Merge remote-tracking branch 'origin/release-v4.2.1'

jordanschnell · Jul 22, 2020 · f311cd5 · f311cd5
2 parents 0d88b58 + b158a15
commit f311cd5
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: 'Issues are typically for demonstrable errors in the software. User problems
+  with a build should be directed to the WRF Forum: forum.mmm.ucar.edu'
+title: ''
+labels: ''
+assignees: davegill
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Use compiler and version '....'
+2. Use namelist options '....'
+3. Output is '....'
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Attachments**
+If applicable, attach supporting files: namelist.input, rsl.* files, etc.
+
+**Additional context**
+Add any other context about the problem here, such as:
+   - This used to work with a previous version.
+   - The documentation is different from the exhibited behavior.
diff --git a/.github/PULL_REQUEST_TEMPLATE b/.github/PULL_REQUEST_TEMPLATE
@@ -1,23 +1,25 @@
-Use this template to give a detailed message describing the change you want to make to the code.
-If you are unclear on what should be written here, see  https://github.com/wrf-model/WRF/wiki/Making-a-good-pull-request-message for more guidance
-
-The title of this pull request should be a brief "purpose" for this change.
-
---- Delete this line and those above before hitting "Create pull request" ---
+The first line should be a single-line "purpose" for this change
 
 TYPE: choose one of [bug fix, enhancement, new feature, feature removed, no impact, text only]
 
-KEYWORDS: approximately 3 to 6 words (more is always better) related to your commit, separated by commas
+KEYWORDS: 5 to 10 words related to commit, separated by commas
 
 SOURCE: Either "developer's name (affiliation)" .XOR. "internal" for a WRF Dev committee member
 
-DESCRIPTION OF CHANGES: One or more paragraphs describing problem, solution, and required changes.
+DESCRIPTION OF CHANGES:
+Problem:
+Generally or specifically, what was wrong and needed to be addressed?
+
+Solution:
+What was down algorithmically and in the source code to address the problem?
 
-ISSUE: For use when this PR closes an issue. For example, if this PR closes issue number 123
+ISSUE: For use when this PR closes an issue.
 Fixes #123
 
 LIST OF MODIFIED FILES: list of changed files (use `git diff --name-status master` to get formatted list)
 
-TESTS CONDUCTED: Explicitly state if a WTF and or other tests were run, or are pending. For more complicated changes please be explicit!
+TESTS CONDUCTED: 
+1. Do mods fix problem? How can that be demonstrated, and was that test conducted?
+2. Are the Jenkins tests all passing?
 
 RELEASE NOTE: Include a stand-alone message suitable for the inclusion in the minor and annual releases. A publication citation is appropriate.
diff --git a/README b/README
@@ -1,4 +1,4 @@
-WRF Model Version 4.2
+WRF Model Version 4.2.1
 
 http://www2.mmm.ucar.edu/wrf/users/
 

diff --git a/Registry/Registry.EM_COMMON b/Registry/Registry.EM_COMMON
@@ -872,7 +872,7 @@ state    real   G_URB2D         ij    misc        1         -       rd=(interp_f
 state    real   RN_URB2D        ij    misc        1         -       rd=(interp_fcnm)u=(copy_fcnm)       "RN_URB"  "NET RADIATION ON URBAN SFC"         "W m{-2}"
 state    real   TS_URB2D        ij    misc        1         -       rd=(interp_fcnm)u=(copy_fcnm)       "TS_URB"  "SKIN TEMPERATURE"          "K"
 state    real   FRC_URB2D       ij    misc        1         -     i012rd=(interp_fcnm)u=(copy_fcnm)      "FRC_URB2D"  "URBAN FRACTION"         "dimensionless"
-state    integer   UTYPE_URB2D  ij    misc        1         -     rd=(interp_fcnm)u=(copy_fcnm)       "UTYPE_URB"  "URBAN TYPE"         "dimensionless"
+state    integer   UTYPE_URB2D  ij    misc        1         -     rd=(interp_fcni)u=(copy_fcni)       "UTYPE_URB"  "URBAN TYPE"         "dimensionless"
 state    real   TRB_URB4D       i{umap1}j   misc       1         Z     r      "TRB_URB4D" "ROOF LAYER TEMPERATURE"          "K"
 state    real   TW1_URB4D       i{umap2}j   misc       1         Z     r      "TW1_URB4D" "WALL LAYER TEMPERATURE"          "K"
 state    real   TW2_URB4D       i{umap2}j   misc       1         Z     r      "TW2_URB4D" "WALL LAYER TEMPERATURE"          "K"
@@ -1763,7 +1763,7 @@ state    real   LH_URB2D_mosaic   i{mocat}j     misc        1         -     r
 state    real   G_URB2D_mosaic    i{mocat}j     misc        1         -     r     "G_URB2D_mosaic"               "GROUND HEAT FLUX  AT THE SURFACE"    "W m-2"
 state    real   RN_URB2D_mosaic   i{mocat}j     misc        1         -     r     "RN_URB2D_mosaic"              "NET RADIATION"                       "W m-2"
 
