valyte 0.1.8__tar.gz → 0.1.11__tar.gz

{valyte-0.1.8/valyte.egg-info → valyte-0.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: valyte
-Version: 0.1.8
+Version: 0.1.11
 Summary: A comprehensive CLI tool for VASP pre-processing (Supercells, K-points) and post-processing (DOS, Band Structure plotting)
 Home-page: https://github.com/nikyadav002/Valyte-Project
 Author: Nikhil
@@ -42,6 +42,7 @@ Requires-Dist: seekpath
   - VBM alignment to 0 eV.
   - Color-coded bands (Purple for VB, Teal for CB).
   - High-symmetry path labels from KPOINTS.
+- **IPR Analysis**: Compute Inverse Participation Ratio from PROCAR to analyze wavefunction localization.
 - **Publication Quality**: Clean aesthetics, custom fonts (Arial, Helvetica, Times New Roman), high DPI output.
 
 ## Installation
@@ -113,6 +114,9 @@ valyte supercell 3 3 1 -i POSCAR_primitive -o POSCAR_3x3x1
 
 Automatically generate a KPOINTS file with high-symmetry paths for band structure calculations.
 
+> [!TIP]
+> **Smart K-Path Generation (New in v0.1.7+)**: Valyte now automatically determines the standard path (e.g., `\Gamma - Y - V` for Monoclinic cells) using the **Bradley-Cracknell** convention by default. This ensures clean, publication-ready labels without external dependencies.
+
 ```bash
 valyte band kpt-gen [options]
 ```
@@ -121,12 +125,20 @@ valyte band kpt-gen [options]
 - `-i`, `--input`: Input POSCAR file (default: `POSCAR`).
 - `-n`, `--npoints`: Points per segment (default: `40`).
 - `-o`, `--output`: Output filename (default: `KPOINTS`).
+- `--mode`: Path convention. Options: `bradcrack` (Default), `seekpath`, `latimer_munro`, `setyawan_curtarolo`.
 
 **Example:**
 ```bash
-valyte band kpt-gen -n 60 -i POSCAR_relaxed -o KPOINTS_band
+# Default (Smart/BradCrack)
+valyte band kpt-gen -n 60
+
+# Explicitly use Seekpath convention
+valyte band kpt-gen --mode seekpath
 ```
 
+> [!IMPORTANT]
+> The command will generate a **`POSCAR_standard`** file. You **MUST** use this structure for your band structure calculation (i.e., `cp POSCAR_standard POSCAR`) because the K-path corresponds to this specific orientation. Using your original POSCAR may result in incorrect paths.
+
 ### 🕸️ Generate K-Points (Interactive)
 
 Generate a `KPOINTS` file for SCF calculations interactively.
@@ -141,6 +153,38 @@ This command will prompt you for:
 
 It automatically calculates the optimal grid based on your `POSCAR` structure.
 
+---
+
+### 🧪 Generate POTCAR
+
+Generate a `POTCAR` file based on the species in your `POSCAR`.
+
+```bash
+valyte potcar [options]
+```
+
+**Options:**
+- `-i`, `--input`: Input POSCAR file (default: `POSCAR`).
+- `-o`, `--output`: Output filename (default: `POTCAR`).
+- `--functional`: Functional to use (default: `PBE`). Options include `PBE`, `PBE_52`, `PBE_54`, `LDA`, etc.
+
+**Example:**
+```bash
+# Generate POTCAR using default PBE functional
+valyte potcar
+
+# Use a specific functional
+valyte potcar --functional PBE_54
+
+# Specify input and output files
+valyte potcar -i POSCAR_relaxed -o POTCAR_new
+```
+
+> [!IMPORTANT]
+> **Pymatgen Configuration Required**: This command requires Pymatgen to be configured with your VASP pseudopotential directory. Set `PMG_VASP_PSP_DIR` in your `~/.pmgrc.yaml` file. See the [Pymatgen documentation](https://pymatgen.org/installation.html#potcar-setup) for setup instructions.
+
+---
+
 #### 2. Plot Band Structure
 
