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Diagnostic output #334

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nichannah opened this issue Jul 7, 2016 · 1 comment
Closed

Diagnostic output #334

nichannah opened this issue Jul 7, 2016 · 1 comment

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@nichannah
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Presently the user can request that a diagnostic output on z-star vertical coords through the diag table. MOM6 regrids the output during the post() call. This issue will extend this functionality to support support both isopycnal (rho) and terrain following (sigma) coordinates.

It may also make sense to do code cleanup / refactoring of the diagnostic vertical regridding code. Perhaps this can be split into a separate file, e.g. src/framework/MOM_diag_regrid.F90

This issue will be tested here: NOAA-GFDL/MOM6-examples#98
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Jul 13, 2016
mom-ocean#334 get diagnostic regrid prototype compiling.
fa29a65
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Jul 14, 2016
mom-ocean#334 get diagnostic regrid prototype compiling.
0fd4920
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Jul 14, 2016
mom-ocean#334 in-progress work on remapping diagnostics to sigma vert…
70ea6ac 
…ical coords.
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Jul 15, 2016
Prototyping diagnostic regridding code. mom-ocean#334
781e94d
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Jul 15, 2016
beginning to split out grid generation into per-column. mom-ocean#334
88c8ae0
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Jul 15, 2016
Prototyping diagnostic regridding code. mom-ocean#334
c6467e2
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Aug 1, 2016
@nichannah
beginning to split out grid generation into per-column. mom-ocean#334
a683340
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Aug 1, 2016
@nichannah
Prototyping diagnostic regridding code. mom-ocean#334
87f193a
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Aug 4, 2016
@nichannah
Diagnostic regridding for zstar, sigma and rho vertical coordinates. m…
76dd200 
…om-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 8, 2016
@nichannah
Correct available_diags for vertically remapped diagnostics. mom-ocea…
b1c6d1c 
…n#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 8, 2016
@nichannah
Split out slight and hycom1 grid generation into columns. Not complete.
7a4050c 
mom-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 9, 2016
@nichannah
Complete slight and hycom1 grid column generation. mom-ocean#334
0495c05
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Aug 10, 2016
@nichannah
beginning to split out grid generation into per-column. mom-ocean#334
c358b7e
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 10, 2016
@nichannah
Split out slight and hycom1 grid generation into columns. Not complete.
85d9677 
mom-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 10, 2016
@nichannah
Complete slight and hycom1 grid column generation. mom-ocean#334
35fed81
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 11, 2016
@nichannah
mom-ocean#334 Print diag hint on h change error for remapping.
ea7728d
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 11, 2016
@nichannah
mom-ocean#334 h has changed, update diag for vertical remapping.
edbd0e6
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Aug 30, 2016
@nichannah
beginning to split out grid generation into per-column. mom-ocean#334
c39d592
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 30, 2016
@nichannah
Split out slight and hycom1 grid generation into columns. Not complete.
25304cd 
mom-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Aug 30, 2016
@nichannah
Complete slight and hycom1 grid column generation. mom-ocean#334
6e31ccf
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Sep 5, 2016
@nichannah
Diagnostic regridding for zstar, sigma and rho vertical coordinates. m…
e401fdf 
…om-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Sep 5, 2016
@nichannah
Correct available_diags for vertically remapped diagnostics. mom-ocea…
df6cd17 
…n#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Sep 5, 2016
@nichannah
Extend vertical remapping to handle SLIGHT and HYCOM1. mom-ocean#334
5240529
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Sep 20, 2016
Remove unused code and add/improve comments after aja/diag_interp_and…
f059eb5 
…_extrinsic merge. mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 1, 2016
Better diagnostic debugging and fixed subroutine name for correctness. …
3bd0add 
…mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 1, 2016
Don't pass temporary axes variable to register_diag_field(). mom-ocea…
57c7abe 
…n#334.
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 1, 2016
Improved checking for vertical grid definition input, also layer var …
b1b2381 
…must be given. mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 1, 2016
Don't pass temporary axes variable to register_diag_field(). mom-ocea…
fc6942f 
…n#334.
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 1, 2016
Compiler error: fix dummy argument intent. mom-ocean#334
604540b
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 1, 2016
Whitespace and formatting fixes. mom-ocean#334
b2f8d18
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 2, 2016
Add some masking for vertically remapped diags based on on bathymetry. …
d7016e8 
…mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 2, 2016
Whitespace and formatting fixes. mom-ocean#334
7bb14ed
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 2, 2016
Whitespace and comment fixes. mom-ocean#334.
1057172
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 2, 2016
Change names of several old z coord diags to be the same as regular d…
42670b4 
…iags. mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 2, 2016
Add some masking for vertically remapped diags based on on bathymetry. …
593de0a 
…mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 2, 2016
Merge dev/master fixing conflicts. mom-ocean#334.
2072bfe
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 3, 2016
Fix merge mistake. mom-ocean#334
fdb4caf
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 4, 2016
Variable renaming, whitespace and documentation. mom-ocean#334
8fb94a2
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 4, 2016
Diagnostic vertical remapping performance improvement. Only activate …
32586a4 
…vertical

