only:gru_struc                               ! gru-hru mapping structures
  USE globalData,only:structInfo                              ! information on the data structures
@@ -71,6 +66,7 @@ subroutine summa_defineOutputFiles(modelTimeStep, summa1_struc, err, message)
  implicit none
  ! dummy variables
  integer(i4b),intent(in)               :: modelTimeStep      ! time step index
+ logical(lgt),intent(in)               :: using_buffer       ! flag for will do buffered write
  type(summa1_type_dec),intent(inout)   :: summa1_struc       ! master summa data structure
  integer(i4b),intent(out)              :: err                ! error code
  character(*),intent(out)              :: message            ! error message
@@ -122,28 +118,32 @@ subroutine summa_defineOutputFiles(modelTimeStep, summa1_struc, err, message)
  ! *****************************************************************************
 
  ! define the file
- call def_output(summaVersion,buildTime,gitBranch,gitHash,nGRU,nHRU,gru_struc(1)%hruInfo(1)%nSoil,fileout,err,cmessage)
+ call def_output(using_buffer,summaVersion,buildTime,gitBranch,gitHash,nGRU,nHRU,fileout,err,cmessage)
  if(err/=0)then; message=trim(message)//trim(cmessage); return; endif
 
- ! write parameters for each HRU
+ ! write parameters with no time dimension
  do iGRU=1,nGRU
 
-  ! write HRU parameters
+  ! write HRU parameters, all written to timestep frequency file
   do iHRU=1,gru_struc(iGRU)%hruCount
    do iStruct=1,size(structInfo)
     select case(trim(structInfo(iStruct)%structName))
-     case('attr'); call writeParm(gru_struc(iGRU)%hruInfo(iHRU)%hru_ix,attrStruct%gru(iGRU)%hru(iHRU),attr_meta,err,cmessage)
-     case('type'); call writeParm(gru_struc(iGRU)%hruInfo(iHRU)%hru_ix,typeStruct%gru(iGRU)%hru(iHRU),type_meta,err,cmessage)
-     case('mpar'); call writeParm(gru_struc(iGRU)%hruInfo(iHRU)%hru_ix,mparStruct%gru(iGRU)%hru(iHRU),mpar_meta,err,cmessage)
+     case('attr'); call writeParam(gru_struc(iGRU)%hruInfo(iHRU)%hru_ix,attrStruct%gru(iGRU)%hru(iHRU),attr_meta,err,cmessage)
+     case('type'); call writeParam(gru_struc(iGRU)%hruInfo(iHRU)%hru_ix,typeStruct%gru(iGRU)%hru(iHRU),type_meta,err,cmessage)
+     case('mpar'); call writeParam(gru_struc(iGRU)%hruInfo(iHRU)%hru_ix,mparStruct%gru(iGRU)%hru(iHRU),mpar_meta,err,cmessage)
     end select
     if(err/=0)then; message=trim(message)//trim(cmessage)//'['//trim(structInfo(iStruct)%structName)//']'; return; endif
    end do  ! (looping through structures)
   end do  ! (looping through HRUs)
 
-  ! write GRU parameters
-  call writeParm(iGRU,bparStruct%gru(iGRU),bpar_meta,err,cmessage)
-  if(err/=0)then; message=trim(message)//trim(cmessage); return; endif
-
+  ! write GRU parameters, all written to timestep frequency file
+  do iStruct=1,size(structInfo)
+   select case(trim(structInfo(iStruct)%structName))
+    case('bpar'); call writeParam(iGRU,bparStruct%gru(iGRU),bpar_meta,err,cmessage)
+   end select
+   if(err/=0)then; message=trim(message)//trim(cmessage)//'['//trim(structInfo(iStruct)%structName)//']'; return; endif
+  end do  ! (looping through structures)
+
  end do  ! (looping through GRUs)
 
  ! end associate statements

build/source/driver/summa_driver.f90

@@ -23,7 +23,7 @@ program summa_driver
 
   ! * module access *
   ! data types
-  USE nrtype                                                  ! variable types, etc.
+  USE nr_type                                                 ! variable types, etc.
   USE summa_type, only: summa1_type_dec                       ! master summa data type
   ! subroutines and functions: model setup
   USE summa_init, only: summa_initialize                      ! used to allocate/initialize summa data structures