(regcm-core) : fix for idynamic 3 in ICBC for correct geolocation of staggered wind components, add option --enable-parallel-nc to test NC3 parallel output through Parallel NetCDF inside NetCDF, fix surface ps error in idynamic 1. Add hash module. Small development in moloch code.

Author: graziano-giuliani

Main/Makefile.am

@@ -135,7 +135,7 @@ mod_bdycod.o : mod_bdycod.F90 mod_atm_interface.o mod_che_interface.o mod_dynpar
 mod_che_interface.o : mod_che_interface.F90 mod_atm_interface.o mod_rad_interface.o mod_che_bdyco.o mod_che_bionit.o mod_che_carbonaer.o mod_che_common.o mod_che_cumtran.o mod_che_drydep.o mod_che_dust.o mod_che_emission.o mod_che_linox.o mod_che_indices.o mod_che_mppio.o mod_che_ncio.o mod_che_param.o mod_che_species.o mod_che_start.o mod_che_tend.o mod_realkinds.o mod_runparams.o mod_regcm_types.o
 mod_cu_interface.o : mod_cu_interface.F90 mod_atm_interface.o mod_che_interface.o mod_cu_bm.o mod_cu_common.o mod_cu_em.o mod_cu_grell.o mod_cu_kf.o mod_cu_kuo.o mod_cu_tables.o mod_cu_tiedtke.o mod_dynparam.o mod_intkinds.o mod_memutil.o mod_realkinds.o mod_regcm_types.o mod_runparams.o mod_regcm_types.o mod_constants.o mod_cu_bm.o mod_cu_common.o mod_cu_em.o mod_cu_grell.o mod_cu_kuo.o mod_cu_tables.o mod_cu_tiedtke.o mod_cu_kf.o mod_cu_shallow.o mod_realkinds.o mod_mppparam.o clwfromt.inc
 mod_diffusion.o : mod_diffusion.F90 mod_atm_interface.o mod_dynparam.o mod_intkinds.o mod_memutil.o mod_mppparam.o mod_realkinds.o mod_runparams.o mod_service.o mod_constants.o
-mod_header.o : mod_header.F90 mod_constants.o mod_date.o mod_intkinds.o mod_mppparam.o mod_realkinds.o mod_stdio.o $(REGCM_ROOT)/version
+mod_header.o : mod_header.F90 mod_constants.o mod_date.o mod_intkinds.o mod_dynparam.o mod_mppparam.o mod_realkinds.o mod_stdio.o $(REGCM_ROOT)/version
 mod_init.o : mod_init.F90 mod_atm_interface.o mod_bdycod.o mod_che_interface.o mod_constants.o mod_cu_interface.o mod_dynparam.o mod_intkinds.o mod_lm_interface.o mod_mpmessage.o mod_mppparam.o mod_ncio.o mod_outvars.o mod_pbl_interface.o mod_micro_interface.o mod_rad_interface.o mod_realkinds.o mod_runparams.o mod_savefile.o mod_service.o mod_slabocean.o mod_sun.o rrtmg_lw_init.o rrtmg_sw_init.o mod_slice.o mod_diffusion.o mod_sound.o mod_massck.o pfesat.inc pfwsat.inc clwfromt.inc
 if DO_COMPILE_LIBCLM
 mod_lm_interface.o : mod_lm_interface.F90 clm_time_manager.o clm_varctl.o clm_varsur.o mod_atm_interface.o mod_bats_common.o mod_che_common.o mod_che_interface.o mod_clm.o mod_memutil.o mod_mpmessage.o mod_mppparam.o mod_mtrxclm.o mod_ocn_common.o mod_outvars.o mod_regcm_types.o mod_runparams.o mod_service.o perf_mod.o restFileMod.o spmdMod.o pfesat.inc pfwsat.inc wlh.inc evpt.inc
@@ -151,9 +151,9 @@ mod_ncio.o : mod_ncio.F90 mod_domain.o mod_dynparam.o mod_ensemble.o mod_memutil
 mod_oasis.o : mod_oasis.F90 mod_atm_interface.o mod_realkinds.o
