TB2J 0.9.9.9__py3-none-any.whl → 0.9.9.10__py3-none-any.whl

TB2J/magnon/magnon_band.py

@@ -0,0 +1,180 @@
+"""Module for handling magnon band structure data and plotting."""
+from dataclasses import dataclass
+from pathlib import Path
+from typing import List, Optional, Tuple, Union
+import json
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+@dataclass
+class MagnonBand:
+    """Magnon band structure data and plotting functionality.
+
+    Parameters
+    ----------
+    energies : np.ndarray
+        Band energies of shape (nkpts, nbands)
+    kpoints : np.ndarray
+        k-points coordinates of shape (nkpts, 3)
+    kpath_labels : List[Tuple[int, str]]
+        List of (index, label) tuples for special k-points
+    special_points : dict
+        Dictionary mapping k-point names to their coordinates
+    xcoords : Optional[Union[np.ndarray, List[np.ndarray]]]
+        x-coordinates for plotting. Can be continuous or segmented.
+    """
+
+    energies: np.ndarray
+    kpoints: np.ndarray
+    kpath_labels: List[Tuple[int, str]]
+    special_points: dict
+    xcoords: Optional[Union[np.ndarray, List[np.ndarray]]] = None
+
+    def __post_init__(self):
+        """Convert input arrays to numpy arrays and set default x-coordinates."""
+        self.energies = np.array(self.energies)
+        self.kpoints = np.array(self.kpoints)
+        
+        if self.xcoords is None:
+            self.xcoords = np.arange(len(self.kpoints))
+
+    def plot(self, ax=None, filename=None, show=False, **kwargs):
+        """Plot the magnon band structure.
+
+        Parameters
+        ----------
+        ax : matplotlib.axes.Axes, optional
+            Matplotlib axes for plotting. If None, creates new figure.
+        filename : str, optional
+            If provided, saves plot to this file.
+        show : bool, optional
+            Whether to show the plot on screen. Default is False.
+        **kwargs : dict
+            Additional arguments passed to plot function:
+            - linewidth: float, default 1.5
+            - color: str, default 'blue'
+            - linestyle: str, default '-'
+
+        Returns
+        -------
+        matplotlib.axes.Axes
+            The axes object containing the plot
+        """
+        if ax is None:
+            fig, ax = plt.subplots(constrained_layout=True)
+
+        # Plot settings
+        linewidth = kwargs.pop('linewidth', 1.5)
+        color = kwargs.pop('color', 'blue')
+        linestyle = kwargs.pop('linestyle', '-')
+
+        # Plot bands
+        if isinstance(self.xcoords, list):  # Segmented path
+            start_idx = 0
+            for x in self.xcoords:
+                nbands = x.shape[0]
+                segment_bands = self.energies[start_idx:start_idx + nbands].T
+                for band in segment_bands:
+                    ax.plot(
+                        x,
+                        band[start_idx:start_idx + nbands],
+                        linewidth=linewidth,
+                        color=color,
+                        linestyle=linestyle,
+                        **kwargs,
+                    )
+                start_idx += nbands
+            ax.set_xlim([self.xcoords[0][0], self.xcoords[-1][-1]])
+        else:  # Continuous path
+            for band in self.energies.T:
+                ax.plot(
+                    self.xcoords,
+                    band,
+                    linewidth=linewidth,
+                    color=color,
+                    linestyle=linestyle,
+                    **kwargs,
+                )
+            ax.set_xlim([self.xcoords[0], self.xcoords[-1]])
+
+        # Set y-limits with padding
+        bmin, bmax = self.energies.min(), self.energies.max()
+        ymin = bmin - 0.05 * abs(bmin - bmax)
+        ymax = bmax + 0.05 * abs(bmax - bmin)
+        ax.set_ylim([ymin, ymax])
+
+        # Add k-point labels and vertical lines
+        kpoint_pos = [i for i, _ in self.kpath_labels]
+        kpoint_labels = [label for _, label in self.kpath_labels]
+        ax.set_xticks(kpoint_pos)
+        ax.set_xticklabels(kpoint_labels)
+        ax.vlines(
+            x=kpoint_pos,
+            ymin=ymin,
+            ymax=ymax,
+            color='black',
+            linewidth=linewidth / 5,
+        )
+
+        ax.set_ylabel('Energy (meV)')
+
+        if filename is not None:
+            plt.savefig(filename, dpi=300, bbox_inches='tight')
+        if show:
+            plt.show()
+
+        return ax
+
+    def save(self, filename: str):
+        """Save band structure data to a JSON file.
+
+        Parameters
+        ----------
+        filename : str
+            Output filename (will append .json if needed)
+        """
+        if not filename.endswith('.json'):
+            filename = filename + '.json'
+
+        data = {
+            'kpoints': self.kpoints.tolist(),
+            'energies': self.energies.tolist(),
+            'kpath_labels': [(int(i), str(l)) for i, l in self.kpath_labels],
+            'special_points': {k: v.tolist() for k, v in self.special_points.items()},
+            'xcoords': self.xcoords.tolist() if isinstance(self.xcoords, np.ndarray)
+                      else [x.tolist() for x in self.xcoords] if self.xcoords is not None
+                      else None,
+        }
+
+        with open(filename, 'w') as f:
+            json.dump(data, f, indent=2)
+
+    @classmethod
+    def load(cls, filename: str) -> 'MagnonBand':
+        """Load band structure from a JSON file.
+
+        Parameters
+        ----------
+        filename : str
+            Input JSON filename
+
+        Returns
+        -------
+        MagnonBand
+            Loaded band structure object
+        """
+        with open(filename) as f:
+            data = json.load(f)
+
+        # Convert lists back to numpy arrays
+        data['kpoints'] = np.array(data['kpoints'])
+        data['energies'] = np.array(data['energies'])
+        if data['xcoords'] is not None:
+            if isinstance(data['xcoords'][0], list):  # Segmented path
+                data['xcoords'] = [np.array(x) for x in data['xcoords']]
+            else:  # Continuous path
+                data['xcoords'] = np.array(data['xcoords'])
+        data['special_points'] = {k: np.array(v) for k, v in data['special_points'].items()}
+
+        return cls(**data)

