Merge pull request #489 from MFraters/sphinx_manual_User_manual_basic…

…_starter_tutorial_v2

Sphinx manual user manual basic starter tutorial

CHANGELOG.md

@@ -37,6 +37,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Added operation options `add`, `substract` and `replace defined only` to the the composition plugins \[Menno Fraters; 2023-02-17; [#474](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/474)\]
 - Added a new compositional model for subducting slab models such that ensures a smooth transition of compositional value from one part of a compositional layer to the other side of the layer. This is based on Arushi Saxena's fault composition plugin with the same name ([#356](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/356)) \[Menno Fraters; 2023-02-18; [#477](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/356)\]
 - If World Builder is configured with MPI it now reads input files on a single process and distributes them via MPI to other processes to reduce I/O load. This can be extended in the future to other input files. \[Rene Gassmoeller; 2023-04-13; [#480](github.com/GeodynamicWorldBuilder/WorldBuilder/pull/480)\]
+- Added a new html manual based on Sphinx, inculding a new tutorial which was designed from scratch to get new users up to speed quickly. It also contains a much structure to add cookbooks, developer and other documentation in the future. \[Menno Fraters; 2023-05-31; [#379](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/489), [#379](https://github.com/GeodynamicWorldBuilder/WorldBuilder/issues/379) the related pull request mentioned in that issue.\]
 
 ### Changed
 - The World Builder Visualizer will now use zlib compression for vtu files by default. If zlib is not available binary output will be used. \[Menno Fraters; 2021-06-26; [#282](github.com/GeodynamicWorldBuilder/WorldBuilder/pull/282)\]

doc/sphinx/GWB_parameter_listings/world_builder_file/index.md

@@ -1,5 +1,5 @@
 
-(part:GWB_parameter_listings:chap:world_builer_file:sec:index)=
+(part:GWB_parameter_listings:chap:world_builder_file:sec:index)=
 The World Builder file
 ======================
 

doc/sphinx/_static/gwb_input_files/BST_02_minimal_box.grid

@@ -0,0 +1,22 @@
+# ouput variables
+grid_type = cartesian
+dim = 3
+compositions = 4
+
+# domain of the grid
+x_min = -1000e3
+x_max = 2000e3 
+y_min = 0e3
+y_max = 1000e3 
+z_min = 0 
+z_max = 600e3 
+
+# low res grid properties
+n_cell_x = 150 
+n_cell_y = 50
+n_cell_z = 30
+
+# shown grid properties
+# n_cell_x = 300 
+# n_cell_y = 100
+# n_cell_z = 60

doc/sphinx/_static/gwb_input_files/BST_04_overriding_plate.grid

@@ -0,0 +1,22 @@
+# ouput variables
+grid_type = cartesian
+dim = 3
+compositions = 4
+
+# domain of the grid
+x_min = -1000e3
+x_max = 2000e3 
+y_min = 0e3
+y_max = 1000e3 
+z_min = 0 
+z_max = 600e3 
+
+# low res grid properties
+n_cell_x = 150 
+n_cell_y = 50
+n_cell_z = 30
+
+# shown grid properties
+# n_cell_x = 300 
+# n_cell_y = 100
+# n_cell_z = 60

doc/sphinx/_static/gwb_input_files/BST_05_limit_depth.grid

@@ -0,0 +1,22 @@
+# ouput variables
+grid_type = cartesian
+dim = 3
+compositions = 4
+
+# domain of the grid
+x_min = -1000e3
+x_max = 2000e3 
+y_min = 0e3
+y_max = 1000e3 
+z_min = 0 
+z_max = 600e3 
+
+# low res grid properties
+n_cell_x = 150 
+n_cell_y = 50
+n_cell_z = 30
+
+# shown grid properties
+# n_cell_x = 300 
+# n_cell_y = 100
+# n_cell_z = 60

doc/sphinx/_static/gwb_input_files/BST_3_limit_depth.wb → doc/sphinx/_static/gwb_input_files/BST_05_limit_depth.wb

@@ -6,11 +6,11 @@
     {
        "model":"oceanic plate", "name":"Overriding Plate", "max depth":100e3, 
        "coordinates":[[0,0],[0,1000e3],[1500e3,1000e3],[1600e3,350e3],[1500e3,0]],
-       "temperature models":
+       "temperature models":[{"model":"uniform", "temperature":293}],
+       "composition models":
          [
-           {"model":"uniform", "temperature":293, "max depth":50e3}
-         ],
-       "composition models":[{"model":"uniform", "compositions":[0]}]
+           {"model":"uniform", "compositions":[0], "max depth":50e3}
+         ]
     }
   ]
 }

