* Deprecate zsalinity, mostly with ifdef and comments first for testing

* Deprecate zsalinity, remove code

* Add warning message for deprecated zsalinity

* Update Icepack to #f5e093f5148554674 (deprecate zsalinity)

…ICE-Consortium#850)

* Extend restart output controls, provide multiple streams for possible
output frequencies.  Convert dumpfreq, dumpfreq_n, dumpfreq_base to
arrays.

Modify histfreq_base to make it an array as well.  Now each history stream
can have it's own base time (init or zero).

Update documentation.

* Clean up implementation and documentation

* Update PR to check github actions

…ICE-Consortium#856)

* merge latest master (#4)

* Isotopes for CICE (CICE-Consortium#423)

Co-authored-by: apcraig <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>

* updated orbital calculations needed for cesm

* fixed problems in updated orbital calculations needed for cesm

* update CICE6 to support coupling with UFS

* put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied

* Convergence on ustar for CICE. (CICE-Consortium#452) (#5)

* Add atmiter_conv to CICE

* Add documentation

* trigger build the docs

Co-authored-by: David A. Bailey <[email protected]>

* update icepack submodule

* Revert "update icepack submodule"

This reverts commit e70d1ab.

* update comp_ice.backend with temporary ice_timers fix

* Fix threading problem in init_bgc

* Fix additional OMP problems

* changes for coldstart running

* Move the forapps directory

* remove cesmcoupled ifdefs

* Fix logging issues for NUOPC

* removal of many cpp-ifdefs

* fix compile errors

* fixes to get cesm working

* fixed white space issue

* Add restart_coszen namelist option

* update icepack submodule

* change Orion to orion in backend

remove duplicate print lines from ice_transport_driver

* add -link_mpi=dbg to debug flags (#8)

* cice6 compile (#6)

* enable debug build. fix to remove errors

* fix an error in comp_ice.backend.libcice

* change Orion to orion for machine identification

* changes for consistency w/ current emc-cice5 (#13)

Update to emc/develop fork to current CICE consortium 

Co-authored-by: David A. Bailey <[email protected]>
Co-authored-by: Tony Craig <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: Mariana Vertenstein <[email protected]>
Co-authored-by: apcraig <[email protected]>
Co-authored-by: Philippe Blain <[email protected]>

* Fixcommit (#14)

Align commit history between emc/develop and cice-consortium/master

* Update CICE6 for integration to S2S


* add wcoss_dell_p3 compiler macro

* update to icepack w/ debug fix

* replace SITE with MACHINE_ID

* update compile scripts

* Support TACC stampede (#19)

* update icepack

* add ice_dyn_vp module to CICE_InitMod

* update gitmodules, update icepack

* Update CICE to consortium master (#23)

updates include:

* deprecate upwind advection (CICE-Consortium#508)
* add implicit VP solver (CICE-Consortium#491)

* update icepack

* switch icepack branches

* update to icepack master but set abort flag in ITD routine
to false

* update icepack

* Update CICE to latest Consortium master (#26)


update CICE and Icepack

* changes the criteria for aborting ice for thermo-conservation errors
* updates the time manager
* fixes two bugs in ice_therm_mushy
* updates Icepack to Consortium master w/ flip of abort flag for troublesome IC cases

* add cice changes for zlvs (#29)

* update icepack and pointer

* update icepack and revert gitmodules

* Fix history features

- Fix bug in history time axis when sec_init is not zero.
- Fix issue with time_beg and time_end uninitialized values.
- Add support for averaging with histfreq='1' by allowing histfreq_n to be any value
  in that case.  Extend and clean up construct_filename for history files.  More could
  be done, but wanted to preserve backwards compatibility.
- Add new calendar_sec2hms to converts daily seconds to hh:mm:ss.  Update the
  calchk calendar unit tester to check this method
- Remove abort test in bcstchk, this was just causing problems in regression testing
- Remove known problems documentation about problems writing when istep=1.  This issue
  does not exist anymore with the updated time manager.
- Add new tests with hist_avg = false.  Add set_nml.histinst.

* revert set_nml.histall

* fix implementation error

* update model log output in ice_init

* Fix QC issues

- Add netcdf ststus checks and aborts in ice_read_write.F90
- Check for end of file when reading records in ice_read_write.F90 for
  ice_read_nc methods
- Update set_nml.qc to better specify the test, turn off leap years since we're cycling
  2005 data
- Add check in c ice.t-test.py to make sure there is at least 1825 files, 5 years of data
- Add QC run to base_suite.ts to verify qc runs to completion and possibility to use
  those results directly for QC validation
- Clean up error messages and some indentation in ice_read_write.F90

* Update testing

- Add prod suite including 10 year gx1prod and qc test
- Update unit test compare scripts

* update documentation

* reset calchk to 100000 years

* update evp1d test

* update icepack

* update icepack

* add memory profiling (#36)


* add profile_memory calls to CICE cap

* update icepack

* fix rhoa when lowest_temp is 0.0

* provide default value for rhoa when imported temp_height_lowest
(Tair) is 0.0
* resolves seg fault when frac_grid=false and do_ca=true

* update icepack submodule

* Update CICE for latest Consortium master (#38)


    * Implement advanced snow physics in icepack and CICE
    * Fix time-stamping of CICE history files
    * Fix CICE history file precision

