diff --git a/Example_1_NZ.m b/Examples/Example_1_NZ.m
similarity index 100%
rename from Example_1_NZ.m
rename to Examples/Example_1_NZ.m
diff --git a/Example_2_NY.m b/Examples/Example_2_NY.m
similarity index 100%
rename from Example_2_NY.m
rename to Examples/Example_2_NY.m
diff --git a/Example_3_ECGC.m b/Examples/Example_3_ECGC.m
similarity index 100%
rename from Example_3_ECGC.m
rename to Examples/Example_3_ECGC.m
diff --git a/Example_4_PRVI.m b/Examples/Example_4_PRVI.m
similarity index 100%
rename from Example_4_PRVI.m
rename to Examples/Example_4_PRVI.m
diff --git a/Example_5_JBAY.m b/Examples/Example_5_JBAY.m
similarity index 100%
rename from Example_5_JBAY.m
rename to Examples/Example_5_JBAY.m
diff --git a/Example_5b_JBAY_w_weirs.m b/Examples/Example_5b_JBAY_w_weirs.m
similarity index 100%
rename from Example_5b_JBAY_w_weirs.m
rename to Examples/Example_5b_JBAY_w_weirs.m
diff --git a/Example_6_GBAY.m b/Examples/Example_6_GBAY.m
similarity index 100%
rename from Example_6_GBAY.m
rename to Examples/Example_6_GBAY.m
diff --git a/Example_6b_GBAY_w_floodplain.m b/Examples/Example_6b_GBAY_w_floodplain.m
similarity index 100%
rename from Example_6b_GBAY_w_floodplain.m
rename to Examples/Example_6b_GBAY_w_floodplain.m
diff --git a/Example_7_Global.m b/Examples/Example_7_Global.m
similarity index 100%
rename from Example_7_Global.m
rename to Examples/Example_7_Global.m
diff --git a/README.md b/README.md
index 54707ded..e9eca2be 100644
--- a/README.md
+++ b/README.md
@@ -4,16 +4,6 @@
## IMPORTANT NOTE:
This is the default and recommended `PROJECTION` branch. Please use it unless you otherwise require legacy (`MASTER` branch) or the absolute newest features (`DEV` branch).
-## `DISCLAIMER: `
-The boundary of the meshing domain must be a polygon (first point equals the last and non-self intersecting) but it does not need to be simplified. Read the user guide for more information about the inputs.
-
-
- 
- 
- 
- 
- 
-
OceanMesh2D is a set of user-friendly MATLAB functions to generate two-dimensional (2D) unstructured meshes for coastal ocean circulation problems. These meshes are based on a variety of feature driven geometric and bathymetric mesh size functions, which are generated according to user-defined parameters. Mesh generation is achieved through a force-balance algorithm combined with a number of topological improvement strategies aimed at improving the worst case triangle quality. The software embeds the mesh generation process into an object-orientated framework that contains pre- and post-processing workflows, which makes mesh generation flexible, reproducible, and script-able.
## `Code framework`
@@ -36,12 +26,12 @@ Download the data for the following examples [here](https://drive.google.com/ope
in addition to [here](http://www.soest.hawaii.edu/pwessel/gshhg/gshhg-shp-2.3.7.zip) for the GSHHG ESRI shapefile and here: "ftp://topex.ucsd.edu/pub/srtm15_plus/SRTM15+V2.nc" for the latest SRTM15_PLUS global topobathy DEM.
```
-Featured in ┌╼ Example_1_NZ.m %<- A simple mesh around South Island New Zealand that uses GSHHS shoreline.
-user guide ├── Example_2_NY.m %<- A high-resolution mesh around the New York/Manhattan area that uses a DEM created from LiDAR data.
- └── Example_3_ECGC.m %<- Builds a mesh for the western North Atlantic with a local high-resolution nest around New York
-Featured in ┌╼ Example_4_PRVI.m %<- Builds a mesh for the western North Atlantic with three high-resolution nests around Peurto Rico and US Virgin Islands
-Geoscientific Model ├── Example_5_JBAY.m %<- An extremely high-fidelity (15-m) mesh from LiDAR data around Jamaica Bay with CFL-limiting.
-Development paper[1]└── Example_6_GBAY.m %<- An example of the polyline/thalweg mesh size function along the Houston Ship Channel.
+Featured in ┌╼ Examples/Example_1_NZ.m %<- A simple mesh around South Island New Zealand that uses GSHHS shoreline.
+user guide ├── Examples/Example_2_NY.m %<- A high-resolution mesh around the New York/Manhattan area that uses a DEM created from LiDAR data.
+ └── Examples/Example_3_ECGC.m %<- Builds a mesh for the western North Atlantic with a local high-resolution nest around New York
+Featured in ┌╼ Examples/Example_4_PRVI.m %<- Builds a mesh for the western North Atlantic with three high-resolution nests around Peurto Rico and US Virgin Islands
+Geoscientific Model ├── Examples/Example_5_JBAY.m %<- An extremely high-fidelity (15-m) mesh from LiDAR data around Jamaica Bay with CFL-limiting.
