proposed parameter file changes (including PR #279)

[rgknox]

The following are the super-set of current proposed changes to the default parameter file. Some of the changes, particularly those related to spread terms, and removal of grass spread are already slated for modification in #279.

In issue #263 we also start discussing removing the "fates_" namespace to parameters.

parameter cdl file

Diff between proposed and master:

diff fates_params_2troppftclones.c171005.cdl fates_params_2troppftclones.c170913.cdl
1c1
< netcdf fates_params_2troppftclones.c171005 {
---
> netcdf fates_params_2troppftclones.c170913 {
154,159c154,156
< double fates_dbh_maxheight(fates_pft) ;
< fates_dbh_maxheight:long_name = "the diameter (if any) corresponding to maximum height or stature, diameters may increase beyond this" ;
< fates_dbh_maxheight:units = "cm" ;
< double fates_dbh_mature(fates_pft) ;
< fates_dbh_mature:long_name = "the diameter (if any) where the plant will start extra clonal allocation to the seed pool" ;
< fates_dbh_mature:units = "cm" ;
---
> double fates_max_dbh(fates_pft) ;
> fates_max_dbh:long_name = "the diameter corresponding to maximum height or stature, diameters may increase beyond this" ;
> fates_max_dbh:units = "cm" ;
228a226,228
> double fates_allom_d2bl_slascaler(fates_pft) ;
> fates_allom_d2bl_slascaler:long_name = "allometric SLA_top scalar on bleaf term" ;
> fates_allom_d2bl_slascaler:units = "" ;
235,240d234
< double fates_allom_d2ca_coefficient_max(fates_pft) ;
< fates_allom_d2ca_coefficient_max:long_name = "max (savanna) dbh to area multiplier factor where: area = n*d2ca_coeff*dbh^beta" ;
< fates_allom_d2ca_coefficient_max:units = "m2 cm^(-1/beta)" ;
< double fates_allom_d2ca_coefficient_min(fates_pft) ;
< fates_allom_d2ca_coefficient_min:long_name = "min (forest) dbh to area multiplier factor where: area = n*d2ca_coeff*dbh^beta" ;
< fates_allom_d2ca_coefficient_min:units = "m2 cm^(-1/beta)" ;
291a286,288
> double fates_grass_spread(fates_scalar) ;
> fates_grass_spread:long_name = "dbh to area multiplier factor where: area = pi*n*grass_spread*dbh^beta" ;
> fates_grass_spread:units = "none" ;
297a295,300
> double fates_maxspread(fates_scalar) ;
> fates_maxspread:long_name = "maximum ratio of dbh to canopy area (used in initializing NBG cohorts)" ;
> fates_maxspread:units = "cm/m2" ;
> double fates_minspread(fates_scalar) ;
> fates_minspread:long_name = "minimum ratio of dbh to canopy area" ;
> fates_minspread:units = "cm/m2" ;
307,309d309
< double fates_canopy_closure_thresh(fates_scalar) ;
< fates_canopy_closure_thresh:long_name = "tree canopy coverage at which crown area allometry changes from savanna to forest value" ;
< fates_canopy_closure_thresh:units = "unitless" ;
488c488
< fates_logging_collateral_frac:long_name = "Fraction of large stems in upperstory that die from logging collateral damage" ;
---
> fates_logging_collateral_frac:long_name = "Fraction of stems killed due to collateral damage per event" ;
490,492d489
< double fates_logging_coll_under_frac(fates_scalar) ;
< fates_logging_coll_under_frac:long_name = "Fraction of stems killed in the understory when logging generates disturbance" ;
< fates_logging_coll_under_frac:units = "fraction" ;
619,621c616
< fates_dbh_maxheight = 150, 150 ;
<
< fates_dbh_mature = 150, 150 ;
---
> fates_max_dbh = 150, 150 ;
663c658
< fates_allom_d2bl1 = 0.07, 0.07 ;
---
> fates_allom_d2bl1 = 0.028, 0.028 ;
668a664,665
> fates_allom_d2bl_slascaler = 0.03, 0.03 ;
>
673,676d669
< fates_allom_d2ca_coefficient_max = 0.656846381604825, 0.656846381604825 ;
<
< fates_allom_d2ca_coefficient_min = 0.338111885296947, 0.338111885296947 ;
<
710a704,705
> fates_grass_spread = 0.18 ;
>
714a710,713
> fates_maxspread = 0.3 ;
>
> fates_minspread = 0.18 ;
>
721,722d719
< fates_canopy_closure_thresh = 0.8 ;
<
879,880d875
< fates_logging_coll_under_frac = 0.55983 ;
<
883c878
< fates_logging_event_code = -30 ;
---
> fates_logging_event_code = 1 ;

