finalized many of the things

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

Author: zerothi

S_02/run.ipynb

@@ -66,7 +66,7 @@
     "# Energy grid to calculate the PDOS on\n",
     "# E_min = -20 eV\n",
     "# E_max = 15 eV\n",
-    "# Gaussian width 0.2 eV\n",
+    "# Gaussian width: \\sigma 2 ^{1/2} = 0.2 eV\n",
     "# Number of points: 3500 (spacing of 0.01 eV)\n",
     "%block Projected.DensityOfStates\n",
     "-20.00 15.00 0.200 3500 eV\n",
@@ -129,7 +129,7 @@
     "\n",
     "    Search the API documentation for the `MonkhorstPack.asaverage` method and figure out what it does. Note, there are other `MonkhorstPack.as*` methods, these are all extremely usefull when calculating a large quantity of data in a Brillouin-zone object.\n",
     "5. Compare the Siesta PDOS with sisl PDOS, why are they different?  \n",
-    "   *HINT*: It is not related to the eigenspectrum. Check the API for the `PDOS` method."
+    "   *HINT*: $\\sigma$. Check the API for the `PDOS` method."
    ]
   },
   {

S_03/run.ipynb

@@ -21,9 +21,9 @@
     "\n",
     "The basic principle of plotting the real-space wave functions may be written as this (for a given $\\mathbf k$-point):\n",
     "\\begin{equation}\n",
-    "   \\psi_i(\\mathbf k, \\mathbf r) = \\sum_\\nu e^{i\\mathbf k \\cdot \\mathbf r_\\nu}|\\psi(\\mathbf k)\\rangle_{i\\nu} \\phi_\\nu(\\mathbf r - \\mathbf r_\\nu),\n",
+    "   \\psi_i(\\mathbf k, \\mathbf r) = \\sum_\\nu e^{i\\mathbf k \\cdot \\mathbf r_\\nu}c_{i\\nu}\\phi_\\nu(\\mathbf r - \\mathbf r_\\nu),\n",
     "\\end{equation}\n",
-    "where $|\\psi(\\mathbf k)\\rangle_{i\\nu}$ is the $\\nu$ basis orbital coefficient for the $i$th eigenstate and $\\phi_\\nu(\\mathbf r - \\mathbf r_\\nu)$ is the basis orbital $\\nu$ centered at $\\mathbf r_\\nu$.\n",
+    "where $c_{i\\nu}=\\langle\\tilde\\phi_\\nu|\\psi_i\\rangle$ is the coefficient for the $i$th eigenstate and $\\nu$ basis orbital and $\\phi_\\nu(\\mathbf r - \\mathbf r_\\nu)$ is the basis orbital $\\nu$ centered at $\\mathbf r_\\nu$.\n",
     "\n",
     "`sisl` will in most cases, automatically read the necessary information from a Siesta run to be able to construct the $\\phi_\\nu$ basis functions in real-space. If the basis-information is not available `sisl` will inform you when trying to calculate real-space quantities.\n",
     "\n",

install_tutorial.sh

@@ -24,7 +24,7 @@ function _help {
     echo "  $0 download"
     echo ""
     echo "During the download part a new directory will be created:"
-    echo "  $home/TBT-TS-sisl-workshop"
+    echo "  $HOME/TBT-TS-sisl-workshop"
     echo ""
 }
 
@@ -62,10 +62,10 @@ case "x$OSTYPE" in
 	esac
 	;;
 esac
+
 action=install
 case $1 in
     install)
-	echo nothing > /dev/null
 	# do nothing, we use the OS to determine stuff
 	action=install
 	;;
@@ -150,7 +150,6 @@ function linux_install {
 	echo ""
 	echo "PLEASE RESTART YOUR SHELL!"
     fi
-    exit 0
 }
 
 
@@ -206,7 +205,6 @@ function macos_install {
 	    echo "Please try and get pip to work and re-run the installation proceduce."
 	fi
     fi
-    exit 0
 }
 
 function install_warning {

presentations/01/device.tex

@@ -52,6 +52,10 @@ \subsection{NEGF Algorithm in TBtrans}
             \node[fdf] {\%endblock}; \\
         };
       \end{scope}
+      \begin{scope}[xshift=8cm,yshift=1cm]
+        \node[anchor=north,fill=black!70!white,text=white,align=center,text width=4.5cm] (A)
+        at (0,0) {Always!\\\mbox{}\\\texttt{tbtrans -fdf TBT.Analyze}};
+      \end{scope}
     \end{tikzpicture}
 
     \item TBtrans does everything else by it-self