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Fix for openmp #5

Merged
merged 3 commits into from
Mar 13, 2014
Merged

Fix for openmp #5

merged 3 commits into from
Mar 13, 2014

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Zhi-Liang
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openmp updates for MOM_kappa_shear.F90 and MOM_vert_friction.F90

adcroft added a commit that referenced this pull request Mar 13, 2014
@adcroft
Merge pull request #5 from CommerceGov/user/z1l/openmp
7962e88 
All tests passed after issuing:
 git checkout user/z1l/openmp
 git merge dev/master
Merging using github UI rather than command line.
@adcroft adcroft merged commit 7962e88 into dev/master Mar 13, 2014
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
Merge pull request #5 from CommerceGov/usr/nnz/fix_analysis_template
e794854 
- Corrects environment and imports needed for MIDAS.
- Fixes EKE script.
- Fixes #2.
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
MOM6: Merge pull request mom-ocean#578 from NCAR/dev/ncar
8b801de 
- NOAA-GFDL/MOM6@ae22a0f Merge pull request mom-ocean#578 from NCAR/dev/ncar
- NOAA-GFDL/MOM6@f4f882f Merge pull request mom-ocean#23 from gustavo-marques/combine_mct_modules
- NOAA-GFDL/MOM6@a85b728 Merge MCT modules
- NOAA-GFDL/MOM6@ba5b5ba Merge pull request mom-ocean#22 from gustavo-marques/check_fluxes
- NOAA-GFDL/MOM6@f5a8483 Adds option to write restart files
- NOAA-GFDL/MOM6@8745b4b Fills additional IOB fluxes
- NOAA-GFDL/MOM6@f6b22ff Merge branch 'dev/ncar' into check_fluxes
- NOAA-GFDL/MOM6@369d5d6 Merge pull request mom-ocean#21 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@2582e0a Adds run paramaters to control SW decomposition
- NOAA-GFDL/MOM6@58f78b9 Fill IOB, some fluxes still need to be checked
- NOAA-GFDL/MOM6@06a30ab Fixed clock and timing
- NOAA-GFDL/MOM6@1bca79b Merge pull request mom-ocean#20 from gustavo-marques/fix_merge
- NOAA-GFDL/MOM6@fb89b08 Adds code that got lost during merge
- NOAA-GFDL/MOM6@7480492 Merge pull request mom-ocean#19 from gustavo-marques/new_merge
- NOAA-GFDL/MOM6@be1e6cf Merge branch 'dev/master' into dev/ncar
- NOAA-GFDL/MOM6@76565cb Merge pull request mom-ocean#17 from gustavo-marques/fix_ssh_slopes
- NOAA-GFDL/MOM6@c04f081 Fix ssh slope calculation
- NOAA-GFDL/MOM6@17d4586 Merge pull request mom-ocean#16 from adcroft/ncar-cherry-picked-fixes
- NOAA-GFDL/MOM6@be46fee (*)Fixes gprime(1) when no layer coordinates are set
- NOAA-GFDL/MOM6@fccb7ae Avoids a SEGV when OBC are not in use with bi-harmonic friction
- NOAA-GFDL/MOM6@f42c970 Merge pull request mom-ocean#15 from gustavo-marques/small_fixes
- NOAA-GFDL/MOM6@31787c2 Adds reference to set_time that was lost during a conflict handling
- NOAA-GFDL/MOM6@d77936e Fix intent(inout) in ice_ocean_boundary
- NOAA-GFDL/MOM6@b403edd Merge pull request mom-ocean#14 from gustavo-marques/docs
- NOAA-GFDL/MOM6@4d346ca Merge branch 'dev/ncar' into docs
- NOAA-GFDL/MOM6@f7c26a5 Clean the module and start doxygenizing it
- NOAA-GFDL/MOM6@cd58e2a Merge pull request mom-ocean#13 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@37a53bc reorganize file structure
- NOAA-GFDL/MOM6@e6c5ddd Merge pull request mom-ocean#12 from gustavo-marques/fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@6b6289a Remove trailing whitespace
- NOAA-GFDL/MOM6@7ce40e5 Fix undefined reference to fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@d517719 Merge branch 'dev/ncar' into fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@b69ab33 Filling ice_ocean_bnd - Draft
- NOAA-GFDL/MOM6@a306c90 Merge pull request mom-ocean#11 from adcroft/use-ocn-public-for-surface
- NOAA-GFDL/MOM6@c83e238 Correct indexing when using ocean_public_type
- NOAA-GFDL/MOM6@1f39c84 Replaces use of "surface" with "ocean_public_type"
- NOAA-GFDL/MOM6@5cd8d7a Filling ice_ocean_bnd, still needs work
- NOAA-GFDL/MOM6@3ceef26 Merge pull request mom-ocean#10 from adcroft/sketch-out-mct-run
- NOAA-GFDL/MOM6@714e8d6 Adds placeholders for stepping foward MOM
- NOAA-GFDL/MOM6@7f2207c Merge pull request #7 from adcroft/fix-mct-whitespace
- NOAA-GFDL/MOM6@a1db77f Cleans up white space
- NOAA-GFDL/MOM6@5700d67 Merge pull request #6 from adcroft/add-use-only-for-imports
- NOAA-GFDL/MOM6@beac3ed Adds "only" for all use statements
- NOAA-GFDL/MOM6@231d19e Merge pull request #5 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@3a923a2 Got initialization working
- NOAA-GFDL/MOM6@8b38141 Wrapped global data
- NOAA-GFDL/MOM6@970f848 added debugging
- NOAA-GFDL/MOM6@2540ed8 Filled empty subroutines in ocn_comp_mct.F90
- NOAA-GFDL/MOM6@ed3ed30 Added ocn_import_export module
- NOAA-GFDL/MOM6@aba7dc2 Completed ocn_init_mct
- NOAA-GFDL/MOM6@5df3bc3 Added method to point ponters to members of ocean_state_type
- NOAA-GFDL/MOM6@57e6086 Added methods to return domain/grid shape
- NOAA-GFDL/MOM6@37e7356 Added ocn_import_export.F90
- NOAA-GFDL/MOM6@2b794da Merge pull request #4 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@fbd405b Added coupler indices module
- NOAA-GFDL/MOM6@fa86163 Merge pull request #3 from NCAR/dev/gfdl
- NOAA-GFDL/MOM6@e8f2999 Merge pull request #2 from gustavo-marques/temp_salt_z_init_file
- NOAA-GFDL/MOM6@86936ba Adds option to read initial temp and salt from separate files
- NOAA-GFDL/MOM6@54f7976 Most initialization working
- NOAA-GFDL/MOM6@426357c Time and calendar initialization in ocn_comp_mct.F90
- NOAA-GFDL/MOM6@346097d Moved blank ocn_comp_mct.F90
- NOAA-GFDL/MOM6@405fecb Merge pull request #1 from gustavo-marques/ice_shelf
- NOAA-GFDL/MOM6@711a613 Removes frazil's contribution to evaporation
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@adcroft
MOM6: Merge branch 'dev/master' into dev/gfdl
3f17d14 
- Updates MOM_parameter_doc files.

