make all inter-notebook links relative

gforsyth · gforsyth · commit f28e7e2bd62d · 2016-10-18T12:04:36.000-04:00
not hardcoded to static versions on nbviewer
diff --git a/lessons/02_Step_2.ipynb b/lessons/02_Step_2.ipynb
@@ -91,7 +91,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The code snippet below is *unfinished*. We have copied over the line from [Step 1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb) that executes the time-stepping update. Can you edit this code to execute the non-linear convection instead?"
+    "The code snippet below is *unfinished*. We have copied over the line from [Step 1](./01_Step_1.ipynb) that executes the time-stepping update. Can you edit this code to execute the non-linear convection instead?"
    ]
   },
   {
diff --git a/lessons/03_CFL_Condition.ipynb b/lessons/03_CFL_Condition.ipynb
@@ -27,7 +27,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Did you experiment in Steps [1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb) and [2](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/02_Step_2.ipynb) using different parameter choices? If you did, you probably ran into some unexpected behavior. Did your solution ever blow up? (In my experience, CFD students *love* to make things blow up.)\n",
+    "Did you experiment in Steps [1](./01_Step_1.ipynb) and [2](./02_Step_2.ipynb) using different parameter choices? If you did, you probably ran into some unexpected behavior. Did your solution ever blow up? (In my experience, CFD students *love* to make things blow up.)\n",
     "\n",
     "You are probably wondering why changing the discretization parameters affects your solution in such a drastic way. This notebook complements our [interactive CFD lessons](https://github.com/barbagroup/CFDPython) by discussing the CFL condition. And learn more by watching Prof. Barba's YouTube lectures (links below). "
    ]
@@ -45,7 +45,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For the first few steps, we've been using the same general initial and boundary conditions.  With the parameters we initially suggested, the grid has 41 points and the timestep is 0.25 seconds.  Now, we're going to experiment with increasing the size of our grid.  The code below is identical to the code we used in [Step 1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb), but here it has been bundled up in a function so that we can easily examine what happens as we adjust just one variable: **the grid size**."
+    "For the first few steps, we've been using the same general initial and boundary conditions.  With the parameters we initially suggested, the grid has 41 points and the timestep is 0.25 seconds.  Now, we're going to experiment with increasing the size of our grid.  The code below is identical to the code we used in [Step 1](./01_Step_1.ipynb), but here it has been bundled up in a function so that we can easily examine what happens as we adjust just one variable: **the grid size**."
    ]
   },
   {
diff --git a/lessons/04_Step_3.ipynb b/lessons/04_Step_3.ipynb
@@ -27,7 +27,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You should have completed Steps [1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb) and [2](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/02_Step_2.ipynb) before continuing. This IPython notebook continues the presentation of the **12 steps to Navier-Stokes**, the practical module taught in the interactive CFD class of [Prof. Lorena Barba](http://lorenabarba.com). "
+    "You should have completed Steps [1](./01_Step_1.ipynb) and [2](./02_Step_2.ipynb) before continuing. This IPython notebook continues the presentation of the **12 steps to Navier-Stokes**, the practical module taught in the interactive CFD class of [Prof. Lorena Barba](http://lorenabarba.com). "
    ]
   },
   {
diff --git a/lessons/05_Step_4.ipynb b/lessons/05_Step_4.ipynb
@@ -51,7 +51,7 @@
     "\n",
     "As you can see, it is a combination of non-linear convection and diffusion. It is surprising how much you learn from this neat little equation! \n",
     "\n",
-    "We can discretize it using the methods we've already detailed in Steps [1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb) to [3](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/04_Step_3.ipynb).  Using forward difference for time, backward difference for space and our 2nd-order method for the second derivatives yields:\n",
