Merge tag 'dev/gfdl/2018.08.25' into ESM4-maintenance

dev/gfdl/2018.08.25

24106e5 icebergs: Merge pull request NOAA-GFDL#59 from wfcooke/user/wfc/calving_restart_timestamp
2741a88 MOM6: Merge pull request #844 from adcroft/avoid-domain_aux-for-wind-stagger
b864fed MOM6: Merge branch 'Hallberg-NOAA-streamline_restore_state' into dev/gfdl
5dcd7c3 SIS2: +Temporarily avoid new update_ocean_model args
f45003c Use IO_LAYOUT=2,2 in global_ALE
5007183 MOM6: Merge pull request #841 from adcroft/fix-oob-restart-filename
f6ae30c MOM6: Merge pull request #839 from MJHarrison-GFDL/rotation_angle_diagnostic
e795958 Merge branch 'Hallberg-NOAA-use_stress_mag' into dev/gfdl
9f11b05 Updated examples with use_stress_mag
d11c6a4 SIS2: Merge branch 'Hallberg-NOAA-add_stress_mag' into dev/gfdl
98b627c Merge branch 'dev/master' into dev/gfdl
78cfb2d MOM6: Merge pull request #820 from adcroft/fix-doxy-1.8.4
7e5d936 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
fbe2918 MOM6: Merge pull request #820 from adcroft/fix-doxy-1.8.4
ed36e93 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
054912d Merge branch 'dev/master' into dev/gfdl
9025815 MOM6: Merge branch 'gustavo-marques-update_KPP' into dev/master
aeda3c9 SIS2: Merge branch 'Hallberg-NOAA-dOxyGenize_SIS2' into dev/gfdl
e937dd8 Merge branch 'Hallberg-NOAA-vertex_shearmix' into dev/gfdl
ea2a6be MOM6: Merge pull request #801 from Hallberg-NOAA/vertex_shearmix
ab45a7d Merge branch 'vertex_shearmix' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-vertex_shearmix
7632200 MOM6: Merge pull request #799 from adcroft/aniso-hor-visc
4bac59b Update examples with VERTEX_SHEAR
a2162e4 MOM6: Merge branch 'ESMG-cleaning' into dev/gfdl
f894815 MOM6: *Merge branch 'ESMG-dev/esmg' into dev/gfdl
f1e9681 Merge branch 'dev/master' into dev/gfdl
5d17daf MOM6: Merge pull request #787 from NOAA-GFDL/dev-master-candidate-2018-06-03
48d4f8d MOM6: Merge branch 'dev/master' into dev/gfdl
0a13ed9 MOM6: Merge branch 'gustavo-marques-add_old_double_diffusion' into dev/master
f2aa2bd MOM6: Merge branch 'gustavo-marques-legacy_diabatic_driver' into dev/master
20799a1 MOM6: Merge pull request #774 from NOAA-GFDL/dev-master-candidate-2018-05-15
72580e8 MOM6: Merge branch 'ESMG-dev/esmg' into dev/gfdl
bed9677 Merge branch 'adcroft-disable-kpp-in-single-col-bml' into dev/gfdl
f2fd688 Disable KPP in single_column/BML experiment
dc9b61d gitlab: Adds testing of MOM6_parameter_doc and updates coverage
d84538c MOM6: Merge pull request #760 from ESMG/dev/esmg
3bcc768 MOM6: Merge branch 'MJHarrison-GFDL-MOM6_DA_rename' into dev/gfdl
ae71364 Travis: added script to build with OpenMP
c465130 mkmf: Updated to allow -l option
7339de5 MOM6: Merge branch 'Hallberg-NOAA-correct_reset_dtbt' into dev/gfdl
28a4377 Merge branch 'correct_reset_dtbt' of https://github.com/Hallberg-NOAA/MOM6-examples into Hallberg-NOAA-correct_reset_dtbt
b06285a MOM6: Merge branch 'MJHarrison-GFDL-MOM6_DA' into dev/gfdl
c903983 MOM6: Merged dev/ncar & dev/master into dev/gfdl
1091210 MOM6: Merged dev/ncar into dev/master
fd12185 Revert "mkmf: Updated to latest version on master branch"
2beb300 mkmf: Updated to latest version on master branch
4c080d1 MOM6: (*)Do not recalculate DTBT every coupled timestep
b40aa92 MOM6: Merge branch 'breichl-breichl/user/bgr/waves_update' into dev/gfdl

