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Update CICE for latest Consortium master #38

Merged
merged 29 commits into from
Sep 16, 2021
Merged

Update CICE for latest Consortium master #38

merged 29 commits into from
Sep 16, 2021

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DeniseWorthen
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@DeniseWorthen DeniseWorthen commented Aug 20, 2021 •
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Fixes CICE Issue #37
Fixes CICE Issue #33
Fixes CICE Issue #35

Waiting on Icepack PR #6

JFLemieux73 and others added 20 commits July 14, 2021 16:15
@JFLemieux73
New fig for Bgrid + minor modifs to comments and doc (CICE-Consortium…
e6bdf86 
…#616)
@apcraig
- Update Onyx port after significant Onyx system update (CICE-Consort…
0489cfd 
…ium#617)

- Update unit test output and scripts to differentiate completed runs and successful testing better
- sumchk is not passing on Onyx due to issues in the global reduction at real*16 and real*4.  This seems to be a software bug in mpich and a report has been issued to Onyx admins.
@apcraig
Fix 1x1 and 2x2 blocksize error (CICE-Consortium#618)
36799ec 
- Fix 1x1 and 2x2 non-bit-for-bit results.  It turns out the 1x1 and 2x2 blocks were
  bit-for-bit physicallly.  The problem was that a set of blocks were "land block eliminated"
  near the equator incorrectly.  These blocks never have sea ice form, so it's not a problem
  scientifically, but it changes the masking and restart files.  The fix is a one line change
  in ice_domain.F90 which that sets the minimum "flat" value to 1.  This error could only
  happen in cases where the blocks were within 0.5 degrees of the equator, and a set of
  conditions were required where an active gridcell was set to inactive which then resulted
  in the entire block being eliminated.
- Update the initialization of ARRAY_G in the gather_global_ext interfaces.  Get rid of
  older, more complex approach which left some blocks uninitialized.
- Set psalt(n) to zero by default.  Was uninitialized in cases where vice=0.
- Add a test to check bit-for-bit in log files for 1x1 blocks with bfbflag set to reprosum.
@rgrumbine
Develop (CICE-Consortium#620)
a35724c 
* port to gaea
@TillRasmussen @srethmeier @apcraig
Bug fixed 1d evp (CICE-Consortium#568)
0ccdea1 
* Initialization of global HTE and HTN arrays with ghost cells on master task to avoid gathering constant arrays when running EVP 1D implementation. This solves issue with departure errors resulting from erroneous initialization of full land blocks in EVP 1D gathering. Correct initialization of remaining variables for full land blocks in EVP 1D gathering.

* Reverted configuration/scripts/cice.batch.csh to resolve bad auto merge of file. Machine 'freya' was double in file.

* Spell error corrected (CICE-Consortium#568 (comment)).

* Redundant initializations to default values removed (CICE-Consortium#568 (comment)). @mhrib questions to default value settings removed.

* Subroutine primary_grid_lengths_global_ext moved from ice_grid module to MPI and serial implementations of ice_boundary modules (CICE-Consortium#568 (comment)). Please note duplication of subroutine.

* Added 1d solver to be fully integrated. Removed kevp=102 bypass.
Clean up. Changed namelist parameter kevp to evp_algorithm

* General cleanup of ice_dyn_evp_1d module (CICE-Consortium#568 (comment) and CICE-Consortium#568 (comment))

* Modified documentation in order to comply with modifications of evp 1d

* Uncommenting of numainit parallelization removed and domp_init moved before numainit to ensure correct initialization. Additional cleanup of code.

* renamed set_nml.evp_algorithm to set_nml.evp1d
added test to base test

* rm set_nml.kevp102

* Naming of variable se is not logical. Changed to sse which is the same
as the global variable

* Alignment of NUMA-aware array splitting between threads

* Initialization of global HTE and HTN arrays with ghost cells on master task to avoid gathering constant arrays when running EVP 1D implementation. This solves issue with departure errors resulting from erroneous initialization of full land blocks in EVP 1D gathering. Correct initialization of remaining variables for full land blocks in EVP 1D gathering.

* Reverted configuration/scripts/cice.batch.csh to resolve bad auto merge of file. Machine 'freya' was double in file.

* Spell error corrected (CICE-Consortium#568 (comment)).

* Redundant initializations to default values removed (CICE-Consortium#568 (comment)). @mhrib questions to default value settings removed.

* Subroutine primary_grid_lengths_global_ext moved from ice_grid module to MPI and serial implementations of ice_boundary modules (CICE-Consortium#568 (comment)). Please note duplication of subroutine.

* Added 1d solver to be fully integrated. Removed kevp=102 bypass.
Clean up. Changed namelist parameter kevp to evp_algorithm

* General cleanup of ice_dyn_evp_1d module (CICE-Consortium#568 (comment) and CICE-Consortium#568 (comment))

* Modified documentation in order to comply with modifications of evp 1d

* Uncommenting of numainit parallelization removed and domp_init moved before numainit to ensure correct initialization. Additional cleanup of code.

* renamed set_nml.evp_algorithm to set_nml.evp1d
added test to base test

* rm set_nml.kevp102

* Naming of variable se is not logical. Changed to sse which is the same
as the global variable

* Alignment of NUMA-aware array splitting between threads

* Fix bad scaling of calculation of tinyarea. Different order of multiplication causes small differences in result

* Fix evp 1d masking issues

- There are relatively rare cases/gridcells where stress (tmask) and stepu (umask) are advanced
without the other.  The 1d evp implementation was not addressing this issue, so skiptcell was added
to the 1d evp (similar to skipucell) to mask out cells separately for stress and stepu.  This
fixed a few non bit-for-bit cases in testing.

- Cleaned up some indentation and other minor issues in 1d evp.

- Updated the evp_algorithm log output in ice_init.

* Some minor revisions in the documentation as suggested by @apcraig (CICE-Consortium#568 (review)) plus some additional minor spelling corrections.

Co-authored-by: Stefan Rethmeier <[email protected]>
Co-authored-by: Till Rasmussen <[email protected]>
Co-authored-by: Stefan Rethmeier <[email protected]>
Co-authored-by: apcraig <[email protected]>
@apcraig
Fix history features
441f693 
- 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.
@apcraig
revert set_nml.histall
15763d8
@apcraig
fix implementation error
b3364a6
@apcraig
update model log output in ice_init
96d5851
@eclare108213 @proteanplanet @apcraig
Advanced snow physics driver (CICE-Consortium#621)
2a692af 
* initial snow redist/metamorph tracer implementation (no physics)

* add rhosmin, snwlvlfac to namelist, change init_snow to init_snowtracers

* updating format labels due to changes in Consortium master

* add calls to new snow physics routines

* update_state after step_snow

* fix optional in update_state

* wrap step_snow and update_state with tr_snow conditional

* snow interactions with thermo (except dEdd)

* conflict warning

* adding snwgrain namelist flag

* use snwredist=bulk instead of 30percent, fix array errors, init snow tracer values, add namelist flags to ice_in

* aging lookup table for dry metamorphism (version for testing)

* add/clean up diagnostics, begin debugging restart implementation

* fixing restarts

* add snow tests to base_suite

* add history; minor cleanup

* fix step_therm1 interface

* io fixes for snow1

* bug fix for snow diagnostics

* fix line continuation

* refactor bgc diagnostics as in Icepack

* add snowtable implementation

* cleaning up snow test options

* send rsnw tracer to dEdd; initialize snow tracers; update -s options for snow

* broadcast new snow diagnostics

* new snow tests require 5 snow layers and therefore can not start from standard initial condition files with nslyr=1

* update icepack

* use local variable for rsnow to prevent array out-of-bound error; cleanup

* updating documentation and some code comments

* documentation:  index

* fix history output; include but comment out code for averaging based on snow presence; set rsnw_fall in ice_in for default dEdd and include relevant snow parameters in options files; update doc; clean up

* minor cleanup, especially documentation

* update icepack

Co-authored-by: Andrew Roberts <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: apcraig <[email protected]>
@apcraig
Fix QC issues
7b5c2b4 
- 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
@apcraig
Update testing
c5794b4 
- Add prod suite including 10 year gx1prod and qc test
- Update unit test compare scripts
@apcraig
update documentation
eaa3c3a
@apcraig
reset calchk to 100000 years
e31ce7e
@apcraig
update evp1d test
83068c7
@apcraig
Merge branch 'master' of https://github.com/cice-consortium/cice into…
3fd897e 
… tmB
@DeniseWorthen
update icepack
4373d3d
@DeniseWorthen
Merge remote-tracking branch 'TCraig/tmB' into feature/updcice
71f4fe6
@apcraig
Fix QC test, fix bug in history time axis, fix history output averagi…
26d917a 
…ng for timestep output (CICE-Consortium#624)

* 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
@DeniseWorthen
Merge remote-tracking branch 'Consortium/master' into feature/updcice
aeb473a
@DeniseWorthen DeniseWorthen self-assigned this Aug 20, 2021
@DeniseWorthen DeniseWorthen mentioned this pull request Aug 20, 2021
Merged
14 tasks
DeniseWorthen and others added 6 commits August 26, 2021 17:20
@DeniseWorthen
Merge branch 'NOAA-EMC:emc/develop' into feature/updcice
397b4bd
@apcraig
Fix history single/double precision issues (CICE-Consortium#628)
cb7d616 
* Fix history single/double precision issues

- Fix io_netcdf.  Double precision output was passed thru a single precision variable
  before writing so the precision in the output was lost.  This is now fixed.  Single
  and double precision netcdf output now reflects the internal model data correctly.

- Fix io_pio2.  Single precision output with pio2 was producing garbage for both netcdf
  and pnetcdf cases.  This is not the case with pio1.  Several changes were needed.
  - The iodesc initialization has to differentiate single or double target variables
  - The write_darray has to explicitly send a single or double array

- Migrated to spval_dbl fills everywhere data is a double type, mostly in ice_history.F90.

- Created a ice_write_hist_fill method in both io_netcdf and io_pio2 to improve reuse.

Ran io_suite on cheyenne and checked that values are produced correctly for each case.