TB2J/magnon/plot.py

@@ -6,10 +6,23 @@ class BandsPlot:
     _UNITS = "meV"
     _NSYSTEMS = 1
 
-    def __init__(self, bands, kpath, **kwargs):
-        self.bands = bands
+    def __init__(self, bands, kpath, xlist=None, **kwargs):
+        """Initialize BandsPlot.
+        
+        Parameters
+        ----------
+        bands : array_like
+            Band energies
+        kpath : list of (index, label) tuples
+            K-point labels and their indices
+        xlist : list of arrays, optional
+            X-coordinates for segmented paths. If None, uses range(nbands)
+        **kwargs : dict
+            Additional plotting options
+        """
+        self.bands = bands * 1000  # Convert to meV
         self.kpath = kpath
-        self.bands *= 1000
+        self.xlist = xlist
 
         plot_options = kwargs
         self.linewidth = plot_options.pop("linewidth", 1.5)
@@ -19,29 +32,55 @@ class BandsPlot:
         self.plot_options = plot_options
 
     def plot(self, filename=None):
-        fig, axs = plt.subplots(1, self._NSYSTEMS, constrained_layout=True)
+        """Plot the band structure.
 
-        kdata = np.arange(self.bands.shape[0])
-        for band in self.bands.T:
-            axs.plot(
-                kdata,
-                band,
-                linewidth=self.linewidth,
-                color=self.color,
-                **self.plot_options,
-            )
+        Parameters
+        ----------
+        filename : str, optional
+            If provided, saves the plot to this file
+        """
+        fig, axs = plt.subplots(1, self._NSYSTEMS, constrained_layout=True)
 
+        # Get min/max for y-axis limits
         bmin, bmax = self.bands.min(), self.bands.max()
-        ymin, ymax = (
-            bmin - 0.05 * np.abs(bmin - bmax),
-            bmax + 0.05 * np.abs(bmax - bmin),
-        )
-
+        ymin = bmin - 0.05 * np.abs(bmin - bmax)
+        ymax = bmax + 0.05 * np.abs(bmax - bmin)
         axs.set_ylim([ymin, ymax])
-        axs.set_xlim([0, kdata[-1]])
 
