Merge branch 'hotfix-v8.2.3'

This merge addresses several issues in the MPAS-Atmosphere model and in the MPAS
infrastructure. Specific changes include:

 * Correction of the pool from which lbc_scalar constituent indices are obtained
   in the init_atm_thompson_aerosols_lbc routine. Rather than obtaining
   index_nifa and index_nwfa from the state pool, the indices of lbc_nifa and
   lbc_nwfa should be obtained from the lbc_state pool. (PR #1249)

 * Correction to the computation of the soil temperature (TSLB) in the Noah-MP
   land surface scheme through the addition of initialization of the soil liquid
   water (SH2O) in the noahmp_init subroutine in module
   mpas_atmphys_lsm_noahmpinit.F prior to calling NoahmpInitMain. (PR #1244)

 * Correction of the units of the fields 'greenfrac', 'shdmin', 'shdmax',
   'vegfra', and 'albedo12m' from "unitless" to "percent" in the
   init_atmosphere and atmosphere core Registry.xml files. Also, a correction to
   the spelling of 'greenness' in several places. (PR #1248)

 * Removal of a duplicate allocation of indexToEdgeID % array in the
   mpas_io_setup_edge_block_fields routine that was the source of a memory leak.
   (PR #1258)

 * Fix for a memory leak in mpas_block_creator_build_cell_halos by deallocating
   the cellLimitField field before the routine returns. (PR #1264)

 * Fix for a bug in the logic for determining when decompositions can be reused
   by the SMIOL library. In almost any practical situation, however, this bug
   created no issues. (PR #1288)

 * Changes in the init_atmosphere core to provide more reliable error messages
   in case config_nfglevels is not set to a value that is at least as large as
   the number of vertical levels in the first-guess intermediate file. (PR #1291)

 * Correction of the loop for Noah-MP snow initialization, capping snow water
   equivalent maximum at 2000 mm. (PR #1300)

 * Fix for a bug in the horizontal 2nd-order filter for the CAM upper absorbing
   layer, where the wrong level in the kdiff field was being used when enforcing
   a lower-bound on kdiff. This absorbing layer is active only when
   config_mpas_cam_coef > 0.0. (PR #1302)

 * Fix in the mountain wave idealized test case initialization when multiple MPI
   tasks are used. The 'xc' variable, which represents the center-point location
   of the mountain, was previously computed based on the maximum xCell values
   local to an MPI task, leading to inconsistent values on each MPI rank. By
   finding the maximum of xCell over all MPI ranks and ensuring that all MPI
   ranks use this global maximum, the terrain field is computed consistently
   between serial and parallel runs of the init_atmosphere_model program for the
   mountain wave test case (config_init_case = 6). (PR #1312)

 * Correction to the calculation of the 2-meter diagnostics (T2M, TH2M, and Q2)
   when using the Noah-MP land surface scheme. While the computation of 2-meter
   diagnostics is the same for Noah and Noah-MP over oceans, it is different
   between the two land surface schemes over land. In Noah-MP, the 2-meter
   diagnostics are weighted as functions of their respective diagnostics over
   bare soil and over vegetation. The updated diagnostics for Noah and Noah-MP
   are now computed in the new file mpas_atmphys_sfc_diagnostics.F. (PR #1242)

 * Fix to provide consistency in the ringing behavior of recurring alarms after
   their reference time has been adjusted with a call to
   mpas_adjust_alarm_to_reference_time. Now, adjusting the reference time for an
   alarm will always leave that alarm in a state such that it is considered by
   the mpas_is_alarm_ringing routine to be ringing at the current time. With
   this fix, limited-area simulations can be restarted at times between LBC
   updates, provided the reference_time attribute for the 'lbc_in' stream is set
   to the simulation initial time in the streams.atmosphere file. (PR #1290).

