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use default(none) for all OMP directives. PGI has a memory leak issue if... #19

Merged
merged 4 commits into from
May 22, 2014
Merged

use default(none) for all OMP directives. PGI has a memory leak issue if... #19

merged 4 commits into from
May 22, 2014

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Zhi-Liang
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... using default(private). This will benefit future development

@adcroft adcroft merged commit 341a350 into dev/master May 22, 2014
gustavo-marques pushed a commit to gustavo-marques/MOM6 that referenced this pull request Aug 1, 2017
@alperaltuntas
Merge pull request mom-ocean#19 from gustavo-marques/new_merge
7480492 
Merging latest dev/master into dev/ncar
nikizadehgfdl pushed a commit to nikizadehgfdl/MOM6 that referenced this pull request 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 pushed a commit to nikizadehgfdl/MOM6 that referenced this pull request 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
marshallward pushed a commit to Hallberg-NOAA/MOM6 that referenced this pull request Dec 1, 2021
@adcroft @marshallward
Fix out-of-bounds k index in PPM flux
ceb181f 
- An errant use of the porous face area led to an out-of-bounds k-index
  reported in NOAA-GFDL#19.
- Closes mom-ocean#19
marshallward pushed a commit to Hallberg-NOAA/MOM6 that referenced this pull request Jan 29, 2022
@kshedstrom
Esmg docs (mom-ocean#57)
65998cd 
* additions for stochastic physics and ePBL perts

* cleanup of code and enhancement of ePBL perts

* Update MOM_diabatic_driver.F90

remove conflict with dev/emc

* Update MOM_diabatic_driver.F90

further resolve conflict

* Update MOM_diabatic_driver.F90

put id_sppt_wts, etc back.

* add stochy_restart writing to mom_cap

* additions for stochy restarts

* clean up debug statements

* clean up code

* fix non stochastic ePBL calculation

* re-write of stochastic code to remove CPP directives

* remove blank link in MOM_diagnostics

* clean up MOM_domains

* make stochastics optional

* correct coupled_driver/ocean_model_MOM.F90 and other cleanup

* clean up of code for MOM6 coding standards

* remove stochastics container

* revert MOM_domains.F90

* clean up of mom_ocean_model_nuopc.F90

* remove PE_here from mom_ocean_model_nuopc.F90

* remove debug statements

* stochastic physics re-write

* move stochastics to external directory

* doxygen cleanup

* add write_stoch_restart_ocn to MOM_stochastics

* add logic to remove incrments from restart if outside IAU window

* revert logic wrt increments

* add comments

* update to gfdl 20210806 (mom-ocean#74)

* remove white space and fix comment

* Update MOM_oda_incupd.F90

remove unused index bounds, and fix sum_h2 loop.

Co-authored-by: pjpegion <Philip.Pegion@noaa.gov>
Co-authored-by: Marshall Ward <marshall.ward@noaa.gov>

* Fussing with zotero.bib.

Getting a warning about a repeated bibliography entry for adcroft2004.
Rob thinks this is a hash failure.

* Still fussing with zotero.bib

- it was complaining about the (unused) Kasahara reference.

* Several little things, one is making sponge less verbose.

- Pointing to OBC wiki file from the lateral parameterizations doc.

- Using the MOM6 verbosity to control the time_interp verbosity.

- Making the check for negative water depths more informative.

* return a more accurate error message in MOM_stochasics

* Working on boundary layer docs.

* Done with EPBL docs?

* Undoing some patches from others

* Cleaning up too-new commits

* Adding in that SAL commit again.

* correction on type in directory name

* Added some to vertical viscisity doc.

* Cleaned up whitespace leftover from porous topomerge.

- Spacing within expressions was uneven and made multiplation look like
  POW functions. Leftover from merging NOAA-GFDL#3.
- No answer changes.

* Fix out-of-bounds k index in PPM flux

- An errant use of the porous face area led to an out-of-bounds k-index
  reported in NOAA-GFDL#19.
- Closes mom-ocean#19

* Adding Channel drag figure

* Take cite out of figure caption.

* Copyright year 2022
gustavo-marques pushed a commit to gustavo-marques/MOM6 that referenced this pull request May 6, 2022
@jskenigson
Stanley scheme in mixed_layer_restrat, vert_fill in stoch_eos, code c…
90e795d 
…leanup (mom-ocean#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 (mom-ocean#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>
gustavo-marques pushed a commit to gustavo-marques/MOM6 that referenced this pull request May 17, 2022
@iangrooms @pjpegion @jskenigson
Corrections to cell-averaged density computation (mom-ocean#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 (mom-ocean#10)

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

* Missing then added

* Merge Ian Grooms Tvar Discretization (mom-ocean#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 (mom-ocean#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 (mom-ocean#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 (mom-ocean#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 (mom-ocean#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 (mom-ocean#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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@Zhi-Liang @adcroft