Merge CliMA#1321 CliMA#1359

1321: More pedagogical computation of continuity equation r=blallen a=blallen # Description @jm-c pointed out that our current method for computing the continuity equation `∇u = 0` is a little counterintuitive. Here is one possible change we can make to improve the clarity while maintaining computational efficiency at the cost of some extra memory usage. 1359: Yt/boyd vandeven r=thomasgibson a=slifer50 # Description Addition of the Boyd-Vandeven filter. Co-authored-by: Brandon Allen <ballen@mit.edu> Co-authored-by: yassine <yassinetissaoui@gmail.com>
blallen · Jul 21, 2020 · 4f09146 · 4f09146
3 parents fc35827 + f72c4e4 + 02278e4
commit 4f09146
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diff --git a/docs/src/APIs/Numerics/Meshes/Mesh.md b/docs/src/APIs/Numerics/Meshes/Mesh.md
@@ -75,6 +75,7 @@ There are methods used to cleanup state vectors.
 
 ```@docs
 Filters.CutoffFilter
+Filters.BoydVandevenFilter
 Filters.ExponentialFilter
 Filters.TMARFilter
 ```

diff --git a/experiments/OceanBoxGCM/ocean_gyre.jl b/experiments/OceanBoxGCM/ocean_gyre.jl
@@ -97,11 +97,7 @@ function run_ocean_gyre(; imex::Bool = false, BC = nothing, nt = 0, refDat = ())
 
     nt_freq = 620
     cb = ClimateMachine.StateCheck.sccreate(
-        [
-            (solver_config.Q, "Q"),
-            (solver_config.dg.state_auxiliary, "s_aux"),
-            (solver_config.dg.state_gradient_flux, "s_gflux"),
-        ],
+        [(solver_config.Q, "Q"), (solver_config.dg.state_auxiliary, "s_aux")],
         nt_freq;
         prec = 12,
     )
@@ -146,50 +142,8 @@ end
     #   Ocean floor BCs,
     #   Surface BCc
     # )
-    boundary_conditions = [
-        (
-            OceanBC(Impenetrable(NoSlip()), Insulating()),
-            OceanBC(Impenetrable(NoSlip()), Insulating()),
-            OceanBC(Penetrable(KinematicStress()), TemperatureFlux()),
-        ),
-        (
-            OceanBC(Impenetrable(FreeSlip()), Insulating()),
-            OceanBC(Impenetrable(NoSlip()), Insulating()),
-            OceanBC(Penetrable(KinematicStress()), TemperatureFlux()),
-        ),
-        (
-            OceanBC(Impenetrable(NoSlip()), Insulating()),
-            OceanBC(Impenetrable(FreeSlip()), Insulating()),
-            OceanBC(Penetrable(KinematicStress()), TemperatureFlux()),
-        ),
-        (
-            OceanBC(Impenetrable(FreeSlip()), Insulating()),
-            OceanBC(Impenetrable(FreeSlip()), Insulating()),
-            OceanBC(Penetrable(KinematicStress()), TemperatureFlux()),
-        ),
-        (
-            OceanBC(Impenetrable(NoSlip()), Insulating()),
-            OceanBC(Impenetrable(NoSlip()), Insulating()),
-            OceanBC(Penetrable(FreeSlip()), TemperatureFlux()),
-        ),
-        (
-            OceanBC(Impenetrable(FreeSlip()), Insulating()),
-            OceanBC(Impenetrable(NoSlip()), Insulating()),
-            OceanBC(Penetrable(FreeSlip()), TemperatureFlux()),
-        ),
-        (
-            OceanBC(Impenetrable(NoSlip()), Insulating()),
-            OceanBC(Impenetrable(FreeSlip()), Insulating()),
-            OceanBC(Penetrable(FreeSlip()), TemperatureFlux()),
-        ),
-        (
-            OceanBC(Impenetrable(FreeSlip()), Insulating()),
-            OceanBC(Impenetrable(FreeSlip()), Insulating()),
-            OceanBC(Penetrable(FreeSlip()), TemperatureFlux()),
-        ),
-    ]
+
     ## By default test with a couple of standard bc's
-    #  Prior block shows that many other combinations are possible
     #  - noslip on sides and bottom
     #  - freeslip on sides and no-slipt on bottom
     boundary_conditions = [

