Merge pull request #3 from bartnijssen/martynpclark-feature/rootDensity

Martynpclark feature/root density

build/source/driver/multi_driver.f90

@@ -116,6 +116,7 @@ program multi_driver
 integer(i4b)              :: jStep=0                        ! index of model output
 ! define the re-start file
 logical(lgt)              :: printRestart                   ! flag to print a re-start file
+integer(i4b),parameter    :: ixRestart_iy=1000              ! named variable to print a re-start file once per year
 integer(i4b),parameter    :: ixRestart_im=1001              ! named variable to print a re-start file once per month
 integer(i4b),parameter    :: ixRestart_id=1002              ! named variable to print a re-start file once per day
 integer(i4b),parameter    :: ixRestart_never=1003           ! named variable to print a re-start file never
@@ -378,8 +379,6 @@ program multi_driver
   ! read forcing data
   call read_force(istep,iHRU,err,message); call handle_err(err,message)
  end do  ! (end looping through HRUs)
- print*, time_data%var
-
 
  ! *****************************************************************************
  ! (7) create a new NetCDF output file, and write parameters and forcing data
@@ -500,8 +499,9 @@ program multi_driver
   ! ****************************************************************************
   ! define the need to calculate the re-start file
   select case(ixRestart)
-   case(ixRestart_im);    printRestart = (time_data%var(iLookTIME%id) == 1 .and. time_data%var(iLookTIME%ih) == 1  .and. time_data%var(iLookTIME%imin) == 0)
-   case(ixRestart_id);    printRestart = (time_data%var(iLookTIME%ih) == 1 .and. time_data%var(iLookTIME%imin) == 0)
+   case(ixRestart_iy);    printRestart = (time_data%var(iLookTIME%im) == 1 .and. time_data%var(iLookTIME%id) == 1 .and. time_data%var(iLookTIME%ih) == 0  .and. time_data%var(iLookTIME%imin) == 0)
+   case(ixRestart_im);    printRestart = (time_data%var(iLookTIME%id) == 1 .and. time_data%var(iLookTIME%ih) == 0 .and. time_data%var(iLookTIME%imin) == 0)
+   case(ixRestart_id);    printRestart = (time_data%var(iLookTIME%ih) == 0 .and. time_data%var(iLookTIME%imin) == 0)
    case(ixRestart_never); printRestart = .false.
    case default; call handle_err(20,'unable to identify option for the restart file')
   end select

build/source/dshare/multiconst.f90

@@ -51,6 +51,7 @@ MODULE multiconst
  REAL(DP), PARAMETER         :: secprday     =   86400._dp       ! number of seconds in a day
  REAL(DP), PARAMETER         :: secprhour    =    3600._dp       ! number of seconds in an hour
  REAL(DP), PARAMETER         :: secprmin     =      60._dp       ! number of seconds in a minute
- integer(i4b),parameter      :: integerMissing = -9999           ! value for mising integer
+ REAL(DP), PARAMETER         :: minprhour    =      60._dp       ! number of minutes in an hour
+ integer(i4b),parameter      :: integerMissing = -9999           ! value for missing integer
 
 END MODULE multiconst

build/source/engine/coupled_em.f90

@@ -1192,7 +1192,7 @@ subroutine printRestartFile(&
  write(timeString,'(a,i4,3(a,i2.2))') '_',time_data%var(iLookTIME%iyyy),'-',time_data%var(iLookTIME%im),'-',time_data%var(iLookTIME%id),'-',time_data%var(iLookTIME%ih)
 
  ! define the file name
- filename = trim(OUTPUT_PATH)//trim(filepref)//trim(timeString)//trim(output_fileSuffix)//'.txt'
+ filename = trim(OUTPUT_PATH)//trim(OUTPUT_PREFIX)//'_'//trim(filepref)//trim(timeString)//trim(output_fileSuffix)//'.txt'
  !print*, trim(filename)
  !pause
 

