# biogeochemistry **URL:** https://forum.croco-ocean.org/c/biogeochemistry/10.md [Latest](https://forum.croco-ocean.org/latest.md) · [Categories](https://forum.croco-ocean.org/categories.md) · [Tags](https://forum.croco-ocean.org/tags.md) --- ## [Documentation for configuring a realistic coastal CROCO-PISCES scenario with river nutrients](https://forum.croco-ocean.org/t/documentation-for-configuring-a-realistic-coastal-croco-pisces-scenario-with-river-nutrients/463)
**Author:** [@Konstantinos\_K](https://forum.croco-ocean.org/u/Konstantinos_K)\ **Replies:** 1\ **Last updated:** [October 26, 2026, 10:18pm UTC](https://forum.croco-ocean.org/t/documentation-for-configuring-a-realistic-coastal-croco-pisces-scenario-with-river-nutrients/463 "2026-10-26T22:18:11Z")
Hi I am trying to create a realistic coastal scenario with CROCO and PISCES that includes nutrients and organic material input from a river. I tried to find an example either from the documentation or the training cou… --- ## [CROCO\_PISCES; PSOURCE - used; DIC - NaN values - in Climatology RUN](https://forum.croco-ocean.org/t/croco-pisces-psource-used-dic-nan-values-in-climatology-run/7598)
**Author:** [@sridevi2024](https://forum.croco-ocean.org/u/sridevi2024)\ **Replies:** 5\ **Last updated:** [March 17, 2026, 5:20am UTC](https://forum.croco-ocean.org/t/croco-pisces-psource-used-dic-nan-values-in-climatology-run/7598 "2026-03-17T05:20:55Z")
Hi CROCO-PISCES Users, My aim is to simulate CROCO coupled with PISCES over the northern Indian Ocean. I defined dust input as True and PSOURCE also activated. In Climatology RUN, after the time step of 127 month onw… --- ## [Erroneous DIC calculation using PISCES in CROCO v2.1.2](https://forum.croco-ocean.org/t/erroneous-dic-calculation-using-pisces-in-croco-v2-1-2/7564)
**Author:** [@lcbernardo](https://forum.croco-ocean.org/u/lcbernardo)\ **Replies:** 7\ **Last updated:** [March 12, 2026, 6:37am UTC](https://forum.croco-ocean.org/t/erroneous-dic-calculation-using-pisces-in-croco-v2-1-2/7564 "2026-03-12T06:37:52Z")
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 biogeoche… --- ## [CROCO-PISCES with AGRIF - gfortran causing runtime errors](https://forum.croco-ocean.org/t/croco-pisces-with-agrif-gfortran-causing-runtime-errors/7587)
**Author:** [@jvmcgovern](https://forum.croco-ocean.org/u/jvmcgovern)\ **Replies:** 3\ **Last updated:** [March 6, 2026, 6:30am UTC](https://forum.croco-ocean.org/t/croco-pisces-with-agrif-gfortran-causing-runtime-errors/7587 "2026-03-06T06:30:26Z")
Hi there, I can get CROCO-PISCES and CROCO-AGRIF working fine on the HPC system I’m using. The HPC system only provides the gnu compiler stack. I’m getting a lot of runtime errors, such as: Fortran runtime error: A… --- ## [utility of DIURNAL\_INPUT\_SRFLX option in PISCES](https://forum.croco-ocean.org/t/utility-of-diurnal-input-srflx-option-in-pisces/231)
**Author:** [@rreboreda](https://forum.croco-ocean.org/u/rreboreda)\ **Replies:** 10\ **Last updated:** [January 26, 2026, 11:57am UTC](https://forum.croco-ocean.org/t/utility-of-diurnal-input-srflx-option-in-pisces/231 "2026-01-26T11:57:00Z")
Hi, I would like to know what is the purpose of the option DIURNAL\_INPUT\_SRFLX avaliable in cppdefs.h when running PISCES. I get it is something related to the shortwave radiation at the surface, but what does it change… --- ## [PISCES and segmentation fault error and river position](https://forum.croco-ocean.org/t/pisces-and-segmentation-fault-error-and-river-position/7528)
