Add namelist control of PIO options

.github/PULL_REQUEST_TEMPLATE.md

@@ -29,4 +29,4 @@ please refer to: <https://github.com/CICE-Consortium/About-Us/wiki/Resource-Inde
     - [ ] No, does the documentation need to be updated at a later time?
         - [ ] Yes
         - [ ] No 
-- [ ] Please provide any additional information or relevant details below:
+- [ ] Please document the changes in detail, including _why_ the changes are made.  This will become part of the PR commit log.

.github/workflows/test-cice.yml

@@ -147,9 +147,11 @@ jobs:
         run: |
           cd $HOME/cice-dirs/input
           wget --progress=dot:giga https://zenodo.org/record/3728358/files/CICE_data_gx3_grid_ic-20200320.tar.gz && tar xvfz CICE_data_gx3_grid_ic-20200320.tar.gz
-          wget --progress=dot:giga https://zenodo.org/record/3728362/files/CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz && tar xvfz CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz
-          wget --progress=dot:giga https://zenodo.org/record/3728364/files/CICE_data_gx3_forcing_JRA55-20200320.tar.gz && tar xvfz CICE_data_gx3_forcing_JRA55-20200320.tar.gz
+          wget --progress=dot:giga https://zenodo.org/records/10419929/files/CICE_data_gx3_forcing_JRA55_200501_20231220.tar.gz && tar xvfz CICE_data_gx3_forcing_JRA55_200501_20231220.tar.gz
           pwd
+          cd CICE_data/forcing/gx3/JRA55/8XDAILY
+          ln -s JRA55_gx3_03hr_forcing_200501.nc JRA55_gx3_03hr_forcing_2005.nc
+          cd $HOME/cice-dirs/input
           ls -alR
 #      - name: run case
 #        run: |

cicecore/cicedyn/analysis/ice_history.F90

@@ -3,7 +3,8 @@
 !
 ! The following variables are currently hard-wired as snapshots
 !   (instantaneous rather than time-averages):
-!   divu, shear, sig1, sig2, sigP, trsig, mlt_onset, frz_onset, hisnap, aisnap
+!   divu, shear, vort, sig1, sig2, sigP, trsig, mlt_onset,
+!   frz_onset, hisnap, aisnap
 !
 ! Options for histfreq: '1','h','d','m','y','x', where x means that
 !   output stream will not be used (recommended for efficiency).
@@ -597,6 +598,7 @@ subroutine init_hist (dt)
       call broadcast_scalar (f_strength, master_task)
       call broadcast_scalar (f_divu, master_task)
       call broadcast_scalar (f_shear, master_task)
+      call broadcast_scalar (f_vort, master_task)
       call broadcast_scalar (f_sig1, master_task)
       call broadcast_scalar (f_sig2, master_task)
       call broadcast_scalar (f_sigP, master_task)
@@ -1312,14 +1314,19 @@ subroutine init_hist (dt)
 
          call define_hist_field(n_divu,"divu","%/day",tstr2D, tcstr, &
              "strain rate (divergence)",                           &
-             "none", secday*c100, c0,                              &
+             "divu is instantaneous, on T grid", secday*c100, c0,                              &
              ns1, f_divu)
 
          call define_hist_field(n_shear,"shear","%/day",tstr2D, tcstr, &
              "strain rate (shear)",                                  &
-             "none", secday*c100, c0,                                &
+             "shear is instantaneous, on T grid", secday*c100, c0,                                &
              ns1, f_shear)
 
+         call define_hist_field(n_vort,"vort","%/day",tstr2D, tcstr, &
+             "strain rate (vorticity)",                                  &
+             "vort is instantaneous, on T grid", secday*c100, c0,                                &
+             ns1, f_vort)
+
          select case (grid_ice)
          case('B')
             description = ", on U grid  (NE corner values)"
@@ -2623,14 +2630,16 @@ subroutine accum_hist (dt)
          if (f_strength(1:1)/= 'x') &
              call accum_hist_field(n_strength,iblk, strength(:,:,iblk), a2D)
 
-! The following fields (divu, shear, sig1, and sig2) will be smeared
+! The following fields (divu, shear, vort, sig1, and sig2) will be smeared
 !  if averaged over more than a few days.
 ! Snapshots may be more useful (see below).
 
