Initial commit

aditya3012/Animate_func.py

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+import numpy
+from matplotlib import pyplot
+import math
+from matplotlib import rcParams
+rcParams['font.family'] = 'serif'
+rcParams['font.size'] =16
+from matplotlib import animation
+from IPython.display import HTML
+
+
+nx =201
+dx =0.2
+nt= 300
+x = numpy.linspace(0,10,nx)
+D =1
+alpha = 1
+
+u= numpy.zeros(nx)
+lbound = numpy.where(x <= 1)
+ubound = numpy.where(x >= 0)            
+bounds = numpy.intersect1d(lbound, ubound)
+u[bounds]=1       
+
+fig = pyplot.figure(figsize=(8,6))
+ax = pyplot.axes(xlim=(0,10),ylim=(0,1.5))
+ax.set_xlabel('$x$')
+ax.set_ylabel('$u$')
+#ax.text(0,-0.25,'See how the curve levels off at u =1',color='red')
+ax.annotate('See how the curve',color='black',wrap= True, xy=(7,1),xytext=(3,1.3))
+ax.annotate('levels off at u =1',color='black',wrap= True,xy=(7,1),xytext=(3,1.2),arrowprops =dict(facecolor='black', shrink =0.04))
+line = ax.plot([],[],color='c',ls=':',lw=3)[0]
+
+
+
+def CatchtheFisherwaveanimate(n):
+    dt =0.0003
+    un= numpy.zeros_like(u)
+    ax.text(6,0.3,'Absence of gene',color='green')
+    ax.fill_between(x,un,1.5, color='aqua')
+    ax.fill_between(x,u,0, color='green')
+    for n in range (nt):
+        un= numpy.copy(u)
+        u[1:-1] = un[1:-1] \
+                + D * dt/dx**2 * (un[2:] - 2*un[1:-1] + un[0:-2]) \
+                + alpha * un[1:-1] * dt * (1 - un[1:-1])       
+        u[0] = u[1] 
+        u[-1] = u[-2]
+        line.set_data(x,u)
+
+anim = animation.FuncAnimation(fig,CatchtheFisherwaveanimate,\
+                               frames=nt,interval=60)

aditya3012/Animate_mutantgene.py

@@ -0,0 +1,45 @@
+import numpy
+from matplotlib import pyplot
+import math
+from matplotlib import rcParams
+rcParams['font.family'] = 'serif'
+rcParams['font.size'] =16
+from matplotlib import animation
+from IPython.display import HTML
+
+
+nx =200
+dx =0.1
+nt= 350
+x = numpy.linspace(-10,10,nx)
+D =1
+alpha = 1
+
+u = numpy.zeros(nx)
+lbound = numpy.where(x >= -2)
+ubound = numpy.where(x <= 2)
+bounds = numpy.intersect1d(lbound, ubound)
+u[bounds]=0.01
+
+fig = pyplot.figure(figsize=(8,6))
+ax = pyplot.axes(xlim=(-10,10),ylim=(0,1.5))
+ax.set_xlabel('$x$')
+ax.set_ylabel('$u$')
+#ax.text(0,-0.25,'See how the curve levels off at u =1',color='red')
+line = ax.plot([],[],color='c',ls=':',lw=3)[0]
+
+def CatchtheFisherwaveanimate(n):
+    dt =0.0001
+    un= numpy.zeros_like(u)
+    ax.fill_between(x,u,0,interpolate=True, color='blue')
+    ax.text(-2.5,.8,'Sickle cell gene',color='white')
+    for n in range (nt):
+        un= numpy.copy(u)
+        u[1:-1] = un[1:-1] \
+                + D * dt/dx**2 * (un[2:] - 2*un[1:-1] + un[0:-2]) \
+                + alpha * un[1:-1] * dt * (1 - un[1:-1])       
+        u[0] = u[1] 
+        u[-1] = u[-2]
+        line.set_data(x,u)
+anim = animation.FuncAnimation(fig,CatchtheFisherwaveanimate,\
+                               frames=nt,interval=50)

