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zerothizerothi
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Signed-off-by: Nick Papior <nickpapior@gmail.com>
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‎presentations/01/RUN.fdf‎

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TBT.k [ 3 1 1 ]
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TBT.DOS.A
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TBT.Current.Orb
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TBT.HS DEVICE.nc
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%block TBT.Elec.Left
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HS ELEC.nc
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semi-inf-direction -a2
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electrode-position 1
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%endblock
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%block TBT.Elec.Right
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HS ELEC.nc
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semi-inf-direction +a2
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electrode-position end -1
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%endblock
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‎presentations/01/run.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from __future__ import print_function\n",
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"import sisl\n",
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"import numpy as np\n",
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"import matplotlib.pyplot as plt\n",
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"%matplotlib inline"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Example of the $k$-point sampling for TBtrans."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"chain = sisl.Geometry([0]*3, sisl.Atom(1, R=1.), sc=[1, 1, 10])\n",
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"chain.set_nsc([3, 3, 1])\n",
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"\n",
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"# Transport along y-direction\n",
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"chain = chain.tile(20, 0)\n",
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"He = sisl.Hamiltonian(chain)\n",
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"He.construct(([0.1, 1.1], [0, -1]))\n",
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"Hd = He.tile(20, 1)\n",
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"He.write('ELEC.nc')\n",
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"Hd.write('DEVICE.nc')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"with open('RUN.fdf', 'w') as f:\n",
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" f.write(\"\"\"\n",
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"TBT.k [ 3 1 1 ]\n",
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"\n",
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"TBT.DOS.A\n",
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"TBT.Current.Orb\n",
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"\n",
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"TBT.HS DEVICE.nc\n",
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"%block TBT.Elec.Left\n",
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" HS ELEC.nc\n",
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" semi-inf-direction -a2\n",
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" electrode-position 1\n",
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"%endblock\n",
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"%block TBT.Elec.Right\n",
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" HS ELEC.nc\n",
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" semi-inf-direction +a2\n",
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" electrode-position end -1\n",
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"%endblock\n",
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" \"\"\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Run these two executables:\n",
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"\n",
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" tbtrans -D TRS RUN.fdf\n",
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" tbtrans -D NO_TRS -fdf TBT.Symmetry.TimeReversal:f RUN.fdf"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"trs = sisl.get_sile('TRS/siesta.TBT.nc')\n",
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"no_trs = sisl.get_sile('NO_TRS/siesta.TBT.nc')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"def plot_bond(tbt, E):\n",
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" xy = tbt.geometry.xyz[:, :2]\n",
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" vector = tbt.vector_current(0, E)[:, :2]\n",
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" atom = tbt.atom_current(0, E)\n",
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" # Normalize atomic current\n",
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" atom += 1\n",
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" atom *= 10 / atom.max()\n",
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" plt.scatter(xy[:, 0], xy[:, 1], atom);\n",
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" plt.quiver(xy[:, 0], xy[:, 1], vector[:, 0], vector[:, 1]);\n",
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" plt.gca().get_xaxis().set_visible(False)\n",
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" plt.gca().get_yaxis().set_visible(False)\n",
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" plt.tight_layout()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_bond(trs, 1.)\n",
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"plt.savefig('fig/trs.png')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"plot_bond(no_trs, 1.)\n",
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"plt.savefig('fig/no_trs.png')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 2",
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"language": "python",
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"name": "python2"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎presentations/02/chemical.tex‎

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%\node[fdf,ind] (NP-1) {contour.eq.pole.n $\langle \mathrm{int}\rangle_1$}; \\
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\node[fdf,ind] {contour.eq}; \\
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\node[fdf,iind] {begin}; \\
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\only<5->{
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\node[fdf,lmark,iiind] (C-chem-1) {C-chem-1}; \\
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\node[fdf,lmark,iiind] (L-chem-1) {L-chem-1}; \\
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}
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\only<1-4>{
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\node[fdf,iiind] (C-chem-1) {C-chem-1}; \\
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\node[fdf,iiind] (L-chem-1) {L-chem-1}; \\
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}
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\node[fdf,iind] {end}; \\
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\node[fdf] {\%endblock}; \\
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};

