{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Simple Metallic Chain\n",
    "\n",
    "This notebook demonstrates a quantum transport calculation using the JunPy package. The goal is to compute the density of states and transmission values for a two-probe device. We manually construct the tight-binding Hamiltonian by setting the onsite energies and hopping parameters.\n",
    "\n",
    "## Import Necessary Libraries\n",
    "\n",
    "We use the built-in module `junpy.factory.stack` to create a simple two-probe device and its tight-binding Hamiltonian."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import junpy as jp\n",
    "from junpy.factory import stack\n",
    "%config InlineBackend.figure_format = 'svg'\n",
    "%config InlineBackend.rc = {'font.size': 12}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Build Device\n",
    "\n",
    "For demonstration, we assume there are 3 sites in the central region and 1 site in each of the left and right electrode unit cells. The spin-polarized onsite energies for each site are set to `np.array([[-0.5, 0], [0, 0.5]])`, where `-0.5` corresponds to spin-up and `0.5` corresponds to spin-down. The hopping energies are set to `-1`. The spin polarization angles are aligned along the $z$ direction, with values set to `0` radians."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# on-site energy\n",
    "eA = np.array([[-0.5, 0], [0, 0.5]])\n",
    "eB = np.array([[-0.5, 0], [0, 0.5]])\n",
    "eC = np.array([[-0.5, 0], [0, 0.5]])\n",
    "\n",
    "# hopping energy\n",
    "t = np.array([[-1, 0], [0, -1]])\n",
    "\n",
    "# spin polarization angle in unit of radian\n",
    "sA, sB, sC,  = 0, 0, 0"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We first create an empty builder using `stack.TwoProbeDeviceBuilder()` to construct the device:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "builder = stack.TwoProbeDeviceBuilder()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The following statements construct the Hamiltonian parameters for the two-probe device. Here, `builder.L`, `builder.C`, and `builder.R` represent the left, central, and right regions, respectively. The left and right regions are semi-infinite electrodes. To construct the Fermi function, we need to set the reservoir chemical potential and temperature. In this example, the reservoir chemical potentials are set to `0`, and the temperatures are set to `100` K. For each region, the `add(energy, hopping, nsites, spin, bias)` function is used to create a layer containing the Hamiltonian parameters. Here, `energy` refers to the onsite energy, `hopping` specifies the hopping energy, `nsites` is the number of sites in the layer, `spin` is the spin polarization angle in radians, and `bias` represents the energy shift of the onsite energy."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# left electrode\n",
    "builder.L.set(chemicalPotential=0, temperature=100)\n",
    "builder.L.add(eA, t, nsites=1, spin=sA, bias=0)\n",
    "\n",
    "# central region\n",
    "builder.C.add(eA, t, nsites=1, spin=sA, bias=0)\n",
    "builder.C.add(eB, t, nsites=3, spin=sB, bias=0)\n",
    "builder.C.add(eC, t, nsites=1, spin=sC, bias=0)\n",
    "\n",
    "# right electrode\n",
    "builder.R.set(chemicalPotential=0, temperature=100)\n",
    "builder.R.add(eC, t, nsites=1, spin=sC, bias=0)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The coupling energies between the layers also need to be specified. We assume that all coupling energies are set to `t`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# define coupling between layers\n",
    "builder.set_layer_coupling(all=t)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The default transport direction is the $z$ direction. To construct a 2D or 3D device, we can set the translation symmetry in the $x$ and $y$ directions. In this example, we construct a simple 1D two-probe device, so the translation symmetry is disabled."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# define translation symmetry\n",
