Merge pull request #89 from climbfuji/update_gsl_develop_from_main

Update gsl/develop from main 2021/05/21

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+# Description
+
+Provide a clear and concise description of the bug and what behavior you are expecting.
+
+## Steps to Reproduce
+
+Please provide detailed steps for reproducing the issue.
+
+1. step 1
+2. step 2
+3. see the bug...
+
+## Additional Context
+
+Please provide any relevant information about your setup. This is important in case the issue is not reproducible except for under certain conditions.
+
+* Machine
+* Compiler
+* Suite Definition File or Scheme
+* Reference other issues or PRs in other repositories that this is related to, and how they are related.
+
+## Output
+
+Please include any relevant log files, screenshots or other output here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+## Description
+Provide a clear and concise description of the problem to be solved.
+
+## Solution
+Add a clear and concise description of the proposed solution.
+
+## Alternatives (optional)
+If applicable, add a description of any alternative solutions or features you've considered.
+
+## Related to (optional)
+Directly reference any issues or PRs in this or other repositories that this is related to, and describe how they are related.

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,22 @@
+## Description of Changes: 
+One or more paragraphs describing the problem, solution, and required changes.
+
+## Tests Conducted: 
+Explicitly state what tests were run on these changes, or if any are still pending (for README or other text-only changes, just put "None required". Make note of the compilers used, the platform/machine, and other relevant details as necessary. For more complicated changes, or those resulting in scientific changes, please be explicit!  
+**OR** Add any links to tests conducted. For example, "See ufs-community/ufs-weather-model/pull/<pr_number>"
+
+## Dependencies:
+Add any links to parent PRs (e.g. SCM and/or UFS PRs) or submodules (e.g. rte-rrtmgp). For example:
+- NCAR/ccpp-framework/pull/<pr_number>
+- NOAA-EMC/fv3atm/pull/<pr_number>
+- ufs-community/ufs-weather-model/pull/<pr_number>
+
+## Documentation:
+Does this PR add new capabilities that need to be documented or require modifications to the existing documentation?  If so, brief supporting material can be provided here. Contact the CODEOWNERS if your PR requires extensive updates to the documentation.  See https://github.com/NCAR/ccpp-doc for Technical Documentation or https://dtcenter.org/community-code/common-community-physics-package-ccpp/documentation for the latest Scientific Documentation.
+
+## Issue (optional): 
+If this PR is resolving or referencing one or more issues, in this repository or elewhere, list them here. For example, "Fixes issue mentioned in #123" or "Related to bug in https://github.com/NCAR/other_repository/pull/63"
+
+## Contributors (optional): 
+If others have contributed to this work aside from the PR author, list them here
+

physics/GFS_DCNV_generic.F90

@@ -26,14 +26,14 @@ subroutine GFS_DCNV_generic_pre_run (im, levs, ldiag3d, qdiag3d, do_cnvgwd, cplc
 