 !        if (f_divu   (1:1) /= 'x') &
 !             call accum_hist_field(n_divu,    iblk, divu(:,:,iblk), a2D)
 !        if (f_shear  (1:1) /= 'x') &
 !             call accum_hist_field(n_shear,   iblk, shear(:,:,iblk), a2D)
+!        if (f_vort  (1:1) /= 'x') &
+!             call accum_hist_field(n_vort,    iblk, vort(:,:,iblk), a2D)
 !        if (f_sig1   (1:1) /= 'x') &
 !             call accum_hist_field(n_sig1,    iblk, sig1(:,:,iblk), a2D)
 !        if (f_sig2   (1:1) /= 'x') &
@@ -3967,6 +3976,7 @@ subroutine accum_hist (dt)
               if (.not. tmask(i,j,iblk)) then ! mask out land points
                  if (n_divu     (ns) /= 0) a2D(i,j,n_divu(ns),     iblk) = spval_dbl
                  if (n_shear    (ns) /= 0) a2D(i,j,n_shear(ns),    iblk) = spval_dbl
+                 if (n_vort     (ns) /= 0) a2D(i,j,n_vort(ns),     iblk) = spval_dbl
                  if (n_sig1     (ns) /= 0) a2D(i,j,n_sig1(ns),     iblk) = spval_dbl
                  if (n_sig2     (ns) /= 0) a2D(i,j,n_sig2(ns),     iblk) = spval_dbl
                  if (n_sigP     (ns) /= 0) a2D(i,j,n_sigP(ns),     iblk) = spval_dbl
@@ -3996,6 +4006,8 @@ subroutine accum_hist (dt)
                        divu (i,j,iblk)*avail_hist_fields(n_divu(ns))%cona
                  if (n_shear    (ns) /= 0) a2D(i,j,n_shear(ns),iblk)     = &
                        shear(i,j,iblk)*avail_hist_fields(n_shear(ns))%cona
+                 if (n_vort     (ns) /= 0) a2D(i,j,n_vort(ns),iblk)      = &
+                       vort(i,j,iblk)*avail_hist_fields(n_vort(ns))%cona
                  if (n_sig1     (ns) /= 0) a2D(i,j,n_sig1(ns),iblk)      = &
                        sig1 (i,j,iblk)*avail_hist_fields(n_sig1(ns))%cona
                  if (n_sig2     (ns) /= 0) a2D(i,j,n_sig2(ns),iblk)      = &

cicecore/cicedyn/analysis/ice_history_shared.F90

@@ -4,7 +4,8 @@
 !
 ! The following variables are currently hard-wired as snapshots
 !   (instantaneous rather than time-averages):
-!   divu, shear, sig1, sig2, sigP, trsig, mlt_onset, frz_onset, hisnap, aisnap
+!   divu, shear, vort, sig1, sig2, sigP, trsig, mlt_onset,
+!   frz_onset, hisnap, aisnap
 !
 ! Options for histfreq: '1','h','d','m','y','x', where x means that
 !   output stream will not be used (recommended for efficiency).
@@ -48,18 +49,23 @@ module ice_history_shared
          history_dir   , & ! directory name for history file
          incond_dir        ! directory for snapshot initial conditions
 
-      character (len=char_len_long), public :: &
-         pointer_file      ! input pointer file for restarts
-
       character (len=char_len), public :: &
          version_name
 
       character (len=char_len), public :: &
-         history_format
+         history_format      , & ! history format, cdf1, cdf2, cdf5, etc
+         history_rearranger      ! history file rearranger, box or subset for pio
 
       character (len=char_len), public :: &
          hist_suffix(max_nstrm)  ! appended to 'h' in filename when not 'x'
 