**Author:** [@popoli](https://forum.croco-ocean.org/u/popoli)\ **Replies:** 0\ **Last updated:** [December 30, 2025, 12:16pm UTC](https://forum.croco-ocean.org/t/pisces-and-segmentation-fault-error-and-river-position/7528 "2025-12-30T12:16:13Z")
hello everyone i have a problem with pisces when i activate agrif to run pisces with nested child grid, i face this error. Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for t… --- ## [PISCES and Segmentation fault](https://forum.croco-ocean.org/t/pisces-and-segmentation-fault/7387)
**Author:** [@Catalina](https://forum.croco-ocean.org/u/Catalina)\ **Replies:** 7\ **Last updated:** [July 17, 2025, 2:26pm UTC](https://forum.croco-ocean.org/t/pisces-and-segmentation-fault/7387 "2025-07-17T14:26:04Z")
Hi everyone! I had a problem when PISCES ran. After the model started calculating, the following appeared: MAIN: started time-stepping STEP time\[DAYS\] DIC ALK OXY POC … --- ## [Interior nudging for non active (non T,S) tracers](https://forum.croco-ocean.org/t/interior-nudging-for-non-active-non-t-s-tracers/7258)
**Author:** [@Konstantinos\_K](https://forum.croco-ocean.org/u/Konstantinos_K)\ **Replies:** 0\ **Last updated:** [March 5, 2025, 2:35pm UTC](https://forum.croco-ocean.org/t/interior-nudging-for-non-active-non-t-s-tracers/7258 "2025-03-05T14:35:32Z")
Hi, Currently there are interior nudging options as explained on this post: For SST: #undef BULK\_FLUX leads to #define QCORRECTION which corrects surface heat flux with SST nudging. For ACTIVE tracers (T,S): T,S yo… --- ## [Issue with time varying river BGC tracer reading](https://forum.croco-ocean.org/t/issue-with-time-varying-river-bgc-tracer-reading/404)
**Author:** [@jvmcgovern](https://forum.croco-ocean.org/u/jvmcgovern)\ **Replies:** 17\ **Last updated:** [February 27, 2025, 4:37pm UTC](https://forum.croco-ocean.org/t/issue-with-time-varying-river-bgc-tracer-reading/404 "2025-02-27T16:37:31Z")
Hi, I’m experiencing an issue at present with CROCO-PISCES coupled. Running CROCO alone doesn’t cause an issue with river data reading (time varying T/S are read fine and model runs fine). However, when I turn on PISCES… --- ## [Problem with make\_dust.m](https://forum.croco-ocean.org/t/problem-with-make-dust-m/940)
**Author:** [@sebainzunza](https://forum.croco-ocean.org/u/sebainzunza)\ **Replies:** 1\ **Last updated:** [December 9, 2024, 1:21pm UTC](https://forum.croco-ocean.org/t/problem-with-make-dust-m/940 "2024-12-09T13:21:37Z")
Hi, I’m trying to run make\_dust.m but it gives an error reading file ‘DUST\_INCA\_new\_r360x180.nc’ since it is not present in croco\_tools/DATASETS\_CROCOTOOLS/WOAPISCES or anywhere else. I’m replacing it with dust\_INCA\_mon… --- ## [NF\_FWRITE ERROR: nf\_put\_vara netCDF error code = -60 mynode = 5](https://forum.croco-ocean.org/t/nf-fwrite-error-nf-put-vara-netcdf-error-code-60-mynode-5/878)
**Author:** [@Catalina](https://forum.croco-ocean.org/u/Catalina)\ **Replies:** 6\ **Last updated:** [November 12, 2024, 7:19pm UTC](https://forum.croco-ocean.org/t/nf-fwrite-error-nf-put-vara-netcdf-error-code-60-mynode-5/878 "2024-11-12T19:19:48Z")
Hi everyone! I’ve benn working with biology lately. Using NPZD and now PISCES light. The same thing happened with both giving this error: \[…\] 116000 8972.16667 2.2656067E+03 2.3696804E+00 1.7205821E+02 4.5360569E-03 … --- ## [PISCES blow-up during high freshwater input conditions](https://forum.croco-ocean.org/t/pisces-blow-up-during-high-freshwater-input-conditions/783)