doc/sphinx/_static/gwb_input_files/BST_06_oceanic_plate_temperature.grid

@@ -0,0 +1,22 @@
+# ouput variables
+grid_type = cartesian
+dim = 3
+compositions = 4
+
+# domain of the grid
+x_min = -1000e3
+x_max = 2000e3 
+y_min = 0e3
+y_max = 1000e3 
+z_min = 0 
+z_max = 600e3 
+
+# low res grid properties
+n_cell_x = 150 
+n_cell_y = 50
+n_cell_z = 30
+
+# shown grid properties
+# n_cell_x = 300 
+# n_cell_y = 100
+# n_cell_z = 60

doc/sphinx/_static/gwb_input_files/BST_06_oceanic_plate_temperature.wb

@@ -0,0 +1,20 @@
+{
+  "version":"0.5",
+  "coordinate system":{"model":"cartesian"},
+  "features":
+  [
+    {
+       "model":"oceanic plate", "name":"Overriding Plate", "max depth":100e3, 
+       "coordinates":[[0,0],[0,1000e3],[1500e3,1000e3],[1600e3,350e3],[1500e3,0]],
+       "temperature models":
+         [
+           {"model":"half space model", "max depth":100e3, "spreading velocity":0.04, 
+            "ridge coordinates":[[[400e3,-1],[-100e3,2000e3]]]}
+         ],
+       "composition models":
+         [
+           {"model":"uniform", "compositions":[0], "max depth":50e3}
+         ]
+    }
+  ]
+}

doc/sphinx/_static/gwb_input_files/BST_07_subducting_plate_oceanic_part.grid

@@ -0,0 +1,22 @@
+# ouput variables
+grid_type = cartesian
+dim = 3
+compositions = 4
+
+# domain of the grid
+x_min = -1000e3
+x_max = 2000e3 
+y_min = 0e3
+y_max = 1000e3 
+z_min = 0 
+z_max = 600e3 
+
+# low res grid properties
+n_cell_x = 150 
+n_cell_y = 50
+n_cell_z = 30
+
+# shown grid properties
+# n_cell_x = 300 
+# n_cell_y = 100
+# n_cell_z = 60

doc/sphinx/_static/gwb_input_files/BST_07_subducting_plate_oceanic_part.wb

@@ -0,0 +1,27 @@
+{
+  "version":"0.5",
+  "coordinate system":{"model":"cartesian"},
+  "features":
+  [
+    {
+       "model":"oceanic plate", "name":"Overriding Plate", "max depth":100e3, 
+       "coordinates":[[0,0],[0,1000e3],[1500e3,1000e3],[1600e3,350e3],[1500e3,0]],
+       "temperature models":
+         [
+           {"model":"half space model", "max depth":100e3, "spreading velocity":0.04, 
+            "ridge coordinates":[[[400e3,-1],[-100e3,2000e3]]]}
+         ],
+       "composition models":
+         [
+           {"model":"uniform", "compositions":[0], "max depth":50e3}
+         ]
+    },
+    {
+      "model":"oceanic plate", "name":"Subducting Oceanic plate", "max depth":100e3, 
+      "coordinates":[[2000e3,0],[2000e3,1000e3],[1500e3,1000e3],[1600e3,350e3],[1500e3,0]],
+      "temperature models":[{"model":"linear", "max depth":100e3}],
+       "composition models":[{"model":"uniform", "compositions":[3], "max depth":50e3},
+                             {"model":"uniform", "compositions":[1], "min depth":50e3}]
+    }
+  ]
+}

doc/sphinx/_static/gwb_input_files/BST_08_passive_margin_variable_depth.grid

@@ -0,0 +1,22 @@
+# ouput variables
+grid_type = cartesian
+dim = 3
+compositions = 4
+
+# domain of the grid
+x_min = -1000e3
+x_max = 2000e3 
+y_min = 0e3
+y_max = 1000e3 
+z_min = 0 
+z_max = 600e3 
+
+# low res grid properties
+n_cell_x = 150 
+n_cell_y = 50
+n_cell_z = 30
+
+# shown grid properties
+# n_cell_x = 300 
+# n_cell_y = 100
+# n_cell_z = 60

