Merge pull request #82 from freude/develop

Develop
freude · Dec 19, 2019 · a653615 · a653615
2 parents ee7e300 + 1dcd768
commit a653615
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Showing 12 changed files with 249 additions and 258 deletions.
diff --git a/docs/Nanonet.pdf b/docs/Nanonet.pdf
diff --git a/docs/source/atom_chains.ipynb b/docs/source/atom_chains.ipynb
@@ -23,7 +23,8 @@
       "| |\\  | (_| | | | | (_) | |\\  |  __/ |_ \n",
       "|_| \\_|\\__,_|_| |_|\\___/|_| \\_|\\___|\\__|\n",
       "                                        \n",
-      "\n"
+      "\n",
+      "Vesion 1.0\n"
      ]
     }
    ],
@@ -43,7 +44,7 @@
    "source": [
     "## Adding new species\n",
     "\n",
-    "Let us define two atoms, called A and B, each has a silgle $s$ orbital and diffrrent energies -1 eV and -0.7 eV."
+    "Let us define two atoms, called A and B, each has a single $s$ orbital and diffrrent energies -1 eV and -0.7 eV."
    ]
   },
   {
@@ -58,22 +59,6 @@
     "b.add_orbital(title='s', energy=-0.7, )"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Now we define a set of of orbitals for tight-binding computations:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "tb.Orbitals.orbital_sets = {'A': a, 'B': b}"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -83,7 +68,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -103,7 +88,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +105,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -168,8 +153,8 @@
       "---------------------------------\n",
       "\n",
       "Unique distances: \n",
-      "    1. Ang between atoms A and B\n",
       "    1. Ang between atoms B and A\n",
+      "    1. Ang between atoms A and B\n",
       "---------------------------------\n",
       "\n"
      ]
@@ -181,7 +166,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -221,7 +206,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -252,7 +237,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -269,7 +254,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {

diff --git a/docs/source/bismuth_bulk.ipynb b/docs/source/bismuth_bulk.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Band structure of bulk bismuth"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -15,7 +22,8 @@
       "| |\\  | (_| | | | | (_) | |\\  |  __/ |_ \n",
       "|_| \\_|\\__,_|_| |_|\\___/|_| \\_|\\___|\\__|\n",
       "                                        \n",
-      "\n"
+      "\n",
+      "Vesion 1.0\n"
      ]
     }
    ],
@@ -24,6 +32,13 @@
     "from tb import set_tb_params, get_k_coords"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Below we set a LCAO sp3 basis set for Bi atoms."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
@@ -46,8 +61,14 @@
     "bi_orb.add_orbital(\"py\", energy=-0.486,\n",
     "                   principal=0, orbital=1, magnetic=1, spin=1)\n",
     "bi_orb.add_orbital(\"pz\", energy=-0.486,\n",
-    "                   principal=0, orbital=1, magnetic=0, spin=1)\n",
-    "Orbitals.orbital_sets = {'Bi': bi_orb}"
+    "                   principal=0, orbital=1, magnetic=0, spin=1)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The primitive cell of crystalline bismuth has two atoms:"
    ]
   },
   {
@@ -204,7 +225,7 @@
     {
      "data": {
       "text/plain": [
-       "<tb.hamiltonian.Hamiltonian at 0x7f1fb3f32470>"
+       "<tb.hamiltonian.Hamiltonian at 0x7f17b588ce48>"
       ]
      },
      "execution_count": 8,
@@ -282,7 +303,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -337,7 +358,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