 Plot the electronic band structure from `vasprun.xml`.
@@ -205,4 +249,30 @@ valyte dos -e Fe "Fe(d)"
 valyte dos ./vasp_data --xlim -5 5 -o my_dos.png
 ```
 
+---
+
+### 📐 Compute IPR (Inverse Participation Ratio)
+
+Compute the Inverse Participation Ratio (IPR) from VASP `PROCAR` to analyze wavefunction localization.
+
+```bash
+valyte ipr
+```
+
+This interactive command will:
+1. Read the `PROCAR` file from the current directory.
+2. Display the number of k-points, bands, and atoms.
+3. Prompt you for **band indices** to analyze (e.g., `5 6 7` or `5-7`).
+4. Optionally show per-k-point IPR values.
+5. Save results to `ipr_procar.dat`.
+
+**Output Columns:**
+- **Band**: Band index.
+- **Energy**: Average energy (eV) across k-points.
+- **IPR**: Inverse Participation Ratio (higher = more localized).
+- **N_eff**: Effective number of atoms (1/IPR).
+
+> [!TIP]
+> Use IPR to identify localized defect states. A state localized on a single atom has IPR ≈ 1.0 and N_eff ≈ 1. Delocalized band states have small IPR and large N_eff.
+
 </details>

{valyte-0.1.8 → valyte-0.1.11}/README.md

@@ -23,6 +23,7 @@
   - VBM alignment to 0 eV.
   - Color-coded bands (Purple for VB, Teal for CB).
   - High-symmetry path labels from KPOINTS.
+- **IPR Analysis**: Compute Inverse Participation Ratio from PROCAR to analyze wavefunction localization.
 - **Publication Quality**: Clean aesthetics, custom fonts (Arial, Helvetica, Times New Roman), high DPI output.
 
 ## Installation
@@ -94,6 +95,9 @@ valyte supercell 3 3 1 -i POSCAR_primitive -o POSCAR_3x3x1
 
 Automatically generate a KPOINTS file with high-symmetry paths for band structure calculations.
 
+> [!TIP]
+> **Smart K-Path Generation (New in v0.1.7+)**: Valyte now automatically determines the standard path (e.g., `\Gamma - Y - V` for Monoclinic cells) using the **Bradley-Cracknell** convention by default. This ensures clean, publication-ready labels without external dependencies.
+
 ```bash
 valyte band kpt-gen [options]
 ```
@@ -102,12 +106,20 @@ valyte band kpt-gen [options]
 - `-i`, `--input`: Input POSCAR file (default: `POSCAR`).
 - `-n`, `--npoints`: Points per segment (default: `40`).
 - `-o`, `--output`: Output filename (default: `KPOINTS`).
+- `--mode`: Path convention. Options: `bradcrack` (Default), `seekpath`, `latimer_munro`, `setyawan_curtarolo`.
 
 **Example:**
 ```bash
-valyte band kpt-gen -n 60 -i POSCAR_relaxed -o KPOINTS_band
+# Default (Smart/BradCrack)
+valyte band kpt-gen -n 60
+
+# Explicitly use Seekpath convention
+valyte band kpt-gen --mode seekpath
 ```
 
+> [!IMPORTANT]
+> The command will generate a **`POSCAR_standard`** file. You **MUST** use this structure for your band structure calculation (i.e., `cp POSCAR_standard POSCAR`) because the K-path corresponds to this specific orientation. Using your original POSCAR may result in incorrect paths.
+
 ### 🕸️ Generate K-Points (Interactive)
 
 Generate a `KPOINTS` file for SCF calculations interactively.
@@ -122,6 +134,38 @@ This command will prompt you for:
 
 It automatically calculates the optimal grid based on your `POSCAR` structure.
 
+---
+
+### 🧪 Generate POTCAR
+
+Generate a `POTCAR` file based on the species in your `POSCAR`.
+
+```bash
+valyte potcar [options]
+```
+
+**Options:**
+- `-i`, `--input`: Input POSCAR file (default: `POSCAR`).
+- `-o`, `--output`: Output filename (default: `POTCAR`).
+- `--functional`: Functional to use (default: `PBE`). Options include `PBE`, `PBE_52`, `PBE_54`, `LDA`, etc.
+
+**Example:**
+```bash
+# Generate POTCAR using default PBE functional
+valyte potcar
+
+# Use a specific functional
+valyte potcar --functional PBE_54
+
+# Specify input and output files
+valyte potcar -i POSCAR_relaxed -o POTCAR_new
+```
+
+> [!IMPORTANT]
+> **Pymatgen Configuration Required**: This command requires Pymatgen to be configured with your VASP pseudopotential directory. Set `PMG_VASP_PSP_DIR` in your `~/.pmgrc.yaml` file. See the [Pymatgen documentation](https://pymatgen.org/installation.html#potcar-setup) for setup instructions.
+
+---
+
 #### 2. Plot Band Structure
 
 Plot the electronic band structure from `vasprun.xml`.
@@ -186,4 +230,30 @@ valyte dos -e Fe "Fe(d)"
 valyte dos ./vasp_data --xlim -5 5 -o my_dos.png
 ```
 
