initial clean-up of presentations

Signed-off-by: Nick Papior <nickpapior@gmail.com>

Author: zerothi

S_03/run.ipynb

@@ -42,7 +42,7 @@
     "4. Read the entry about the `EigenstateElectron` in the [sisl](http://zerothi.github.io/sisl/docs/latest/api-generated/sisl.physics.html#electrons-electron).  \n",
     "   Figure out which method you should use in order to calculate the real-space wavefunction.  \n",
     "   Use the below method (`plot_grid`) to plot a cut through the wavefunction grid.\n",
-    "   *HINT*: this may be a useful grid `grid = Grid(0.01, sc=H.geometry.sc)`\n",
+    "   *HINT*: this may be a useful grid `grid = Grid(0.05, sc=H.geometry.sc)`\n",
     "5. If you **don't** see a warning like this:\n",
     "\n",
     "        info:0: SislInfo: wavefunction: summing 18 different state coefficients, will continue silently!\n",
@@ -51,7 +51,7 @@
     "   *HINT*: If you have VMD/XCrySDen on your laptop it may be *fun* to plot the real-space quantities using cube files, if you want, figure out how to save the `Grid` into a cube/xsf file.\n",
     "6. Try and *play* with the supercell you pass to the `Grid` initialization and plot the wavefunction for different sizes of the grid.  \n",
     "    What do you see for increasing size of grids? Are there any periodicites, if so, what is the periodicity and why?\n",
-    "7. Calculate the eigenstates such that the wavefunction has a periodicity of $3\\times2$ along the first/second lattice vector.  \n",
+    "7. Calculate the eigenstates such that the wavefunctions has a periodicity of $3$ along the first lattice vector and $2$ along the second lattice vector (only plot one of the eigenstates)  \n",
     "   *HINT*: $e^{i\\mathbf k \\cdot \\mathbf R}$"
    ]
   },
@@ -84,9 +84,11 @@
     "        im = ax.contourf(x, y, grid.grid[:, :, z_index])\n",
     "        ax.set_xlabel(r'$x$ [Ang]'); ax.set_ylabel(r'$y$ [Ang]')\n",
     "    # Also plot the atomic coordinates\n",
-    "    xyz = grid.geometry.xyz\n",
-    "    for ax in axs:\n",
-    "        ax.scatter(xyz[:, 0], xyz[:, 1], 50, 'k', alpha=.6)\n",
+    "    try:\n",
+    "        xyz = grid.geometry.xyz\n",
+    "        for ax in axs:\n",
+    "            ax.scatter(xyz[:, 0], xyz[:, 1], 50, 'k', alpha=.6)\n",
+    "    except: pass\n",
     "    fig.colorbar(im);"
    ]
   },

TS_04/run.ipynb

@@ -172,7 +172,7 @@
    "metadata": {},
    "source": [
     "- TranSiesta's method of setting boundary conditions for $N$-electrodes is extremely crude since it only fixes the potential on the electrodes. Instead of letting TranSiesta apply the boundary conditions we can provide an external solution to the Poisson problem with *proper* boundary conditions of the electrodes.  \n",
-    "  Below is a method to solve the Poisson problem in Python using `pyamg` (you need to install this `pip install pyamg`, otherwise ask and you'll get the final output). It takes quite some time, so be patient.  \n",
+    "  Below is a method to solve the Poisson problem in Python using `pyamg`. It takes quite some time, so be patient.  \n",
     "  You don't need to understand the below script (but I won't hold you back if you want to carefully read it through ;))"
    ]
   },
@@ -260,7 +260,8 @@
     "         tbtrans -L guess_0.5 -V 0.5:eV -D guess_0.5 RUN.fdf > TBT_guess_0.5.out\n",
     "         tbtrans -L no_guess_0.5 -V 0.5:eV -D no_guess_0.5 RUN.fdf > TBT_no_guess_0.5.out\n",
     "      \n",
-    "     Plot the two transmissions and density of states, are they the same?"
+    "     Plot the two transmissions and density of states, are they the same?\n",
+    "- If you have VMD/XCrySDen installed try out the command-line utility `sgrid` to create a cube file containing the potential profile, [this page](http://zerothi.github.io/sisl/docs/latest/scripts/sgrid.html) may be useful."
    ]
   },
   {

install_tutorial.sh

@@ -104,8 +104,11 @@ esac
 # Function for installation on Linux
 function linux_install {
 