 * Correction of an indexing error for rvcuten in code blocks specific to the
   Grell-Freitas scheme in the convection driver. Specifically, in the
   convection_from_MPAS and convection_to_MPAS routines, rvcuten used (k,k) as
   indexing in a loop, where (k,i) is needed. Since the Grell-Freitas scheme
   does not provide momentum tendencies, the changes in this merge have no
   impact on results. (PR #1283)

Author: mgduda

README.md

@@ -1,4 +1,4 @@
-MPAS-v8.2.2
+MPAS-v8.2.3
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

src/core_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" core_abbrev="atm" version="8.2.2">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="8.2.3">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->
@@ -3451,10 +3451,10 @@
                 <var name="landmask" type="integer"  dimensions="nCells" units="unitless"
                      description="land-ocean mask (1=land ; 0=ocean)"/>
 
-                <var name="shdmin" type="real" dimensions="nCells" units="unitless"
+                <var name="shdmin" type="real" dimensions="nCells" units="percent"
                      description="minimum fractional coverage of annual green vegetation fraction"/>
 
-                <var name="shdmax" type="real" dimensions="nCells" units="unitless"
+                <var name="shdmax" type="real" dimensions="nCells" units="percent"
                      description="maximum fractional coverage of annual green vegetation fraction"/>
 
                 <var name="snoalb" type="real"  dimensions="nCells" units="unitless"
@@ -3463,11 +3463,11 @@
                 <var name="ter" type="real" dimensions="nCells" units="m"
                      description="terrain height"/>
 
-                <var name="albedo12m" type="real" dimensions="nMonths nCells" units="unitless"
+                <var name="albedo12m" type="real" dimensions="nMonths nCells" units="percent"
                      description="monthly-mean climatological surface albedo"/>
 
-                <var name="greenfrac" type="real" dimensions="nMonths nCells" units="unitless"
-                     description="monthly-mean climatological greeness fraction"/>
+                <var name="greenfrac" type="real" dimensions="nMonths nCells" units="percent"
+                     description="monthly-mean climatological greenness fraction"/>
 
                 <var name="dzs" type="real" dimensions="nSoilLevels nCells Time" units="m"
                      description="soil layer thickness"/>
@@ -3493,7 +3493,7 @@
                 <var name="tmn" type="real" dimensions="nCells Time" units="K"
                      description="deep soil temperature"/>
 
-                <var name="vegfra" type="real" dimensions="nCells Time" units="unitless"
+                <var name="vegfra" type="real" dimensions="nCells Time" units="percent"
                      description="vegetation fraction"/>
 
                 <var name="seaice" type="real" dimensions="nCells Time" units="unitless"

src/core_atmosphere/dynamics/mpas_atm_time_integration.F

@@ -4692,7 +4692,7 @@ subroutine atm_compute_dyn_tend_work(nCells, nEdges, nVertices, nVertLevels_dumm
                do k = nVertLevels-config_number_cam_damping_levels + 1, nVertLevels
                   visc2cam = 4.0*2.0833*config_len_disp*config_mpas_cam_coef
                   visc2cam = visc2cam*(1.0-real(nVertLevels-k)/real(config_number_cam_damping_levels))
-                  kdiff(k  ,iCell) = max(kdiff(nVertLevels  ,iCell),visc2cam)
+                  kdiff(k  ,iCell) = max(kdiff(k  ,iCell),visc2cam)
                end do
             end do
 

src/core_atmosphere/physics/Makefile

@@ -48,6 +48,7 @@ OBJS = \
 	mpas_atmphys_packages.o            \
 	mpas_atmphys_rrtmg_lwinit.o        \
 	mpas_atmphys_rrtmg_swinit.o        \
+	mpas_atmphys_sfc_diagnostics.o     \
 	mpas_atmphys_todynamics.o          \
 	mpas_atmphys_update_surface.o      \
 	mpas_atmphys_update.o              \
@@ -103,6 +104,7 @@ mpas_atmphys_driver.o: \
 	mpas_atmphys_driver_oml.o \
 	mpas_atmphys_constants.o \
 	mpas_atmphys_interface.o \
+	mpas_atmphys_sfc_diagnostics.o \
 	mpas_atmphys_update.o \
 	mpas_atmphys_vars.o
 
