notebooks/2021-08-26-Magnetic Structure Generation as Input for Initial DFT Calculations.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "2feb87ef",
   "metadata": {},
   "source": [
    "# Magnetic Structure Generation as Input for Initial DFT Calculations\n",
    "\n",
    "_Author: Shivam Beniwal_\n",
    "\n",
    "Date: 26 August 2021"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f8548d15",
   "metadata": {},
   "source": [
    "## Introduction\n",
    "\n",
    "This notebook demonstrates a helpful method from the pymatgen magnetism analyzer module to add magnetic information to a structure as an input to a DFT run where the outcome of the calculation is dependent on the initial magnetic structure, and/or requires some magnetic moment as starting point. This can be extremely useful in case of newly predicted structures."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e167481e",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
    "# !pip install pymatgen==2022.7.19\n",
    "from __future__ import annotations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4622d496",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pymatgen.analysis.magnetism.analyzer import CollinearMagneticStructureAnalyzer\n",
    "from pymatgen.ext.matproj import MPRester\n",
    "from pymatgen.symmetry.analyzer import SpacegroupAnalyzer\n",
    "from pymatgen.util.testing import PymatgenTest"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "299fd4df",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Full Formula (Li4 Fe4 P4 O16)\n",
      "Reduced Formula: LiFePO4\n",
      "abc   :   4.744800   6.065770  10.410370\n",
      "angles:  90.501790  90.000190  90.003620\n",
      "pbc   :       True       True       True\n",
      "Sites (28)\n",
      "  #  SP          a        b        c\n",
      "---  ----  -------  -------  -------\n",
      "  0  Li    1e-05    0.99999  0.99999\n",
      "  1  Li    0.99999  0.5      1e-05\n",
      "  2  Li    0.49999  0.99999  0.5\n",
      "  3  Li    0.50002  0.5      0.5\n",
      "  4  Fe    0.52507  0.25344  0.21884\n",
      "  5  Fe    0.02508  0.74654  0.28116\n",
      "  6  Fe    0.97497  0.25346  0.71884\n",
      "  7  Fe    0.47493  0.74653  0.78116\n",
      "  8  P     0.58205  0.75169  0.09444\n",
      "  9  P     0.08207  0.2483   0.40556\n",
      " 10  P     0.91794  0.75174  0.59443\n",
      " 11  P     0.41793  0.24828  0.90557\n",
      " 12  O     0.29156  0.25112  0.04317\n",
      " 13  O     0.25851  0.75043  0.09622\n",
      " 14  O     0.71346  0.95594  0.1658\n",
      " 15  O     0.71627  0.5486   0.16562\n",
      " 16  O     0.21629  0.4514   0.33438\n",
      " 17  O     0.21345  0.04406  0.33419\n",
      " 18  O     0.75852  0.24955  0.40378\n",
      " 19  O     0.79157  0.7489   0.45682\n",
      " 20  O     0.20845  0.2511   0.54316\n",
      " 21  O     0.24149  0.75046  0.59622\n",
      " 22  O     0.78658  0.95602  0.66577\n",
      " 23  O     0.78367  0.54867  0.66564\n",
      " 24  O     0.28366  0.45133  0.83436\n",
      " 25  O     0.28658  0.04399  0.83423\n",
      " 26  O     0.74149  0.24958  0.90378\n",
      " 27  O     0.70842  0.74889  0.95684\n"
     ]
    }
   ],
   "source": [
    "# Specify location of CIF on your device\n",
    "structure = PymatgenTest.get_structure(\"LiFePO4\")\n",
    "print(structure)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e5fc1f62",
   "metadata": {},
   "source": [
    "## Add magmoms to initial structure\n",
    "\n",
    "Here we define magnetic moments of individual species present in the structure, if not already present. Refer to pymatgen [docs](https://pymatgen.org/pymatgen.analysis.magnetism.analyzer.html) for more information on options available for the argument overwrite_magmom_mode. Here we add magmoms for all sites in the structure irrespective of input structure, suitable for a spin-polarized (a.k.a 'magnetic') calculation.\n",
    "\n",
    "This is particularly interesting in case of either attempting a ferromagnetic calculation or an antiferromagnetic calculation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7c7b6ea0",