diff --git a/experiments/OceanBoxGCM/refvals/ocean_gyre_refvals.jl b/experiments/OceanBoxGCM/refvals/ocean_gyre_refvals.jl
@@ -26,10 +26,9 @@
 #
 #   Now for real!
 #
-#! format: off
 
-    refVals=[]
-    refPrecs=[]
+refVals = []
+refPrecs = []
 
 # SC ========== Test number 1 reference values and precision match template. =======
 # SC ========== /home/cnh/projects/cm/experiments/OceanBoxGCM/ocean_gyre.jl test reference values ======================================
@@ -42,48 +41,86 @@
 #  [         :                :          :        :      :          :           ],
 # ]
 varr = [
- [       "Q",   "u[1]", -7.88803234115370288659e-02,  6.54328011157667283060e-02,  2.01451525264660777012e-03,  1.24588716783015467093e-02 ],
- [       "Q",   "u[2]", -8.71605274310934263760e-02,  1.47505267452495314462e-01,  5.63158201082454307890e-03,  1.28959719954838437916e-02 ],
- [       "Q",       :η, -4.73491408441974459542e-01,  4.02693687285993751068e-01, -6.49059970676089264836e-05,  2.21689928090662985438e-01 ],
- [       "Q",       :θ,  4.24292935192304451839e-04,  9.24539353455580759089e+00,  2.49938206627401893201e+00,  2.17986626392490689952e+00 ],
- [   "s_aux",       :y,  0.00000000000000000000e+00,  4.00000000000000046566e+06,  1.99999999999999976717e+06,  1.15573163901915703900e+06 ],
- [   "s_aux",       :w, -2.22086406767055965930e-04,  2.00575090959195941574e-04,  2.53168866096191178104e-07,  1.66257132341925427171e-05 ],
- [   "s_aux",    :pkin, -9.00869877619915215838e-01,  0.00000000000000000000e+00, -3.33171488779369640021e-01,  2.54740287894525019308e-01 ],
- [   "s_aux",     :wz0, -2.96608015794916532427e-05,  3.66759042312538147113e-05,  3.78116102589123325624e-10,  1.07073256826409470244e-05 ],
- [ "s_gflux", "ν∇u[1]", -1.98765276856145908790e-02,  1.92976912753076192131e-02,  9.31995586073550077850e-09,  2.84016926475062683050e-04 ],
- [ "s_gflux", "ν∇u[2]", -8.60188027210821715141e-03,  2.03898608650850965418e-02,  1.44279862042391183595e-05,  7.01831343135553482361e-04 ],
- [ "s_gflux", "ν∇u[3]", -2.36999031942582461820e-05,  3.39171933774427215489e-05,  1.79310417841609871239e-08,  3.03350466717279338539e-06 ],
- [ "s_gflux", "ν∇u[4]", -3.27811105688537093861e-02,  3.33776923250933485465e-02, -8.41954909635648634245e-06,  9.93067541524441646170e-04 ],
- [ "s_gflux", "ν∇u[5]", -3.19705003898926379269e-02,  3.94072309121676778859e-03, -2.09915474589233714674e-06,  4.56596518968874199012e-04 ],
- [ "s_gflux", "ν∇u[6]", -3.84552825296212839770e-05,  3.30579003830798668533e-05, -6.85753430789401392363e-08,  3.41712910764070301712e-06 ],
- [ "s_gflux", "κ∇θ[1]", -1.90663030661463762938e-03,  1.59419367775516821958e-03, -2.07346812692515548133e-05,  1.38241222633447261199e-04 ],
- [ "s_gflux", "κ∇θ[2]", -1.17846832845764997420e-03,  3.03333905110560143534e-03,  9.95380871168155762288e-04,  8.10649417649871592909e-04 ],
- [ "s_gflux", "κ∇θ[3]", -1.91676759182478058212e-05,  6.14879473708830387359e-05, -4.12675761035662034755e-07,  1.91038619046619808554e-06 ],
