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update icepack and fix NYGLOB setting #80

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merged 1 commit into from
Feb 9, 2018
Merged

update icepack and fix NYGLOB setting #80

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1 change: 1 addition & 0 deletions cice.setup
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Original file line number Diff line number Diff line change
Expand Up @@ -531,6 +531,7 @@ setenv ICE_MACHCOMP ${machcomp}
setenv ICE_RUNDIR ${ICE_MACHINE_WKDIR}/${casename}
setenv ICE_GRID ${grid}
setenv ICE_NXGLOB ${ICE_DECOMP_NXGLOB}
setenv ICE_NYGLOB ${ICE_DECOMP_NYGLOB}
setenv ICE_NTASKS ${task}
setenv ICE_NTHRDS ${thrd}
setenv ICE_DECOMP ${ICE_DECOMP_DECOMP}
Expand Down
15 changes: 6 additions & 9 deletions cicecore/cicedynB/general/ice_step_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -145,9 +145,9 @@ subroutine step_therm1 (dt, iblk)
meltsn, melttn, meltbn, congeln, snoicen, uatm, vatm, &
wind, rhoa, potT, Qa, zlvl, strax, stray, flatn, fsensn, fsurfn, fcondtopn, &
flw, fsnow, fpond, sss, mlt_onset, frz_onset, &
frain, Tair, coszen, strairxT, strairyT, fsurf, fcondtop, fsens, &
frain, Tair, strairxT, strairyT, fsurf, fcondtop, fsens, &
flat, fswabs, flwout, evap, Tref, Qref, Uref, fresh, fsalt, fhocn, &
fswthru, meltt, melts, meltb, meltl, congel, snoice, frazil, &
fswthru, meltt, melts, meltb, meltl, congel, snoice, &
flatn_f, fsensn_f, fsurfn_f, fcondtopn_f
use ice_flux_bgc, only: dsnown, faero_atm, faero_ocn
use ice_grid, only: lmask_n, lmask_s
Expand Down Expand Up @@ -324,7 +324,7 @@ subroutine step_therm1 (dt, iblk)
fswthrun (i,j,:,iblk), fswabs (i,j, iblk), &
flwout (i,j, iblk), &
Sswabsn (i,j,:,:,iblk), Iswabsn (i,j,:,:,iblk), &
flw (i,j, iblk), coszen (i,j, iblk), &
flw (i,j, iblk), &
fsens (i,j, iblk), fsensn (i,j,:,iblk), &
flat (i,j, iblk), flatn (i,j,:,iblk), &
evap (i,j, iblk), &
Expand All @@ -337,11 +337,10 @@ subroutine step_therm1 (dt, iblk)
dhsn (i,j,:,iblk), ffracn (i,j,:,iblk), &
meltt (i,j, iblk), melttn (i,j,:,iblk), &
meltb (i,j, iblk), meltbn (i,j,:,iblk), &
meltl (i,j, iblk), &
melts (i,j, iblk), meltsn (i,j,:,iblk), &
congel (i,j, iblk), congeln (i,j,:,iblk), &
snoice (i,j, iblk), snoicen (i,j,:,iblk), &
dsnown (i,j,:,iblk), frazil (i,j, iblk), &
dsnown (i,j,:,iblk), &
lmask_n (i,j, iblk), lmask_s (i,j, iblk), &
mlt_onset (i,j, iblk), frz_onset (i,j, iblk), &
yday, prescribed_ice)
Expand Down Expand Up @@ -1085,7 +1084,7 @@ subroutine biogeochemistry (dt, iblk)
use ice_domain_size, only: nblyr, nilyr, nslyr, n_algae, n_zaero, ncat, &
n_doc, n_dic, n_don, n_fed, n_fep
use ice_flux, only: meltbn, melttn, congeln, snoicen, &
sst, sss, fsnow, meltsn, hmix, salinz
sst, sss, fsnow, meltsn
use ice_flux_bgc, only: hin_old, flux_bio, flux_bio_atm, faero_atm, &
nit, amm, sil, dmsp, dms, algalN, doc, don, dic, fed, fep, zaeros, hum
use ice_state, only: aicen_init, vicen_init, aicen, vicen, vsnon, &
Expand Down Expand Up @@ -1207,8 +1206,6 @@ subroutine biogeochemistry (dt, iblk)
sss (i,j, iblk), &
fsnow (i,j, iblk), &
meltsn (i,j,:, iblk), &
hmix (i,j, iblk), &
salinz (i,j,1:nilyr, iblk), &
hin_old (i,j,:, iblk), &
flux_bio (i,j,1:nbtrcr, iblk), &
flux_bio_atm(i,j,1:nbtrcr, iblk), &
Expand All @@ -1220,7 +1217,7 @@ subroutine biogeochemistry (dt, iblk)
aice0 (i,j, iblk), &
trcrn (i,j,1:ntrcr,:,iblk), &
vsnon_init (i,j,:, iblk), &
skl_bgc, icepack_max_algae, icepack_max_nbtrcr)
skl_bgc)