-state    integer   mosaic_cat_index  iuj        misc        1         Z     i012rd=(interp_mask_land_field:lu_index)u=(copy_fcnm)    "mosaic_cat_index"          "  "   ""
+state    integer   mosaic_cat_index  iuj        misc        1         Z     i012rd=(interp_fcni)u=(copy_fcni)    "mosaic_cat_index"          "  "   ""
 state    real      landusef2         iuj        misc        1         Z     i012rdu                                                  "LANDUSEF2"      "sorted landuse fraction"  ""
 
 # State vector for etampnew microphysics. Must be declared state because it is not read-once and is needed for restarting.
@@ -2782,6 +2782,7 @@ state integer nodyn_dummy - dyn_nodyn -  -  -  "" "" ""
 # Turbine drag physics.
 rconfig   integer     windfarm_opt        namelist,physics      max_domains    0       rh       "windfarm_opt"                ""      ""
 rconfig   integer     windfarm_ij         namelist,physics      1              0       rh       "windfarm_ij"                ""      ""
+rconfig   real        windfarm_tke_factor namelist,physics      1              0.25    rh       "windfarm_tke_factor"        ""      ""
 #
 # Ideal case selection
 rconfig   integer     ideal_case          namelist,ideal        1              0       rh       "ideal_case"                 ""      ""
@@ -3062,7 +3063,7 @@ package   icedepth_one   seaice_thickness_opt==1     -             state:icedept
 #Time series options for text output
 package   notseries             process_time_series==0                 -             -
 package   tseries               process_time_series==1                 -             state:ts_hour,ts_u,ts_v,ts_q,ts_t,ts_psfc,ts_glw,ts_gsw,ts_hfx,ts_lh,ts_tsk,ts_tslb,ts_clw,ts_rainc,ts_rainnc,ts_u_profile,ts_v_profile,ts_gph_profile,ts_th_profile,ts_p_profile,ts_w_profile
-package   tseries_add_solar     process_time_series==2                 -             state:ts_hour,ts_u,ts_v,ts_q,ts_t,ts_psfc,ts_glw,ts_gsw,ts_hfx,ts_lh,ts_tsk,ts_tslb,ts_clw,ts_rainc,ts_rainnc,ts_u_profile,ts_v_profile,ts_gph_profile,ts_th_profile,ts_cldfrac2d,ts_wvp,ts_lwp,ts_iwp,ts_swp,ts_lwp_tot,ts_iwp_tot,ts_swp_tot,ts_re_qc,ts_re_qi,ts_re_qs,ts_re_qc_tot,ts_re_qi_tot,ts_re_qs_tot,ts_tau_qc,ts_tau_qi,ts_tau_qs,ts_tau_qc_tot,ts_tau_qi_tot,ts_tau_qs_tot,ts_cbaseht,ts_ctopht,ts_cbaseht_tot,ts_ctopht_tot,ts_clrnidx
+package   tseries_add_solar     process_time_series==2                 -             state:ts_hour,ts_u,ts_v,ts_q,ts_t,ts_psfc,ts_glw,ts_gsw,ts_hfx,ts_lh,ts_tsk,ts_tslb,ts_clw,ts_rainc,ts_rainnc,ts_u_profile,ts_v_profile,ts_gph_profile,ts_th_profile,ts_cldfrac2d,ts_wvp,ts_lwp,ts_iwp,ts_swp,ts_lwp_tot,ts_iwp_tot,ts_swp_tot,ts_re_qc,ts_re_qi,ts_re_qs,ts_re_qc_tot,ts_re_qi_tot,ts_re_qs_tot,ts_tau_qc,ts_tau_qi,ts_tau_qs,ts_tau_qc_tot,ts_tau_qi_tot,ts_tau_qs_tot,ts_cbaseht,ts_ctopht,ts_cbaseht_tot,ts_ctopht_tot,ts_clrnidx,ts_p_profile,ts_w_profile
 