@@ -223,6 +225,10 @@ mpas_atmphys_rrtmg_swinit.o: \
 	mpas_atmphys_constants.o \
 	mpas_atmphys_utilities.o
 
+mpas_atmphys_sfc_diagnostics.o: \
+	mpas_atmphys_constants.o \
+	mpas_atmphys_vars.o
+
 mpas_atmphys_todynamics.o: \
 	mpas_atmphys_constants.o \
 	mpas_atmphys_vars.o

src/core_atmosphere/physics/Registry_noahmp.xml

@@ -360,12 +360,18 @@
       <var name="t2mbxy" type="real" dimensions="nCells Time" units="K"
                 description="2-meter temperature over bare ground" missing_value="-9999.0"/>
 
+      <var name="t2mxy" type="real" dimensions="nCells Time" units="K"
+                description="grid-mean 2-meter temperature" missing_value="-9999.0"/>
+
       <var name="q2mvxy" type="real" dimensions="nCells Time" units="kg kg^{-1}"
                 description="2-meter water vapor mixing ratio over canopy" missing_value="-9999.0"/>
 
       <var name="q2mbxy" type="real" dimensions="nCells Time" units="kg kg^{-1}"
                 description="2-meter water vapor mixing ratio over bare ground" missing_value="-9999.0"/>
 
+      <var name="q2mxy" type="real" dimensions="nCells Time" units="kg kg^{-1}"
+                description="grid-mean 2-meter water vapor mixing ratio" missing_value="-9999.0"/>
+
       <var name="tradxy" type="real" dimensions="nCells Time" units="K"
                 description="surface radiative temperature" missing_value="-9999.0"/>
 

src/core_atmosphere/physics/mpas_atmphys_driver.F

@@ -23,6 +23,7 @@ module mpas_atmphys_driver
  use mpas_atmphys_driver_oml
  use mpas_atmphys_constants
  use mpas_atmphys_interface
+ use mpas_atmphys_sfc_diagnostics,only: atmphys_sfc_diagnostics
  use mpas_atmphys_update
  use mpas_atmphys_vars, only: l_camlw,l_conv,l_radtlw,l_radtsw
  use mpas_timer
@@ -296,14 +297,21 @@ subroutine physics_driver(domain,itimestep,xtime_s)
           enddo
        endif
 
-       call allocate_seaice
+       call allocate_seaice(block%configs)
 !$OMP PARALLEL DO
        do thread=1,nThreads
           call driver_seaice(block%configs,diag_physics,sfc_input, &
                              cellSolveThreadStart(thread),cellSolveThreadEnd(thread))
        enddo
 !$OMP END PARALLEL DO
-       call deallocate_seaice
+       call deallocate_seaice(block%configs)
+
+!$OMP PARALLEL DO
+       do thread=1,nThreads
+          call atmphys_sfc_diagnostics(block%configs,mesh,diag,diag_physics,sfc_input,output_noahmp, &
+                           cellSolveThreadStart(thread),cellSolveThreadEnd(thread))
+       enddo
+!$OMP END PARALLEL DO
     endif
 
     !call to pbl schemes:

src/core_atmosphere/physics/mpas_atmphys_driver_convection.F

@@ -744,7 +744,7 @@ subroutine convection_from_MPAS(dt_dyn,configs,mesh,sfc_input,diag_physics,tend_
              rqvblten_p(i,k,j)  = rqvblten(k,i)
              rqvdynten_p(i,k,j) = rqvdynten(k,i)
              rucuten_p(i,k,j)   = rucuten(k,i)
-             rvcuten_p(i,k,j)   = rvcuten(k,k)
+             rvcuten_p(i,k,j)   = rvcuten(k,i)
           enddo
        enddo
        enddo
@@ -941,7 +941,7 @@ subroutine convection_to_MPAS(configs,diag_physics,tend_physics,its,ite)
              qc_cu(k,i)    = qccu_p(i,k,j)
              qi_cu(k,i)    = qicu_p(i,k,j)
              rucuten(k,i)  = rucuten_p(i,k,j)
-             rvcuten(k,k)  = rvcuten_p(i,k,j)
+             rvcuten(k,i)  = rvcuten_p(i,k,j)
           enddo
        enddo
        enddo