- NOAA-GFDL/MOM6@cde6d3f Merge branch 'dev/master' into dev/gfdl
- NOAA-GFDL/MOM6@ae22a0f Merge pull request mom-ocean#578 from NCAR/dev/ncar
- NOAA-GFDL/MOM6@f4f882f Merge pull request mom-ocean#23 from gustavo-marques/combine_mct_modules
- NOAA-GFDL/MOM6@a85b728 Merge MCT modules
- NOAA-GFDL/MOM6@ba5b5ba Merge pull request mom-ocean#22 from gustavo-marques/check_fluxes
- NOAA-GFDL/MOM6@f5a8483 Adds option to write restart files
- NOAA-GFDL/MOM6@8745b4b Fills additional IOB fluxes
- NOAA-GFDL/MOM6@f6b22ff Merge branch 'dev/ncar' into check_fluxes
- NOAA-GFDL/MOM6@369d5d6 Merge pull request mom-ocean#21 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@2582e0a Adds run paramaters to control SW decomposition
- NOAA-GFDL/MOM6@58f78b9 Fill IOB, some fluxes still need to be checked
- NOAA-GFDL/MOM6@06a30ab Fixed clock and timing
- NOAA-GFDL/MOM6@1bca79b Merge pull request mom-ocean#20 from gustavo-marques/fix_merge
- NOAA-GFDL/MOM6@fb89b08 Adds code that got lost during merge
- NOAA-GFDL/MOM6@7480492 Merge pull request mom-ocean#19 from gustavo-marques/new_merge
- NOAA-GFDL/MOM6@be1e6cf Merge branch 'dev/master' into dev/ncar
- NOAA-GFDL/MOM6@76565cb Merge pull request mom-ocean#17 from gustavo-marques/fix_ssh_slopes
- NOAA-GFDL/MOM6@c04f081 Fix ssh slope calculation
- NOAA-GFDL/MOM6@17d4586 Merge pull request mom-ocean#16 from adcroft/ncar-cherry-picked-fixes
- NOAA-GFDL/MOM6@be46fee (*)Fixes gprime(1) when no layer coordinates are set
- NOAA-GFDL/MOM6@fccb7ae Avoids a SEGV when OBC are not in use with bi-harmonic friction
- NOAA-GFDL/MOM6@f42c970 Merge pull request mom-ocean#15 from gustavo-marques/small_fixes
- NOAA-GFDL/MOM6@31787c2 Adds reference to set_time that was lost during a conflict handling
- NOAA-GFDL/MOM6@d77936e Fix intent(inout) in ice_ocean_boundary
- NOAA-GFDL/MOM6@b403edd Merge pull request mom-ocean#14 from gustavo-marques/docs
- NOAA-GFDL/MOM6@4d346ca Merge branch 'dev/ncar' into docs
- NOAA-GFDL/MOM6@f7c26a5 Clean the module and start doxygenizing it
- NOAA-GFDL/MOM6@cd58e2a Merge pull request mom-ocean#13 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@37a53bc reorganize file structure
- NOAA-GFDL/MOM6@e6c5ddd Merge pull request mom-ocean#12 from gustavo-marques/fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@6b6289a Remove trailing whitespace
- NOAA-GFDL/MOM6@7ce40e5 Fix undefined reference to fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@d517719 Merge branch 'dev/ncar' into fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@b69ab33 Filling ice_ocean_bnd - Draft
- NOAA-GFDL/MOM6@a306c90 Merge pull request mom-ocean#11 from adcroft/use-ocn-public-for-surface
- NOAA-GFDL/MOM6@c83e238 Correct indexing when using ocean_public_type
- NOAA-GFDL/MOM6@1f39c84 Replaces use of "surface" with "ocean_public_type"
- NOAA-GFDL/MOM6@5cd8d7a Filling ice_ocean_bnd, still needs work
- NOAA-GFDL/MOM6@3ceef26 Merge pull request mom-ocean#10 from adcroft/sketch-out-mct-run
- NOAA-GFDL/MOM6@714e8d6 Adds placeholders for stepping foward MOM
- NOAA-GFDL/MOM6@7f2207c Merge pull request #7 from adcroft/fix-mct-whitespace
- NOAA-GFDL/MOM6@a1db77f Cleans up white space
- NOAA-GFDL/MOM6@5700d67 Merge pull request #6 from adcroft/add-use-only-for-imports
- NOAA-GFDL/MOM6@beac3ed Adds "only" for all use statements
- NOAA-GFDL/MOM6@231d19e Merge pull request #5 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@3a923a2 Got initialization working
- NOAA-GFDL/MOM6@8b38141 Wrapped global data
- NOAA-GFDL/MOM6@970f848 added debugging
- NOAA-GFDL/MOM6@2540ed8 Filled empty subroutines in ocn_comp_mct.F90
- NOAA-GFDL/MOM6@ed3ed30 Added ocn_import_export module
- NOAA-GFDL/MOM6@aba7dc2 Completed ocn_init_mct
- NOAA-GFDL/MOM6@5df3bc3 Added method to point ponters to members of ocean_state_type
- NOAA-GFDL/MOM6@57e6086 Added methods to return domain/grid shape
- NOAA-GFDL/MOM6@37e7356 Added ocn_import_export.F90
- NOAA-GFDL/MOM6@2b794da Merge pull request #4 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@fbd405b Added coupler indices module
- NOAA-GFDL/MOM6@fa86163 Merge pull request #3 from NCAR/dev/gfdl
- NOAA-GFDL/MOM6@e8f2999 Merge pull request #2 from gustavo-marques/temp_salt_z_init_file
- NOAA-GFDL/MOM6@86936ba Adds option to read initial temp and salt from separate files
- NOAA-GFDL/MOM6@54f7976 Most initialization working
- NOAA-GFDL/MOM6@426357c Time and calendar initialization in ocn_comp_mct.F90
- NOAA-GFDL/MOM6@346097d Moved blank ocn_comp_mct.F90
- NOAA-GFDL/MOM6@405fecb Merge pull request #1 from gustavo-marques/ice_shelf
- NOAA-GFDL/MOM6@711a613 Removes frazil's contribution to evaporation
nikizadehgfdl referenced this pull request in nikizadehgfdl/MOM6 Oct 9, 2017
@jkrasting
Merge pull request #5 from NOAA-GFDL/dev/gfdl
b6a25d3 
Merge from dev/gfdl
menzel-gfdl pushed a commit to menzel-gfdl/MOM6 that referenced this pull request Nov 5, 2018
@wrongkindofdoctor
Merge pull request mom-ocean#5 from NOAA-GFDL/dev/gfdl
975262d 
Latest MOM6 updates
Hallberg-NOAA pushed a commit that referenced this pull request Apr 12, 2019
@jkrasting
Merge pull request #5 from NOAA-GFDL/dev/gfdl
8bf6c9e 
Sync dev/gfdl with NOAA-GFDL version of repository
@kshedstrom kshedstrom mentioned this pull request Apr 23, 2019
Merged
gustavo-marques referenced this pull request in ashao/MOM6 Sep 17, 2019
@alperaltuntas
Merge pull request #5 from NCAR/dev/ncar
fda9848 
update dev/ncar
AndrewWittenberg pushed a commit to AndrewWittenberg/MOM6 that referenced this pull request Feb 6, 2020
@wfcooke
Merge pull request mom-ocean#5 from wfcooke/user/wfc_mjh/salt_flux_ad…
eb88576 
…d_fix