+---
+
+### 📐 Compute IPR (Inverse Participation Ratio)
+
+Compute the Inverse Participation Ratio (IPR) from VASP `PROCAR` to analyze wavefunction localization.
+
+```bash
+valyte ipr
+```
+
+This interactive command will:
+1. Read the `PROCAR` file from the current directory.
+2. Display the number of k-points, bands, and atoms.
+3. Prompt you for **band indices** to analyze (e.g., `5 6 7` or `5-7`).
+4. Optionally show per-k-point IPR values.
+5. Save results to `ipr_procar.dat`.
+
+**Output Columns:**
+- **Band**: Band index.
+- **Energy**: Average energy (eV) across k-points.
+- **IPR**: Inverse Participation Ratio (higher = more localized).
+- **N_eff**: Effective number of atoms (1/IPR).
+
+> [!TIP]
+> Use IPR to identify localized defect states. A state localized on a single atom has IPR ≈ 1.0 and N_eff ≈ 1. Delocalized band states have small IPR and large N_eff.
+
 </details>

valyte-0.1.11/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"

{valyte-0.1.8 → valyte-0.1.11}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name="valyte",
-    version="0.1.8",
+    version="0.1.11",
     packages=find_packages(),
     install_requires=[
         "numpy",

valyte-0.1.11/valyte/band.py

@@ -0,0 +1,247 @@
+"""Band structure KPOINTS generation."""
+
+import os
+import json
+import numpy as np
+import seekpath
+from pymatgen.core import Structure
+from pymatgen.symmetry.bandstructure import HighSymmKpath
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+try:
+    from importlib.resources import files as ilr_files
+except ImportError:
+    from importlib_resources import files as ilr_files
+
+from valyte.potcar import generate_potcar
+
+
+def generate_band_kpoints(poscar_path="POSCAR", npoints=40, output="KPOINTS", symprec=0.01, mode="bradcrack"):
+    """Generate a line-mode KPOINTS file for band structure calculations."""
+
+    if not os.path.exists(poscar_path):
+        raise FileNotFoundError(f"{poscar_path} not found")
+
+    mode = (mode or "bradcrack").lower()
+
+    structure = Structure.from_file(poscar_path)
+
+    if mode == "bradcrack":
+        try:
+            kpath = BradCrackKpath(structure, symprec=symprec)
+            prim_std = kpath.prim
+            path = kpath.path
+            kpoints = kpath.kpoints
+
+            standard_filename = "POSCAR_standard"
+            prim_std.to(filename=standard_filename)
+        except Exception as e:
+            raise RuntimeError(f"Error generating Bradley-Cracknell path: {e}")
+    else:
+        try:
+            if mode == "seekpath":
+                mode = "hinuma"
+
+            sga = SpacegroupAnalyzer(structure, symprec=symprec)
+            prim_std = sga.get_primitive_standard_structure()
+        except Exception as e:
+            raise RuntimeError(f"Error during standardization: {e}")
+
+        try:
+            kpath = HighSymmKpath(prim_std, path_type=mode, symprec=symprec)
+
+            standard_filename = "POSCAR_standard"
+            prim_std.to(filename=standard_filename)
+
+            path = kpath.kpath["path"]
+            kpoints = kpath.kpath["kpoints"]
+        except Exception as e:
+            raise RuntimeError(f"Error generating K-path: {e}")
+
+    try:
+        with open(output, "w") as f:
+            f.write("KPOINTS for Band Structure\n")
+            f.write(f"{npoints}\n")
+            f.write("Line-mode\n")
+            f.write("Reciprocal\n")
