TB2J 0.9.9.9__py3-none-any.whl → 0.9.9.12__py3-none-any.whl

TB2J/magnon/magnon_band.py

@@ -0,0 +1,185 @@
+"""Module for handling magnon band structure data and plotting."""
+
+import json
+from dataclasses import dataclass
+from typing import List, Optional, Tuple, Union
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+@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, shift=0.0,**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]+shift,
+                        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+shift,
+                    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/magnon_math.py

@@ -32,6 +32,7 @@ def get_rotation_arrays(magmoms, u=uz):
     v = magmoms
     n = np.cross(u, v)
     n /= np.linalg.norm(n, axis=-1).reshape(dim, 1)
+    #z = u #np.repeat(u, dim, axis=0)
     z = np.repeat(u, dim, axis=0)
     A = np.stack([z, np.cross(n, z), n], axis=1)
     B = np.stack([v, np.cross(n, v), n], axis=1)

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 +1,151 @@
+#!/usr/bin/env python
+from __future__ import division
+
+import ase
+import matplotlib.pyplot as plt
+import numpy as np
+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-0.9.9.12.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-0.9.9.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9.9
+Version: 0.9.9.12
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,10 +21,12 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.2.3
+Requires-Dist: HamiltonIO>=0.2.4
 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-0.9.9.12.dist-info}/RECORD

@@ -1,17 +1,17 @@
 TB2J/Jdownfolder.py,sha256=n5BeQCYP4mD9JsAPeE1F3ZKKR3SUxADfDbaG_rzi77k,9658
-TB2J/Jtensor.py,sha256=t6OsqrSlYW6Im4H7ykVAW8Al_pFXN4C5yj2UEsV6r7g,3181
+TB2J/Jtensor.py,sha256=Wi06AAbfKFU6f2a2jkFr9zU2cwwfVroajTp-dwCtkTE,3160
 TB2J/MAE.py,sha256=fM8U-Dgp9HcQOEeC_kyZV1oVrygBvcux9BraUXVouvY,10994
-TB2J/MAEGreen.py,sha256=Iq4hlZrKEOycPvpV66_t13WIcJ1FJgBS79NleXYpFzw,15528
+TB2J/MAEGreen.py,sha256=DHoU6nlM0Fk42T_SYd_s-VafB6wCZNzVzRXhuv-hCwM,15762
 TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
 TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
-TB2J/__init__.py,sha256=AuZFEUeBNk8Hny02OhG2Y1omWiUh5m4XffiIIrWZkoI,24
+TB2J/__init__.py,sha256=TcMW0FTsZFR9McJTh8TBwZl2lylHc2uwsxVV9PsgSwY,25
 TB2J/anisotropy.py,sha256=0zmvXkmDmakbBOwGYLa3IIkv5cE99SHLAQJsGoZz7JQ,25463
 TB2J/basis.py,sha256=DFo6_QUwjBwisP6zGxvoO0lpGTMDPAOkiL9giNCjOjA,1558
 TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=zLHQZZ3hhgLkLFPATCraLOJyLJKLC0fba_L_5sRz23o,3246
 TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
-TB2J/exchange.py,sha256=P0GR2mlb-c_59fM_rFmc2C5zN8G7z5-cCsI7YAN5Aik,26980
+TB2J/exchange.py,sha256=rJ7XeHOo6j9A0alauM2XQ5DvTO741dq_pDQQxyyn8mE,26981
 TB2J/exchangeCL2.py,sha256=P7bklMXVYX_tn9DbjEPqeTir1SeZyfPBIP1fhWUzLmY,11419
 TB2J/exchange_params.py,sha256=VW9nGVio6M_Ub9-36L_LExhjgdD1E_joYpI8AxmM360,8029
 TB2J/exchange_pert.py,sha256=jmFMtQbYa_uczM4VAeS6TijkIHRFIqEzZJswzE9Wfuo,8523
@@ -19,7 +19,7 @@ TB2J/exchange_qspace.py,sha256=ZL68qBGFUaQ9BsSPsJaaoWOr9RssPiqX34R_9I3nk_8,8436
 TB2J/gpaw_wrapper.py,sha256=aJ--9Dtyq7jOP1Hkh-Sh1nWcfXm6zKcljOCO0DNCAr0,6890
 TB2J/green.py,sha256=ySXjoV3Cj_E2C41dRfc3TkS7M4vmM6qcHXkt-_-jxsY,17071
 TB2J/greentest.py,sha256=2ISSfhor9ecSEOi_E6b4Cv26wEIQlwlzca0ru8z44_E,1603
-TB2J/io_merge.py,sha256=E1_GfAB2HGpW-ipaO2lqU9SvaslwkiLxssn4DqJpMT8,6899
+TB2J/io_merge.py,sha256=xj5sIo5o62HYwSnijGycem_rAc8kSzY-HI2IJDRhzyE,7405
 TB2J/kpoints.py,sha256=9L7tBarFBHoIhpuc9zuwA6HdnlgH834SQrPek4yRoWk,3191
 TB2J/myTB.py,sha256=ok_B4my29bOIghMSZfx0Es6G8FaXaIiLP4gPxTdSj00,17659
 TB2J/mycfr.py,sha256=ZF1PEE2khlKd_4gPyMkoNXepX3XqwWAL2kDbRJNVX-Y,3908
@@ -43,32 +43,34 @@ TB2J/interfaces/__init__.py,sha256=4tiLoXQ73Nlyi9L4j8jJXOYzXluVNPxQZkwfkQZEGHg,3
 TB2J/interfaces/gpaw_interface.py,sha256=GCDlJ-hRWfChvWwsgBDYSmVqO4sH9HAuGZTV9GqgN6c,1504
 TB2J/interfaces/lawaf_interface.py,sha256=PieLnmppdafOYsgeHznqOou1g9L1sam5jOm3KaObdqo,4408
 TB2J/interfaces/manager.py,sha256=PQMLEfMCT5GnDWSl2nI4JOgRPm_fysyR-6Y6l97xWcw,860
-TB2J/interfaces/siesta_interface.py,sha256=nkb8CTjHtv3DgMok4njyiaE-vDGDJFCjLHat71R_Z48,7561
+TB2J/interfaces/siesta_interface.py,sha256=Y4rRn_MRZUOI4y4btgCKTtVy8iXrSpaBuK7SMCJ1C2o,7594
 TB2J/interfaces/wannier90_interface.py,sha256=qzRgXUBb7t1Aiegrl_RV51BB8csdtVM0EP0Z4pjmTcs,4467
 TB2J/interfaces/abacus/__init__.py,sha256=leas71oCvM_HxrF4gnO5A_VKcJmDAgsI1BUctLU3OBw,177
 TB2J/interfaces/abacus/abacus_api.py,sha256=lNV4LNkLcKw7Zux4MQYM9wnh3eFTlcSqbf4Pb7pqhrk,7243
 TB2J/interfaces/abacus/abacus_wrapper.py,sha256=bQFnvvy-0hruTavH_VspMk1wD32t2UFybEkCgwkwle0,11941
 TB2J/interfaces/abacus/gen_exchange_abacus.py,sha256=v-AUHGkJWeMNf4D5A4wOpCjM6DygQsFB6SWu-BGdTxM,3262
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