Restart refactor

Merge branch 'rgknox-restart-refactor'

This change-group completes a first version of a refactored restart
process that conforms to our new interface design. The general
approach was to re-use as much of the design of the history restart
process, ie using a vector list of objects to hold all of the restart
information along with its recent refactors.

Design points:

FatesHistoryDimensionsMod -> FatesIODimensionsMod, which contains
types and procedures that handle setting up the dimensioning for BOTH
history and restarts.

FatesHistoryVariableKindMod -> FatesIOVariableKindMod, which now
contains the types and procedures associated with the "dimension-kind"
structures, for BOTH history and restarts.

Some local constants such as the number of dimensions and dim-kinds
were re-tooled a little so that history and restarts have their own.

Some procedures of different classes were using the same name, which
was confusing, changed name for different classes.

The fates_bounds_type was moved to FatesIODimensionsMod, this seems
consistent as it is a holding place for dimensioning information
(bounds).

The registry of variables was cleaned-up regarding variable names,
long names and units.

Fixes: #129

User interface changes?: no

Code review:

Testing:

  rgknox

    Test suite: lawrencium-lr3 (intel), edTest, clm_short_45
    Test baseline: 2ac7960
    Test namelist changes: none
    Test answer changes: none, b4b

    Test summary: all PASS

  andre:
    Test suite: ed - yellowstone gnu, intel, pgi
                     hobart nag
    Test baseline: ed-clm-5c5928f
    Test namelist changes: none
    Test answer changes: no bit for bit
    Test summary: all tests pass

    Test suite: aux_clm40, aux_clm45 -
                          yellowstone gnu, intel, pgi
                          hobart nag
    Test baseline: clm4_5_12_r195
    Test namelist changes: none
    Test answer changes: bit for bit except for ed compsets
    Test summary: all tests pass except ed compsets which have
                  diverged from r195.

components/clm/src/ED/biogeochem/EDCohortDynamicsMod.F90

@@ -13,7 +13,7 @@ module EDCohortDynamicsMod
   use EDGrowthFunctionsMod  , only : c_area, tree_lai
   use EDTypesMod            , only : ed_site_type, ed_patch_type, ed_cohort_type
   use EDTypesMod            , only : fusetol, cp_nclmax
-  use EDtypesMod            , only : ncwd, numcohortsperpatch, udata
+  use EDtypesMod            , only : ncwd, maxcohortsperpatch, udata
   use EDtypesMod            , only : sclass_ed,nlevsclass_ed,AREA
   use EDtypesMod            , only : min_npm2, min_nppatch, min_n_safemath
   !
@@ -626,7 +626,7 @@ subroutine fuse_cohorts(patchptr)
     iterate = 1
     fusion_took_place = 0   
     currentPatch => patchptr
-    maxcohorts = numCohortsPerPatch
+    maxcohorts = maxCohortsPerPatch
 
     !---------------------------------------------------------------------!
     !  Keep doing this until nocohorts <= maxcohorts                         !

components/clm/src/ED/biogeochem/EDPatchDynamicsMod.F90

@@ -9,7 +9,7 @@ module EDPatchDynamicsMod
   use clm_varctl           , only : iulog 
   use pftconMod            , only : pftcon
   use EDCohortDynamicsMod  , only : fuse_cohorts, sort_cohorts, insert_cohort
-  use EDtypesMod           , only : ncwd, n_dbh_bins, ntol, numpft_ed, area, dbhmax, numPatchesPerCol
+  use EDtypesMod           , only : ncwd, n_dbh_bins, ntol, numpft_ed, area, dbhmax, maxPatchesPerCol
   use EDTypesMod           , only : ed_site_type, ed_patch_type, ed_cohort_type, udata
   use EDTypesMod           , only : min_patch_area, cp_numlevgrnd, cp_numSWb
   !
@@ -1018,7 +1018,7 @@ subroutine fuse_patches( csite )
     !---------------------------------------------------------------------
 
     !maxpatch = 4  
-    maxpatch = numPatchesPerCol
+    maxpatch = maxPatchesPerCol
 
     currentSite => csite 
 

components/clm/src/ED/biogeophys/EDPhotosynthesisMod.F90

@@ -54,7 +54,7 @@ subroutine Photosynthesis_ED (nsites, sites,bc_in,bc_out,dtime)
     use EDTypesMod        , only : ed_cohort_type
     use EDTypesMod        , only : ed_site_type
     use EDTypesMod        , only : numpft_ed
-    use EDTypesMod        , only : numpatchespercol
+    use EDTypesMod        , only : maxpatchespercol
     use EDTypesMod        , only : cp_numlevsoil
     use EDTypesMod        , only : cp_nlevcan
     use EDTypesMod        , only : cp_nclmax
@@ -105,9 +105,9 @@ subroutine Photosynthesis_ED (nsites, sites,bc_in,bc_out,dtime)
     real(r8) :: ci                                ! intracellular leaf CO2 (Pa)
     real(r8) :: lnc(mxpft)                        ! leaf N concentration (gN leaf/m^2)
 
