Update world builder to version v1.0.0

geodynamics · Aug 21, 2024 · 71b5d4f · 71b5d4f
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diff --git a/contrib/world_builder/CHANGELOG.md b/contrib/world_builder/CHANGELOG.md
@@ -9,6 +9,17 @@ Add new entries a the bottom of the current list in the subheading. Item format:
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.0]
+### Added
+- Added the ability to calculate the water content within the oceanic plate feature and the subducting plate feature. The implementation samples the temperature within the feature, calculates a lithostatic pressure, and determines the water content using parameterized phase diagrams for 4 different lithologies: sediment, mid ocean ridge basalt (MORB), gabbro, and peridotite from [Tian et al., 2019](https://doi.org/10.1029/2019GC008488). \[Daniel Douglas; 2024-08-20; [#661](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/661)\]
+- Added a `random uniform distribution deflected` grains model for all features that allows an initial texture computed from a random uniform distribution of rotation matrices applied to a given orientation specified as a set of Euler angles or a rotation matrix. \[Yijun Wang; 2024-06-06; [#713](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/713)\]
+### Changed
+- In the "mass conserving" model, change the name of the entry "plate velocity" to "spreading velocity" \[Haoyuan Li; 2024-03-11; [#694](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/694)\]
+- The Windows MinGW/CYGWIN install options are no longer supported. You are recommended to use Linux subsystems for Windows or the visual studio compiler instead on Windows. \[Menno Fraters; 2024-08-01; #[743](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/743), #[744](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/744)\]
+
+### Fixed
+
+
 ## [0.6.0]
 ### Added
 - Implemented the framework that will allow the mass conserving temperature model to account for the the movement of a spreading center through time. \[Daniel Douglas; Haoyuan Li; 2024-02-29; [#654](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/654)\]
@@ -50,7 +61,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - A new input parameter and associated functions which define the maximum depth of a model. This allows the world builder to create a complete picture of the world. \[Menno Fraters; 2021-11-08; [#367](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/367) and [#331](https://github.com/GeodynamicWorldBuilder/WorldBuilder/issues/331)\]
 - A one of type which can create a JSON schema entry where one of several types can be chosen. \[Menno Fraters; 2022-03-26; [#396](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/396)\]
 - A value at points type which can read in an array containing a value and a list of points from the input. \[Menno Fraters; 2022-03-26; [#396](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/396)\]
-- A surface object which can take an array of value at points and create an interpolation through delaunay triangulation (with the delaunator library which was added) and a KD-Tree and barycentric linear interplation. \[Menno Fraters, KD-Tree with help of Oliver Kreylos; 2022-03-26; [#396](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/396)\]
+- A surface object which can take an array of value at points and create an interpolation through delaunay triangulation (with the delaunator library which was added) and a KD-Tree and barycentric linear interpolation. \[Menno Fraters, KD-Tree with help of Oliver Kreylos; 2022-03-26; [#396](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/396)\]
 - The option to make min and max depth into variable surfaces for all area features (continental plate, oceanic plate and mantle layer) and their temperature, composition and grain plugins. \[Menno Fraters; 2022-03-26; [#366](https://github.com/GeodynamicWorldBuilder/WorldBuilder/issues/366) and [#396](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/396)\]
 - The option to the WordBuilderApp to input 3D spherical coordinates \[Menno Fraters; 2022-03-26; [#396](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/396)\]
 - An equal operator (operator==) for the point class, which compares two points with an espilon. \[Menno Fraters; 2022-03-26; [#396](https://github.com/GeodynamicWorldBuilder/WorldBuilder/pull/396)\]

diff --git a/contrib/world_builder/CITATION b/contrib/world_builder/CITATION
@@ -1,3 +1,15 @@
+
+@article{GWB_2024_JOSS,
+title = {The Geodynamic World Builder: A planetary structure creator for the geosciences},
+author = {Fraters, M. and Billen, M., and Gassmöller, R. and Saxena, A. and Heister, T. and Li, H., and Douglas, D., and Dannberg J., and Bangerth W. and Wang, Y.},
+doi = {10.21105/joss.06671},
+url = {https://doi.org/10.21105/joss.06671},
+year = {2024},
+publisher = {The Open Journal},
+pages = {6671},
+journal = {Journal of Open Source Software}
+}
+
 @Article{se-10-1785-2019,
 AUTHOR = {Fraters, M. and Thieulot, C. and van den Berg, A. and Spakman, W.},
 TITLE = {The Geodynamic World Builder: a solution for complex initial conditions in numerical modeling},
@@ -10,14 +22,24 @@ URL = {https://se.copernicus.org/articles/10/1785/2019/},
 DOI = {10.5194/se-10-1785-2019}
 }
 