       integer, intent(in) :: im, levs, nsamftrac, ntqv, index_of_process_dcnv, dtidx(:,:)
       logical, intent(in) :: ldiag3d, qdiag3d, do_cnvgwd, cplchm
-      real(kind=kind_phys), dimension(im,levs), intent(in)    :: gu0
-      real(kind=kind_phys), dimension(im,levs), intent(in)    :: gv0
-      real(kind=kind_phys), dimension(im,levs), intent(in)    :: gt0
-      real(kind=kind_phys), dimension(:,:,:),   intent(inout) :: gq0
-      real(kind=kind_phys), dimension(im,levs), intent(inout) :: save_u
-      real(kind=kind_phys), dimension(im,levs), intent(inout) :: save_v
-      real(kind=kind_phys), dimension(im,levs), intent(inout) :: save_t
-      real(kind=kind_phys), dimension(:,:,:),   intent(inout) :: save_q
+      real(kind=kind_phys), dimension(:,:),   intent(in)    :: gu0
+      real(kind=kind_phys), dimension(:,:),   intent(in)    :: gv0
+      real(kind=kind_phys), dimension(:,:),   intent(in)    :: gt0
+      real(kind=kind_phys), dimension(:,:,:), intent(inout) :: gq0
+      real(kind=kind_phys), dimension(:,:),   intent(inout) :: save_u
+      real(kind=kind_phys), dimension(:,:),   intent(inout) :: save_v
+      real(kind=kind_phys), dimension(:,:),   intent(inout) :: save_t
+      real(kind=kind_phys), dimension(:,:,:), intent(inout) :: save_q
       ! dqdti only allocated if cplchm is .true.
       real(kind=kind_phys), dimension(:,:),     intent(inout) :: dqdti
       character(len=*), intent(out) :: errmsg
@@ -99,8 +99,8 @@ end subroutine GFS_DCNV_generic_post_finalize
 !> \section arg_table_GFS_DCNV_generic_post_run Argument Table
 !! \htmlinclude GFS_DCNV_generic_post_run.html
 !!
-    subroutine GFS_DCNV_generic_post_run (im, levs, lssav, ldiag3d, ras, cscnv,   &
-      frain, rain1, dtf, cld1d, save_u, save_v, save_t, gu0, gv0, gt0,            &
+    subroutine GFS_DCNV_generic_post_run (im, levs, lssav, ldiag3d, qdiag3d, ras, &
+      cscnv, frain, rain1, dtf, cld1d, save_u, save_v, save_t, gu0, gv0, gt0,     &
       ud_mf, dd_mf, dt_mf, con_g, npdf3d, num_p3d, ncnvcld3d, nsamftrac,          &
       rainc, cldwrk, upd_mf, dwn_mf, det_mf, dtend, dtidx, index_of_process_dcnv, &
       index_of_temperature, index_of_x_wind, index_of_y_wind, ntqv, gq0, save_q,  &
@@ -113,31 +113,26 @@ subroutine GFS_DCNV_generic_post_run (im, levs, lssav, ldiag3d, ras, cscnv,   &
       implicit none
 
       integer, intent(in) :: im, levs, nsamftrac
-      logical, intent(in) :: lssav, ldiag3d, ras, cscnv
+      logical, intent(in) :: lssav, ldiag3d, qdiag3d, ras, cscnv
       logical, intent(in) :: flag_for_dcnv_generic_tend
 
       real(kind=kind_phys), intent(in) :: frain, dtf
-      real(kind=kind_phys), dimension(im), intent(in) :: rain1, cld1d
-      real(kind=kind_phys), dimension(im,levs), intent(in) :: save_u, save_v, save_t
-      real(kind=kind_phys), dimension(im,levs), intent(in) :: gu0, gv0, gt0
-      real(kind=kind_phys), dimension(:,:,:), intent(in)   :: gq0, save_q
-      real(kind=kind_phys), dimension(im,levs), intent(in) :: ud_mf, dd_mf, dt_mf
+      real(kind=kind_phys), dimension(:),     intent(in) :: rain1, cld1d
+      real(kind=kind_phys), dimension(:,:),   intent(in) :: save_u, save_v, save_t
+      real(kind=kind_phys), dimension(:,:),   intent(in) :: gu0, gv0, gt0
+      real(kind=kind_phys), dimension(:,:,:), intent(in) :: gq0, save_q
+      real(kind=kind_phys), dimension(:,:),   intent(in) :: ud_mf, dd_mf, dt_mf
       real(kind=kind_phys), intent(in) :: con_g
       integer, intent(in) :: npdf3d, num_p3d, ncnvcld3d
 
-      real(kind=kind_phys), dimension(im), intent(inout) :: rainc, cldwrk
-      ! dtend, upd_mf, dwn_mf, det_mf only allocated if ldiag3d == .true.
+      real(kind=kind_phys), dimension(:),   intent(inout) :: rainc, cldwrk
       real(kind=kind_phys), dimension(:,:), intent(inout) :: upd_mf, dwn_mf, det_mf
-      real(kind=kind_phys), dimension(im,levs), intent(inout) :: cnvw, cnvc
+      real(kind=kind_phys), dimension(:,:), intent(inout) :: cnvw, cnvc
 
       real(kind=kind_phys), dimension(:,:,:), intent(inout) :: dtend
       integer, intent(in) :: dtidx(:,:), index_of_process_dcnv, index_of_temperature, &
            index_of_x_wind, index_of_y_wind, ntqv
 
