[pre-commit.ci] auto fixes from pre-commit.com hooks

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Author: pre-commit-ci[bot]

docs/source/content/defect-finder.ipynb

@@ -25,10 +25,8 @@
     "from pathlib import Path\n",
     "\n",
     "import numpy as np\n",
-    "from pymatgen.io.vasp import Locpot\n",
     "\n",
     "TEST_FILES = Path(\"../../../tests/test_files\")\n",
-    "import glob\n",
     "\n",
     "from pymatgen.analysis.defects.finder import DefectSiteFinder\n",
     "from pymatgen.core.structure import Structure\n",
@@ -37,11 +35,10 @@
     "finder = DefectSiteFinder()\n",
     "\n",
     "for q in range(-1, 3):\n",
-    "    fname = f\"{str(TEST_FILES)}/v_N_GaN/q={q}/CONTCAR.gz\"\n",
+    "    fname = f\"{TEST_FILES!s}/v_N_GaN/q={q}/CONTCAR.gz\"\n",
     "    struct = Structure.from_file(fname)\n",
     "    fpos = finder.get_defect_fpos(defect_structure=struct, base_structure=base_struct)\n",
-    "    fpos -= np.round(fpos)\n",
-    "    print(fpos)"
+    "    fpos -= np.round(fpos)"
    ]
   },
   {

docs/source/content/defining-defects.ipynb

@@ -58,7 +58,7 @@
     "if (\n",
     "    bulk.lattice == bulk.get_primitive_structure().lattice\n",
     "):  # check that you have the primitive structure\n",
-    "    print(\"The bulk unit cell is the unique primitive WS cell\")"
+    "    pass"
    ]
   },
   {
@@ -92,7 +92,7 @@
     "mg_ga_defect0 = Substitution(structure=bulk, site=mg_site0)\n",
     "mg_ga_defect1 = Substitution(structure=bulk, site=mg_site1)\n",
     "if mg_ga_defect0 == mg_ga_defect1:\n",
-    "    print(\"The two Mg_Ga defects are equivalent.\")"
+    "    pass"
    ]
   },
   {
@@ -125,14 +125,10 @@
     "vac_defect1 = Vacancy(structure=bulk, site=n_site0)\n",
     "vac_defect2 = Vacancy(structure=bulk, site=n_site1)\n",
     "if vac_defect0 != vac_defect1:\n",
-    "    print(\n",
-    "        f\"The two vacancies {vac_defect0.name} and {vac_defect1.name} are not equivalent.\"\n",
-    "    )\n",
+    "    pass\n",
     "\n",
     "if vac_defect2 == vac_defect1:\n",
-    "    print(\n",
-    "        f\"The two vacancies {vac_defect2.name} and {vac_defect1.name} are equivalent.\"\n",
-    "    )"
+    "    pass"
    ]
   },
   {
@@ -260,8 +256,8 @@
     "\n",
     "chgcar = Chgcar.from_file(TEST_FILES / \"CHGCAR.Fe3O4.vasp\")\n",
     "cig = ChargeInterstitialGenerator()\n",
-    "for defect in cig.generate(chgcar, insert_species=[\"H\"]):\n",
-    "    print(defect)"
+    "for _defect in cig.generate(chgcar, insert_species=[\"H\"]):\n",
+    "    pass"
    ]
   },
   {
@@ -279,8 +275,8 @@
    },
    "outputs": [],
    "source": [
-    "for defect in generate_all_native_defects(chgcar):\n",
-    "    print(defect)"
+    "for _defect in generate_all_native_defects(chgcar):\n",
+    "    pass"
    ]
   },
   {

docs/source/content/formation-energy.ipynb

@@ -59,9 +59,9 @@
    "outputs": [],
    "source": [
     "import warnings\n",
+    "\n",
     "from monty.serialization import loadfn\n",
     "from pymatgen.analysis.defects.thermo import FormationEnergyDiagram\n",
-    "from pymatgen.io.vasp import Vasprun\n",
     "\n",
     "warnings.filterwarnings(\"ignore\")\n",
     "\n",
@@ -129,10 +129,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "for i, p in enumerate(fed.chempot_limits):\n",
-    "    print(f\"Limits for the chemical potential changes for point {i}\")\n",
-    "    for k,v in p.items():\n",
-    "        print(f\"Δμ_{k} = {v:.2f} eV\")"
+    "for _i, p in enumerate(fed.chempot_limits):\n",
+    "    for _k, _v in p.items():\n",
+    "        pass"
    ]
   },
   {
@@ -164,10 +163,11 @@
    "outputs": [],
    "source": [
     "from pymatgen.analysis.defects.corrections.freysoldt import plot_plnr_avg\n",
+    "\n",
     "plot_data = fed.defect_entries[1].corrections_metadata[\"freysoldt\"][\"plot_data\"]\n",
     "plot_plnr_avg(plot_data[0], title=\"Lattice Direction 1\")\n",
     "plot_plnr_avg(plot_data[1], title=\"Lattice Direction 2\")\n",
-    "plot_plnr_avg(plot_data[2], title=\"Lattice Direction 3\")\n"
+    "plot_plnr_avg(plot_data[2], title=\"Lattice Direction 3\")"
    ]
   }
  ],