enddo ! i
enddo ! j
Expand Down
10 changes: 3 additions & 7 deletions cicecore/shared/ice_init_column.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -721,7 +721,7 @@ subroutine init_bgc()
do j = jlo, jhi
do i = ilo, ihi

call icepack_init_bgc(dt, ncat, nblyr, nilyr, ntrcr_o, &
call icepack_init_bgc(ncat, nblyr, nilyr, ntrcr_o, &
cgrid, igrid, ntrcr, nbtrcr, &
sicen(:,:), trcrn_bgc(:,:), sss(i,j, iblk), &
ocean_bio_all(i,j,:,iblk))
Expand Down Expand Up @@ -824,7 +824,6 @@ subroutine init_zbgc

integer (kind=int_kind), dimension(icepack_max_algae) :: &
nlt_bgc_N , & ! algae
nlt_bgc_C , & !
nlt_bgc_chl

integer (kind=int_kind), dimension(icepack_max_doc) :: &
Expand All @@ -845,7 +844,6 @@ subroutine init_zbgc

integer (kind=int_kind), dimension(icepack_max_algae) :: &
nt_bgc_N , & ! diatoms, phaeocystis, pico/small
nt_bgc_C , & ! diatoms, phaeocystis, pico/small
nt_bgc_chl ! diatoms, phaeocystis, pico/small

integer (kind=int_kind), dimension(icepack_max_doc) :: &
Expand Down Expand Up @@ -1676,10 +1674,8 @@ subroutine init_zbgc

! vectors of size icepack_max_algae
nlt_bgc_N(:) = 0
nlt_bgc_C(:) = 0
nlt_bgc_chl(:) = 0
nt_bgc_N(:) = 0
nt_bgc_C(:) = 0
nt_bgc_chl(:) = 0