-@misc{gwb-doi-v0.4.0,
-  title        = {{The Geodynamic World Builder} v0.4.0 [software]},
+@misc{gwb-doi-v1.0.0,
+  title        = {{The Geodynamic World Builder} v0.6.0 [software]},
   author       = {Menno Fraters and
                   others},
-  month        = jun,
-  year         = 2021,
-  DOI          = {10.5281/zenodo.5014808},
-  URL          = {https://doi.org/10.5281/zenodo.5014808},
+  month        = aug,
+  year         = 2024,
+  DOI          = {10.5281/zenodo.13352667},
+  URL          = {https://doi.org/10.5281/zenodo.13352667},
+}
+
+@misc{gwb-doi-v0.6.0,
+  title        = {{The Geodynamic World Builder} v0.6.0 [software]},
+  author       = {Menno Fraters and
+                  others},
+  month        = mar,
+  year         = 2024,
+  DOI          = {10.5281/zenodo.10794862},
+  URL          = {https://doi.org/10.5281/zenodo.10794862},
 }
 
 @misc{gwb-doi-v0.5.0,
@@ -30,14 +52,12 @@ DOI = {10.5194/se-10-1785-2019}
   URL          = {https://doi.org/10.5281/zenodo.7998525},
 }
 
-@misc{gwb-doi-v0.6.0,
-  title        = {{The Geodynamic World Builder} v0.6.0 [software]},
+@misc{gwb-doi-v0.4.0,
+  title        = {{The Geodynamic World Builder} v0.4.0 [software]},
   author       = {Menno Fraters and
                   others},
-  month        = mar,
-  year         = 2024,
-  DOI          = {10.5281/zenodo.10794862},
-  URL          = {https://doi.org/10.5281/zenodo.10794862},
-}
-
-
+  month        = jun,
+  year         = 2021,
+  DOI          = {10.5281/zenodo.5014808},
+  URL          = {https://doi.org/10.5281/zenodo.5014808},
+}
diff --git a/contrib/world_builder/CMakeLists.txt b/contrib/world_builder/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.13.4)
+cmake_minimum_required(VERSION 2.8.12)
 
 project(WorldBuilder C CXX)
 
@@ -107,7 +107,7 @@ else()
 endif()
 
 if(USE_MPI)
-  message(STATUS "Using MPI.")
+  message(STATUS "Using MPI found in: ${MPI_INCLUDE_PATH}")
   include_directories(${MPI_INCLUDE_PATH})
 else()
   message(STATUS "Not using MPI.")
@@ -371,7 +371,7 @@ if (NOT MSVC AND NOT APPLE)
       # cmake vesrion 3.12.0 introduces COMPILE_LANGUAGE:FORTRAN, otherwise this would be >=2.8.12
       if(NOT ${CMAKE_VERSION} VERSION_LESS "3.9.0")
         SET(WB_COMPILER_OPTIONS_PRIVATE -pedantic -Wall -Wextra  
-        $<$<COMPILE_LANGUAGE:CXX>:-Wmost -Wconversion -Wunreachable-code -Wuninitialized -Wmissing-braces -Wunused-parameter -Wold-style-cast -Wshadow -Wfloat-equal -Wpointer-arith -Wwrite-strings
+        $<$<COMPILE_LANGUAGE:CXX>:-Wmost  -Wunreachable-code -Wuninitialized -Wmissing-braces -Wunused-parameter -Wold-style-cast -Wshadow -Wfloat-equal -Wpointer-arith -Wwrite-strings
         -Wsynth -Wsign-compare -Woverloaded-virtual -Wliteral-range -Wparentheses -Wunused-local-typedefs -Wcast-qual -fstrict-aliasing -Werror=uninitialized -Wundef 
         -Wcast-align -Wmissing-declarations -Wredundant-decls -Wdiv-by-zero -Wdisabled-optimization -Wswitch-default -Wunused>)
 