docs/source/content/freysoldt-correction.ipynb

@@ -71,17 +71,14 @@
     "        defect_structure=defect_locpot.structure, base_structure=bulk_locpot.structure\n",
     "    )\n",
     "    center -= np.round(center)\n",
-    "    print(f\"Computing Freysoldt Correction for: q={q}\")\n",
-    "    print(f\"center={center}\")\n",
     "    freysoldt_results[q] = get_freysoldt_correction(\n",
     "        q=q,\n",
     "        dielectric=5,\n",
     "        bulk_locpot=bulk_locpot,\n",
     "        defect_locpot=defect_locpot,\n",
     "        defect_frac_coords=center,\n",
     "    )\n",
-    "    align = np.mean(list(freysoldt_results[q].metadata[\"alignments\"].values()))\n",
-    "    print(f\"alignment correction: {align}\")\n"
+    "    align = np.mean(list(freysoldt_results[q].metadata[\"alignments\"].values()))"
    ]
   },
   {
@@ -103,7 +100,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def plot_sxd_output(q, direction, C, ax):\n",
+    "def plot_sxd_output(q, direction, C, ax) -> None:\n",
     "    \"\"\"Read the vline-eV-a#.dat files computed by the `sxdefectalign` program.\n",
     "\n",
     "    Args:\n",
@@ -114,7 +111,7 @@
     "    \"\"\"\n",
     "    v_line_file = DEFECT_DIR / f\"q={q}/vline-eV-a{direction}.dat\"\n",
     "    # split the file into blocks based on the location of the string \"&\"\n",
-    "    with open(v_line_file, \"r\") as f:\n",
+    "    with open(v_line_file) as f:\n",
     "        blocks = f.read().split(\"&\")\n",
     "\n",
     "    # convert each block into a list of lines and convert to a numpy array\n",
@@ -134,7 +131,7 @@
     "    ax.legend()\n",
     "\n",
     "\n",
-    "def comparison_plots(q):\n",
+    "def comparison_plots(q) -> None:\n",
     "    \"\"\"\"\"\"\n",
     "    fig, axs = plt.subplots(3, 2, figsize=(15, 15), sharey=True)\n",
     "    for direction in range(3):\n",
@@ -210,7 +207,7 @@
    "outputs": [],
    "source": [
     "def get_sxd_result(q):\n",
-    "    \"\"\"Read the output of sxdefectalign\"\"\"\n",
+    "    \"\"\"Read the output of sxdefectalign.\"\"\"\n",
     "    fname = str(DEFECT_DIR / f\"q={q}/corr_align.out\")\n",
     "    gen = reverse_readfile(fname)\n",
     "    line = next(gen)\n",
@@ -225,8 +222,7 @@
    "source": [
     "for q in range(-1, 3):\n",
     "    python_res = freysoldt_results[q].correction_energy\n",
-    "    sxd_res = get_sxd_result(q)\n",
-    "    print(f\"python: {python_res:0.4f} / sxdefectalign: {sxd_res:0.4f}\")"
+    "    sxd_res = get_sxd_result(q)"
    ]
   }
  ],

