Added folder for wiki images.

Author: rbanerjee20

fdm-devito-notebooks/01_vib/vib_app.ipynb

@@ -15,7 +15,7 @@
     "<!-- 0D blood flow? -->\n",
     "<!-- waves: 1D blood flow -->\n",
     "<!-- general particle laws and velocity verlet, make exercises -->\n",
-    "<!-- see <htthinspace .://en.wikipedia.org/wiki/Velocity_Verlet> -->\n",
+    "<!-- see <http://en.wikipedia.org/wiki/Velocity_Verlet> -->\n",
     "\n",
     "# Applications of vibration models\n",
     "<div id=\"vib:app\"></div>\n",
@@ -814,7 +814,7 @@
     "In fact (and not surprising!) Figures [vib:app:pendulum:fig_problem](#vib:app:pendulum:fig_problem) and\n",
     "[vib:app:pendulum:fig_forces](#vib:app:pendulum:fig_forces) were drawn using Pysketcher.\n",
     "The details of the drawings are explained in the\n",
-    "[Pysketcher tutorial](htthinspace .://hplgit.github.io/pysketcher/doc/web/index.html).\n",
+    "[Pysketcher tutorial](http://hplgit.github.io/pysketcher/doc/web/index.html).\n",
     "Here, we outline how this type of sketch can be used to create an animated\n",
     "free body diagram during the motion of a pendulum.\n",
     "\n",
@@ -2071,9 +2071,9 @@
     "<https://github.com/hplgit/bumpy>. You may start looking at the\n",
     "\"tutorial\":\n",
     "% if FORMAT == 'pdflatex':\n",
-    "\"htthinspace .://hplgit.github.io/bumpy/doc/pub/bumpy.pdf\".\n",
+    "\"http://hplgit.github.io/bumpy/doc/pub/bumpy.pdf\".\n",
     "% else:\n",
-    "\"htthinspace .://hplgit.github.io/bumpy/doc/pub/bumpy.html\".\n",
+    "\"http://hplgit.github.io/bumpy/doc/pub/bumpy.html\".\n",
     "% endif\n",
     "\n",
     "## Bouncing ball\n",
@@ -2172,7 +2172,7 @@
     "\n",
     "1. The ball impacts the ground, recognized by a sufficiently large negative\n",
     "   velocity ($v<-\\epsilon_v$). The velocity then changes sign and is\n",
-    "   reduced by a factor $C_R$, known as the [coefficient of restitution](htthinspace .://en.wikipedia.org/wiki/Coefficient_of_restitution).\n",
+    "   reduced by a factor $C_R$, known as the [coefficient of restitution](http://en.wikipedia.org/wiki/Coefficient_of_restitution).\n",
     "   For plotting purposes, one may set $h=0$.\n",
     "\n",
     "2. The motion stops, recognized by a sufficiently small velocity\n",
@@ -4916,7 +4916,7 @@
     "\n",
     "    v[0] = V\n",
     "    u[0] = I\n",
-    "    # Compare with eq 22 in htthinspace .://arxiv.org/pdf/cond-mat/0110585.pdf\n",
+    "    # Compare with eq 22 in http://arxiv.org/pdf/cond-mat/0110585.pdf\n",
     "    for n in range(0, Nt):\n",
     "        u_ = u[n] + xi*dt*v[n]\n",
     "        v_ = v[n] + 0.5*(1-2*lambda_)*dt*g(u_, v[n])\n",
@@ -5074,7 +5074,7 @@
     "\n",
     "    v[0] = V\n",
     "    u[0] = I\n",
-    "    # Compare with eq 22 in htthinspace .://arxiv.org/pdf/cond-mat/0110585.pdf\n",
+    "    # Compare with eq 22 in http://arxiv.org/pdf/cond-mat/0110585.pdf\n",
     "    for n in range(0, Nt):\n",
     "        u_ = u[n] + xi*dt*v[n]\n",
     "        v_ = v[n] + 0.5*(1-2*lambda_)*dt*g(u_, v[n])\n",

