Breaking CMIP6 backward compatibility through bugfixes - iHAMOCC ready for NorESM2.1 #315
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* FIX: impose no-flux boundary condition at surface for fdust This bugfix potentially affects the sediment burrying rate
Merge branch 'master' into 'feature-hamocc_beyond-CMIP6'
Bug fixes for denitrification stoichiometry and C-isotopes in the sediment
Introducing a static 3D sediment porosity field that can be optionally read in with effects on molecular pore water diffusion and shifting.
…sedbypass=true` (#198) * Removing bodensed - Initialization of sediment parameters and fields now in mo_sedmnt
Make the surface mixed layer depth fractional index `hOBL` available for use in iHAMOCC, and adjust the internal iHAMOCC index `kmle` according to `hOBL`. Default value `kmle = 2` is retained for consistency with isopycnic coordinates.
* Fixing the reading of variable porosity input field in preparation for the NorESM 2.0.6 release Cherry-picked from private Ncycleprivate branch 0d56930e2fdd62caba964d375b57304942568926 * Provide number of layers (3rd dim) via ks and not hard-coded * minor clean-up
…ions (default off).
* add pCO2m (moist), CO2 piston velocity and solubility output - caution: kwco2 piston velocity now really holds only piston velocity (and not times solubility)
* Add variables used by PNETCDF to explicit use staements. * Move implicit none statments * update explicit use statement for pnetcdf
Fixed sediment clay units.
Merge from master
* Dynamic mapping of pore water tracers to ocean tracers (#192) * Initial restructuring of sediment-related tracer declaration and initialization * Introducing mapping function * Remove unncessary comments * Fixed diagnostics bug and updated index naming * Added initial support for NUOPC driver. * Lon-lat variable sediment porosity (#189) Introducing a static 3D sediment porosity field that can be optionally read in with effects on molecular pore water diffusion and shifting. * Added wave forcing fields. * Renamed folder for MCT driver. * Moved MCT specific file from drivers/cpl_share/ to drivers/mct/. * Rename drivers/mct/mod_swtfrz.F to drivers/mct/mod_swtfrz.F90. * Rewrite to drivers/mct/mod_swtfrz.F90 to free format Fortran. * Remove redundant definition of kOBL. * Redefine kOBL, cast as integer * Fixing variable sediment porosity - field initialization in case of `sedbypass=true` (#198) * Removing bodensed - Initialization of sediment parameters and fields now in mo_sedmnt * Hamocc hybrid coord2 (#179) Make the surface mixed layer depth fractional index `hOBL` available for use in iHAMOCC, and adjust the internal iHAMOCC index `kmle` according to `hOBL`. Default value `kmle = 2` is retained for consistency with isopycnic coordinates. * Fix porosity read (#201) * Fixing the reading of variable porosity input field in preparation for the NorESM 2.0.6 release Cherry-picked from private Ncycleprivate branch 0d56930e2fdd62caba964d375b57304942568926 * Provide number of layers (3rd dim) via ks and not hard-coded * minor clean-up * Correct unit of diagnostic variable dp_trc. * Made conservation and checksum diagnostics selectable by namelist options (default off). * pCO2, Piston velocity and solubility output (#202) * add pCO2m (moist), CO2 piston velocity and solubility output - caution: kwco2 piston velocity now really holds only piston velocity (and not times solubility) * Bugfix pnetcdf (#208) * Add variables used by PNETCDF to explicit use staements. * Move implicit none statments * update explicit use statement for pnetcdf * fixed units and renamed calcium burial to CaCO3 burial (#212) Fixed sediment clay units. * Add option for surface pH output (#221) * Remove unused parameters in wrt* subroutine calls in ncout_hamocc.F90 * Import get_bgc_namelist only in subroutine where it is needed. (#225) Co-authored-by: Mats Bentsen <[email protected]> Co-authored-by: Tomas Torsvik <[email protected]> Co-authored-by: Tomas Torsvik <[email protected]> Co-authored-by: Jörg Schwinger <[email protected]>
Fixing a missing ' that only showed up when using `cisonew`
* Dynamic mapping of pore water tracers to ocean tracers (#192) * Initial restructuring of sediment-related tracer declaration and initialization * Introducing mapping function * Remove unncessary comments * Fixed diagnostics bug and updated index naming * Added initial support for NUOPC driver. * Lon-lat variable sediment porosity (#189) Introducing a static 3D sediment porosity field that can be optionally read in with effects on molecular pore water diffusion and shifting. * Added wave forcing fields. * Renamed folder for MCT driver. * Moved MCT specific file from drivers/cpl_share/ to drivers/mct/. * Rename drivers/mct/mod_swtfrz.F to drivers/mct/mod_swtfrz.F90. * Rewrite to drivers/mct/mod_swtfrz.F90 to free format Fortran. * Remove redundant definition of kOBL. * Redefine kOBL, cast as integer * Fixing variable sediment