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cicecore: correct initial condition metadata (CICE-Consortium#818)
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* ice_history_write: fix initial condition metadata under 'hist_avg'

When writing averaged history outputs (hist_avg=.true.), this setting
also affects the initial condition. Even if the actual data variables
written to the initial condition are not averaged (they are taken
more or less directly from the restart or the hard-coded defaults,
modulo aggregation over categories), their attributes ('cell_method' and
'time_rep') imply they are averaged, and the 'bound' attribute of the
'time' variable refers to the 'time_bounds' variable.

Make the metadata of the initial condition more correct by:
- not writing the 'time_bounds' variable (and the corresponding 'd2' dimension)
- not writing the 'bounds' attribute of the 'time' variable
- not writing the 'cell_method' attributes of each variable
- writing the 'time_rep' attribute of each variable as 'instantaneous'
instead of 'averaged'.

Do this by checking 'write_ic' at all places where we check for the
value of 'hist_avg' to write the above variables and attributes in each
of the 3 IO backends (binary, netcdf, pio2).

* drivers/{nemo_concepts,standalone}: write initial condition at initial time

In CICE_InitMod::cice_init, we call ice_calendar::advance_timestep
before writing the initial condition, such that the 'time' variable in
the initial condition is not zero; it has a value of 1*dt (the model
time step). The initial condition filename also reflects this, since
'msec' (model seconds) also has a value of 1*dt and is used in
ice_history_shared::construct_filename. This leads to the initial
condition filename not corresponding to the model initialization
date/time but rather 1*dt later.

Since we call 'accum_hist' after initializing the forcing, any forcing
field written to the initial condition has values corresponding to
msec=dt, whereas the ice state corresponds to msec=0, leading to an
inconsistency.

Fix that by calling 'accum_hist' to write the initial condition _before_
calling 'advance_timestep'. Since we now call 'accum_hist' before
initializing the forcing, any forcing field written to the initial
condition have its default, hard-coded value, instead of its value at
time=dt. An improvement would be to read the forcing at time=dt, write
the initial condition, advance the time step, and read the forcing
again, but let's not complicate things too much for now.

(cherry picked from commit 9a55ad9)

Cherry-pick notes:

There were some conflicts in io_{netcdf,pio2}/ice_history_write.F90 due
to 26d917a (Fix QC test, fix bug in history time axis, fix history
output averaging for timestep output (CICE-Consortium#624), 2021-08-19), since that
commit enabled averaging over multiple time steps and thus removed the
assumption that histfreq(ns) = '1' means hist_avg = .false.. I also had
to add additional changes to 'ice_history_write'  in the conditions that
are checked before writing the NetCDF attributes since we do not yet
have the 'ice_write_hist_attrs' subroutine added in 078aab4 (Merge
cgridDEV branch including C grid implementation and other fixes (CICE-Consortium#715),
2022-05-10).

Closes: https://gitlab.science.gc.ca/concepts/CICE/issues/19
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@phil-blain
phil-blain committed Mar 16, 2023
1 parent 9ffccf4 commit f52140e
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17 changes: 9 additions & 8 deletions cicecore/cicedynB/infrastructure/io/io_binary/ice_history_write.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -158,6 +158,7 @@ subroutine ice_write_hist(ns)
trim(avail_hist_fields(n)%vcomment)

if (histfreq(ns) == '1' .or. .not. hist_avg &
.or. write_ic &
.or. n==n_divu(ns) .or. n==n_shear(ns) & ! snapshots
.or. n==n_sig1(ns) .or. n==n_sig2(ns) &
.or. n==n_sigP(ns) .or. n==n_trsig(ns) &
Expand Down Expand Up @@ -186,7 +187,7 @@ subroutine ice_write_hist(ns)
write (nu_hdr, 994) nrec,trim(avail_hist_fields(n)%vname), &
trim(avail_hist_fields(n)%vdesc),trim(avail_hist_fields(n)%vunit),nn

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
write (nu_hdr, 996) nrec,trim(avail_hist_fields(n)%vname), &
'time_rep','instantaneous'
else
Expand All @@ -210,7 +211,7 @@ subroutine ice_write_hist(ns)
write (nu_hdr, 993) nrec,trim(avail_hist_fields(n)%vname), &
trim(avail_hist_fields(n)%vdesc),trim(avail_hist_fields(n)%vunit),k