 mod_output.o : mod_output.F90 mod_atm_interface.o mod_bdycod.o mod_capecin.o mod_che_interface.o mod_che_output.o mod_cu_interface.o mod_dynparam.o mod_header.o mod_intkinds.o mod_lm_interface.o mod_mpmessage.o mod_mppparam.o mod_ncout.o mod_pbl_interface.o mod_micro_interface.o mod_rad_interface.o mod_realkinds.o mod_runparams.o mod_savefile.o mod_service.o mod_slabocean.o mod_split.o pfwsat.inc pfesat.inc
 if DO_COMPILE_LIBCLM45
-mod_params.o : mod_params.F90 mod_advection.o mod_atm_interface.o mod_bdycod.o mod_che_interface.o mod_clm_regcm.o mod_cu_interface.o mod_domain.o mod_lm_interface.o mod_mpmessage.o mod_mppparam.o mod_ncio.o mod_ncout.o mod_pbl_interface.o mod_micro_interface.o mod_rad_interface.o mod_runparams.o mod_savefile.o mod_service.o mod_slabocean.o mod_sldepparam.o mod_slice.o mod_split.o mod_tendency.o mod_nhinterp.o mod_diffusion.o mod_sladvection.o mod_timer.o
+mod_params.o : mod_params.F90 mod_advection.o mod_atm_interface.o mod_bdycod.o mod_che_interface.o mod_clm_regcm.o mod_cu_interface.o mod_domain.o mod_lm_interface.o mod_mpmessage.o mod_mppparam.o mod_ncio.o mod_ncout.o mod_pbl_interface.o mod_micro_interface.o mod_rad_interface.o mod_runparams.o mod_savefile.o mod_service.o mod_slabocean.o mod_sldepparam.o mod_slice.o mod_split.o mod_tendency.o mod_nhinterp.o mod_diffusion.o mod_sladvection.o mod_timer.o mod_moloch.o
 else
-mod_params.o : mod_params.F90 mod_advection.o mod_atm_interface.o mod_bdycod.o mod_che_interface.o mod_cu_interface.o mod_domain.o mod_lm_interface.o mod_mpmessage.o mod_mppparam.o mod_ncio.o mod_ncout.o mod_pbl_interface.o mod_micro_interface.o mod_rad_interface.o mod_runparams.o mod_savefile.o mod_service.o mod_slabocean.o mod_sldepparam.o mod_slice.o mod_split.o mod_tendency.o mod_nhinterp.o mod_sound.o mod_diffusion.o mod_sladvection.o mod_timer.o
+mod_params.o : mod_params.F90 mod_advection.o mod_atm_interface.o mod_bdycod.o mod_che_interface.o mod_cu_interface.o mod_domain.o mod_lm_interface.o mod_mpmessage.o mod_mppparam.o mod_ncio.o mod_ncout.o mod_pbl_interface.o mod_micro_interface.o mod_rad_interface.o mod_runparams.o mod_savefile.o mod_service.o mod_slabocean.o mod_sldepparam.o mod_slice.o mod_split.o mod_tendency.o mod_nhinterp.o mod_sound.o mod_diffusion.o mod_sladvection.o mod_timer.o mod_moloch.o
 endif
 mod_pbl_interface.o : mod_pbl_interface.F90 mod_atm_interface.o mod_che_common.o mod_che_interface.o mod_constants.o mod_dynparam.o mod_memutil.o mod_mppparam.o mod_pbl_common.o mod_pbl_holtbl.o mod_pbl_uwtcm.o mod_realkinds.o mod_regcm_types.o mod_runparams.o mod_service.o mod_pbl_gfs.o mod_pbl_myj.o
 mod_micro_interface.o : mod_micro_interface.F90 mod_realkinds.o mod_service.o mod_constants.o mod_dynparam.o mod_memutil.o mod_mppparam.o mod_regcm_types.o mod_runparams.o mod_micro_nogtom.o mod_micro_subex.o mod_micro_wsm5.o mod_cloud_subex.o mod_cloud_xuran.o mod_cloud_thomp.o mod_cloud_guli2007.o pfesat.inc pfwsat.inc clwfromt.inc mod_atm_interface.o mod_che_interface.o wlh.inc