build/source/engine/derivforce.f90

@@ -32,6 +32,7 @@ module derivforce_module
  subroutine derivforce(err,message)
  USE multiconst,only:Tfreeze                                 ! freezing point of pure water (K)
  USE multiconst,only:secprhour                               ! number of seconds in an hour
+ USE multiconst,only:minprhour                               ! number of minutes in an hour
  USE data_struc,only:data_step                               ! length of the data step (s)
  USE data_struc,only:time_data,forc_data                     ! forcing data structures
  USE data_struc,only:attr_data,mpar_data,mvar_data           ! model data structures
@@ -49,6 +50,8 @@ subroutine derivforce(err,message)
  ! variables for cosine of the solar zenith angle
  integer(i4b),pointer          :: im                         ! month
  integer(i4b),pointer          :: id                         ! day
+ integer(i4b),pointer          :: ih                         ! hour
+ integer(i4b),pointer          :: imin                       ! minute
  real(dp)                      :: ahour                      ! hour at start of time step
  real(dp)                      :: dataStep                   ! data step (hours)
  real(dp),parameter            :: slope=0._dp                ! terrain slope (assume flat)
@@ -115,8 +118,8 @@ subroutine derivforce(err,message)
  ! assign pointers to radiation geometry variables
  im        => time_data%var(iLookTIME%im)                           ! month
  id        => time_data%var(iLookTIME%id)                           ! day
- dataStep   = data_step/secprhour                                   ! time step (hours)
- ahour      = real(time_data%var(iLookTIME%ih),kind(dp)) - dataStep ! hour at start of time step
+ ih        => time_data%var(iLookTIME%ih)                           ! hour
+ imin      => time_data%var(iLookTIME%imin)                         ! minute
  latitude  => attr_data%var(iLookATTR%latitude)                     ! latitude (degrees north
  cosZenith => mvar_data%var(iLookMVAR%scalarCosZenith)%dat(1)       ! average cosine of the zenith angle over time step DT
  ! assign pointers to model forcing data
@@ -148,18 +151,24 @@ subroutine derivforce(err,message)
  scalarCO2air = co2Factor * airpres  ! atmospheric co2 concentration (Pa)
  scalarO2air  = o2Factor * airpres   ! atmospheric o2 concentration (Pa)
 
+ ! compute the decimal hour at the start of the time step
+ dataStep = data_step/secprhour  ! time step (hours)
+ ahour    = real(ih,kind(dp)) + real(imin,kind(dp))/minprhour - data_step/secprhour  ! decimal hour (start of the step)
+
  ! compute the cosine of the solar zenith angle
  call clrsky_rad(im,id,ahour,dataStep,   &  ! intent(in): time variables
                  slope,azimuth,latitude, &  ! intent(in): location variables
                  hri,cosZenith)             ! intent(out): cosine of the solar zenith angle
+ !write(*,'(a,1x,4(i2,1x),3(f9.3,1x))') 'im,id,ih,imin,ahour,dataStep,cosZenith = ', &
+ !                                       im,id,ih,imin,ahour,dataStep,cosZenith
  ! check that we don't have considerable shortwave when the zenith angle is low
  ! NOTE: this is likely because the data are not in local time
- if(cosZenith < epsilon(cosZenith) .and. SWRadAtm > 100._dp)then
-  message=trim(message)//'SWRadAtm > 100 W m-2 when cos zenith angle is zero -- check that forcing data are in local time, '//&
-                         'that the time stamp in forcing data is at the end of the data interval, and that the lat-lon '//&
-                         'in the site characteristix file is correct'
-  err=20; return
- endif
+ !if(cosZenith < epsilon(cosZenith) .and. SWRadAtm > 200._dp)then
+ ! message=trim(message)//'SWRadAtm > 200 W m-2 when cos zenith angle is zero -- check that forcing data are in local time, '//&
+ !                        'that the time stamp in forcing data is at the end of the data interval, and that the lat-lon '//&
+ !                        'in the site characteristix file is correct'
+ ! err=20; return
+ !endif
  ! ensure solar radiation is zero between sunset and sunrise
  ! NOTE: also ensure that sw radiation is positive
  if(cosZenith <= 0._dp .or. SWRadAtm < 0._dp) SWRadAtm = 0._dp

build/source/engine/read_force.f90

@@ -148,9 +148,12 @@ subroutine read_force(istep,iHRU,err,message)
                   time_data%var(iLookTIME%ih),              & ! input  = hour
                   time_data%var(iLookTIME%imin),dsec,       & ! input  = minute/second
                   juldayFirst,err,cmessage)                   ! output = julian day (fraction of day) + error control
+  write(*,'(a,i4,1x,4(i2,1x))') 'firstTime: iyyy, im, id, ih, imin = ', time_data%var
   ! compute the start index
   iStart = nint( (dJulianStart - juldayFirst)*secprday/data_step )
+  print*, 'iStartIndex = ', iStart
   if(iStart < 0)then
+   print*, 'iStart = ', iStart
    message=trim(message)//'simulation start time is before the first time index in the datafile ['//trim(infile)//']'
    err=20; return
   endif
@@ -160,6 +163,10 @@ subroutine read_force(istep,iHRU,err,message)
     read(unt,'(a)',iostat=err)
     if(err/=0)then; err=20; message=trim(message)//'problemLineRead[is there any data within the simulation period?]'; return; endif
    end do
+  ! iStart=0, then need to back up because of data read in the next block
+  else
+   backspace(unit=unt,iostat=err)
+   if(err/=0)then; err=20; message=trim(message)//'problemRewindingFile: iStart=0'; return; endif
   endif
   ! handle situation where istep>1
   if (istep>1) then