diff --git a/docs/source/block_tridiagonal_and_sorting.ipynb b/docs/source/block_tridiagonal_and_sorting.ipynb
diff --git a/docs/source/bulk_silicon.ipynb b/docs/source/bulk_silicon.ipynb
@@ -52,7 +52,8 @@
       "| |\\  | (_| | | | | (_) | |\\  |  __/ |_ \n",
       "|_| \\_|\\__,_|_| |_|\\___/|_| \\_|\\___|\\__|\n",
       "                                        \n",
-      "\n"
+      "\n",
+      "Vesion 1.0\n"
      ]
     }
    ],
@@ -160,7 +161,7 @@
     {
      "data": {
       "text/plain": [
-       "<tb.hamiltonian.Hamiltonian at 0x7f810519c208>"
+       "<tb.hamiltonian.Hamiltonian at 0x7ff9855deb70>"
       ]
      },
      "execution_count": 4,
@@ -308,7 +309,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -360,7 +361,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

diff --git a/docs/source/chain_greens_function.ipynb b/docs/source/chain_greens_function.ipynb
diff --git a/docs/source/notebooks.rst b/docs/source/notebooks.rst
@@ -10,5 +10,5 @@ Learning by examples
    silicon_nanowire.ipynb
    bismuth_bulk.ipynb
    chain_greens_function.ipynb
-
+   block_tridiagonal_and_sorting.ipynb    
 