.gitignore

@@ -21,3 +21,5 @@ seaice.stats.*
 .ipynb_checkpoints
 # Ignore anything labeled ignore
 *.ignore
+# Ignore lcov files
+lcov.*

.gitlab-ci.yml

@@ -0,0 +1,48 @@
+parameter_files:
+  tags:
+    - ncrc3
+    - ncrc4
+  script:
+    # Install / update testing scripts
+    - git clone https://github.com/adcroft/MRS.git build_MRS
+    # Recursively clone submodules
+    - git submodule sync --recursive && git submodule update --init --recursive
+    # Clone other components
+    - test -d src/LM3 || make -f build_MRS/Makefile.clone CONFIGS=. clone_gfdl -s
+    # Create mannifest of experiments to run
+    - git clone http://gitlab.gfdl.noaa.gov/ogrp/Gaea-stats-MOM6-examples.git tests && mv tests/regressions . && rm -rf tests
+    - bash build_MRS/generate_manifest.sh . > manifest.mk && rm -rf regressions
+    # Build executables
+    - time make -f build_MRS/Makefile.build build_gnu CONFIGS=. -s -j
+    # Run standard tests
+    - echo "make -f build_MRS/Makefile.run gnu_all MEMORY=dynamic_symmetric CONFIGS=. -s -j" > job.sh
+    - msub -l partition=c3:c4,nodes=25,walltime=00:08:00,qos=norm -q debug -S /bin/tcsh -j oe -A gfdl_o -z -o log.$CI_PIPELINE_ID -N mom6_examples_test -K job.sh
+    # Check status of doc files
+    - git status
+    - git diff --exit-code
+
+coverage:
+  tags:
+    - ncrc3
+    - ncrc4
+  script:
+    # Install / update testing scripts
+    - git clone https://github.com/adcroft/MRS.git build_MRS
+    # Recursively clone submodules
+    - git submodule sync --recursive && git submodule update --init --recursive
+    # Clone other components
+    - test -d src/LM3 || make -f build_MRS/Makefile.clone CONFIGS=. clone_gfdl -s
+    # Create mannifest of experiments to run
+    - git clone http://gitlab.gfdl.noaa.gov/ogrp/Gaea-stats-MOM6-examples.git tests && mv tests/regressions . && rm -rf tests
+    - bash build_MRS/generate_manifest.sh . > manifest.mk && rm -rf regressions
+    # Build executables
+    - time make -f build_MRS/Makefile.build coverage_gnu CONFIGS=. EXTRA_MAKE_ARGS="FFLAGS_COVERAGE=--coverage LDFLAGS_COVERAGE=--coverage" -s -j
+    # Run standard tests
+    - echo "time make -f build_MRS/Makefile.coverage gnu_ocean_only gnu_ice_ocean_SIS2 MEMORY=dynamic_symmetric CONFIGS=." > job.sh
+    - msub -l partition=c3:c4,nodes=15,walltime=00:37:00,qos=norm -q debug -S /bin/tcsh -j oe -A gfdl_o -z -o log.$CI_PIPELINE_ID -N mom6_coverage -K job.sh
+    # Process lcov files
+    - make -f build_MRS/Makefile.coverage CONFIGS=. coverage
+    # Post to codecov
+    - cd src/MOM6 ; curl -s https://codecov.io/bash > codecov.sh
+    - GITLAB_CI=""
+    - PWD=`pwd` bash codecov.sh -t $CODECOV_TOKEN -X gcov