* update formatting
@DeniseWorthen
update icepack
a1b3375
@DeniseWorthen
Merge remote-tracking branch 'Consortium/master' into feature/updcice
7d2139c
@apcraig
Update gx1prod, Icepack, version number (CICE-Consortium#629)
6e89728 
* update gx1prod, update version number to 6.3

* update Icepack

* update gx1prod15 to start at 1995
@DeniseWorthen
Merge remote-tracking branch 'Consortium/master' into feature/updcice
cd021b5
@DeniseWorthen
fix rhoa when lowest_temp is 0.0
5cb78cd 
* 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
@DeniseWorthen
update icepack submodule
d0a45a2
@DeniseWorthen DeniseWorthen merged commit 2540695 into NOAA-EMC:emc/develop Sep 16, 2021
DeniseWorthen added a commit to DeniseWorthen/CICE that referenced this pull request Nov 8, 2022
@DeniseWorthen @apcraig
@dabail10 @eclare108213 @MinsukJi-NOAA @phil-blain
Add wave-ice coupling to nuopc/cmeps driver (CICE-Consortium#782)
251ca48 
* merge latest master (NOAA-EMC#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) (NOAA-EMC#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 (NOAA-EMC#8)

* cice6 compile (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#19)

* update icepack

* add ice_dyn_vp module to CICE_InitMod

* update gitmodules, update icepack

* Update CICE to consortium master (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#40)

* switch to icepack master at consortium

* recreate cap update branch (NOAA-EMC#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 (NOAA-EMC#45)

* Update CICE to Consortium/main (NOAA-EMC#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 (NOAA-EMC#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

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]>
DeniseWorthen added a commit to DeniseWorthen/CICE that referenced this pull request Sep 1, 2023
@DeniseWorthen @apcraig
@dabail10 @eclare108213 @MinsukJi-NOAA @phil-blain @junwang-noaa
Add logging features to nuopc/cmeps cap; deprecates zsalinity in cap (C…
e8a69ab 
…ICE-Consortium#856)

* merge latest master (NOAA-EMC#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) (NOAA-EMC#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 (NOAA-EMC#8)

* cice6 compile (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#19)

* update icepack

* add ice_dyn_vp module to CICE_InitMod

* update gitmodules, update icepack

* Update CICE to consortium master (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#40)

* switch to icepack master at consortium

* recreate cap update branch (NOAA-EMC#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 (NOAA-EMC#45)

* Update CICE to Consortium/main (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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]>
DeniseWorthen added a commit to DeniseWorthen/CICE that referenced this pull request Sep 18, 2023
@DeniseWorthen
Squashed commit of the following:
94525d6 
commit 2ed3c05
Author: Denise Worthen <[email protected]>
Date:   Thu Sep 7 15:00:21 2023 -0400

    Update CICE from Consortium/main, add run-time and history-write logging (NOAA-EMC#65)

commit d41c61d
Author: Denise Worthen <[email protected]>
Date:   Wed Aug 2 17:09:26 2023 -0400

    Update CICE from Consortium/main (NOAA-EMC#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)

commit 5840cd1
Merge: 6671e32 7df80ba
Author: Denise Worthen <[email protected]>
Date:   Wed Mar 22 07:43:35 2023 -0400

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit 6671e32
Merge: ee68d3f d73bb8b
Author: Denise Worthen <[email protected]>
Date:   Tue Mar 7 12:56:52 2023 -0500

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit ee68d3f
Merge: dd25b0f e628a9a
Author: Denise Worthen <[email protected]>
Date:   Tue Mar 7 12:56:33 2023 -0500

    Merge branch 'emc/develop' into feature/updcice

commit e628a9a
Author: Denise Worthen <[email protected]>
Date:   Mon Jan 23 07:58:06 2023 -0500

    Update CICE for latest Consortium/main (NOAA-EMC#56)

commit dd25b0f
Merge: ed472ab 506614d
Author: Denise Worthen <[email protected]>
Date:   Sat Jan 14 12:00:15 2023 -0500

    Merge branch 'test' into feature/updcice

commit 506614d
Merge: 7757945 0bf0fdc
Author: Denise Worthen <[email protected]>
Date:   Sat Jan 14 11:58:19 2023 -0500

    Merge remote-tracking branch 'CICE-Consortium/main' into test

commit ed472ab
Author: denise.worthen <[email protected]>
Date:   Mon Jan 9 12:53:05 2023 +0000

    fix for nudiag_set

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

commit ce2298e
Merge: ad8d577 0bf0fdc
Author: denise.worthen <[email protected]>
Date:   Wed Jan 4 14:50:34 2023 -0500

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit ad8d577
Merge: 90a8b62 b16d7fd
Author: Denise Worthen <[email protected]>
Date:   Tue Dec 6 14:22:06 2022 -0500

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit 90a8b62
Merge: fe16051 7757945
Author: Denise Worthen <[email protected]>
Date:   Tue Dec 6 13:37:51 2022 -0500

    Merge branch 'NOAA-EMC:emc/develop' into feature/updcice

commit 7757945
Author: Denise Worthen <[email protected]>
Date:   Fri Nov 25 08:58:08 2022 -0500

    Update CICE (NOAA-EMC#54)

    * update to include recent PRs to Consortium/main

commit fe16051
Merge: b11bfb4 9808b51
Author: Denise Worthen <[email protected]>
Date:   Wed Nov 16 07:59:58 2022 -0500

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit b11bfb4
Merge: b893ee9 251ca48
Author: Denise Worthen <[email protected]>
Date:   Tue Nov 8 09:07:10 2022 -0500

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit b893ee9
Author: denise.worthen <[email protected]>
Date:   Wed Nov 2 15:45:10 2022 -0600

    add initializationsin ice_state

    * initialize vsnon/vsnon_init and vicen/vicen_init

commit 2e68b9e
Merge: d6d081a 3820cde
Author: Denise Worthen <[email protected]>
Date:   Wed Nov 2 12:14:34 2022 -0400

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit d6d081a
Merge: 1f70caf 968a0ed
Author: Denise Worthen <[email protected]>
Date:   Wed Nov 2 12:13:52 2022 -0400

    Merge branch 'emc/develop' into feature/updcice

commit 968a0ed
Author: Denise Worthen <[email protected]>
Date:   Tue Aug 30 12:51:07 2022 -0400

    Add wave-cice coupling; update to Consortium main (NOAA-EMC#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)

commit 1f70caf
Merge: 73cc18c fea412a
Author: denise.worthen <[email protected]>
Date:   Sat Aug 20 10:52:22 2022 -0400

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit 73cc18c
Merge: cc0f89c 471c010
Author: denise.worthen <[email protected]>
Date:   Thu Jun 23 17:42:49 2022 -0400

    Merge remote-tracking branch 'Consortium/main' into feature/addCgridfixes

commit cc0f89c
Author: denise.worthen <[email protected]>
Date:   Wed Jun 22 14:13:25 2022 -0600

    remove inserted whitespace for uvelE,N and vvelE,N

commit 9e2dd69
Author: denise.worthen <[email protected]>
Date:   Wed Jun 22 13:07:56 2022 -0600

    respond to review comments

commit 26498db
Author: denise.worthen <[email protected]>
Date:   Mon Jun 20 15:27:46 2022 -0600

    fix debug failure when grid_ice=C

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

commit 2d5487a
Author: denise.worthen <[email protected]>
Date:   Mon Jun 13 11:56:40 2022 -0600

    change F->S for ocean velocities and tilts

commit a38df37
Merge: ab95d2d 7705e13
Author: denise.worthen <[email protected]>
Date:   Mon Jun 13 09:34:45 2022 -0400

    Merge remote-tracking branch 'Consortium/main' into feature/addCgridfixes

commit ab95d2d
Merge: cbc6046 c334aee
Author: denise.worthen <[email protected]>
Date:   Thu Jun 2 15:48:31 2022 -0400

    Merge remote-tracking branch 'Consortium/main' into feature/addCgridfixes

commit cbc6046
Author: denise.worthen <[email protected]>
Date:   Mon May 23 19:07:39 2022 -0600

    remove added haloupdates

    * baselines pass with these extra halo updates removed

commit ae50efe
Author: denise.worthen <[email protected]>
Date:   Sun May 22 16:30:00 2022 -0600

    fixes for cgrid repro

commit dd158e2
Author: denise.worthen <[email protected]>
Date:   Sat May 14 13:59:26 2022 +0000

    replace save_init with step_prep in CICE_RunMod

commit 247dc1d
Author: denise.worthen <[email protected]>
Date:   Sat May 14 09:01:12 2022 -0400

    fix comment, fix env for orion and hera

commit 4b28dfe
Merge: c660075 078aab4
Author: denise.worthen <[email protected]>
Date:   Sat May 14 08:58:48 2022 -0400

    Merge remote-tracking branch 'Consortium/main' into feature/addCgrid

commit c660075
Author: Denise Worthen <[email protected]>
Date:   Tue May 10 15:28:44 2022 -0400

    Update CICE to Consortium/main (NOAA-EMC#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

commit 27dfd1b
Author: Denise Worthen <[email protected]>
Date:   Thu Feb 24 11:19:10 2022 -0500

    Update CICE to latest Consortium/main (NOAA-EMC#45)

commit 8ff0fb2
Author: denise.worthen <[email protected]>
Date:   Tue Nov 30 05:11:57 2021 -0500

    duplicate gitmodule style for icepack

commit abbebab
Author: denise.worthen <[email protected]>
Date:   Tue Nov 30 05:10:24 2021 -0500

    remove 2 extraneous lines

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

commit 7a0b65e
Merge: 55bf9f4 8d4a3c6
Author: denise.worthen <[email protected]>
Date:   Mon Nov 29 19:06:29 2021 -0500

    Merge branch 'emc/develop' into feature/updcice

commit 55bf9f4
Merge: d83c67b 2b85126
Author: denise.worthen <[email protected]>
Date:   Mon Nov 29 18:50:34 2021 -0500

    Merge remote-tracking branch 'Consortium/main' into feature/updcice

commit 8d4a3c6
Author: Denise Worthen <[email protected]>
Date:   Mon Nov 22 09:06:56 2021 -0500

    recreate cap update branch (NOAA-EMC#42)

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

commit d83c67b
Merge: 8a88024 d95bd51
Author: Denise Worthen <[email protected]>
Date:   Tue Oct 12 14:16:31 2021 -0400

    Merge branch 'NOAA-EMC:emc/develop' into feature/updcice

commit d95bd51
Author: Denise Worthen <[email protected]>
Date:   Fri Oct 1 09:42:49 2021 -0400

    Use CICE-Consortium/Icepack master (NOAA-EMC#40)

    * switch to icepack master at consortium

commit 8a88024
Merge: d0a45a2 2540695
Author: Denise Worthen <[email protected]>
Date:   Mon Sep 20 09:28:26 2021 -0400