add MJHarrison-GFDL salt_flux_add_fix to SPEAR codeset
marshallward added a commit that referenced this pull request Sep 30, 2020
@marshallward
Merge pull request #5 from MJHarrison-GFDL/tc4_ice_shelf
d319e07 
Tc4 ice shelf
SMoorthi-emc pushed a commit to SMoorthi-emc/MOM6 that referenced this pull request Mar 2, 2021
@DeniseWorthen
Merge pull request mom-ocean#5 from NOAA-EMC/dev/emc
fb02b3a 
merge to latest dev/emc
@Hallberg-NOAA Hallberg-NOAA mentioned this pull request Mar 26, 2021
Merged
marshallward pushed a commit that referenced this pull request Mar 31, 2021
@Hallberg-NOAA
Merge pull request #5 from marshallward/FMS2_io_writes
81c48cb 
Explicit domain decomposition of horizontal axes
marshallward pushed a commit that referenced this pull request Aug 6, 2021
@jiandewang
Merge pull request #5 from pjpegion/patch-1
3fb3a4c 
Update MOM_oda_incupd.F90
herrwang0 pushed a commit to herrwang0/MOM6 that referenced this pull request Nov 29, 2021
@Hallberg-NOAA
Add initialization tests using CS%initialized
be50361 
  Added a new variable, initialized, to the control structures of modules that
had been testing for an allocated control structure to verify that it had been
initialized before it was going to be used, and then duplicated the tests using
this new variable.  This was done to enable us to go ahead with MOM6 PR mom-ocean#5,
which eliminated many of these checks when converting the control structures
from pointers in the parent modules to elements that are always there, and then
passing them as simple types instead of as pointers.  If we decide that we do
not need these tests after all, we can easily delete them, but until this is
discussed, this commit avoids losing the messages, as it was easier to do it
this way instead of trying to recreate them after they had been removed.  All
answers and output are bitwise identical.
herrwang0 pushed a commit to herrwang0/MOM6 that referenced this pull request Nov 29, 2021
@Hallberg-NOAA
Merge pull request mom-ocean#5 from marshallward/no_more_pointers
b2f6678 
Redefine ~500 pointers as local or stack variables
gustavo-marques pushed a commit that referenced this pull request Jun 29, 2022
@iangrooms @pjpegion @jskenigson
Corrections to cell-averaged density computation (#213)
8f97b3d 
* initial hooks for stochastic EOS modifications