coupled_AM2_LM3_SIS/CM2G63L/MOM_parameter_doc.layout

@@ -51,10 +51,10 @@ NIPROC = 10                     !
                                 ! The number of processors in the x-direction. With
                                 ! STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
 NJPROC = 6                      !
-                                ! The number of processors in the x-direction. With
+                                ! The number of processors in the y-direction. With
                                 ! STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
 LAYOUT = 10, 6                  !
-                                ! The processor layout that was acutally used.
+                                ! The processor layout that was actually used.
 IO_LAYOUT = 1, 1                ! default = 1
                                 ! The processor layout to be used, or 0,0 to automatically
                                 ! set the io_layout to be the same as the layout.

coupled_AM2_LM3_SIS/CM2G63L/MOM_parameter_doc.short

@@ -103,7 +103,6 @@ TOPO_CONFIG = "file"            !
                                 !     seamount - Gaussian bump for spontaneous motion test case.
                                 !     dumbbell - Sloshing channel with reservoirs on both ends.
                                 !     shelfwave - exponential slope for shelfwave test case.
-                                !     supercritical - flat but with 8.95 degree land mask.
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
@@ -393,15 +392,36 @@ Z_OUTPUT_GRID_FILE = "OM3_zgrid.nc" ! default = ""
 ! === module MOM_diabatic_driver ===
 ! The following parameters are used for diabatic processes.
 
-! === module MOM_KPP ===
-! This is the MOM wrapper to CVmix:KPP
-! See http://code.google.com/p/cvmix/
+! === module MOM_CVMix_KPP ===
+! This is the MOM wrapper to CVMix:KPP
+! See http://cvmix.github.io/
 
-! === module MOM_diffConvection ===
-! This module implements enhanced diffusivity as a
-! function of static stability, N^2.
-CONVECTION%
-%CONVECTION
+! === module MOM_tidal_mixing ===
+! Vertical Tidal Mixing Parameterization
+INT_TIDE_DISSIPATION = True     !   [Boolean] default = False
+                                ! If true, use an internal tidal dissipation scheme to
+                                ! drive diapycnal mixing, along the lines of St. Laurent
+                                ! et al. (2002) and Simmons et al. (2004).
+INT_TIDE_DECAY_SCALE = 300.3003003003003 !   [m] default = 500.0
+                                ! The decay scale away from the bottom for tidal TKE with
+                                ! the new coding when INT_TIDE_DISSIPATION is used.
+KAPPA_ITIDES = 6.28319E-04      !   [m-1] default = 6.283185307179586E-04
+                                ! A topographic wavenumber used with INT_TIDE_DISSIPATION.
+                                ! The default is 2pi/10 km, as in St.Laurent et al. 2002.
+KAPPA_H2_FACTOR = 0.75          !   [nondim] default = 1.0
+                                ! A scaling factor for the roughness amplitude with nINT_TIDE_DISSIPATION.
+TKE_ITIDE_MAX = 0.1             !   [W m-2] default = 1000.0
+                                ! The maximum internal tide energy source availble to mix
+                                ! above the bottom boundary layer with INT_TIDE_DISSIPATION.
+READ_TIDEAMP = True             !   [Boolean] default = False
+                                ! If true, read a file (given by TIDEAMP_FILE) containing
+                                ! the tidal amplitude with INT_TIDE_DISSIPATION.
+H2_FILE = "sgs_h2.nc"           !
+                                ! The path to the file containing the sub-grid-scale
+                                ! topographic roughness amplitude with INT_TIDE_DISSIPATION.
+
+! === module MOM_CVMix_conv ===
+! Parameterization of enhanced mixing due to convection via CVMix
 