    Merge branch 'NOAA-EMC:emc/develop' into feature/updcice

commit 2540695
Author: Denise Worthen <[email protected]>
Date:   Thu Sep 16 08:28:30 2021 -0400

    Update CICE for latest Consortium master (NOAA-EMC#38)

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

commit d0a45a2
Author: denise.worthen <[email protected]>
Date:   Thu Sep 16 07:44:22 2021 -0400

    update icepack submodule

commit 5cb78cd
Author: denise.worthen <[email protected]>
Date:   Wed Sep 15 09:15:42 2021 -0400

    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

commit cd021b5
Merge: 7d2139c 6e89728
Author: denise.worthen <[email protected]>
Date:   Wed Sep 1 19:39:06 2021 -0400

    Merge remote-tracking branch 'Consortium/master' into feature/updcice

commit 7d2139c
Merge: a1b3375 cb7d616
Author: denise.worthen <[email protected]>
Date:   Tue Aug 31 14:08:06 2021 -0400

    Merge remote-tracking branch 'Consortium/master' into feature/updcice

commit a1b3375
Author: denise.worthen <[email protected]>
Date:   Tue Aug 31 14:07:50 2021 -0400

    update icepack

commit 397b4bd
Merge: aade124 7f089d0
Author: Denise Worthen <[email protected]>
Date:   Thu Aug 26 17:20:25 2021 -0400

    Merge branch 'NOAA-EMC:emc/develop' into feature/updcice

commit 7f089d0
Author: Denise Worthen <[email protected]>
Date:   Mon Aug 23 08:19:25 2021 -0400

    add memory profiling (NOAA-EMC#36)

    * add profile_memory calls to CICE cap

commit aade124
Author: denise.worthen <[email protected]>
Date:   Fri Aug 20 08:14:44 2021 -0400

    update icepack

commit aeb473a
Merge: 71f4fe6 26d917a
Author: denise.worthen <[email protected]>
Date:   Fri Aug 20 08:03:58 2021 -0400

    Merge remote-tracking branch 'Consortium/master' into feature/updcice

commit 71f4fe6
Merge: 4373d3d 3fd897e
Author: denise.worthen <[email protected]>
Date:   Sun Aug 15 11:04:41 2021 -0400

    Merge remote-tracking branch 'TCraig/tmB' into feature/updcice

commit 4373d3d
Author: denise.worthen <[email protected]>
Date:   Sun Aug 15 11:04:01 2021 -0400

    update icepack

commit 3fd897e
Merge: 83068c7 2a692af
Author: apcraig <[email protected]>
Date:   Fri Aug 13 16:24:01 2021 -0600

    Merge branch 'master' of https://github.com/cice-consortium/cice into tmB

commit 83068c7
Author: apcraig <[email protected]>
Date:   Fri Aug 13 09:24:49 2021 -0600

    update evp1d test

commit e31ce7e
Author: apcraig <[email protected]>
Date:   Fri Aug 13 09:00:01 2021 -0600

    reset calchk to 100000 years

commit eaa3c3a
Author: apcraig <[email protected]>
Date:   Thu Aug 12 23:53:55 2021 -0600

    update documentation

commit c5794b4
Author: apcraig <[email protected]>
Date:   Thu Aug 12 23:49:05 2021 -0600

    Update testing

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

commit 7b5c2b4
Author: apcraig <[email protected]>
Date:   Thu Aug 12 16:57:18 2021 -0600

    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

commit 96d5851
Author: apcraig <[email protected]>
Date:   Wed Aug 11 13:26:01 2021 -0600

    update model log output in ice_init

commit b3364a6
Author: apcraig <[email protected]>
Date:   Tue Aug 10 22:21:33 2021 -0600

    fix implementation error

commit 15763d8
Author: apcraig <[email protected]>
Date:   Tue Aug 10 17:14:25 2021 -0600

    revert set_nml.histall

commit 441f693
Author: apcraig <[email protected]>
Date:   Tue Aug 10 17:04:56 2021 -0600

    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.

commit 55586f7
Author: denise.worthen <[email protected]>
Date:   Tue Jul 20 11:21:12 2021 -0400

    update icepack and revert gitmodules

commit 1721728
Merge: 9057817 85531cf
Author: denise.worthen <[email protected]>
Date:   Fri Jul 2 09:49:24 2021 -0400

    Merge remote-tracking branch 'Consortium/master' into feature/updcice

commit 9057817
Merge: f3b2652 995f3af
Author: denise.worthen <[email protected]>
Date:   Thu Jun 24 08:34:26 2021 -0400

    Merge remote-tracking branch 'Consortium/master' into feature/updcice

commit f3b2652
Author: denise.worthen <[email protected]>
Date:   Thu Jun 24 08:32:44 2021 -0400

    update icepack and pointer

commit 0c39047
Merge: 9a76541 d1f2d15
Author: denise.worthen <[email protected]>
Date:   Thu Jun 24 08:30:26 2021 -0400

    Merge branch 'emc/develop' into feature/updcice

commit d1f2d15
Merge: 74e7b58 9d88d92
Author: denise.worthen <[email protected]>
Date:   Fri Jun 11 09:13:53 2021 -0400

    Merge remote-tracking branch 'upstream/emc/develop' into emc/develop

commit 9d88d92
Author: Denise Worthen <[email protected]>
Date:   Thu Jun 10 18:08:12 2021 -0400

    add cice changes for zlvs (NOAA-EMC#29)

commit 74e7b58
Merge: b52e91c 519d339
Author: denise.worthen <[email protected]>
Date:   Sat Jun 5 17:35:52 2021 -0400

    Merge remote-tracking branch 'upstream/emc/develop' into emc/develop

commit 519d339
Author: Denise Worthen <[email protected]>
Date:   Fri Jun 4 16:41:08 2021 -0400

    Update CICE to latest Consortium master (NOAA-EMC#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

commit 9a76541
Author: denise.worthen <[email protected]>
Date:   Fri Jun 4 16:01:59 2021 -0400

    update icepack

commit d8fb6d9
Author: denise.worthen <[email protected]>
Date:   Wed Jun 2 16:57:19 2021 -0400

    switch icepack branches

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

commit 51db2f9
Merge: b52e91c bd512d4
Author: denise.worthen <[email protected]>
Date:   Tue Jun 1 09:17:15 2021 -0400

    Merge remote-tracking branch 'Consortium/master' into feature/updcice

commit b52e91c
Merge: 840e931 2eca569
Author: denise.worthen <[email protected]>
Date:   Mon Apr 5 08:40:40 2021 -0400

    Merge remote-tracking branch 'upstream/emc/develop' into emc/develop

commit 2eca569
Author: denise.worthen <[email protected]>
Date:   Mon Apr 5 08:29:35 2021 -0400

    update icepack

commit 66546ae
Merge: 1e4d393 5a0a559
Author: denise.worthen <[email protected]>
Date:   Sun Mar 14 09:27:54 2021 -0400

    Merge remote-tracking branch 'Consortium/master' into feature/updcice

commit 1e4d393
Merge: 2a0f332 f773ef3
Author: denise.worthen <[email protected]>
Date:   Sun Mar 14 09:19:52 2021 -0400

    Merge remote-tracking branch 'upstream/emc/develop' into feature/updcice

commit 840e931
Merge: 23cdee7 f773ef3
Author: denise.worthen <[email protected]>
Date:   Tue Nov 10 10:44:16 2020 -0500

    Merge remote-tracking branch 'upstream/emc/develop' into emc/develop

commit f773ef3
Author: Denise Worthen <[email protected]>
Date:   Tue Nov 10 10:37:11 2020 -0500

    Update CICE to consortium master (NOAA-EMC#23)

    updates include:

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

commit 2a0f332
Author: denise.worthen <[email protected]>
Date:   Tue Nov 10 10:29:03 2020 -0500

    update gitmodules, update icepack

commit 41afe74
Author: denise.worthen <[email protected]>
Date:   Fri Oct 30 17:47:51 2020 +0000

    add ice_dyn_vp module to CICE_InitMod

commit 2515f77
Merge: 1e4f42b 12fdb47
Author: denise.worthen <[email protected]>
Date:   Fri Oct 30 11:14:19 2020 -0400

    Merge remote-tracking branch 'consortium/master' into feature/updcice

commit 1e4f42b
Author: denise.worthen <[email protected]>
Date:   Fri Oct 30 11:13:17 2020 -0400

    update icepack

commit 23cdee7
Merge: 8129aab ac617cd
Author: denise.worthen <[email protected]>
Date:   Thu Oct 8 07:17:42 2020 -0400

    Merge remote-tracking branch 'upstream/emc/develop' into emc/develop

commit ac617cd
Author: Minsuk Ji <[email protected]>
Date:   Thu Oct 8 07:13:14 2020 -0400

    Support TACC stampede (NOAA-EMC#19)

commit 8129aab
Merge: 6d30789 c0a2e2d
Author: denise.worthen <[email protected]>
Date:   Mon Aug 31 13:29:35 2020 -0400

    Merge remote-tracking branch 'consortium/master' into emc/develop

commit 6d30789
Merge: 5dcfca8 285985c
Author: denise.worthen <[email protected]>
Date:   Mon Aug 31 16:59:48 2020 +0000

    Merge remote-tracking branch 'upstream/emc/develop' into emc/develop

commit 285985c
Author: Denise Worthen <[email protected]>
Date:   Mon Aug 31 12:53:02 2020 -0400

    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

commit 5dcfca8
Merge: 5ecde75 4d7ba5b
Author: denise.worthen <[email protected]>
Date:   Thu Aug 13 13:06:16 2020 -0400

    Merge remote-tracking branch 'upstream/emc/develop' into emc/develop

commit 4d7ba5b
Merge: d81a834 eb77517
Author: denise.worthen <[email protected]>
Date:   Thu Aug 13 12:57:55 2020 -0400

    Merge remote-tracking branch 'upstream/master' into emc/develop

commit d81a834
Author: Denise Worthen <[email protected]>
Date:   Thu Aug 13 09:40:18 2020 -0400

    Fixcommit (NOAA-EMC#14)

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

commit 5ecde75
Merge: 88cc2fd bdf1a1f
Author: denise.worthen <[email protected]>
Date:   Wed Aug 12 16:24:04 2020 -0400

    Merge remote-tracking branch 'upstream/emc/develop' into emc/develop

commit bdf1a1f
Author: Denise Worthen <[email protected]>
Date:   Wed Aug 12 15:55:21 2020 -0400

    changes for consistency w/ current emc-cice5 (NOAA-EMC#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]>

commit 88cc2fd
Merge: c084de4 003aae0
Author: denise.worthen <[email protected]>
Date:   Wed Aug 5 18:35:50 2020 -0400

