Merge pull request #264 from brown-ccv/dev-to-master

Dev to master
brown-ccv · Apr 10, 2024 · e20bd2e · e20bd2e · cpaniaguam · Apr 10, 2024
2 parents 5d564f3 + 08fe6e1
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diff --git a/Project.toml b/Project.toml
@@ -25,6 +25,7 @@ CSV = "0.10.9"
 DataFrames = "1.5.0"
 DifferentialEquations = "7.7.0"
 IterableTables = "1.0.0"
+Memoize = "0.4.4"
 Parameters = "0.12.3"
 Plots = "1.38.9"
 Roots = "2.0.7"

diff --git a/README.md b/README.md
@@ -73,21 +73,18 @@ julia> depth = 8e3
 
 julia> # Run simulation
 julia> dataframe = chamber(composition, end_time, log_volume_km3, InitialConc_H2O, InitialConc_CO2, log_vfr, depth)
-470×11 DataFrame
- Row │ time            P+dP       T        eps_g       V          rho_m    rho_x    X_CO2     total_mass  total_mass_H2O  total_mass_CO2
-     │ Float64         Float64    Float64  Float64     Float64    Float64  Float64  Float64   Float64     Float64         Float64
-─────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
-   1 │      0.0        2.1582e8   1046.71  0.00558159  1.58489e9  2400.0   2600.0   0.346043  3.83394e12      1.54039e11       3.85098e9
-   2 │ 100000.0        2.15824e8  1046.71  0.00558131  1.58489e9  2400.0   2600.0   0.34605   3.83395e12      1.54039e11       3.85099e9
-   3 │      7.62058e5  2.15848e8  1046.71  0.0055795   1.5849e9   2400.01  2600.01  0.346101  3.83397e12      1.5404e11        3.85101e9
-   4 │      2.83015e6  2.15924e8  1046.71  0.00557383  1.58491e9  2400.03  2600.03  0.346259  3.83405e12      1.54044e11       3.85109e9
-   5 │      4.89825e6  2.16e8     1046.71  0.00556818  1.58492e9  2400.04  2600.05  0.346418  3.83413e12      1.54047e11       3.85117e9
-  ⋮  │       ⋮             ⋮         ⋮         ⋮           ⋮         ⋮        ⋮        ⋮          ⋮             ⋮               ⋮
- 467 │      2.9764e9   2.23039e8  1043.45  0.00561742  1.58776e9  2401.81  2601.96  0.337852  3.8504e12       1.547e11         3.86751e9
- 468 │      2.9864e9   2.23399e8  1043.44  0.00559152  1.58782e9  2401.9   2602.06  0.338571  3.85078e12      1.54716e11       3.86789e9
- 469 │      2.9964e9   2.2376e8   1043.43  0.00556579  1.58788e9  2401.99  2602.15  0.339287  3.85116e12      1.54731e11       3.86828e9
- 470 │      3.0e9      2.23889e8  1043.43  0.00555656  1.5879e9   2402.02  2602.18  0.339545  3.8513e12       1.54737e11       3.86841e9
-                                                                                                                         461 rows omitted
+470×12 DataFrame
+ Row │ time            P+dP       T        eps_g       V          rho_m    rho_x    X_CO2     total_mass  total_mass_H2O  total_mass_CO2  eps_x    
+     │ Float64         Float64    Float64  Float64     Float64    Float64  Float64  Float64   Float64     Float64         Float64         Float64  
+─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+   1 │      0.0        2.1582e8   1046.71  0.00558159  1.58489e9  2400.0   2600.0   0.346043  3.83394e12      1.54039e11       3.85098e9  0.146696
+   2 │ 100000.0        2.15824e8  1046.71  0.00558131  1.58489e9  2400.0   2600.0   0.34605   3.83395e12      1.54039e11       3.85099e9  0.146696
+   3 │      7.61993e5  2.15848e8  1046.71  0.0055795   1.5849e9   2400.01  2600.01  0.346101  3.83397e12      1.5404e11        3.85101e9  0.146698
+  ⋮  │       ⋮             ⋮         ⋮         ⋮           ⋮         ⋮        ⋮        ⋮          ⋮             ⋮               ⋮            ⋮
+ 468 │      2.98643e9  2.23399e8  1043.44  0.00559005  1.58782e9  2401.9   2602.06  0.33863   3.85078e12      1.54716e11       3.8679e9   0.167628
+ 469 │      2.99643e9  2.23759e8  1043.43  0.00556433  1.58788e9  2401.99  2602.15  0.339346  3.85116e12      1.54731e11       3.86828e9  0.16766
+ 470 │      3.0e9      2.23888e8  1043.43  0.00555519  1.5879e9   2402.02  2602.18  0.339601  3.8513e12       1.54737e11       3.86842e9  0.167671
+                                                                                                                                   464 rows omitted
 ```
 As noted, the `chamber` function returns a DataFrame containing the solution data with columns described above. Additionally, it automatically creates a directory named with the current timestamp (by default) to store the output files including figures and CSV data files.
 
@@ -104,16 +101,18 @@ julia> depth = 8e3
 julia> output_dirname = "MyDirname"
 
 julia> chamber(composition, end_time, log_volume_km3, InitialConc_H2O, InitialConc_CO2, log_vfr, depth, output_dirname)
-458×11 DataFrame
- Row │ time            P+dP       T        eps_g       V          rho_m    rho_x    X_CO2     total_mass  total_mass_H2O  total_mass_CO2 
-     │ Float64         Float64    Float64  Float64     Float64    Float64  Float64  Float64   Float64     Float64         Float64        
-─────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
-   1 │      0.0        2.1582e8   1405.74  0.00139209  1.58489e9  2420.0   2900.0   0.859079  3.94439e12      3.94903e10       3.94903e9
-   2 │ 100000.0        2.15823e8  1405.74  0.00139197  1.58489e9  2420.0   2900.0   0.859081  3.9444e12       3.94903e10       3.94903e9
-  ⋮  │       ⋮             ⋮         ⋮         ⋮           ⋮         ⋮        ⋮        ⋮          ⋮             ⋮               ⋮
- 457 │      2.99798e9  2.22224e8  1401.01  0.00138553  1.58951e9  2421.66  2901.99  0.856719  3.97782e12      3.98249e10       3.98249e9
- 458 │      3.0e9      2.22284e8  1401.01  0.00138339  1.58952e9  2421.68  2902.01  0.856746  3.9779e12       3.98257e10       3.98257e9
-                                                                                                                         454 rows omitted
+458×12 DataFrame
+ Row │ time            P+dP       T        eps_g       V          rho_m    rho_x    X_CO2     total_mass  total_mass_H2O  total_mass_CO2  eps_x    
+     │ Float64         Float64    Float64  Float64     Float64    Float64  Float64  Float64   Float64     Float64         Float64         Float64  
+─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+   1 │      0.0        2.1582e8   1405.74  0.00139209  1.58489e9  2420.0   2900.0   0.859079  3.94439e12      3.94903e10       3.94903e9  0.149114
+   2 │ 100000.0        2.15823e8  1405.74  0.00139197  1.58489e9  2420.0   2900.0   0.859081  3.9444e12       3.94903e10       3.94903e9  0.149115
+   3 │      6.31887e5  2.1584e8   1405.74  0.00139134  1.5849e9   2420.0   2900.01  0.859088  3.94442e12      3.94905e10       3.94905e9  0.149122
+  ⋮  │       ⋮             ⋮         ⋮         ⋮           ⋮         ⋮        ⋮        ⋮          ⋮             ⋮               ⋮            ⋮
+ 456 │      2.98793e9  2.21924e8  1401.0   0.00139538  1.58945e9  2421.59  2901.91  0.856613  3.97744e12      3.98211e10       3.98211e9  0.17412
+ 457 │      2.99793e9  2.22224e8  1401.01  0.00138474  1.58951e9  2421.66  2902.0   0.856745  3.97782e12      3.9825e10        3.9825e9   0.174241
+ 458 │      3.0e9      2.22286e8  1401.01  0.00138255  1.58952e9  2421.68  2902.01  0.856772  3.9779e12       3.98258e10       3.98258e9  0.174266
+                                                                                                                                   452 rows omitted
 ```
 The output directory specified by `output_dirname` contains the generated files.
 