+    "We can discretize it using the methods we've already detailed in Steps [1](./01_Step_1.ipynb) to [3](./04_Step_3.ipynb).  Using forward difference for time, backward difference for space and our 2nd-order method for the second derivatives yields:\n",
     "\n",
     "$$\\frac{u_i^{n+1}-u_i^n}{\\Delta t} + u_i^n \\frac{u_i^n - u_{i-1}^n}{\\Delta x} = \\nu \\frac{u_{i+1}^n - 2u_i^n + u_{i-1}^n}{\\Delta x^2}$$\n",
     "\n",
diff --git a/lessons/07_Step_5.ipynb b/lessons/07_Step_5.ipynb
@@ -27,7 +27,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Up to now, all of our work has been in one spatial dimension (Steps [1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb) to [4](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/05_Step_4.ipynb)). We can learn a lot in just 1D, but let's grow up to flatland: two dimensions. \n",
+    "Up to now, all of our work has been in one spatial dimension (Steps [1](./01_Step_1.ipynb) to [4](./05_Step_4.ipynb)). We can learn a lot in just 1D, but let's grow up to flatland: two dimensions. \n",
     "\n",
     "In the following exercises, you will extend the first four steps to 2D. To extend the 1D finite-difference formulas to partial derivatives in 2D or 3D, just apply the definition: a partial derivative with respect to $x$ is the variation in the $x$ direction *at constant* $y$.\n",
     "\n",
diff --git a/lessons/08_Step_6.ipynb b/lessons/08_Step_6.ipynb
@@ -27,7 +27,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You should have completed your own code for [Step 5](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/07_Step_5.ipynb) before continuing to this lesson. As with Steps 1 to 4, we will build incrementally, so it's important to complete the previous step!\n",
+    "You should have completed your own code for [Step 5](./07_Step_5.ipynb) before continuing to this lesson. As with Steps 1 to 4, we will build incrementally, so it's important to complete the previous step!\n",
     "\n",
     "We continue ..."
    ]
diff --git a/lessons/11_Defining_Function_in_Python.ipynb b/lessons/11_Defining_Function_in_Python.ipynb
@@ -211,9 +211,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Remember our short detour on using [array operations with NumPy](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/07_Step_5.ipynb)?\n",
+    "Remember our short detour on using [array operations with NumPy](./07_Step_5.ipynb)?\n",
     "\n",
-    "Well, there are a few more ways to make your scientific codes in Python run faster. We recommend the article on the Technical Discovery blog about [Speeding Up Python](http://technicaldiscovery.blogspot.com/2011/06/speeding-up-python-numpy-cython-and.html) (June 20, 2011), which talks about NumPy, Cython and Weave. It uses as example the Laplace equation (which we will solve in [Step 9](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/12_Step_9.ipynb)) and makes neat use of defined functions.\n",
+    "Well, there are a few more ways to make your scientific codes in Python run faster. We recommend the article on the Technical Discovery blog about [Speeding Up Python](http://technicaldiscovery.blogspot.com/2011/06/speeding-up-python-numpy-cython-and.html) (June 20, 2011), which talks about NumPy, Cython and Weave. It uses as example the Laplace equation (which we will solve in [Step 9](./12_Step_9.ipynb)) and makes neat use of defined functions.\n",
     "\n",
     "But a recent new way to get fast Python codes is [Numba](http://numba.pydata.org). We'll learn a bit about that after we finish the **12 steps to Navier-Stokes**.\n",
     "\n",
diff --git a/lessons/12_Step_9.ipynb b/lessons/12_Step_9.ipynb
@@ -27,7 +27,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In the previous step, we solved the [2D Burgers' equation](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/10_Step_8.ipynb): an important equation in the study of fluid mechanics because it contains the full convective nonlinearity of the flow equations. With that exercise, we also build the experience to incrementatlly code a Navier-Stokes solver.\n",
+    "In the previous step, we solved the [2D Burgers' equation](./10_Step_8.ipynb): an important equation in the study of fluid mechanics because it contains the full convective nonlinearity of the flow equations. With that exercise, we also build the experience to incrementatlly code a Navier-Stokes solver.\n",
     "\n",
     "In the next two steps, we will solve Laplace and then Poisson equation. We will then put it all together!"