+    [
+        "Q",
+        "u[1]",
+        -7.88803234115370288659e-02,
+        6.54328011157667283060e-02,
+        2.01451525264660777012e-03,
+        1.24588716783015467093e-02,
+    ],
+    [
+        "Q",
+        "u[2]",
+        -8.71605274310934263760e-02,
+        1.47505267452495314462e-01,
+        5.63158201082454307890e-03,
+        1.28959719954838437916e-02,
+    ],
+    [
+        "Q",
+        :η,
+        -4.73491408441974459542e-01,
+        4.02693687285993751068e-01,
+        -6.49059970676089264836e-05,
+        2.21689928090662985438e-01,
+    ],
+    [
+        "Q",
+        :θ,
+        4.24292935192304451839e-04,
+        9.24539353455580759089e+00,
+        2.49938206627401893201e+00,
+        2.17986626392490689952e+00,
+    ],
+    [
+        "s_aux",
+        :y,
+        0.00000000000000000000e+00,
+        4.00000000000000046566e+06,
+        1.99999999999999976717e+06,
+        1.15573163901915703900e+06,
+    ],
+    [
+        "s_aux",
+        :w,
+        -2.22086406767055965930e-04,
+        2.00575090959195941574e-04,
+        2.53168866096191178104e-07,
+        1.66257132341925427171e-05,
+    ],
+    [
+        "s_aux",
+        :pkin,
+        -9.00869877619915215838e-01,
+        0.00000000000000000000e+00,
+        -3.33171488779369640021e-01,
+        2.54740287894525019308e-01,
+    ],
+    [
+        "s_aux",
+        :wz0,
+        -2.96608015794916532427e-05,
+        3.66759042312538147113e-05,
+        3.78116102589123325624e-10,
+        1.07073256826409470244e-05,
+    ],
 ]
 parr = [
- [       "Q",   "u[1]",    12,    12,    12,    12 ],
- [       "Q",   "u[2]",    12,    12,    12,    12 ],
- [       "Q",       :η,    12,    12,    12,    12 ],
- [       "Q",       :θ,    12,    12,    12,    12 ],
- [   "s_aux",       :y,    12,    12,    12,    12 ],
- [   "s_aux",       :w,    12,    12,    12,    12 ],
- [   "s_aux",    :pkin,    12,    12,    12,    12 ],
- [   "s_aux",     :wz0,    12,    12,     8,    12 ],
- [ "s_gflux", "ν∇u[1]",    12,    12,     8,    12 ],
- [ "s_gflux", "ν∇u[2]",    12,    12,    12,    12 ],
- [ "s_gflux", "ν∇u[3]",    12,    12,    12,    12 ],
- [ "s_gflux", "ν∇u[4]",    12,    12,    12,    12 ],
- [ "s_gflux", "ν∇u[5]",    12,    12,    12,    12 ],
- [ "s_gflux", "ν∇u[6]",    12,    12,    12,    12 ],
- [ "s_gflux", "κ∇θ[1]",    12,    12,    12,    12 ],
- [ "s_gflux", "κ∇θ[2]",    12,    12,    12,    12 ],
- [ "s_gflux", "κ∇θ[3]",    12,    12,    12,    12 ],
+    ["Q", "u[1]", 12, 12, 12, 12],
+    ["Q", "u[2]", 12, 12, 12, 12],
+    ["Q", :η, 12, 12, 12, 12],
+    ["Q", :θ, 12, 12, 12, 12],
+    ["s_aux", :y, 12, 12, 12, 12],
+    ["s_aux", :w, 12, 12, 12, 12],
+    ["s_aux", :pkin, 12, 12, 12, 12],
+    ["s_aux", :wz0, 12, 12, 8, 12],
 ]
 # END SCPRINT
 # SC ====================================================================================
 
