Add option for surface pH output #221
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jmaerz
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Jan 6, 2023
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Looks generally ok to me. The question is generally, if you want to generate the time mean ph, or ph of time mean H+ concentration, though (which can make a -likely subtle- difference). Only minor thing: one could rename 'h+' to 'H+' in the netcdf variable units (as in '-log10(H+)').
TomasTorsvik
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Jan 6, 2023
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Thanks, Jöran and Tomas for reviewing this quickly! @jmaerz I also just got aware that we do not save the average pH, but the log10 of the average H+ concentration. Since this has been done always like this for the 3d-pH field in HAMOCC (at least in Bergen), I implemented it consistent with the 3d fields. I am not sure how large the difference is. If there is a difference, one should have the option for both average H+ and average pH. I have changed h+ to H+. |
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* 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 <mben@norceresearch.no> Co-authored-by: Tomas Torsvik <tomas.torsvik.work@gmail.com> Co-authored-by: Tomas Torsvik <43031053+TomasTorsvik@users.noreply.github.com> Co-authored-by: Jörg Schwinger <jorg.schwinger@norceresearch.no>
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* 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 <mben@norceresearch.no> Co-authored-by: Tomas Torsvik <tomas.torsvik.work@gmail.com> Co-authored-by: Mehmet Ilicak <milicak@itu.edu.tr> Co-authored-by: Tomas Torsvik <43031053+TomasTorsvik@users.noreply.github.com> Co-authored-by: Jörg Schwinger <jorg.schwinger@norceresearch.no>
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* Dynamic mapping of pore water tracers to ocean tracers (NorESMhub#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 (NorESMhub#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` (NorESMhub#198) * Removing bodensed - Initialization of sediment parameters and fields now in mo_sedmnt * Hamocc hybrid coord2 (NorESMhub#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 (NorESMhub#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 (NorESMhub#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 (NorESMhub#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 (NorESMhub#212) Fixed sediment clay units. * Add option for surface pH output (NorESMhub#221) * Remove unused parameters in wrt* subroutine calls in ncout_hamocc.F90 * Import get_bgc_namelist only in subroutine where it is needed. (NorESMhub#225) Co-authored-by: Mats Bentsen <mben@norceresearch.no> Co-authored-by: Tomas Torsvik <tomas.torsvik.work@gmail.com> Co-authored-by: Tomas Torsvik <43031053+TomasTorsvik@users.noreply.github.com> Co-authored-by: Jörg Schwinger <jorg.schwinger@norceresearch.no>
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…b#232) * Dynamic mapping of pore water tracers to ocean tracers (NorESMhub#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 (NorESMhub#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` (NorESMhub#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 (NorESMhub#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 (NorESMhub#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 (NorESMhub#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 (NorESMhub#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 (NorESMhub#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 (NorESMhub#221) * Remove unused parameters in wrt* subroutine calls in ncout_hamocc.F90 * Import get_bgc_namelist only in subroutine where it is needed. (NorESMhub#225) * fix missing ' (NorESMhub#228) Fixing a missing ' that only showed up when using `cisonew` --------- Co-authored-by: Mats Bentsen <mben@norceresearch.no> Co-authored-by: Tomas Torsvik <tomas.torsvik.work@gmail.com> Co-authored-by: Mehmet Ilicak <milicak@itu.edu.tr> Co-authored-by: Tomas Torsvik <43031053+TomasTorsvik@users.noreply.github.com> Co-authored-by: Jörg Schwinger <jorg.schwinger@norceresearch.no>
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Has been tested with and without natDIC option.