adding descriptions to all notebooks

ggebbie · Jul 6, 2024 · acb2f5a · acb2f5a
1 parent a26559f
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Showing 5 changed files with 151 additions and 21 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/budget_examples/EulerianVolumeBudgetExample.ipynb b/budget_examples/EulerianVolumeBudgetExample.ipynb
@@ -1,5 +1,19 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Computing the Eulerian Volume Budget for an Arbitrary Cell in ECCO V4r4"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Load in packages and relevant LLC90 grid information"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 9,
@@ -60,6 +74,13 @@
     "cell_volumes = get_cell_volumes(area, cell_depths);"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Load in $u, v$, and $w$ from directory"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 27,
@@ -68,7 +89,10 @@
    "source": [
     "#define experimennt\n",
     "expname = \"iter129_bulkformula\"\n",
-    "get_data_files(xx, expname) = filter(x -> occursin(\"data\",x),searchdir(diagpath[expname],xx))\n",
+    "diagnostics_directory = diagpath[expname]\n",
+    "\n",
+    "#filter function\n",
+    "get_data_files(xx, expname) = filter(x -> occursin(\"data\",x),searchdir(diagnostics_directory,xx))\n",
     "\n",
     "#define the file names\n",
     "datafilelist_uvw  = get_data_files(\"trsp_3d_set1\", expname);\n",
@@ -79,13 +103,20 @@
     "u, v, w = extract_eulerian_velocities(diagpath, expname, fnameuvw, γ);"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Compute in $\\nabla_H \\cdot u_H$ and $\\frac{\\partial w}{\\partial z}$ using MeshArrays.jl and ECCOtour.jl"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 23,
    "metadata": {},
    "outputs": [],
    "source": [
-    "Utrsp, Vtrsp = UVtoTrsp(u, v, Γ, γ)\n",
+    "Utrsp, Vtrsp = UVtoTrsp(u, v, Γ, γ) #convert velocities to volume fluxes\n",
     "Wtrsp = w .* area32;\n",
     "\n",
     "UV_conv3D = MeshArray(γ,Float32,50);\n",
@@ -95,6 +126,13 @@
     "calc_W_conv3D!(Wtrsp, W_conv3D) #vertical diffusive converegence\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Select arbitrary grid cell and plot an instantaneous snapshot of the volume budget"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 26,
@@ -723,7 +761,7 @@
     }
    ],
    "source": [
-    "select_cell(x) = x[4, 20][110, 45]\n",
+    "select_cell(x::MeshArray) = x[4, 20][110, 45]\n",
     "\n",
     "vars = [select_cell(UV_conv3D), \n",
     "        select_cell(W_conv3D)] \n",