+      integer (kind=int_kind), public :: &
+         history_iotasks     , & ! iotasks, root, stride defines io pes for pio
+         history_root        , & ! iotasks, root, stride defines io pes for pio
+         history_stride      , & ! iotasks, root, stride defines io pes for pio
+         history_deflate     , & ! compression level for hdf5/netcdf4
+         history_chunksize(2) ! chunksize for hdf5/netcdf4
+
       !---------------------------------------------------------------
       ! Instructions for adding a field: (search for 'example')
       !     Here or in ice_history_[process].F90:
@@ -267,7 +273,7 @@ module ice_history_shared
            f_strocnxE  = 'x', f_strocnyE   = 'x', &
            f_strintxE  = 'x', f_strintyE   = 'x', &
            f_taubxE    = 'x', f_taubyE     = 'x', &
-           f_strength  = 'm', &
+           f_strength  = 'm', f_vort       = 'm', &
            f_divu      = 'm', f_shear      = 'm', &
            f_sig1      = 'm', f_sig2       = 'm', &
            f_sigP      = 'm', &
@@ -434,7 +440,7 @@ module ice_history_shared
 !          f_strocnxE,  f_strocnyE , &
 !          f_strintxE,  f_strintyE , &
 !          f_taubxE,    f_taubyE   , &
-           f_strength,  &
+           f_strength,  f_vort     , &
            f_divu,      f_shear    , &
            f_sig1,      f_sig2     , &
            f_sigP,      &
@@ -626,7 +632,7 @@ module ice_history_shared
            n_strocnxE   , n_strocnyE   , &
            n_strintxE   , n_strintyE   , &
            n_taubxE     , n_taubyE     , &
-           n_strength   , &
+           n_strength   , n_vort       , &
            n_divu       , n_shear      , &
            n_sig1       , n_sig2       , &
            n_sigP       , &