src/core_atmosphere/physics/mpas_atmphys_driver_lsm_noahmp.F

@@ -84,11 +84,11 @@ subroutine lsm_noahmp_fromMPAS(configs,mesh,diag,diag_physics,diag_physics_noahm
 
 
 !--- local OUT pointers (with no Noah LSM equivalent as defined in WRF):
- real(kind=RKIND),dimension(:),pointer:: t2mvxy,t2mbxy,q2mvxy,q2mbxy,tradxy,neexy,gppxy,nppxy,fvegxy,runsfxy,  &
-                                         runsbxy,ecanxy,edirxy,etranxy,fsaxy,firaxy,aparxy,psnxy,savxy,sagxy,  &
-                                         rssunxy,rsshaxy,bgapxy,wgapxy,tgvxy,tgbxy,chvxy,chbxy,shgxy,shcxy,    &
-                                         shbxy,evgxy,evbxy,ghvxy,ghbxy,irgxy,ircxy,irbxy,trxy,evcxy,chleafxy,  &
-                                         chucxy,chv2xy,chb2xy,rs,qtdrain
+ real(kind=RKIND),dimension(:),pointer:: tradxy,neexy,gppxy,nppxy,fvegxy,runsfxy,runsbxy,ecanxy,edirxy,  &
+                                         etranxy,fsaxy,firaxy,aparxy,psnxy,savxy,sagxy,rssunxy,rsshaxy,  &
+                                         bgapxy,wgapxy,tgvxy,tgbxy,chvxy,chbxy,shgxy,shcxy,shbxy,evgxy,  &
+                                         evbxy,ghvxy,ghbxy,irgxy,ircxy,irbxy,trxy,evcxy,chleafxy,chucxy, &
+                                         chv2xy,chb2xy,rs,qtdrain
 
 
 !--- local OUT additional variables:
@@ -375,10 +375,6 @@ subroutine lsm_noahmp_fromMPAS(configs,mesh,diag,diag_physics,diag_physics_noahm
 
 !--- initialization of OUT (with no Noah LSM equivalent as defined in WRF), i.e.
 !    see lines 242-290 in module NoahmpIOVarType.F90):
- call mpas_pool_get_array(output_noahmp,'t2mvxy'  ,t2mvxy  )
- call mpas_pool_get_array(output_noahmp,'t2mbxy'  ,t2mbxy  )
- call mpas_pool_get_array(output_noahmp,'q2mvxy'  ,q2mvxy  )
- call mpas_pool_get_array(output_noahmp,'q2mbxy'  ,q2mbxy  )
  call mpas_pool_get_array(output_noahmp,'tradxy'  ,tradxy  )
  call mpas_pool_get_array(output_noahmp,'neexy'   ,neexy   )
  call mpas_pool_get_array(output_noahmp,'gppxy'   ,gppxy   )
@@ -423,10 +419,6 @@ subroutine lsm_noahmp_fromMPAS(configs,mesh,diag,diag_physics,diag_physics_noahm
  call mpas_pool_get_array(output_noahmp,'qtdrain',qtdrain  )
 
  do i = its,ite
-    mpas_noahmp%t2mvxy(i)   = t2mvxy(i)
-    mpas_noahmp%t2mbxy(i)   = t2mbxy(i)
-    mpas_noahmp%q2mvxy(i)   = q2mvxy(i)
-    mpas_noahmp%q2mbxy(i)   = q2mbxy(i)
     mpas_noahmp%tradxy(i)   = tradxy(i)
     mpas_noahmp%neexy(i)    = neexy(i)
     mpas_noahmp%gppxy(i)    = gppxy(i)
@@ -685,11 +677,11 @@ subroutine lsm_noahmp_toMPAS(diag_physics,diag_physics_noahmp,output_noahmp,sfc_
 
