Claude/3d export vertical chunking 9jb nb#221

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tomsail wants to merge 84 commits into

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tomsail:claude/3d-export-vertical-chunking-9jbNB

Commits on May 22, 2026

Minor change in aspect ratio script

josephzhang8
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tomsail
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Re-org gen_vqs_1.f90 for usability

josephzhang8
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update EPA MBM model setup

wzhengui
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Minor changes in MARSH; output from WWM for check

josephzhang8
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Restored Core/gen_version.py for gnu make

josephzhang8
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Update manual

josephzhang8
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More updates on manual

josephzhang8
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Update WWM manual link

josephzhang8
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Added checks in Fairall air-sea exchange.

josephzhang8
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Make Fairall default in make also

josephzhang8
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Feature ugrid (#204)

platipodium
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Added conditional for 2D header info (iof_ugrid>0)

josephzhang8
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restored Fairall as default

josephzhang8
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Add live manual for SCHISM in ESMF docs

josephzhang8
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Fix link formatting in ESMF documentation

josephzhang8
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added CR version of hotstart from hycom

cseaton
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added comment to CR hotstart gen

cseaton
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edit of notes

josephzhang8
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Fix veg_lai and veg_cw type declaration: integer -> real (#205)

jreniel
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Added hotstart-only generation from hycom for CR

cseaton
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fix error in computing diagonistic variable oMT in ICM

wzhengui
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minor edit on EPA MBM setup

wzhengui
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Revised flex veg option (including MARSH); tested with lab cases

josephzhang8
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update notes

josephzhang8
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tomsail
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Added lon/lat option for script eq_diameter_aspect_ratio.f90

josephzhang8
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tomsail
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minor edit on EPA MBM setup

wzhengui
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Moved ghost exchange in USE_ATMOS

josephzhang8
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Added iref_ts=2 that allows user to specify scaling (ramp-down) factor

josephzhang8
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add notes

josephzhang8
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Impose bound for air-water T in shallows

josephzhang8
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tomsail
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Update notes

josephzhang8
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tomsail
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STOFS3D-Atl scripts. Reorganized and added new functions in the Atl setup scripts and put them in a new folder (STOFS-3D-Atl-Setup) alongside the old one (STOFS-3D-Atl-shadow-VIMS). Both are kept f…

feiye-vims
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tomsail
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STOFS3D-Atl scripts: Added a README for the new setup workflow.

feiye-vims
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Revised read_staout.f90 to output nc per NOAA request

josephzhang8
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minor notes

josephzhang8
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notes edits

josephzhang8
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Fix mpi_bcast for ieg_source_flowpath_ids with correct size

jduckerOWP
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Update SCHISM_BMI_GRID_SOURCE_ELEMENTS loop indices to use nsources_bmi

jduckerOWP
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update EPA MBM parameter setup

wzhengui
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Fixed a bug in MICE I/O and added notes for hotstart. Thx, Qian!

Joseph Zhang
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Added attribites and station coord in staout

josephzhang8
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added notes

josephzhang8
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added gnu make for kuro. At the moment, the scribe IO does not work

josephzhang8
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added notes on compiling scribe IO under gnu make

josephzhang8
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turn off PETSc as default

josephzhang8
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Changed sequence for atmos update under USE_ATMOS

josephzhang8
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updated compiler name on kuro

josephzhang8
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:memo: Updates docs workflow (#212)

jamal919
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Fix size allocations for water level boundaries to avoid memory corruption during concurrent execution of SCHISM BMI

jduckerOWP
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Refactor boundary array allocations and add MPI barriers to SCHISM BMI Driver Test

jduckerOWP
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PETSc works with OLDIO and NOPARM at the moment. Will work to have

josephzhang8
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Ursa(NOAA-RDHPC) CMake conf. file (#213)

felicio93
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notes

josephzhang8
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Resolved conflict for FABM mask

platipodium
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Make sure to not initialize must-be-nonnegative (like PAR) with missing_values (which is FABM default -1e20)

platipodium
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tomsail
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Guard vertical loops in FABM against kbe(iz) = zero, which leads to crashes on some systems

platipodium
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tomsail
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Fix (recurrent) unbalenced _FABM_MASK_TYPE_ macro

platipodium
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tomsail
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Added a simple script to manipulate SMS map

josephzhang8
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PDAF manual

josephzhang8
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edits on PDAF manual

josephzhang8
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add new figs

josephzhang8
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tomsail
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edit PDAF manual

josephzhang8
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tomsail
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edit PDAF manual

josephzhang8
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bug fixes with initial CICE implementation (#215)

SmithJos13
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Edit Joey Smith's PR: exchange tau_oi(2,npa)

josephzhang8
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Typos in units

josephzhang8
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Bug fix in WWM hotstart; c/o Zhiyun Du

josephzhang8
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minor edits

josephzhang8
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added Spherepack into SCHISM for SAL; not working yet

josephzhang8
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Add Spherepack sources

josephzhang8
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fixed compile flag for gcc

josephzhang8
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Moved zcor station output to its own file to reduce size

josephzhang8
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Finished revising iout_sta=2; tested

josephzhang8
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Modifications for CICE coupling (#218)

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Update i.c. & b.c. scripts for T<0 (ice)

josephzhang8
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Make ice-ocean drag spatially varying

josephzhang8
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Update notes

josephzhang8
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STOFS3D-Atl scripts: save final updates on the old shadow forecast scripts (STOFS3D-Atl-v3.1 or earlier).

feiye-vims
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tomsail
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STOFS-3D scripts: Reorganized the setup package to support future STOFS-3D versions (v3.1 and beyond), while maintaining compatibility with previous versions. The previous STOFS-3D-Atl-shadow-VIMS …

feiye-vims
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STOFS-3D scripts: Added the STOFS-3D-Atl-Setup scripts.

feiye-vims
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tomsail
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STOFS-3D scripts: minor updates on the README and pyproject.toml.

feiye-vims
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STOFS-3D scripts: Added more updates from v7.4; minor changes in README.

feiye-vims
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Chunk 3D netCDF outputs along the vertical dimension

claude
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tomsail
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remove legacy term
tomsail
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