    Merge remote-tracking branch 'upstream/master' into emc/develop

commit c084de4
Merge: 86b8dab b055c7f
Author: denise.worthen <[email protected]>
Date:   Fri Jul 17 17:24:15 2020 -0400

    Merge remote-tracking branch 'upstream/master' into emc/develop

commit 86b8dab
Merge: 9bdb9ad 8f37bfc
Author: denise.worthen <[email protected]>
Date:   Fri Jul 17 13:15:25 2020 +0000

    Merge remote-tracking branch 'upstream/emc/develop' into HEAD

commit 8f37bfc
Author: Minsuk Ji <[email protected]>
Date:   Fri Jul 17 09:05:06 2020 -0400

    cice6 compile (NOAA-EMC#6)

    * enable debug build. fix to remove errors

    * fix an error in comp_ice.backend.libcice

    * change Orion to orion for machine identification

commit 9bdb9ad
Merge: 916c6af c22c6d5
Author: denise.worthen <[email protected]>
Date:   Wed Jul 15 13:15:02 2020 -0400

    Merge remote-tracking branch 'CICE-Consortium/master' into emc/develop

commit 916c6af
Author: Denise Worthen <[email protected]>
Date:   Tue Jul 14 08:18:33 2020 -0400

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

commit 8ff4ee0
Author: denise.worthen <[email protected]>
Date:   Tue Jul 7 15:46:57 2020 -0400

    change Orion to orion in backend

    remove duplicate print lines from ice_transport_driver

commit 4e8cc79
Merge: f92bef3 93f0e86
Author: denise.worthen <[email protected]>
Date:   Tue Jul 7 15:32:13 2020 -0400

    Merge remote-tracking branch 'upstream/nuopc' into emc/develop

commit f92bef3
Author: denise.worthen <[email protected]>
Date:   Tue Jul 7 15:20:45 2020 -0400

    update icepack submodule

commit 93f0e86
Merge: 8ebdda9 6b4a277
Author: David A. Bailey <[email protected]>
Date:   Tue Jul 7 13:19:36 2020 -0600

    Merge pull request NOAA-EMC#5 from ESCOMP/coszen

    Add restart_coszen namelist option

commit 6b4a277
Merge: 27dd3b7 8ebdda9
Author: David A. Bailey <[email protected]>
Date:   Tue Jul 7 13:19:22 2020 -0600

    Merge branch 'nuopc' into coszen

commit 50bf856
Merge: 3bb3694 fcf8989
Author: denise.worthen <[email protected]>
Date:   Tue Jul 7 15:03:30 2020 -0400

    Merge remote-tracking branch 'upstream/master'

commit 27dd3b7
Author: David Bailey <[email protected]>
Date:   Tue Jul 7 12:40:33 2020 -0600

    Add restart_coszen namelist option

commit 8ebdda9
Merge: e4c989c 30a81cc
Author: David A. Bailey <[email protected]>
Date:   Tue Jul 7 12:39:20 2020 -0600

    Merge pull request NOAA-EMC#4 from mvertens/nuopc

    cleanup changes to nuopc branch

commit 30a81cc
Author: Mariana Vertenstein <[email protected]>
Date:   Tue Jul 7 12:17:21 2020 -0600

    fixed white space issue

commit e4c989c
Merge: 178693a fcf8989
Author: David Bailey <[email protected]>
Date:   Mon Jul 6 10:24:24 2020 -0600

    Merge branch 'master' of https://github.com/CICE-Consortium/CICE into nuopc

commit aea1aa8
Merge: 178693a 41855fd
Author: Mariana Vertenstein <[email protected]>
Date:   Sat Jul 4 15:04:13 2020 -0600

    update to latest nuopc changes

commit 41855fd
Author: Mariana Vertenstein <[email protected]>
Date:   Sat Jul 4 14:29:12 2020 -0600

    fixes to get cesm working

commit 3a1b88b
Author: denise.worthen <[email protected]>
Date:   Sat Jul 4 13:25:48 2020 -0600

    fix compile errors

commit b4afd2e
Author: Mariana Vertenstein <[email protected]>
Date:   Sat Jul 4 11:59:19 2020 -0600

    removal of many cpp-ifdefs

commit 178693a
Merge: 902e883 c762336
Author: David Bailey <[email protected]>
Date:   Thu Jul 2 15:28:07 2020 -0600

    Merge branch 'nuopc' of https://github.com/ESCOMP/CICE into nuopc

commit 902e883
Author: David Bailey <[email protected]>
Date:   Thu Jul 2 15:27:55 2020 -0600

    Fix logging issues for NUOPC

commit 6bccf71
Author: denise.worthen <[email protected]>
Date:   Thu Jul 2 13:19:25 2020 -0600

    remove cesmcoupled ifdefs

commit c762336
Author: David Bailey <[email protected]>
Date:   Thu Jul 2 11:36:49 2020 -0600

    Move the forapps directory

commit 46fcfba
Author: denise.worthen <[email protected]>
Date:   Thu Jul 2 05:24:54 2020 -0600

    changes for coldstart running

commit 73e7774
Author: David Bailey <[email protected]>
Date:   Wed Jul 1 14:41:27 2020 -0600

    Fix additional OMP problems

commit ad03424
Author: David Bailey <[email protected]>
Date:   Wed Jul 1 12:52:00 2020 -0600

    Fix threading problem in init_bgc

commit 239c7de
Merge: b4da8a6 415df0e
Author: David Bailey <[email protected]>
Date:   Wed Jul 1 12:50:38 2020 -0600

    Merge branch 'nuopc' of https://github.com/ESCOMP/CICE into nuopc

commit b4da8a6
Merge: 6affdcf 55ca18b
Author: David Bailey <[email protected]>
Date:   Wed Jul 1 12:50:14 2020 -0600

    Merge branch 'master' of https://github.com/CICE-Consortium/CICE into nuopc

commit 415df0e
Merge: b5a6058 6affdcf
Author: David Bailey <[email protected]>
Date:   Wed Jul 1 10:08:07 2020 -0600

    Merge branch 'nuopc' of https://github.com/ESCOMP/CICE into nuopc

commit b5a6058
Merge: 7848fdf 55ca18b
Author: David Bailey <[email protected]>
Date:   Wed Jul 1 10:07:31 2020 -0600

    Merge branch 'master' of https://github.com/CICE-Consortium/CICE into nuopc

commit 6affdcf
Merge: 7848fdf c6c20bf
Author: David Bailey <[email protected]>
Date:   Mon Jun 29 15:31:28 2020 -0600

    Merge branch 'master' of https://github.com/CICE-Consortium/CICE into nuopc

commit 089f60f
Author: denise.worthen <[email protected]>
Date:   Thu Jun 25 15:18:56 2020 +0000

    update comp_ice.backend with temporary ice_timers fix

commit 6982ee4
Merge: 308a1d4 7848fdf
Author: denise.worthen <[email protected]>
Date:   Thu Jun 25 14:03:59 2020 +0000

    Merge remote-tracking branch 'upstream/nuopc' into HEAD

commit 7848fdf
Merge: 7e43703 f532dd9
Author: David Bailey <[email protected]>
Date:   Wed Jun 24 15:46:15 2020 -0600

    Merge branch 'master' of https://github.com/CICE-Consortium/CICE into nuopc

commit 308a1d4
Author: denise.worthen <[email protected]>
Date:   Mon Jun 22 15:05:32 2020 -0600

    Revert "update icepack submodule"

    This reverts commit e70d1ab.

commit e70d1ab
Author: denise.worthen <[email protected]>
Date:   Mon Jun 22 14:58:13 2020 -0600

    update icepack submodule

commit f41f1e9
Merge: 7ac0e3d 7e43703
Author: denise.worthen <[email protected]>
Date:   Mon Jun 22 20:52:39 2020 +0000

    Merge remote-tracking branch 'upstream/nuopc' into HEAD

commit 3bb3694
Author: Denise Worthen <[email protected]>
Date:   Fri Jun 5 13:32:44 2020 -0400

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

    * Add atmiter_conv to CICE

    * Add documentation

    * trigger build the docs

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

commit 397e588
Merge: d46d691 2054d09
Author: denise.worthen <[email protected]>
Date:   Tue Jun 2 12:31:56 2020 -0400

    Merge remote-tracking branch 'upstream/master'

commit 7e43703
Merge: 80c9e6e 53715ea
Author: David A. Bailey <[email protected]>
Date:   Tue May 26 09:15:51 2020 -0600

    Merge pull request NOAA-EMC#3 from mvertens/mvertens/nuopc

    changes to satisfy ufsatm and cesm requirements for pot temp and density from atm

commit 53715ea
Author: Mariana Vertenstein <[email protected]>
Date:   Sun May 24 18:06:06 2020 -0600

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

commit 80c9e6e
Merge: 8f0b5ee bce31c2
Author: David Bailey <[email protected]>
Date:   Tue May 19 09:09:00 2020 -0600

    Merge branch 'master' of https://github.com/CICE-Consortium/CICE into nuopc

commit 7ac0e3d
Merge: 10e7c20 8f0b5ee
Author: Denise Worthen <[email protected]>
Date:   Tue May 12 10:02:58 2020 -0400

    Merge pull request #1 from ESCOMP/nuopc

commit 8f0b5ee
Merge: 10e7c20 ce8e5a9
Author: David A. Bailey <[email protected]>
Date:   Sun May 10 08:24:19 2020 -0600

    Merge pull request #2 from apcraig/ufs01

    Update CICE for coupling with UFS

commit ce8e5a9
Author: apcraig <[email protected]>
Date:   Sat May 9 21:29:22 2020 -0600

    update CICE6 to support coupling with UFS

commit 10e7c20
Author: Mariana Vertenstein <[email protected]>
Date:   Wed Apr 29 16:36:09 2020 -0600

    fixed problems in updated orbital calculations needed for cesm

commit 183218a
Author: Mariana Vertenstein <[email protected]>
Date:   Thu Apr 23 17:43:35 2020 -0600

    updated orbital calculations needed for cesm

commit d46d691
Author: Denise Worthen <[email protected]>
Date:   Wed Apr 22 14:48:08 2020 -0400

    merge latest master (NOAA-EMC#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]>

commit 71d2ded
Merge: 99470ed 9ac1863
Author: Denise Worthen <[email protected]>
Date:   Thu Apr 2 15:13:02 2020 -0400