    ]
@@ -116,7 +116,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Remember the lesson on writing [functions with Python](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/11_Defining_Function_in_Python.ipynb)? We will use that style of code in this exercise.\n",
+    "Remember the lesson on writing [functions with Python](./11_Defining_Function_in_Python.ipynb)? We will use that style of code in this exercise.\n",
     "\n",
     "We're going to define two functions: one that plots our data in a 3D projection plot and the other that iterates to solve for $p$ until the change in the [L1 Norm](http://en.wikipedia.org/wiki/Norm_(mathematics)#Taxicab_norm_or_Manhattan_norm) of $p$ is less than a specified value.   "
    ]
@@ -333,7 +333,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The [next step](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/13_Step_10.ipynb) will be to solve Poisson's equation. Watch **Video Lesson 11** on You Tube to understand why we need Poisson's equation in CFD."
+    "The [next step](./13_Step_10.ipynb) will be to solve Poisson's equation. Watch **Video Lesson 11** on You Tube to understand why we need Poisson's equation in CFD."
    ]
   },
   {
diff --git a/lessons/13_Step_10.ipynb b/lessons/13_Step_10.ipynb
@@ -58,7 +58,7 @@
     "\n",
     "So, unlinke the Laplace equation, there is some finite value inside the field that affects the solution. Poisson's equation acts to \"relax\" the initial sources in the field.\n",
     "\n",
-    "In discretized form, this looks almost the same as [Step 9](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/12_Step_9.ipynb), except for the source term:\n",
+    "In discretized form, this looks almost the same as [Step 9](./12_Step_9.ipynb), except for the source term:\n",
     "\n",
     "$$\\frac{p_{i+1,j}^{n}-2p_{i,j}^{n}+p_{i-1,j}^{n}}{\\Delta x^2}+\\frac{p_{i,j+1}^{n}-2 p_{i,j}^{n}+p_{i,j-1}^{n}}{\\Delta y^2}=b_{i,j}^{n}$$\n",
     "\n",
@@ -135,7 +135,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "With that, we are ready to advance the initial guess in pseudo-time. How is the code below different from the function used in [Step 9](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/12_Step_9.ipynb) to solve Laplace's equation?"
+    "With that, we are ready to advance the initial guess in pseudo-time. How is the code below different from the function used in [Step 9](./12_Step_9.ipynb) to solve Laplace's equation?"
    ]
   },
   {
@@ -164,7 +164,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Maybe we could reuse our plotting function from [Step 9](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/12_Step_9.ipynb), don't you think?"
+    "Maybe we could reuse our plotting function from [Step 9](./12_Step_9.ipynb), don't you think?"
    ]
   },
   {
diff --git a/lessons/14_Optimizing_Loops_with_Numba.ipynb b/lessons/14_Optimizing_Loops_with_Numba.ipynb
@@ -41,7 +41,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "You will recall from our exploration of [array operations with NumPy](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/06_Array_Operations_with_NumPy.ipynb) that there are large speed gains to be had from implementing our discretizations using NumPy-optimized array operations instead of many nested loops.  \n",
+      "You will recall from our exploration of [array operations with NumPy](./06_Array_Operations_with_NumPy.ipynb) that there are large speed gains to be had from implementing our discretizations using NumPy-optimized array operations instead of many nested loops.  \n",
       "\n",
       "[Numba](http://numba.pydata.org/) is a tool that offers another approach to optimizing our Python code.  Numba is a library for Python which turns Python functions into C-style compiled functions using LLVM.  Depending on the original code and the size of the problem, Numba can provide a significant speedup over NumPy optimized code.\n",
       "\n",
diff --git a/lessons/15_Step_11.ipynb b/lessons/15_Step_11.ipynb
@@ -35,7 +35,7 @@
     "\n",
     "This represents three scalar equations, one for each velocity component $(u,v,w)$. But we will solve it in two dimensions, so there will be two scalar equations.\n",
     "\n",
-    "Remember the continuity equation? This is where the [Poisson equation](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/13_Step_10.ipynb) for pressure comes in!"