Main/mod_atm_interface.F90

@@ -770,7 +770,7 @@ subroutine allocate_domain(dom)
       call getmem2d(dom%dlat,jde1,jde2,ide1,ide2,'storage:dlat')
       call getmem2d(dom%dlon,jde1,jde2,ide1,ide2,'storage:dlon')
       if ( idynamic == 3 ) then
-        call getmem2d(dom%clv,jce1,jce2,ice1,ice2,'storage:clv')
+        call getmem2d(dom%clv,jce1,jce2,ice1ga,ice2ga,'storage:clv')
         call getmem2d(dom%fmyu,jce1,jce2,ice1,ice2,'storage:fmyu')
       end if
       call getmem2d(dom%msfx,jd1,jd2,id1,id2,'storage:msfx')

Main/mod_header.F90

@@ -24,6 +24,7 @@ module mod_header
   use mod_constants
   use mod_mppparam
   use mod_date
+  use mod_dynparam , only : nproc
   use mod_stdio
 
   implicit none
@@ -116,6 +117,7 @@ subroutine finaltime(myid)
       write(cdata,'(i0.4,"-",i0.2,"-",i0.2," ",i0.2,":",i0.2,":",i0.2,a)') &
             tval(1), tval(2), tval(3), tval(5), tval(6), tval(7), czone
       write (stdout,*) ': this run stops at  : ', trim(cdata)
+      write (stdout,*) ': Run has been completed using ', nproc, ' processors.'
       write (stdout,*) ': Total elapsed seconds of run : ', &
                 (finish_time - start_time)
     end if

Main/mod_moloch.F90

@@ -58,6 +58,8 @@ module mod_moloch
   real(rkx) , pointer , dimension(:,:,:) :: ux , vx , wx
   real(rkx) , pointer , dimension(:,:,:) :: tkex
 
+  public allocate_moloch
+
   contains
 
 #include <cpmf.inc>
@@ -137,8 +139,9 @@ end subroutine filt3d
 
       subroutine advection
         implicit none
-        integer(ik4) :: i , j , k
+        integer(ik4) :: i , j , k , n
         real(rkx) :: dz
+        real(rkx) , pointer , dimension(:,:,:) :: ptr
 
         dz = hzita / real(kz,rkx)
 
@@ -243,10 +246,22 @@ subroutine advection
                     mddom%clv,mddom%fmyu)
         call wafone(wx,mo_atm%u,mo_atm%v,dx,dx,dz,dt, &
                     mddom%clv,mddom%fmyu)
+        do n = 1 , nqx
+          call assignpnt(mo_atm%qx,ptr,n)
+          call wafone(ptr,mo_atm%u,mo_atm%v,dx,dx,dz,dt, &
+                      mddom%clv,mddom%fmyu)
+        end do
         if ( ibltyp == 2 ) then
           call wafone(tkex,mo_atm%u,mo_atm%v,dx,dx,dz,dt, &
                       mddom%clv,mddom%fmyu)
         end if
+        if ( ichem == 1 ) then
+          do n = 1 , ntr
+            call assignpnt(mo_atm%trac,ptr,n)
+            call wafone(ptr,mo_atm%u,mo_atm%v,dx,dx,dz,dt, &
+                        mddom%clv,mddom%fmyu)
+          end do
+        end if
 
         call exchange_lr(ux,2,jce1,jce2,ice1,ice2,1,kz)
         call exchange_bt(vx,2,jce1,jce2,ice1,ice2,1,kz)