+        # Plot bands
+        if self.xlist is not None:
+            # Plot segments
+            start_idx = 0
+            for x in self.xlist:
+                nbands = x.shape[0]
+                segment_bands = self.bands[start_idx:start_idx + nbands].T
+                for band in segment_bands:
+                    axs.plot(
+                        x,
+                        band[start_idx:start_idx + nbands],
+                        linewidth=self.linewidth,
+                        color=self.color,
+                        **self.plot_options,
+                    )
+                start_idx += nbands
+            # Set xlim to cover all segments
+            axs.set_xlim([self.xlist[0][0], self.xlist[-1][-1]])
+        else:
+            # Standard continuous plotting
+            kdata = np.arange(self.bands.shape[0])
+            for band in self.bands.T:
+                axs.plot(
+                    kdata,
+                    band,
+                    linewidth=self.linewidth,
+                    color=self.color,
+                    **self.plot_options,
+                )
+            axs.set_xlim([0, kdata[-1]])
+
+        # Add k-point labels and vertical lines
         kpoint_labels = list(zip(*self.kpath))
-        axs.set_xticks(*kpoint_labels, fontsize=self.ticksize)
+        axs.set_xticks(kpoint_labels[0], kpoint_labels[1], fontsize=self.ticksize)
         axs.vlines(
             x=kpoint_labels[0],
             ymin=ymin,
@@ -55,4 +94,4 @@ class BandsPlot:
         if filename is None:
             plt.show()
         else:
-            fig.save(filename, dpi=300, bbox_inches="tight")
+            plt.savefig(filename, dpi=300, bbox_inches="tight")

TB2J/mathutils/auto_kpath.py

@@ -0,0 +1,154 @@
+ #!/usr/bin/env python
+from __future__ import division
+import ase
+import matplotlib.pyplot as plt
+import numpy as np
+from ase.geometry import cell_to_cellpar, cellpar_to_cell
+from ase.dft.kpoints import get_special_points, parse_path_string
+from ase.cell import Cell
+from ase.dft.kpoints import bandpath
+
+# from minimulti.spin.hamiltonian import SpinHamiltonian
+# from minimulti.spin.mover import SpinMover
+
+
+def group_band_path(bp, eps=1e-8, shift=0.15):
+    """Groups band paths by separating segments with small distances between points.
+
+    Parameters
+    ----------
+    bp : ASE.cell.BandPath
+        The band path object containing k-points and special points
+    eps : float, optional
+        The threshold distance below which points are considered to be in the same group.
+        Default is 1e-8.
+    shift : float, optional
+        The shift distance to apply between different segments for visualization.
+        Default is 0.15.
+
+    Returns
+    -------
+    tuple
+        Contains:
+        - xlist : list of arrays
+            The x-coordinates for each segment, shifted for visualization
+        - kptlist : list of arrays
+            The k-points for each segment
+        - Xs : array
+            The x-coordinates of special points, shifted for visualization
+        - knames : list
+            The names of special k-points
+    """
+    xs, Xs, knames = bp.get_linear_kpoint_axis()
+    kpts = bp.kpts
+
+    m = xs[1:] - xs[:-1] < eps
+    segments = [0] + list(np.where(m)[0] + 1) + [len(xs)]
+
+    # split Xlist
+    xlist, kptlist = [], []
+    for i, (start, end) in enumerate(zip(segments[:-1], segments[1:])):
+        kptlist.append(kpts[start:end])
+        xlist.append(xs[start:end] + i * shift)