+    "Remember the continuity equation? This is where the [Poisson equation](./13_Step_10.ipynb) for pressure comes in!"
    ]
   },
   {
diff --git a/lessons/18_Burgers_equation.ipynb b/lessons/18_Burgers_equation.ipynb
@@ -14,7 +14,7 @@
       "Evaluating Burgers Equation with different CFD Schemes\n",
       "===\n",
       "\n",
-      "We've already examined Burgers equation in both 1D and 2D ([Step 4](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/05_Step_4.ipynb) and [Step 8](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/10_Step_8.ipynb), respectively).  Here we are going to restrict ourselves to the 1D Burgers equation and examine the role that different schemes play in discretizing non-linear 1st order hyperbolic equations.  "
+      "We've already examined Burgers equation in both 1D and 2D ([Step 4](./05_Step_4.ipynb) and [Step 8](./10_Step_8.ipynb), respectively).  Here we are going to restrict ourselves to the 1D Burgers equation and examine the role that different schemes play in discretizing non-linear 1st order hyperbolic equations.  "
      ]
     },
     {

Original file line number	Diff line number	Diff line change
`@@ -91,7 +91,7 @@`
`91`	`91`	`"cell_type": "markdown",`
`92`	`92`	`"metadata": {},`
`93`	`93`	`"source": [`
`94`		`- "The code snippet below is unfinished. We have copied over the line from [Step 1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb) that executes the time-stepping update. Can you edit this code to execute the non-linear convection instead?"`
	`94`	`+ "The code snippet below is unfinished. We have copied over the line from [Step 1](./01_Step_1.ipynb) that executes the time-stepping update. Can you edit this code to execute the non-linear convection instead?"`
`95`	`95`	`]`
`96`	`96`	`},`
`97`	`97`	`{`
Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,7 @@`
`27`	`27`	`"cell_type": "markdown",`
`28`	`28`	`"metadata": {},`
`29`	`29`	`"source": [`
`30`		`- "Did you experiment in Steps [1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb) and [2](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/02_Step_2.ipynb) using different parameter choices? If you did, you probably ran into some unexpected behavior. Did your solution ever blow up? (In my experience, CFD students love to make things blow up.)\n",`
	`30`	`+ "Did you experiment in Steps [1](./01_Step_1.ipynb) and [2](./02_Step_2.ipynb) using different parameter choices? If you did, you probably ran into some unexpected behavior. Did your solution ever blow up? (In my experience, CFD students love to make things blow up.)\n",`
`31`	`31`	`"\n",`
`32`	`32`	`"You are probably wondering why changing the discretization parameters affects your solution in such a drastic way. This notebook complements our [interactive CFD lessons](https://github.com/barbagroup/CFDPython) by discussing the CFL condition. And learn more by watching Prof. Barba's YouTube lectures (links below). "`
`33`	`33`	`]`
`@@ -45,7 +45,7 @@`
`45`	`45`	`"cell_type": "markdown",`
`46`	`46`	`"metadata": {},`
`47`	`47`	`"source": [`
`48`		- "For the first few steps, we've been using the same general initial and boundary conditions. With the parameters we initially suggested, the grid has 41 points and the timestep is 0.25 seconds. Now, we're going to experiment with increasing the size of our grid. The code below is identical to the code we used in [Step 1](http://nbviewer.ipython.org/urls/github.com/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb), but here it has been bundled up in a function so that we can easily examine what happens as we adjust just one variable: the grid size."
	`48`	`+ "For the first few steps, we've been using the same general initial and boundary conditions. With the parameters we initially suggested, the grid has 41 points and the timestep is 0.25 seconds. Now, we're going to experiment with increasing the size of our grid. The code below is identical to the code we used in [Step 1](./01_Step_1.ipynb), but here it has been bundled up in a function so that we can easily examine what happens as we adjust just one variable: the grid size."`
`49`	`49`	`]`
`50`	`50`	`},`
`51`	`51`	`{`