    Merge pull request NOAA-EMC#3 from CICE-Consortium/master

commit 99470ed
Merge: 0338d04 7e2a1d9
Author: Denise Worthen <[email protected]>
Date:   Sat Mar 7 10:03:29 2020 -0500

    Merge pull request #2 from CICE-Consortium/master

commit 0338d04
Merge: b5134ad 7e11a34
Author: Denise Worthen <[email protected]>
Date:   Tue Feb 25 08:43:10 2020 -0500

    Merge pull request #1 from CICE-Consortium/master
Merge branch 'emc/develop' into feature/main6.4.2
DeniseWorthen added a commit to DeniseWorthen/CICE that referenced this pull request Sep 22, 2023
@DeniseWorthen
Update CICE for latest Consortium master (NOAA-EMC#38)
9d5fdb1 
    * Implement advanced snow physics in icepack and CICE
    * Fix time-stamping of CICE history files
    * Fix CICE history file precision
DeniseWorthen added a commit to DeniseWorthen/CICE that referenced this pull request Apr 7, 2024
@DeniseWorthen
Squashed commit of the following:
b75b8a9 
commit f36559256eb08272cdfe0706c45e0824e00fb37b
Author: Denise Worthen <[email protected]>
Date:   Sun Apr 7 09:50:39 2024 -0400

    fix bad merge

    * this fixes a block of code w/in a CESMCOUPLED ifdef block

commit cbac04dad1f79eb51900dab8bf6aaa7cddbe82a1
Merge: 5a56c38 7d4e5de
Author: Denise Worthen <[email protected]>
Date:   Wed Apr 3 16:05:31 2024 -0400

    Merge branch 'emc/develop' into feature/pio_options

commit 5a56c38a0d73bf16ddf2024a23f3f3fe4432007a
Author: Denise Worthen <[email protected]>
Date:   Wed Apr 3 15:44:33 2024 -0400

    update with last emc/develop change

commit aca835755aa82ead50040ea7e43ec63619667054
Author: Tony Craig <[email protected]>
Date:   Thu Feb 22 08:55:44 2024 -0800

    Update IO formats and add new IO namelist controls (#928)

    This provides new features for CICE IO both thru netCDF and PIO.  New namelist are added to control history and restart format, hdf5 compression and chunking, the PIO rearranger, and PIO IO task control.  Separate controls are provided for history and restart files.  The namelist changes are for

      _history_format, restart_format
      history_rearranger, restart_rearranger
      history_iotasks, history_root, history_stride, restart_iotasks, restart_root, and restart_stride
      history_chunksize, history_deflate, restart_chunksize, restart_deflate._

    In particular,

    - Update restart_format and history_format options to 'cdf1', 'cdf2', 'cdf5', 'hdf5', 'pnetcdf1', 'pnetcdf2', 'pnetcdf5', 'default'.  The old options, 'default', 'pio_netcdf', and 'pio_pnetcdf' are still supported and backwards compatible with lcdf64, but are deprecated and no longer documented.  The old options and old namelist lcdf64 are covered by the new options.  Support of the old options should be removed in the future.  Note that some problems were discovered when opening files with hdf5 format but reading non-hdf5 files with a spack built PIO/netCDF.  As a result, the format specified for the restart read is always 'cdf1' which provides flexibility and robustness across software installs, although it may result in serial reads of hdf5 files when a parallel read could be done.
    - Deprecate lcdf64 namelist.  This namelist is no longer needed and is covered by the new restart_format and history_format options.  The namelist still exists and is backwards compatible with the old 'default', 'pio_netcdf', and 'pio_pnetcdf' format options, but is no longer documented.  This should be removed in the future.
    - Add new namelist to control PIO pe/task setup (iotasks, root, stride) for history and restart.  These settings control the PIO IO tasks.  The root, stride, and iotasks are consistent with the MPI communicator.  root=0 is the first MPI task.  These control PIO IO performance and are usually a function of things like the IO and node hardware.  See PIO for more information.  CICE computes PIO iotask, root, and stride defaults for cases where -99 is passed in for some or all of these namelist.  Those defaults are somewhat constrained by a bug in PIO, https://github.com/NCAR/ParallelIO/issues/1986.  The current implementation avoids the bug by limiting the iotasks for some MPI task counts.  This is noted in ice_pio.F90.
    - Add new namelist to control PIO rearranger (rearranger) for history and restart.  Supports 'box', 'subset', and 'default'.  These control how PIO rearrangment is carried out.  default is equivalent to box and the box generally performs better.  See PIO for more information.
    - Add new namelist to support hdf5 compression and chunking (deflate, chunksize) for history and restart.  The deflate controls file compression and is an integer between 0 and 9 where 0 means no compression and 9 is maximum compression.   Generally, the higher the number, the slower the IO and the smaller the file, but the optimal setting depends on the contents of the file.  Chunksize provides a performance control for the hdf5 parallel writes.  It is a 2d array and is associated with the size of the piece of the array written by hdf5.  hdf5 can be read and written in parallel, but that depends on how netCDF and PIO are built.  Note that prior version of PIO, including PIO1, do not support the hdf5 compression and chunking thru the PIO interface.
    - Add new namelist settings (set_nml files) and update the io_suite to cover the new IO options.  Remove old namelist settings associated with the deprecated format options and the lcdf64 namelist.  These deprecated feature are no longer tested.
    - Update documentation to add new namelist and IO features.
    - Update the nuopc/cmeps driver code to support the new features.
    - Update the default ice_in to add the new namelist.
    - Update the derecho netcdf module to a version that supports hdf5.
    - Clean up some code formatting (indentation)

    ---------

    Co-authored-by: Anton Steketee <[email protected]>

commit 9e9e5b3fabd88c429c4632baa8235187129e2dd7
Author: Philippe Blain <[email protected]>
Date:   Mon Feb 19 14:08:37 2024 -0500

    ug_testing.rst: also mention checking the base suite results (#934)

    In the "End-To-End Testing Procedure" section of the user guide, we
    instruct users to run a base suite and a test suite, but only mention
    checking the results of the test suite.

    Also mention checking the results of the base suite first, to make sure
    everything passes before checking the test suite.

    Suggested-by: Jean-Francois Lemieux <[email protected]>

commit 095e62a9342df74261b90fcb7a20d2ecdae2c5bc
Author: Tony Craig <[email protected]>
Date:   Mon Feb 12 14:49:02 2024 -0800

    Update PULL_REQUEST_TEMPLATE to request detailed information (#931)

    Update PULL_REQUEST_TEMPLATE to request detailed information about changes associated with the PR. This will be useful for the commit log when squash merging the PR.
    ---------

    Co-authored-by: Philippe Blain <[email protected]>

commit 1a00e5e4e967c8429a7753ac3597f9c1476cf6b7
Author: David A. Bailey <[email protected]>
Date:   Mon Feb 5 16:22:11 2024 -0700

    Fix for ice_mesh_mod with grid variables removed (#929)

commit 7a4b95e6deec0ec72c1da35a23ae1eb3ffe3d077
Author: Tony Craig <[email protected]>
Date:   Mon Jan 22 11:12:13 2024 -0800

    Update pio and netcdf error checks (#927)

    Update pio and netcdf error checks

    ---------

    Co-authored-by: anton-climate <[email protected]>
    Co-authored-by: Anton Steketee <[email protected]>

commit 6449f40c41aa1a5c00096696202d7bd7ebd2a69a
Author: JFLemieux73 <[email protected]>
Date:   Thu Jan 11 19:17:20 2024 +0000

    Add vorticity as a diagnostic output (#924)

    * Added new variable vort for vorticity output

    * Added calc of diag vorticity for evp, vp and eap for B, C and CD grids

    * updated doc and ice_in file for new vorticity variable

    * Changed output frequency of vorticity from m to x

    * Added f_vort to set_nml.histall and set_nml.histdbg

    * Specified location of divu, shear and vort in ice_history.F90

    ---------

    Co-authored-by: Tony Craig <[email protected]>

commit a20bfddf7a1260dbb61241e0838c678d2eecf972
Author: David A. Bailey <[email protected]>
Date:   Thu Jan 11 11:07:36 2024 -0700

    scamn bugfix for nuopc driver (#926)

    Co-authored-by: John Truesdale <[email protected]>

commit 1314e17b4213c6ce9424eab80763edf4b2ae867f
Author: TRasmussen <[email protected]>
Date:   Thu Jan 11 18:25:52 2024 +0100

    First round of housekeeping on ice_grid (#921)

    * removal of unused variables.

    * moved xav to transport. Could remove commented code. Could remove xav and yav as they are zero

    * Move derived parameters and only allocate if needed

    * bugfixes for cxp, cyp...

    * fix index and remove commented code in ice_grid

    * new version of transport_remap. xav, yav array where needed. xxav, yyav parameter

    * Removed comments rom ice_transport_remap and arrays for nonuniform grids

commit 37f9a98b1b6529bc957fb888bd00348ab61c8b32
Author: Tony Craig <[email protected]>
Date:   Thu Dec 21 07:15:02 2023 -0800

    Fix single channel debug failure, Update github actions testing (#922)

    * update ghactions testing

    * refactor min/max global reductions, code away from huge which was giving MPI some problems.

commit b14cedfaed8b81500fc5422cfc44b6d80e5893ef
Author: David A. Bailey <[email protected]>
Date:   Tue Nov 28 15:10:16 2023 -0700

    ice_history: allow per-stream suffix for history filenames (#912)

    * Add capability for h extension

    * Update documentation for hist_str

    * Change hist_str to hist_suffix

    * Change in default namelist

    * Update doc/source/cice_index.rst

    Co-authored-by: Philippe Blain <[email protected]>

    * One more hist_str

    ---------

    Co-authored-by: Philippe Blain <[email protected]>

commit 21fab166fd2b8e903df366dbc1c518dabd08c23f
Author: Tony Craig <[email protected]>
Date:   Tue Nov 28 10:04:36 2023 -0800

    Update Icepack to #f6ff8f7c4d4cb6f (#913)

    * Update Icepack to #f6ff8f7c4d4cb6f

    Split the developer guide infrastructure section from the dynamics documentation

    Add a coding standard section to the documentation

    Add a couple sentences about the state of the parameter nghost to the documentation

    Update opticep to use the latest main code for the unit test

    * update documentation

commit 509e2c33e95e3a2370dc406fb2fe4d06192420a6
Author: Philippe Blain <[email protected]>
Date:   Thu Nov 23 13:09:04 2023 -0500

    ice_history: refactor CMIP history variables (#906)

    * ice_flux: zero-initialize divu and shear in init_history_dyn

    'divu' and 'shear' are accessed in 'accum_hist' when writing the initial
    condition before they are initialized at the start of {eap, evp,
    implicit_solver}. This leads to runtime error when compiling with NaN
    initialization.