diff --git a/budget_examples/HeatBudgetExample copy.ipynb b/budget_examples/HeatBudgetExample copy.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Computing the Heat Budget for an Arbitrary Cell in ECCO V4r4"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 5,
@@ -32,6 +39,13 @@
     "include(\"../src/config_exp.jl\");"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Load in packages and relevant LLC90 grid information"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 13,
@@ -78,21 +92,11 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 14,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "1992.0:0.08333333333333333:2018.0"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": []
+   "source": [
+    "#### Load in $\\theta, \\eta$. Also load in advective and diffusive heat fluxes"
+   ]
   },
   {
    "cell_type": "code",
@@ -102,7 +106,8 @@
    "source": [
     "#define experimennt\n",
     "expname = \"iter129_bulkformula\"\n",
-    "get_data_files(xx, expname) = filter(x -> occursin(\"data\",x),searchdir(diagpath[expname],xx))\n",
+    "diagnostic_directory = diagpath[expname] #directory that contains the data\n",
+    "get_data_files(xx, expname) = filter(x -> occursin(\"data\",x),searchdir(diagnostic_directory,xx))\n",
     "\n",
     "#define the file names\n",
     "datafilelist_H  = get_data_files(\"trsp_3d_set2\", expname)\n",
@@ -161,6 +166,13 @@
     "κzθp1, wθp1 = extract_vertical_heatbudget(diagpath, expname , fnameRp1, γ);"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Compute vertical and horizontal heat convergences"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 44,
@@ -189,6 +201,15 @@
     "calc_W_conv3D!(κzθp1, κzθ_convp1) #vertical advective converegence"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Select arbitrary grid cell and plot an monthly snapshot of the heat budget. Since we are not using daily snapshots of $\\eta$ and $\\theta$, the RHS and LHS are not guaranteed to balance. \n",
+    "\n",
+    "*It is pretty close sometimes though!*"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 45,
@@ -1288,7 +1309,7 @@
     "vars = vars ./ select_cell(cell_volumes)\n",
     "push!(vars, select_cell(dθdt))\n",
     "\n",
-    "labels = [\"∇ₕ⋅(κ ∇ₕθ)\", \"∇ₕ⋅(uₕθ)\", \"∂(wθ)/∂z\", \"∂(κ(∂θ/∂z))/∂z\", \"GTF\", \"Approx\\ndθ/dt\", \"dθ/dt\"]\n",
+    "labels = [\"∇ₕ⋅(κ ∇ₕθ)\", \"-∇ₕ⋅(uₕθ)\", \"∂(wθ)/∂z\", \"∂(κ(∂θ/∂z))/∂z\", \"GTF\", \"Approx\\ndθ/dt\", \"dθ/dt\"]\n",
     "\n",
     "fig, ax = plt.subplots(figsize = (10, 4))\n",
     "sns.barplot(x=labels, y=vars, ax = ax)\n",

diff --git a/budget_examples/ResidualVolumeBudgetExample.ipynb b/budget_examples/ResidualVolumeBudgetExample.ipynb
@@ -1,8 +1,22 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Computing the Eulerian Volume Budget for an Arbitrary Cell in ECCO V4r4"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Load in packages and relevant LLC90 grid information"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -59,6 +73,13 @@
     "cell_volumes = get_cell_volumes(area, cell_depths);"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Load in $u, v$, $w$, $u^*, v^*$, and $w^*$ from directory"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 19,
@@ -108,6 +129,13 @@
     "wres = w .+ wb"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Compute in $\\nabla_H \\cdot u^{res}_H$ and $\\frac{\\partial w^{res}}{\\partial z}$ using MeshArrays.jl and ECCOtour.jl"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 20,
@@ -124,6 +152,13 @@
     "calc_W_conv3D!(Wrestrsp, Wres_conv3D) #vertical diffusive converegence"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Select arbitrary grid cell and plot a monthly snapshot of the volume budget"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 21,

diff --git a/diagnostic_examples/Interpolations.ipynb b/diagnostic_examples/Interpolations.ipynb
@@ -1,5 +1,19 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Interpolating native ECCO V4r4 onto a $0.5^\\circ$ grid using MeshArrays.jl and ECCOtour.jl"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Load in packages and relevant LLC90 grid information"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -12,7 +26,8 @@
     "      LaTeXStrings\n",
     "using PythonCall\n",
     "import PythonPlot as plt\n",
-    "# plt.matplotlib.rcParams[\"figure.dpi\"] = 50\n",
+    "\n",
+    "plt.matplotlib.rcParams[\"figure.dpi\"] = 50\n",
     "# plt.pygui(false)\n",
     "\n",
     "matplotlib = pyimport(\"matplotlib\")\n",
@@ -60,6 +75,13 @@
     "Depth = Γ.Depth;"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Plot the depth of each column in ECCO V4r4 (as best we can)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 19,
@@ -80,6 +102,13 @@
     "display(fig)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Interpolate onto a regular grid"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 4,
@@ -99,6 +128,13 @@
     "DD = reshape(DD, size(lon));"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Plot interpolated depths, *looks pretty good*! "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 5,