+    # Update lists
+    sudo apt-get update
+
     # First ensure that the correct packages are installed
-    for p in gcc gfortran libhdf5-dev libnetcdf-dev libnetcdff-dev python-dev python-tk python-pip python-pip-whl libatlas3-base liblapack3 libfreetype6-dev libpng12-dev
+    for p in gcc gfortran libhdf5-dev libnetcdf-dev libnetcdff-dev python-dev python-tk python-pip python-pip-whl libatlas3-base liblapack3 libfreetype6-dev libpng-dev
     do
 	sudo apt-get install $p
     done
@@ -217,6 +220,16 @@ function install_warning {
     sleep 3
 }
 
+function install_test_sisl {
+    echo ""
+    echo " Will try and run sisl"
+    echo "    import sisl ; print(sisl.geom.graphene())"
+    python -c "import sisl ; print(sisl.geom.graphene())"
+    if [ $? -ne 0 ]; then
+	echo "Failed running sisl, please mail the organizer with the error message (unless some of the installations failed)"
+    fi
+}
+
 if [ $action == install ]; then
     # os will be download
     case $os in
@@ -229,6 +242,7 @@ if [ $action == install ]; then
 	    macos_install
 	    ;;
     esac
+    install_test_sisl
 
     exit 0
 fi

presentations/01/electrodes.tex

@@ -311,7 +311,7 @@ \subsection{Electrodes}
       \;
       \sum_{
           \mathclap{
-              \substack{j\\
+              \substack{j=1\\
                   k_j=k_n+2\pi\frac{j-1}{nR}
               }
           }
@@ -324,15 +324,15 @@ \subsection{Electrodes}
         &
         \cdots
         &
-        e^{-i nk_jR}
+        e^{-i (n-1)k_jR}
         \\
         e^{i k_jR}
         &
         1
         &
         \cdots
         &
-        e^{-i (n-1)k_jR}
+        e^{-i (n-2)k_jR}
         \\
         \vdots
         &
@@ -342,10 +342,10 @@ \subsection{Electrodes}
         &
         \vdots
         \\
-        e^{i nk_jR}
-        &
         e^{i (n-1)k_jR}
         &
+        e^{i (n-2)k_jR}
+        &
         \cdots
         &1
       \end{bmatrix}
@@ -362,7 +362,7 @@ \subsection{Electrodes}
   \framesubtitle{Bloch's theorem}
 
   \begin{itemize}
-    \item Atomic ordering is important, see sisl \texttt{Geometry.repeat} for details
+    \item Atomic ordering is important, see sisl \texttt{Geometry.tile} for details
     \item $k$-point sampling is important, \emph{has} to sample equivalently
   \end{itemize}
 

presentations/01/green.tex

@@ -93,20 +93,26 @@ \subsection{Rules of integration}
           \begin{tikzpicture}[my fill/.style={fill=good},
             font=\footnotesize]
             \begin{axis}[width=.7\textwidth,height=3.5cm,%
+              my eta/.style={forget plot, only marks, mark=*, opacity=0.9, mark size=2pt},
               xmin=-1,xmax=1,ymin=0,xlabel=Energy]
               \addplot[black,smooth,my fill] table {../data/lorentzian.dat};
               \addlegendentry{$\mathfrak{L}$}
               \draw[<->] (axis cs:-0.05, {.5/0.05}) -- node[below=5pt] {$2\eta$}
               (axis cs:0.05,{.5/0.05});
               \node[my fill] at (axis cs:0.5, 10) {$\int=\pi$};
+              \only<4->{
+                  \addplot[my eta,color=good] table {../data/lorentzian_1o5eta.dat};
+                  \addplot[my eta,color=bad] table {../data/lorentzian_5eta.dat};
+                  \addplot[my eta,color=ok] table {../data/lorentzian_eta.dat};
+              }
             \end{axis}
           \end{tikzpicture}
         \end{center}
     }
 
