Starting to add contet

docs/about.md

@@ -0,0 +1,33 @@
+---
+title: What is morphologica?
+layout: home
+permalink: /about
+order: 1
+---
+
+morphologica is a library of header-only C++ code.
+
+If you're a C++ developer and you want to draw runtime graphs, surface plots or scatter plots that are **fast**, you are a member of the target demographic.
+
+morphologica provides **simulation support facilities** for simulations of dynamical systems, agent-based models or, in fact, any program that needs dynamic, runtime visualization.
+
+It helps with:
+
+* **OpenGL Visualizations of your program while it runs**. A modern OpenGL visualization
+  scheme called **[morph::Visual](https://github.com/ABRG-Models/morphologica/blob/main/morph/Visual.h)**
+  provides the ability to visualise 2D and 3D graphs
+  of surfaces, lines, bars, scatter plots and quiver plots with minimal
+  processing overhead.
+
+* **Configuration**: morphologica allows you to easily set up a simulation
+  parameter configuration system, using the JSON reading and writing
+  abilities of **[morph::Config](https://github.com/ABRG-Models/morphologica/blob/main/morph/Config.h)**. ([morph::Config Example](https://github.com/ABRG-Models/morphologica/blob/main/examples/jsonconfig.cpp))
+
+* **Saving data from your simulation**. morphologica provides a set of
+  easy-to-use convenience wrappers (**[morph::HdfData](https://github.com/ABRG-Models/morphologica/blob/main/morph/HdfData.h)**) around the HDF5 C
+  API. By saving data in a standard format, it is easy to access
+  simulation data in python, MATLAB or Octave for analysis and graphing. ([HdfData Example](https://github.com/ABRG-Models/morphologica/blob/main/examples/hdfdata.cpp))
+
+# What is this site for?
+
+It's to help you to learn how to use the classes in morphologica in your own numerical simulations and data analysis programs.

docs/core_classes/colourmap.md

@@ -0,0 +1,6 @@
+---
+title: morph::ColourMap
+layout: page
+permalink: /core/colourmap
+---
+morph::ColourMap provides a set of colour maps to indicate numerical values with graded colours.

docs/core_classes/index.md

@@ -0,0 +1,20 @@
+---
+title: Core maths classes
+layout: page
+permalink: /core/
+---
+As I developed the data-vis features of morphologica, I found I needed functionality that I've used repeatedly in many programs.
+The most basic was a simple mathematical vector class, [morph::vec](/core/vec), which was essential for computing locations within the 3D graphics environment.
+
+As the project progressed, I developed a number of these classes for handling mathematical operations with a convenient interface:
+
+* [morph::vec](/core/vec) A mathematical vector class of a fixed size
+* [morph::vvec](/core/vvec) A 'variable vector' class
+* [morph::mathconst](/core/mathconst) Templated mathematical constants
+* [morph::RandUniform](/core/random) Random number generation
+* [morph::Scale](/core/scale) A class to scale numbers (log/linear scaling)
+* [morph::ColourMap](/core/colourmap) When you visualise, you will need colour maps
+* [morph::Matrix22](/core/matrix33) 2x2 matrix operations
+* [morph::Matrix33](/core/matrix33) 3x3 matrix operations
+* [morph::TransformMatrix](/core/transformmatrix) 4x4 matrix operations are common in graphics systems
+* [morph::Quaternion](/core/quaternion) Quaternions are also commonly used for graphics

docs/core_classes/range.md

@@ -0,0 +1,6 @@
+---
+title: morph::range
+layout: page
+permalink: /core/range
+---
+morph::range is a useful little class for specifying a range of values.

docs/core_classes/scale.md

@@ -0,0 +1,6 @@
+---
+title: morph::Scale
+layout: page
+permalink: /core/scale
+---
+morph::Scale is for scaling numbers.

docs/core_classes/vec.md

@@ -0,0 +1,48 @@
+---
+layout: page
+title: morph::vec
+permalink: /core/vec/
+---
+
+A fixed-size mathematical vector class. Derives from `std::array`.
+
+```c++
+#include <morph/vec.h>
+```
+Create like an `std::array`:
+
+```c++
+morph::vec<int, 4> v1 = { 1, 2, 3, 4 };
+```
+but you can do maths:
+
+```c++
+morph::vec<int, 4> v1 = { 1, 2, 3, 4 };
+morph::vec<int, 4> v3 = v1 + v2; // element-wise addition
+```
+
+It's really useful to be able to do vector maths:
+
+```c++
+morph::vec<float, 3> u1 = { 1.0f, 0.0f, 0.0f };
+morph::vec<float, 3> u2 = { 0.0f, 1.0f, 0.0f };
+morph::vec<float, 3> u3 = u1.cross (u2);
+morph::vec<float, 3> u4 = u1 - u2;
+float dp = u1.dot (u3);
+```
+
+See these programs for more example usage: [tests/testvec](https://github.com/ABRG-Models/morphologica/blob/main/tests/testvec.cpp), [tests/testvecElementOps](https://github.com/ABRG-Models/morphologica/blob/main/tests/testvecElementOps.cpp).
+
+## Using morph::vec as a key in std::map or within an std::set
+
+Although morph::vec derives from std::array, you **can't use it as a key in an std::map**.
+
+```c++
+// Bad!
+std::map<morph::vec<int, 2>, myclass> some_map;
+
+// Also Bad!
+std::set<morph::vec<int, 2>> some_set;
+```
+
+The reason for this is that the less-than operation is redefined, but `std::set` and `std::map` depend upon less-than for their functionality. In std::array, less-than is lexicographic. See this file for a workaround, in which you specify that you want to use morph::vec's lexicographics less-than: [tests/testvec_asmapkey](https://github.com/ABRG-Models/morphologica/blob/main/tests/testvec_asmapkey.cpp).