**Author:** [@lcbernardo](https://forum.croco-ocean.org/u/lcbernardo)\ **Replies:** 7\ **Last updated:** [October 30, 2024, 1:42am UTC](https://forum.croco-ocean.org/t/pisces-blow-up-during-high-freshwater-input-conditions/783 "2024-10-30T01:42:38Z")
Hi everyone, I have been trying to run a sub-regional ROMS+PISCES simulation using CROCO version 1.3.1 for an area which contains various features such as straits, small islands, and embayment areas. I have been experim… --- ## [CROCO and FABM](https://forum.croco-ocean.org/t/croco-and-fabm/470)
**Author:** [@jvmcgovern](https://forum.croco-ocean.org/u/jvmcgovern)\ **Replies:** 5\ **Last updated:** [September 17, 2024, 11:11am UTC](https://forum.croco-ocean.org/t/croco-and-fabm/470 "2024-09-17T11:11:16Z")
Hi I’m wondering if any work has been done to make CROCO compatible with FABM? Best regards --- ## [PISCES time step frequency](https://forum.croco-ocean.org/t/pisces-time-step-frequency/778)
**Author:** [@Konstantinos\_K](https://forum.croco-ocean.org/u/Konstantinos_K)\ **Replies:** 4\ **Last updated:** [August 12, 2024, 7:43am UTC](https://forum.croco-ocean.org/t/pisces-time-step-frequency/778 "2024-08-12T07:43:03Z")
Hi, I am assuming that the setting below found in the “namelist\_pisces\_ref” file containing parameters for PISCES is supposed to give the option to have a different time step (relative to the CROCO time step?) only for … --- ## [PISCES blow-up after switching from TPXO7 to TPXO9.5](https://forum.croco-ocean.org/t/pisces-blow-up-after-switching-from-tpxo7-to-tpxo9-5/438)
**Author:** [@jvmcgovern](https://forum.croco-ocean.org/u/jvmcgovern)\ **Replies:** 3\ **Last updated:** [May 27, 2024, 9:15pm UTC](https://forum.croco-ocean.org/t/pisces-blow-up-after-switching-from-tpxo7-to-tpxo9-5/438 "2024-05-27T21:15:24Z")
Hi All, My CROCO-PISCES model (km-scale, 20 layers) is blowing up since I switched my tidal forcing from TPXO7 to TPXO9.5. The motivation to switch between them is the apparent errors in M2 tides from TPXO7 in my domain… --- ## [Diagnostic TS and BIO](https://forum.croco-ocean.org/t/diagnostic-ts-and-bio/481)
**Author:** [@Pizarro-Koch](https://forum.croco-ocean.org/u/Pizarro-Koch)\ **Replies:** 0\ **Last updated:** [August 24, 2023, 12:45pm UTC](https://forum.croco-ocean.org/t/diagnostic-ts-and-bio/481 "2023-08-24T12:45:03Z")
Hi. I’m runnig croco model with MPI (climatology), the physics and biogeochemistry works well, however, when active the diagnostic TS and BIO there is a error: The first month it works good, but at the second month the… --- ## [PISCES diagnostics (WRT)](https://forum.croco-ocean.org/t/pisces-diagnostics-wrt/103)
**Author:** [@ftagklis](https://forum.croco-ocean.org/u/ftagklis)\ **Replies:** 0\ **Last updated:** [May 28, 2019, 4:35pm UTC](https://forum.croco-ocean.org/t/pisces-diagnostics-wrt/103 "2019-05-28T16:35:03Z")
Hi croco users, I am facing an issue while trying to write avg diagnostics\_bio files. Whenever I restart from a history or restart files, the model starts writing diagnostics again from diagbio.0000.nc. History and a… --- ## [Error when running with EBUS after compilation, 2nd nesting](https://forum.croco-ocean.org/t/error-when-running-with-ebus-after-compilation-2nd-nesting/478)