fdm-devito-notebooks/01_vib/vib_gen.ipynb

@@ -939,7 +939,7 @@
     "[hpl 1: odespy for the generalized problem]\n",
     "\n",
     "<!-- Discussion of which method is best: -->\n",
-    "<!-- <htthinspace .://gamedev.stackexchange.com/questions/33694/pros-and-cons-of-different-integrators> -->\n",
+    "<!-- <http://gamedev.stackexchange.com/questions/33694/pros-and-cons-of-different-integrators> -->\n",
     "\n",
     "## The Stoermer-Verlet algorithm for the generalized model\n",
     "<div id=\"vib:model2x2:gen:StormerVerlet\"></div>\n",

fdm-devito-notebooks/01_vib/vib_undamped.ipynb

@@ -264,7 +264,7 @@
     "successively for $n=1,2,\\ldots,N_t-1$. This numerical scheme sometimes\n",
     "goes under the name\n",
     "Stoermer's\n",
-    "method, [Verlet integration](htthinspace .://en.wikipedia.org/wiki/Verlet_integration), or the Leapfrog method\n",
+    "method, [Verlet integration](http://en.wikipedia.org/wiki/Verlet_integration), or the Leapfrog method\n",
     "(one should note\n",
     "that Leapfrog is used for many quite different methods for quite\n",
     "different differential equations!).\n",
@@ -951,7 +951,7 @@
     "\n",
     "### Visualizing convergence rates with slope markers\n",
     "\n",
-    "Tony S. Yu has written a script [`plotslopes.py`](htthinspace .://goo.gl/A4Utm7)\n",
+    "Tony S. Yu has written a script [`plotslopes.py`](http://goo.gl/A4Utm7)\n",
     "that is very useful to indicate the slope of a graph, especially\n",
     "a graph like $\\ln E = r\\ln \\Delta t + \\ln C$ arising from the model\n",
     "$E=C\\Delta t^r$. A copy of the script resides in the \"`src/vib`\": \"${src_vib}\"\n",
@@ -1429,12 +1429,12 @@
     "by the mouse. For example, we can show four periods of several signals in\n",
     "several plots and then scroll with the mouse through the rest of the\n",
     "simulation *simultaneously* in all the plot windows.\n",
-    "The [Bokeh](htthinspace .://bokeh.pydata.org/en/latest) plotting library offers such tools, but the plots must be displayed in\n",
+    "The [Bokeh](http://bokeh.pydata.org/en/latest) plotting library offers such tools, but the plots must be displayed in\n",
     "a web browser. The documentation of Bokeh is excellent, so here we just\n",
     "show how the library can be used to compare a set of $u$ curves corresponding\n",
     "to long time simulations. (By the way, the guidance to correct\n",
     "pronunciation of Bokeh in\n",
-    "the [documentation](htthinspace .://bokeh.pydata.org/en/0.10.0/docs/faq.html#how-do-you-pronounce-bokeh) and on [Wikipedia](https://en.wikipedia.org/wiki/Bokeh) is not directly compatible with a [YouTube video](https://www.youtube.com/watch?v=OR8HSHevQTM)...).\n",
+    "the [documentation](http://bokeh.pydata.org/en/0.10.0/docs/faq.html#how-do-you-pronounce-bokeh) and on [Wikipedia](https://en.wikipedia.org/wiki/Bokeh) is not directly compatible with a [YouTube video](https://www.youtube.com/watch?v=OR8HSHevQTM)...).\n",
     "\n",
     "Imagine we have performed experiments for a set of $\\Delta t$ values.\n",
     "We want each curve, together with the exact solution, to appear in\n",
@@ -1965,7 +1965,7 @@
    "source": [
     "The last line follows from the relation\n",
     "$\\cos x - 1 = -2\\sin^2(x/2)$ (try `cos(x)-1` in\n",
-    "[wolframalpha.com](htthinspace .://www.wolframalpha.com) to see the formula).\n",
+    "[wolframalpha.com](http://www.wolframalpha.com) to see the formula).\n",
     "\n",
     "The scheme ([7](#vib:ode1:step4))\n",
     "with $u^n=Ie^{i\\tilde\\omega\\Delta t\\, n}$ inserted now gives"
@@ -2301,7 +2301,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "by L'Hopital's rule. This result could also been computed [WolframAlpha](htthinspace .://www.wolframalpha.com/input/?i=%282%2Fx%29*asin%28w*x%2F2%29+as+x-%3E0), or\n",
+    "by L'Hopital's rule. This result could also been computed [WolframAlpha](http://www.wolframalpha.com/input/?i=%282%2Fx%29*asin%28w*x%2F2%29+as+x-%3E0), or\n",
     "we could use the limit functionality in `sympy`:"
    ]
   },
@@ -2498,7 +2498,7 @@
     "([18](#vib:ode1:tildeomega)) may be larger than 1, i.e., $\\omega\\Delta\n",
     "t/2 > 1$. In this case, $\\sin^{-1}(\\omega\\Delta t/2)$ has a complex\n",
     "value and therefore $\\tilde\\omega$ becomes complex.  Type, for\n",
-    "example, `asin(x)` in [wolframalpha.com](htthinspace .://www.wolframalpha.com) to see basic properties of $\\sin^{-1}\n",
+    "example, `asin(x)` in [wolframalpha.com](http://www.wolframalpha.com) to see basic properties of $\\sin^{-1}\n",
     "(x)$).\n",
     "\n",
     "A complex $\\tilde\\omega$ can be written $\\tilde\\omega = \\tilde\\omega_r\n",
@@ -4320,7 +4320,7 @@
     "The scheme\n",
     "([54](#vib:model2x2:EulerCromer:veq1b))-([55](#vib:model2x2:EulerCromer:ueq1b))\n",
     "goes under several names: forward-backward scheme, [semi-implicit\n",
-    "Euler method](htthinspace .://en.wikipedia.org/wiki/Semi-implicit_Euler_method),\n",
+    "Euler method](http://en.wikipedia.org/wiki/Semi-implicit_Euler_method),\n",
     "semi-explicit Euler, symplectic Euler,\n",
     "Newton-Stoermer-Verlet,\n",
     "and Euler-Cromer.  We shall stick to the latter name.\n",