+Development paper[1]└── Examples/Example_6_GBAY.m %<- An example of the polyline/thalweg mesh size function along the Houston Ship Channel.
```
@@ -51,7 +41,7 @@ All pull requests are tested with Jenkins on a local host. However, to ensure th
## `References!`
-If you make use of `OceanMesh2D` please include a reference to the following:
+If you make use of `OceanMesh2D` please include a reference to [1], and to any of [2]-[4] if pertinent:
```
[1] - Roberts, K. J., Pringle, W. J., and Westerink, J. J., 2019.
@@ -65,7 +55,17 @@ If you make use of `OceanMesh2D` please include a reference to the following:
[4] - Roberts, Keith J., Pringle W.J., Westerink J. J. Contreras, M.T., Wirasaet, D., 2019.
On the automatic and a priori design of unstructured mesh resolution for coastal ocean circulation models,
Ocean Modelling, 144, 101509. https://doi.org/10.1016/j.ocemod.2019.101509
+
+```
+## `DISCLAIMER: `
+The boundary of the meshing domain must be a polygon (first point equals the last and non-self intersecting) but it does not need to be simplified. Read the user guide for more information about the inputs.
-
-```
+## `GALLERY: `
+
+ 
+ 
+ 
+ 
+ 
+
diff --git a/OceanMesh2D_User_Guide_July42019.pdf b/UserGuide/OceanMesh2D_User_Guide_July42019.pdf
similarity index 100%
rename from OceanMesh2D_User_Guide_July42019.pdf
rename to UserGuide/OceanMesh2D_User_Guide_July42019.pdf
diff --git a/Example1.png b/imgs/Example1.png
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rename from Example1.png
rename to imgs/Example1.png
diff --git a/Globalocean.jpg b/imgs/Globalocean.jpg
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rename from Globalocean.jpg
rename to imgs/Globalocean.jpg
diff --git a/ResoNA.png b/imgs/ResoNA.png
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rename from ResoNA.png
rename to imgs/ResoNA.png
diff --git a/VizGilgo.png b/imgs/VizGilgo.png
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rename from VizGilgo.png
rename to imgs/VizGilgo.png
diff --git a/global.jpeg b/imgs/global.jpeg
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rename from global.jpeg
rename to imgs/global.jpeg
diff --git a/nesting.png b/imgs/nesting.png
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rename from nesting.png
rename to imgs/nesting.png
diff --git a/maketiny.m b/maketiny.m
deleted file mode 100644
index a008508d..00000000
--- a/maketiny.m
+++ /dev/null
@@ -1,64 +0,0 @@
-clearvars; close all; clc;
-
-boubox = [-73.9647 40.5696
- -73.9650 40.5569
- -73.9334 40.5569
- -73.9342 40.5731
- -73.9644 40.5731
- -73.9647 40.5696] ;
-
-weir{1} = [-73.9537 40.5568 0.0002
- -73.9541 40.5632 0
- -73.9545 40.5704 0
- -73.9546 40.5731 0];
-
-gdat = geodata('bbox',boubox,'h0',25,'outer',boubox,'mainland',boubox,'weirs',weir) ;
-
-plot(gdat) ;
-
-fh = edgefx('geodata',gdat,'dis',0.15) ;
-
-plot(fh) ;
-
-mshopts = meshgen('bou',gdat,'ef',fh,'plot_on',1,'proj','equi') ;
-mshopts = mshopts.build ;
-m = mshopts.grd ;
-
-plot(m,'tri') ;
-
-%%
-m = makens(m,'outer',0) ;
-
-m = makens(m,'weirs',gdat) ;
-%%
-m.b = m.p(:,1)*0 + 3 ;
-
-m = Calc_tau0(m) ;
-
-pos = [-73.9534 40.5566
- -73.9536 40.5589
- -73.9543 40.5716
- -73.9543 40.5734
- -73.9334 40.5733
- -73.9329 40.5563] ;
-
-% make the right side all dry at the start
-in = inpoly(m.p,pos) ;
-
-ss(:,1) = m.p(:,1)*0 ;
-
-ss(in,1) = 1;
-
-m = Calc_f13_inpoly(m,'surface_submergence_state',[],[],[],ss) ;
-
-% jack up the friction on the right too
-cf(:,1) = m.p(:,1)*0 + 0.025 ;
-
-cf(in,1) = 0.06;
-
-m = Calc_f13_inpoly(m,'mannings_n_at_sea_floor',[],[],[],cf) ;
-
-%%
-m = renum(m) ;
-
-write(m,'tiny2') ;
\ No newline at end of file
diff --git a/weirs_cell.mat b/weirs_cell.mat
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index a6a5c874..00000000
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diff --git a/weirs_struct.mat b/weirs_struct.mat
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index 1ed347e6..00000000
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