coordinate remapping there if diagnostics that use the given coordinate. This
saves time on target grid updates. mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 7, 2016
Whitespace changes. mom-ocean#334
caf702d
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 7, 2016
Make diagnostic default missing value same as other parts of the model.
2b3dba6 
mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 9, 2016
Fix masking used by vertically remapped diagnostics. mom-ocean#334
f817665
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 10, 2016
Fix masking used by vertically remapped diagnostics. mom-ocean#334
8ca897c
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 10, 2016
Fix masking used by vertically remapped diagnostics. mom-ocean#334
50efe07
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 16, 2016
Don't asser that masks are correctly attached. This is not needed for…
3b4c534 
… _zold diags. mom-ocean#334
nichannah pushed a commit to nichannah/MOM6 that referenced this issue Nov 17, 2016
Fix masking for vertically remapped diagnostics. mom-ocean#334
b701b8b
nichannah added a commit to nichannah/MOM6 that referenced this issue Nov 28, 2016
@nichannah
Remove support for diagnostic horizontal averaging on Z interfaces. m…
58b26a0 
…om-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Nov 28, 2016
@nichannah
Fix subroutine name in error string. mom-ocean#334
c32946c
nichannah added a commit to nichannah/MOM6 that referenced this issue Dec 8, 2016
@nichannah
Fix variable intent compilation error in dev/master. mom-ocean#334
a4031da
nichannah added a commit to nichannah/MOM6 that referenced this issue Dec 16, 2016
@nichannah
Allow horizontally_average_diag_field to be called by both native and…
47bed87 
… remapped diagnostics. mom-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Dec 16, 2016
@nichannah
Fix diagnostic umo_2d post. This diag was being registered but not po…
0fd8f70 
…sted properly. mom-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Dec 16, 2016
@nichannah
Fix diagnostic (v)umo_2d post. These diags were being registered but …
5d701f0 
…not posted properly. mom-ocean#334
nichannah added a commit to nichannah/MOM6 that referenced this issue Dec 16, 2016
@nichannah
Fix diagnostic (v)umo_2d post. These diags were being registered but …
d0f0e7a 
…not posted properly. mom-ocean#334
nikizadehgfdl pushed a commit to nikizadehgfdl/MOM6 that referenced this issue Oct 9, 2017
@adcroft
MOM6: Merge branch 'gustavo-marques-MOM_F90_FIX' into dev/master
00b9226 
- NOAA-GFDL/MOM6@2a50035 Merge branch 'gustavo-marques-MOM_F90_FIX' into dev/master
- NOAA-GFDL/MOM6@d7aa18b Refactor of gustavo-marques-MOM_F90_FIX
- NOAA-GFDL/MOM6@a2835a9 Merge branch 'MOM_F90_FIX' of https://github.com/gustavo-marques/MOM6 into gustavo-marques-MOM_F90_FIX
- NOAA-GFDL/MOM6@c8986f6 Merge branch 'nicjhan-334-kernelise-grid-build' into dev/master
- NOAA-GFDL/MOM6@753098a Merge branch '334-kernelise-grid-build' of https://github.com/nicjhan/MOM6 into nicjhan-334-kernelise-grid-build
- NOAA-GFDL/MOM6@1e373d9 Minor re-factor of diag_mediator()
- NOAA-GFDL/MOM6@b1b3554 Added new kernel reintegrate_column()
- NOAA-GFDL/MOM6@b1ccc5a Renamed unitTests to unit_tests
- NOAA-GFDL/MOM6@17a3f80 Added new module MOM_diag_vkernels
- NOAA-GFDL/MOM6@6e31ccf Complete slight and hycom1 grid column generation. mom-ocean#334
- NOAA-GFDL/MOM6@25304cd Split out slight and hycom1 grid generation into columns. Not complete. mom-ocean#334
- NOAA-GFDL/MOM6@c39d592 beginning to split out grid generation into per-column. mom-ocean#334
- NOAA-GFDL/MOM6@fc1b184 Updated comments in MOM_diag_mediator.F90
- NOAA-GFDL/MOM6@f44b798 Added cell_measures for static fields depth_ocean and wet
- NOAA-GFDL/MOM6@571b397 Implemented "interp_method = 'none'" for vector/q-point locations
- NOAA-GFDL/MOM6@909264b Merge branch 'user/nnz/openmpfixes_devmaster_20160809' into dev/master
- NOAA-GFDL/MOM6@f7507a4 Merge branch 'dev/master' into user/nnz/openmpfixes_devmaster_20160809
- NOAA-GFDL/MOM6@fd296ae Implemented cell_measure area for h-point variables
nikizadehgfdl pushed a commit to nikizadehgfdl/MOM6 that referenced this issue Oct 9, 2017
@adcroft
MOM6: Moved to flat (no subdirs) mode for doxygen
83415bc 
- NOAA-GFDL/MOM6@90d31ed Moved to flat (no subdirs) mode for doxygen
- NOAA-GFDL/MOM6@fd533dc Added draft of Diagnostics page
- NOAA-GFDL/MOM6@5bd2cfc Implemented xy-averaged diagnostics for interface data
- NOAA-GFDL/MOM6@ff858c7 Corrected variable names (changed extrinsic to extensive)
- NOAA-GFDL/MOM6@3aa0e78 Fix "edges" attribute for dimension variable in z-diag output
- NOAA-GFDL/MOM6@c32946c Fix subroutine name in error string. mom-ocean#334
- NOAA-GFDL/MOM6@58b26a0 Remove support for diagnostic horizontal averaging on Z interfaces. mom-ocean#334
nikizadehgfdl pushed a commit to nikizadehgfdl/MOM6 that referenced this issue Oct 9, 2017
@adcroft
MOM6: Finalizing merge of nicjhan-334-rho-sigma-diagnostic-regridding
6dcf7cf 
- Updates available_diags