 ! === module MOM_entrain_diffusive ===
 MAX_ENT_IT = 20                 ! default = 5
@@ -439,24 +459,19 @@ BBL_MIXING_AS_MAX = False       !   [Boolean] default = True
                                 ! If true, take the maximum of the diffusivity from the
                                 ! BBL mixing and the other diffusivities. Otherwise,
                                 ! diffusiviy from the BBL_mixing is simply added.
-HENYEY_IGW_BACKGROUND = True    !   [Boolean] default = False
-                                ! If true, use a latitude-dependent scaling for the near
-                                ! surface background diffusivity, as described in
-                                ! Harrison & Hallberg, JPO 2008.
-N2_FLOOR_IOMEGA2 = 0.0          !   [nondim] default = 1.0
-                                ! The floor applied to N2(k) scaled by Omega^2:
-                                !   If =0., N2(k) is simply positive definite.
-                                !   If =1., N2(k) > Omega^2 everywhere.
+
+! === module MOM_bkgnd_mixing ===
+! Adding static vertical background mixing coefficients
 KD = 2.0E-05                    !   [m2 s-1]
                                 ! The background diapycnal diffusivity of density in the
                                 ! interior. Zero or the molecular value, ~1e-7 m2 s-1,
                                 ! may be used.
 KD_MIN = 2.0E-06                !   [m2 s-1] default = 2.0E-07
                                 ! The minimum diapycnal diffusivity.
-INT_TIDE_DISSIPATION = True     !   [Boolean] default = False
-                                ! If true, use an internal tidal dissipation scheme to
-                                ! drive diapycnal mixing, along the lines of St. Laurent
-                                ! et al. (2002) and Simmons et al. (2004).
+HENYEY_IGW_BACKGROUND = True    !   [Boolean] default = False
+                                ! If true, use a latitude-dependent scaling for the near
+                                ! surface background diffusivity, as described in
+                                ! Harrison & Hallberg, JPO 2008.
 DISSIPATION_N0 = 1.0E-07        !   [W m-3] default = 0.0
                                 ! The intercept when N=0 of the N-dependent expression
                                 ! used to set a minimum dissipation by which to determine
@@ -465,23 +480,6 @@ DISSIPATION_N1 = 6.0E-04        !   [J m-3] default = 0.0
                                 ! The coefficient multiplying N, following Gargett, used to
                                 ! set a minimum dissipation by which to determine a lower
                                 ! bound of Kd (a floor): B in eps_min = A + B*N
-INT_TIDE_DECAY_SCALE = 300.3003003003003 !   [m] default = 0.0
-                                ! The decay scale away from the bottom for tidal TKE with
-                                ! the new coding when INT_TIDE_DISSIPATION is used.
-KAPPA_ITIDES = 6.28319E-04      !   [m-1] default = 6.283185307179586E-04
-                                ! A topographic wavenumber used with INT_TIDE_DISSIPATION.
-                                ! The default is 2pi/10 km, as in St.Laurent et al. 2002.
-KAPPA_H2_FACTOR = 0.75          !   [nondim] default = 1.0
-                                ! A scaling factor for the roughness amplitude with nINT_TIDE_DISSIPATION.
-TKE_ITIDE_MAX = 0.1             !   [W m-2] default = 1000.0
-                                ! The maximum internal tide energy source availble to mix
-                                ! above the bottom boundary layer with INT_TIDE_DISSIPATION.
-READ_TIDEAMP = True             !   [Boolean] default = False
-                                ! If true, read a file (given by TIDEAMP_FILE) containing
-                                ! the tidal amplitude with INT_TIDE_DISSIPATION.
-H2_FILE = "sgs_h2.nc"           !
-                                ! The path to the file containing the sub-grid-scale
-                                ! topographic roughness amplitude with INT_TIDE_DISSIPATION.
 
 ! === module MOM_kappa_shear ===
 ! Parameterization of shear-driven turbulence following Jackson, Hallberg and Legg, JPO 2008
@@ -495,6 +493,9 @@ MAX_RINO_IT = 25                !   [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.