   "metadata": {},
   "outputs": [],
   "source": [
    "magmom = CollinearMagneticStructureAnalyzer(\n",
    "    structure, overwrite_magmom_mode=\"replace_all_if_undefined\"\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "94b18ea1",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Assume an initial ferromagnetic order\n",
    "fm_structure = magmom.get_ferromagnetic_structure(make_primitive=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "64729507",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Full Formula (Li4 Fe4 P4 O16)\n",
      "Reduced Formula: LiFePO4\n",
      "abc   :   4.744800   6.065770  10.410370\n",
      "angles:  90.501790  90.000190  90.003620\n",
      "pbc   :       True       True       True\n",
      "Sites (28)\n",
      "  #  SP          a        b        c    magmom\n",
      "---  ----  -------  -------  -------  --------\n",
      "  0  Li    1e-05    0.99999  0.99999         0\n",
      "  1  Li    0.99999  0.5      1e-05           0\n",
      "  2  Li    0.49999  0.99999  0.5             0\n",
      "  3  Li    0.50002  0.5      0.5             0\n",
      "  4  Fe    0.52507  0.25344  0.21884         5\n",
      "  5  Fe    0.02508  0.74654  0.28116         5\n",
      "  6  Fe    0.97497  0.25346  0.71884         5\n",
      "  7  Fe    0.47493  0.74653  0.78116         5\n",
      "  8  P     0.58205  0.75169  0.09444         0\n",
      "  9  P     0.08207  0.2483   0.40556         0\n",
      " 10  P     0.91794  0.75174  0.59443         0\n",
      " 11  P     0.41793  0.24828  0.90557         0\n",
      " 12  O     0.29156  0.25112  0.04317         0\n",
      " 13  O     0.25851  0.75043  0.09622         0\n",
      " 14  O     0.71346  0.95594  0.1658          0\n",
      " 15  O     0.71627  0.5486   0.16562         0\n",
      " 16  O     0.21629  0.4514   0.33438         0\n",
      " 17  O     0.21345  0.04406  0.33419         0\n",
      " 18  O     0.75852  0.24955  0.40378         0\n",
      " 19  O     0.79157  0.7489   0.45682         0\n",
      " 20  O     0.20845  0.2511   0.54316         0\n",
      " 21  O     0.24149  0.75046  0.59622         0\n",
      " 22  O     0.78658  0.95602  0.66577         0\n",
      " 23  O     0.78367  0.54867  0.66564         0\n",
      " 24  O     0.28366  0.45133  0.83436         0\n",
      " 25  O     0.28658  0.04399  0.83423         0\n",
      " 26  O     0.74149  0.24958  0.90378         0\n",
      " 27  O     0.70842  0.74889  0.95684         0\n"
     ]
    }
   ],
   "source": [
    "print(fm_structure)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "56698524",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Ordering.FM\n"
     ]
    }
   ],
   "source": [
    "order = magmom.ordering  # Useful if magnetic order is unknown or not user-defined\n",
    "print(order)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cb607211",
   "metadata": {},
   "source": [
    "## Get space group information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c3e09dbc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'2/m'"
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "spa = SpacegroupAnalyzer(structure)\n",
    "spa.get_point_group_symbol()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "10867b71",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'P2_1/c'"
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "spa.get_space_group_symbol()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4a8ec0de",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"# generated using pymatgen\\ndata_LiFePO4\\n_symmetry_space_group_name_H-M   'P 1'\\n_cell_length_a   4.74480000\\n_cell_length_b   6.06577000\\n_cell_length_c   10.41037000\\n_cell_angle_alpha   90.50179000\\n_cell_angle_beta   90.00019000\\n_cell_angle_gamma   90.00362000\\n_symmetry_Int_Tables_number   1\\n_chemical_formula_structural   LiFePO4\\n_chemical_formula_sum   'Li4 Fe4 P4 O16'\\n_cell_volume   299.60796771\\n_cell_formula_units_Z   4\\nloop_\\n _symmetry_equiv_pos_site_id\\n _symmetry_equiv_pos_as_xyz\\n  1  'x, y, z'\\nloop_\\n _atom_site_type_symbol\\n _atom_site_label\\n _atom_site_symmetry_multiplicity\\n _atom_site_fract_x\\n _atom_site_fract_y\\n _atom_site_fract_z\\n _atom_site_occupancy\\n  Li  Li0  1  0.00001000  0.99999000  0.99999000  1.0\\n  Li  Li1  1  0.99999000  0.50000000  0.00001000  1.0\\n  Li  Li2  1  0.49999000  0.99999000  0.50000000  1.0\\n  Li  Li3  1  0.50002000  0.50000000  0.50000000  1.0\\n  Fe  Fe4  1  0.52507000  0.25344000  0.21884000  1.0\\n  Fe  Fe5  1  0.02508000  0.74654000  0.28116000  1.0\\n  Fe  Fe6  1  0.97497000  0.25346000  0.71884000  1.0\\n  Fe  Fe7  1  0.47493000  0.74653000  0.78116000  1.0\\n  P  P8  1  0.58205000  0.75169000  0.09444000  1.0\\n  P  P9  1  0.08207000  0.24830000  0.40556000  1.0\\n  P  P10  1  0.91794000  0.75174000  0.59443000  1.0\\n  P  P11  1  0.41793000  0.24828000  0.90557000  1.0\\n  O  O12  1  0.29156000  0.25112000  0.04317000  1.0\\n  O  O13  1  0.25851000  0.75043000  0.09622000  1.0\\n  O  O14  1  0.71346000  0.95594000  0.16580000  1.0\\n  O  O15  1  0.71627000  0.54860000  0.16562000  1.0\\n  O  O16  1  0.21629000  0.45140000  0.33438000  1.0\\n  O  O17  1  0.21345000  0.04406000  0.33419000  1.0\\n  O  O18  1  0.75852000  0.24955000  0.40378000  1.0\\n  O  O19  1  0.79157000  0.74890000  0.45682000  1.0\\n  O  O20  1  0.20845000  0.25110000  0.54316000  1.0\\n  O  O21  1  0.24149000  0.75046000  0.59622000  1.0\\n  O  O22  1  0.78658000  0.95602000  0.66577000  1.0\\n  O  O23  1  0.78367000  0.54867000  0.66564000  1.0\\n  O  O24  1  0.28366000  0.45133000  0.83436000  1.0\\n  O  O25  1  0.28658000  0.04399000  0.83423000  1.0\\n  O  O26  1  0.74149000  0.24958000  0.90378000  1.0\\n  O  O27  1  0.70842000  0.74889000  0.95684000  1.0\\nloop_\\n _atom_site_moment_label\\n _atom_site_moment_crystalaxis_x\\n _atom_site_moment_crystalaxis_y\\n _atom_site_moment_crystalaxis_z\\n  Fe4  -5.00000000  0.00000000  0.00000000\\n  Fe5  -5.00000000  0.00000000  0.00000000\\n  Fe6  -5.00000000  0.00000000  0.00000000\\n  Fe7  -5.00000000  0.00000000  0.00000000\\n\""
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fm_structure.to(filename=\"lfp.mcif\")  # Save the structure in magCIF format."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8703b5d7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Full Formula (Li4 Fe4 P4 O16)\n",
      "Reduced Formula: LiFePO4\n",
      "abc   :   4.744800   6.065770  10.410370\n",
      "angles:  90.501790  90.000190  90.003620\n",
      "pbc   :       True       True       True\n",
      "Sites (28)\n",
      "  #  SP               a        b        c\n",
      "---  ---------  -------  -------  -------\n",
      "  0  Li,spin=0  1e-05    0.99999  0.99999\n",
      "  1  Li,spin=0  0.99999  0.5      1e-05\n",
      "  2  Li,spin=0  0.49999  0.99999  0.5\n",
      "  3  Li,spin=0  0.50002  0.5      0.5\n",
      "  4  Fe,spin=5  0.52507  0.25344  0.21884\n",
      "  5  Fe,spin=5  0.02508  0.74654  0.28116\n",
      "  6  Fe,spin=5  0.97497  0.25346  0.71884\n",
      "  7  Fe,spin=5  0.47493  0.74653  0.78116\n",
      "  8  P,spin=0   0.58205  0.75169  0.09444\n",
      "  9  P,spin=0   0.08207  0.2483   0.40556\n",
      " 10  P,spin=0   0.91794  0.75174  0.59443\n",
      " 11  P,spin=0   0.41793  0.24828  0.90557\n",
      " 12  O,spin=0   0.29156  0.25112  0.04317\n",
      " 13  O,spin=0   0.25851  0.75043  0.09622\n",
      " 14  O,spin=0   0.71346  0.95594  0.1658\n",
      " 15  O,spin=0   0.71627  0.5486   0.16562\n",
      " 16  O,spin=0   0.21629  0.4514   0.33438\n",
      " 17  O,spin=0   0.21345  0.04406  0.33419\n",
      " 18  O,spin=0   0.75852  0.24955  0.40378\n",
      " 19  O,spin=0   0.79157  0.7489   0.45682\n",
      " 20  O,spin=0   0.20845  0.2511   0.54316\n",
      " 21  O,spin=0   0.24149  0.75046  0.59622\n",
      " 22  O,spin=0   0.78658  0.95602  0.66577\n",
      " 23  O,spin=0   0.78367  0.54867  0.66564\n",
      " 24  O,spin=0   0.28366  0.45133  0.83436\n",
      " 25  O,spin=0   0.28658  0.04399  0.83423\n",