-      ! The following arrays may not be allocated, depending on certain flags and microphysics schemes.
-      ! Since Intel 15 crashes when passing unallocated arrays to arrays defined with explicit shape,
-      ! use assumed-shape arrays. Note that Intel 18 and GNU 6.2.0-8.1.0 tolerate explicit-shape arrays
-      ! as long as these do not get used when not allocated (it is still invalid Fortran code, though).
       real(kind=kind_phys), dimension(:,:), intent(inout) :: cnvw_phy_f3d, cnvc_phy_f3d
 
       character(len=*), intent(out) :: errmsg
@@ -209,13 +204,15 @@ subroutine GFS_DCNV_generic_post_run (im, levs, lssav, ldiag3d, ras, cscnv,   &
           endif
 
           ! convective mass fluxes
-          do k=1,levs
-            do i=1,im
-              upd_mf(i,k)  = upd_mf(i,k)  + ud_mf(i,k) * (con_g*frain)
-              dwn_mf(i,k)  = dwn_mf(i,k)  + dd_mf(i,k) * (con_g*frain)
-              det_mf(i,k)  = det_mf(i,k)  + dt_mf(i,k) * (con_g*frain)
+          if(qdiag3d) then
+            do k=1,levs
+              do i=1,im
+                upd_mf(i,k)  = upd_mf(i,k)  + ud_mf(i,k) * (con_g*frain)
+                dwn_mf(i,k)  = dwn_mf(i,k)  + dd_mf(i,k) * (con_g*frain)
+                det_mf(i,k)  = det_mf(i,k)  + dt_mf(i,k) * (con_g*frain)
+              enddo
             enddo
-          enddo
+          endif
         endif ! if (ldiag3d)
 
       endif ! if (lssav)

physics/GFS_DCNV_generic.meta

@@ -228,6 +228,14 @@
   type = logical
   intent = in
   optional = F
+[qdiag3d]
+  standard_name = flag_tracer_diagnostics_3D
+  long_name = flag for 3d tracer diagnostic fields
+  units = flag
+  dimensions = ()
+  type = logical
+  intent = in
+  optional = F
 [ras]
   standard_name = flag_for_ras_deep_convection
   long_name = flag for ras convection scheme

physics/GFS_GWD_generic.F90

@@ -1,11 +1,14 @@
-!> \file GFS_GWD_generic.f
+!> \file GFS_GWD_generic.F90
 !! This file contains the CCPP-compliant orographic gravity wave
 !! drag pre interstitial codes.
 
 module GFS_GWD_generic_pre
 
 contains
 
+!! \section arg_table_GFS_GWD_generic_pre_init Argument Table
+!! \htmlinclude GFS_GWD_generic_pre_init.html
+!!
       subroutine GFS_GWD_generic_pre_init()
       end subroutine GFS_GWD_generic_pre_init
 
@@ -29,15 +32,15 @@ subroutine GFS_GWD_generic_pre_run(                               &
       implicit none
 
       integer, intent(in) :: im, levs, nmtvr
-      real(kind=kind_phys), intent(in) :: mntvar(im,nmtvr)
+      real(kind=kind_phys), intent(in) :: mntvar(:,:)
 
       real(kind=kind_phys), intent(out) ::                              &
-     &  oc(im), oa4(im,4), clx(im,4),                                   &
+     &  oc(:), oa4(:,:), clx(:,:),                                      &
      &  varss(:), ocss(:), oa4ss(:,:), clxss(:,:),                      &
-     &  theta(im), sigma(im), gamma(im), elvmax(im)
+     &  theta(:), sigma(:), gamma(:), elvmax(:)
 
       logical, intent(in) :: lssav, ldiag3d, flag_for_gwd_generic_tend
-      real(kind=kind_phys), intent(in) :: dtdt(im,levs), dudt(im,levs), dvdt(im,levs)
+      real(kind=kind_phys), intent(in) :: dtdt(:,:), dudt(:,:), dvdt(:,:)
       ! dtend only allocated only if ldiag3d is .true.
       real(kind=kind_phys), intent(inout) :: dtend(:,:,:)
       integer, intent(in) :: dtidx(:,:), index_of_temperature,          &
@@ -141,6 +144,9 @@ subroutine GFS_GWD_generic_pre_run(                               &
       end subroutine GFS_GWD_generic_pre_run
 !> @}
 