+
+            for subpath in path:
+                for i in range(len(subpath) - 1):
+                    start_label = subpath[i]
+                    end_label = subpath[i + 1]
+
+                    start_coords = kpoints[start_label]
+                    end_coords = kpoints[end_label]
+
+                    f.write(
+                        f"{start_coords[0]:10.6f} {start_coords[1]:10.6f} {start_coords[2]:10.6f} ! {start_label}\n"
+                    )
+                    f.write(
+                        f"{end_coords[0]:10.6f} {end_coords[1]:10.6f} {end_coords[2]:10.6f} ! {end_label}\n"
+                    )
+                    f.write("\n")
+
+        print(f"Generated {output} ({' - '.join([' - '.join(seg) for seg in path])})")
+        print(f"Generated {standard_filename} (Standardized Primitive Cell)")
+        print("IMPORTANT: Use POSCAR_standard for the band calculation.")
+    except Exception as e:
+        raise RuntimeError(f"Error writing KPOINTS file: {e}")
+
+    try:
+        print("Generating default POTCAR (PBE)...")
+        generate_potcar(poscar_path=poscar_path, functional="PBE", output="POTCAR")
+    except Exception as e:
+        print(f"Warning: could not generate POTCAR: {e}")
+        print("Proceeding without POTCAR generation.")
+
+
+class BradCrackKpath:
+    """Bradley-Cracknell K-path generation using SeeK-path output."""
+
+    def __init__(self, structure, symprec=0.01):
+        self.structure = structure
+        self.symprec = symprec
+
+        sga = SpacegroupAnalyzer(structure, symprec=symprec)
+        self._spg_data = sga.get_symmetry_dataset()
+
+        cell = (
+            structure.lattice.matrix,
+            structure.frac_coords,
+            [s.specie.number for s in structure],
+        )
+
+        self._seek_data = seekpath.get_path(cell, symprec=symprec)
+
+        prim_lattice = self._seek_data["primitive_lattice"]
+        prim_pos = self._seek_data["primitive_positions"]
+        prim_types = self._seek_data["primitive_types"]
+
+        z_to_specie = {s.specie.number: s.specie for s in structure}
+        prim_species = [z_to_specie[z] for z in prim_types]
+
+        self.prim = Structure(prim_lattice, prim_species, prim_pos)
+
+        conv_lattice = self._seek_data["conv_lattice"]
+        conv_pos = self._seek_data["conv_positions"]
+        conv_types = self._seek_data["conv_types"]
+        conv_species = [z_to_specie[z] for z in conv_types]
+        self.conv = Structure(conv_lattice, conv_species, conv_pos)
+
+        self._get_bradcrack_path()
+
+    def _get_bradcrack_path(self):
+        a, b, c = self.conv.lattice.abc
+        angles = self.conv.lattice.angles
+
+        angles_r = [round(x, 3) for x in angles]
+        unique_val = min(angles_r, key=angles_r.count)
+        unique = angles_r.index(unique_val)
+
+        spg_symbol = self._spg_data["international"]
+        spg_number = self._spg_data["number"]
+
+        lattice_type = self.get_lattice_type(spg_number)
+        bravais = self._get_bravais_lattice(spg_symbol, lattice_type, a, b, c, unique)
+
+        json_file = ilr_files("valyte.data").joinpath("bradcrack.json")
+        with json_file.open("r") as f:
+            data = json.load(f)
+
+        if bravais not in data:
+            raise ValueError(f"Bravais lattice code '{bravais}' not found in BradCrack data.")
+