**Author:** [@Gandy](https://forum.croco-ocean.org/u/Gandy)\ **Replies:** 9\ **Last updated:** [August 23, 2023, 3:14pm UTC](https://forum.croco-ocean.org/t/error-when-running-with-ebus-after-compilation-2nd-nesting/478 "2023-08-23T15:14:54Z")
Im using the script below to run the model (second nesting), but Im getting this error: ERROR: keyword not found: diagbioFlux\_history\_fields ERROR: keyword not found: diagbioVSink\_history\_fields ERROR: keyword not fou… --- ## [interannual runs for biogeochemical simulations](https://forum.croco-ocean.org/t/interannual-runs-for-biogeochemical-simulations/476)
**Author:** [@Apriansyah\_Hakim](https://forum.croco-ocean.org/u/Apriansyah_Hakim)\ **Replies:** 1\ **Last updated:** [August 18, 2023, 4:56pm UTC](https://forum.croco-ocean.org/t/interannual-runs-for-biogeochemical-simulations/476 "2023-08-18T16:56:30Z")
Hello CROCO model developers, Is it possible to do interannual runs for biogeochemical simulations? Is there a special toolbox to do so? Thank you. --- ## [pisces compilation error](https://forum.croco-ocean.org/t/pisces-compilation-error/469)
**Author:** [@yxli](https://forum.croco-ocean.org/u/yxli)\ **Replies:** 1\ **Last updated:** [June 21, 2023, 1:10pm UTC](https://forum.croco-ocean.org/t/pisces-compilation-error/469 "2023-06-21T13:10:46Z")
Hi! I follow the tutorial step by step,however I met the following errors when trying to compile crocs after open the pisces key. And my configuration without pisces is compiled and run very successful. Can anybody he… --- ## [ln\_river in PISCES](https://forum.croco-ocean.org/t/ln-river-in-pisces/433)
**Author:** [@lsuocean](https://forum.croco-ocean.org/u/lsuocean)\ **Replies:** 0\ **Last updated:** [February 10, 2023, 3:50pm UTC](https://forum.croco-ocean.org/t/ln-river-in-pisces/433 "2023-02-10T15:50:59Z")
Hello friends, There is a flag ln\_river in PISCES. If river-borne nutrients are already in croco\_runoff.nc and .in file, does ln\_river still have to be activated? In the code, rivdin rivdip … are used if ln\_river is act… --- ## [PISCES status: v1 or v2](https://forum.croco-ocean.org/t/pisces-status-v1-or-v2/430)
**Author:** [@jvmcgovern](https://forum.croco-ocean.org/u/jvmcgovern)\ **Replies:** 2\ **Last updated:** [January 25, 2023, 2:11pm UTC](https://forum.croco-ocean.org/t/pisces-status-v1-or-v2/430 "2023-01-25T14:11:25Z")
Hi All, I’m wondering can I get clarification as to which version of PISCES is packaged with CROCO? v1 (Aumont et al 2005) or v2 (Aumont et al 2015). Best regards, Joe --- ## [pisces segmentation runtime error](https://forum.croco-ocean.org/t/pisces-segmentation-runtime-error/415)
**Author:** [@ify](https://forum.croco-ocean.org/u/ify)\ **Replies:** 8\ **Last updated:** [December 8, 2022, 10:25am UTC](https://forum.croco-ocean.org/t/pisces-segmentation-runtime-error/415 "2022-12-08T10:25:57Z")
Hi Everyone, Big thanks for dev team and the update of the croco code and tools. I try testing a PISCES run with v1.3. After successfully compiling, I ran into this issue during my run: \*\*\* Total number of p… --- ## [PISCES and psource， read in error](https://forum.croco-ocean.org/t/pisces-and-psource-read-in-error/407)
**Author:** [@Isa\_Su](https://forum.croco-ocean.org/u/Isa_Su)\ **Replies:** 1\ **Last updated:** [November 4, 2022, 4:37pm UTC](https://forum.croco-ocean.org/t/pisces-and-psource-read-in-error/407 "2022-11-04T16:37:11Z")
Hi, I am working with croco-pisces, and there is only a large river in our model domain. I am using the psource defined in croco\_inter.in, and the model runs very successfully without PISCES. However, the ‘read in err… --- ## [PISCES and psource， read in error](https://forum.croco-ocean.org/t/pisces-and-psource-read-in-error/406)