- NOAA-GFDL/MOM6@5afba32 Fixed continuation character (again!)
- NOAA-GFDL/MOM6@a4031da Fix variable intent compilation error in dev/master. mom-ocean#334
- NOAA-GFDL/MOM6@c838594 Re-enable support for diagnostic horizonal averaging on Z interfaces and layers.
nikizadehgfdl pushed a commit to nikizadehgfdl/MOM6 that referenced this issue Oct 9, 2017
@adcroft
MOM6: Moved mass transport diagnostics to right point in algorithm
034145c 
- NOAA-GFDL/MOM6@d19edfb Moved mass transport diagnostics to right point in algorithm
- NOAA-GFDL/MOM6@aa488c0 Merge branch 'nicjhan-334-diagnostic-regridding-fixes' into dev/master
- NOAA-GFDL/MOM6@fc6162a Fix FPE when diagnosing MEKE bottom drag function
- NOAA-GFDL/MOM6@c063650 Merge branch '334-diagnostic-regridding-fixes' of https://github.com/nicjhan/MOM6 into nicjhan-334-diagnostic-regridding-fixes
- NOAA-GFDL/MOM6@d0f0e7a Fix diagnostic (v)umo_2d post. These diags were being registered but not posted properly. mom-ocean#334
- NOAA-GFDL/MOM6@47bed87 Allow horizontally_average_diag_field to be called by both native and remapped diagnostics. mom-ocean#334
- NOAA-GFDL/MOM6@af85249 +Optionally append a suffix to NIPROC in logs
@Hallberg-NOAA
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This capability has been implemented.

nikizadehgfdl pushed a commit to nikizadehgfdl/MOM6 that referenced this issue Mar 29, 2023
@Hallberg-NOAA @marshallward
Fix indexing bugs in get_field_nc (mom-ocean#334)
37389b5 
Fixed two horizontal indexing bugs in `get_field_nc`, where the difference
between the array starting index (always 1 in this subroutine) and the values
in the handle argument were not being taken into account when the array was
being passed in with only its computational domain.

Also initialized the internal `unlim_index` array in `get_netcdf_fields` to fix
a problem with using an uninitialized array that was being flagged when run in
debug mode.

With this commit, the model is once again reproducing the expected answers when
rescaling is applied for vertical distances or time.

Co-authored-by: Marshall Ward <marshall.ward@gmail.com>
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@nichannah @Hallberg-NOAA