Merge branch 'Mar5bar:main' into main

Author: Mar5bar

.gitattributes

@@ -0,0 +1,2 @@
+*.md linguist-language=Markdown
+*.markdown linguist-language=Markdown

_user-guide/advanced-options.md

@@ -549,7 +549,7 @@ Forward and backward differences can also be computed with second-order numerica
 
 Throughout VisualPDE, you can make use of the special functions `sin`, `cos`, `tan`, `exp`, `log`, `sqrt`, `sinh`, `cosh`, `tanh` and `H`, where the latter is a [Heaviside function](https://en.wikipedia.org/wiki/Heaviside_step_function) smoothed over the interval $[-1,1]$ (see the [GLSL reference](https://registry.khronos.org/OpenGL-Refpages/gl4/html/smoothstep.xhtml) for details). All function arguments should be surrounded by parentheses, e.g. `sin(x)`. You can also use `min` and `max` as functions with two arguments, which return the minimum or maximum of their arguments, e.g. `min(u,1)` returns the minimum of $u$ and 1. If you wish to raise the output of a function to a power, you must enclose the function in parentheses, e.g. write `(cos(x))^2`, not `cos(x)^2`. You can also use `mod(a,b)` to compute the remainder of $a$ upon division by $b$ (see the [GLSL reference](https://registry.khronos.org/OpenGL-Refpages/gl4/html/mod.xhtml) for details).
 
-A [bump function](https://en.m.wikipedia.org/wiki/Bump_function) with compact support can be used via the syntax `Bump(X, Y, radius)` (or `Bump(X, radius)` in 1D), which localises a bump of unit maximum of the given radius at the point $(X, Y)$.
+A [bump function](https://en.m.wikipedia.org/wiki/Bump_function) with compact support can be used via the syntax `Bump(X, Y, radius)` (or `Bump(X, radius)` in 1D, with `Y` implicitly set to `L_y/2`), which localises a bump of unit maximum of the given radius at the point $(X, Y)$.
 
 A [bivariate Gaussian function](https://en.wikipedia.org/wiki/Multivariate_normal_distribution) can be used with similar syntax to the bump function: `Gauss(X, Y, s)` is a correctly normalised Gaussian function centred at $(X,Y)$ with standard deviation `s`. The extended syntax `Gauss(X, Y, s_x, s_y)` produces a potentially asymmetric Gaussian with standard deviations `s_x` and `s_y` in the $x$ and $y$ directions, with zero correlation. Correlation can be specified via `Gauss(X, Y, s_x, s_y, r)`, where `r` is the correlation between the two directions.
 

sim/scripts/RD/main.js

@@ -1769,6 +1769,9 @@ async function VisualPDE(url) {
       imageSourceBlend: {
         type: "t",
       },
+      isTwoD: {
+        type: "bool",
+      },
       L: {
         type: "f",
       },
@@ -3058,6 +3061,7 @@ async function VisualPDE(url) {
         Midnight: "midnight",
         Pastels: "pastels",
         Pride: "pride",
+        "Red-green": "redGreen",
         Retro: "retro",
         "Simply blue": "blue",
         "Snow Ghost": "snowghost",
@@ -8120,6 +8124,7 @@ async function VisualPDE(url) {
       }
     }
     if (options.dimension == 1) options.minY = "0.0";
+    uniforms.isTwoD.value = options.dimension == 2;
     resize();
     setRDEquations();
     setEquationDisplayType();

sim/scripts/RD/presets.js

@@ -3315,13 +3315,13 @@ presets["bacteriaInAReach2D"] = {
   domainViaIndicatorFun: true,
   imagePathOne: "./images/river.png",
   kineticParams:
-    "c0 = 0.1 in [0, 1];c1 = 0 in [0, 1];k = 0.006 in [0, 0.05];u = 1 in [0.1, 4];",
+    "c0 = 0.5 in [0, 1];c1 = 0 in [0, 1];k = 0.006 in [0, 0.05];u = 1 in [0.1, 4];",
   maxColourValue: "5",
   overlayExpr: "I_S",
   parent: "bacteriaInAReach",
   plotType: "plane",
   reactionStr_1:
-    "-u*C_xb - 5*(0.4*L_y-y)*C_y/L_y - k*C + c0*0.1*Bump(0,L_y/2,L/20) + c1*0.1*Bump(L_x/2,0.7*L_y,L/20)",
+    "-u*C_xb - 5*(0.4*L_y-y)*C_y/L_y - k*C + c0*0.1*Bump(0,L_y/2,L/20)/u + c1*0.1*Bump(L_x/2,0.7*L_y,L/20)/u",
   views: [
     {
       name: "Concentration",
@@ -3340,15 +3340,16 @@ presets["bacteriaInAReach"] = {
   brushAction: "smoothadd",
   brushRadius: "20",
   brushType: "vline",
-  brushValue: "min(0.02, 1-C)",
+  brushValue: "min(1, max(0,5-C))",
   colourbar: true,
-  colourmap: "turbo",
+  colourmap: "redGreen",
   comboStr_1: "Left: Dirichlet = c0; Right: Ghost = 0;",
   diffusionStr_1_1: "0",
   diffusionStr_2_2: "0",
   dimension: "1",
   domainScale: "320",
   dt: 0.01,
+  flippedColourmap: true,
   initCond_1: "0",
   initCond_2: "0",
   kineticParams:

sim/scripts/auxiliary_GLSL_funs.js

@@ -1,6 +1,7 @@
 // auxiliary_GLSL_funs.js
 export function auxiliary_GLSL_funs() {
   return `const float pi = 3.141592653589793;
+  uniform bool isTwoD;
   float H(float VALUE) 
     {
         float RES = smoothstep(-0.01, 0.01, VALUE);
@@ -33,7 +34,11 @@ export function auxiliary_GLSL_funs() {
     }
 
     float Bump(float x, float y, float MX, float MY, float MAXR) {
-      float RADIUSSQ = ((x-MX)*(x-MX)+(y-MY)*(y-MY)) / (MAXR*MAXR);
+      float yDiff = 0.0;
+      if (isTwoD) {
+        yDiff = y - MY;
+      }
+      float RADIUSSQ = ((x-MX)*(x-MX)+(yDiff)*(yDiff)) / (MAXR*MAXR);
       if (RADIUSSQ < 1.0) {
         return exp(1.0-1.0/(1.0-RADIUSSQ));
       } else {

sim/scripts/colourmaps.js

@@ -1,6 +1,13 @@
 export function getColours(sel) {
   let colours = [];
   switch (sel) {
+    case "redGreen":
+      colours.push([0.89, 0.07, 0.18, 0.0]);
+      colours.push([0.95, 0.53, 0.24, 0.25]);
+      colours.push([0.93, 0.82, 0.31, 0.5]);
+      colours.push([0.62, 0.82, 0.32, 0.75]);
+      colours.push([0.11, 0.64, 0.23, 1.0]);
+      break;
     case "fireOnTerrain":
       colours.push([0.51, 0.36, 0.33, 0.0]);
       colours.push([1, 0.99, 0.59, 0.45]);