+!! \section arg_table_GFS_GWD_generic_pre_finalize Argument Table
+!! \htmlinclude GFS_GWD_generic_pre_finalize.html
+!!
       subroutine GFS_GWD_generic_pre_finalize()
       end subroutine GFS_GWD_generic_pre_finalize
 
@@ -216,6 +222,9 @@ subroutine GFS_GWD_generic_post_run(lssav, ldiag3d, dtf, dusfcg, dvsfcg, dudt, d
     end subroutine GFS_GWD_generic_post_run
 !> @}
 
+!! \section arg_table_GFS_GWD_generic_post_finalize Argument Table
+!! \htmlinclude GFS_GWD_generic_post_finalize.html
+!!
     subroutine GFS_GWD_generic_post_finalize()
     end subroutine GFS_GWD_generic_post_finalize
 

physics/GFS_GWD_generic.meta

@@ -162,7 +162,7 @@
   dimensions = (horizontal_loop_extent,vertical_dimension)
   type = real
   kind = kind_phys
-  intent = inout
+  intent = in
   optional = F
 [dvdt]
   standard_name = tendency_of_y_wind_due_to_model_physics
@@ -171,7 +171,7 @@
   dimensions = (horizontal_loop_extent,vertical_dimension)
   type = real
   kind = kind_phys
-  intent = inout
+  intent = in
   optional = F
 [dtdt]
   standard_name = tendency_of_air_temperature_due_to_model_physics

physics/GFS_MP_generic.F90

@@ -12,18 +12,19 @@ end subroutine GFS_MP_generic_pre_init
 !> \section arg_table_GFS_MP_generic_pre_run Argument Table
 !! \htmlinclude GFS_MP_generic_pre_run.html
 !!
-      subroutine GFS_MP_generic_pre_run(im, levs, ldiag3d, qdiag3d, do_aw, ntcw, nncl, ntrac, gt0, gq0, save_t, save_q, errmsg, errflg)
+      subroutine GFS_MP_generic_pre_run(im, levs, ldiag3d, qdiag3d, do_aw, ntcw, nncl, &
+                                        ntrac, gt0, gq0, save_t, save_q, errmsg, errflg)
 !
       use machine,               only: kind_phys
 
       implicit none
-      integer,                                          intent(in) :: im, levs, ntcw, nncl, ntrac
-      logical,                                          intent(in) :: ldiag3d, qdiag3d, do_aw
-      real(kind=kind_phys), dimension(im, levs),        intent(in) :: gt0
-      real(kind=kind_phys), dimension(im, levs, ntrac), intent(in) :: gq0
+      integer,                                intent(in) :: im, levs, ntcw, nncl, ntrac
+      logical,                                intent(in) :: ldiag3d, qdiag3d, do_aw
+      real(kind=kind_phys), dimension(:,:),   intent(in) :: gt0
+      real(kind=kind_phys), dimension(:,:,:), intent(in) :: gq0
 
-      real(kind=kind_phys), dimension(im, levs),        intent(inout) :: save_t
-      real(kind=kind_phys), dimension(im, levs, ntrac), intent(inout) :: save_q
+      real(kind=kind_phys), dimension(:,:),   intent(inout) :: save_t
+      real(kind=kind_phys), dimension(:,:,:), intent(inout) :: save_q
 
       character(len=*), intent(out) :: errmsg
       integer, intent(out) :: errflg
@@ -102,42 +103,41 @@ subroutine GFS_MP_generic_post_run(im, levs, kdt, nrcm, ncld, nncl, ntcw, ntrac,
       logical, intent(in) :: cal_pre, lssav, ldiag3d, qdiag3d, cplflx, cplchm
       integer, intent(in) :: index_of_temperature,index_of_process_mp
 