+        self.bradcrack_data = data[bravais]
+        self.kpoints = self.bradcrack_data["kpoints"]
+        self.path = self.bradcrack_data["path"]
+
+    def get_lattice_type(self, number):
+        if 1 <= number <= 2:
+            return "triclinic"
+        if 3 <= number <= 15:
+            return "monoclinic"
+        if 16 <= number <= 74:
+            return "orthorhombic"
+        if 75 <= number <= 142:
+            return "tetragonal"
+        if 143 <= number <= 167:
+            if number in [146, 148, 155, 160, 161, 166, 167]:
+                return "rhombohedral"
+            return "trigonal"
+        if 168 <= number <= 194:
+            return "hexagonal"
+        if 195 <= number <= 230:
+            return "cubic"
+        return "unknown"
+
+    def _get_bravais_lattice(self, spg_symbol, lattice_type, a, b, c, unique):
+        if lattice_type == "triclinic":
+            return "triclinic"
+
+        if lattice_type == "monoclinic":
+            if "P" in spg_symbol:
+                if unique == 0:
+                    return "mon_p_a"
+                if unique == 1:
+                    return "mon_p_b"
+                if unique == 2:
+                    return "mon_p_c"
+            if "C" in spg_symbol:
+                if unique == 0:
+                    return "mon_c_a"
+                if unique == 1:
+                    return "mon_c_b"
+                if unique == 2:
+                    return "mon_c_c"
+
+        if lattice_type == "orthorhombic":
+            if "P" in spg_symbol:
+                return "orth_p"
+            if "A" in spg_symbol or "C" in spg_symbol:
+                if a > b:
+                    return "orth_c_a"
+                if b > a:
+                    return "orth_c_b"
+            if "F" in spg_symbol:
+                inv_a2 = 1 / a**2
+                inv_b2 = 1 / b**2
+                inv_c2 = 1 / c**2
+                if (inv_a2 < inv_b2 + inv_c2) and (inv_b2 < inv_c2 + inv_a2) and (inv_c2 < inv_a2 + inv_b2):
+                    return "orth_f_1"
+                if inv_c2 > inv_a2 + inv_b2:
+                    return "orth_f_2"
+                if inv_b2 > inv_a2 + inv_c2:
+                    return "orth_f_3"
+                if inv_a2 > inv_c2 + inv_b2:
+                    return "orth_f_4"
+            if "I" in spg_symbol:
+                if a > b and a > c:
+                    return "orth_i_a"
+                if b > a and b > c:
+                    return "orth_i_b"
+                if c > a and c > b:
+                    return "orth_i_c"
+
+        if lattice_type == "tetragonal":
+            if "P" in spg_symbol:
+                return "tet_p"
+            if "I" in spg_symbol:
+                return "tet_i_a" if a > c else "tet_i_c"
+
+        if lattice_type in ["trigonal", "hexagonal", "rhombohedral"]:
+            if "R" in spg_symbol:
+                return "trig_r_a" if a > np.sqrt(2) * c else "trig_r_c"
+            if "P" in spg_symbol:
+                if unique == 0:
+                    return "trig_p_a"
+                if unique == 2:
+                    return "trig_p_c"
+
+        if lattice_type == "cubic":
+            if "P" in spg_symbol:
+                return "cubic_p"
+            if "I" in spg_symbol:
+                return "cubic_i"
+            if "F" in spg_symbol:
+                return "cubic_f"
+
+        return "unknown"