    Zero-initialize 'divu' and 'shear' in init_history_dyn, where the
    related variable 'strength' is already zero-initialized.

    * ice_history_shared: disallow 'x' in history frequency variables f_*'

    In the current code, nothing prevents users from leaving 'x' along with
    active frequencies in the individual namelist history frequency
    variables, for example:

        f_aice = 'xmd'

    This configuration does not work correctly, however. The corresponding
    history fields are correctly defined in
    ice_history_shared::define_hist_field, but since the calls to
    ice_history_shared::accum_hist_field in ice_history::accum_hist are only
    done after checking that the first element of each frequency variable is
    not 'x', the corresponding variables in the history files are all zero.

    Prevent that behaviour by actually disallowing 'x' in history frequency
    variables if any other frequencies are active. To implement that, add a
    check in the loop in define_hist_field, which loops through vhistfreq,
    (corresponding to f_aice, etc. in ice_history). Since this subroutine
    initializes 'id(:)' to zero and then writes a (non-zero) index in 'id'
    for any active frequency, it suffices to check that all previous indices
    are non-zero.

    * ice_history: remove uneeded conditions around CMIP history variables

    In ice_history::accum_hist, after the calls to accum_hist, we loop on
    the different output streams, and on the history variables in the
    avail_hist_fields array, to mask out land points and convert units for
    each output variable.

    Since 3c99e106 (Update CICE with CMIP changes. (#191), 2018-09-27), we
    also use this loop to do a special treatment for some CMIP variables
    (namely, averaging them only for time steps where ice is present, and
    masking points where ice is absent).

    This adjustment is done if the corresponding output frequency variable
    (f_sithick, etc.) does not have 'x' as its first element, and if the
    corresponding index in avail_hist_field for that variable/frequency
    (n_sithick(ns)) is not zero. Both conditions are in fact uneeded since
    they are always true.

    The first condition is always true because if the variable is found in
    the avail_hist_field array, which is ensured by the condition on line
    3645, then necessarily its corresponding namelist output frequency won't
    have 'x' as its first character (since this is enforced in
    ice_history_shared::define_hist_field).

    The second condition is always true because if the variable is found in
    the avail_hist_field array, then necessarily its index in that array,
    n_<var>(ns), is non-zero (see ice_history_shared::define_hist_field).

    Remove these uneeded conditions. This commit is best viewed with

        git show --color-moved --color-moved-ws=allow-indentation-change

    * ice_history: use loop index directly for CMIP variables

    In ice_history::accum_hist, there is a special treatment for some CMIP
    variables where they are averaged only for time steps where ice is
    present, and points where there is no ice are masked. This is done on
    the loop on output streams (with loop index n).

    This special averaging is done by accessing a2D and a3Dc using the
    variable n_<var>(ns), which corresponds to the index in the
    avail_hist_field array where this history variable/frequency is defined.
    By construction, this index correponds to the loop index 'n', for both
    the 2D and the 3D loops. Simplify the code by using 'n' directly.

    * ice_history_shared: add two logical components to ice_hist_field

    At the end of ice_history::accum_hist, we do a special processing for
    some CMIP variables: we average them only for time steps where ice is
    present, and also mask ice-free points. The code to do that is repeated
    for each variable to which it applies.

    In order to reduce code duplication, let's introduce two new logical
    components to our 'ice_hist_field' type, defaulting them to .false., and make them optional
    arguments in ice_history_shared::define_hist_field. This allows us to
    avoid defining them for each output variable. We'll set them for CMIP
    variables in a following commit.

    * ice_history: set avg_ice_present, mask_ice_free_points for relevant CMIP variables

    In the previous commit, we added two components to type ice_hist_field
    (avg_ice_present and mask_ice_free_points), relating to some special
    treatment for CMIP variables (whether to average only for time steps
    where the ice is present and to mask ice-free points).

    Set these to .true. in the call to 'define_hist_field' for the relevant
    2D variables [1], and set only 'avg_ice_present' to .true. for the 3D
    variables siitdthick and siitdsnthick, corresponding to the code under
    the "Mask out land points and convert units" loop in
    ice_history::accum_hist.

    [1]
    sithick
    siage
    sisnthick
    sitemptop
    sitempsnic
    sitempbot
    siu
    siv
    sidmasstranx
    sistrxdtop
    sistrydtop
    sistrxubot
    sistryubot
    sicompstren
    sispeed
    sidir
    sialb
    sihc
    siflswdtop
    siflswutop
    siflswdbot
    sifllwdtop
    sifllwutop
    siflsenstop
    siflsensupbot
    sifllatstop
    siflcondtop
    siflcondbot
    sipr
    sifb
    siflsaltbot
    siflfwbot
    siflfwdrain
    sidragtop
    sirdgthick
    siforcetiltx
    siforcetilty
    siforcecoriolx
    siforcecorioly
    siforceintstrx
    siforceintstry

    * ice_history: use avg_ice_present, mask_ice_free_points to reduce duplication

    Some CMIP variables are processed differently in
    ice_history::accum_hist: they are averaged only for time steps when ice
    is present, and points where ice is absent are masked. This processing
    is repeated for each of these variables in the 2D and 3Dc loops.

    To reduce code duplication, use the new components avg_ice_present and
    mask_ice_free_points of ice_hist_field to perform this processing only
    for variables that were defined accordingly. The relevant variables
    already have those components defined as of the previous commit.

    Note that we still need a separate loop for the variable 'sialb' (sea
    ice albedo) to mask points below the horizon.

commit 1cf109b7c350f119e8e3cd8bd918fa31e61d829c
Author: David A. Bailey <[email protected]>
Date:   Mon Nov 20 14:03:59 2023 -0700

    Change to dealloc_grid in CICE_InitMod.F90 (#911)

commit d14bb694f2f8df4e74361a9df999e82eaa44fc8b
Author: Mads Hvid Ribergaard <[email protected]>
Date:   Fri Nov 17 16:39:01 2023 +0100

    Add missing logical "timer_stats" (#910)

    Co-authored-by: Mads Hvid Ribergaard <[email protected]>

commit 8573ba8ab196c1e357a101462b16bd92128461b1
Author: TRasmussen <[email protected]>
Date:   Thu Nov 16 22:12:07 2023 +0100

    New 1d evp solver (#895)

    * New 1d evp solver

    * Small changes incl timer names and inclued private/publice in ice_dyn_core1d

    * fixed bug on gnu debug

    * moved halo update to evp1d, added deallocation, fixed bug

    * fixed deallocation dyn_evp1d

    * bugfix deallocate

    * Remove gather strintx and strinty

    * removed 4 test with evp1d and c/cd grid

    * Update of evp1d implementation

    - Rename halo_HTE_HTN to global_ext_halo and move into ice_grid.F90
    - Generalize global_ext_halo to work with any nghost size (was hardcoded for nghost=1)
    - Remove argument from dyn_evp1d_init, change to "use" of global grid variables
    - rename pgl_global_ext to save_ghte_ghtn
    - Update allocation of G_HTE, G_HTN
    - Add dealloc_grid to deallocate G_HTE and G_HTN at end of initialization
    - Add calls to dealloc_grid to all CICE_InitMod.F90 subroutines
    - Make dimension of evp1d arguments implicit size more consistently
    - Clean up indentation and formatting a bit

    * Clean up trailing blanks

    * resolved name conflicts

    * 1d grid var name change

    ---------

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

commit 5d09123865b5e8b47ba9d3c389b23743d84908c1
Author: Mads Hvid Ribergaard <[email protected]>
Date:   Fri Nov 10 01:17:24 2023 +0100

    Rename sum to asum, as "sum" is also a generic fortran function (#905)

    Co-authored-by: Mads Hvid Ribergaard <[email protected]>

commit 4450a3e8c64bc07d1173eb3e341cd8dea91d5068
Author: Tony Craig <[email protected]>
Date:   Fri Oct 27 22:22:43 2023 -0700

    Update Icepack to latest version, does not affect CICE (#903)

commit ea241fa81a53b614f54cf5c2dad93bda20b72a78
Author: Tony Craig <[email protected]>
Date:   Fri Oct 27 16:27:15 2023 -0700

    Update version, remove trailing blanks (#901)

commit 32f233d9728b4e453c0f02fb79a188517a8d5ed4
Author: Tony Craig <[email protected]>
Date:   Fri Oct 27 16:27:01 2023 -0700

    Update Icepack, add snicar and snicartest tests (#902)

commit 0484dcd1410920f26375b7c280500a5bd16173e9
Author: Tony Craig <[email protected]>
Date:   Fri Oct 27 09:24:52 2023 -0700

    Split N/E grid computation out of Tlonlat, create NElonlat subroutine. (#899)

    * Split N/E grid computation out of Tlonlat, create NElonlat subroutine.

    See https://github.com/CICE-Consortium/CICE/issues/897

    When TLON, TLAT, ANGLET are on the CICE grid, Tlonlat is NOT called.  This
    meant N and E grid info was never computed.  This would fail during history
    writing with invalid values in N and E grid arrays.  And it would also
    cause problem if the C-grid were run with this type of CICE grid.

    There are no test grids that have TLON, TLAT, ANGLET on them, so this
    error was not found in standard test suites.  This was detected by
    users.

    * Add gx3 grid/kmt files with TLON, TLAT, ANGLET netcdf grid test.

    The grid and kmt files were produced from a gx3 history file.  Results
    are not bit-for-bit with the standard gx3 runs, but seem to be roundoff
    different initially (as expected).

commit 0b5ca0911edaf6081ba891f4287af14ceb201c9f
Author: Tony Craig <[email protected]>
Date:   Thu Oct 26 19:33:19 2023 -0700

    Revert "Add 5-band dEdd shortwave tests (#896)" (#900)

    This reverts commit b4abca479cd548c3e600a6c645447d5ba9464422.

commit 2e13606558f7ce71633274bc38630caa23de3392
Author: Philippe Blain <[email protected]>
Date:   Thu Oct 26 13:24:37 2023 -0400

    doc: update histfreq_base and hist_avg descriptions (#898)

    * doc: ug_implementation.rst: do not use curly quotes

    The namelist excerpt in section 'History' of the Implementation part of
    the user guide uses curly quotes (’) instead of regular straight quotes
    ('). This is probably a remnant of the LaTeX version of the doc. These
    quotes can't be used in Fortran and so copy pasting from the doc to the
    namelist causes runtime failures. Use straigth quotes instead.