fdm-devito-notebooks/02_wave/wave1D_fd2.ipynb

@@ -79,7 +79,7 @@
     "Boundary conditions\n",
     "that specify the value of $\\partial u/\\partial n$\n",
     "(or shorter $u_n$) are known as\n",
-    "[Neumann](htthinspace .://en.wikipedia.org/wiki/Neumann_boundary_condition) conditions, while [Dirichlet conditions](htthinspace .://en.wikipedia.org/wiki/Dirichlet_conditions)\n",
+    "[Neumann](http://en.wikipedia.org/wiki/Neumann_boundary_condition) conditions, while [Dirichlet conditions](http://en.wikipedia.org/wiki/Dirichlet_conditions)\n",
     "refer to specifications of $u$.\n",
     "When the values are zero ($\\partial u/\\partial n=0$ or $u=0$) we speak\n",
     "about *homogeneous* Neumann or Dirichlet conditions.\n",
@@ -241,7 +241,6 @@
     "## Implementation of Neumann conditions\n",
     "<div id=\"wave:pde2:Neumann:impl\"></div>\n",
     "\n",
-    "\n",
     "We have seen in the preceding section\n",
     "that the special formulas for the boundary points\n",
     "arise from replacing $u_{i-1}^n$ by $u_{i+1}^n$ when computing\n",
@@ -342,6 +341,9 @@
     "write $n=0$ and $t_0$ rather than $n=\\mathcal{I}_t^0$. We also avoid notation\n",
     "like $x_{\\mathcal{I}_x^{-1}}$ and will instead use $x_i$, $i={\\mathcal{I}_x^{-1}}$.\n",
     "\n",
+    "[wave:pde2:Neumann:impl](#wave:pde2:Neumann:impl)\n",
+    "\n",
+    "\n",
     "The Python code associated with index sets applies the following\n",
     "conventions:\n",
     "\n",
@@ -473,7 +475,7 @@
    "source": [
     "**Notice.**\n",
     "\n",
-    "The program [`wave1D_dn.py`](${src_wave}/wave1D/wave1D_dn.py)\n",
+    "The program [`wave1D_dn.py`](src-wave/wave1D/python/wave1D_dn.py)\n",
     "applies the index set notation and\n",
     "solves the 1D wave equation $u_{tt}=c^2u_{xx}+f(x,t)$ with\n",
     "quite general boundary and initial conditions:\n",
@@ -2192,7 +2194,7 @@
     "More details on storing the solution in files appear in\n",
     "in\n",
     "the document\n",
-    "[Scientific software engineering; wave equation case](htthinspace .://tinyurl.com/k3sdbuv/pub/softeng2)\n",
+    "[Scientific software engineering; wave equation case](http://tinyurl.com/k3sdbuv/pub/softeng2)\n",
     "[[Langtangen_deqbook_softeng2]](#Langtangen_deqbook_softeng2).\n",
     "\n",
     "## Pulse propagation in two media\n",