build/source/engine/read_pinit.f90

@@ -75,6 +75,7 @@ subroutine read_pinit(filenm,isLocal,mpar_meta,parFallback,err,message)
  ! build filename and update error message
  infile = trim(SETNGS_PATH)//trim(filenm)
  message=trim(message)//'file='//trim(infile)//' - '
+ write(*,'(a)') trim(infile)
  ! open file
  call file_open(trim(infile),unt,err,cmessage)
  if(err/=0)then; message=trim(message)//trim(cmessage); return; endif

build/source/engine/systemSolv.f90

@@ -307,7 +307,6 @@ subroutine systemSolv(&
  real(dp)                        :: dCanopyEvaporation_dCanLiq   ! derivative in canopy evaporation w.r.t. canopy liquid water content (s-1)
  ! energy fluxes and derivatives for the snow and soil domains
  real(dp),dimension(nLayers)     :: ssdNetNrgFlux                ! net energy flux for each layer (J m-3 s-1)
- real(dp),dimension(0:nLayers)   :: iLayerNrgFlux                ! energy flux at the layer interfaces (W m-2)
  real(dp),dimension(0:nLayers)   :: dNrgFlux_dTempAbove          ! derivatives in the flux w.r.t. temperature in the layer above (J m-2 s-1 K-1)
  real(dp),dimension(0:nLayers)   :: dNrgFlux_dTempBelow          ! derivatives in the flux w.r.t. temperature in the layer below (J m-2 s-1 K-1)
  ! liquid water fluxes and derivatives for the vegetation domain
@@ -1716,6 +1715,7 @@ subroutine computFlux(&
   mLayerColumnOutflow     => mvar_data%var(iLookMVAR%mLayerColumnOutflow)%dat       ,&  ! intent(out): [dp(:)] column outflow from each soil layer (m3 s-1)
 
   ! soil fluxes
+  iLayerNrgFlux           => mvar_data%var(iLookMVAR%iLayerNrgFlux)%dat             ,&  ! intent(out): [dp(0:)] vertical energy flux at the interface of snow and soil layers
   iLayerLiqFluxSnow       => mvar_data%var(iLookMVAR%iLayerLiqFluxSnow)%dat         ,&  ! intent(out): [dp(0:)] vertical liquid water flux at snow layer interfaces (-)
   iLayerLiqFluxSoil       => mvar_data%var(iLookMVAR%iLayerLiqFluxSoil)%dat         ,&  ! intent(out): [dp(0:)] vertical liquid water flux at soil layer interfaces (-)
   mLayerBaseflow          => mvar_data%var(iLookMVAR%mLayerBaseflow)%dat            ,&  ! intent(out): [dp(:)] baseflow from each soil layer (m s-1)

build/source/engine/time_utils.f90

@@ -73,7 +73,6 @@ subroutine extractTime(refdate,iyyy,im,id,ih,imin,dsec,err,message)
  if (istart+(iend-2)==n) then
   ih=0; imin=0; dsec=0._dp; return
  endif
- print*, 'iyyy, im, id = ', iyyy, im, id
 
  ! get the hour (":" at end of hour)
  istart = istart+iend
@@ -92,6 +91,7 @@ subroutine extractTime(refdate,iyyy,im,id,ih,imin,dsec,err,message)
  if(istart > len_trim(refdate)) return
  iend   = index(refdate(istart:n)," ")
  read(refdate(istart:n),*) dsec
+ write(*,'(a,i4,1x,4(i2,1x))') 'refdate: iyyy, im, id, ih, imin = ', iyyy, im, id, ih, imin
 
  contains
 

docs/howto/summa_and_git_howto.md

@@ -18,7 +18,7 @@ In general, if you plan to apply the model rather than work directly on the sour
 If you plan on contributing to model development or would like a systematic way to incorporate updates to the SUMMA source code, we encourage you to use Git. The following sections are designed to get you started using Git and working with the SUMMA source code repository.
 