    * doc: ug_implementation.rst: align histfreq_n with histfreq

    Align frequencies with their respective streams, which makes the example
    clearer.

    * doc: ug_implementation.rst: avoid "now" and "still"

    The documentation talks about the current version of the code, so it is
    unnecessary to use words like "now" and "still" to talk about the model
    features. Remove them.

    * doc: ug_implementation.rst: mention histfreq_base and hist_avg are per-stream

    In 35ec167d (Add functionality to change hist_avg for each stream
    (#827), 2023-05-17), hist_avg was made into an array, allowing each
    stream to individually be set to instantaneous or averaged mode. The
    first paragraph of the "History" section of the user guide was updated,
    but another paragraph a little below was not.

    In 933b148c (Extend restart output controls, provide multiple frequency
    options (#850), 2023-08-24), histfreq_base was also made into an array,
    but the "History" section of the user guide was not updated.

    Adjust the wording of the doc to reflect the fact that both hist_avg and
    histfreq_base are per-stream. Also adjust the namelist excerpt to make
    histfreq_base an array, and align hist_avg with it.

    * doc: ug_implementation.rst: refer to 'timemanager' after mentioning histfreq_base

    In 34dc6670 (Namelist option for time axis position. (#839),
    2023-07-06), the namelist option hist_time_axis was added, and the
    "History" section of the user guide updated to mention it.

    The added sentence, however, separates the mention of 'histfreq_base'
    and the reference to the "Time manager" section, which explains the
    different allowed values for that variable. Move the reference up so
    both are next to each other.

commit b4abca479cd548c3e600a6c645447d5ba9464422
Author: Tony Craig <[email protected]>
Date:   Thu Oct 26 08:54:40 2023 -0700

    Add 5-band dEdd shortwave tests (#896)

commit 624c28b19b443c031ea862e3e5d2c16387777ddc
Author: Philippe Blain <[email protected]>
Date:   Thu Oct 26 11:52:26 2023 -0400

    ice_dyn_evp: pass 'grid_location' for LKD seabed stress on C grid (#893)

    When the C grid support was added in 078aab48 (Merge cgridDEV branch
    including C grid implementation and other fixes (#715), 2022-05-10),
    subroutine ice_dyn_shared::seabed_stress_factor_LKD gained a
    'grid_location' optional argument to indicate where to compute
    intermediate quantities and the seabed stress itself (originally added
    in 0f9f48b9 (ice_dyn_shared: add optional 'grid_location' argument to
    seabed_stress_factor_LKD, 2021-11-17)). This argument was however
    forgotten in ice_dyn_evp::evp when this subroutine was adapted for the C
    grid in 48c07c66 (ice_dyn_evp: compute seabed stress factor at CD-grid
    locations, 2021-11-17), such that currently the seabed stress is not
    computed at the correct grid location for the C and CD grids.

    Fix that by correctly passing the 'grid_location' argument. Note that
    the dummy argument is incorrectly declared as 'intent(inout)' in the
    subroutine, so change that to 'intent(in)' so we can pass in character
    constants.

    Closes: https://github.com/CICE-Consortium/CICE/issues/891

commit d3698fb46fc23a81b1df8dba676a5a74d7e96a39
Author: daveh150 <[email protected]>
Date:   Wed Oct 25 16:34:35 2023 -0500

    Add atm_data_version to allow JRA55 forcing filenames to have a unique version string (#876)

    * Add jra55date to allow JRA55 forcing to have creation date in file name

    * Changed jra55_date to atm_data_date. Added atm_data_date to docs.

    * Change jra55_date to atm_data_date. Update JRA55_files to include atm_data_date in file. Update case scripts/namelist.

    * change atm_data_date to atm_data_version. Update set_nml.tx1 default to corrected forcing version

    * Update doc to have atm_data_version in proper alphabetical order

    * Re-add set_nml.jra55. Deleted accitentally

    * Fix type-o in atm_data_dir documentation

    * Add atm_data_version to set_nml.jra55

    * fix spacing after changing atm_data_date to atm_data_version

    * Change atm_data_date to atm_data_version

    * Comment out JRA55 file debugging

    * Update dg_forcing docs to describe atm_data_version string

    * Uncomment JRA55 filename check. Added check for debug_forcing before writing output

    * Correct doc format/links in dg_forcing.rst

commit 8916b9ff2c58a3a095235bb5b4ce7e8a68f76e87
Author: Tony Craig <[email protected]>
Date:   Wed Oct 18 14:08:21 2023 -0700

    Update update_ocn_f implementation, Add cpl_frazil namelist (#889)

    * Update update_ocn_f implementation

    Add cpl_frazil namelist

    Add update_ocn_f and cpl_frazil to icepack_init_parameters call, set these
    values inside Icepack at initialization.

    Remove update_ocn_f argument from icepack_step_therm2 call

    Update runtime_diags and accum_hist to account for new Icepack and
    cpl_frazil implementation.  These may need an addition update later.

    * Update documentation

commit 6ba070f7e7027f9fd2cc32f2dbe10c9854511d93
Author: Tony Craig <[email protected]>
Date:   Wed Oct 18 12:35:08 2023 -0700

    Update Documentation to clarify Namelist Inputs (#888)

    * Update Documentation to clarify Namelist Inputs

    * Update documentation

commit a9d6dc75f47a2898f1800ad4ddd96c4992e3bed0
Author: Tony Craig <[email protected]>
Date:   Wed Oct 18 10:47:01 2023 -0700

    Update input data area for Derecho, switch to campaign (#890)

commit 5ddb74dfb8724ff90aa7e806d5bfcfb4a0990762
Author: Tony Craig <[email protected]>
Date:   Wed Oct 18 10:46:40 2023 -0700

    Remove cicedynB link (#887)

    Update documentation

commit 96b43fb458fe00696d9532e547a3c5bff113f9f9
Author: Tony Craig <[email protected]>
Date:   Wed Oct 18 10:46:25 2023 -0700

    Update Icepack CPP USE_SNICARHC to NO_SNICARHC and update logic (#886)

    Update Icepack to version #0c548120ce44382 Oct 16, 2023 includes NO_SNICARHC

commit 48a92ef6dd6bf7884ec8a16b2c082345accae385
Author: Tony Craig <[email protected]>
Date:   Fri Oct 13 14:22:03 2023 -0700

    Remove use of the deprecated "_old" tfrz_options in set_nml files.  This (#883)

    changes answers for some test cases, as expected.

    Update tfrz_option implementation to not allow _old options.

commit 276563041ea6a2b6b4c70cbfa5173fb85db7b47f
Author: Tony Craig <[email protected]>
Date:   Thu Oct 12 12:41:17 2023 -0700

    Add perlmutter gnu, intel, cray port (#882)

commit deb247bcec381615d01006bfa15dddf3a4f068fd
Author: Tony Craig <[email protected]>
Date:   Thu Oct 5 12:50:32 2023 -0700

    Update CICE for E3SM Icepack modifications (#879)

    * Update CICE to run with eclare108213/Icepack branch snicar (#100)

    * Update CICE to run with eclare108213/Icepack branch snicar

    - including https://github.com/eclare108213/Icepack/pull/13, Sept 11, 2022
    - Passes full CICE test suite on cheyenne with 3 compilers except alt04 changes
      answers for all compilers and all tests.  CICE #fea412a55f was baseline.
    - Icepack submodule still points to standard version on main, need to be
      swapped manually to appropriate development version.

    * Remove faero_optics

    * update ciceexe string to account for USE_SNICARHC CPP

    * Update documentation

    * Update test suite to add modal testing

    * Point Icepack submodule to cice-consortium/E3SM-icepack-initial-integration

    Update to snicar branch merge, #8aef3f785ce

    * Add E3SM namelists for CICE. (#101)

    * New e3sm and e3smbgc namelist options

    * Update E3SM test options

    * Add a simple e3sm test suite

    * atmbndy is not actually different

    * Additional changes

    * add Tliquidus_max namelist parameter to CICE

    * Add Tf argument to icepack interfaces

    * Add constant option for tfrz_option

    * Fix some diagnostic prints and add to additional drivers

    * Update messages and change option in alt01

    * Update implementation for latest version of Icepack

    - Update tfrz_option, add _old options for backwards bit-for-bit
    - Fix unittests
    - Add hi_min to namelist and tests

    * Update Icepack

    * Update to E3SM-Project/Icepack/cice-consortium/E3SM-icepack-initial-integration including Icepack1.3.3 release, Dec 15, 2022.

    * Update Icepack to E3SM-Project/Icepack #87db73ba6d93747a9, current head of cice-consortium/E3SM-icepack-initial-integration Feb 3, 2023

    * Update boxchan1e and boxchan1n tests to tfrz_option = 'mushy_old' to recover Consortium main results

    Update Icepack to the latest hash on E3SM-Project Icepack cice-consortium/E3SM-icepack-initial-integration, #96f2fc707fc743d7

    Prior commit was a merge from CICE Consortium Main, #d466031001cf447bcd64220c842dcd2707f61e9, Sept 29, 2023

    * remove icepack

    * update icepack

    ---------

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

commit d466031001cf447bcd64220c842dcd2707f61e90
Author: Tony Craig <[email protected]>
Date:   Fri Sep 29 12:08:53 2023 -0700

    Add single grid channel capability and test for C-grid (#875)

    * Added code for transport in one grid cell wide channels

    * Update remap advection to support transport in single gridcell channels

    Add single grid east and north channel configurations and tests

    * Update documentation

    * Remove temporary code comments

    ---------

    Co-authored-by: Jean-Francois Lemieux <[email protected]>

commit 55342ca7cb4a1be511ade6249e349cb8a8095881
Author: Dougie Squire <[email protected]>
Date:   Tue Sep 26 03:49:09 2023 +1000

    Fix mesh mask check in nuopc/cmeps cap (#873)

commit a5bb4f9a0c180e325e2a5480832f588dbfdd25ec
Author: Denise Worthen <[email protected]>
Date:   Fri Sep 15 16:01:00 2023 -0400

    switch to cesm-style field names (#869)

commit 01ed4db7c4e5857768a37e8b1fd7472ab5121827
Author: JFLemieux73 <[email protected]>
Date:   Fri Sep 15 19:59:55 2023 +0000

    More accurate calculation of areafact in remapping (#849)

    * 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]>

commit 06282a538e03599aed27bc3c5506ccc31a590069
Author: Tony Craig <[email protected]>
Date:   Fri Sep 8 11:26:45 2023 -0700

    Update version to 6.4.2 (#864)

    Update License and Copyright

    Update Icepack for version/copyright

commit 714bab97540e5b75c0f2b6c11cd061277cdb322d
Author: Tony Craig <[email protected]>
Date:   Thu Sep 7 14:20:29 2023 -0700

    Update Cheyenne and Derecho ports (#863)

    * 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

commit cbbac74cd9073dce8eb44fa23cabb573913aa44f
Author: David A. Bailey <[email protected]>
Date:   Tue Sep 5 14:22:59 2023 -0600

    Only print messages in CAP on master task (#861)

commit 32dc48eae101749b437bd777c18830e3c397b17a
Author: Tony Craig <[email protected]>
Date:   Thu Aug 31 13:05:54 2023 -0700

    Update Icepack to #23b6c1272b50d42ca, Aug 30, 2023 (#857)

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

commit e8a69abde90b99fc6528d469b8698506a99f6e2a
Author: Denise Worthen <[email protected]>
Date:   Mon Aug 28 16:00:41 2023 -0400

    Add logging features to nuopc/cmeps cap; deprecates zsalinity in cap (#856)

    * merge latest master (#4)

    * Isotopes for CICE (#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. (#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 e70d1abcbeb4351195a2b81c6ce3f623c936426c.