   \end{block}
 
-  \uncover<3>{\hfill\hyperlink{DOS<3>}{\beamergotobutton{Return to DOS}}}
+  \uncover<3->{\hfill\hyperlink{DOS<3>}{\beamergotobutton{Return to DOS}}}
 
 \end{frame}
 

presentations/01/talk.tex

@@ -4,12 +4,12 @@
 \graphicspath{{fig/}}
 \usepackage[export]{adjustbox}
 
-\institute[2017, Nick R. Papior; DTU Nanotech]{\begin{tikzpicture}
+\institute[2018, Nick R. Papior; DTU Nanotech]{\begin{tikzpicture}
       \node[shape=rectangle split,rectangle split parts=2,anchor=base] at (0,0)
       {DTU: sisl, TBtrans and TranSiesta workshop};
     \end{tikzpicture}}
 
-\date{25. October 2017}
+\date{20. November 2018}
 \title{Non-equilibrium Green function theory: 1 \& 2}
 \author{Nick R. Papior}
 

presentations/02/negf.tex

@@ -283,6 +283,9 @@ \subsection{Numeric integration}
 
 \end{frame}
 
+
+\pgfplotsset{my c/.style={/tikz/color=#1, /tikz/fill=#1}}
+
 \begin{frame}
   \frametitle{Numeric integration}
   \framesubtitle{Algorithms}
@@ -309,11 +312,11 @@ \subsection{Numeric integration}
         xlabel={Real Energy [eV]},
         ylabel={Imaginary Energy [eV]}]
         \only<1>{
-        \addplot+[red!70!black] table {../data/siesta_30_simpson.dat};}
+        \addplot+[my c=red!70!black] table {../data/siesta_30_simpson.dat};}
         \only<2>{
-        \addplot+[blue!70!black] table {../data/siesta_30_legendre.dat};}
+        \addplot+[my c=blue!70!black] table {../data/siesta_30_legendre.dat};}
         \only<3->{
-        \addplot+[green!70!black] table {../data/siesta_30_legendre_right.dat};}
+        \addplot+[my c=green!70!black] table {../data/siesta_30_legendre_right.dat};}
       \end{axis}
     \end{tikzpicture}
   \end{center}

presentations/02/talk.tex

@@ -3,12 +3,12 @@
 \graphicspath{{fig/}{fig-defence/}{paper-fig/}}
 \usepackage[export]{adjustbox}
 
-\institute[2017, Nick R. Papior; DTU Nanotech]{\begin{tikzpicture}
+\institute[2018, Nick R. Papior; DTU Nanotech]{\begin{tikzpicture}
       \node[shape=rectangle split,rectangle split parts=2,anchor=base] at (0,0)
       {DTU: sisl, TBtrans and TranSiesta workshop};
     \end{tikzpicture}}
 
-\date{26. October 2016}
+\date{20. November 2018}
 \title{TBtrans/TranSiesta for smarties}
 \author{Nick R. Papior}
 

presentations/03/algorithms.tex presentations/04/algorithms.texpresentations/03/algorithms.tex renamed to presentations/04/algorithms.tex

@@ -272,7 +272,7 @@ \subsection{The omnipotent pivoting scheme?}
   \framesubtitle{Analyzing the sparsity pattern}
 
   \begin{center}
-    \texttt{transiesta -fdf TS.Analyze RUN.fdf}
+    \texttt{siesta -fdf TS.Analyze RUN.fdf}
   \end{center}
 
   \begin{itemize}[<+->]