-    real(r8) :: kc( numpatchespercol )            ! Michaelis-Menten constant for CO2 (Pa)
-    real(r8) :: ko( numpatchespercol )            ! Michaelis-Menten constant for O2 (Pa)
-    real(r8) :: co2_cp( numpatchespercol )        ! CO2 compensation point (Pa)
+    real(r8) :: kc( maxpatchespercol )            ! Michaelis-Menten constant for CO2 (Pa)
+    real(r8) :: ko( maxpatchespercol )            ! Michaelis-Menten constant for O2 (Pa)
+    real(r8) :: co2_cp( maxpatchespercol )        ! CO2 compensation point (Pa)
 
     ! ---------------------------------------------------------------
     ! TO-DO: bbbopt is slated to be transferred to the parameter file

components/clm/src/ED/biogeophys/EDSurfaceAlbedoMod.F90

@@ -12,7 +12,7 @@ module EDSurfaceRadiationMod
 
   use EDtypesMod        , only : ed_patch_type, ed_site_type
   use EDtypesMod        , only : numpft_ed
-  use EDtypesMod        , only : numPatchesPerCol
+  use EDtypesMod        , only : maxPatchesPerCol
   use shr_kind_mod      , only : r8 => shr_kind_r8
   use shr_log_mod       , only : errMsg => shr_log_errMsg
   use FatesInterfaceMod , only : bc_in_type, &
@@ -74,8 +74,8 @@ subroutine ED_Norman_Radiation (nsites, sites, bc_in, bc_out )
       real(r8) :: k_dir(numpft_ed)                              ! Direct beam extinction coefficient
       real(r8) :: tr_dir_z(cp_nclmax,numpft_ed,cp_nlevcan)         ! Exponential transmittance of direct beam radiation through a single layer
       real(r8) :: tr_dif_z(cp_nclmax,numpft_ed,cp_nlevcan)         ! Exponential transmittance of diffuse radiation through a single layer
-      real(r8) :: forc_dir(numPatchesPerCol,cp_maxSWb)
-      real(r8) :: forc_dif(numPatchesPerCol,cp_maxSWb)
+      real(r8) :: forc_dir(maxPatchesPerCol,cp_maxSWb)
+      real(r8) :: forc_dif(maxPatchesPerCol,cp_maxSWb)
       real(r8) :: weighted_dir_tr(cp_nclmax)
       real(r8) :: weighted_fsun(cp_nclmax)
       real(r8) :: weighted_dif_ratio(cp_nclmax,cp_maxSWb)
@@ -93,8 +93,8 @@ subroutine ED_Norman_Radiation (nsites, sites, bc_in, bc_out )
       real(r8) :: abs_rad(cp_maxSWb)                               !radiation absorbed by soil
       real(r8) :: tr_soili                                      ! Radiation transmitted to the soil surface.
       real(r8) :: tr_soild                                      ! Radiation transmitted to the soil surface.
-      real(r8) :: phi1b(numPatchesPerCol,numpft_ed)      ! Radiation transmitted to the soil surface.
-      real(r8) :: phi2b(numPatchesPerCol,numpft_ed)
+      real(r8) :: phi1b(maxPatchesPerCol,numpft_ed)      ! Radiation transmitted to the soil surface.
+      real(r8) :: phi2b(maxPatchesPerCol,numpft_ed)
       real(r8) :: laisum                                        ! cumulative lai+sai for canopy layer (at middle of layer)
       real(r8) :: angle
 
@@ -107,8 +107,8 @@ subroutine ED_Norman_Radiation (nsites, sites, bc_in, bc_out )
       integer  :: fp,iv,s      ! array indices
       integer  :: ib               ! waveband number
       real(r8) :: cosz             ! 0.001 <= coszen <= 1.000
-      real(r8) :: chil(numPatchesPerCol)     ! -0.4 <= xl <= 0.6
-      real(r8) :: gdir(numPatchesPerCol)    ! leaf projection in solar direction (0 to 1)
+      real(r8) :: chil(maxPatchesPerCol)     ! -0.4 <= xl <= 0.6
+      real(r8) :: gdir(maxPatchesPerCol)    ! leaf projection in solar direction (0 to 1)
 
       !-----------------------------------------------------------------------
 

components/clm/src/ED/main/EDInitMod.F90

@@ -54,10 +54,6 @@ subroutine zero_site( site_in )
     site_in%oldest_patch     => null() ! pointer to oldest patch at the site
     site_in%youngest_patch   => null() ! pointer to yngest patch at the site
 
-    ! INDICES 
-    site_in%lat              = nan
-    site_in%lon              = nan
-
     ! DISTURBANCE
     site_in%disturbance_rate = 0._r8  ! site level disturbance rates from mortality and fire.
     site_in%dist_type        = 0      ! disturbance dist_type id.