    "builder.set_translationSymmetry(x=False, y=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Once the construction is finished, use `create_device` to build the device."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# create device\n",
    "device = builder.create_device()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Calculate Density of States"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "tags": [
     "hide-output"
    ]
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "JunPy version---------------------------: 0.15.0.post29+ga5b3260\n",
      "Parallelization information\n",
      "    BLAS Vendor-----------------------------: MKL\n",
      "    Total number of MPI processes-----------: 1\n",
      "    OMP_NUM_THREADS-------------------------: 1\n",
      "    MKL_NUM_THREADS-------------------------: unset\n",
      "    OPENBLAS_NUM_THREADS--------------------: unset\n",
      "Calculating density of states... (2024-08-14 20:01:57)\n",
      "    Device information\n",
      "        bias (mu2-mu1)--------------------------: 0\n",
      "        central.numberOfSites-------------------: 5\n",
      "        central.spinType------------------------: SpinType.GeneralSpin\n",
      "        lead1.numberOfSites---------------------: 1\n",
      "        lead1.spinType--------------------------: SpinType.GeneralSpin\n",
      "        lead1.direction-------------------------: -3\n",
      "        lead1.temperature-----------------------: 100\n",
      "        lead1.chemicalPotential-----------------: 0\n",
      "        lead2.numberOfSites---------------------: 1\n",
      "        lead2.spinType--------------------------: SpinType.GeneralSpin\n",
      "        lead2.direction-------------------------: 3\n",
      "        lead2.temperature-----------------------: 100\n",
      "        lead2.chemicalPotential-----------------: 0\n",
      "    Energy sampling\n",
      "        samplingName----------------------------: CustomSampling\n",
      "        range-----------------------------------: [-3.0000e+00, 3.0000e+00]\n",
      "        number----------------------------------: 61\n",
      "    K-space sampling\n",
      "        samplingName----------------------------: SymmetryKspaceSampling\n",
      "        gridNumber------------------------------: (1, 1, 1)\n",
      "        isTimeReversalSymmetry------------------: True\n",
      "        numReducedKpoints-----------------------: 1\n",
      "    Runtime message\n",
      "        Integrate over energy and k-space...\n",
      "            Start MPI execution...\n",
      "            -->   6.6% finished (Elapsed time: 0:00:00.004573)\n",
      "            -->  11.5% finished (Elapsed time: 0:00:00.001699)\n",
      "            -->  16.4% finished (Elapsed time: 0:00:00.001630)\n",
      "            -->  21.3% finished (Elapsed time: 0:00:00.001487)\n",
      "            -->  26.2% finished (Elapsed time: 0:00:00.001480)\n",
      "            -->  31.1% finished (Elapsed time: 0:00:00.001430)\n",
      "            -->  36.1% finished (Elapsed time: 0:00:00.001932)\n",
      "            -->  41.0% finished (Elapsed time: 0:00:00.001499)\n",
      "            -->  45.9% finished (Elapsed time: 0:00:00.001404)\n",
      "            -->  50.8% finished (Elapsed time: 0:00:00.001315)\n",
      "            -->  55.7% finished (Elapsed time: 0:00:00.001314)\n",
      "            -->  60.7% finished (Elapsed time: 0:00:00.001766)\n",
      "            -->  65.6% finished (Elapsed time: 0:00:00.001617)\n",
      "            -->  70.5% finished (Elapsed time: 0:00:00.001195)\n",
      "            -->  75.4% finished (Elapsed time: 0:00:00.001387)\n",
      "            -->  80.3% finished (Elapsed time: 0:00:00.001412)\n",
      "            -->  85.2% finished (Elapsed time: 0:00:00.001434)\n",
