Erroneous DIC calculation using PISCES in CROCO v2.1.2

biogeochemistry
1

Hi everyone,

I am trying to update my model setup previously run on CROCOv1.3.1 to the more recent CROCO v2.1.2 and have been encountering problems in the calculation of dissolved organic carbon (DIC) when the biogeochemical model PISCES is activated. As far as I can confirm, I am using the same settings and initial and boundary conditions as my previous setup, but right from the start of the run, the calculated DIC increases to a much larger value and behaves erratically over time compared to runs using CROCOv.1.3.1. I have attached a time series plot comparison at a selected point to clarify what I mean:

CROCOv212_DICcomparison
CROCOv212_DICcomparison6694×2264 245 KB

Might anyone have encountered a similar issue before? As always, I would greatly appreciate any help and guidance.

Lawrence

2

Hi,
which key you used in ? can you please check with only quota+ sediment
( ln_sed_2way = .false.) with standard nampisext and without PSOURCE_NCFILE etc. and make a plot. in code DIC used as jpdic , you can check related code (please check if they have redundant in used cases or not).
PISCES code many cpp key as well many namelist stuff not related with CROCO, what I find many similar code related to NEMO.
you can see that the model start perfectly in the first time-step but after that the problem start.
Thank you.

3

Thank you for the suggestions. I am just using the standard version of PISCES for now with the following settings in my cppdefs.h:

                      /*   Choice of Biology models   */
# ifdef BIOLOGY
#  define  PISCES
#  undef  BIO_NChlPZD
#  undef  BIO_N2ChlPZD2
#  undef BIO_BioEBUS
                      /*   Biology options    */
#  ifdef PISCES
#   undef  DIURNAL_INPUT_SRFLX
#   define key_pisces
#   undef key_ligand
#   undef key_pisces_quota
#   undef key_pisces_npzd
#   undef key_sediment
#  endif
#  ifdef BIO_NChlPZD
#   define OXYGEN
#  endif
#  ifdef BIO_BioEBUS
#   define NITROUS_OXIDE
#  endif

As for my PISCES namelists, the boolean options set to ‘true’ are:

ln_sink_mus = .true. ! MUSCL sinking scheme
ln_ironsed = .true. ! boolean for Fe input from sediments

Also, at the bottom of the ‘namelist_pisces_ref’ file, there is a whole set of options set to ‘true’:
!-----------------------------------------------------------------------
&nampisdbg ! Namelist parameters for debugging
!-----------------------------------------------------------------------
ln_bio = .true. ! Enable biological processes
ln_flx = .true. ! Enable air-sea gas exchange
ln_sed = .true. ! Enable sediment mobilisation processes
ln_lys = .true. ! Enable carbonate chemistry
ln_sink = .true. ! Enable vertical sinking
ln_fechem = .true. ! Enable Iron chemistry
ln_prod = .true. ! Enable Phyptoplankton growth rate
ln_mort = .true. ! Enable Phyptoplankton mortality
ln_micro = .true. ! Enable microzooplankton
ln_meso = .true. ! Enable mesozooplankton
ln_poc = .true. ! Enable organic particles processes
ln_agg = .true. ! Enable particles Aggregation
ln_rem = .true. ! Enable Remineralisation
ln_diaz = .true. ! Enable diazotrophy

This list of options is not included in the PISCES namelist for CROCO version 1.3.1 so I do not know which can likely cause a large change in the DIC calculation.

Nevertheless, my initial run had PSOURCE_NCFILE and other options related to rivers activated, so I will try to run without any river sources to see how it changes the results.

4

As I mention use quota+ sediment
( ln_sed_2way = .false.).
As per my understanding about jpdic and discussion with my friend from Indian Institute of Technology, Kharagpur, India. He suggested to me there 200+ bugs in CROCO and 100+ bugs in PISCES. He sent me some fixes and tests for my simulation for gulf of mexico. I hope it will help your simulation . If you share your email address I can share it with you. :+1:
Thank you

1 Like
5

Thank you for your reply. I have never used the quota or sediment before so I will try to activate them. I expect to run into some compiling issues initially, but once I have been able to resolve these and test some more configurations, I will will try to contact you directly regarding the fixes you mentioned.