last changes for the 2018 tutorial

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

Author: zerothi

TB_02/run.ipynb

@@ -285,9 +285,9 @@
    "source": [
     "## Exercises\n",
     "\n",
-    "- Try and create a big graphene flake with an associated Hamiltonian 100,000 atoms. When doing this it is essential you only construct the minimal graphene flake (otherwise creating such a big Hamiltonian will take several minutes). Then use `tile` or `repeat` to expand to the big system.\n",
     "- Go to `In [4]` and change `H.write('ELEC.nc')` to `H.write('ELEC.TSHS')`, then adapt `RUN.fdf` file to let the left electrode read the electronic structure from the `TSHS` file instead. Redo the calculation and check if the output is the same.\n",
-    "- Try and change the on-site term of _one_ of the device atoms, then redo the calculation. What is the (periodic) effect of changing the on-site for one atom?"
+    "- Try and change the on-site term of _one_ of the device atoms, then redo the calculation. What is the (periodic) effect of changing the on-site for one atom?\n",
+    "- Try and create a big graphene flake with an associated Hamiltonian 100,000 atoms. When doing this it is essential you only construct the minimal graphene flake (otherwise creating such a big Hamiltonian will take several minutes). Then use `tile` or `repeat` to expand to the big system. If you try to run transport on this device it will take forever, and may even crash. To handle such big systems you may use the fdf-flag `TBT.Atoms.Device` to limit the calculation region (advice is to *not* do the calculation). "
    ]
   },
   {

TB_06/run.ipynb

@@ -151,8 +151,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "device = device.add_vacuum(100, 0).add_vacuum(100, 1)\n",
-    "device = device.translate( device.center(what='cell') )\n",
+    "device = device.add_vacuum(70, 0).add_vacuum(20, 1)\n",
+    "device = device.translate( device.center(what='cell') - device.center(what='xyz') )\n",
     "device.write('device.xyz')"
    ]
   },
@@ -363,21 +363,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.14"
+   "pygments_lexer": "ipython3",
+   "version": "3.7.1"
   }
  },
  "nbformat": 4,

TB_07/run.ipynb

@@ -116,8 +116,8 @@
     "device = H.geom\n",
     "xy = sisl.Hamiltonian(device)\n",
     "for ia in device:\n",
-    "    # Get all connecting elements (edges discards connections to it-self)\n",
-    "    edges = H.edges(ia)\n",
+    "    # Get all connecting elements (including it-self)\n",
+    "    edges = H.edges(ia, exclude=[])\n",
     "    # Calculate the vector between edges and ia:\n",
     "    #    xyz[edges, :] - xyz[ia, :]\n",
     "    Rij = device.Rij(ia, edges)\n",

TS_02/run.ipynb

@@ -89,7 +89,7 @@
     "5. An additional analysis (before going to the transport calculations) is to calculate the potential drop in the junction. In sisl this is easy:\n",
     "```\n",
     "v0 = sisl.Grid.read('TS_0/ElectrostaticPotential.grid.nc')\n",
-    "vd = (sisl.Grid.read('TS_0.5/ElectrostaticPotential.grid.nc') - v0) * sisl.unit.siesta.unit_convert('Ry', 'eV')\n",
+    "vd = (sisl.Grid.read('TS_0.5/ElectrostaticPotential.grid.nc') - v0)\n",
     "``` \n",
     "`vd` then contains the potential profile (in eV). To save it as a linear average bias file (remember transport is along first lattice vector) you can execute the following:\n",
     "```\n",
@@ -143,7 +143,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Remember to think about why applying a bias to a bulk system is wrong. If you can't immediately figure this out, try and create a longer system by replacing `device = elec.tile(3, axis=0)` with, say: `device = elec.tile(6, axis=0)` and redo the calculation for a given bias."
+    "**TIME**: A remark on this exercise. Think why applying a bias to a bulk system is wrong. If you can't immediately figure this out, try and create a longer system by replacing `device = elec.tile(3, axis=0)` with, say: `device = elec.tile(6, axis=0)` and redo the calculation for a given bias. Then compare the potential profiles."
    ]
   },
   {