      "            -->  90.2% finished (Elapsed time: 0:00:00.001451)\n",
      "            -->  95.1% finished (Elapsed time: 0:00:00.001334)\n",
      "            --> 100.0% finished (Elapsed time: 0:00:00.001556)\n",
      "            Wait for other processes...\n",
      "            --> finished (Elapsed time: 0:00:00.000186)\n",
      "            Gather results from other processes...\n",
      "            --> finished (Elapsed time: 0:00:00.000293)\n",
      "    Density of states report\n",
      "            Energy_eV       D_up-up       D_dn-dn    D_Re-up-dn    D_Im-up-dn\n",
      "        -3.000000e+00  1.256112e-03  9.353190e-05  0.000000e+00  0.000000e+00\n",
      "        -2.900000e+00  2.050678e-03  1.113836e-04  0.000000e+00  0.000000e+00\n",
      "        -2.800000e+00  3.807053e-03  1.340980e-04  0.000000e+00  0.000000e+00\n",
      "        -2.700000e+00  8.907812e-03  1.634881e-04  0.000000e+00  0.000000e+00\n",
      "        -2.600000e+00  3.611755e-02  2.022652e-04  0.000000e+00  0.000000e+00\n",
      "        -2.500000e+00  5.699298e+00  2.546209e-04  0.000000e+00  0.000000e+00\n",
      "        -2.400000e+00  2.635411e+00  3.272927e-04  0.000000e+00  0.000000e+00\n",
      "        -2.300000e+00  1.839267e+00  4.316354e-04  0.000000e+00  0.000000e+00\n",
      "        -2.200000e+00  1.511842e+00  5.879337e-04  0.000000e+00  0.000000e+00\n",
      "        -2.100000e+00  1.326195e+00  8.352035e-04  0.000000e+00  0.000000e+00\n",
      "        -2.000000e+00  1.203896e+00  1.256112e-03  0.000000e+00  0.000000e+00\n",
      "        -1.900000e+00  1.115984e+00  2.050678e-03  0.000000e+00  0.000000e+00\n",
      "        -1.800000e+00  1.049216e+00  3.807053e-03  0.000000e+00  0.000000e+00\n",
      "        -1.700000e+00  9.966793e-01  8.907812e-03  0.000000e+00  0.000000e+00\n",
      "        -1.600000e+00  9.544100e-01  3.611755e-02  0.000000e+00  0.000000e+00\n",
      "        -1.500000e+00  9.199549e-01  5.699298e+00  0.000000e+00  0.000000e+00\n",
      "        -1.400000e+00  8.916953e-01  2.635411e+00  0.000000e+00  0.000000e+00\n",
      "        -1.300000e+00  8.685007e-01  1.839267e+00  0.000000e+00  0.000000e+00\n",
      "        -1.200000e+00  8.495421e-01  1.511842e+00  0.000000e+00  0.000000e+00\n",
      "        -1.100000e+00  8.341881e-01  1.326195e+00  0.000000e+00  0.000000e+00\n",
      "        -1.000000e+00  8.219456e-01  1.203896e+00  0.000000e+00  0.000000e+00\n",
      "        -9.000000e-01  8.124258e-01  1.115984e+00  0.000000e+00  0.000000e+00\n",
      "        -8.000000e-01  8.053250e-01  1.049216e+00  0.000000e+00  0.000000e+00\n",
      "        -7.000000e-01  8.004137e-01  9.966793e-01  0.000000e+00  0.000000e+00\n",
      "        -6.000000e-01  7.975308e-01  9.544100e-01  0.000000e+00  0.000000e+00\n",
      "        -5.000000e-01  7.965804e-01  9.199549e-01  0.000000e+00  0.000000e+00\n",
      "        -4.000000e-01  7.975308e-01  8.916953e-01  0.000000e+00  0.000000e+00\n",
      "        -3.000000e-01  8.004137e-01  8.685007e-01  0.000000e+00  0.000000e+00\n",
      "        -2.000000e-01  8.053250e-01  8.495421e-01  0.000000e+00  0.000000e+00\n",
      "        -1.000000e-01  8.124258e-01  8.341881e-01  0.000000e+00  0.000000e+00\n",
      "         0.000000e+00  8.219456e-01  8.219456e-01  0.000000e+00  0.000000e+00\n",
      "         1.000000e-01  8.341881e-01  8.124258e-01  0.000000e+00  0.000000e+00\n",
      "         2.000000e-01  8.495421e-01  8.053250e-01  0.000000e+00  0.000000e+00\n",
      "         3.000000e-01  8.685007e-01  8.004137e-01  0.000000e+00  0.000000e+00\n",
      "         4.000000e-01  8.916953e-01  7.975308e-01  0.000000e+00  0.000000e+00\n",
      "         5.000000e-01  9.199549e-01  7.965804e-01  0.000000e+00  0.000000e+00\n",
      "         6.000000e-01  9.544100e-01  7.975308e-01  0.000000e+00  0.000000e+00\n",
      "         7.000000e-01  9.966793e-01  8.004137e-01  0.000000e+00  0.000000e+00\n",