 # WRF-HAILCAST
 state    real   HAILCAST_DHAIL1   ij     misc        1         -      r          "HAILCAST_DHAIL1"     "WRF-HAILCAST Hail Diameter, 1st rank order"     "mm"

diff --git a/Registry/Registry.NMM b/Registry/Registry.NMM
@@ -1433,6 +1433,7 @@ rconfig   integer     ysu_topdown_pblmix  namelist,physics      max_domains    0
 rconfig   integer     shinhong_tke_diag   namelist,physics      max_domains    0       rh       "shinhong_tke_diag"             ""      ""
 rconfig   integer     windfarm_opt        namelist,physics      max_domains    0       rh       "windfarm_opt"                ""      ""
 rconfig   integer     windfarm_ij         namelist,physics      1              0       rh       "windfarm_ij"                ""      ""
+rconfig   real        windfarm_tke_factor namelist,physics      1              0.25    rh       "windfarm_tke_factor"        ""      ""
 rconfig   integer     mfshconv            namelist,physics      max_domains    1        rh       "mfshconv"         "To activate mass flux scheme with qnse, 1=true; 0=false"      ""
 rconfig   real    BLDT                    namelist,physics	max_domains    0       h    "BLDT"          ""      ""
 rconfig   integer     cu_physics          namelist,physics	max_domains    0       rh0123       "cu_physics"            ""      ""

diff --git a/Registry/registry.clm b/Registry/registry.clm
@@ -1,14 +1,14 @@
 # CLM Variables
 
-state   integer NUMC           ij       misc      1          Z     rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)           "NUMC"     "NUMBER OF COLUMN SUBGRIDS"   " "
-state   integer NUMP           ij       misc      1          Z     rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)           "NUMP"     "NUMBER OF PFT SUBGRIDS"   " "
+state   integer NUMC           ij       misc      1          Z     rd=(interp_fcni)u=(copy_fcni)           "NUMC"     "NUMBER OF COLUMN SUBGRIDS"   " "
+state   integer NUMP           ij       misc      1          Z     rd=(interp_fcni)u=(copy_fcni)           "NUMP"     "NUMBER OF PFT SUBGRIDS"   " "
 state   real    SABV           ij       misc      1          Z     h                                                           "SABV"     "NET VEGETATION SOLAR RADIATION" "W m-2"
 state   real    SABG           ij       misc      1          Z     h                                                           "SABG"     "NET SOIL SOLAR RADIATION"       "W m-2"
 state   real    LWUP           ij       misc      1          Z     h                                                           "LWUP"     "OUTGOING LONGWAVE RADIATION"    "W m-2"
 state  real     LHSOI          i4j      misc      1          Z      h                                                           "LHSOI"           "LH from soil"              "W/m^2"
 state  real     LHVEG          i4j      misc      1          Z      h                                                           "LHVEG"           "LH from vegetation"        "W/m^2"
 state  real     LHTRAN         i4j      misc      1          Z      h                                                           "LHTRAN"          "LH from transpiration"     "W/m^2"
-state   integer SNL            i4j      misc      1          Z     rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)           "SNL"      "NUMBER OF SNOW LAYERS"   " "
+state   integer SNL            i4j      misc      1          Z     rd=(interp_fcni)u=(copy_fcni)           "SNL"      "NUMBER OF SNOW LAYERS"   " "
 state   real    SNOWDP         i4j      misc      1          Z     rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)           "SNOWDP"   "SUBGRID SNOW DEPTH"              "m"
 state   real    WTC            i4j      misc      1          Z     rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)           "WTC"      "COLUMN WEIGHT"                "fraction"
 state   real    WTP            i4j      misc      1          Z     rd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)           "WTP"      "PFT WEIGHT"                   "fraction"