Main/mod_params.F90

@@ -48,6 +48,7 @@ module mod_params
   use mod_sldepparam
   use mod_sound
   use mod_timer
+  use mod_moloch
   use mod_timefilter
 
   implicit none
@@ -622,52 +623,56 @@ subroutine param
 #endif
       end if
 
-      upstream_mode = .true.
-      stability_enhance = .true.
-      if ( idynamic == 2 ) then
-        gnu1 = 0.1000_rkx
-        gnu2 = 0.1000_rkx
-        diffu_hgtf = 0
-      else
-        gnu1 = 0.0625_rkx
-        gnu2 = 0.0625_rkx
-        diffu_hgtf = 1
-      end if
-      ckh = 1.0_rkx
-      adyndif = 1.0_rkx
-      uoffc = 0.250_rkx
-      t_extrema = 5.0_rkx
-      q_rel_extrema = 0.20_rkx
-      rewind(ipunit)
-      read (ipunit, nml=dynparam, iostat=iretval, err=104)
-      if ( iretval /= 0 ) then
-        write(stdout,*) 'Using default dynamical parameters.'
-#ifdef DEBUG
-      else
-        write(stdout,*) 'Read dynparam OK'
-#endif
-      end if
-
-      if ( idynamic == 2 ) then
+      if ( idynamic < 3 ) then
+        upstream_mode = .true.
+        stability_enhance = .true.
+        if ( idynamic == 2 ) then
+          gnu1 = 0.1000_rkx
+          gnu2 = 0.1000_rkx
+          diffu_hgtf = 0
+        else if ( idynamic == 1 ) then
+          gnu1 = 0.0625_rkx
+          gnu2 = 0.0625_rkx
+          diffu_hgtf = 1
+        end if
+        ckh = 1.0_rkx
+        adyndif = 1.0_rkx
+        uoffc = 0.250_rkx
+        t_extrema = 5.0_rkx
+        q_rel_extrema = 0.20_rkx
         rewind(ipunit)
-        read (ipunit, nml=nonhydroparam, iostat=iretval, err=105)
+        read (ipunit, nml=dynparam, iostat=iretval, err=104)
         if ( iretval /= 0 ) then
-          write(stdout,*) 'Using default non-hydrostatc parameters.'
+          write(stdout,*) 'Using default dynamical parameters.'
 #ifdef DEBUG
         else
-          write(stdout,*) 'Read nonhydroparam OK'
+          write(stdout,*) 'Read dynparam OK'
 #endif
         end if
-      else
-        rewind(ipunit)
-        read (ipunit, nml=hydroparam, iostat=iretval, err=106)
-        if ( iretval /= 0 ) then
-          write(stdout,*) 'Using default hydrostatc parameters.'
+
+        if ( idynamic == 2 ) then
+          rewind(ipunit)
+          read (ipunit, nml=nonhydroparam, iostat=iretval, err=105)
+          if ( iretval /= 0 ) then
+            write(stdout,*) 'Using default non-hydrostatc parameters.'
 #ifdef DEBUG
-        else
-          write(stdout,*) 'Read hydroparam OK'
+          else
+            write(stdout,*) 'Read nonhydroparam OK'
 #endif
+          end if
+        else if ( idynamic == 1 ) then
+          rewind(ipunit)
+          read (ipunit, nml=hydroparam, iostat=iretval, err=106)
+          if ( iretval /= 0 ) then
+            write(stdout,*) 'Using default hydrostatc parameters.'
+#ifdef DEBUG
+          else
+            write(stdout,*) 'Read hydroparam OK'
+#endif
+          end if
         end if
+      else
+        ! Moloch dynamic
       end if
 
       ! Hack. permanently disable seasonal albedo.
@@ -1108,7 +1113,9 @@ subroutine param
     call bcast(ichem)
     call bcast(ntr)
 