      "         8.000000e-01  1.049216e+00  8.053250e-01  0.000000e+00  0.000000e+00\n",
      "         9.000000e-01  1.115984e+00  8.124258e-01  0.000000e+00  0.000000e+00\n",
      "         1.000000e+00  1.203896e+00  8.219456e-01  0.000000e+00  0.000000e+00\n",
      "         1.100000e+00  1.326195e+00  8.341881e-01  0.000000e+00  0.000000e+00\n",
      "         1.200000e+00  1.511842e+00  8.495421e-01  0.000000e+00  0.000000e+00\n",
      "         1.300000e+00  1.839267e+00  8.685007e-01  0.000000e+00  0.000000e+00\n",
      "         1.400000e+00  2.635411e+00  8.916953e-01  0.000000e+00  0.000000e+00\n",
      "         1.500000e+00  5.699298e+00  9.199549e-01  0.000000e+00  0.000000e+00\n",
      "         1.600000e+00  3.611755e-02  9.544100e-01  0.000000e+00  0.000000e+00\n",
      "         1.700000e+00  8.907812e-03  9.966793e-01  0.000000e+00  0.000000e+00\n",
      "         1.800000e+00  3.807053e-03  1.049216e+00  0.000000e+00  0.000000e+00\n",
      "         1.900000e+00  2.050678e-03  1.115984e+00  0.000000e+00  0.000000e+00\n",
      "         2.000000e+00  1.256112e-03  1.203896e+00  0.000000e+00  0.000000e+00\n",
      "         2.100000e+00  8.352035e-04  1.326195e+00  0.000000e+00  0.000000e+00\n",
      "         2.200000e+00  5.879337e-04  1.511842e+00  0.000000e+00  0.000000e+00\n",
      "         2.300000e+00  4.316354e-04  1.839267e+00  0.000000e+00  0.000000e+00\n",
      "         2.400000e+00  3.272927e-04  2.635411e+00  0.000000e+00  0.000000e+00\n",
      "         2.500000e+00  2.546209e-04  5.699298e+00  0.000000e+00  0.000000e+00\n",
      "         2.600000e+00  2.022652e-04  3.611755e-02  0.000000e+00  0.000000e+00\n",
      "         2.700000e+00  1.634881e-04  8.907812e-03  0.000000e+00  0.000000e+00\n",
      "         2.800000e+00  1.340980e-04  3.807053e-03  0.000000e+00  0.000000e+00\n",
      "         2.900000e+00  1.113836e-04  2.050678e-03  0.000000e+00  0.000000e+00\n",
      "         3.000000e+00  9.353190e-05  1.256112e-03  0.000000e+00  0.000000e+00\n",
      "Calculation of density of states finished (2024-08-14 20:01:57)\n",
      "Elapsed time----------------------------: 0:00:00.054571\n"
     ]
    }
   ],
   "source": [
    "calcr_dos = jp.DensityOfStates(\n",
    "    device=device,\n",
    "    energies=np.linspace(-3, 3, 61),\n",
    "    kpoints=jp.SymmetryKspaceSampling((1,1,1)),\n",
    "    etaSigma=0.01)\n",
    "jp.run(calcr_dos, savefile=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
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   ],
   "source": [
    "# shape: (#kpoints, #energies, #spin)\n",
    "dos = calcr_dos.densityOfStates(spin='diag')\n",
    "\n",
    "plt.plot(calcr_dos.energies, dos[0,:,0], '.-', label='spin-up')\n",
    "plt.plot(calcr_dos.energies, dos[0,:,1], '.-', label='spin-down')\n",
    "plt.xlabel('Energy (eV)')\n",
    "plt.ylabel('DOS (1/eV)')\n",
    "plt.legend()\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Calculate Transmission"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "tags": [
     "hide-output"
    ]
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "JunPy version---------------------------: 0.15.0.post29+ga5b3260\n",
      "Parallelization information\n",
      "    BLAS Vendor-----------------------------: MKL\n",
      "    Total number of MPI processes-----------: 1\n",
      "    OMP_NUM_THREADS-------------------------: 1\n",
      "    MKL_NUM_THREADS-------------------------: unset\n",
      "    OPENBLAS_NUM_THREADS--------------------: unset\n",
      "Calculating transmission... (2024-08-14 20:02:20)\n",
      "    Device information\n",
      "        bias (mu2-mu1)--------------------------: 0\n",
      "        central.numberOfSites-------------------: 5\n",
      "        central.spinType------------------------: SpinType.GeneralSpin\n",
      "        lead1.numberOfSites---------------------: 1\n",
