Convert Marker from namedtuple to py class

abipy/abio/inputs.py

@@ -814,7 +814,7 @@ def escape(text):
                 for name in names:
                     value = vars[name]
                     if mnemonics and value is not None:
-                        print(f"{name=}")
+                        #print(f"{name=}")
                         app(escape("#### <" + var_database[name].mnemonics + ">"))
 
                     # Build variable, convert to string and append it

abipy/core/kpoints.py

@@ -101,7 +101,6 @@ def issamek(k1, k2, atol=None):
     """
     k1 = np.asarray(k1)
     k2 = np.asarray(k2)
-    #if k1.shape != k2.shape:
 
     return is_integer(k1 - k2, atol=atol)
 
@@ -416,15 +415,12 @@ def kpoints_indices(frac_coords, ngkpt, check_mesh=0) -> np.ndarray:
         ngkpt:
         check_mesh:
     """
+
     # Transforms kpt in its corresponding reduced number in the interval [0,1[
     k_indices = [np.round((kpt % 1) * ngkpt) for kpt in frac_coords]
     k_indices = np.array(k_indices, dtype=int)
 
-    for kpt, inds in zip(frac_coords, k_indices):
-        if np.any(inds >= ngkpt):
-            print(f"{kpt=}, {np.round(kpt % 1)=} {inds=})")
-            #raise ValueError("")
-
+    # Debug secction.
     if check_mesh:
         print(f"kpoints_indices: Testing whether k-points belong to the {ngkpt =} mesh")
         ierr = 0
@@ -435,7 +431,12 @@ def kpoints_indices(frac_coords, ngkpt, check_mesh=0) -> np.ndarray:
                 ierr += 1; print(kpt, "-->", same_k)
         if ierr:
             raise ValueError("Wrong mapping")
-        print("Check succesful!")
+
+        #for kpt, inds in zip(frac_coords, k_indices):
+        #    if np.any(inds >= ngkpt):
+        #        raise ValueError(f"inds >= nkgpt for {kpt=}, {np.round(kpt % 1)=} {inds=})")
+
+        print("Check succesfull!")
 
     return k_indices
 

abipy/core/structure.py

@@ -1301,7 +1301,6 @@ def check_image(structure, site):
 
         # If the centrosymmetry is broken at a given atomic site of the given structure,
         # returns False. Else, return True
-
         sites = self.sites
 
         for s1 in sites:

abipy/dfpt/phonons.py

@@ -1123,7 +1123,8 @@ def plot(self, ax=None, units="eV", qlabels=None, branch_range=None, match_bands
         self.plot_ax(ax, branch_range, units=units, match_bands=match_bands, **kwargs)
 
         if points is not None:
-            ax.scatter(points.x, np.array(points.y), s=np.abs(points.s), marker="o", c="b")
+            ax.scatter(points.x, np.array(points.y), s=np.abs(points.s),
+                        marker=points.marker, c=points.color, alpha=points.alpha)
 
         if temp is not None:
             # Scatter plot with Bose-Einstein occupation factors for T = temp
@@ -2940,7 +2941,7 @@ def __init__(self, filepath: str):
             path: path to the file
         """
         super().__init__(filepath)
-        self.reader = PHBST_Reader(filepath)
+        self.reader = self.r = PHBST_Reader(filepath)
 
         # Initialize Phonon bands and add metadata from ncfile
         self._phbands = PhononBands.from_file(filepath)
@@ -2982,7 +2983,7 @@ def phbands(self) -> PhononBands:
 
     def close(self) -> None:
         """Close the file."""
-        self.reader.close()
+        self.r.close()
 
     @lazy_property
     def params(self) -> dict:
@@ -3623,12 +3624,16 @@ def __init__(self, filepath: str):
         # Open the file, read data and create objects.
         super().__init__(filepath)
 
-        self.reader = r = PhdosReader(filepath)
-        self.wmesh = r.wmesh
+        self.reader = self.r = PhdosReader(filepath)
+        self.wmesh = self.r.wmesh
 
     def close(self) -> None:
         """Close the file."""
-        self.reader.close()
+        self.r.close()
+
+    @lazy_property
+    def qptrlatt(self):
+        return self.r.read_value("qptrlatt")
 
     @lazy_property
     def params(self) -> dict:
@@ -3666,12 +3671,12 @@ def to_string(self, verbose: int = 0) -> str:
     @lazy_property
     def structure(self) -> Structure:
         """|Structure| object."""
-        return self.reader.structure
+        return self.r.structure
 
     @lazy_property
     def phdos(self) -> PhononDos:
         """|PhononDos| object."""
-        return self.reader.read_phdos()
+        return self.r.read_phdos()
 
     @lazy_property
     def pjdos_symbol(self):
@@ -3680,15 +3685,15 @@ def pjdos_symbol(self):
         where PhononDos is the contribution to the total DOS summed over atoms
         with chemical symbol `symbol`.
         """
-        return self.reader.read_pjdos_symbol_dict()
+        return self.r.read_pjdos_symbol_dict()
 
     @lazy_property
     def msqd_dos(self):
         """
         |MsqDos| object with Mean square displacement tensor in cartesian coords.
         Allows one to calculate Debye Waller factors by integration with 1/omega and the Bose-Einstein factor.
         """
-        return self.reader.read_msq_dos()
+        return self.r.read_msq_dos()
 
