Merge pull request #3 from NCAR/modularize_infiltration_p2

Rename things related to saturated surface runoff

Renames the module, derived type, variables and methods related to
saturated surface runoff. The rename qflx_sat_surf ->
qflx_sat_excess_surf was suggested at a ctsm meeting. The other renames
are to be consistent with that and consistent with
InfiltrationExcessRunoffMod.

Also, remove a long yellowstone test, change PE count for cheyenne:
Removing this long test that sometimes exceeds the 2-hour limit I give
it (other times it takes just slightly less than 2 hours):
ERS_Ly5_P60x1.f10_f10_musgs.IHistClm50BgcCrop.yellowstone_intel.clm-cropMonthOutput. We
still have an identical test on cheyenne. Also, increase the PE count on
cheyenne to use two full nodes, rather than a partial node.

ChangeLog_branch

@@ -1,4 +1,100 @@
 ===============================================================
+Tag name: ctsm_n07_clm4_5_16_r249
+Originator(s): sacks
+Date: Aug 22, 2017
+One-line Summary: Rename things related to saturated surface runoff
+
+Purpose of changes
+------------------
+
+Renames the module, derived type, variables and methods related to saturated
+surface runoff. The rename qflx_sat_surf -> qflx_sat_excess_surf was suggested
+at a ctsm meeting. The other renames are to be consistent with that and
+consistent with InfiltrationExcessRunoffMod.
+
+Also, remove a long yellowstone test, change PE count for cheyenne: Removing
+this long test that sometimes exceeds the 2-hour limit I give it (other times it
+takes just slightly less than 2 hours):
+ERS_Ly5_P60x1.f10_f10_musgs.IHistClm50BgcCrop.yellowstone_intel.clm-cropMonthOutput. We
+still have an identical test on cheyenne. Also, increase the PE count on
+cheyenne to use two full nodes, rather than a partial node.
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+
+CLM testing:
+
+  build-namelist tests:
+
+    yellowstone - not run
+
+  unit-tests (components/clm/src):
+
+    yellowstone - not run
+
+  tools-tests (components/clm/test/tools):
+
+    yellowstone - not run
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     yellowstone - not run
+
+  regular tests (aux_clm):
+
+    yellowstone_intel - pass
+    yellowstone_pgi - pass
+    yellowstone_gnu - pass
+    cheyenne_intel - pass
+    hobart_nag - pass
+    hobart_pgi - pass
+    hobart_intel - pass
+
+CLM tag used for the baseline comparisons: ctsm_n06_clm4_5_16_r249
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+
+Detailed list of changes
+------------------------
+
+List any svn externals directories updated (cime, rtm, mosart, cism, etc.): none
+
+List all files eliminated:
+
+========= Renamed
+D       components/clm/src/biogeophys/SurfRunoffSatMod.F90
+
+List all files added and what they do:
+
+========= Renamed
+A       components/clm/src/biogeophys/SaturatedExcessRunoffMod.F90
+
+List all existing files that have been modified, and describe the changes:
+
+========= Renames
+M       components/clm/src/biogeochem/CNDriverMod.F90
+M       components/clm/src/biogeochem/CNFireBaseMod.F90
+M       components/clm/src/biogeochem/CNFireLi2014Mod.F90
+M       components/clm/src/biogeochem/CNFireLi2016Mod.F90
+M       components/clm/src/biogeochem/CNFireMethodMod.F90
+M       components/clm/src/biogeochem/CNFireNoFireMod.F90
+M       components/clm/src/biogeochem/CNVegetationFacade.F90
+M       components/clm/src/biogeophys/HydrologyNoDrainageMod.F90
+M       components/clm/src/biogeophys/InfiltrationExcessRunoffMod.F90
+M       components/clm/src/biogeophys/SoilHydrologyMod.F90
+M       components/clm/src/main/clm_driver.F90
+M       components/clm/src/main/clm_instMod.F90
+
+========= Remove a yellowstone test, tweak a cheyenne test, as described above
+M       components/clm/cime_config/testdefs/testlist_clm.xml
+
+===============================================================
+===============================================================
 Tag name: ctsm_n06_clm4_5_16_r249
 Originator(s): sacks
 Date: Aug 21, 2017