      "        lead1.spinType--------------------------: SpinType.GeneralSpin\n",
      "        lead1.direction-------------------------: -3\n",
      "        lead1.temperature-----------------------: 100\n",
      "        lead1.chemicalPotential-----------------: 0\n",
      "        lead2.numberOfSites---------------------: 1\n",
      "        lead2.spinType--------------------------: SpinType.GeneralSpin\n",
      "        lead2.direction-------------------------: 3\n",
      "        lead2.temperature-----------------------: 100\n",
      "        lead2.chemicalPotential-----------------: 0\n",
      "    Energy sampling\n",
      "        samplingName----------------------------: CustomSampling\n",
      "        range-----------------------------------: [-3.0000e+00, 3.0000e+00]\n",
      "        number----------------------------------: 61\n",
      "    K-space sampling\n",
      "        samplingName----------------------------: SymmetryKspaceSampling\n",
      "        gridNumber------------------------------: (1, 1, 1)\n",
      "        isTimeReversalSymmetry------------------: True\n",
      "        numReducedKpoints-----------------------: 1\n",
      "    Runtime message\n",
      "        Integrate over energy and k-space...\n",
      "            Start MPI execution...\n",
      "            -->   6.6% finished (Elapsed time: 0:00:00.003585)\n",
      "            -->  11.5% finished (Elapsed time: 0:00:00.001882)\n",
      "            -->  16.4% finished (Elapsed time: 0:00:00.001779)\n",
      "            -->  21.3% finished (Elapsed time: 0:00:00.002063)\n",
      "            -->  26.2% finished (Elapsed time: 0:00:00.001690)\n",
      "            -->  31.1% finished (Elapsed time: 0:00:00.001729)\n",
      "            -->  36.1% finished (Elapsed time: 0:00:00.002109)\n",
      "            -->  41.0% finished (Elapsed time: 0:00:00.002407)\n",
      "            -->  45.9% finished (Elapsed time: 0:00:00.001634)\n",
      "            -->  50.8% finished (Elapsed time: 0:00:00.001618)\n",
      "            -->  55.7% finished (Elapsed time: 0:00:00.001521)\n",
      "            -->  60.7% finished (Elapsed time: 0:00:00.001520)\n",
      "            -->  65.6% finished (Elapsed time: 0:00:00.001730)\n",
      "            -->  70.5% finished (Elapsed time: 0:00:00.002024)\n",
      "            -->  75.4% finished (Elapsed time: 0:00:00.001649)\n",
      "            -->  80.3% finished (Elapsed time: 0:00:00.001612)\n",
      "            -->  85.2% finished (Elapsed time: 0:00:00.001697)\n",
      "            -->  90.2% finished (Elapsed time: 0:00:00.002344)\n",
      "            -->  95.1% finished (Elapsed time: 0:00:00.001554)\n",
      "            --> 100.0% finished (Elapsed time: 0:00:00.001243)\n",
      "            Wait for other processes...\n",
      "            --> finished (Elapsed time: 0:00:00.000009)\n",
      "            Gather results from other processes...\n",
      "            --> finished (Elapsed time: 0:00:00.000113)\n",
      "    Transmission report\n",
      "            Energy_eV       T_up-up       T_dn-dn    T_Re-up-dn    T_Im-up-dn\n",
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      "        -2.800000e+00  1.073804e-10  1.618547e-14  0.000000e+00  0.000000e+00\n",
      "        -2.700000e+00  6.715972e-10  2.915862e-14  0.000000e+00  0.000000e+00\n",
      "        -2.600000e+00  1.020449e-08  5.441482e-14  0.000000e+00  0.000000e+00\n",
      "        -2.500000e+00  4.826224e-01  1.057711e-13  0.000000e+00  0.000000e+00\n",
      "        -2.400000e+00  1.000000e+00  2.156665e-13  0.000000e+00  0.000000e+00\n",
      "        -2.300000e+00  1.000000e+00  4.655865e-13  0.000000e+00  0.000000e+00\n",
      "        -2.200000e+00  1.000000e+00  1.077732e-12  0.000000e+00  0.000000e+00\n",
      "        -2.100000e+00  1.000000e+00  2.723300e-12  0.000000e+00  0.000000e+00\n",
