…#616)

…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.

- 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.

* port to gaea

* 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 <str@dmi.dk>
Co-authored-by: Till Rasmussen <tar@11glvp2.usr.local>
Co-authored-by: Stefan Rethmeier <stefan@rethmeier.dk>
Co-authored-by: apcraig <anthony.p.craig@gmail.com>

- 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.

* 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 <afroberts@lanl.gov>
Co-authored-by: Elizabeth Hunke <eclare@pn2003333.lanl.gov>
Co-authored-by: apcraig <anthony.p.craig@gmail.com>

- 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

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

… tmB

…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

* 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

* update gx1prod, update version number to 6.3

* update Icepack

* update gx1prod15 to start at 1995

* 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