cime_config/testdefs/testlist_clm.xml

@@ -1088,9 +1088,8 @@
       <test name="ERP_Ly3_P72x2">
         <machine compiler="intel" testtype="aux_clm" testmods="clm/cropMonthOutput" comment="Multi-year global test of transient crops together with transient glaciers. Use no-evolve glaciers with ERP test">cheyenne</machine>
       </test>
-      <test name="ERS_Ly5_P60x1">
+      <test name="ERS_Ly5_P72x1">
         <machine compiler="intel" testtype="aux_clm" testmods="clm/cropMonthOutput" comment="Want a multi-year global test of transient crops; also want a multi-year transient restart test. Using P60x1 and ERS rather than ERP to get faster turnaround of this long-running test">cheyenne</machine>
-        <machine compiler="intel" testtype="aux_clm" testmods="clm/cropMonthOutput" comment="Want a multi-year global test of transient crops; also want a multi-year transient restart test. Using P60x1 and ERS rather than ERP to get faster turnaround of this long-running test">yellowstone</machine>
       </test>
     </grid>
   </compset>

src/biogeochem/CNDriverMod.F90

@@ -36,7 +36,7 @@ module CNDriverMod
   use PhotosynthesisMod               , only : photosyns_type
   use ch4Mod                          , only : ch4_type
   use EnergyFluxType                  , only : energyflux_type
-  use SurfRunoffSatMod                , only : surf_runoff_sat_type
+  use SaturatedExcessRunoffMod        , only : saturated_excess_runoff_type
   !
   ! !PUBLIC TYPES:
   implicit none
@@ -91,7 +91,7 @@ subroutine CNDriverNoLeaching(bounds,
        soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst,                &
        atm2lnd_inst, waterstate_inst, waterflux_inst,                                      &
        canopystate_inst, soilstate_inst, temperature_inst, crop_inst, ch4_inst,            &
-       dgvs_inst, photosyns_inst, surf_runoff_sat_inst, energyflux_inst,                   &
+       dgvs_inst, photosyns_inst, saturated_excess_runoff_inst, energyflux_inst,                   &
        nutrient_competition_method, cnfire_method)
     !
     ! !DESCRIPTION:
@@ -175,7 +175,7 @@ subroutine CNDriverNoLeaching(bounds,
     type(ch4_type)                          , intent(in)    :: ch4_inst
     type(dgvs_type)                         , intent(inout) :: dgvs_inst
     type(photosyns_type)                    , intent(in)    :: photosyns_inst
-    type(surf_runoff_sat_type)              , intent(in)    :: surf_runoff_sat_inst
+    type(saturated_excess_runoff_type)      , intent(in)    :: saturated_excess_runoff_inst
     type(energyflux_type)                   , intent(in)    :: energyflux_inst
     class(nutrient_competition_method_type) , intent(inout) :: nutrient_competition_method
     class(cnfire_method_type)               , intent(inout) :: cnfire_method
@@ -737,7 +737,7 @@ subroutine CNDriverNoLeaching(bounds,
 
     call t_startf('CNFire')
     call cnfire_method%CNFireArea(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-         atm2lnd_inst, energyflux_inst, surf_runoff_sat_inst, waterstate_inst, &
+         atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterstate_inst, &
          cnveg_state_inst, cnveg_carbonstate_inst, &
          totlitc_col=soilbiogeochem_carbonstate_inst%totlitc_col(begc:endc), &
          decomp_cpools_vr_col=soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), &

src/biogeochem/CNFireBaseMod.F90

@@ -35,7 +35,7 @@ module CNFireBaseMod
   use CNVegNitrogenFluxType              , only : cnveg_nitrogenflux_type
   use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
   use EnergyFluxType                     , only : energyflux_type
-  use SurfRunoffSatMod                   , only : surf_runoff_sat_type
+  use SaturatedExcessRunoffMod           , only : saturated_excess_runoff_type
   use WaterstateType                     , only : waterstate_type
   use GridcellType                       , only : grc
   use ColumnType                         , only : col
@@ -263,7 +263,7 @@ end subroutine CNFireInterp
 