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
write (nu_hdr, 996) nrec,trim(avail_hist_fields(n)%vname), &
'time_rep','instantaneous'
else
Expand All @@ -234,7 +235,7 @@ subroutine ice_write_hist(ns)
write (nu_hdr, 993) nrec,trim(avail_hist_fields(n)%vname), &
trim(avail_hist_fields(n)%vdesc),trim(avail_hist_fields(n)%vunit),nn,k

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
write (nu_hdr, 996) nrec,trim(avail_hist_fields(n)%vname), &
'time_rep','instantaneous'
else
Expand All @@ -258,7 +259,7 @@ subroutine ice_write_hist(ns)
write (nu_hdr, 993) nrec,trim(avail_hist_fields(n)%vname), &
trim(avail_hist_fields(n)%vdesc),trim(avail_hist_fields(n)%vunit),nn,k

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
write (nu_hdr, 996) nrec,trim(avail_hist_fields(n)%vname), &
'time_rep','instantaneous'
else
Expand All @@ -282,7 +283,7 @@ subroutine ice_write_hist(ns)
write (nu_hdr, 993) nrec,trim(avail_hist_fields(n)%vname), &
trim(avail_hist_fields(n)%vdesc),trim(avail_hist_fields(n)%vunit),nn,k

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
write (nu_hdr, 996) nrec,trim(avail_hist_fields(n)%vname), &
'time_rep','instantaneous'
else
Expand All @@ -307,7 +308,7 @@ subroutine ice_write_hist(ns)
write (nu_hdr, 993) nrec,trim(avail_hist_fields(n)%vname), &
trim(avail_hist_fields(n)%vdesc),trim(avail_hist_fields(n)%vunit),nn,k

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
write (nu_hdr, 996) nrec,trim(avail_hist_fields(n)%vname), &
'time_rep','instantaneous'
else
Expand All @@ -333,7 +334,7 @@ subroutine ice_write_hist(ns)
write (nu_hdr, 993) nrec,trim(avail_hist_fields(n)%vname), &
trim(avail_hist_fields(n)%vdesc),trim(avail_hist_fields(n)%vunit),nn,k

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
write (nu_hdr, 996) nrec,trim(avail_hist_fields(n)%vname), &
'time_rep','instantaneous'
else
Expand All @@ -359,7 +360,7 @@ subroutine ice_write_hist(ns)
write (nu_hdr, 993) nrec,trim(avail_hist_fields(n)%vname), &
trim(avail_hist_fields(n)%vdesc),trim(avail_hist_fields(n)%vunit),nn,k

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
write (nu_hdr, 996) nrec,trim(avail_hist_fields(n)%vname), &
'time_rep','instantaneous'
else
Expand Down
27 changes: 14 additions & 13 deletions cicecore/cicedynB/infrastructure/io/io_netcdf/ice_history_write.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ subroutine ice_write_hist (ns)
! define dimensions
!-----------------------------------------------------------------

if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
status = nf90_def_dim(ncid,'d2',2,boundid)
if (status /= nf90_noerr) call abort_ice(subname// &
'ERROR: defining dim d2')
Expand Down Expand Up @@ -237,7 +237,7 @@ subroutine ice_write_hist (ns)
call abort_ice(subname//'ERROR: invalid calendar settings')
endif

if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
status = nf90_put_att(ncid,varid,'bounds','time_bounds')
if (status /= nf90_noerr) call abort_ice(subname// &
'ERROR: time bounds')
Expand All @@ -247,7 +247,7 @@ subroutine ice_write_hist (ns)
! Define attributes for time bounds if hist_avg is true
!-----------------------------------------------------------------

if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
dimid(1) = boundid
dimid(2) = timid
status = nf90_def_var(ncid,'time_bounds',lprecision,dimid(1:2),varid)
Expand Down Expand Up @@ -563,7 +563,7 @@ subroutine ice_write_hist (ns)
!-----------------------------------------------------------------
! Add cell_methods attribute to variables if averaged
!-----------------------------------------------------------------
if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
if (TRIM(avail_hist_fields(n)%vname)/='sig1' &
.or.TRIM(avail_hist_fields(n)%vname)/='sig2' &
.or.TRIM(avail_hist_fields(n)%vname)/='sistreave' &
Expand All @@ -576,6 +576,7 @@ subroutine ice_write_hist (ns)
endif