* remove debug statements

* add documentation

* Change ampltiude from 0.39 to sqrt(.39)

* remove global_indexing logic from stoch_eos_init

* switch to using MOM_random and add restart capability

* update random sequence to update each each time-step

* remove tseed0 from MOM_random (leftover from debugging)

* Added necessary submodules and S^2, T^2 diagnostics to MOM_diagnostics

* Added diagnostics for outputting variables related to the stochastic parameterization.

* Diagnostics in MOM_PressureForce_FV updated for stochastic (rather than deterministic) Stanley SGS T variance parameterization.

* Added parentheses for reproducibility.

* Changed diagnostics to account for possible absence of stoch_eos_pattern in MOM_PressureForce_FV,
when deterministic parameterization is on.

* remove mom6_da_hooks and geoKdTree from pkg

* add stochastic compoment to MOM_thickness_diffuse

* fix array size declaration and post_data

* Corrected indexing of loops in MOM_calc_varT

* Changed how parameterization of SGS T variance (deterministic and stochastic) is switched on in PGF and thickness diffusion codes

* Corrected a few typos

* Cleaned up indices, redundant diagnostic, printing

* Fixed diagnostic IDs

* Fixed diagnostics typo

* Corrected indices in calculation of tv%varT

* Minor index fix

* Corrected bug in pressure in Stanley diagnostics

* Fixed whitespace error

* Stoch eos clock (#5)

*Added a clock for the Stanley parameterization

Co-authored-by: jkenigson <jkenigso@gmail.com>

* add halo update to random pattern

* Update MOM_stoch_eos.F90

Fix bug for looping over compute domain (is -> isc etc.)