docs/source/content/nonradiative.ipynb

@@ -21,8 +21,10 @@
    "source": [
     "# disable warnings\n",
     "import warnings\n",
+    "\n",
     "warnings.filterwarnings(\"ignore\", category=UserWarning)\n",
     "from pathlib import Path\n",
+    "\n",
     "import numpy as np\n",
     "from matplotlib import pyplot as plt\n",
     "from pymatgen.analysis.defects.ccd import HarmonicDefect, get_SRH_coefficient"
@@ -63,12 +65,6 @@
     "hd0 = HarmonicDefect.from_directories(\n",
     "    directories=dirs01,\n",
     "    store_bandstructure=True,\n",
-    ")\n",
-    "print(f\"The relaxed structure is in dirs01[{hd0.relaxed_index}]\")\n",
-    "print(hd0)\n",
-    "print(\n",
-    "    f\"The spin channel ({hd0.spin}) is also automaticalliy determined by the \"\n",
-    "    \"IPR, by taking the spin channel who's defect states have the lowest average IPR across the different k-points.\"\n",
     ")"
    ]
   },
@@ -184,9 +180,7 @@
    "outputs": [],
    "source": [
     "wswq_dir = TEST_FILES / \"ccd_0_-1\" / \"wswqs\"\n",
-    "print(f\"The parsed WSWQ files are: {[f.name for f in wswq_dir.glob('WSWQ*')]}\")\n",
-    "hd0.read_wswqs(TEST_FILES / \"ccd_0_-1\" / \"wswqs\")\n",
-    "print(f\"Parsed {len(hd0.wswqs)} WSWQ files.\")\n"
+    "hd0.read_wswqs(TEST_FILES / \"ccd_0_-1\" / \"wswqs\")"
    ]
   },
   {
@@ -205,11 +199,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(f\"The automatically determined defect electronic states are: {hd0.defect_band} \"\n",
-    "    \"(with [band, k-point, spin] indexing).\")\n",
-    "epME = hd0.get_elph_me(defect_state=(138, 1, 1))\n",
-    "print(f\"The resulting array of shape {epME.shape} contains the matrix elements from the \"\n",
-    "    \"defect state to all other states at the same k-point.\")\n"
+    "epME = hd0.get_elph_me(defect_state=(138, 1, 1))"
    ]
   },
   {
@@ -233,7 +223,7 @@
     "hd1 = HarmonicDefect.from_directories(\n",
     "    directories=dirs10,\n",
     "    store_bandstructure=True,\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -252,7 +242,9 @@
    "outputs": [],
    "source": [
     "T = np.linspace(100, 1000, 20)\n",
-    "srh_c = get_SRH_coefficient(initial_state=hd0, final_state=hd1, defect_state=(138, 1, 1), T=T, dE=0.3)\n",
+    "srh_c = get_SRH_coefficient(\n",
+    "    initial_state=hd0, final_state=hd1, defect_state=(138, 1, 1), T=T, dE=0.3\n",
+    ")\n",
     "plt.plot(T, srh_c)\n",
     "plt.xlabel(\"Temperature [K]\")\n",
     "plt.ylabel(\"SRH coefficient [cm$^{-3}$s$^{-1}$]\");"