-    if ( idynamic == 2 ) then
+    if ( idynamic == 3 ) then
+      ! Moloch paramters here
+    else if ( idynamic == 2 ) then
       call bcast(base_state_pressure)
       call bcast(logp_lrate)
       call bcast(ifupr)
@@ -1519,6 +1526,8 @@ subroutine param
 
     if ( idynamic == 2 ) then
       call allocate_mod_sound
+    else if ( idynamic == 3 ) then
+      call allocate_moloch
     end if
 
     call allocate_mod_diffusion
@@ -2396,6 +2405,8 @@ subroutine param
     if ( idynamic == 2 ) then
       call make_reference_atmosphere
       call compute_full_coriolis_coefficients
+    else if ( idynamic == 3 ) then
+      call compute_latfac
     end if
 
     if ( iboudy < 0 .or. iboudy > 5 ) then
@@ -2624,6 +2635,17 @@ subroutine compute_full_coriolis_coefficients
         end if
       end subroutine compute_full_coriolis_coefficients
 
+      subroutine compute_latfac
+        implicit none
+        integer :: i , j
+        do i = ice1 , ice2
+          do j = jce1 , jce2
+            mddom%clv(j,i) = cos(mddom%xlat(j,i))
+            mddom%clv(j,i) = 1.0_rkx/cos(mddom%xlat(j,i))
+          end do
+        end do
+      end subroutine compute_latfac
+
       recursive integer function gcd_rec(u,v) result(gcd)
         implicit none
         integer , intent(in) :: u , v

Main/mpplib/mod_regcm_types.F90

@@ -127,6 +127,8 @@ module mod_regcm_types
     real(rkx) , pointer , dimension(:,:,:) :: pai
     real(rkx) , pointer , dimension(:,:,:) :: tetav
     real(rkx) , pointer , dimension(:,:,:) :: tke
+    real(rkx) , pointer , dimension(:,:,:,:) :: qx
+    real(rkx) , pointer , dimension(:,:,:,:) :: trac
   end type atmosphere
 
   type reference_atmosphere

PreProc/ICBC/mod_write.F90

@@ -229,6 +229,10 @@ subroutine writef(idate)
     integer(ik4) :: ivar , k
     real(rkx) :: dx
 
+    if ( idynamic == 1 ) then
+      ps4 = (ps4+ptop)*d_10
+    end if
+
     if ( idynamic == 2 ) then
       dx = ds * d_1000
       call meandiv(u4,v4,pd4,msfd,sigmah,dsigma,jx,iy,kz,dx,jx-1,iy-1)

PreProc/Terrain/mod_maps.F90

@@ -25,7 +25,7 @@ module mod_maps
 
   real(rkx) , pointer , dimension(:,:) :: coriol , dlat , dlon ,   &
                    dmap , htgrid , lndout , mask , dpth , snowam , &
-                   smoist , texout , xlat , xlon , xmap , ps0
+                   smoist , texout , xlat , xlon , xmap , ps0 , askip
   real(rkx) , pointer , dimension(:,:,:) :: frac_tex , rmoist
   real(rkx) , pointer , dimension(:,:,:) :: pr0 , t0 , rho0 , z0
   real(rkx) , pointer , dimension(:,:,:) :: zeta , fmz
@@ -72,6 +72,7 @@ subroutine prepare_grid(jx,iy,kz,ntex,nsoil,idyn)
       call getmem3d(rho0,1,jx,1,iy,1,kz+1,'maps:rho0')
       call getmem3d(z0,1,jx,1,iy,1,kz+1,'maps:z0')
     else if ( idyn == 3 ) then
+      call getmem2d(askip,1,jx,1,iy,'maps:askip')
       call getmem1d(zita,1,kz+1,'maps:zita')
       call getmem1d(ak,1,kz+1,'maps:ak')
       call getmem1d(bk,1,kz+1,'maps:bk')