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

commit 933b148cb141a16d74615092af62c3e8d36777a2
Author: Tony Craig <[email protected]>
Date:   Thu Aug 24 10:23:56 2023 -0700

    Extend restart output controls, provide multiple frequency options (#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

commit 357103a2df0428089d54bdacf9eab621a5e1f710
Author: Tony Craig <[email protected]>
Date:   Tue Aug 22 11:27:28 2023 -0700

    Deprecate zsalinity (#851)

    * 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)

commit 8322416793ae2b76c2bafa9c7b9b108c289ede9d
Author: Elizabeth Hunke <[email protected]>
Date:   Fri Aug 18 17:34:24 2023 -0600

    Updates to advanced snow physics implementation (#852)

    * Replace tr_snow flag with snwredist, snwgrain in some places (tr_snow is still used more generally).  Fix intent(out) compile issue in ice_read_write.F90. Replace badger with chicoma machine files.

    * update icepack to 86cae16d1b7c4c4f8

    ---------

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

commit 7e8dc5b2aeffe98a6a7fd91dbb8e93ced1e3369c
Author: Tony Craig <[email protected]>
Date:   Thu Aug 10 13:06:41 2023 -0700

    Update conda_macos to fix problems with Github Actions testing (#853)

    * test ghactions

    * update master to main in github actions

commit 4cb296c4003014fe57d6d00f86868a78a532fc95
Author: JFLemieux73 <[email protected]>
Date:   Tue Jul 25 16:11:33 2023 +0000

    Modification of edge mask computation when l_fixed_area=T in horizontal remapping (#833)

    * Use same method whether l_fixed_area=T or F to compute masks for edge fluxes

    * Corrected typo in comment

    * Cosmetic (indentation) change in ice_transport_remap.F90

    * Set l_fixed_area value depending of grid type

    * Modifs to the doc for l_fixed_area

    * Use umask for uvel,vvel initialization for boxslotcyl and change grid avg type from S to A in init_state

    * Temporary changes before next PR: l_fixed_area=F for B and C grid

    * Temporary changes before next PR: remove paragraph in the doc

    * Small modifs: l_fixed_area and grid_ice are defined in module ice_transport_remap

commit 9f42a620e9e642c637d8f04441bacb5835ebf0b7
Author: Tony Craig <[email protected]>
Date:   Thu Jul 20 14:59:42 2023 -0700

    Update Icepack to Consortium main #4728746, July 18 2023 (#846)

    - fix optional arguments issues
    - fix hsn_new(1) bug

    Update optargs unit test, add new test cases

    Add opticep unit test, to test CICE calls to Icepack without optional arguments.
    Add new comparison option to comparelog.csh to compare a unit test with
    a standard CICE test.

    Update unittest_suite

    Update documentation about optional arguments and unit tests

commit f9d3002c86e11ca18b06382fc2d0676c9a945223
Author: Tony Craig <[email protected]>
Date:   Thu Jul 13 16:01:26 2023 -0700

    Add support for JRA55do (#843)

    * updating paths for local nrlssc builds

    * Add jra55do forcing option

    * Updated env.nrlssc_gnu for new local directory structure

    * Added JRA55do to file names. Added comments for each variable name at top of JRA55do_???_files subroutine

    * Make JRA55 forcing to use common subroutines. Search atm_data_type for specific cases

    * remove extraneous 'i' variable in JRA55_files

    * Changed JRA55 filename JRA55_grid instead of grid at end of filename

    * Add jra55do tests to base_suite and quick_suite. This is done via set_nml options.

    * Update forcing implementation to provide a little more flexibility for
    JRA55, JRA55do, and ncar bulk atm forcing files.

    * Update documentation

    * update Onyx port

    * Update forcing documentation

    Initial port to derecho_intel

    * clean up blank spaces

    ---------

    Co-authored-by: daveh150 <[email protected]>

commit 766ff8d9606ae08bdd34ac2b36b6b068464c7e71
Author: Tony Craig <[email protected]>
Date:   Tue Jul 11 07:53:22 2023 -0700

    Update Icepack to #d024340f19676b July 6, 2023 (#841)

    Remove deprecated COREII LYq forcing

    Remove deprecated print_points_state

    Update links in rst documentation to point to main, not master

commit 34dc66707f6b691b1689bf36689591af3e8df270
Author: David A. Bailey <[email protected]>
Date:   Thu Jul 6 21:46:58 2023 -0600

    Namelist option for time axis position. (#839)

    * Add option to change location in interval of time axis

    * Only use hist_time_axis when hist_avg is true

    * Add more comments and information in the documentation

    * Add a check on hist_time_axis as well as a global attribute

    * Abort if hist_time_axis is not set correctly.

commit 7eb4dd7e7e2796c5718061d06b86ff602b9d29cc
Author: Tony Craig <[email protected]>
Date:   Tue Jun 20 09:40:55 2023 -0700

    Update .readthedocs.yaml, add pdf (#837)

    * update readthedocs.yaml, turn on pdf

    * update readthedocs.yaml, turn on pdf

    * update readthedocs.yaml, turn on pdf

    * update readthedocs.yaml, turn on pdf

commit 8e2aab217ece5fae933a1f2ad6e0d6ab81ecad8a
Author: David A. Bailey <[email protected]>
Date:   Tue Jun 20 08:54:25 2023 -0600

    Fix for mesh check in CESM driver (#830)

    * Fix for mesh check in CESM driver

    * Slightly different way to evaluate longitude difference

    * Slightly different way to evaluate longitude difference

    * Put the abs inside the mod

    * Add abort calls back in

commit b98b8ae899fb2a1af816105e05470b829f8b3294
Author: Tony Craig <[email protected]>
Date:   Wed May 24 09:56:10 2023 -0700

    Update Icepack to #6703bc533c968 May 22, 2023 (#829)

    Remove trailing blanks via automated tool in some Fortran files

commit 35ec167dc6beee685a6e9485b8a1db3604d566bd
Author: David A. Bailey <[email protected]>
Date:   Wed May 17 14:56:26 2023 -0600

    Add functionality to change hist_avg for each stream (#827)

    * Add functionality to change hist_avg for each stream

    * Fix some documentation

    * Try to fix sphinx problem

    * Fix hist_avg documentation

    * Add some metadata changes to time and time_bounds

commit 5b0418a9f6d181d668ddebdc2c540566529e4125
Author: Tony Craig <[email protected]>
Date:   Wed Apr 5 13:29:21 2023 -0700

    Update global reduction implementation to improve performance, fix VP bug (#824)

    * Update global reduction implementation to improve performance, fix VP bug

    This was mainly done for situations like VP that need a fast global sum.
    The VP global sum is still slightly faster than the one computed in the
    infrastructure, so kept that implementation.  Found a bug in the workspace_y
    calculation in VP that was fixed.  Also found that the haloupdate call
    as part of the precondition step generally improves VP performance, so removed
    option to NOT call the haloupdate there.

    Separately, fixed a bug in the tripoleT global sum implementation, added
    a tripoleT global sum unit test, and resynced ice_exit.F90, ice_reprosum.F90,
    and ice_global_reductions.F90 between serial and mpi versions.

    - Refactor global sums to improve performance, move if checks outside do loops
    - Fix bug in tripoleT global sums, tripole seam masking
    - Update VP solver, use local global sum more often
    - Update VP solver, fix bug in workspace_y calculation
    - Update VP solver, always call haloupdate during precondition
    - Refactor ice_exit.F90 and sync serial and mpi versions
    - Sync ice_reprosum.F90 between serial and mpi versions
    - Update sumchk unit test to handle grids better
    - Add tripoleT sumchk test

    * Update VP global sum to exclude local implementation with tripole grids

commit 942449751275ebd884abb5752d03d7ea64b72664
Author: David A. Bailey <[email protected]>
Date:   Thu Mar 23 16:46:05 2023 -0600

    Fix CESMCOUPLED compile issue in icepack. (#823)

    * Fix CESMCOUPLED compile problem in icepack
DeniseWorthen added a commit to DeniseWorthen/CICE that referenced this pull request May 10, 2024
@DeniseWorthen
Update CICE for latest Consortium master (NOAA-EMC#38)
64d9b9e 
    * Implement advanced snow physics in icepack and CICE
    * Fix time-stamping of CICE history files
    * Fix CICE history file precision
DeniseWorthen added a commit to DeniseWorthen/CICE that referenced this pull request May 10, 2024
@DeniseWorthen
Update CICE for latest Consortium master (NOAA-EMC#38)
955ef8d 
    * Implement advanced snow physics in icepack and CICE
    * Fix time-stamping of CICE history files
    * Fix CICE history file precision
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@MinsukJi-NOAA MinsukJi-NOAA MinsukJi-NOAA approved these changes

@junwang-noaa junwang-noaa junwang-noaa approved these changes

@binli2337 binli2337 Awaiting requested review from binli2337

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@DeniseWorthen @junwang-noaa @MinsukJi-NOAA @JFLemieux73 @apcraig @rgrumbine @TillRasmussen @eclare108213