abitutorials/lobster.ipynb

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    "Back to the main [Index](index.ipynb) <a id=\"top\"></a>"
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   "source": [
    "# Analyzing Lobster output files with AbiPy"
   ]
  },
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   "source": [
    "This example shows how to analyze the output files\n",
    "produced by [Lobster](http://schmeling.ac.rwth-aachen.de/cohp)\n",
    "\n",
    "Use \n",
    "\n",
    "    abiopen.py FILE \n",
    "    \n",
    "with the `--expose` or `--print` for a command line interface\n",
    "and `--notebook` to generate a jupyter notebook from a lobster `FILE`.\n",
    "\n",
    "Note: The code in this notebook requires abipy >= 0.6\n",
    "\n",
    "## Table of Contents\n",
    "[[back to top](#top)]\n",
    "\n",
    "- [How to analyze the COHPCAR file](#How-to-analyze-the-COHPCAR-file)\n",
    "- [How to analyze the DOSCAR file](#How-to-analyze-the-DOSCAR-file)\n",
    "- [Analyzing all Lobster output files](#Analyzing-all-Lobster-output-files-with-LobsterAnalyzer)\n",
    "\n",
    "Let's start by importing the basic modules needed for this tutorial."
   ]
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    "# Use this at the beginning of your script so that your code will be compatible with python3\n",
    "from __future__ import print_function, division, unicode_literals\n",
    "\n",
    "import warnings \n",
    "warnings.filterwarnings(\"ignore\")  # Ignore warnings\n",
    "\n",
    "from abipy import abilab\n",
    "abilab.enable_notebook() # This line tells AbiPy we are running inside a notebook\n",
    "import abipy.data as abidata\n",
    "\n",
    "# This line configures matplotlib to show figures embedded in the notebook.\n",
    "# Replace `inline` with `notebook` in classic notebook\n",
    "%matplotlib inline   \n",
    "\n",
    "# Option available in jupyterlab. See https://github.com/matplotlib/jupyter-matplotlib\n",
    "#%matplotlib widget  "
   ]
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## How to analyze the COHPCAR file  \n",
    "[[back to top](#top)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
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   "outputs": [
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     "text": [
      "\n",
      "COHP: Number of energies: 401, from -14.035 to 6.015 (eV) with E_fermi set 0 (was 2.298)\n",
      "has_partial_projections: True, nsppol: 1\n",
      "Number of pairs: 2\n",
      "[0] Ga@0 --> As@1\n",
      "[1] As@1 --> Ga@0\n"
     ]
    }
   ],
   "source": [
    "# Path to one of the reference file shipped with AbiPy\n",
    "import os\n",
    "dirpath = os.path.join(abidata.dirpath, \"refs\", \"lobster_gaas\")\n",
    "filename = os.path.join(dirpath, \"GaAs_COHPCAR.lobster.gz\")\n",
    "\n",
    "# Open the COHPCAR.lobster file (same API for COOPCAR.lobster)\n",
    "cohp_file = abilab.abiopen(filename)\n",
    "print(cohp_file)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To plot the COHP averaged over all atom pairs specified:"
   ]
  },
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   "cell_type": "code",
   "execution_count": 12,
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   "source": [
    "cohp_file.plot(title=\"GaAs COHP\");"
   ]
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   "source": [
    "To plot the integrated COHP averaged over all atom pairs:"
   ]
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    "cohp_file.plot(what=\"i\", title=\"GaAs integrated COHP\");"
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   "source": [
    "To plot the total overlap for all sites listed in `from_site_index`"
   ]
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   "source": [
    "cohp_file.plot_site_pairs_total(from_site_index=[0, 1], title=\"COHP total overlap for site index 0\");"
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   "source": [
    "To plot partial crystal orbital projections for all sites listed in `from_site_index`:"
   ]
  },
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    "cohp_file.plot_site_pairs_partial(from_site_index=[0, 1], \n",
    "                                  title=\"COHP with orbital projections from site index 0\", \n",
    "                                  fontsize=6, tight_layout=True);"
   ]
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   "source": [
    "#cohp_file.plot_average_pairs(with_site_index=[0]);"
   ]
  },
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   "cell_type": "markdown",
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   "source": [
    "Use `abiopen` to open the MDF:"
   ]
  },
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## How to analyze the ICOHPLIST file  \n",
    "[[back to top](#top)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
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   "outputs": [
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     "text": [
      "Number of pairs: 2\n",
      "index0  index1 type0 type1  spin  average distance n_bonds    pair\n",
      "     0       1    Ga    As     0 -4.36062  2.49546    None  (0, 1)\n",
      "     1       0    As    Ga     0 -4.36062  2.49546    None  (1, 0)\n"
     ]
    }
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   "source": [
    "# Path to one of the AbiPy file\n",
    "dirpath = os.path.join(abidata.dirpath, \"refs\", \"lobster_gaas\")\n",
    "filename = os.path.join(dirpath, \"GaAs_ICOHPLIST.lobster.gz\")\n",
    "\n",
    "# Open the ICOHPCAR.lobster file.\n",
    "icohp_file = abilab.abiopen(filename)\n",
    "print(icohp_file)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## How to analyze the DOSCAR file  \n",
    "[[back to top](#top)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
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     "text": [
      "Number of energies: 401, from -14.035 to 6.015 (eV) with E_fermi set to 0 (was 2.298)\n",
      "nsppol: 1\n",
      "Number of sites in projected DOS: 2\n",
      "0 --> {4s, 4p_y, 4p_z, 4p_x}\n",
      "1 --> {4s, 4p_y, 4p_z, 4p_x}\n"
     ]
    }
   ],
   "source": [
    "dirpath = os.path.join(abidata.dirpath, \"refs\", \"lobster_gaas\")\n",
    "filename = os.path.join(dirpath, \"GaAs_DOSCAR.lobster.gz\")\n",
    "\n",
    "# Open the ICOHPCAR.lobster file.\n",
    "doscar = abilab.abiopen(filename)\n",
    "print(doscar)"
   ]
  },
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   "execution_count": 19,
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   "source": [
    "doscar.plot();"
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   "source": [
    "doscar.plot_pdos_site(site_index=[0, 1]);"
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   "source": [
    "## Analyzing all Lobster output files with LobsterAnalyzer\n",
    "[[back to top](#top)]\n",
    "\n",
    "Let's assume we have a directory with lobster output files \n",
    "for COOP, COHP, DOS and we need to produce plots showing all these results altogether.\n",
    "In this case, one can use the `LobsterAnalyzer` object and initialize it from the directory\n",
    "containing the output files."