* Avoid unnessary computations on halo (MOM_stoch_eos) and code clean-up (MOM_thickness_diffuse)

* Removed halo updates before determ param calc

* Update MOM_stoch_eos.F90

Removed unnecessary code

* Bug - indices are transposed

* Changed Stanley stochastic coefficient from exp(X) to exp(aX) (#9)

* Changed Stanley stochastic coefficient from exp(X) to exp(aX)

* Extra spaces removed

* Stoch eos init fix (#10)

* Don't bother calculating tv%varT if stanley_coeff<0

* Missing then added

* Merge Ian Grooms Tvar Discretization (#11)

* Update MOM_stoch_eos.F90

In progress updating stencil for$ | dx \times \nabla T|^2$ calculation

* New discretization of |dx\circ\nablaT|^2

Co-authored-by: Ian Grooms <ian.grooms@colorado.edu>

* Multiplied tvar%SGS by grid cell thickness ratio

* Added limiter for tv%varT

* Stoch eos ncar linear disc (#12)

* Update MOM_stoch_eos.F90

In progress updating stencil for$ | dx \times \nabla T|^2$ calculation

* New discretization of |dx\circ\nablaT|^2

* AR1 timescale land mask

Adds land mask to the computation of the AR1 decorrelation time

* Update dt in call to MOM_stoch_eos_run

The call to `MOM_stoch_eos_run` (which time steps the noise) is from within `step_MOM_dynamics`. `step_MOM_dynamics` advances on time step `dt` (per line 957), but the noise is updated using `dt_thermo`. It seems more appropriate to update the noise using `dt`, since it gets called from within `step_MOM_dynamics`.

* Fixed the units for r_sm_H

* Remove vestigial declarations

The variables `hl`, `Tl`, `mn_T`, `mn_T2`, and `r_sm_H` are no longer used, so I removed their declarations and an OMP private clause

Co-authored-by: Ian Grooms <ian.grooms@colorado.edu>

* Update MOM_thickness_diffuse.F90

Changed index for soft convention

* Update CVMix-src

* Ensure use_varT, etc., initialized

* Don't register stanley diagnostics if scheme is off

* Stanley density second derivs at h pts (#15)

* Change discretization of Stanley correction (drho_dT_dT at h points)

* Limit Stanley noise, shrink limiting value

* Revert t variance discretization

* Reverted variable declarations

* Stanley scheme in mixed_layer_restrat, vert_fill in stoch_eos, code cleanup (#19)

* Test Stanley EOS param in mixed_layer_restrat

* Fix size of TS cov, S var in Stanley calculate_density calls

* Test move stanley scheme initialization

* Added missing openMP directives

* Revert Stanley tvar discretization (#18)

* Perform vertical filling in calculation of T variance

* Variable declaration syntax error, remove scaling from get_param

* Fix call to vert_fill_TS

* Code cleanup, whitespace cleanup

Co-authored-by: Jessica Kenigson <jessicak@cheyenne1.cheyenne.ucar.edu>

* Use Stanley (2020) variance; scheme off at coast

* Comment clean-up

* Remove factor of 0.5 in Tvar

* Don't calculate Stanley diagnostics on halo

* Change start indices in stanley_density_1d

* Stanley param in MOM_isopycnal_slopes (#22)

Stanley param in MOM_isopycnal_slopes and thickness diffuse index fix

* Set eady flag to true if use_stored_slopes is true

* Cleanup, docs, whitespace

* Docs and whitespace

* Docs and whitespace

* Docs and whitespace

* Whitespace cleanup

* Whitespace cleanup

* Clean up whitespace

* Docs cleanup

* use_stanley

* Update MOM_lateral_mixing_coeffs.F90

* Adds link to another TEOS10 module

* Set Stanley off for testing

* Line continuation

Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: Philip Pegion <Philip.Pegion@noaa.gov>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne6.cheyenne.ucar.edu>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne3.cheyenne.ucar.edu>
Co-authored-by: jkenigson <jkenigso@gmail.com>
Co-authored-by: jskenigson <jessica.kenigson@colorado.edu>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne1.cheyenne.ucar.edu>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne5.cheyenne.ucar.edu>
Co-authored-by: Philip Pegion <ppegion@Philips-MacBook-Pro.local>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne4.cheyenne.ucar.edu>
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2 participants
@Zhi-Liang @adcroft