if (histfreq(ns) == '1' .or. .not. hist_avg &
.or. write_ic &
.or. n==n_divu(ns) .or. n==n_shear(ns) & ! snapshots
.or. n==n_sig1(ns) .or. n==n_sig2(ns) &
.or. n==n_sigP(ns) .or. n==n_trsig(ns) &
Expand Down Expand Up @@ -634,13 +635,13 @@ subroutine ice_write_hist (ns)
!-----------------------------------------------------------------
! Add cell_methods attribute to variables if averaged
!-----------------------------------------------------------------
if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
status = nf90_put_att(ncid,varid,'cell_methods','time: mean')
if (status /= nf90_noerr) call abort_ice(subname// &
'ERROR: defining cell methods for '//avail_hist_fields(n)%vname)
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = nf90_put_att(ncid,varid,'time_rep','instantaneous')
else
status = nf90_put_att(ncid,varid,'time_rep','averaged')
Expand Down Expand Up @@ -875,13 +876,13 @@ subroutine ice_write_hist (ns)
!-----------------------------------------------------------------
! Add cell_methods attribute to variables if averaged
!-----------------------------------------------------------------
if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
status = nf90_put_att(ncid,varid,'cell_methods','time: mean')
if (status /= nf90_noerr) call abort_ice(subname// &
'ERROR: defining cell methods for '//avail_hist_fields(n)%vname)
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = nf90_put_att(ncid,varid,'time_rep','instantaneous')
else
status = nf90_put_att(ncid,varid,'time_rep','averaged')
Expand Down Expand Up @@ -936,13 +937,13 @@ subroutine ice_write_hist (ns)
!-----------------------------------------------------------------
! Add cell_methods attribute to variables if averaged
!-----------------------------------------------------------------
if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
status = nf90_put_att(ncid,varid,'cell_methods','time: mean')
if (status /= nf90_noerr) call abort_ice(subname// &
'ERROR: defining cell methods for '//avail_hist_fields(n)%vname)
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = nf90_put_att(ncid,varid,'time_rep','instantaneous')
else
status = nf90_put_att(ncid,varid,'time_rep','averaged')
Expand Down Expand Up @@ -997,13 +998,13 @@ subroutine ice_write_hist (ns)
!-----------------------------------------------------------------
! Add cell_methods attribute to variables if averaged
!-----------------------------------------------------------------
if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
status = nf90_put_att(ncid,varid,'cell_methods','time: mean')
if (status /= nf90_noerr) call abort_ice(subname// &
'ERROR: defining cell methods for '//avail_hist_fields(n)%vname)
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = nf90_put_att(ncid,varid,'time_rep','instantaneous')
else
status = nf90_put_att(ncid,varid,'time_rep','averaged')
Expand Down Expand Up @@ -1098,7 +1099,7 @@ subroutine ice_write_hist (ns)
! write time_bounds info
!-----------------------------------------------------------------

if (hist_avg) then
if (hist_avg .and. .not. write_ic) then
status = nf90_inq_varid(ncid,'time_bounds',varid)
if (status /= nf90_noerr) call abort_ice(subname// &
'ERROR: getting time_bounds id')
Expand Down
43 changes: 22 additions & 21 deletions cicecore/cicedynB/infrastructure/io/io_pio2/ice_history_write.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,7 @@ subroutine ice_write_hist (ns)
! define dimensions
!-----------------------------------------------------------------

if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_def_dim(File,'d2',2,boundid)
endif

Expand Down Expand Up @@ -224,12 +224,12 @@ subroutine ice_write_hist (ns)
call abort_ice(subname//'ERROR: invalid calendar settings')
endif

if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'bounds','time_bounds')
endif

! Define attributes for time_bounds if hist_avg is true
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
dimid2(1) = boundid
dimid2(2) = timid
!sgl status = pio_def_var(File,'time_bounds',pio_real,dimid2,varid)
Expand Down Expand Up @@ -473,7 +473,7 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
if (TRIM(avail_hist_fields(n)%vname)/='sig1' &
.or.TRIM(avail_hist_fields(n)%vname)/='sig2' &
.or.TRIM(avail_hist_fields(n)%vname)/='sistreave' &
Expand All @@ -484,6 +484,7 @@ subroutine ice_write_hist (ns)
endif