 ### Git resources
-If you are SUMMA familiar with Git yet, we encourage you to spend a few minutes getting antiquated with the system before you starting working with the SUMMA source code and Git. It's not difficult to use and a few minutes of learning about Git will go along way in helping you manage your code development.
+If you are not familiar with Git yet, we encourage you to spend a few minutes getting acquainted with the system before you starting working with the SUMMA source code and Git. It's not difficult to use and a few minutes of learning about Git will go along way in helping you manage your code development.
 
 There are a number of good Git learning resources that will provide a basic introduction to the version control system.
 * http://git-scm.com/about
@@ -84,7 +84,7 @@ then you are not in a Git repository (note that the top level directory in a Git
 
 Assign the truth repo to a remote tracking branch called `upstream`, which will allow you easily pull in changes that are made in the truth repo and keep your clone in-sync with that version. Once you get more familiar with Git, you will be able to control which updates to include:
 
-    git remote add --tracking upstream https://github.com/NCAR/summa.git
+    git remote add upstream https://github.com/NCAR/summa.git
 
 #### Step 4. Sync your clone with the truth repo
 
@@ -189,7 +189,7 @@ The SUMMA administrator and other developers will review your pull request and d
 
 ### Git workflow
 
-For us to leverage Git to its full potential, we have implemented a Git-oriented workflow. This requires developers to adhere to a few rules regarding branch names and merge requests. A full description of the workflow we use can be found [here](https://github.com/NCAR/summa/docs/summa_git_workflow.md).
+For us to leverage Git to its full potential, we have implemented a Git-oriented workflow. This requires developers to adhere to a few rules regarding branch names and merge requests. A full description of the workflow we use can be found [here](https://github.com/NCAR/summa/blob/master/docs/howto/summa_git_workflow.md).
 
 
 

docs/howto/summa_git_workflow.md

@@ -36,9 +36,9 @@ Although anyone could create these branches, they are designed for the preparati
  * Feature branch – feature/{feature_name}
  * Hotfix branch – hotfix/{hotfix_name}
  * Release branch – release/{release_name}
- * Support branch – support/VIC.{base_release_number}.{feature_branch_name}
- * Release name – VIC.{major.minor.patch}
- * Support release name - VIC.{base_release_number}.{feature_branch_name}.{##}
+ * Support branch – support/SUMMA.{base_release_number}.{feature_branch_name}
+ * Release name – SUMMA.{major.minor.patch}
+ * Support release name - SUMMA.{base_release_number}.{feature_branch_name}.{##}
 
 ## User Permissions
 Using Github to host the central or truth repository of our models allows us to easily control contributor permissions. Currently we split permission levels into 3 levels, Owners, Model Admins, and Developers.
@@ -47,7 +47,7 @@ Using Github to host the central or truth repository of our models allows us to
 
  2. Model Admins have full access to specific repositories. They may push, pull, or make administrative changes to those repositories associated with their model. However, they should generally not push to the truth repo directly. Instead, they should fork, clone, edit locally, update their fork and then issue a pull request. This pull request should preferably be reviewed by someone else before it is merged.
 
- 3. Developers have read-only access (pull, clone, fork) to any of the publically listed repositories under the UW-hydro name. If a developer would like a feature branch merged into the main repository, a pull request must be submitted and a Model Admin may merge it in.
+ 3. Developers have read-only access (pull, clone, fork) to any of the publicly listed repositories under the UW-hydro name. If a developer would like a feature branch merged into the main repository, a pull request must be submitted and a Model Admin may merge it in.
 
 ## Workflow examples
 
@@ -67,7 +67,7 @@ The process would be as follows:
 
  * Add the main SUMMA repo as the upstream remote, so you can easily merge changes that are made in the main SUMMA repo into your own local repo
 
-        git add remote upstream git@github.com:NCAR/summa.git
+        git remote add upstream git@github.com:NCAR/summa.git
 
  * Checkout the `develop` branch
 
@@ -81,7 +81,7 @@ The process would be as follows:
 
         git push
 
- * Now make as many changes as you need to, commit them to your local repo and push them to your remote on GitHub. This is just like any other work you would do using Git. Once everything is working and eevrything is sufficiently tested, you will be ready to share your code with others.
+ * Now make as many changes as you need to, commit them to your local repo and push them to your remote on GitHub. This is just like any other work you would do using Git. Once everything is working and everything is sufficiently tested, you will be ready to share your code with others.
 
 
  * Before you do that, merge any changes that have been made in the develop branch in the main SUMMA repo into the `feature/resistance` branch of your local repo. Assuming you are already on the `feature/resistance` branch: