diff --git a/A_01/run.ipynb b/A_01/run.ipynb index e415093..52412d9 100644 --- a/A_01/run.ipynb +++ b/A_01/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -46,7 +45,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/A_02/run.ipynb b/A_02/run.ipynb index d291dae..37458a0 100644 --- a/A_02/run.ipynb +++ b/A_02/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -146,7 +145,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/A_03/run.ipynb b/A_03/run.ipynb index 8eca9df..a580211 100644 --- a/A_03/run.ipynb +++ b/A_03/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -50,7 +49,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/A_04/run.ipynb b/A_04/run.ipynb index 3723b0c..f265025 100644 --- a/A_04/run.ipynb +++ b/A_04/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -82,7 +81,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/A_05/run.ipynb b/A_05/run.ipynb index 6553878..91150d3 100644 --- a/A_05/run.ipynb +++ b/A_05/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -170,7 +169,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/S_01/run.ipynb b/S_01/run.ipynb index 2917dfb..5d95358 100644 --- a/S_01/run.ipynb +++ b/S_01/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -133,7 +132,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/S_02/run.ipynb b/S_02/run.ipynb index 8068b18..9d3510a 100644 --- a/S_02/run.ipynb +++ b/S_02/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -166,7 +165,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/S_03/run.ipynb b/S_03/run.ipynb index 6fd15e9..b2978d1 100644 --- a/S_03/run.ipynb +++ b/S_03/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -126,7 +125,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TB_01/run.ipynb b/TB_01/run.ipynb index e653faa..06e89ce 100644 --- a/TB_01/run.ipynb +++ b/TB_01/run.ipynb @@ -13,7 +13,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -376,7 +375,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TB_02/run.ipynb b/TB_02/run.ipynb index d630ef6..471b735 100644 --- a/TB_02/run.ipynb +++ b/TB_02/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -319,7 +318,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TB_03/run.ipynb b/TB_03/run.ipynb index 1fce6eb..1350024 100644 --- a/TB_03/run.ipynb +++ b/TB_03/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -203,7 +202,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TB_04/run.ipynb b/TB_04/run.ipynb index 09248d8..ae0489a 100644 --- a/TB_04/run.ipynb +++ b/TB_04/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -319,7 +318,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TB_05/run.ipynb b/TB_05/run.ipynb index 3d726de..6e58990 100644 --- a/TB_05/run.ipynb +++ b/TB_05/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "from matplotlib import animation\n", @@ -237,7 +236,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TB_06/run.ipynb b/TB_06/run.ipynb index 4a1e75e..efe82a6 100644 --- a/TB_06/run.ipynb +++ b/TB_06/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -377,7 +376,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TB_07/run.ipynb b/TB_07/run.ipynb index 2f5b5d7..b976344 100644 --- a/TB_07/run.ipynb +++ b/TB_07/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import math\n", "import sisl\n", "import numpy as np\n", @@ -291,7 +290,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TB_08/run.ipynb b/TB_08/run.ipynb index 2a845e7..a795166 100644 --- a/TB_08/run.ipynb +++ b/TB_08/run.ipynb @@ -6,13 +6,11 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import math\n", "import tqdm\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", - "from functools import partial\n", "%matplotlib inline" ] }, @@ -23,12 +21,15 @@ "In TBtrans and TranSiesta one is capable of performing real space transport calculations by using real space self-energies (see [here](https://doi.org/10.1103/PhysRevB.100.195417)). \n", "Currently the real space self-energy calculation *has* to be performed in `sisl` since it is not implemented in TranSiesta.\n", "\n", + "A real space self-energy is a $\\mathbf k$ averaged self-energy which can emulate *any* 2D or 3D electrode. I.e. for an STM junction a tip and a surface. In such a system the surface could be modelled using the real space self-energy to remove mirror effects of STM tips.\n", + "\n", "The basic principle for calculating the real space self-energy is the Brillouin zone integral:\n", "\\begin{equation}\n", " \\mathbf G_{\\mathcal R}(E) = \\int_{\\mathrm{BZ}}\\mathbf G_\\mathbf k\n", "\\end{equation}\n", "In this example we will construct an STM tip probing a graphene flake.\n", "\n", + "\n", "---\n", "\n", "We start by creating the graphene tight-binding model." diff --git a/TS_01/run.ipynb b/TS_01/run.ipynb index a36c7ad..267d1d1 100644 --- a/TS_01/run.ipynb +++ b/TS_01/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -157,7 +156,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TS_02/run.ipynb b/TS_02/run.ipynb index 18a1748..5380c60 100644 --- a/TS_02/run.ipynb +++ b/TS_02/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -201,7 +200,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TS_03/run.ipynb b/TS_03/run.ipynb index c3a29a9..298a2d0 100644 --- a/TS_03/run.ipynb +++ b/TS_03/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -107,7 +106,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TS_04/run.ipynb b/TS_04/run.ipynb index fabb4b8..53563b9 100644 --- a/TS_04/run.ipynb +++ b/TS_04/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -297,7 +296,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/TS_05/run.ipynb b/TS_05/run.ipynb index d522e4f..7f17a2e 100644 --- a/TS_05/run.ipynb +++ b/TS_05/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -133,7 +132,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/presentations/01/run.ipynb b/presentations/01/run.ipynb index a6b0248..546f4d4 100644 --- a/presentations/01/run.ipynb +++ b/presentations/01/run.ipynb @@ -6,7 +6,6 @@ "metadata": {}, "outputs": [], "source": [ - "from __future__ import print_function\n", "import sisl\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", @@ -135,21 +134,21 @@ ], "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": "3.7.3" } }, "nbformat": 4, diff --git a/tutorial.ipynb b/tutorial.ipynb index 00f330d..aa37b2f 100644 --- a/tutorial.ipynb +++ b/tutorial.ipynb @@ -78,7 +78,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "All tutorials are hosted online [here (version 2018)](https://github.com/zerothi/ts-tbt-sisl-tutorial/tree/2018)." + "All tutorials are hosted online [here (version 2020)](https://github.com/zerothi/ts-tbt-sisl-tutorial/tree/2020)." ] }, { @@ -125,7 +125,10 @@ "- [TB 7](TB_07/run.ipynb) \n", " Advanced exercise of *manipulation* of a predefined Hamiltonian. This example will cover how to add a magnetic field to a tight-binding Hamiltonian. This may be accomblished by using the $\\delta\\mathbf H$/$\\delta\\boldsymbol\\Sigma$ method.\n", " \n", - " \n", + "- [TB 8](TB_08/run.ipynb) \n", + " Advanced exercise for creating *real space self-energies*. This example will cover how to remove $\\mathbf k$-point sampling using real space methods.\n", + "\n", + "\n", "### Siesta\n", "\n", "Siesta has many utilities to post-process output such as, calculating DOS from the eigenspectrum, analyzing real-space charge and plotting molecular orbitals/wavefunctions (for experienced Siesta users `denchar` should be a familiar name). These tutorials shows how to use `sisl` to do the same analysis. It may be useful to read [this page](http://zerothi.github.io/sisl/docs/latest/api-generated/sisl.io.html#siesta-siesta) which contains the current list of files that `sisl` may interact with.\n", @@ -200,7 +203,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.7.3" } }, "nbformat": 4,