-    append!(refVals ,[ varr ] )
-    append!(refPrecs,[ parr ] )
+append!(refVals, [varr])
+append!(refPrecs, [parr])
 
 # SC ========== Test number 2 reference values and precision match template. =======
 # SC ========== /home/cnh/projects/cm/experiments/OceanBoxGCM/ocean_gyre.jl test reference values ======================================
@@ -96,47 +133,83 @@ parr = [
 #  [         :                :          :        :      :          :           ],
 # ]
 varr = [
- [       "Q",   "u[1]", -3.08415268094245687003e-01,  3.31683879748177812274e-01,  2.34355645025035056947e-03,  1.38278493625595393784e-02 ],
- [       "Q",   "u[2]", -9.30330187375882494694e-02,  1.45773331490709479041e-01,  6.38739141648009701308e-03,  1.38107523198905141754e-02 ],
- [       "Q",       :η, -4.60215148246349181615e-01,  3.97155090993862369686e-01, -1.05814653709044253051e-04,  2.14356824554893188317e-01 ],
- [       "Q",       :θ,  3.90305009874997816885e-04,  9.28488770009523101123e+00,  2.49938688339290848717e+00,  2.17986650147491722862e+00 ],
- [   "s_aux",       :y,  0.00000000000000000000e+00,  4.00000000000000046566e+06,  1.99999999999999976717e+06,  1.15573163901915703900e+06 ],
- [   "s_aux",       :w, -2.65432487944419423249e-04,  2.51335486222488370053e-04,  3.34985017281366756292e-07,  1.98256782258218657716e-05 ],
- [   "s_aux",    :pkin, -9.01203660410079376852e-01,  0.00000000000000000000e+00, -3.33173652152760846334e-01,  2.54737286187841360796e-01 ],
- [   "s_aux",     :wz0, -3.16776291712146345464e-05,  3.89428424525183031852e-05,  4.05688221636862481177e-10,  1.10561449663397378925e-05 ],
- [ "s_gflux", "ν∇u[1]", -6.91411158656193985950e-02,  6.71894067927724242262e-02,  1.93151282317531301526e-08,  3.67871498890457999768e-04 ],
- [ "s_gflux", "ν∇u[2]", -6.41072589623675609394e-02,  5.93158959821227672188e-03, -1.72612717858599068401e-05,  1.09370391833557892812e-03 ],
- [ "s_gflux", "ν∇u[3]", -7.40852152420143496942e-05,  7.70630509235797829829e-05,  1.94096112473072846645e-08,  3.35721658566900582726e-06 ],
- [ "s_gflux", "ν∇u[4]", -2.77618725100101104708e-02,  2.76053769492804849939e-02,  8.37000168929151316390e-06,  1.04649435866464054871e-03 ],
- [ "s_gflux", "ν∇u[5]", -3.57980327012049140412e-02,  4.20082014423407961584e-03, -2.26270579934147913334e-06,  5.16063361553070450508e-04 ],
- [ "s_gflux", "ν∇u[6]", -3.87729590851969090591e-05,  3.38326906830031177748e-05, -7.64232106453937395084e-08,  3.42855062975519724920e-06 ],
- [ "s_gflux", "κ∇θ[1]", -2.63114521554794764460e-03,  3.13139570197398927828e-03, -2.58270397697685688597e-05,  1.80489106756528977114e-04 ],
- [ "s_gflux", "κ∇θ[2]", -4.29150657020392189284e-03,  3.20181945576268351533e-03,  9.94194034856019440149e-04,  8.13274467049271117605e-04 ],
- [ "s_gflux", "κ∇θ[3]", -3.08119171379054497821e-05,  9.12508944783092335127e-05, -4.12575332587978521639e-07,  1.92043362474637987870e-06 ],
+    [
+        "Q",
+        "u[1]",
+        -3.08415268094245687003e-01,