! vectors of size icepack_max_dic
Expand Down Expand Up @@ -2182,14 +2178,14 @@ subroutine init_zbgc
nt_fbri_in=nt_fbri, &
nt_bgc_Nit_in=nt_bgc_Nit, nt_bgc_Am_in=nt_bgc_Am, nt_bgc_Sil_in=nt_bgc_Sil, &
nt_bgc_DMS_in=nt_bgc_DMS, nt_bgc_PON_in=nt_bgc_PON, nt_bgc_S_in=nt_bgc_S, &
nt_bgc_N_in=nt_bgc_N, nt_bgc_C_in=nt_bgc_C, nt_bgc_chl_in=nt_bgc_chl, &
nt_bgc_N_in=nt_bgc_N, nt_bgc_chl_in=nt_bgc_chl, &
nt_bgc_DOC_in=nt_bgc_DOC, nt_bgc_DON_in=nt_bgc_DON, nt_bgc_DIC_in=nt_bgc_DIC, &
nt_zaero_in=nt_zaero, nt_bgc_DMSPp_in=nt_bgc_DMSPp, nt_bgc_DMSPd_in=nt_bgc_DMSPd, &
nt_bgc_Fed_in=nt_bgc_Fed, nt_bgc_Fep_in=nt_bgc_Fep, nt_zbgc_frac_in=nt_zbgc_frac, &
nlt_zaero_sw_in=nlt_zaero_sw, nlt_chl_sw_in=nlt_chl_sw, nlt_bgc_Sil_in=nlt_bgc_Sil, &
nlt_bgc_N_in=nlt_bgc_N, nlt_bgc_Nit_in=nlt_bgc_Nit, nlt_bgc_Am_in=nlt_bgc_Am, &
nlt_bgc_DMS_in=nlt_bgc_DMS, nlt_bgc_DMSPp_in=nlt_bgc_DMSPp, nlt_bgc_DMSPd_in=nlt_bgc_DMSPd, &
nlt_bgc_C_in=nlt_bgc_C, nlt_bgc_chl_in=nlt_bgc_chl, nlt_zaero_in=nlt_zaero, &
nlt_bgc_chl_in=nlt_bgc_chl, nlt_zaero_in=nlt_zaero, &
nlt_bgc_DIC_in=nlt_bgc_DIC, nlt_bgc_DOC_in=nlt_bgc_DOC, nlt_bgc_PON_in=nlt_bgc_PON, &
nlt_bgc_DON_in=nlt_bgc_DON, nlt_bgc_Fed_in=nlt_bgc_Fed, nlt_bgc_Fep_in=nlt_bgc_Fep, &
nt_bgc_hum_in=nt_bgc_hum, nlt_bgc_hum_in=nlt_bgc_hum, &
Expand Down
2 changes: 1 addition & 1 deletion icepack
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Submodule icepack updated 68 files
+3 −0 .gitignore
+27 −14 .travis.yml
+9 −7 README.md
+4 −14 columnphysics/icepack_aerosol.F90
+0 −1 columnphysics/icepack_age.F90
+126 −159 columnphysics/icepack_algae.F90
+15 −23 columnphysics/icepack_atmo.F90
+37 −62 columnphysics/icepack_brine.F90
+0 −1 columnphysics/icepack_firstyear.F90
+1 −3 columnphysics/icepack_flux.F90
+0 −1 columnphysics/icepack_intfc.F90
+27 −31 columnphysics/icepack_itd.F90
+0 −1 columnphysics/icepack_kinds.F90
+3 −6 columnphysics/icepack_mechred.F90
+2 −6 columnphysics/icepack_meltpond_cesm.F90
+2 −6 columnphysics/icepack_meltpond_lvl.F90
+4 −10 columnphysics/icepack_meltpond_topo.F90
+4 −4 columnphysics/icepack_mushy_physics.F90
+1 −2 columnphysics/icepack_ocean.F90
+17 −26 columnphysics/icepack_orbital.F90
+0 −1 columnphysics/icepack_parameters.F90
+11 −16 columnphysics/icepack_shortwave.F90
+1 −6 columnphysics/icepack_therm_0layer.F90
+5 −10 columnphysics/icepack_therm_bl99.F90
+1 −15 columnphysics/icepack_therm_itd.F90
+50 −82 columnphysics/icepack_therm_mushy.F90
+1 −8 columnphysics/icepack_therm_shared.F90
+27 −40 columnphysics/icepack_therm_vertical.F90
+4 −5 columnphysics/icepack_tracers.F90
+0 −1 columnphysics/icepack_warnings.F90
+25 −43 columnphysics/icepack_zbgc.F90
+7 −13 columnphysics/icepack_zbgc_shared.F90
+33 −43 columnphysics/icepack_zsalinity.F90
+7 −11 configuration/driver/icedrv_InitMod.F90
+13 −15 configuration/driver/icedrv_RunMod.F90
+1 −11 configuration/driver/icedrv_calendar.F90
+1 −2 configuration/driver/icedrv_constants.F90
+6 −13 configuration/driver/icedrv_diagnostics.F90
+10 −20 configuration/driver/icedrv_diagnostics_bgc.F90
+1 −1 configuration/driver/icedrv_flux.F90
+23 −25 configuration/driver/icedrv_forcing.F90
+4 −23 configuration/driver/icedrv_forcing_bgc.F90
+3 −20 configuration/driver/icedrv_init.F90
+9 −15 configuration/driver/icedrv_init_column.F90
+10 −15 configuration/driver/icedrv_restart.F90
+7 −7 configuration/driver/icedrv_restart_bgc.F90
+1 −1 configuration/driver/icedrv_state.F90
+14 −32 configuration/driver/icedrv_step.F90
+10 −0 configuration/scripts/icepack.batch.csh
+39 −0 configuration/scripts/machines/Macros.hobart_nag
+17 −0 configuration/scripts/machines/env.hobart_nag
+22 −4 configuration/scripts/tests/report_results.csh
+17 −0 configuration/scripts/tests/travis_suite.ts
+ − doc/.DS_Store
+7 −21 doc/source/developer_guide/dg_col_phys.rst
+264 −0 doc/source/developer_guide/dg_documentation.rst
+2 −2 doc/source/developer_guide/dg_driver.rst
+1 −0 doc/source/developer_guide/index.rst
+12 −11 doc/source/icepack_index.rst
+3 −1 doc/source/intro/major_updates.rst
+48 −0 doc/source/master_list.bib
+3 −5 doc/source/science_guide/sg_bgc.rst
+25 −15 doc/source/science_guide/sg_boundary_forcing.rst
+0 −0 doc/source/user_guide/index.rst
+10 −7 doc/source/user_guide/ug_case_settings.rst
+1 −1 doc/source/user_guide/ug_implementation.rst
+99 −6 doc/source/user_guide/ug_running.rst
+25 −26 doc/source/user_guide/ug_testing.rst