@@ -380,7 +380,7 @@ if (NOT MSVC AND NOT APPLE)
         endif ()
 
       else()
-        SET(WB_COMPILER_OPTIONS_PRIVATE "-pedantic -Wall -Wextra -Wmost -Wconversion -Wunreachable-code -Wuninitialized -Wmissing-braces -Wunused-parameter -Wold-style-cast -Wshadow -Wfloat-equal -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Woverloaded-virtual -Wliteral-range -Wparentheses -Wunused-local-typedefs -Wcast-qual -fstrict-aliasing -Werror=uninitialized -Wundef -Wcast-align -Wmissing-declarations -Wredundant-decls -Wdiv-by-zero -Wdisabled-optimization -Wswitch-default -Wunused")
+        SET(WB_COMPILER_OPTIONS_PRIVATE "-pedantic -Wall -Wextra -Wmost -Wunreachable-code -Wuninitialized -Wmissing-braces -Wunused-parameter -Wold-style-cast -Wshadow -Wfloat-equal -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Woverloaded-virtual -Wliteral-range -Wparentheses -Wunused-local-typedefs -Wcast-qual -fstrict-aliasing -Werror=uninitialized -Wundef -Wcast-align -Wmissing-declarations -Wredundant-decls -Wdiv-by-zero -Wdisabled-optimization -Wswitch-default -Wunused")
 
         if (${FORCE_COLORED_OUTPUT})
           SET(WB_COMPILER_OPTIONS_PRIVATE "-fcolor-diagnostics ${WB_COMPILER_OPTIONS_PRIVATE}")
@@ -396,15 +396,16 @@ if (NOT MSVC AND NOT APPLE)
 
       # Preventing issues with older cmake compilers (<3.7) which do not support VERSION_GREATER_EQUAL
       # cmake vesrion 3.12.0 introduces COMPILE_LANGUAGE:FORTRAN, otherwise this would be >=2.8.12
+      # -Warith-conversion was added in gcc 10, add back in when the minimum becomes gcc 10.
       if(NOT ${CMAKE_VERSION} VERSION_LESS "3.9.0")
-        SET(WB_COMPILER_OPTIONS_PRIVATE -pedantic -Wall -Wextra  $<$<COMPILE_LANGUAGE:CXX>:-Wunused-variable -Wmissing-braces -Wunused-parameter -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Woverloaded-virtual -Wno-placement-new -Wno-literal-suffix -Wno-parentheses -Wno-unused-local-typedefs -Wcast-qual -fstrict-aliasing -Wmaybe-uninitialized -Werror=maybe-uninitialized -Wparentheses -Wfloat-equal -Wundef -Wcast-align -Wlogical-op -Wmissing-declarations -Wredundant-decls -Wdiv-by-zero -Wdisabled-optimization -Wswitch-default -Wno-unused>)
+        SET(WB_COMPILER_OPTIONS_PRIVATE -pedantic -Wall -Wextra  $<$<COMPILE_LANGUAGE:CXX>:-Wunused-variable -Wold-style-cast -Wconversion -Wsign-conversion -Wmissing-braces -Wunused-parameter -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Woverloaded-virtual -Wno-placement-new -Wno-literal-suffix -Wno-parentheses -Wno-unused-local-typedefs -Wcast-qual -fstrict-aliasing -Wmaybe-uninitialized -Werror=maybe-uninitialized -Wparentheses -Wfloat-equal -Wundef -Wcast-align -Wlogical-op -Wmissing-declarations -Wredundant-decls -Wdiv-by-zero -Wdisabled-optimization -Wswitch-default -Wno-unused>)
 
         if (${FORCE_COLORED_OUTPUT})
-          SET(WB_COMPILER_OPTIONS_PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-fdiagnostics-color=always> ${WB_COMPILER_OPTIONS_PRIVATE})
+          SET(WB_COMPILER_OPTIONS_PRIVATE -fdiagnostics-color=always ${WB_COMPILER_OPTIONS_PRIVATE})
         endif()
 
       else()
-        SET(WB_COMPILER_OPTIONS_PRIVATE "-pedantic -Wall -Wextra -Wunused-variable -Wmissing-braces -Wunused-parameter -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Woverloaded-virtual -Wno-placement-new -Wno-literal-suffix -Wno-parentheses -Wno-unused-local-typedefs -Wcast-qual -fstrict-aliasing -Wmaybe-uninitialized -Werror=maybe-uninitialized -Wparentheses -Wfloat-equal -Wundef -Wcast-align -Wlogical-op -Wmissing-declarations -Wredundant-decls -Wdiv-by-zero -Wdisabled-optimization -Wswitch-default -Wno-unused>")
+        SET(WB_COMPILER_OPTIONS_PRIVATE "-pedantic -Wall -Wextra -Wold-style-cast -Wconversion -Wsign-conversion -Wunused-variable -Wmissing-braces -Wunused-parameter -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Woverloaded-virtual -Wno-placement-new -Wno-literal-suffix -Wno-parentheses -Wno-unused-local-typedefs -Wcast-qual -fstrict-aliasing -Wmaybe-uninitialized -Werror=maybe-uninitialized -Wparentheses -Wfloat-equal -Wundef -Wcast-align -Wlogical-op -Wmissing-declarations -Wredundant-decls -Wdiv-by-zero -Wdisabled-optimization -Wswitch-default -Wno-unused>")
 