cicecore/cicedyn/dynamics/ice_dyn_eap.F90

@@ -109,7 +109,7 @@ subroutine eap (dt)
           seabed_stress_factor_LKD, seabed_stress_factor_prob, &
           seabed_stress_method, seabed_stress, &
           stack_fields, unstack_fields, iceTmask, iceUmask, &
-          fld2, fld3, fld4
+          fld2, fld3, fld4, dxhy, dyhx, cxp, cyp, cxm, cym
       use ice_flux, only: rdg_conv, strairxT, strairyT, &
           strairxU, strairyU, uocn, vocn, ss_tltx, ss_tlty, fmU, &
           strtltxU, strtltyU, strocnxU, strocnyU, strintxU, strintyU, taubxU, taubyU, &
@@ -118,10 +118,10 @@ subroutine eap (dt)
           stressp_1, stressp_2, stressp_3, stressp_4, &
           stressm_1, stressm_2, stressm_3, stressm_4, &
           stress12_1, stress12_2, stress12_3, stress12_4
-      use ice_grid, only: tmask, umask, dxT, dyT, dxhy, dyhx, cxp, cyp, cxm, cym, &
+      use ice_grid, only: tmask, umask, dxT, dyT, dxU, dyU, &
           tarear, uarear, grid_average_X2Y, &
           grid_atm_dynu, grid_atm_dynv, grid_ocn_dynu, grid_ocn_dynv
-      use ice_state, only: aice, aiU, vice, vsno, uvel, vvel, divu, shear, &
+      use ice_state, only: aice, aiU, vice, vsno, uvel, vvel, divu, shear, vort, &
           aice_init, aice0, aicen, vicen, strength
       use ice_timers, only: timer_dynamics, timer_bound, &
           ice_timer_start, ice_timer_stop
@@ -195,6 +195,7 @@ subroutine eap (dt)
             rdg_shear(i,j,iblk) = c0 ! always zero. Could be moved
             divu (i,j,iblk) = c0
             shear(i,j,iblk) = c0
+            vort(i,j,iblk)  = c0
             e11(i,j,iblk) = c0
             e12(i,j,iblk) = c0
             e22(i,j,iblk) = c0
@@ -433,6 +434,7 @@ subroutine eap (dt)
                               arlx1i,               denom1,               &
                               uvel      (:,:,iblk), vvel      (:,:,iblk), &
                               dxT       (:,:,iblk), dyT       (:,:,iblk), &
+                              dxU       (:,:,iblk), dyU       (:,:,iblk), &
                               dxhy      (:,:,iblk), dyhx      (:,:,iblk), &
                               cxp       (:,:,iblk), cyp       (:,:,iblk), &
                               cxm       (:,:,iblk), cym       (:,:,iblk), &
@@ -448,6 +450,7 @@ subroutine eap (dt)
                               stress12_1(:,:,iblk), stress12_2(:,:,iblk), &
                               stress12_3(:,:,iblk), stress12_4(:,:,iblk), &
                               shear     (:,:,iblk), divu      (:,:,iblk), &
+                              vort      (:,:,iblk),                       &
                               e11       (:,:,iblk), e12       (:,:,iblk), &
                               e22       (:,:,iblk),                       &
                               s11       (:,:,iblk), s12       (:,:,iblk), &
@@ -1162,6 +1165,7 @@ subroutine stress_eap  (nx_block,   ny_block,       &
                               arlx1i,     denom1,         &
                               uvel,       vvel,           &
                               dxT,        dyT,            &
+                              dxU,        dyU,            &
                               dxhy,       dyhx,           &
                               cxp,        cyp,            &
                               cxm,        cym,            &
@@ -1175,6 +1179,7 @@ subroutine stress_eap  (nx_block,   ny_block,       &
                               stress12_1, stress12_2,     &
                               stress12_3, stress12_4,     &
                               shear,      divu,           &
+                              vort,                       &
                               e11,        e12,            &
                               e22,                        &
                               s11,        s12,            &
@@ -1206,6 +1211,8 @@ subroutine stress_eap  (nx_block,   ny_block,       &
          vvel     , & ! y-component of velocity (m/s)
          dxT      , & ! width of T-cell through the middle (m)
          dyT      , & ! height of T-cell through the middle (m)
+         dxU      , & ! width of U-cell through the middle (m)
+         dyU      , & ! height of U-cell through the middle (m)
          dxhy     , & ! 0.5*(HTE - HTW)
          dyhx     , & ! 0.5*(HTN - HTS)
          cyp      , & ! 1.5*HTE - 0.5*HTW
@@ -1226,6 +1233,7 @@ subroutine stress_eap  (nx_block,   ny_block,       &
       real (kind=dbl_kind), dimension (nx_block,ny_block), intent(inout) :: &
          shear    , & ! strain rate II component (1/s)
          divu     , & ! strain rate I component, velocity divergence (1/s)
+         vort     , & ! vorticity (1/s)
          e11      , & ! components of strain rate tensor (1/s)
          e12      , & !
          e22      , & !
@@ -1255,6 +1263,7 @@ subroutine stress_eap  (nx_block,   ny_block,       &
          divune, divunw, divuse, divusw            , & ! divergence
          tensionne, tensionnw, tensionse, tensionsw, & ! tension
          shearne, shearnw, shearse, shearsw        , & ! shearing
+         dvdxn, dvdxs, dudye, dudyw                , & ! for vorticity calc
          ssigpn, ssigps, ssigpe, ssigpw            , &
          ssigmn, ssigms, ssigme, ssigmw            , &
          ssig12n, ssig12s, ssig12e, ssig12w        , &
@@ -1357,6 +1366,13 @@ subroutine stress_eap  (nx_block,   ny_block,       &
                  (tensionne + tensionnw + tensionse + tensionsw)**2 &
                 +  (shearne +   shearnw +   shearse +   shearsw)**2)
 
+            ! vorticity
+            dvdxn = dyU(i,j)*vvel(i,j) - dyU(i-1,j)*vvel(i-1,j)
+            dvdxs = dyU(i,j-1)*vvel(i,j-1) - dyU(i-1,j-1)*vvel(i-1,j-1)
+            dudye = dxU(i,j)*uvel(i,j) - dxU(i,j-1)*uvel(i,j-1)
+            dudyw = dxU(i-1,j)*uvel(i-1,j) - dxU(i-1,j-1)*uvel(i-1,j-1)
+            vort(i,j) = p5*tarear(i,j)*(dvdxn + dvdxs - dudye - dudyw)
+
             divu(i,j) = p25*(divune + divunw + divuse + divusw) * tarear(i,j)
             rdg_conv(i,j)  = -min(p25*(alpharne + alpharnw &
                                      + alpharsw + alpharse),c0) * tarear(i,j)