doc/sphinx/_static/gwb_input_files/BST_08_passive_margin_variable_depth.wb

@@ -0,0 +1,39 @@
+{
+  "version":"0.5",
+  "coordinate system":{"model":"cartesian"},
+  "features":
+  [
+    {
+       "model":"oceanic plate", "name":"Overriding Plate", "max depth":100e3, 
+       "coordinates":[[0,0],[0,1000e3],[1500e3,1000e3],[1600e3,350e3],[1500e3,0]],
+       "temperature models":
+         [
+           {"model":"half space model", "max depth":100e3, "spreading velocity":0.04, 
+            "ridge coordinates":[[[400e3,-1],[-100e3,2000e3]]]}
+         ],
+       "composition models":[{"model":"uniform", "compositions":[0], "max depth":50e3}]
+    },
+    {
+       "model":"continental plate", "name":"Passive margin", "max depth":[[200e3]], 
+       "coordinates":[[-1000e3,0],[-1000e3,1000e3],[0,1000e3],[0,0]],
+       "temperature models":
+         [
+           {"model":"linear", "max depth":[[100e3],[200e3,[[-250e3,0],[-750e3,1000e3]]]]}
+         ],
+       "composition models":
+         [
+           {"model":"uniform", "compositions":[3], 
+            "max depth":[[100e3],[200e3,[[-250e3,0],[-750e3,1000e3]]]]},
+           {"model":"uniform", "compositions":[1], 
+            "min depth":[[100e3],[200e3,[[-250e3,0],[-750e3,1000e3]]]]}
+         ]
+    },
+    {
+      "model":"oceanic plate", "name":"Subducting Oceanic plate", "max depth":100e3, 
+      "coordinates":[[2000e3,0],[2000e3,1000e3],[1500e3,1000e3],[1600e3,350e3],[1500e3,0]],
+      "temperature models":[{"model":"linear", "max depth":100e3}],
+       "composition models":[{"model":"uniform", "compositions":[3], "max depth":50e3},
+                             {"model":"uniform", "compositions":[1], "min depth":50e3}]
+    }
+  ]
+}

doc/sphinx/_static/gwb_input_files/BST_09_adding_mantle_layer.grid

@@ -0,0 +1,22 @@
+# ouput variables
+grid_type = cartesian
+dim = 3
+compositions = 5
+
+# domain of the grid
+x_min = -1000e3
+x_max = 2000e3 
+y_min = 0e3
+y_max = 1000e3 
+z_min = 0 
+z_max = 600e3 
+
+# low res grid properties
+n_cell_x = 150 
+n_cell_y = 50
+n_cell_z = 30
+
+# shown grid properties
+# n_cell_x = 300 
+# n_cell_y = 100
+# n_cell_z = 60

doc/sphinx/_static/gwb_input_files/BST_09_adding_mantle_layer.wb

@@ -0,0 +1,44 @@
+{
+  "version":"0.5",
+  "coordinate system":{"model":"cartesian"},
+  "features":
+  [
+    {
+       "model":"mantle layer", "name":"upper mantle", "max depth":660e3,
+       "coordinates":[[-1000e3,0],[-1000e3,1000e3],[3000e3,1000e3],[3000e3,0]],
+       "composition models":[{"model":"uniform", "compositions":[4]}]
+    },
+    {
+       "model":"oceanic plate", "name":"Overriding Plate", "max depth":100e3, 
+       "coordinates":[[0,0],[0,1000e3],[1500e3,1000e3],[1600e3,350e3],[1500e3,0]],
+       "temperature models":
+         [
+           {"model":"half space model", "max depth":100e3, "spreading velocity":0.04, 
+            "ridge coordinates":[[[400e3,-1],[-100e3,2000e3]]]}
+         ],
+       "composition models":[{"model":"uniform", "compositions":[0], "max depth":50e3}]
+    },
+    {
+       "model":"continental plate", "name":"Passive margin", "max depth":[[200e3]], 
+       "coordinates":[[-1000e3,0],[-1000e3,1000e3],[0,1000e3],[0,0]],
+       "temperature models":
+         [
+           {"model":"linear", "max depth":[[100e3],[200e3,[[-250e3,0],[-750e3,1000e3]]]]}
+         ],
+       "composition models":
+         [
+           {"model":"uniform", "compositions":[3], 
+            "max depth":[[100e3],[200e3,[[-250e3,0],[-750e3,1000e3]]]]},
+           {"model":"uniform", "compositions":[1], 
+            "min depth":[[100e3],[200e3,[[-250e3,0],[-750e3,1000e3]]]]}
+         ]
+    },
+    {
+      "model":"oceanic plate", "name":"Subducting Oceanic plate", "max depth":100e3, 
+      "coordinates":[[2000e3,0],[2000e3,1000e3],[1500e3,1000e3],[1600e3,350e3],[1500e3,0]],
+      "temperature models":[{"model":"linear", "max depth":100e3}],
+       "composition models":[{"model":"uniform", "compositions":[3], "max depth":50e3},
+                             {"model":"uniform", "compositions":[1], "min depth":50e3}]
+    }
+  ]
+}

doc/sphinx/_static/gwb_input_files/BST_10_adding_basic_subducting_plate.grid

@@ -0,0 +1,22 @@
+# ouput variables
+grid_type = cartesian
+dim = 3
+compositions = 4
+
+# domain of the grid
+x_min = -1000e3
+x_max = 2000e3 
+y_min = 0e3
+y_max = 1000e3 
+z_min = 0 
+z_max = 600e3 
+
+# low res grid properties
+n_cell_x = 150 
+n_cell_y = 50
+n_cell_z = 30
+
+# shown grid properties
+# n_cell_x = 300 
+# n_cell_y = 100
+# n_cell_z = 60