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MARBL version with explicit calcifiers #330
MARBL version with explicit calcifiers #330
Commits on Jul 6, 2017
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kristenkrumhardt committed
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Commits on Jul 18, 2017
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Added explicit calcifier cocco, else-if statements
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Commits on Jul 19, 2017
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Added QCaCO3_max_exp parameter, modified cocco/sp growth parms
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Modified parameters, need sp to be more competitive.
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Commits on Jul 20, 2017
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Change parms back to the way they were with v2, except kNO3 for sp
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Commits on Jul 21, 2017
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Parms changed: increased cocco kNO3, decreased cocco thetaNmax, incre…
…ased cocco gQfe_0
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Commits on Jul 24, 2017
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Increased thetaNmax for coccos
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Lower alphaPI and thetaNmax for coccos, lower KFe for diat, higher PC…
…ref for diat
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Commits on Jul 25, 2017
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diat PCref is now 5.2, diat kFe is 0.5
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Lower cocco gQfe_0 to 15., cocco alphaPI increased to 0.30
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Commits on Aug 2, 2017
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Added modulation of calcification by Plim,CO2,temp and growth rate by…
… C lim
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Commits on Aug 3, 2017
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More modifications to try to get modulated calcification and Clim to …
…work.
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Commits on Aug 4, 2017
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Fixed some bugs related to calcification and C limitation of coccos
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Commits on Aug 7, 2017
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reinstated increased pic/poc with Plim, modified parms to make coccos…
… slightly more competitive
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Commits on Aug 8, 2017
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further decreased KFe for coccos and increased thetaNmax to 3.2 for c…
…occos
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Commits on Aug 9, 2017
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decreased kCO2 for cocco, decreased Kno3 for cocco, increased alphaPI…
… for cocco
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Made a special Tfunc for coccos
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Commits on Aug 10, 2017
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decreased competitive ability of coccos, given new Tfunc
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made the Tfunc for coccos to version 2 (not so advantageous)
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Commits on Aug 11, 2017
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lowered max growth rate for coccos
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Commits on Aug 15, 2017
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Kristen Krumhardt committed
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made light lim cocco same as for diat and really efficient Kfe for co…
…ccos
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coccos have the same light parms as diatoms, but with super efficent …
…Kfe and with the blue Tfunc for coccos
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Commits on Aug 16, 2017
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kristenkrumhardt committed
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Commits on Aug 29, 2017
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Kristen Krumhardt committed
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Commits on Aug 30, 2017
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kristenkrumhardt committed
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Commits on Aug 31, 2017
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kristenkrumhardt committed
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Commits on Sep 1, 2017
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kristenkrumhardt committed
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going back to version 20 parms
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Commits on Sep 2, 2017
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kristenkrumhardt committed
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Commits on Sep 3, 2017
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put my light parms like Cara's
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Commits on Sep 5, 2017
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kristenkrumhardt committed
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thetaNmax for cocco same as sp, lowered KNO3 for cocco, increased KSi…
…O3 for diat
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adjusting a bunch of parms to make coccos more competitive
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Commits on Sep 6, 2017
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adjusted light parms and some nutrient kms to make coccos more compet…
…itive
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Commits on Sep 7, 2017
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change cocco grazing function to sigmoidal
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after adding grazing, need to make Km for nuts bigger for coccos/less…
… for sp
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made sp more competitive nutrient-wise
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Commits on Sep 8, 2017
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try making sp with sigmoidal grazing too
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changed everyone to sigmoidal grazing
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Commits on Sep 9, 2017
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made max growth rate for coccos 4.5 d-1, a few other adjustments in p…
…arms (too much cocco)
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Commits on Sep 10, 2017
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lower alphaPI for coccos, higher Kms for coccos, lower KNO3 for sp
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Commits on Sep 11, 2017
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coccos were still too much, adjusted alphaPI, PCref, grazing
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Commits on Sep 12, 2017
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kristenkrumhardt committed
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Commits on Sep 13, 2017
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grazing parms identical between sp and cocco, changing back to sigmoi…
…dal grazing
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identical sp and cocco grazing parms, michaelis-menten grazing
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Commits on Sep 19, 2017
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Merge branch 'master' into modify_Tfunc
Conflicts: src/Makefile src/marbl_config_mod.F90 src/marbl_diagnostics_mod.F90 src/marbl_interface_private_types.F90 src/marbl_mod.F90 src/marbl_parms.F90 src/marbl_sizes.F90 tests/driver_src/Makefile
Kristen Krumhardt committedSep 19, 2017 Configuration menu - View commit details
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Commits on Sep 20, 2017
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making changes in the marbl master for coccos
Kristen Krumhardt committedSep 20, 2017 Configuration menu - View commit details
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Commits on Mar 16, 2018
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Fixed picpoc calculations so they cannot go negative
Kristen Krumhardt committedMar 16, 2018 Configuration menu - View commit details
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Commits on Apr 24, 2018
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Slightly modified Tfunc_cocco, Tfunc_cocco modifies cocco mortality, …
…CaCO2 dissolution in zooplankton guts increased to 0.7
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Merge pull request #1 from mnlevy1981/modify_Tfunc
Modify tfunc
kristenkrumhardt authoredApr 24, 2018 Configuration menu - View commit details
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fixed a few bugs concerning C limitation in marbl_diagnostics; fixed …
…bug concerning temperature in marbl_mod; changed default settings.yaml to accomodate coccos
Kristen Krumhardt committedApr 24, 2018 Configuration menu - View commit details
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Commits on Jul 23, 2018
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add CaCO3_prod to output, add cocco_C_lim to output
Kristen Krumhardt committedJul 23, 2018 Configuration menu - View commit details
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Commits on Feb 20, 2019
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Merge branch 'development' into modify_Tfunc
Conflicts: src/marbl_diagnostics_mod.F90 src/marbl_mod.F90 src/marbl_pft_mod.F90 src/marbl_settings_mod.F90
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add kco2 to autotroph settings
Kristen Krumhardt committedFeb 20, 2019 Configuration menu - View commit details
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Commits on May 15, 2019
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Bring latest development branch in modify_Tfunc
Includes SPECTRA support
Kristen Krumhardt committedMay 15, 2019 Configuration menu - View commit details
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Commits on May 30, 2019
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Add is_carbon_limited to autotroph_settings_type
Also, only include C_lim diagnostics for carbon limited diagnostics.