TS_03/run.ipynb

@@ -20,7 +20,7 @@
     "Create the input required for a full TranSiesta calculation. Here you should create your first system with these settings:\n",
     "\n",
     "- A pristine bulk Carbon-chain system.\n",
-    "- The Carbon-chain should have a bond-length of $1.5\\,\\mathrm{Ang}$\n",
+    "- The Carbon-chain should have a bond-length of $1.5\\,\\mathrm{Ang}$ and lots of vacuum in the transverse directions (to make it a chain)\n",
     "- You should decide in which direction the semi-infinite directions are.\n",
     "\n",
     "Please use the script `tselecs.sh` to create the relevant input for TranSiesta.  \n",

TS_04/run.ipynb

@@ -100,8 +100,8 @@
    "outputs": [],
    "source": [
     "xy = tbt.geometry.xyz[:, :]\n",
-    "J12 = # fill in the corresponding code here ()\n",
-    "plt.quiver(xy[:, 0], xy[:, 1], J12[:, 0], J12[:, 1]);"
+    "J1 = # fill in the corresponding code here ()\n",
+    "plt.quiver(xy[:, 0], xy[:, 1], J1[:, 0], J1[:, 1]);"
    ]
   },
   {
@@ -160,7 +160,15 @@
    "outputs": [],
    "source": [
     "# Read in the two different grids:\n",
-    "grid0 = sisl.get_sile('siesta.VH').read_grid()\n",
+    "grid0 = sisl.get_sile('siesta.VH').read_grid()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "no_guess = sisl.get_sile('no_guess_0.5.VH').read_grid()\n",
     "# Specify the geometry so we can add the atoms to the plot\n",
     "no_guess.set_geometry(device)\n",
@@ -240,7 +248,7 @@
     "# the sparse matrix may be *VERY* big).\n",
     "# small trick to not have the solution array twice.\n",
     "del grid.grid\n",
-    "grid.grid = solve(A, b).reshape(shape[0])\n",
+    "grid.grid = solve(A, b).reshape(shape.ravel())\n",
     "grid.write('V.TSV.nc')"
    ]
   },

presentations/01/options.tex

@@ -20,7 +20,7 @@ \subsection{fdf input}
 TBT.DOS.Gf true
 TBT.ElectronicTemperature 25. meV
 %block TBT.k
-...
+ ...
 %endblock
 \end{verbatim}
 

presentations/01/talk.tex

@@ -31,7 +31,7 @@
     \item Danish tap water is safe to drink, don't waste money on buying expensive bottled
     water
 
-    \item Start at 9 each day, sandwiches at 12 (not Friday), cake at 14/15
+    \item Start at 9 each day, sandwiches at 12 (no sandwiche Friday), cake at 14/15
 
     \item Poster session Wednesday at 17:30 in 341/342, dinner at 19:00
 
@@ -40,9 +40,17 @@
     \item Please ask questions during the workshop, you are here to learn!
 
     \item If there are things not covered in the tutorial, please ask and I will try and
-    prepare a \emph{mini} tutorial for the last day.
+    prepare a \emph{mini} tutorial for the last day
 
   \end{itemize}
+
+  \uncover<+->{
+      \begin{center}
+        \large
+        sisl is \emph{not} a static code! It evolves due to comments of users, so if you
+        have a comment/suggestion/correction, please do so!
+      \end{center}
+  }
 
 \end{frame}
 

presentations/03/talk.tex

@@ -8,8 +8,8 @@
       {DTU: sisl, TBtrans and TranSiesta workshop};
     \end{tikzpicture}}
 
-\date{20. November 2018}
-\title{TBtrans/TranSiesta for smarties}
+\date{21. November 2018}
+\title{Introduction to TranSiesta and NEGF}
 \author{Nick R. Papior}
 
 \begin{document}

presentations/04/talk.tex

@@ -1,13 +1,14 @@
 \input ../common.tex
+\logo{\includegraphics[angle=90,height=3cm]{villum}}
 
-\graphicspath{{fig/}}
+\graphicspath{{fig/}{../fig/}}
 
 \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{21/22. November 2018}
+\date{22. November 2018}
 \title{$N_\idxE>2$ NEGF calculations using TranSiesta}
 \author{Nick R. Papior}