fdm-devito-notebooks/02_wave/wave1D_prog.ipynb

@@ -1194,7 +1194,7 @@
     "in principle, be performed simultaneously.  That is, vectorization not\n",
     "only speeds up the code on serial computers, but also makes it easy to\n",
     "exploit parallel computing. Actually, there are Python tools like\n",
-    "[Numba](htthinspace .://numba.pydata.org) that can automatically turn\n",
+    "[Numba](http://numba.pydata.org) that can automatically turn\n",
     "vectorized code into parallel code.\n",
     "\n",
     "\n",

fdm-devito-notebooks/02_wave/wave2D_prog.ipynb

@@ -912,10 +912,10 @@
     "more powerful and with higher visual quality).\n",
     "\n",
     "The official documentation of the `mlab` module is provided in two\n",
-    "places, one for the [basic functionality](htthinspace .://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html)\n",
-    "and one for [further functionality](htthinspace .://docs.enthought.com/mayavi/mayavi/auto/mlab_other_functions.html).\n",
+    "places, one for the [basic functionality](http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html)\n",
+    "and one for [further functionality](http://docs.enthought.com/mayavi/mayavi/auto/mlab_other_functions.html).\n",
     "Basic [figure\n",
-    "handling](htthinspace .://docs.enthought.com/mayavi/mayavi/auto/mlab_figure.html)\n",
+    "handling](http://docs.enthought.com/mayavi/mayavi/auto/mlab_figure.html)\n",
     "is very similar to the one we know from Matplotlib.  Just as for\n",
     "Matplotlib, all plotting commands you do in `mlab` will go into the\n",
     "same figure, until you manually change to a new figure.\n",

fdm-devito-notebooks/02_wave/wave_analysis.ipynb

@@ -323,7 +323,7 @@
     "known as the *Nyquist frequency*.\n",
     "Within the range of\n",
     "relevant frequencies $(0,\\pi/\\Delta x]$ one defines\n",
-    "the [discrete Fourier transform](htthinspace .://en.wikipedia.org/wiki/Discrete_Fourier_transform), using $N_x+1$ discrete frequencies:"
+    "the [discrete Fourier transform](http://en.wikipedia.org/wiki/Discrete_Fourier_transform), using $N_x+1$ discrete frequencies:"
    ]
   },
   {

fdm-devito-notebooks/02_wave/wave_app.ipynb

@@ -834,7 +834,7 @@
     "([22](#wave:app:sound:prho)) is a constitutive law relating\n",
     "density to pressure by thermodynamic considerations.\n",
     "A typical model\n",
-    "for ([22](#wave:app:sound:prho)) is the so-called [isentropic relation](htthinspace .://en.wikipedia.org/wiki/Isentropic_process), valid for\n",
+    "for ([22](#wave:app:sound:prho)) is the so-called [isentropic relation](http://en.wikipedia.org/wiki/Isentropic_process), valid for\n",
     "adiabatic processes where there is no heat transfer:"
    ]
   },