valyte-0.1.11/valyte/band_plot.py

@@ -0,0 +1,86 @@
+import os
+import numpy as np
+import matplotlib as mpl
+mpl.use("agg")
+mpl.rcParams["axes.unicode_minus"] = False
+import matplotlib.pyplot as plt
+from pymatgen.io.vasp import BSVasprun
+from pymatgen.electronic_structure.plotter import BSPlotter
+
+
+def plot_band_structure(vasprun_path, kpoints_path=None, output="valyte_band.png",
+                        ylim=None, figsize=(4, 4), dpi=400, font="Arial"):
+    """Plot the electronic band structure from a VASP vasprun.xml."""
+
+    if os.path.isdir(vasprun_path):
+        vasprun_path = os.path.join(vasprun_path, "vasprun.xml")
+
+    font_map = {
+        "arial": "Arial",
+        "helvetica": "Helvetica",
+        "times": "Times New Roman",
+        "times new roman": "Times New Roman",
+    }
+    font = font_map.get(font.lower(), "Arial")
+    mpl.rcParams["font.family"] = font
+    mpl.rcParams["axes.linewidth"] = 1.4
+    mpl.rcParams["font.weight"] = "bold"
+    mpl.rcParams["font.size"] = 14
+    mpl.rcParams["xtick.major.width"] = 1.2
+    mpl.rcParams["ytick.major.width"] = 1.2
+
+    try:
+        vr = BSVasprun(vasprun_path, parse_projected_eigen=False)
+        bs = vr.get_band_structure(kpoints_filename=kpoints_path, line_mode=True)
+    except Exception as e:
+        raise ValueError(f"Failed to load band structure: {e}")
+
+    bs_plotter = BSPlotter(bs)
+    data = bs_plotter.bs_plot_data(zero_to_efermi=True)
+
+    distances = data["distances"]
+    energies = data["energy"]
+    ticks = data["ticks"]
+
+    fig, ax = plt.subplots(figsize=figsize)
+
+    color_vb = "#8e44ad"
+    color_cb = "#2a9d8f"
+
+    for i in range(len(distances)):
+        d = distances[i]
+
+        if isinstance(energies, dict):
+            for spin in energies:
+                for band in energies[spin][i]:
+                    c = color_vb if np.mean(band) <= 0 else color_cb
+                    ax.plot(d, band, color=c, lw=1.5, alpha=1.0)
+        else:
+            for spin in energies[i]:
+                for band in energies[i][spin]:
+                    c = color_vb if np.mean(band) <= 0 else color_cb
+                    ax.plot(d, band, color=c, lw=1.5, alpha=1.0)
+
+    ax.set_xticks(ticks["distance"])
+    clean_labels = [(l or "").replace("$\\mid$", "|") for l in ticks["label"]]
+    ax.set_xticklabels(clean_labels, fontsize=14, fontweight="bold")
+
+    for d in ticks["distance"]:
+        ax.axvline(d, color="k", lw=0.8, ls="-", alpha=0.3)
+
+    ax.axhline(0, color="k", lw=0.8, ls="--", alpha=0.5)
+
+    ax.set_ylabel("Energy (eV)", fontsize=16, fontweight="bold", labelpad=8)
+    if ylim:
+        ax.set_ylim(ylim)
+        yticks = np.arange(np.ceil(ylim[0]), np.floor(ylim[1]) + 1, 1)
+        ax.set_yticks(yticks)
+    else:
+        ax.set_ylim(-4, 4)
+        ax.set_yticks(np.arange(-4, 5, 1))
+
+    ax.set_xlim(distances[0][0], distances[-1][-1])
+
+    plt.tight_layout()
+    plt.savefig(output, dpi=dpi)
+    plt.close(fig)