diff --git a/Registry/registry.noahmp b/Registry/registry.noahmp
@@ -1,5 +1,5 @@
 # For Noah-MP
-state   integer isnowxy    ij      -       1      -     i02rhd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)    "isnow"      "no. of snow layer"                   "m3 m-3"
+state   integer isnowxy    ij      -       1      -     i02rhd=(interp_fcni)u=(copy_fcni)    "isnow"      "no. of snow layer"                   "m3 m-3"
 state    real   tvxy       ij      -       1      -     i02rhd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)    "tv"         "vegetation leaf temperature"         "K"
 state    real   tgxy       ij      -       1      -     i02rhd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)    "tg"         "bulk ground temperature"             "K"
 state    real   canicexy   ij      -       1      -     i02rhd=(interp_mask_field:lu_index,iswater)u=(copy_fcnm)    "canice"     "intercepted ice mass"                "mm"

diff --git a/chem/KPP/clean_kpp b/chem/KPP/clean_kpp
@@ -9,7 +9,7 @@ echo "# DO NOT EDIT! Placeholder for automatically generated file"  >&   configu
 # remove the traces of KPP
 if (-e ../Makefile_org ) then
 cp  -f ../Makefile_org  ../Makefile
-rm -f ../Makfile_org
+rm -f ../Makefile_org
 endif
 
 

diff --git a/chem/rxn.F b/chem/rxn.F
@@ -157,10 +157,11 @@ SUBROUTINE rxn_init( nw, wl )
       integer, intent(in) :: nw
       real, intent(in)    :: wl(nw)
 
-      integer :: astat, m, n
+      integer :: astat, m, n, debug_level
       character(len=256) :: emsg
 
       call set_initialization( status=.true. )
+      call get_wrf_debug_level( debug_level )
 
       if( .not. allocated( xsqy_tab ) ) then
          allocate( xsqy_tab(kj),stat=astat )
@@ -200,7 +201,9 @@ SUBROUTINE rxn_init( nw, wl )
       npht_tab = 2
       call setup_sub_calls( the_subs,npht_tab )
 
-      call diagnostics
+      IF ( 100 .LE. debug_level ) THEN
+        call diagnostics
+      ENDIF
 
       call rdxs_init( nw, wl )
 

diff --git a/dyn_em/module_advect_em.F b/dyn_em/module_advect_em.F
@@ -2,7 +2,7 @@
 !WRF:MODEL_LAYER:DYNAMICS
 !
 #if ( defined(ADVECT_KERNEL) )
-! cpp -traditional -C -P -DADVECT_KERNEL module_advect_em.F > advection_kernel.f90
+! cpp -traditional-cpp -P -DADVECT_KERNEL module_advect_em.F > advection_kernel.f90
 ! gfortran -ffree-form -ffree-line-length-none advection_kernel.f90
 ! ./a.out
 MODULE advection_kernel
@@ -10558,7 +10558,8 @@ PROGRAM feeder
                                             msfty
    REAL , DIMENSION( : ), ALLOCATABLE :: fzm, &
                                   fzp, &
-                                  rdzw, znw,dnw, rdnw, dn, rdn
+                                  rdzw, znw,dnw, rdnw, dn, rdn, &
+                                  c1, c2
    REAL :: rdx, &
            rdy, &
            dt
@@ -10607,6 +10608,8 @@ PROGRAM feeder
    ALLOCATE (rdnw( kms:kme ) )
    ALLOCATE ( dn ( kms:kme ) )
    ALLOCATE (rdn ( kms:kme ) )
+   ALLOCATE ( c1 ( kms:kme ) )
+   ALLOCATE ( c2 ( kms:kme ) )
    PRINT *,'CALL init'
    CALL init ( config_flags)
    CALL tophat ( field , MAX_SCALARS ,&
@@ -10649,6 +10652,10 @@ PROGRAM feeder
     fzp(k) = .5* dnw(k  )/dn(k)
     fzm(k) = .5* dnw(k-1)/dn(k)
    ENDDO
+   DO k = kts,kte
+      c1(k) = 1. ! This is d(B)/d(eta), so assuming no hyb coord
+      c2(k) = 0. ! This (1 - c1)*(p00 - ptop)
+   ENDDO
 