aditya3012/numericalmoocstyle.css

@@ -0,0 +1,152 @@
+<link href='http://fonts.googleapis.com/css?family=Alegreya+Sans:100,300,400,500,700,800,900,100italic,300italic,400italic,500italic,700italic,800italic,900italic' rel='stylesheet' type='text/css'>
+<link href='http://fonts.googleapis.com/css?family=Arvo:400,700,400italic' rel='stylesheet' type='text/css'>
+<link href='http://fonts.googleapis.com/css?family=PT+Mono' rel='stylesheet' type='text/css'>
+<link href='http://fonts.googleapis.com/css?family=Shadows+Into+Light' rel='stylesheet' type='text/css'>
+<link href='http://fonts.googleapis.com/css?family=Nixie+One' rel='stylesheet' type='text/css'>
+<link href='https://fonts.googleapis.com/css?family=Source+Code+Pro' rel='stylesheet' type='text/css'>
+<style>
+
+@font-face {
+    font-family: "Computer Modern";
+    src: url('http://mirrors.ctan.org/fonts/cm-unicode/fonts/otf/cmunss.otf');
+}
+
+#notebook_panel { /* main background */
+    background: rgb(245,245,245);
+}
+
+div.cell { /* set cell width */
+    width: 750px;
+}
+
+div #notebook { /* centre the content */
+    background: #fff; /* white background for content */
+    width: 1000px;
+    margin: auto;
+    padding-left: 0em;
+}
+
+#notebook li { /* More space between bullet points */
+    margin-top:0.8em;
+}
+
+/* draw border around running cells */
+div.cell.border-box-sizing.code_cell.running { 
+    border: 1px solid #111;
+}
+
+/* Put a solid color box around each cell and its output, visually linking them*/
+div.cell.code_cell {
+    background-color: rgb(256,256,256); 
+    border-radius: 0px; 
+    padding: 0.5em;
+    margin-left:1em;
+    margin-top: 1em;
+}
+
+div.text_cell_render{
+    font-family: 'Alegreya Sans' sans-serif;
+    line-height: 140%;
+    font-size: 125%;
+    font-weight: 400;
+    width:600px;
+    margin-left:auto;
+    margin-right:auto;
+}
+
+
+/* Formatting for header cells */
+.text_cell_render h1 {
+    font-family: 'Nixie One', serif;
+    font-style:regular;
+    font-weight: 400;    
+    font-size: 45pt;
+    line-height: 100%;
+    color: rgb(0,51,102);
+    margin-bottom: 0.5em;
+    margin-top: 0.5em;
+    display: block;
+}
+
+.text_cell_render h2 {
+    font-family: 'Nixie One', serif;
+    font-weight: 400;
+    font-size: 30pt;
+    line-height: 100%;
+    color: rgb(0,51,102);
+    margin-bottom: 0.1em;
+    margin-top: 0.3em;
+    display: block;
+}	
+
+.text_cell_render h3 {
+    font-family: 'Nixie One', serif;
+    margin-top:16px;
+    font-size: 22pt;
+    font-weight: 600;
+    margin-bottom: 3px;
+    font-style: regular;
+    color: rgb(102,102,0);
+}
+
+.text_cell_render h4 {    /*Use this for captions*/
+    font-family: 'Nixie One', serif;
+    font-size: 14pt;
+    text-align: center;
+    margin-top: 0em;
+    margin-bottom: 2em;
+    font-style: regular;
+}
+
+.text_cell_render h5 {  /*Use this for small titles*/
+    font-family: 'Nixie One', sans-serif;
+    font-weight: 400;
+    font-size: 16pt;
+    color: rgb(163,0,0);
+    font-style: italic;
+    margin-bottom: .1em;
+    margin-top: 0.8em;
+    display: block;
+}
+
+.text_cell_render h6 { /*use this for copyright note*/
+    font-family: 'PT Mono', sans-serif;
+    font-weight: 300;
+    font-size: 9pt;
+    line-height: 100%;
+    color: grey;
+    margin-bottom: 1px;
+    margin-top: 1px;
+}
+
+.CodeMirror{
+    font-family: "Source Code Pro";
+    font-size: 90%;
+}
+
+.alert-box {
+    padding:10px 10px 10px 36px;
+    margin:5px;
+}
+
+.success {
+    color:#666600;
+    background:rgb(240,242,229);
+}
+</style>
+<script>
+    MathJax.Hub.Config({
+                        TeX: {
+                           extensions: ["AMSmath.js"],
+                           equationNumbers: { autoNumber: "AMS", useLabelIds: true}
+                           },
+                tex2jax: {
+                    inlineMath: [ ['$','$'], ["\\(","\\)"] ],
+                    displayMath: [ ['$$','$$'], ["\\[","\\]"] ]
+                },
+                displayAlign: 'center', // Change this to 'center' to center equations.
+                "HTML-CSS": {
+                    styles: {'.MathJax_Display': {"margin": 4}}
+                }
+        });
+</script>