   !-----------------------------------------------------------------------
   subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       atm2lnd_inst, energyflux_inst, surf_runoff_sat_inst, waterstate_inst, &
+       atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterstate_inst, &
        cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
@@ -280,7 +280,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     integer                               , intent(in)    :: filter_soilp(:) ! filter for soil patches
     type(atm2lnd_type)                    , intent(in)    :: atm2lnd_inst
     type(energyflux_type)                 , intent(in)    :: energyflux_inst
-    type(surf_runoff_sat_type)            , intent(in)    :: surf_runoff_sat_inst
+    type(saturated_excess_runoff_type)    , intent(in)    :: saturated_excess_runoff_inst
     type(waterstate_type)                 , intent(in)    :: waterstate_inst
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst

src/biogeochem/CNFireLi2014Mod.F90

@@ -34,7 +34,7 @@ module CNFireLi2014Mod
   use CNVegNitrogenFluxType              , only : cnveg_nitrogenflux_type
   use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
   use EnergyFluxType                     , only : energyflux_type
-  use SurfRunoffSatMod                   , only : surf_runoff_sat_type
+  use SaturatedExcessRunoffMod           , only : saturated_excess_runoff_type
   use WaterstateType                     , only : waterstate_type
   use GridcellType                       , only : grc                
   use ColumnType                         , only : col                
@@ -83,7 +83,7 @@ end function constructor
 
   !-----------------------------------------------------------------------
   subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       atm2lnd_inst, energyflux_inst, surf_runoff_sat_inst, waterstate_inst, &
+       atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterstate_inst, &
        cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
@@ -106,7 +106,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     integer                               , intent(in)    :: filter_soilp(:) ! filter for soil patches
     type(atm2lnd_type)                    , intent(in)    :: atm2lnd_inst
     type(energyflux_type)                 , intent(in)    :: energyflux_inst
-    type(surf_runoff_sat_type)            , intent(in)    :: surf_runoff_sat_inst
+    type(saturated_excess_runoff_type)    , intent(in)    :: saturated_excess_runoff_inst
     type(waterstate_type)                 , intent(in)    :: waterstate_inst
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
@@ -164,7 +164,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
 
          btran2             => energyflux_inst%btran2_patch                    , & ! Input:  [real(r8) (:)     ]  root zone soil wetness                            
-         fsat               => surf_runoff_sat_inst%fsat_col                   , & ! Input:  [real(r8) (:)     ]  fractional area with water table at surface       
+         fsat               => saturated_excess_runoff_inst%fsat_col           , & ! Input:  [real(r8) (:)     ]  fractional area with water table at surface       
          wf                 => waterstate_inst%wf_col                          , & ! Input:  [real(r8) (:)     ]  soil water as frac. of whc for top 0.05 m         
          wf2                => waterstate_inst%wf2_col                         , & ! Input:  [real(r8) (:)     ]  soil water as frac. of whc for top 0.17 m         
 

src/biogeochem/CNFireLi2016Mod.F90

@@ -34,7 +34,7 @@ module CNFireLi2016Mod
   use CNVegNitrogenFluxType              , only : cnveg_nitrogenflux_type
   use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con
   use EnergyFluxType                     , only : energyflux_type
-  use SurfRunoffSatMod                   , only : surf_runoff_sat_type
+  use SaturatedExcessRunoffMod           , only : saturated_excess_runoff_type
   use WaterstateType                     , only : waterstate_type
   use GridcellType                       , only : grc                
   use ColumnType                         , only : col                
@@ -84,7 +84,7 @@ end function constructor
 
   !-----------------------------------------------------------------------
   subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       atm2lnd_inst, energyflux_inst, surf_runoff_sat_inst, waterstate_inst, &
+       atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterstate_inst, &
        cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
@@ -108,7 +108,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     integer                               , intent(in)    :: filter_soilp(:) ! filter for soil patches
     type(atm2lnd_type)                    , intent(in)    :: atm2lnd_inst
     type(energyflux_type)                 , intent(in)    :: energyflux_inst
-    type(surf_runoff_sat_type)            , intent(in)    :: surf_runoff_sat_inst
+    type(saturated_excess_runoff_type)    , intent(in)    :: saturated_excess_runoff_inst
     type(waterstate_type)                 , intent(in)    :: waterstate_inst
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst
@@ -171,7 +171,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
          fd_pft             => pftcon%fd_pft                                   , & ! Input:
 