* Use CICE-Consortium/Icepack master (#40)

* switch to icepack master at consortium

* recreate cap update branch (#42)


* add debug_model feature
* add required variables and calls for tr_snow

* remove 2 extraneous lines

* remove two log print lines that were removed prior to
merge of driver updates to consortium

* duplicate gitmodule style for icepack

* Update CICE to latest Consortium/main (#45)

* Update CICE to Consortium/main (#48)


Update OpenMP directives as needed including validation via new omp_suite. Fixed OpenMP in dynamics.
Refactored eap puny/pi lookups to improve scalar performance
Update Tsfc implementation to make sure land blocks don't set Tsfc to freezing temp
Update for sea bed stress calculations

* fix comment, fix env for orion and hera

* replace save_init with step_prep in CICE_RunMod

* fixes for cgrid repro

* remove added haloupdates

* baselines pass with these extra halo updates removed

* change F->S for ocean velocities and tilts

* fix debug failure when grid_ice=C

* compiling in debug mode using -init=snan,arrays requires
initialization of variables

* respond to review comments

* remove inserted whitespace for uvelE,N and vvelE,N

* Add wave-cice coupling; update to Consortium main (#51)


* add wave-ice fields
* initialize aicen_init, which turns up as NaN in calc of floediam
export
* add call to icepack_init_wave to initialize wavefreq and dwavefreq
* update to latest consortium main (PR 752)

* add initializationsin ice_state

* initialize vsnon/vsnon_init and vicen/vicen_init

* Update CICE (#54)


* update to include recent PRs to Consortium/main

* fix for nudiag_set

allow nudiag_set to be available outside of cesm; may prefer
to fix in coupling interface

* Update CICE for latest Consortium/main (#56)

* add run time info

* change real(8) to real(dbl)kind)

* fix syntax

* fix write unit

* use cice_wrapper for ufs timer functionality

* add elapsed model time for logtime

* tidy up the wrapper

* fix case for 'time since' at the first advance

* add timer and forecast log

* write timer values to timer log, not nu_diag
* write log.ice.fXXX

* only one time is needed

* modify message written for log.ice.fXXX

* change info in fXXX log file

* Update CICE from Consortium/main (#62)


* Fix CESMCOUPLED compile issue in icepack. (CICE-Consortium#823)
* Update global reduction implementation to improve performance, fix VP bug (CICE-Consortium#824)
* Update VP global sum to exclude local implementation with tripole grids
* Add functionality to change hist_avg for each stream (CICE-Consortium#827)
* Update Icepack to #6703bc533c968 May 22, 2023 (CICE-Consortium#829)
* Fix for mesh check in CESM driver (CICE-Consortium#830)
* Namelist option for time axis position. (CICE-Consortium#839)

* reset timer after Advance to retrieve "wait time"

* add logical control for enabling runtime info

* remove zsal items from cap

* fix typo

---------

Co-authored-by: apcraig <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: Mariana Vertenstein <[email protected]>
Co-authored-by: Minsuk Ji <[email protected]>
Co-authored-by: Tony Craig <[email protected]>
Co-authored-by: Philippe Blain <[email protected]>
Co-authored-by: Jun.Wang <[email protected]>

Includes thin ice enthalpy fix, not bit-for-bit.

* Update cheyenne and derecho ports

cheyenne_intel updated to intel/19/1/1, mpt/2.25
cheyenne_gnu updated to gnu/8.3.0, mpt/2.25
cheyenne_pgi updated to pgi/19.9, mpt/2.22
derecho_intel minor updates
derecho_intelclassic added
derecho_inteloneapi added (not working)
derecho_gnu added
derecho_cray added
derecho_nvhpc added

cheyenne_pgi changed answers

derecho_inteloneapi is not working, compiler issues

fixes automated qc testing on cheyenne

* Update permissions on env.chicoma_intel

Update License and Copyright

Update Icepack for version/copyright

* Modified doc to specify that l_fixed_area is T for C-grid

* Initial modifs to calc areafact based on linear interpolation of left and rigth values

* put back l_fixed_area = .true. for C-grid

* added temporary comments for PR review

* Modified areafac calc for case 1 and case 2

* Corrected minor compilation issues

* Corrected conditions for case 1 to make sure areas add up

* Small modif in l_fixed_area section to ensure only one condition is true

* Modified conditions in locate triangle to be consistent with previous changes for case 1

* Use other edge areafac_c for TL, BL, TR and BR triangles

* Some comments removed

* Fixed out of bounds areafac_ce and now use earea and narea

* Replaced ib,ie,jb,je in locate_triangle using ilo,ihi,jlo,jhi

* Modified areafac for TL1, BL2, TR1 and BR2 for area flux consistency

* Cosmetic changes

* Added comment to explain latest change

* Modification of bugcheck condition for l_fixed_area=T

* update areafac_c, areafac_ce in halo in dynamics

---------

Co-authored-by: apcraig <[email protected]>

…3smup3

Update Branch to Consortium CICE main #55342ca7cb4a1be511ade6249e349cb8a8095881, Sept 27, 2023

Update Icepack to E3SM-Project Icepack cice-consortium/E3SM-icepack-initial-integration #78286bfa0b2f8a9dc446f61a76e7a57499c96715, Sept 26, 2023