docs/source/content/photo-conduct.ipynb

@@ -25,11 +25,14 @@
    "outputs": [],
    "source": [
     "# disable tqdm progress bar\n",
-    "from tqdm import tqdm\n",
     "from functools import partialmethod\n",
+    "\n",
+    "from tqdm import tqdm\n",
+    "\n",
     "tqdm.__init__ = partialmethod(tqdm.__init__, disable=True)\n",
     "# disable warnings\n",
     "import warnings\n",
+    "\n",
     "warnings.filterwarnings(\"ignore\", category=UserWarning)"
    ]
   },
@@ -40,13 +43,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import bisect\n",
+    "import collections\n",
     "from pathlib import Path\n",
-    "from pymatgen.analysis.defects.ccd import HarmonicDefect, get_SRH_coefficient\n",
-    "from pymatgen.io.vasp.optics import DielectricFunctionCalculator, Spin, Vasprun, Waveder\n",
+    "\n",
     "import numpy as np\n",
     "from matplotlib import pyplot as plt\n",
-    "import bisect\n",
-    "import collections\n",
+    "from pymatgen.analysis.defects.ccd import HarmonicDefect\n",
+    "from pymatgen.io.vasp.optics import Spin, Waveder\n",
+    "\n",
     "TEST_FILES = Path(\"../../../tests/test_files/v_Ga/\")"
    ]
   },
@@ -71,9 +76,7 @@
     "dir0 = TEST_FILES / \"ccd_0_-1\" / \"optics\"\n",
     "hd0 = HarmonicDefect.from_directories(directories=[dir0], store_bandstructure=True)\n",
     "# Note the `store_bandstructure=True` argument is required for the matrix element plotting later in the notebook.\n",
-    "# but not required for the dielectric function calculation.\n",
-    "print(f\"The defect band is {hd0.defect_band}\")\n",
-    "print(f\"The vibrational frequency is omega={hd0.omega} in this case is gibberish.\")"
+    "# but not required for the dielectric function calculation."
    ]
   },
   {
@@ -96,36 +99,34 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
-    "def print_eigs(vr, bwind=5, defect_bands = ()):\n",
+    "def print_eigs(vr, bwind=5, defect_bands=()) -> None:\n",
     "    \"\"\"Print the eigenvalues in a small band window around the Fermi level.\n",
     "\n",
     "    Args:\n",
     "        vr (Vasprun): The Vasprun object.\n",
     "        bwind (int): The number of bands above and below the Fermi level to print.\n",
     "        defect_bands (list): A list of tuples of the form (band index, kpt index, spin index)\n",
     "    \"\"\"\n",
-    "    def _get_spin_idx(spin):\n",
+    "\n",
+    "    def _get_spin_idx(spin) -> int:\n",
     "        if spin == Spin.up:\n",
     "            return 0\n",
     "        return 1\n",
+    "\n",
     "    occ = vr.eigenvalues[Spin.up][0, :, 1] * -1\n",
-    "    fermi_idx = bisect.bisect_left(occ, -0.5) \n",
+    "    fermi_idx = bisect.bisect_left(occ, -0.5)\n",
     "    output = collections.defaultdict(list)\n",
     "    for k, spin_eigs in vr.eigenvalues.items():\n",
     "        spin_idx = _get_spin_idx(k)\n",
     "        for kpt in range(spin_eigs.shape[0]):\n",
     "            for ib in range(fermi_idx - bwind, fermi_idx + bwind):\n",
     "                e, o = spin_eigs[kpt, ib, :]\n",
     "                idx = (ib, kpt, spin_idx)\n",
-    "                if idx in defect_bands:\n",
-    "                    e_out = f\"{e:7.4f}*\"\n",
-    "                else:\n",
-    "                    e_out = f\"{e:8.5f}\"\n",
+    "                e_out = f\"{e:7.4f}*\" if idx in defect_bands else f\"{e:8.5f}\"\n",
     "                output[(ib)].append(e_out)\n",
-    "    print(\"band s=0,k=0  s=0,k=1  s=1,k=0  s=1,k=1\")\n",
-    "    for ib, eigs in output.items():\n",
-    "        print(f\"{ib:3d} {' '.join(eigs)}\")\n",
+    "    for ib in output:\n",
+    "        pass\n",
+    "\n",
     "\n",
     "print_eigs(vr=hd0.vrun, defect_bands=hd0.defect_band)"
    ]
@@ -177,7 +178,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "energy, eps_vbm, eps_cbm = hd0.get_dielectric_function(idir=0,jdir=0)\n",
+    "energy, eps_vbm, eps_cbm = hd0.get_dielectric_function(idir=0, jdir=0)\n",
     "# plotting\n",
     "plt.plot(energy, np.imag(eps_vbm), label=\"VBM\")\n",
     "plt.plot(energy, np.imag(eps_cbm), label=\"CBM\")\n",
@@ -216,15 +217,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pymatgen.analysis.defects.plotting.optics import plot_optical_transitions\n",
     "import matplotlib as mpl\n",
+    "from pymatgen.analysis.defects.plotting.optics import plot_optical_transitions\n",
+    "\n",
     "fig, ax = plt.subplots()\n",
-    "cm_ax  = fig.add_axes([0.8,0.1,0.02,0.8])\n",
-    "df_k0, cmap, norm = plot_optical_transitions(hd0, kpt_index=1, band_window=5, x0=3, ax=ax)\n",
-    "df_k1, _, _ = plot_optical_transitions(hd0, kpt_index=0, band_window=5, x0=0, ax=ax, cmap=cmap, norm=norm)\n",
-    "mpl.colorbar.ColorbarBase(cm_ax,cmap=cmap,norm=norm,orientation='vertical')\n",
-    "ax.set_ylabel(\"Energy (eV)\");\n",
-    "ax.set_xticks([0,3])\n",
+    "cm_ax = fig.add_axes([0.8, 0.1, 0.02, 0.8])\n",
+    "df_k0, cmap, norm = plot_optical_transitions(\n",
+    "    hd0, kpt_index=1, band_window=5, x0=3, ax=ax\n",
+    ")\n",
+    "df_k1, _, _ = plot_optical_transitions(\n",
+    "    hd0, kpt_index=0, band_window=5, x0=0, ax=ax, cmap=cmap, norm=norm\n",
+    ")\n",
+    "mpl.colorbar.ColorbarBase(cm_ax, cmap=cmap, norm=norm, orientation=\"vertical\")\n",
+    "ax.set_ylabel(\"Energy (eV)\")\n",
+    "ax.set_xticks([0, 3])\n",
     "ax.set_xticklabels([\"Kpoint-0\", \"Kpoint-1\"])"
    ]
   },