diff --git a/notebooks/images/instructions_5.png b/notebooks/images/instructions_5.png
diff --git a/notebooks/images/instructions_6.png b/notebooks/images/instructions_6.png
diff --git a/notebooks/images/instructions_7.png b/notebooks/images/instructions_7.png
diff --git a/notebooks/notebook_for_chamber.ipynb b/notebooks/notebook_for_chamber.ipynb
@@ -41,7 +41,7 @@
         "set -e\n",
         "\n",
         "#---------------------------------------------------#\n",
-        "JULIA_VERSION=\"1.8.2\"\n",
+        "JULIA_VERSION=\"1.8.5\"\n",
         "JULIA_PACKAGES=\"IJulia Chamber\"\n",
         "JULIA_NUM_THREADS=2\n",
         "#---------------------------------------------------#\n",
@@ -371,6 +371,37 @@
         "depth = 8e3\n",
         "dataframe = chamber(composition, end_time, log_volume_km3, InitialConc_H2O, InitialConc_CO2, log_vfr, depth)"
       ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Save results to your Google Drive\n",
+        "To download the output files, mount your Google Drive by following these steps:\n",
+        "\n",
+        "1. Change the runtime type to Python.\n",
+        "\n",
+        "    <img src=\"images/instructions_5.png\" height=320/>   <img src=\"images/instructions_6.png\" height=250/>\n",
+        "\n",
+        "2. Run the code cell below.\n",
+        "3. Afterward, you can drag the desired output files into the Drive folder.\n",
+        "\n",
+        "    <img src=\"images/instructions_7.png\" height=200/>\n",
+        "\n",
+        "\n",
+        "[Notice] Remember to change the runtime type back to Julia before running other Julia code cells."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "# runtime type: Python\n",
+        "from google.colab import drive\n",
+        "drive.mount('/content/drive')"
+      ]
     }
   ],
   "metadata": {