      " 26  O,spin=0   0.74149  0.24958  0.90378\n",
      " 27  O,spin=0   0.70842  0.74889  0.95684\n"
     ]
    }
   ],
   "source": [
    "spn_structure = (\n",
    "    magmom.get_structure_with_spin()\n",
    ")  # Returns spin decorated values in structure instead of magmom site properties\n",
    "print(spn_structure)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9dc72f40",
   "metadata": {},
   "source": [
    "The above structure is saved as a magCIF with .mcif extension. This can be converted back to a CIF with relevant magnetic information associated with each site. OpenBabel does this easily, on command line write-\n",
    "```\n",
    "obabel -imcif lfp.mcif -ocif -O lfp.cif \n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "130df9f1",
   "metadata": {},
   "source": [
    "## Analyze magnetic moment present in a calculated structure using MAPI\n",
    "\n",
    "In some cases, it might be useful to analyze magnetic behavior of a strucure from the Materials Project database. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e90dcfb8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "31adbcae7a3b46f6af0607be98587806",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Retrieving MaterialsDoc documents:   0%|          | 0/1 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Full Formula (Li4 Fe4 P4 O16)\n",
      "Reduced Formula: LiFePO4\n",
      "abc   :   4.744800   6.065770  10.410370\n",
      "angles:  90.501790  90.000190  90.003620\n",
      "pbc   :       True       True       True\n",
      "Sites (28)\n",
      "  #  SP          a        b        c\n",
      "---  ----  -------  -------  -------\n",
      "  0  Li    1e-05    0.99999  0.99999\n",
      "  1  Li    0.99999  0.5      1e-05\n",
      "  2  Li    0.49999  0.99999  0.5\n",
      "  3  Li    0.50002  0.5      0.5\n",
      "  4  Fe    0.52507  0.25344  0.21884\n",
      "  5  Fe    0.02508  0.74654  0.28116\n",
      "  6  Fe    0.97497  0.25346  0.71884\n",
      "  7  Fe    0.47493  0.74653  0.78116\n",
      "  8  P     0.58205  0.75169  0.09444\n",
      "  9  P     0.08207  0.2483   0.40556\n",
      " 10  P     0.91794  0.75174  0.59443\n",
      " 11  P     0.41793  0.24828  0.90557\n",
      " 12  O     0.29156  0.25112  0.04317\n",
      " 13  O     0.25851  0.75043  0.09622\n",
      " 14  O     0.71346  0.95594  0.1658\n",
      " 15  O     0.71627  0.5486   0.16562\n",
      " 16  O     0.21629  0.4514   0.33438\n",
      " 17  O     0.21345  0.04406  0.33419\n",
      " 18  O     0.75852  0.24955  0.40378\n",
      " 19  O     0.79157  0.7489   0.45682\n",
      " 20  O     0.20845  0.2511   0.54316\n",
      " 21  O     0.24149  0.75046  0.59622\n",
      " 22  O     0.78658  0.95602  0.66577\n",
      " 23  O     0.78367  0.54867  0.66564\n",
      " 24  O     0.28366  0.45133  0.83436\n",
      " 25  O     0.28658  0.04399  0.83423\n",
      " 26  O     0.74149  0.24958  0.90378\n",
      " 27  O     0.70842  0.74889  0.95684\n"
     ]
    }
   ],
   "source": [
    "# Establish rester for accessing Materials API\n",
    "mpr = MPRester()\n",
    "mp_id = \"mp-504263\"  # Previously reported structure; Co replaced at Fe site\n",
    "structure_from_mp = mpr.get_structure_by_material_id(mp_id)\n",
    "print(structure)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "eb53cc57",
   "metadata": {},
   "outputs": [],
   "source": [
    "mgmmnt = CollinearMagneticStructureAnalyzer(\n",
    "    structure_from_mp, overwrite_magmom_mode=\"replace_all_if_undefined\"\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ccedc00c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mgmmnt.is_magnetic"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d400c9af",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'Co': [0.988, 2.739, 2.746, 2.747, 2.762, 2.768]}"
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mgmmnt.magnetic_species_and_magmoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1436c1aa",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
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