          btran2             => energyflux_inst%btran2_patch                    , & ! Input:  [real(r8) (:)     ]  root zone soil wetness                            
-         fsat               => surf_runoff_sat_inst%fsat_col                   , & ! Input:  [real(r8) (:)     ]  fractional area with water table at surface       
+         fsat               => saturated_excess_runoff_inst%fsat_col           , & ! Input:  [real(r8) (:)     ]  fractional area with water table at surface       
          wf2                => waterstate_inst%wf2_col                         , & ! Input:  [real(r8) (:)     ]  soil water as frac. of whc for top 0.17 m         
 
          is_cwd             => decomp_cascade_con%is_cwd                       , & ! Input:  [logical  (:)     ]  TRUE => pool is a cwd pool                         

src/biogeochem/CNFireMethodMod.F90

@@ -96,7 +96,7 @@ end subroutine CNFireInterp_interface
 
   !-----------------------------------------------------------------------
   subroutine CNFireArea_interface (this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       atm2lnd_inst, energyflux_inst, surf_runoff_sat_inst, waterstate_inst, &
+       atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterstate_inst, &
        cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
@@ -107,7 +107,7 @@ subroutine CNFireArea_interface (this, bounds, num_soilc, filter_soilc, num_soil
     use decompMod                          , only : bounds_type
     use atm2lndType                        , only : atm2lnd_type
     use EnergyFluxType                     , only : energyflux_type
-    use SurfRunoffSatMod                   , only : surf_runoff_sat_type
+    use SaturatedExcessRunoffMod           , only : saturated_excess_runoff_type
     use WaterstateType                     , only : waterstate_type
     use CNVegStateType                     , only : cnveg_state_type
     use CNVegCarbonStateType               , only : cnveg_carbonstate_type
@@ -122,7 +122,7 @@ subroutine CNFireArea_interface (this, bounds, num_soilc, filter_soilc, num_soil
     integer                               , intent(in)    :: filter_soilp(:) !  filter for soil patches
     type(atm2lnd_type)                    , intent(in)    :: atm2lnd_inst
     type(energyflux_type)                 , intent(in)    :: energyflux_inst
-    type(surf_runoff_sat_type)            , intent(in)    :: surf_runoff_sat_inst
+    type(saturated_excess_runoff_type)    , intent(in)    :: saturated_excess_runoff_inst
     type(waterstate_type)                 , intent(in)    :: waterstate_inst
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst

src/biogeochem/CNFireNoFireMod.F90

@@ -16,7 +16,7 @@ module CNFireNoFireMod
   use CNVegNitrogenStateType             , only : cnveg_nitrogenstate_type
   use CNVegNitrogenFluxType              , only : cnveg_nitrogenflux_type
   use EnergyFluxType                     , only : energyflux_type
-  use SurfRunoffSatMod                   , only : surf_runoff_sat_type
+  use SaturatedExcessRunoffMod           , only : saturated_excess_runoff_type
   use WaterstateType                     , only : waterstate_type
   use CNFireMethodMod                    , only : cnfire_method_type
   use CNFireBaseMod                      , only : cnfire_base_type
@@ -58,7 +58,7 @@ end function constructor
 
   !-----------------------------------------------------------------------
   subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, &
-       atm2lnd_inst, energyflux_inst, surf_runoff_sat_inst, waterstate_inst, &
+       atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterstate_inst, &
        cnveg_state_inst, cnveg_carbonstate_inst, totlitc_col, decomp_cpools_vr_col, t_soi17cm_col)
     !
     ! !DESCRIPTION:
@@ -76,7 +76,7 @@ subroutine CNFireArea (this, bounds, num_soilc, filter_soilc, num_soilp, filter_
     integer                               , intent(in)    :: filter_soilp(:) ! filter for soil patches
     type(atm2lnd_type)                    , intent(in)    :: atm2lnd_inst
     type(energyflux_type)                 , intent(in)    :: energyflux_inst
-    type(surf_runoff_sat_type)            , intent(in)    :: surf_runoff_sat_inst
+    type(saturated_excess_runoff_type)    , intent(in)    :: saturated_excess_runoff_inst
     type(waterstate_type)                 , intent(in)    :: waterstate_inst
     type(cnveg_state_type)                , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)          , intent(inout) :: cnveg_carbonstate_inst