integration with fabm#18

Draft

plazzari wants to merge 99 commits into

17-integration-with-fabm

Commits on Aug 25, 2025

Adding preliminary example to couple with FABM
plazzari
committed

Commits on Oct 14, 2025

Add leonardo.intel
Marco-Puglia
authored

Commits on Nov 10, 2025

adding include and library paths for FABM
Paolo Lazzari
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first test including fabm module
Paolo Lazzari
committed

Commits on Nov 11, 2025

start including initialization phase of fabm in ogstm
Paolo Lazzari
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Adding Initialize and fabm.yaml read procedure
Paolo Lazzari
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bug fix
Paolo Lazzari
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Commits on Nov 20, 2025

Bug fix, put linking of fabm library in the correct order, to fulfill dependencies
Paolo Lazzari
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add configuration file fabm.yaml to the FABM
Paolo Lazzari
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Commits on Nov 25, 2025

change name of lidata add suffix _ogstm to avoid conflict with fabm
Paolo Lazzari
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Commits on Dec 3, 2025

correct string for FABM path
Paolo Lazzari
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add the range of all bio-optical parameters
Paolo Lazzari
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Commits on Dec 5, 2025

include separate subroutines for native bfm and fabm
Paolo Lazzari
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select coupling with fabm
Paolo Lazzari
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added more initialization functions, the creation of the model is currently in a bad position with the BIOmem allocation function
Paolo Lazzari
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Commits on Jan 15, 2026

include switch between bfm old style and fabm
Paolo Lazzari
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remove bfm code when bfm not active
Paolo Lazzari
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Commits on Jan 16, 2026

Commits on Jan 20, 2026

add test namelists for different BGC-TYPE
Paolo Lazzari
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add configuration column for BGC-TYPE
Paolo Lazzari
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Allows the model to use non parameter definition of BGC matrix sizes
Paolo Lazzari
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Commits on Jan 21, 2026

Retrive size of passive tracers matrixes from FABM
Paolo Lazzari
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Finalize to pass FABM internal variables names and units to OGSTM, namelist.passivetrc not used any more, diagnostic writing activations and frequency hard coded, need to be solved.
Paolo Lazzari
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set no BGC as Default configuration
Paolo Lazzari
committed

Commits on Jan 22, 2026

Fix BFM and DEFAULT compilation in parini.f90
Marco-Puglia
committed

Commits on Jan 26, 2026

copy all the namelist need .optics and .phys when using fabm BGC_TYPE
Paolo Lazzari
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correct not ifdef with propoer syntax
Paolo Lazzari
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allow for greater lenght of restart filenames and variables specification them.
Paolo Lazzari
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Commits on Jan 27, 2026

include variable naming of FABM-BFM
Paolo Lazzari
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hardcode relaxation variables --> need to be implemented better to adapt to FABM,extend files and variables naming to allow for larger strings
Paolo Lazzari
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Commits on Feb 4, 2026

adding module to read ogstm.yaml file, to configure I/O activation and frequency.
Paolo Lazzari
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include cmake options to include yaml modules
Paolo Lazzari
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connect configuration parameter in ogstm.yaml for I/O to operating ones in ogstm, relaxation activation needs to be completed
Paolo Lazzari
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add yaml directives to CMAKE
Paolo Lazzari
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set to default no BFM no FABM
Paolo Lazzari
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Commits on Feb 5, 2026

exclude use of yaml module in default and BFM configurations
Paolo Lazzari
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add controls on ogstm.yaml declaration of tracer, need to be consistent with internal fabm variables
Paolo Lazzari
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script to create template of ogstm.yaml
Paolo Lazzari
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Commits on Feb 10, 2026

fix path and deployment for ogstm.yaml
Paolo Lazzari
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Commits on Feb 11, 2026

define seconds_per_time_unit to prevent error in FABM initialization
Paolo Lazzari
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Commits on Feb 12, 2026

Dump info about restart files read.
Paolo Lazzari
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Start including the environmental dependencies required by FABM.
Paolo Lazzari
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set always at least one HF output otherwise create problems all outputs at 10.e-08.
Paolo Lazzari
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Bug fix on double declared variable.
Paolo Lazzari
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Commits on Feb 16, 2026

Finalize the definition of FABM dependencies.
Paolo Lazzari
committed

Commits on Feb 19, 2026

Improve ogstm.yaml handling in deploy_code.py
plazzari
authored
Include instructions to apply derivatives from FABM
Paolo Lazzari
committed