     @add_fig_kwargs
     def plot_pjdos_type(self, units="eV", stacked=True, colormap="jet", alpha=0.7, exchange_xy=False,
@@ -3851,7 +3856,7 @@ def plot_pjdos_cartdirs_type(self, units="eV", stacked=True, colormap="jet", alp
         cmap = plt.get_cmap(colormap)
 
         # symbol --> [three, number_of_frequencies] in cart dirs
-        pjdos_symbol_rc = self.reader.read_pjdos_symbol_xyz_dict()
+        pjdos_symbol_rc = self.r.read_pjdos_symbol_xyz_dict()
 
         xx = self.phdos.mesh * factor
         for idir, ax in enumerate(ax_list):
@@ -3865,7 +3870,7 @@ def plot_pjdos_cartdirs_type(self, units="eV", stacked=True, colormap="jet", alp
 
             # Plot Type projected DOSes along cartesian direction idir
             cumulative = np.zeros(len(self.wmesh))
-            for itype, symbol in enumerate(self.reader.chemical_symbols):
+            for itype, symbol in enumerate(self.r.chemical_symbols):
                 color = cmap(float(itype) / max(1, ntypat - 1))
                 yy = pjdos_symbol_rc[symbol][idir] / factor
 
@@ -3923,7 +3928,7 @@ def plot_pjdos_cartdirs_site(self, view="inequivalent", units="eV", stacked=True
         cmap = plt.get_cmap(colormap)
 
         # [natom, three, nomega] array with PH-DOS projected over atoms and cartesian directions
-        pjdos_atdir = self.reader.read_pjdos_atdir()
+        pjdos_atdir = self.r.read_pjdos_atdir()
 
         xx = self.phdos.mesh * factor
         for idir, ax in enumerate(ax_list):
@@ -4019,7 +4024,7 @@ def to_pymatgen(self) -> PmgCompletePhononDos:
         total_dos = self.phdos.to_pymatgen()
 
         # [natom, three, nomega] array with PH-DOS projected over atoms and cartesian directions"""
-        pjdos_atdir = self.reader.read_pjdos_atdir()
+        pjdos_atdir = self.r.read_pjdos_atdir()
 
         factor = abu.phfactor_ev2units("thz")
         summed_pjdos = np.sum(pjdos_atdir, axis=1) / factor

abipy/electrons/ebands.py

@@ -185,7 +185,7 @@ def num_leadblanks(string):
             return _TIPS
 
 
-class ElectronTransition(object):
+class ElectronTransition:
     """
     This object describes an electronic transition between two single-particle states.
     """
@@ -516,8 +516,7 @@ def __init__(self, structure, kpoints, eigens, fermie, occfacts, nelect, nspinor
         Args:
             structure: |Structure| object.
             kpoints: |KpointList| instance.
-            eigens: Array-like object with the eigenvalues (eV) stored as [s, k, b]
-                where s: spin , k: kpoint, b: band index
+            eigens: Array-like object with the eigenvalues (eV) stored as [s, k, b] where s: spin , k: kpoint, b: band index
             fermie: Fermi level in eV.
             occfacts: Occupation factors (same shape as eigens)
             nelect: Number of valence electrons in the unit cell.
@@ -798,8 +797,7 @@ def with_points_along_path(self, frac_bounds=None, knames=None, dist_tol=1e-12):
             frac_bounds: [M, 3] array  with the vertexes of the k-path in reduced coordinates.
                 If None, the k-path is automatically selected from the structure.
             knames: List of strings with the k-point labels defining the k-path. It has precedence over frac_bounds.
-            dist_tol: A point is considered to be on the path if its distance from the line
-                is less than dist_tol.
+            dist_tol: A point is considered to be on the path if its distance from the line is less than dist_tol.
 
         Return:
             namedtuple with the following attributes::
@@ -2216,7 +2214,8 @@ def plot(self, spin=None, band_range=None, klabels=None, e0="fermie", ax=None, y
                 self.plot_ax(ax, e0, spin=spin, band=band, **opts)
 
         if points is not None:
-            ax.scatter(points.x, np.array(points.y) - e0, s=np.abs(points.s), marker="o", c="b")
+            ax.scatter(points.x, np.array(points.y) - e0, s=np.abs(points.s),
+                        marker=points.marker, c=points.color, alpha=points.alpha)
 
         if with_gaps and (self.mband > self.nspinor * self.nelect // 2):
             # Show fundamental and direct gaps for each spin.
@@ -2775,7 +2774,6 @@ def plot_with_edos(self, edos, klabels=None, ax_list=None, e0="fermie", points=N
                 * ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
                 *  Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
                 *  None: Don't shift energies, equivalent to ``e0 = 0``
-
             points: Marker object with the position and the size of the marker.
                 Used for plotting purpose e.g. QP energies, energy derivatives...
             with_gaps: True to add markers and arrows showing the fundamental and the direct gap.
@@ -2854,7 +2852,6 @@ def plotly_with_edos(self, edos, klabels=None, fig=None, band_rcd=None, dos_rcd=
                 * ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
                 *  Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
                 *  None: Don't shift energies, equivalent to ``e0 = 0``
-
             points: Marker object with the position and the size of the marker.
                 Used for plotting purpose e.g. QP energies, energy derivatives...
             with_gaps: True to add markers and arrows showing the fundamental and the direct gap.