if (histfreq(ns) == '1' .or. .not. hist_avg &
.or. write_ic &
.or. n==n_divu(ns) .or. n==n_shear(ns) & ! snapshots
.or. n==n_sig1(ns) .or. n==n_sig2(ns) &
.or. n==n_sigP(ns) .or. n==n_trsig(ns) &
Expand Down Expand Up @@ -527,11 +528,11 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'cell_methods','time: mean')
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = pio_put_att(File,varid,'time_rep','instantaneous')
else
status = pio_put_att(File,varid,'time_rep','averaged')
Expand Down Expand Up @@ -569,11 +570,11 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'cell_methods','time: mean')
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = pio_put_att(File,varid,'time_rep','instantaneous')
else
status = pio_put_att(File,varid,'time_rep','averaged')
Expand Down Expand Up @@ -611,11 +612,11 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'cell_methods','time: mean')
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = pio_put_att(File,varid,'time_rep','instantaneous')
else
status = pio_put_att(File,varid,'time_rep','averaged')
Expand Down Expand Up @@ -653,11 +654,11 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'cell_methods','time: mean')
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = pio_put_att(File,varid,'time_rep','instantaneous')
else
status = pio_put_att(File,varid,'time_rep','averaged')
Expand Down Expand Up @@ -695,11 +696,11 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'cell_methods','time: mean')
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = pio_put_att(File,varid,'time_rep','instantaneous')
else
status = pio_put_att(File,varid,'time_rep','averaged')
Expand Down Expand Up @@ -743,11 +744,11 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'cell_methods','time: mean')
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = pio_put_att(File,varid,'time_rep','instantaneous')
else
status = pio_put_att(File,varid,'time_rep','averaged')
Expand Down Expand Up @@ -786,11 +787,11 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'cell_methods','time: mean')
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = pio_put_att(File,varid,'time_rep','instantaneous')
else
status = pio_put_att(File,varid,'time_rep','averaged')
Expand Down Expand Up @@ -830,11 +831,11 @@ subroutine ice_write_hist (ns)
endif

! Add cell_methods attribute to variables if averaged
if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_put_att(File,varid,'cell_methods','time: mean')
endif

if (histfreq(ns) == '1' .or. .not. hist_avg) then
if (histfreq(ns) == '1' .or. .not. hist_avg .or. write_ic) then
status = pio_put_att(File,varid,'time_rep','instantaneous')
else
status = pio_put_att(File,varid,'time_rep','averaged')
Expand Down Expand Up @@ -908,7 +909,7 @@ subroutine ice_write_hist (ns)
! write time_bounds info
!-----------------------------------------------------------------

if (hist_avg .and. histfreq(ns) /= '1') then
if (hist_avg .and. histfreq(ns) /= '1' .and. .not. write_ic) then
status = pio_inq_varid(File,'time_bounds',varid)
time_bounds=(/time_beg(ns),time_end(ns)/)
bnd_start = (/1,1/)
Expand Down
4 changes: 2 additions & 2 deletions cicecore/drivers/direct/nemo_concepts/CICE_InitMod.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -185,6 +185,8 @@ subroutine cice_init
if (trim(runtype) == 'continue' .or. restart) &
call init_shortwave ! initialize radiative transfer

if (write_ic) call accum_hist(dt) ! write initial conditions

! determine the time and date at the end of the first timestep
call advance_timestep()

Expand Down Expand Up @@ -215,8 +217,6 @@ subroutine cice_init
call init_flux_atm ! initialize atmosphere fluxes sent to coupler
call init_flux_ocn ! initialize ocean fluxes sent to coupler

if (write_ic) call accum_hist(dt) ! write initial conditions

end subroutine cice_init

!=======================================================================
Expand Down
4 changes: 2 additions & 2 deletions cicecore/drivers/standalone/cice/CICE_InitMod.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -190,6 +190,8 @@ subroutine cice_init
if (trim(runtype) == 'continue' .or. restart) &
call init_shortwave ! initialize radiative transfer

if (write_ic) call accum_hist(dt) ! write initial conditions

! tcraig, use advance_timestep here
! istep = istep + 1 ! update time step counters
! istep1 = istep1 + 1
Expand Down Expand Up @@ -222,8 +224,6 @@ subroutine cice_init
call init_flux_atm ! initialize atmosphere fluxes sent to coupler
call init_flux_ocn ! initialize ocean fluxes sent to coupler

if (write_ic) call accum_hist(dt) ! write initial conditions

end subroutine cice_init

!=======================================================================
Expand Down

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