+
+    m = Xs[1:] - Xs[:-1] < eps
+
+    s = np.where(m)[0] + 1
+
+    for i in s:
+        Xs[i:] += shift
+
+    return xlist, kptlist, Xs, knames
+
+
+def test_group_band_path():
+    """Visualize the band path grouping functionality.
+    
+    This function demonstrates how group_band_path works by:
+    1. Creating a simple test case (H atom with rectangular cell)
+    2. Generating a band path with 50 points
+    3. Grouping the path segments using group_band_path
+    4. Plotting each segment to visualize how segments are shifted
+    
+    The resulting plot shows:
+    - Each path segment plotted separately
+    - Special k-points labeled on x-axis
+    - Segments shifted relative to each other for clarity
+
+    Note: This is a visualization function rather than a unit test.
+    It helps understand the band path grouping behavior visually.
+    """
+    atoms = ase.Atoms("H", cell=[1, 1, 2])
+    bp = atoms.cell.bandpath(npoints=50)
+    xlist, kptlist, Xs, knames, spk = group_band_path(bp)
+
+    for x, k in zip(xlist, kptlist):
+        plt.plot(x, x)
+
+    plt.xticks(Xs, knames)
+    plt.show()
+
+       
+
+
+def auto_kpath(cell, knames, kvectors=None, npoints=100, supercell_matrix=None):
+    """Generates an automatic k-path for band structure calculations.
+
+    Parameters
+    ----------
+    cell : array_like
+        The unit cell vectors
+    knames : list or None
+        Names of the high-symmetry k-points. If None and kvectors is None,
+        automatically determines the path. If kvectors is provided, these names
+        correspond to the provided k-vectors.
+    kvectors : array_like, optional
+        Explicit k-vectors for the path. If None, vectors are determined from
+        knames or automatically. Default is None.
+    npoints : int, optional
+        Number of k-points along the path. Default is 100.
+    supercell_matrix : array_like, optional
+        Transformation matrix for supercell calculations. If provided, k-points
+        are transformed accordingly. Default is None.
+
+    Returns
+    -------
+    tuple
+        Contains:
+        - xlist : list of arrays
+            The x-coordinates for each path segment
+        - kptlist : list of arrays
+            The k-points for each segment
+        - Xs : array
+            The x-coordinates of special points
+        - knames : list
+            The names of special k-points
+        - spk : dict
+            Dictionary mapping k-point names to their coordinates
+    """
+    if knames is None and kvectors is None:
+        # fully automatic k-path
+        bp = Cell(cell).bandpath(npoints=npoints)
+        spk = bp.special_points
+        xlist, kptlist, Xs, knames = group_band_path(bp)
+    elif knames is not None and kvectors is None:
+        # user specified kpath by name
+        bp = Cell(cell).bandpath(knames, npoints=npoints)
+        spk = bp.special_points
+        kpts = bp.kpts
+        xlist, kptlist, Xs, knames = group_band_path(bp)
+    else:
+        # user spcified kpath and kvector.
+        kpts, x, Xs = bandpath(kvectors, cell, npoints)
+        spk = dict(zip(knames, kvectors))
+        xlist = [x]
+        kptlist = [kpts]
+
+    if supercell_matrix is not None:
+        kptlist = [np.dot(k, supercell_matrix) for k in kptlist]
+    print("High symmetry k-points:")
+    for name, k in spk.items():
+        if name == "G":
+            name = "Gamma"
+        print(f"{name}: {k}")
+    return xlist, kptlist, Xs, knames, spk