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Commits on May 31, 2019
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Make temp_func_form_opt and Tref per-PFT settings
Also, introduce the temp_func_form_opt = 'power' option (which will be used by coccolithophores). Note that this commit changes the default Tref behavior -- rather than depending on temp_func_form_opt (Tref = 30 for q_10 and Tref = 25 for arrhenius), the default is currently based on the PFT shortname and set to 30 for all current PFTs. I have some ideas on how to change the way we apply dependencies to allow Tref to depend on the per-autotroph temp_func_form_opt but haven't implemented that yet.
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Commits on Jun 11, 2019
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Tref is no longer available from input file
Tref is still in the PFT settings_type data structures, but values are derived based on temp_func_form_opt (30 for q_10, 25 for arrhenius, and 0 for power -- note that the power function doesn't use the Tref parameter)
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Remove Tref from default files
MARBL_generate_settings_file was still putting Tref in the input files because it was in the settings file.
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Commits on Jun 13, 2019
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cesm2.1 will match the final configuration of MARBL in the CESM 2.1 release (while future tuning changings will go into settings_latest). The cesm2.1+cocco file will contain settings for Kristen's coccolithophore runs, but in this commit is identical to the latest settings.
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Update values in settings_cesm2.1+cocco.yaml
Something to look at in code review: I added a workaround to marbl_settings_mod.F90 to set PFT_defaults = 'user-specified' if the namelist uses 'CESM2.1+cocco'; I can't use 'CESM2' because that will get the autotroph count wrong, and we intentionally did not hard-code the cocco settings in the fortran code so this seemed like a necessary step.
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Commits on Jun 14, 2019
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Now that we have cesm2.1+cocco settings file, we can set QCaCO3_max to different values when using coccolithophores instead of needing a separate settings variable.
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Commits on Jun 17, 2019
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Re-order compute_temperature_functional_form args
intent(out) variable should be last (also added comments defining dimensions of each argument)
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Update comments in marbl_pft_mod
Some default variable settings were missing the comment to see the CESM NOTE in marbl_settings_mod, others had an incorrect message (claiming the CESM NOTE was in marbl_pft_mod rather than settings_mod). Also, changed the order in which the autotroph settings are set so that it matches the order variables appear in the settings YAML file.
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Commits on Jun 18, 2019
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Merge in code clean-up following review
Several small issues were raised in code review on May 22nd, and this merge fixes most of them
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Commits on Jul 2, 2019
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cleaned up comments in calcification subroutine of marbl_interior_ten…
…dency_mod.F90 and switched CaCO3_PROD output from medium to low in diagnostics_lastest.yaml
Kristen Krumhardt committedJul 2, 2019 Configuration menu - View commit details
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Commits on Jul 5, 2019
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Clean up comments and variable names
Following the refactor to move Tref and temp_func_form_iopt onto the autotroph and zooplankton settings types, the variable Tfunc_ind was no longer an appropriate name (it wasn't just indexing Tfunc). So Tfunc_ind is now PFT_ind (matching the "PFT_cnt" dimension in the comments). I also cleaned up the comments about Tref in the function header to note that the setting is not used when Tfunc is computed with the power function.
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116007e changed diagnostics_latest.yaml but did not change the JSON file
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Commits on Jul 11, 2019
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Missing a space between variable name and '==' operator
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Update PFT_keys in more generic manner
This will make it easier to add additional valid values for PFT_defaults in different settings files
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Clean up python code following review
Fixed poor spacing around operator in MARBL_share.py and also improved the in determining proper values of append_to_keys and PFT_keys in MARBL_settings_file_class.py
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