      "        -2.000000e+00  1.000000e+00  7.716049e-12  0.000000e+00  0.000000e+00\n",
      "        -1.900000e+00  1.000000e+00  2.559462e-11  0.000000e+00  0.000000e+00\n",
      "        -1.800000e+00  1.000000e+00  1.073804e-10  0.000000e+00  0.000000e+00\n",
      "        -1.700000e+00  1.000000e+00  6.715972e-10  0.000000e+00  0.000000e+00\n",
      "        -1.600000e+00  1.000000e+00  1.020449e-08  0.000000e+00  0.000000e+00\n",
      "        -1.500000e+00  1.000000e+00  4.826224e-01  0.000000e+00  0.000000e+00\n",
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      "        -1.200000e+00  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
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      "        -1.000000e+00  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "        -9.000000e-01  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "        -8.000000e-01  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "        -7.000000e-01  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
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      "        -4.000000e-01  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "        -3.000000e-01  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
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      "        -1.000000e-01  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         0.000000e+00  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         1.000000e-01  1.000000e+00  1.000000e+00  0.000000e+00  0.000000e+00\n",
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      "         1.500000e+00  4.826224e-01  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         1.600000e+00  1.020449e-08  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         1.700000e+00  6.715972e-10  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         1.800000e+00  1.073804e-10  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         1.900000e+00  2.559462e-11  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         2.000000e+00  7.716049e-12  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         2.100000e+00  2.723300e-12  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         2.200000e+00  1.077732e-12  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         2.300000e+00  4.655865e-13  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         2.400000e+00  2.156665e-13  1.000000e+00  0.000000e+00  0.000000e+00\n",
      "         2.500000e+00  1.057711e-13  4.826224e-01  0.000000e+00  0.000000e+00\n",
      "         2.600000e+00  5.441482e-14  1.020449e-08  0.000000e+00  0.000000e+00\n",
      "         2.700000e+00  2.915862e-14  6.715972e-10  0.000000e+00  0.000000e+00\n",
      "         2.800000e+00  1.618547e-14  1.073804e-10  0.000000e+00  0.000000e+00\n",
      "         2.900000e+00  9.265870e-15  2.559462e-11  0.000000e+00  0.000000e+00\n",
      "         3.000000e+00  5.451332e-15  7.716049e-12  0.000000e+00  0.000000e+00\n",
      "Calculation of transmission finished (2024-08-14 20:02:20)\n",
      "Elapsed time----------------------------: 0:00:00.046322\n"
     ]
    }
   ],
   "source": [
    "calcr_trans = jp.Transmission(\n",
    "    device=device,\n",
    "    energies=np.linspace(-3, 3, 61),\n",
    "    kpoints=jp.SymmetryKspaceSampling((1,1,1)),\n",
    "    etaSigma=1e-4,\n",
    ")\n",
    "jp.run(calcr_trans, savefile=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
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   "source": [
    "# shape: (#kpoints, #energies, #spin)\n",
    "trans = calcr_trans.transmission(spin='diag')\n",
    "\n",
    "plt.plot(calcr_trans.energies, trans[0,:,0], '.-', label='spin-up')\n",
    "plt.plot(calcr_trans.energies, trans[0,:,1], '.-', label='spin-down')\n",
    "plt.xlabel('Energy (eV)')\n",
    "plt.ylabel('Transmission')\n",
    "plt.legend()\n",
    "plt.show()"
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