   ]
  },
  {
   "cell_type": "code",
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     "text": [
      "================================= COOP File =================================\n",
      "Name: GaAs_COOPCAR.lobster.gz\n",
      "Directory: /Users/gmatteo/git_repos/abipy/abipy/data/refs/lobster_gaas\n",
      "Size: 23.04 kb\n",
      "Access Time: Mon Aug  6 01:15:08 2018\n",
      "Modification Time: Sat Jul 14 00:27:22 2018\n",
      "Change Time: Sat Jul 14 00:27:22 2018\n",
      "\n",
      "COOP: Number of energies: 401, from -14.035 to 6.015 (eV) with E_fermi set 0 (was 2.298)\n",
      "has_partial_projections: True, nsppol: 1\n",
      "Number of pairs: 2\n",
      "[0] Ga@0 --> As@1\n",
      "[1] As@1 --> Ga@0\n",
      "\n",
      "================================= COHP File =================================\n",
      "Name: GaAs_COHPCAR.lobster.gz\n",
      "Directory: /Users/gmatteo/git_repos/abipy/abipy/data/refs/lobster_gaas\n",
      "Size: 24.06 kb\n",
      "Access Time: Mon Aug  6 01:15:08 2018\n",
      "Modification Time: Sat Jul 14 00:27:22 2018\n",
      "Change Time: Sat Jul 14 00:27:22 2018\n",
      "\n",
      "COHP: Number of energies: 401, from -14.035 to 6.015 (eV) with E_fermi set 0 (was 2.298)\n",
      "has_partial_projections: True, nsppol: 1\n",
      "Number of pairs: 2\n",
      "[0] Ga@0 --> As@1\n",
      "[1] As@1 --> Ga@0\n",
      "\n",
      "============================== ICHOHPLIST File ==============================\n",
      "Number of pairs: 2\n",
      "index0  index1 type0 type1  spin  average distance n_bonds    pair\n",
      "     0       1    Ga    As     0 -4.36062  2.49546    None  (0, 1)\n",
      "     1       0    As    Ga     0 -4.36062  2.49546    None  (1, 0)\n",
      "\n",
      "=============================== Lobster DOSCAR ===============================\n",
      "Number of energies: 401, from -14.035 to 6.015 (eV) with E_fermi set to 0 (was 2.298)\n",
      "nsppol: 1\n",
      "Number of sites in projected DOS: 2\n",
      "0 --> {4s, 4p_y, 4p_z, 4p_x}\n",
      "1 --> {4s, 4p_y, 4p_z, 4p_x}\n",
      "\n"
     ]
    }
   ],
   "source": [
    "dirpath = os.path.join(abidata.dirpath, \"refs\", \"lobster_gaas\")\n",
    "\n",
    "# Open the all the lobster files produced in directory dirpath\n",
    "# with the (optional) prefix GaAs_\n",
    "lobana = abilab.LobsterAnalyzer.from_dir(dirpath, prefix=\"GaAs_\")\n",
    "print(lobana.to_string(verbose=1))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To plot COOP + COHP + DOS, use:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
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   "source": [
    "lobana.plot(title=\"COOP + COHP + DOS\");"
   ]
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To plot COHP for all sites in from_site_index and Lobster DOS:"
   ]
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   "source": [
    "lobana.plot_coxp_with_dos(from_site_index=[0, 1]);"
   ]
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      "text/html": [
       "<p>Failed to display Jupyter Widget of type <code>FigureCanvasNbAgg</code>.</p>\n",
       "<p>\n",
       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
       "  that the widgets JavaScript is still loading. If this message persists, it\n",
       "  likely means that the widgets JavaScript library is either not installed or\n",
       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
       "  Widgets Documentation</a> for setup instructions.\n",
       "</p>\n",
       "<p>\n",
       "  If you're reading this message in another frontend (for example, a static\n",
       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
       "  it may mean that your frontend doesn't currently support widgets.\n",
       "</p>\n"
      ],
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       "FigureCanvasNbAgg()"
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     "metadata": {},
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   ],
   "source": [
    "# Plot orbital projections.\n",
    "lobana.plot_coxp_with_dos(from_site_index=[0], with_orbitals=True);"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#lobana.plot_with_ebands(ebands=\"out_GSR.nc\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<div class=\"alert alert-info\" role=\"alert\">\n",
    "For a command line interface, use: `abiview.py lobster .`.\n",
    "Use the `--expose` option to generate plots automatically.\n",
    "</div>\n",
    "\n",
    "Back to the main [Index](index.ipynb)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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