 
 !--- local OUT pointers (with no Noah LSM equivalent as defined in WRF):
- real(kind=RKIND),dimension(:),pointer:: t2mvxy,t2mbxy,q2mvxy,q2mbxy,tradxy,neexy,gppxy,nppxy,fvegxy,runsfxy,  &
-                                         runsbxy,ecanxy,edirxy,etranxy,fsaxy,firaxy,aparxy,psnxy,savxy,sagxy,  &
-                                         rssunxy,rsshaxy,bgapxy,wgapxy,tgvxy,tgbxy,chvxy,chbxy,shgxy,shcxy,    &
-                                         shbxy,evgxy,evbxy,ghvxy,ghbxy,irgxy,ircxy,irbxy,trxy,evcxy,chleafxy,  &
-                                         chucxy,chv2xy,chb2xy,rs,qtdrain
+ real(kind=RKIND),dimension(:),pointer:: t2mvxy,t2mbxy,t2mxy,q2mvxy,q2mbxy,q2mxy,tradxy,neexy,gppxy,nppxy,  &
+                                         fvegxy,runsfxy,runsbxy,ecanxy,edirxy,etranxy,fsaxy,firaxy,aparxy,  &
+                                         psnxy,savxy,sagxy,rssunxy,rsshaxy,bgapxy,wgapxy,tgvxy,tgbxy,chvxy, &
+                                         chbxy,shgxy,shcxy,shbxy,evgxy,evbxy,ghvxy,ghbxy,irgxy,ircxy,irbxy, &
+                                         trxy,evcxy,chleafxy,chucxy,chv2xy,chb2xy,rs,qtdrain
 
 
 !--- local OUT additional variables:
@@ -865,8 +857,10 @@ subroutine lsm_noahmp_toMPAS(diag_physics,diag_physics_noahmp,output_noahmp,sfc_
 !    lines 242-290 in module NoahmpIOVarType.F90:
  call mpas_pool_get_array(output_noahmp,'t2mvxy'  ,t2mvxy  )
  call mpas_pool_get_array(output_noahmp,'t2mbxy'  ,t2mbxy  )
+ call mpas_pool_get_array(output_noahmp,'t2mxy'   ,t2mxy   )
  call mpas_pool_get_array(output_noahmp,'q2mvxy'  ,q2mvxy  )
  call mpas_pool_get_array(output_noahmp,'q2mbxy'  ,q2mbxy  )
+ call mpas_pool_get_array(output_noahmp,'q2mxy'   ,q2mxy   )
  call mpas_pool_get_array(output_noahmp,'tradxy'  ,tradxy  )
  call mpas_pool_get_array(output_noahmp,'neexy'   ,neexy   )
  call mpas_pool_get_array(output_noahmp,'gppxy'   ,gppxy   )
@@ -913,8 +907,10 @@ subroutine lsm_noahmp_toMPAS(diag_physics,diag_physics_noahmp,output_noahmp,sfc_
  do i = its,ite
     t2mvxy(i)   = mpas_noahmp%t2mvxy(i)
     t2mbxy(i)   = mpas_noahmp%t2mbxy(i)
+    t2mxy(i)    = mpas_noahmp%t2mxy(i)
     q2mvxy(i)   = mpas_noahmp%q2mvxy(i)
     q2mbxy(i)   = mpas_noahmp%q2mbxy(i)
+    q2mxy(i)    = mpas_noahmp%q2mxy(i)
     tradxy(i)   = mpas_noahmp%tradxy(i)
     neexy(i)    = mpas_noahmp%neexy(i)
     gppxy(i)    = mpas_noahmp%gppxy(i)