[rosiealice]

Did I miss the discussion of fates_dbh_mature? Does everything do clonal allocation now, or only things where clone_alloc >0 ?

…

On Oct 4, 2017 8:58 PM, "Ryan Knox" ***@***.***> wrote: The following are the super-set of current proposed changes to the default parameter file. Some of the changes, particularly those related to spread terms, and removal of grass spread are already slated for modification in #279 <#279>. In issue #263 <#263> we also start discussing removing the "fates_" namespace to parameters. parameter cdl file <https://drive.google.com/file/d/0B_5e7rc3QoQqTm1wckR0N3ExeTg/view?usp=sharing> Diff between proposed and master: diff fates_params_2troppftclones.c171005.cdl fates_params_2troppftclones.c170913.cdl 1c1 < netcdf fates_params_2troppftclones.c171005 { --- > netcdf fates_params_2troppftclones.c170913 { 154,159c154,156 < double fates_dbh_maxheight(fates_pft) ; < fates_dbh_maxheight:long_name = "the diameter (if any) corresponding to maximum height or stature, diameters may increase beyond this" ; < fates_dbh_maxheight:units = "cm" ; < double fates_dbh_mature(fates_pft) ; < fates_dbh_mature:long_name = "the diameter (if any) where the plant will start extra clonal allocation to the seed pool" ; < fates_dbh_mature:units = "cm" ; --- > double fates_max_dbh(fates_pft) ; > fates_max_dbh:long_name = "the diameter corresponding to maximum height or stature, diameters may increase beyond this" ; > fates_max_dbh:units = "cm" ; 228a226,228 > double fates_allom_d2bl_slascaler(fates_pft) ; > fates_allom_d2bl_slascaler:long_name = "allometric SLA_top scalar on bleaf term" ; > fates_allom_d2bl_slascaler:units = "" ; 235,240d234 < double fates_allom_d2ca_coefficient_max(fates_pft) ; < fates_allom_d2ca_coefficient_max:long_name = "max (savanna) dbh to area multiplier factor where: area = n*d2ca_coeff*dbh^beta" ; < fates_allom_d2ca_coefficient_max:units = "m2 cm^(-1/beta)" ; < double fates_allom_d2ca_coefficient_min(fates_pft) ; < fates_allom_d2ca_coefficient_min:long_name = "min (forest) dbh to area multiplier factor where: area = n*d2ca_coeff*dbh^beta" ; < fates_allom_d2ca_coefficient_min:units = "m2 cm^(-1/beta)" ; 291a286,288 > double fates_grass_spread(fates_scalar) ; > fates_grass_spread:long_name = "dbh to area multiplier factor where: area = pi*n*grass_spread*dbh^beta" ; > fates_grass_spread:units = "none" ; 297a295,300 > double fates_maxspread(fates_scalar) ; > fates_maxspread:long_name = "maximum ratio of dbh to canopy area (used in initializing NBG cohorts)" ; > fates_maxspread:units = "cm/m2" ; > double fates_minspread(fates_scalar) ; > fates_minspread:long_name = "minimum ratio of dbh to canopy area" ; > fates_minspread:units = "cm/m2" ; 307,309d309 < double fates_canopy_closure_thresh(fates_scalar) ; < fates_canopy_closure_thresh:long_name = "tree canopy coverage at which crown area allometry changes from savanna to forest value" ; < fates_canopy_closure_thresh:units = "unitless" ; 488c488 < fates_logging_collateral_frac:long_name = "Fraction of large stems in upperstory that die from logging collateral damage" ; --- > fates_logging_collateral_frac:long_name = "Fraction of stems killed due to collateral damage per event" ; 490,492d489 < double fates_logging_coll_under_frac(fates_scalar) ; < fates_logging_coll_under_frac:long_name = "Fraction of stems killed in the understory when logging generates disturbance" ; < fates_logging_coll_under_frac:units = "fraction" ; 619,621c616 < fates_dbh_maxheight = 150, 150 ; < < fates_dbh_mature = 150, 150 ; --- > fates_max_dbh = 150, 150 ; 663c658 < fates_allom_d2bl1 = 0.07, 0.07 ; --- > fates_allom_d2bl1 = 0.028, 0.028 ; 668a664,665 > fates_allom_d2bl_slascaler = 0.03, 0.03 ; > 673,676d669 < fates_allom_d2ca_coefficient_max = 0.656846381604825, 0.656846381604825 ; < < fates_allom_d2ca_coefficient_min = 0.338111885296947, 0.338111885296947 ; < 710a704,705 > fates_grass_spread = 0.18 ; > 714a710,713 > fates_maxspread = 0.3 ; > > fates_minspread = 0.18 ; > 721,722d719 < fates_canopy_closure_thresh = 0.8 ; < 879,880d875 < fates_logging_coll_under_frac = 0.55983 ; < 883c878 < fates_logging_event_code = -30 ; --- > fates_logging_event_code = 1 ; — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#285>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMWsQ4frWrnsbSHJKiyr024zob2Q_pi2ks5spEXygaJpZM4PugB8> .