tb2j-0.9.9.10.data/scripts/TB2J_plot_magnon_bands.py

@@ -0,0 +1,7 @@
+#!python
+
+
+if __name__ == "__main__":
+    from TB2J.magnon.magnon3 import main
+
+    main()

{tb2j-0.9.9.9.dist-info → tb2j-0.9.9.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9.9
+Version: 0.9.9.10
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -25,6 +25,8 @@ Requires-Dist: HamiltonIO>=0.2.3
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
 Requires-Dist: sisl>=0.9.0
+Requires-Dist: tomli>=2.0.0
+Requires-Dist: tomli-w>=1.0.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{tb2j-0.9.9.9.dist-info → tb2j-0.9.9.10.dist-info}/RECORD

@@ -55,20 +55,22 @@ TB2J/interfaces/abacus/test_density_matrix.py,sha256=bMWWJYtDS57SpPZ-eZXZ9Hr_UK4
 TB2J/interfaces/abacus/test_read_HRSR.py,sha256=W1oO_yigT50Yb5_u-KB_IfTpM7kArGkBuMSMs0H4CTs,1235
 TB2J/interfaces/abacus/test_read_stru.py,sha256=hoKPHVco8vwzC7Gao4bOPCdAPhh29x-9DTJJqRr7AYM,788
 TB2J/io_exchange/__init__.py,sha256=LqEnG67qDVKt4hCUywDEQvUIJ7jsQjmtueOW_J16NOE,54
-TB2J/io_exchange/io_exchange.py,sha256=3swwPeheUog2pLrpBnyx76_AG7pPT8mVNEwv2ZTHoRI,21309
+TB2J/io_exchange/io_exchange.py,sha256=px0FcH_Vx7FfoB2rA3ERXImjfrbYuBB7UImBxg6R_8E,22585
 TB2J/io_exchange/io_multibinit.py,sha256=8PDmWxzGuv-GwJosj2ZTmiyNY_duFVWJ4ekCuSqGdd8,6739
 TB2J/io_exchange/io_tomsasd.py,sha256=NqkAC1Fl-CUnFA21eBzSy_S5F_oeQFJysw4UukQbN8o,4173
 TB2J/io_exchange/io_txt.py,sha256=BMr1eSILlKpgtjvDx7uw2VMAkEKSvGEPNxpaT_zev0I,10547
 TB2J/io_exchange/io_uppasd.py,sha256=bI4iPEgnK4TvCZNvb6x2xYXgjW7pEehCqmcizy2pqFU,3301
-TB2J/io_exchange/io_vampire.py,sha256=59Bq5NZ3z6ACDdZdNrYnLnnKPVsZVqnYx7R6LQvO52E,5725
-TB2J/magnon/__init__.py,sha256=jdUFkOlhrpHRmKavAXVcFdZgtY7lKZVzMPFlLmmCErM,113
+TB2J/io_exchange/io_vampire.py,sha256=u4NZhqoC_JBcVq19WZfBkyM5p8u-OMuRoUrtFIcPp5E,5762
+TB2J/magnon/__init__.py,sha256=Q69duroGIIotgW_71ZdHYarSiJLGAu9NPYgEacUk6eI,117
 TB2J/magnon/io_exchange2.py,sha256=EcC3x6H13qq61WBsr__xKzHDtSvy_dMz1tEdUaqSG2I,23265
-TB2J/magnon/magnon3.py,sha256=GNqJVf73xibVbI9wVvaN2_uigbnNJKbHZxqjICwz3vw,10958
+TB2J/magnon/magnon3.py,sha256=IhuDqqkWP5NzMjaPoVk2C5aw4xIgrxgWfNdrZfoPd70,27064
+TB2J/magnon/magnon_band.py,sha256=S8W0sP-uR0urmi85QZRIDevIYnALUKAd1DPF99KLvAI,6076
 TB2J/magnon/magnon_io.py,sha256=H4bmzCcnh1D3Sb6UBIIKWa6jIrA20dg9lX4wfLXHEjo,1241
 TB2J/magnon/magnon_math.py,sha256=hJ2k24eR4TzdaFMxfxgCr10lWV4GEcfaf2WxhWj-uUk,1320
-TB2J/magnon/plot.py,sha256=kwq9LL0FRVo-SLYNkE-ghlyjz8DZD-c4LAWg8si5GJo,1674
+TB2J/magnon/plot.py,sha256=QxkI2bIs-wF31rUzyxL-SRR_r7XY-gFVLb9SVFnGaJY,3197
 TB2J/magnon/structure.py,sha256=rKefzXgQlEjVvV-A7E2IogVDWwf5egZr3Wxxu6HuJU4,7685
 TB2J/mathutils/__init__.py,sha256=E70Mx8mLXh3DJGmdN3TLWmGYMcsbvKxmgxUbAI6Mzmo,49
+TB2J/mathutils/auto_kpath.py,sha256=9vhb_3iRSYE7eRmY1sVRqkK3i4KzaGAw1w0SmCzIA7Y,5119
 TB2J/mathutils/fermi.py,sha256=72tZ5CptGmYaBUD0xLWltuH7LBXcrMUwODyW6-WqlzI,638
 TB2J/mathutils/fibonacci_sphere.py,sha256=1rqf5n3a9aDjSydA4qGkR1eIeLJKuoblA73cchWJzNg,2342
 TB2J/mathutils/kR_convert.py,sha256=p_9XWJVNanTzTK2rI6KRjTkbSq42la6N448-zJOsMwY,2671
@@ -87,20 +89,21 @@ TB2J/spinham/supercell.py,sha256=y17uUC6r3gQb278FhxIW4CABihfLTvKFj6flyXrCPR8,122
 TB2J/wannier/__init__.py,sha256=7ojCbM84PYv1X1Tbo4NHI-d3gWmQsZB_xiYqbfxVV1E,80
 TB2J/wannier/w90_parser.py,sha256=dbd63LuKyv2DVUzqRINGsbDzEsOxsQyE8_Ear_LQIRg,4620
 TB2J/wannier/w90_tb_parser.py,sha256=qt8pnuprmPp9iIAYwPkPbmEzk6ZPgMq2xognoQp7vwc,4610
-tb2j-0.9.9.9.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
-tb2j-0.9.9.9.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-tb2j-0.9.9.9.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-tb2j-0.9.9.9.data/scripts/TB2J_magnon2.py,sha256=tMa7Fg_Wd2UytnrH3C_AsgGM7BciUW0iy6NiPlWvar8,1920
-tb2j-0.9.9.9.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-tb2j-0.9.9.9.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
-tb2j-0.9.9.9.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
-tb2j-0.9.9.9.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
-tb2j-0.9.9.9.data/scripts/abacus2J.py,sha256=ozYI7qZyja1WEs9oCYVpeYAfVj5PGhehhmdZFcvrd3g,1795
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