docs/vvec.md → docs/core_classes/vvec.md

@@ -1,7 +1,7 @@
 ---
 layout: page
 title: morph::vvec
-permalink: /vvec/
+permalink: /core/vvec/
 ---
 
 This could be a page about the variable vector class vvec.

docs/index.md

@@ -1,32 +1,5 @@
 ---
-title: What is morphologica?
+title: morphologica blog
 layout: home
 permalink: /
 ---
-
-morphologica is a library of header-only C++ code.
-
-If you're a C++ developer and you want to draw runtime graphs, surface plots or scatter plots that are **fast**, you are a member of the target demographic.
-
-morphologica provides **simulation support facilities** for simulations of dynamical systems, agent-based models or, in fact, any program that needs dynamic, runtime visualization.
-
-It helps with:
-
-* **OpenGL Visualizations of your program while it runs**. A modern OpenGL visualization
-  scheme called **[morph::Visual](https://github.com/ABRG-Models/morphologica/blob/main/morph/Visual.h)**
-  provides the ability to visualise 2D and 3D graphs
-  of surfaces, lines, bars, scatter plots and quiver plots with minimal
-  processing overhead.
-
-* **Configuration**: morphologica allows you to easily set up a simulation
-  parameter configuration system, using the JSON reading and writing
-  abilities of **[morph::Config](https://github.com/ABRG-Models/morphologica/blob/main/morph/Config.h)**. ([morph::Config Example](https://github.com/ABRG-Models/morphologica/blob/main/examples/jsonconfig.cpp))
-
-* **Saving data from your simulation**. morphologica provides a set of
-  easy-to-use convenience wrappers (**[morph::HdfData](https://github.com/ABRG-Models/morphologica/blob/main/morph/HdfData.h)**) around the HDF5 C
-  API. By saving data in a standard format, it is easy to access
-  simulation data in python, MATLAB or Octave for analysis and graphing. ([HdfData Example](https://github.com/ABRG-Models/morphologica/blob/main/examples/hdfdata.cpp))
-
-# What is this site for?
-
-It's to help you to learn how to use the classes in morphologica in your own numerical simulations and data analysis programs.

docs/quick.md

@@ -2,6 +2,7 @@
 title: Quick start
 layout: page
 permalink: /quick/
+order: 4
 ---
 
 Quick-start assumption: You're using a Debian flavour of Linux. If you're using a Mac, see [README.build.mac](https://github.com/ABRG-Models/morphologica/tree/main/README.build.mac.md) for help getting dependencies in place. It's [README.build.windows](https://github.com/ABRG-Models/morphologica/tree/main/README.build.windows.md) for Windows users.

docs/who.md

@@ -0,0 +1,6 @@
+---
+title: Who'd need morphologica?
+layout: page
+permalink: /who
+order: 2
+---

docs/why.md

@@ -0,0 +1,19 @@
+---
+title: Why was morphologica developed?
+layout: page
+permalink: /why
+order: 3
+---
+Why expend the time writing an OpenGL visualization system when there are alternatives, like Python's matplotlib already available?
+
+I think the the answers are 'opportunity', 'preference' and 'benefit'.
+
+'Opportunity' because I started a project with Stuart Wilson at the University of Sheffield's Department of Psychology in which we were going to solve reaction-diffusion equations and there was a requirement to plot the results of those computations. I had a free hand in how to go about the work and plenty of time on a 4 year project.
+
+'Preference', because I just don't really like Python very much. I dislike its lack of scope identifiers, which make it awkward to copy blocks of code around and I find the management of Python packages a headache. On the other hand, I do really like C++.
+
+If the resulting visualization system had not had any promise of showing a benefit over matplotlib or MATLAB, I'd still not have started it and would have lived with the least bad alternative. But vizualization based on computer gaming technology had the promise of being lightning fast with minimal use of computational resources. I really wrote morphologica so that I could have insightful graphics while still getting the most I possilbly could out of the CPU hardware I had access to.
+
+Could I have used an alternative C++ plotting system? Possibly. Alternatives include CERN's [Root](https://root.cern/), which looked old-fashioned and byzantine, [VTK](https://vtk.org/) from Kitware, which seemed complex to get started with and [matplot++](https://alandefreitas.github.io/matplotplusplus/), which copies the Python matplotlib API which I never got on with!
+
+What I have ended up with is a library of code which is very easy to incorporate into projects and which can animate 3D plots with very low CPU overhead. It was worth the effort.