-      real(kind=kind_phys),                           intent(in)    :: dtf, frain, con_g
-      real(kind=kind_phys), dimension(im),            intent(in)    :: rain1, xlat, xlon, tsfc
-      real(kind=kind_phys), dimension(im),            intent(inout) :: ice, snow, graupel, rainc
-      real(kind=kind_phys), dimension(im),            intent(in)    :: rain0, ice0, snow0, graupel0
-      real(kind=kind_phys), dimension(im,nrcm),       intent(in)    :: rann
-      real(kind=kind_phys), dimension(im,levs),       intent(in)    :: gt0, prsl, save_t, del
-      real(kind=kind_phys), dimension(im,levs+1),     intent(in)    :: prsi, phii
-      real(kind=kind_phys), dimension(im,levs,ntrac), intent(in)    :: gq0, save_q
-
-      real(kind=kind_phys), dimension(im),      intent(in   ) :: sr
-      real(kind=kind_phys), dimension(im),      intent(inout) :: rain, domr_diag, domzr_diag, domip_diag, doms_diag, tprcp,  &
-                                                                 srflag, cnvprcp, totprcp, totice, totsnw, totgrp, cnvprcpb, &
-                                                                 totprcpb, toticeb, totsnwb, totgrpb, rain_cpl, rainc_cpl,   &
-                                                                 snow_cpl, pwat
-
-      real(kind=kind_phys), dimension(:,:,:),   intent(inout) :: dtend ! only if ldiag3d
+      real(kind=kind_phys),                    intent(in)    :: dtf, frain, con_g
+      real(kind=kind_phys), dimension(:),      intent(in)    :: rain1, xlat, xlon, tsfc
+      real(kind=kind_phys), dimension(:),      intent(inout) :: ice, snow, graupel, rainc
+      real(kind=kind_phys), dimension(:),      intent(in)    :: rain0, ice0, snow0, graupel0
+      real(kind=kind_phys), dimension(:,:),    intent(in)    :: rann
+      real(kind=kind_phys), dimension(:,:),    intent(in)    :: gt0, prsl, save_t, del
+      real(kind=kind_phys), dimension(:,:),    intent(in)    :: prsi, phii
+      real(kind=kind_phys), dimension(:,:,:),  intent(in)    :: gq0, save_q
+
+      real(kind=kind_phys), dimension(:),      intent(in   ) :: sr
+      real(kind=kind_phys), dimension(:),      intent(inout) :: rain, domr_diag, domzr_diag, domip_diag, doms_diag, tprcp,  &
+                                                                srflag, cnvprcp, totprcp, totice, totsnw, totgrp, cnvprcpb, &
+                                                                totprcpb, toticeb, totsnwb, totgrpb, pwat
+      real(kind=kind_phys), dimension(:),      intent(inout) :: rain_cpl, rainc_cpl, snow_cpl
+
+      real(kind=kind_phys), dimension(:,:,:),   intent(inout) :: dtend
       integer,         dimension(:,:), intent(in)    :: dtidx
 
       ! Stochastic physics / surface perturbations
-      real(kind=kind_phys), dimension(im),      intent(inout) :: drain_cpl
-      real(kind=kind_phys), dimension(im),      intent(inout) :: dsnow_cpl
+      real(kind=kind_phys), dimension(:),      intent(inout) :: drain_cpl, dsnow_cpl
 
       ! Rainfall variables previous time step
       integer, intent(in) :: lsm, lsm_ruc, lsm_noahmp
-      real(kind=kind_phys), dimension(im),      intent(inout) :: raincprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: rainncprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: iceprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: snowprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: graupelprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: draincprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: drainncprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: diceprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: dsnowprv
-      real(kind=kind_phys), dimension(im),      intent(inout) :: dgraupelprv
-
-      real(kind=kind_phys),                     intent(in)    :: dtp
+      real(kind=kind_phys), dimension(:),      intent(inout) :: raincprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: rainncprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: iceprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: snowprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: graupelprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: draincprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: drainncprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: diceprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: dsnowprv
+      real(kind=kind_phys), dimension(:),      intent(inout) :: dgraupelprv
+
+      real(kind=kind_phys),                    intent(in)    :: dtp
 
       ! CCPP error handling
       character(len=*), intent(out) :: errmsg

physics/GFS_MP_generic.meta

@@ -297,7 +297,7 @@
   dimensions = (horizontal_loop_extent)
   type = real
   kind = kind_phys
-  intent = in
+  intent = inout
   optional = F
 [rain1]
   standard_name = lwe_thickness_of_explicit_precipitation_amount