+        3.31683879748177812274e-01,
+        2.34355645025035056947e-03,
+        1.38278493625595393784e-02,
+    ],
+    [
+        "Q",
+        "u[2]",
+        -9.30330187375882494694e-02,
+        1.45773331490709479041e-01,
+        6.38739141648009701308e-03,
+        1.38107523198905141754e-02,
+    ],
+    [
+        "Q",
+        :η,
+        -4.60215148246349181615e-01,
+        3.97155090993862369686e-01,
+        -1.05814653709044253051e-04,
+        2.14356824554893188317e-01,
+    ],
+    [
+        "Q",
+        :θ,
+        3.90305009874997816885e-04,
+        9.28488770009523101123e+00,
+        2.49938688339290848717e+00,
+        2.17986650147491722862e+00,
+    ],
+    [
+        "s_aux",
+        :y,
+        0.00000000000000000000e+00,
+        4.00000000000000046566e+06,
+        1.99999999999999976717e+06,
+        1.15573163901915703900e+06,
+    ],
+    [
+        "s_aux",
+        :w,
+        -2.65432487944419423249e-04,
+        2.51335486222488370053e-04,
+        3.34985017281366756292e-07,
+        1.98256782258218657716e-05,
+    ],
+    [
+        "s_aux",
+        :pkin,
+        -9.01203660410079376852e-01,
+        0.00000000000000000000e+00,
+        -3.33173652152760846334e-01,
+        2.54737286187841360796e-01,
+    ],
+    [
+        "s_aux",
+        :wz0,
+        -3.16776291712146345464e-05,
+        3.89428424525183031852e-05,
+        4.05688221636862481177e-10,
+        1.10561449663397378925e-05,
+    ],
 ]
 parr = [
- [       "Q",   "u[1]",    12,    12,    12,    12 ],
- [       "Q",   "u[2]",    12,    12,    12,    12 ],
- [       "Q",       :η,    12,    12,    12,    12 ],
- [       "Q",       :θ,    12,    12,    12,    12 ],
- [   "s_aux",       :y,    12,    12,    12,    12 ],
- [   "s_aux",       :w,    12,    12,    12,    12 ],
- [   "s_aux",    :pkin,    12,    12,    12,    12 ],
- [   "s_aux",     :wz0,    12,    12,     8,    12 ],
- [ "s_gflux", "ν∇u[1]",    12,    12,     8,    12 ],
- [ "s_gflux", "ν∇u[2]",    12,    12,    12,    12 ],
- [ "s_gflux", "ν∇u[3]",    12,    12,    12,    12 ],
- [ "s_gflux", "ν∇u[4]",    12,    12,    12,    12 ],
- [ "s_gflux", "ν∇u[5]",    12,    12,    12,    12 ],
- [ "s_gflux", "ν∇u[6]",    12,    12,    12,    12 ],
- [ "s_gflux", "κ∇θ[1]",    12,    12,    12,    12 ],
- [ "s_gflux", "κ∇θ[2]",    12,    12,    12,    12 ],
- [ "s_gflux", "κ∇θ[3]",    12,    12,    12,    12 ],
+    ["Q", "u[1]", 12, 12, 12, 12],
+    ["Q", "u[2]", 12, 12, 12, 12],
+    ["Q", :η, 12, 12, 12, 12],
+    ["Q", :θ, 12, 12, 12, 12],
+    ["s_aux", :y, 12, 12, 12, 12],
+    ["s_aux", :w, 12, 12, 12, 12],
+    ["s_aux", :pkin, 12, 12, 12, 12],
+    ["s_aux", :wz0, 12, 12, 8, 12],
 ]
 # END SCPRINT
 # SC ====================================================================================
 
-    append!(refVals ,[ varr ] )
-    append!(refPrecs,[ parr ] )
-
-#! format: on
+append!(refVals, [varr])
+append!(refPrecs, [parr])