**Author:** [@Isa\_Su](https://forum.croco-ocean.org/u/Isa_Su)\ **Replies:** 0\ **Last updated:** [October 28, 2022, 2:54pm UTC](https://forum.croco-ocean.org/t/pisces-and-psource-read-in-error/406 "2022-10-28T14:54:23Z")
Hi, I am working with croco-pisces, and there is only a large river in our model domain. I am using the psource defined in croco\_inter.in, and the model runs very successfully without PISCES. However, the ‘read in err… --- ## [PISCES runtime error](https://forum.croco-ocean.org/t/pisces-runtime-error/400)
**Author:** [@jvmcgovern](https://forum.croco-ocean.org/u/jvmcgovern)\ **Replies:** 6\ **Last updated:** [October 17, 2022, 9:00am UTC](https://forum.croco-ocean.org/t/pisces-runtime-error/400 "2022-10-17T09:00:38Z")
Hi all, I previously have run CROCO-PISCES on my current domain of interest, but it was a while back, firstly in climatological mode, and then with Mercator IBI initial and boundary conditions. Now, I’m in the situatio… --- ## [forrtl: severe (174): SIGSEGV, segmentation fault occurred](https://forum.croco-ocean.org/t/forrtl-severe-174-sigsegv-segmentation-fault-occurred/385)
**Author:** [@Isa\_Su](https://forum.croco-ocean.org/u/Isa_Su)\ **Replies:** 0\ **Last updated:** [August 26, 2022, 7:54am UTC](https://forum.croco-ocean.org/t/forrtl-severe-174-sigsegv-segmentation-fault-occurred/385 "2022-08-26T07:54:46Z")
Dear all, I am running the croco-pisces on my Mac, and meeting the following error after I open the PISCES key, however, the physical module is running very successfully before I open the PISCES key. I have attached the… --- ## [Passive tracer with sea-to-air flux](https://forum.croco-ocean.org/t/passive-tracer-with-sea-to-air-flux/382)
**Author:** [@Qingyue](https://forum.croco-ocean.org/u/Qingyue)\ **Replies:** 0\ **Last updated:** [August 12, 2022, 4:56pm UTC](https://forum.croco-ocean.org/t/passive-tracer-with-sea-to-air-flux/382 "2022-08-12T16:56:12Z")
Hi everyone, I have observations with SF5CF3 as tracers and I want to do a simulation. I currently define it as a passive tracer and the model outputs show that the tracer is mostly concentrated at the sea surface. But … --- ## [Error: READ\_INP ERROR while reading block with keyword 'auxiliary\_history\_fields'](https://forum.croco-ocean.org/t/error-read-inp-error-while-reading-block-with-keyword-auxiliary-history-fields/372)
**Author:** [@ify](https://forum.croco-ocean.org/u/ify)\ **Replies:** 8\ **Last updated:** [July 5, 2022, 7:41am UTC](https://forum.croco-ocean.org/t/error-read-inp-error-while-reading-block-with-keyword-auxiliary-history-fields/372 "2022-07-05T07:41:30Z")
Hello everyone, I am trying to configure CROCO for a test case with the simple biogeochemical model BIO\_NChlPZD. I already made all my files correctly and all seem to work well. However, when I try to run the model aft… --- ## [PISCES and river tracers](https://forum.croco-ocean.org/t/pisces-and-river-tracers/355)
**Author:** [@MartinV](https://forum.croco-ocean.org/u/MartinV)\ **Replies:** 0\ **Last updated:** [May 14, 2022, 8:04am UTC](https://forum.croco-ocean.org/t/pisces-and-river-tracers/355 "2022-05-14T08:04:14Z")
Hi everyone! I am trying to run CROCO with PISCES and several rivers. I use the psource netcdf file for discharge and tracer concentrations (cpp flags: PSOURCE PSOURCE\_NCFILE PSOURCE\_NCFILE\_TS). I have defined po4\_src\_… [Next page](https://forum.croco-ocean.org/c/biogeochemistry/10.md?page=1)