[rgknox]

Recap from meeting and explanation of fates_dbh_mature:

We have two processes that have maximum stature thresholds, the capping of heights and increasing allocation to seed biomass at larger sizes. But, with soon to be released options in modular allometry, some schemes are asymptotic and do not need height capping (people might also just want to turn off height capping in non-asymptotic schemes as well). So, the proposal is to split fates_dbh_max into two parameters; one (fates_dbh_maxheight) that sets the dbh at maximum height (if any), and one that specifies the size threshold for increased carbon allocation to seeds (if any, fates_dbh_mature).

By setting these two parameters to the same value as the existing dbh_max parameter, and continuing to use the same allometry scheme, will continue to generate the same results we currently have.

[rgknox]

suggestions on better names for dbh_mature?

fates_dbh_repro_thresh?
fates_dbh_seedalloc ?

Also, will change fates_dbh_maxheight to fates_allom_dbh_maxheight (this is certainly part of the allometry group).

[rosiealice]

I think fates_dbh_repro_threshold would be fine. It's only used once, I think?

…

On 5 October 2017 at 14:18, Ryan Knox ***@***.***> wrote: suggestions on better names for dbh_mature? fates_dbh_repro_thresh? fates_dbh_seedalloc ? Also, will change fates_dbh_maxheight to fates_allom_dbh_maxheight (this is certainly part of the allometry group). — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#285 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMWsQzR6nS0deKQCJMpfAkd4hyiK6dZmks5spTmggaJpZM4PugB8> .

-- ----------------------------------------------------------------- Dr Rosie A. Fisher Staff Scientist Terrestrial Sciences Section Climate and Global Dynamics National Center for Atmospheric Research 1850 Table Mesa Drive Boulder, Colorado, 80305 USA. +1 303-497-1706 http://www.cgd.ucar.edu/staff/rfisher/

[ckoven]

fixed via #287, closing.