    time_step = 5
    dt = time_step
@@ -10668,8 +10675,8 @@ PROGRAM feeder
          CALL advect_scalar    ( field(ims,kms,jms,im), &
                                  field_old(ims,kms,jms,im), &
                                  tendency(ims,kms,jms), &
-                                 ru, rv, rom,                   &
-                                 mut, time_step/3, config_flags,  &
+                                 ru, rv, rom, c1, c2,           &
+                                 mut, time_step/3, config_flags,&
                                  msfux, msfuy, msfvx, msfvy,    &
                                  msftx, msfty,                  &
                                  fzm, fzp,                      &
@@ -10685,8 +10692,8 @@ PROGRAM feeder
          CALL advect_scalar    ( field(ims,kms,jms,im), &
                                  field_old(ims,kms,jms,im), &
                                  tendency(ims,kms,jms), &
-                                 ru, rv, rom,                   &
-                                 mut, time_step/2, config_flags,  &
+                                 ru, rv, rom, c1, c2,           &
+                                 mut, time_step/2, config_flags,&
                                  msfux, msfuy, msfvx, msfvy,    &
                                  msftx, msfty,                  &
                                  fzm, fzp,                      &
@@ -10703,7 +10710,7 @@ PROGRAM feeder
             CALL advect_scalar    ( field(ims,kms,jms,im), &
                                     field_old(ims,kms,jms,im), &
                                     tendency(ims,kms,jms), &
-                                    ru, rv, rom,                   &
+                                    ru, rv, rom, c1, c2,           &
                                     mut, time_step, config_flags,  &
                                     msfux, msfuy, msfvx, msfvy,    &
                                     msftx, msfty,                  &
@@ -10718,7 +10725,8 @@ PROGRAM feeder
                                     tendency(ims,kms,jms), &
                                     h_tendency(ims,kms,jms), &
                                     z_tendency(ims,kms,jms), &
-                                    ru, rv, rom, mut, mub, mu_old, &
+                                    ru, rv, rom, c1, c2, &
+                                    mut, mub, mu_old, &
                                     time_step, config_flags, tenddec, &
                                     msfux, msfuy, msfvx, msfvy, &
                                     msftx, msfty, fzm, fzp, &
@@ -10732,7 +10740,8 @@ PROGRAM feeder
                                     tendency(ims,kms,jms), &
                                     h_tendency(ims,kms,jms), &
                                     z_tendency(ims,kms,jms), &
-                                    ru, rv, rom, mut, mub, mu_old, &
+                                    ru, rv, rom, c1, c2, &
+                                    mut, mub, mu_old, &
                                     config_flags, tenddec, &
                                     msfux, msfuy, msfvx, msfvy, &
                                     msftx, msfty, fzm, fzp, &
@@ -10744,7 +10753,7 @@ PROGRAM feeder
             CALL advect_scalar_weno ( field(ims,kms,jms,im), &
                                    field_old(ims,kms,jms,im), &
                                    tendency(ims,kms,jms), &
-                             ru, rv, rom,                   &
+                             ru, rv, rom, c1, c2,           &
                              mut, time_step, config_flags,  &
                              msfux, msfuy, msfvx, msfvy,    &
                              msftx, msfty,                  &
@@ -10757,7 +10766,7 @@ PROGRAM feeder
             CALL advect_scalar_wenopd ( field(ims,kms,jms,im), &
                                         field_old(ims,kms,jms,im), &
                                         tendency(ims,kms,jms), &
-                                ru, rv, rom,                   &
+                                ru, rv, rom, c1, c2,           &
                                 mut, mub, mu_old,              &
                                 time_step, config_flags,       &
                                 msfux, msfuy, msfvx, msfvy,    &
@@ -10803,7 +10812,7 @@ PROGRAM feeder
    print *,' '
    print *,'Lines to input to gnuplot'
    print *,' '
-   print *,"set term x11"
+   print *,"set terminal x11"
    IF      (config_flags%scalar_adv_opt .EQ. 0 ) THEN
       print *,'set title "Scalar Advection" font ",20"'
    ELSE IF (config_flags%scalar_adv_opt .EQ. 1 ) THEN
@@ -10812,7 +10821,7 @@ PROGRAM feeder
       print *,'set title "Mono Advection" font ",20"'
    ELSE IF (config_flags%scalar_adv_opt .EQ. 3 ) THEN
       print *,'set title "WENO Advection" font ",20"'
-   ELSE IF (config_flags%scalar_adv_opt .EQ. 3 ) THEN
+   ELSE IF (config_flags%scalar_adv_opt .EQ. 4 ) THEN
       print *,'set title "WENO PD Advection" font ",20"'
    END IF
    print *,"set yrange[-20:120]"