         if (${FORCE_COLORED_OUTPUT})
           SET(WB_COMPILER_OPTIONS_PRIVATE "-fdiagnostics-color=always ${WB_COMPILER_OPTIONS_PRIVATE}")
@@ -496,7 +497,7 @@ else()
 endif()
 
 if(${USE_MPI})
-  target_link_libraries (${WB_TARGET} PUBLIC MPI::MPI_CXX)
+  target_link_libraries (${WB_TARGET} PUBLIC MPI::MPI_CXX MPI::MPI_C)
 endif()
 
 if(WB_ENABLE_APPS)
@@ -506,7 +507,7 @@ if(WB_ENABLE_APPS)
     set(_libs ${_libs} ${ZLIB_LIBRARIES})
   endif()
   if (USE_MPI)
-    set(_mpi_dep "PUBLIC MPI::MPI_CXX")
+    set(_mpi_dep "PUBLIC MPI::MPI_CXX MPI::MPI_C")
   else()
     set(_mpi_dep "")
   endif()

diff --git a/contrib/world_builder/VERSION b/contrib/world_builder/VERSION
@@ -1 +1 @@
-0.6.0
+1.0.0
diff --git a/contrib/world_builder/appveyor.yml b/contrib/world_builder/appveyor.yml
@@ -1,4 +1,4 @@
-version: '0.6.0.{build}'
+version: '1.0.0.{build}'
 
 image: Visual Studio 2015
 

diff --git a/contrib/world_builder/cookbooks/2d_cartesian_subduction_rift/2d_cartesian_subduction_rift.wb b/contrib/world_builder/cookbooks/2d_cartesian_subduction_rift/2d_cartesian_subduction_rift.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "cross section":[[0,0],[100,0]],
   "features":
   [

diff --git a/...ookbooks/2d_cartesian_subduction_rift_adiabatic/2d_cartesian_subduction_rift_adiabatic.wb b/...ookbooks/2d_cartesian_subduction_rift_adiabatic/2d_cartesian_subduction_rift_adiabatic.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "cross section":[[0,0],[100,0]],
   "features":
   [

diff --git a/...d_cartesian_subduction_rift_sepran_example/2d_cartesian_subduction_rift_sepran_example.wb b/...d_cartesian_subduction_rift_sepran_example/2d_cartesian_subduction_rift_sepran_example.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "cross section":[[0,0],[100,0]],
   "features":
   [

diff --git a/contrib/world_builder/cookbooks/2d_spherical_subduction_rift/2d_spherical_subduction_rift.wb b/contrib/world_builder/cookbooks/2d_spherical_subduction_rift/2d_spherical_subduction_rift.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "coordinate system":{"model":"spherical", "depth method":"begin segment"},
   "cross section":[[0,0],[10,0]],
   "features":

diff --git a/...ookbooks/2d_spherical_subduction_rift_adiabatic/2d_spherical_subduction_rift_adiabatic.wb b/...ookbooks/2d_spherical_subduction_rift_adiabatic/2d_spherical_subduction_rift_adiabatic.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "coordinate system":{"model":"spherical", "depth method":"begin segment"},
   "cross section":[[0,0],[10,0]],
   "features":

diff --git a/.../world_builder/cookbooks/3d_cartesian_curved_subduction/3d_cartesian_curved_subduction.wb b/.../world_builder/cookbooks/3d_cartesian_curved_subduction/3d_cartesian_curved_subduction.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "potential mantle temperature":1500,
   "thermal expansion coefficient":2.0e-5,
   "maximum distance between coordinates":100000,

diff --git a/.../world_builder/cookbooks/3d_cartesian_double_subduction/3d_cartesian_double_subduction.wb b/.../world_builder/cookbooks/3d_cartesian_double_subduction/3d_cartesian_double_subduction.wb
@@ -1,5 +1,5 @@
 {
-"version": "0.6",
+"version": "1.0",
 "coordinate system":{"model":"cartesian"},
 "features":
 [

diff --git a/contrib/world_builder/cookbooks/3d_cartesian_rift/3d_cartesian_rift.wb b/contrib/world_builder/cookbooks/3d_cartesian_rift/3d_cartesian_rift.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "features":
   [
     {"model":"oceanic plate", "name":"oceanic plate A", "coordinates":[[-1e3,-1e3],[2001e3,-1e3],[2001e3,1000e3],[-1e3,1000e3]],