Commits on Feb 23, 2026

adding mask for terrain points
Paolo Lazzari
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Commits on Mar 2, 2026

initialized aksi short wave radiation, huge values gives overflow need to check more in detail
Paolo Lazzari
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initialized diagnostic to zero to prevent overflow, need to put correct values
Paolo Lazzari
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adding diagnostic data from FABM to OGSTM
Paolo Lazzari
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Commits on Mar 3, 2026

Adding sinking velocity taking the velocity from FABM, all variables possibly sink according to FABM specs
Paolo Lazzari
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Commits on Mar 4, 2026

adding time variable, need to be fixed
Paolo Lazzari
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passing time parameters to FABM
Paolo Lazzari
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Commits on Mar 6, 2026

added new function for day of the year
Paolo Lazzari
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pass to FABM the correct time informations
Paolo Lazzari
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from bfm to bgc flag activation
Paolo Lazzari
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add target and pointer definitions
Paolo Lazzari
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setting diagnostic write default to -> false
Paolo Lazzari
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Commits on Mar 11, 2026

add momentary write
Paolo Lazzari
committed
graphic interface to configure ogstm.yaml
Paolo Lazzari
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Commits on Mar 24, 2026

Adding trcave alternative subroutine for FABM
Paolo Lazzari
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deactivaded recovery of diagnostics from restart in FABM
Paolo Lazzari
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added improved diagnostic allocation according to what is dumped by user, correction of linking functions in FABM initialization by passing pure memeory address
Paolo Lazzari
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ogstm.yaml creation with graphic interface
Paolo Lazzari
committed

Commits on Mar 26, 2026

added a missing space in the cp yaml instruction
Marco-Puglia
committed
switched from the now absent lbfm flag to the new lbgc flag in all the namelist files
Marco-Puglia
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revert to previous version because the change was useless
Marco-Puglia
committed

Commits on Mar 30, 2026

Commits on Apr 7, 2026

Add RosenMacartur model setup
Paolo Lazzari
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Add case for RosenMacartur mode
Paolo Lazzari
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Add GUI for ogstm.yaml file configuration
Paolo Lazzari
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Commits on Apr 15, 2026

extension of variable name strings for output files to 200 digits, bug fix of diadump when high freq not active random output values.
Paolo Lazzari
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bug fix for function DAY_OF_THE_YEAR
Paolo Lazzari
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added different options for var_nc definition of Restoration Mask, this part will be removed, see issue in GitHub
Paolo Lazzari
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Removed write for debug phase
Paolo Lazzari
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set aerosol_air_mass_type from 10 - continental - to 1 - open ocean -
Paolo Lazzari
committed

Commits on Apr 16, 2026

Fixed error message to include the new FABM-BFM flag.
Marco-Puglia
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Select activation of ogstm OASIM model according to FABM.yaml file
Paolo Lazzari
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Commits on Apr 17, 2026

adding automatic selction of atmospheric model from fabm version or BIOPTIMOD version
Paolo Lazzari
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Commits on Apr 21, 2026

Create init files for BFM98
plazzari
committed

Commits on Apr 22, 2026

script to generate vertical profiles for BFM98
plazzari
committed

Commits on Apr 23, 2026

Added the mapping dictionary creator
Marco-Puglia
committed
code cleaning
plazzari
committed
code cleaning
plazzari
committed

Commits on Apr 24, 2026

Added bgc_error.py to house shared error logic and edited the relative files
Marco-Puglia
committed

Commits on Apr 28, 2026

Bug fix on buondary conditions index i->j
Paolo Lazzari
committed
update python script with BFM98
plazzari
committed
correct error message
plazzari
committed
Merge remote-tracking branch 'refs/remotes/origin/17-integration-with-fabm' into 17-integration-with-fabm
Paolo Lazzari
committed

Commits on May 13, 2026

new create_RESTARTS98.py file
Marco-Puglia
committed

Commits on May 15, 2026

utility to create boundary conditions namelists with ogstm-fabm
Paolo Lazzari
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refine utility to create boundary conditions namelists with ogstm-fabm
Paolo Lazzari
committed
new create_ATL98.py file
Marco-Puglia
committed

Commits on May 18, 2026

Commits on May 26, 2026

Script to create 1.aveTimes type files
Paolo Lazzari
committed