fdm-devito-notebooks/02_wave/wave_app_exer.ipynb

@@ -551,9 +551,9 @@
     "Create some fancy 3D visualization of the water waves *and* the subsea hill\n",
     "in [Problem 6: Earthquake-generated tsunami over a 3D hill](#wave:app:exer:tsunami2D:hill).\n",
     "Try to make the hill transparent. Possible visualization tools are\n",
-    "[Mayavi](htthinspace .://code.enthought.com/projects/mayavi/),\n",
-    "[Paraview](htthinspace .://www.paraview.org/), and\n",
-    "[OpenDX](htthinspace .://www.opendx.org/).\n",
+    "[Mayavi](http://code.enthought.com/projects/mayavi/),\n",
+    "[Paraview](http://www.paraview.org/), and\n",
+    "[OpenDX](http://www.opendx.org/).\n",
     "Filename: `tsunami2D_hill_viz`.\n",
     "\n",
     "<!-- --- end exercise --- -->\n",

fdm-devito-notebooks/03_diffu/diffu_app.ipynb

@@ -1098,15 +1098,15 @@
     "## Propagation of electrical signals in the brain\n",
     "\n",
     "\n",
-    "<!-- <htthinspace .://icwww.epfl.ch/~gerstner/SPNM/node17.html> -->\n",
-    "<!-- <htthinspace .://www.uio.no/studier/emner/matnat/ifi/INF5610/h09/Lecture04.pdf> -->\n",
-    "<!-- <htthinspace .://people.mbi.ohio-state.edu/schwemmer.2/Publications/Schwemmer_Dissertation_Final.pdf> -->\n",
+    "<!-- <http://icwww.epfl.ch/~gerstner/SPNM/node17.html> -->\n",
+    "<!-- <http://www.uio.no/studier/emner/matnat/ifi/INF5610/h09/Lecture04.pdf> -->\n",
+    "<!-- <http://people.mbi.ohio-state.edu/schwemmer.2/Publications/Schwemmer_Dissertation_Final.pdf> -->\n",
     "<!-- The book by Peskin & ... -->\n",
     "\n",
     "One can make a model of how electrical signals are propagated along the\n",
     "neuronal fibers that receive synaptic inputs in the brain. The signal\n",
     "propagation is one-dimensional and can, in the simplest cases, be\n",
-    "governed by the [Cable equation](htthinspace .://en.wikipedia.org/wiki/Cable_equation):"
+    "governed by the [Cable equation](http://en.wikipedia.org/wiki/Cable_equation):"
    ]
   },
   {

fdm-devito-notebooks/03_diffu/diffu_exer.ipynb

@@ -171,7 +171,7 @@
     "to zero. Integrate this expression and derive\n",
     "([4](#diffu:exer:estimates:p1:result)).\n",
     "\n",
-    "<!-- <htthinspace .://www.ann.jussieu.fr/~frey/cours/UdC/ma691/ma691_ch6.pdf> -->\n",
+    "<!-- <http://www.ann.jussieu.fr/~frey/cours/UdC/ma691/ma691_ch6.pdf> -->\n",
     "\n",
     "**b)**\n",
     "Now we address a slightly different problem,"

fdm-devito-notebooks/03_diffu/diffu_fd1.ipynb

@@ -1115,7 +1115,7 @@
     "\n",
     "<!-- [movie](${doc_notes}/pub/diffu/html/mov-diffu/diffu1D_u0_FE_plug/movie.ogg) -->\n",
     "<!-- Does not work: -->\n",
-    "<!-- htthinspace .://tinyurl.com/pu5uyfn/pub/diffu/html/mov-diffu/diffu1D_u0_FE_plug/movie.ogg -->\n",
+    "<!-- http://tinyurl.com/pu5uyfn/pub/diffu/html/mov-diffu/diffu1D_u0_FE_plug/movie.ogg -->\n",
     "<!-- Works: -->\n",
     "<!-- https://raw.githubusercontent.com/hplgit/fdm-book/master/doc/.src/book/mov-diffu/diffu1D_u0_FE_plug/movie.ogg -->\n",
     "\n",