diff --git a/docs/source/silicon_nanowire.ipynb b/docs/source/silicon_nanowire.ipynb
@@ -31,7 +31,8 @@
       "| |\\  | (_| | | | | (_) | |\\  |  __/ |_ \n",
       "|_| \\_|\\__,_|_| |_|\\___/|_| \\_|\\___|\\__|\n",
       "                                        \n",
-      "\n"
+      "\n",
+      "Vesion 1.0\n"
      ]
     }
    ],
@@ -59,7 +60,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "The verbosity level is 2\n",
+      "The verbosity level is 1\n",
       "The radius of the neighbourhood is 2.4 Ang\n",
       "\n",
       "---------------------------------\n",
@@ -76,75 +77,10 @@
       "Si7    4.125000    1.375000    4.125000\n",
       "Si8    1.375000    4.125000    4.125000\n",
       "Si9    0.000000    5.500000    0.000000\n",
-      "Si10    2.750000    8.250000    0.000000\n",
-      "Si11    2.750000    5.500000    2.750000\n",
-      "Si12    0.000000    8.250000    2.750000\n",
-      "Si13    1.375000    6.875000    1.375000\n",
-      "Si14    4.125000    9.625000    1.375000\n",
-      "Si15    4.125000    6.875000    4.125000\n",
-      "Si16    1.375000    9.625000    4.125000\n",
-      "Si17    5.500000    0.000000    0.000000\n",
-      "Si18    8.250000    2.750000    0.000000\n",
-      "Si19    8.250000    0.000000    2.750000\n",
-      "Si20    5.500000    2.750000    2.750000\n",
-      "Si21    6.875000    1.375000    1.375000\n",
-      "Si22    9.625000    4.125000    1.375000\n",
-      "Si23    9.625000    1.375000    4.125000\n",
-      "Si24    6.875000    4.125000    4.125000\n",
-      "Si25    5.500000    5.500000    0.000000\n",
-      "Si26    8.250000    8.250000    0.000000\n",
-      "Si27    8.250000    5.500000    2.750000\n",
-      "Si28    5.500000    8.250000    2.750000\n",
-      "Si29    6.875000    6.875000    1.375000\n",
-      "Si30    9.625000    9.625000    1.375000\n",
-      "Si31    9.625000    6.875000    4.125000\n",
-      "Si32    6.875000    9.625000    4.125000\n",
-      "Si33   11.000000    2.750000    2.750000\n",
-      "Si34   11.000000    0.000000    0.000000\n",
-      "Si35   11.000000    8.250000    2.750000\n",
-      "Si36   11.000000    5.500000    0.000000\n",
-      " H1   11.859375    1.890625    1.890625\n",
-      " H2   11.859375    3.609375    3.609375\n",
-      " H3   -0.859375    1.890625    3.609375\n",
-      " H4   -0.859375    3.609375    1.890625\n",
-      " H5   -0.859375    0.859375    4.640625\n",
-      " H6   11.859375    7.390625    1.890625\n",
-      " H7   11.859375    9.109375    3.609375\n",
-      " H8   -0.859375    7.390625    3.609375\n",
-      " H9   -0.859375    9.109375    1.890625\n",
-      " H10   -0.859375    4.640625    0.859375\n",
-      " H11   11.859375    6.359375    0.859375\n",
-      " H12   11.859375    4.640625    4.640625\n",
-      " H13   -0.859375    6.359375    4.640625\n",
-      " H14   11.859375    0.859375    0.859375\n",
-      "Si37    2.750000   11.000000    2.750000\n",
-      "Si38    0.000000   11.000000    0.000000\n",
-      "Si39    8.250000   11.000000    2.750000\n",
-      "Si40    5.500000   11.000000    0.000000\n",
-      " H15    1.890625   -0.859375    3.609375\n",
-      " H16    3.609375   -0.859375    1.890625\n",
-      " H17    1.890625   11.859375    1.890625\n",
-      " H18    3.609375   11.859375    3.609375\n",
-      " H19    0.859375   -0.859375    4.640625\n",
-      " H20    7.390625   -0.859375    3.609375\n",
-      " H21    9.109375   -0.859375    1.890625\n",
-      " H22    7.390625   11.859375    1.890625\n",
-      " H23    9.109375   11.859375    3.609375\n",
-      " H24    4.640625   -0.859375    0.859375\n",
-      " H25    6.359375   11.859375    0.859375\n",
-      " H26    6.359375   -0.859375    4.640625\n",
-      " H27    4.640625   11.859375    4.640625\n",
-      " H28    0.859375   11.859375    0.859375\n",
-      "Si41   11.000000   11.000000    0.000000\n",
-      " H29   -0.859375   -0.859375    0.859375\n",
-      " H30   11.859375   11.859375    0.859375\n",
-      " H31   11.859375   -0.859375    4.640625\n",
-      " H32   -0.859375   11.859375    4.640625\n",
-      " H33   10.140625   11.859375    4.640625\n",
-      " H34   11.859375   10.140625    4.640625\n",
-      " H35   10.140625   -0.859375    0.859375\n",
-      " H36   -0.859375   10.140625    0.859375\n",
-      "\n",
+      "                  .                    \n",
+      "                  .                    \n",
+      "                  .                    \n",
+      "There are 69 more coordinates\n",
       "---------------------------------\n",
       "\n",
       "Basis set \n",
@@ -184,9 +120,9 @@
       "---------------------------------\n",
       "\n",
       "Unique distances: \n",
-      "    1.4885 Ang between atoms H and Si\n",
-      "    1.4885 Ang between atoms Si and H\n",
       "    2.3816 Ang between atoms Si and Si\n",
+      "    1.4885 Ang between atoms Si and H\n",
+      "    1.4885 Ang between atoms H and Si\n",
       "    1.4584 Ang between atoms H and H\n",
       "---------------------------------\n",
       "\n",
@@ -203,7 +139,7 @@
     "PRIMITIVE_CELL = [[0, 0, a_si]]\n",
     "tb.Orbitals.orbital_sets = {'Si': 'SiliconSP3D5S', 'H': 'HydrogenS'}\n",
     "\n",
-    "h = tb.Hamiltonian(xyz='../input_samples/SiNW2.xyz', nn_distance=2.4)\n",
+    "h = tb.Hamiltonian(xyz='../examples/input_samples/SiNW2.xyz', nn_distance=2.4)\n",
     "h.initialize()\n",
     "h.set_periodic_bc(PRIMITIVE_CELL)"
    ]
@@ -216,7 +152,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x7fde8b9a4ac8>"
+       "<matplotlib.image.AxesImage at 0x7f5db7bf2c88>"
       ]
      },
      "execution_count": 3,
@@ -274,7 +210,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -333,7 +269,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,