{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# Phonon calculations with small displacement method\n\nSimple example showing how to calculate the phonon dispersion for bulk aluminum\nusing a 5x5x5 supercell within effective medium theory:\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import matplotlib.pyplot as plt\nimport numpy as np\n\nfrom ase.build import bulk\nfrom ase.calculators.emt import EMT\nfrom ase.phonons import Phonons"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Setup Al crystal\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "atoms = bulk('Al', 'fcc', a=4.05)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Setup phonon calculation with EMT calculator\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "N = 5\nph = Phonons(\n    atoms,\n    EMT(),\n    supercell=(N, N, N),\n    use_mean_minimum_images=True,\n    minimum_image_tol=1e-6,\n)\nph.run()"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Read forces and assemble the dynamical matrix\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "ph.read()\nph.clean()"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Set and plot phonon band-structure along specific path\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "path = atoms.cell.bandpath('GXULGK', npoints=100)\nbs = ph.get_band_structure(path)\n\n# Get phonon DoS\ndos = ph.get_dos(kpts=(20, 20, 20)).sample_grid(npts=100, width=1e-3)\nfig = plt.figure(figsize=(7, 4))\nax = fig.add_axes([0.12, 0.07, 0.67, 0.85])\n\n# Plot phonon band structure and DoS\nemax = 0.035\nbs.plot(ax=ax, emin=0.0, emax=emax)\n\ndosax = fig.add_axes([0.8, 0.07, 0.17, 0.85])\ndosax.fill_between(\n    dos.get_weights(),\n    dos.get_energies(),\n    y2=0,\n    color='grey',\n    edgecolor='k',\n    lw=1,\n)\n\ndosax.set_ylim(0, emax)\ndosax.set_yticks([])\ndosax.set_xticks([])\ndosax.set_xlabel('DoS', fontsize=18)\nplt.show()\n\n# fig.savefig('Al_phonon.png')"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "You can visualize the modes with the following script:\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "# Write modes for specific q-vector to trajectory file\nL = np.array(path.special_points['L'])\nph.write_modes(\n    L / 2.0,\n    branches=[2],\n    repeat=(8, 8, 8),\n    kT=3e-4,\n    center=True,\n)\n\n# Optionally, generate gif animation\n\n# from ase.io.trajectory import Trajectory\n# from ase.io import write\n\n# Temporarily disabled due to matplotlib writer compatibility issue.\n# with Trajectory('phonon.mode.2.traj', 'r') as traj:\n#    write('Al_mode.gif', traj, interval=50,\n#           rotation='-36x,26.5y,-25z')"
      ]
    }
  ],
  "metadata": {
    "kernelspec": {
      "display_name": "Python 3",
      "language": "python",
      "name": "python3"
    },
    "language_info": {
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
      },
      "file_extension": ".py",
      "mimetype": "text/x-python",
      "name": "python",
      "nbconvert_exporter": "python",
      "pygments_lexer": "ipython3",
      "version": "3.14.5"
    }
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  "nbformat": 4,
  "nbformat_minor": 0
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