porosity - field initialization in case of `sedbypass=true` (#198) * Removing bodensed - Initialization of sediment parameters and fields now in mo_sedmnt * This is the first commit of MKS units. All variables in the subroutines have been converted to MKS [meter, kg, seconds] instead of CGS [cm, gram, seconds] with necessary coefficients. The default option which is CGS reproduce old results. The new option MKS cannot reproduce because of machine precision. * Hamocc hybrid coord2 (#179) Make the surface mixed layer depth fractional index `hOBL` available for use in iHAMOCC, and adjust the internal iHAMOCC index `kmle` according to `hOBL`. Default value `kmle = 2` is retained for consistency with isopycnic coordinates. * BLOM CIME cpp updates to run in NorESM * bug fixes for the CGS MKS conversion * cesm thermal forcing bug fixes for reproducibility * BLOM MKS update to export winds into the CESM using proper units. * input values in ocn_in case is updated for mks setup * default cgsmks value changed * Initialize some variables in the k-epsilon model. * Fix porosity read (#201) * Fixing the reading of variable porosity input field in preparation for the NorESM 2.0.6 release Cherry-picked from private Ncycleprivate branch 0d56930e2fdd62caba964d375b57304942568926 * Provide number of layers (3rd dim) via ks and not hard-coded * minor clean-up * Correct unit of diagnostic variable dp_trc. * Made conservation and checksum diagnostics selectable by namelist options (default off). * pCO2, Piston velocity and solubility output (#202) * add pCO2m (moist), CO2 piston velocity and solubility output - caution: kwco2 piston velocity now really holds only piston velocity (and not times solubility) * Bugfix pnetcdf (#208) * Add variables used by PNETCDF to explicit use staements. * Move implicit none statments * update explicit use statement for pnetcdf * fixed units and renamed calcium burial to CaCO3 burial (#212) Fixed sediment clay units. * - Made the "fuk95" configuration work with MKS units. - Removed "CGS" CPP flag. - Changed some unit conversion factors from variables to parameters. - Introduced rho0 (= 1/alpha0) parameter. - Updated copyright statements. * Correct unit conversion of mixed layer depth to pressure. * Updated NorESM coupling scripts for the use of MKS units. * Fixed check of unit system when building as NorESM component. * Add option for surface pH output (#221) * Remove unused parameters in wrt* subroutine calls in ncout_hamocc.F90 * Import get_bgc_namelist only in subroutine where it is needed. (#225) * fix missing ' (#228) Fixing a missing ' that only showed up when using `cisonew` --------- Co-authored-by: Mats Bentsen <[email protected]> Co-authored-by: Tomas Torsvik <[email protected]> Co-authored-by: Mehmet Ilicak <[email protected]> Co-authored-by: Tomas Torsvik <[email protected]> Co-authored-by: Jörg Schwinger <[email protected]>
… history and provide common hook again
Merge latest `master` changes into the `feature-hamocc_beyond-CMIP6` and align commit history again getting a new common hook.
Add missing local parameters to private OMP
Merge master into beyond-CMIP6 branch
JorgSchwinger
approved these changes
Nov 20, 2023
mvertens
approved these changes
Nov 20, 2023
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@mvertens, @JorgSchwinger and @TomasTorsvik : I suspect that we should briefly talk about the tagging during the BLOM core meeting tmw. Any opinion on this @JorgSchwinger? - see also discussion #295. Wrt the regression testing: I would be happy to incorporate the automated regression testing in my daily routine of coding (thus far mainly manually done). I hope that the full support will be available through the NorESM2.1 release. Wrt to specific testcases, I see that some combinations are probably needed - particularly in combination with the hybrid coordinates, at some point potentially with the new SI units, potentially a combination of HAMOCC logicals and potentially wrt to air-sea fluxes. Wrt to merging #314 and #315, I'll wait a bit longer today for Tomas, but I suspect that he's busy with the workshop so that I merge the stuff in the afternoon. |
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I don't have any strong opinion on the tagging-question. Using |
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@JorgSchwinger , ok, thanks for the input on the tagging. I suspect it will be a decision between Mats and Mariana then. |
Properly declare and initialize bifrXX_ini and clean mo_biomod from growth_co2
jmaerz
changed the title
jmaerz
changed the title
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I performed another regression testing between an earlier stage of the |
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This PR breaks CMIP6 backward compatibility since it introduces a few bugfixes to
master:This PR makes
masterready for the NorESM2.1 milestone (at least from the iHAMOCC point of view).