diff --git a/contrib/world_builder/cookbooks/3d_cartesian_transform_fault/3d_cartesian_transform_fault.wb b/contrib/world_builder/cookbooks/3d_cartesian_transform_fault/3d_cartesian_transform_fault.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "surface temperature":273.15,
   "potential mantle temperature":1573.15,
   "thermal expansion coefficient":0,

diff --git a/contrib/world_builder/cookbooks/3d_spherical_subduction/3d_spherical_subduction.wb b/contrib/world_builder/cookbooks/3d_spherical_subduction/3d_spherical_subduction.wb
@@ -1,5 +1,5 @@
 {
-  "version": "0.6",
+  "version": "1.0",
   "coordinate system":{"model":"spherical", "depth method":"begin segment"},
   "cross section":[[0,0],[10,0]],
   "maximum distance between coordinates":0.01,

diff --git a/contrib/world_builder/cookbooks/index.md b/contrib/world_builder/cookbooks/index.md
@@ -6,11 +6,10 @@ This section contains self-contained cookbooks on how to design different geodyn
 
 
 ```{toctree}
-: hidden:
+:hidden:
 
 3d_cartesian_rift/doc/README
 3d_cartesian_transform_fault/doc/README
 simple_subduction_2d_cartesian/doc/README
 simple_subduction_2d_chunk/doc/README
-
 ```
diff --git a/.../world_builder/cookbooks/simple_subduction_2d_cartesian/simple_subduction_2d_cartesian.wb b/.../world_builder/cookbooks/simple_subduction_2d_cartesian/simple_subduction_2d_cartesian.wb
@@ -1,5 +1,5 @@
 {
-  "version":"0.6",
+  "version":"1.0",
   "coordinate system":{"model":"cartesian"},
   "cross section":[[0,0],[8000e3,0]],
   "surface temperature":273, "potential mantle temperature":1573,
@@ -32,22 +32,23 @@
     {"model":"subducting plate", "name":"Slab",   
       "coordinates":[[3500e3,-100e3],[3500e3,100e3]], 
       "dip point":[0,0],"max depth":1000e3,
-	    "segments":[{"length":200e3,"thickness":[300e3],"top truncation":[-50e3],"angle":[0,30]},
-	      {"length":100e3, "thickness":[300e3],"top truncation":[-50e3], "angle":[30,50]},
-	      {"length":500e3, "thickness":[300e3],"top truncation":[-50e3], "angle":[50,50]},
-	      {"length":300e3, "thickness":[300e3],"top truncation":[-50e3], "angle":[50,10]},
-	      {"length":300e3, "thickness":[300e3],"top truncation":[-50e3], "angle":[10,10]}],
-	    "composition models":[
+      "segments":[{"length":200e3,"thickness":[300e3],"top truncation":[-50e3],"angle":[0,30]},
+        {"length":100e3, "thickness":[300e3],"top truncation":[-50e3], "angle":[30,50]},
+        {"length":500e3, "thickness":[300e3],"top truncation":[-50e3], "angle":[50,50]},
+        {"length":300e3, "thickness":[300e3],"top truncation":[-50e3], "angle":[50,10]},
+        {"length":300e3, "thickness":[300e3],"top truncation":[-50e3], "angle":[10,10]}],
+      "composition models":[
         {"model":"uniform", "compositions":[0], "max distance slab top":100e3}],
-	    "temperature models":[{"model":"mass conserving", 
-	      "reference model name": "plate model",
-		    "density":3300, "thermal conductivity":3.3,"adiabatic heating":false,
-		    "plate velocity":0.03,
-		    "ridge coordinates":[[[8000e3,-100e3],[8000e3,100e3]]],
-	 	    "coupling depth":80e3, 
-		    "forearc cooling factor":20.0,
-		    "taper distance":100e3, 
-	 	    "min distance slab top":-200e3, "max distance slab top":300e3}]	 
-	 }      
+      "temperature models":[{"model":"mass conserving", 
+        "reference model name": "plate model",
+        "density":3300, "thermal conductivity":3.3,"adiabatic heating":false,
+        "spreading velocity":0.03,
+        "subducting velocity":0.03,
+        "ridge coordinates":[[[8000e3,-100e3],[8000e3,100e3]]],
+        "coupling depth":80e3, 
+        "forearc cooling factor":20.0,
+        "taper distance":100e3, 
+        "min distance slab top":-200e3, "max distance slab top":300e3}]   
+   }      
   ]
 }