fdm-devito-notebooks/03_diffu/diffu_fd3.ipynb

@@ -987,7 +987,7 @@
     "\n",
     "**`scipy.linalg` versus `numpy.linalg`.**\n",
     "\n",
-    "Quote from the [SciPy documentation](htthinspace .://docs.scipy.org/doc/scipy/reference/tutorial/linalg.html):\n",
+    "Quote from the [SciPy documentation](http://docs.scipy.org/doc/scipy/reference/tutorial/linalg.html):\n",
     "\n",
     "`scipy.linalg` contains all the functions in `numpy.linalg`\n",
     "plus some other more advanced ones not contained in `numpy.linalg`.\n",
@@ -1766,7 +1766,7 @@
     "The `spsolve` function in `scipy.sparse.linalg` is an efficient\n",
     "version of Gaussian elimination suited for matrices described by\n",
     "diagonals.  The algorithm is known as *sparse Gaussian elimination*,\n",
-    "and `spsolve` calls up a well-tested C code called [SuperLU](htthinspace .://crd-legacy.lbl.gov/~xiaoye/SuperLU/).\n",
+    "and `spsolve` calls up a well-tested C code called [SuperLU](http://crd-legacy.lbl.gov/~xiaoye/SuperLU/).\n",
     "\n",
     "The complete code utilizing `spsolve`\n",
     "is found in the `solver_sparse` function in the file\n",

fdm-devito-notebooks/03_diffu/diffu_rw.ipynb

@@ -1010,7 +1010,7 @@
    "source": [
     "What is the gain of the vectorized implementations? One important gain\n",
     "is that each vectorized operation can be automatically parallelized\n",
-    "if one applies a parallel `numpy` library like [Numba](htthinspace .://numba.pydata.org). On a single CPU, however, the speed up of the vectorized operations\n",
+    "if one applies a parallel `numpy` library like [Numba](http://numba.pydata.org). On a single CPU, however, the speed up of the vectorized operations\n",
     "is also significant. With $N=1,000$ and 50,000 repeated walks,\n",
     "the two vectorized versions run about 25 and 18 times faster than the scalar\n",
     "version, with `random_walks1D_vec1` being fastest.\n",
@@ -1381,7 +1381,7 @@
    "metadata": {},
    "source": [
     "Positions beyond the limits of the $x$ axis appear with a value.\n",
-    "[A long file](htthinspace .://bit.ly/1UbULeH)\n",
+    "[A long file](http://bit.ly/1UbULeH)\n",
     "contains the complete ascii plot corresponding to the\n",
     "function `run_random_walk` above.\n",
     "<!-- \"https://github.com/hplgit/fdm-book/blob/master/doc/.src/chapters/diffu/fig-diffu/rw_ascii.txt\" -->\n",

fdm-devito-notebooks/05_nonlin/nonlin_exer.ipynb

@@ -1321,7 +1321,7 @@
     "each cell, expand the answer and simplify. You can ask `sympy` for\n",
     "LaTeX code and render it either by creating a LaTeX document and\n",
     "compiling it to a PDF document or by using\n",
-    "<htthinspace .://latex.codecogs.com> to display LaTeX formulas in a web\n",
+    "<http://latex.codecogs.com> to display LaTeX formulas in a web\n",
     "page. Here are some appropriate Python statements\n",
     "for the latter purpose:"
    ]
@@ -1351,9 +1351,9 @@
     "# page with an interactive editor and display area where the\n",
     "# formula can be further edited\n",
     "text = \"\"\"\n",
-    "<a href=\"htthinspace .://www.codecogs.com/eqnedit.php?latex=%(html_code)s\"\n",
+    "<a href=\"http://www.codecogs.com/eqnedit.php?latex=%(html_code)s\"\n",
     " target=\"_blank\">\n",
-    "<img src=\"htthinspace .://latex.codecogs.com/gif.latex?%(html_code)s\"\n",
+    "<img src=\"http://latex.codecogs.com/gif.latex?%(html_code)s\"\n",
     " title=\"%(latex_code)s\"/>\n",
     "</a>\n",
     " \"\"\" % vars()\n",