‎presentations/02/negf.tex‎

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xlabel={Energy [eV]},
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ylabel={Weight}]
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\only<1>{
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\addplot[gen,good,domain=-.3:.3,samples=25] {1./(exp((x-0.25)/0.01) + 1)-
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1./(exp((x+0.25)/0.01) + 1)};
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\addplot[gen,bad,domain=-.55:.55,samples=30] {1./(exp((x-0.5)/0.01)
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%\addplot[gen,bad,domain=-.3:.3,samples=25] {1./(exp((x-0.25)/0.01) + 1)-
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% 1./(exp((x+0.25)/0.01) + 1)};
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\addplot[gen,good,domain=-.55:.55,samples=30] {1./(exp((x-0.5)/0.01)
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+ 1)- 1./(exp((x+0.5)/0.01) + 1)};
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\draw[<->,good,very thick] (axis cs:-.25, 0.3) -- (axis cs:.25,0.3) node[midway,above]
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{$n_F(\E+0.25\,\mathrm{eV}) - n_F(\E-0.25\,\mathrm{eV})$};
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\draw[<->,bad,very thick] (axis cs:-.5, 1.3) -- (axis cs:.5,1.3) node[midway,above]
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%\draw[<->,bad,very thick] (axis cs:-.25, 0.3) -- (axis cs:.25,0.3) node[midway,above]
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%{$n_F(\E+0.25\,\mathrm{eV}) - n_F(\E-0.25\,\mathrm{eV})$};
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\draw[<->,good,very thick] (axis cs:-.5, 1.3) -- (axis cs:.5,1.3) node[midway,above]
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{$n_F(\E+0.5\,\mathrm{eV}) - n_F(\E-0.5\,\mathrm{eV})$};
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\node[below left] at (rel axis cs:.9,.9) {2 different $\mu$};
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}

‎presentations/02/summary.tex‎

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\item Run TranSiesta on device at $V=0$
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\item \textbf{ENSURE CONVERGENCE}
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\item !!! \textbf{ENSURE CONVERGENCE} !!!
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\item Step-by-step increase/decrease the bias and copy the \texttt{siesta.TSDE} from
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the nearest lower bias to the folder for restart capability

‎presentations/02/talk.tex‎

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\tableofcontents
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\end{frame}
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\input steps.tex
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\input negf.tex
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\input contour.tex
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\input chemical.tex
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\input steps.tex
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\input summary.tex
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\end{document}

‎tutorial.ipynb‎

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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Help on method tile in module sisl.geometry:\n",
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"\n",
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"tile(self, reps, axis) unbound sisl.geometry.Geometry method\n",
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" Tile the geometry to create a bigger one\n",
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" \n",
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" The atomic indices are retained for the base structure.\n",
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" \n",
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" Parameters\n",
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" ----------\n",
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" reps : int\n",
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" number of tiles (repetitions)\n",
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" axis : int\n",
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" direction of tiling, 0, 1, 2 according to the cell-direction\n",
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" \n",
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" Examples\n",
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" --------\n",
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" >>> geom = Geometry([[0, 0, 0], [0.5, 0, 0]], sc=1.)\n",
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" >>> g = geom.tile(2,axis=0)\n",
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" >>> print(g.xyz)\n",
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" [[ 0. 0. 0. ]\n",
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" [ 0.5 0. 0. ]\n",
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" [ 1. 0. 0. ]\n",
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" [ 1.5 0. 0. ]]\n",
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" >>> g = geom.tile(2,0).tile(2,axis=1)\n",
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" >>> print(g.xyz)\n",
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" [[ 0. 0. 0. ]\n",
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" [ 0.5 0. 0. ]\n",
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" [ 1. 0. 0. ]\n",
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" [ 1.5 0. 0. ]\n",
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" [ 0. 1. 0. ]\n",
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" [ 0.5 1. 0. ]\n",
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" [ 1. 1. 0. ]\n",
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" [ 1.5 1. 0. ]]\n",
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" \n",
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" See Also\n",
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" --------\n",
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" repeat : equivalent but different ordering of final structure\n",
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"\n"
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]
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}
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],
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"source": [
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"%pdoc sisl.Geometry.tile\n",
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"help(sisl.Geometry.tile)"
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"- [Advanced 04](A04/run.ipynb) \n",
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" Create a 3rd nearest neighbour graphene model."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {

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