Update references, minor fixes

README.rst

@@ -29,9 +29,9 @@ If you use the implementation of the local Chern marker in periodic boundary con
 
   N. Baù and A. Marrazzo
   Local Chern marker for periodic systems
-  `accepted in PRB, arxiv (2023)`_
+  `Phys. Rev. B 109, 014206 (2024)`_
 
-.. _accepted in PRB, arxiv (2023): https://doi.org/10.48550/arXiv.2310.15783
+.. _Phys. Rev. B 109, 014206 (2024): https://doi.org/10.1103/PhysRevB.109.014206
 
 If you use the implementation of the localization marker:
 

docs/changelog.rst

@@ -15,7 +15,7 @@ The functions of previous versions have been updated in order to work with this
 
 * Introduced three main classes :python:`Model`, :python:`Supercell` and :python:`FiniteModel` which are aimed at the creation of the specific model.
 * Introduced the interface with `Wannier90 <https://wannier.org/>`_ through `WannierBerri <https://wannier-berri.org/index.html>`_, which allows to read Wannier Hamiltonians.
-* Introduced the PBC local Chern marker for periodic system in a supercell, as defined in Ref. `Baù-Marrazzo (2023) <https://arxiv.org/abs/2310.15783>`_.
+* Introduced the PBC local Chern marker for periodic system in a supercell, as defined in Ref. `Baù-Marrazzo (2023) <https://doi.org/10.1103/PhysRevB.109.014206>`_.
 * Introduced the localization marker for finite systems, as defined in Ref. `Marrazzo-Resta (2019) <https://doi.org/10.1103/PhysRevLett.122.166602>`_.
 * Introduced the possibility of add disorder in the system both by an on-site uniformly distributed random term (Anderson disorder) and by vacancies in the lattice.
 

docs/index.rst

@@ -13,7 +13,7 @@ Welcome to StraWBerryPy!
 **StraWBerryPy** (Single-poinT and local invaRiAnts for Wannier Berriologies in Python) is a Python package to calculate topological invariants and quantum-geometrical quantities in non-crystalline topological insulators. 
 
 StraWBerryPy can work with periodic and finite systems in tight-binding.
-In periodic boundary conditions (PBCs), the code implements the single-point formulas for the Chern number `[Ceresoli-Resta] <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.76.012405>`_ and the single-point spin Chern number `[Favata-Marrazzo] <https://iopscience.iop.org/article/10.1088/2516-1075/acba6f/meta>`_ in the supercell framework. In PBCs, it is also possible to calculate the local Chern marker within periodic boundary conditions `[Baù-Marrazzo] <https://arxiv.org/abs/2310.15783>`_.
+In periodic boundary conditions (PBCs), the code implements the single-point formulas for the Chern number `[Ceresoli-Resta] <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.76.012405>`_ and the single-point spin Chern number `[Favata-Marrazzo] <https://iopscience.iop.org/article/10.1088/2516-1075/acba6f/meta>`_ in the supercell framework. In PBCs, it is also possible to calculate the local Chern marker within periodic boundary conditions `[Baù-Marrazzo] <https://doi.org/10.1103/PhysRevB.109.014206>`_.
 In addition, StraWBerryPy can handle finite systems (such as bounded samples and heterostructures) in open boundary conditions (OBCs) and can compute the local Chern marker `[Bianco-Resta] <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.241106>`_ and the localization marker `[Marrazzo-Resta] <https://doi.org/10.1103/PhysRevLett.122.166602>`_ .
 
 The code provides dedicated interfaces to the tight-binding engines `PythTB <http://www.physics.rutgers.edu/pythtb/>`_ and `TBmodels <https://tbmodels.greschd.ch/en/latest/>`_. Latest version of StraWBerryPy implements the calculation of single-point topological invariants with ab initio Wannier Hamiltonians, which are read in the format produced by `Wannier90 <https://wannier.org/>`_ through `WannierBerri <https://wannier-berri.org/index.html>`_.

docs/tutorial.rst

@@ -37,7 +37,7 @@ In order to add disorder and vacancies to a given model we can use the following
     model.add_onsite_disorder(w = 3, seed = rng_seed)
 
     # Add 15 random vacancies to the lattice
-    vacncies = strawberrypy.utils.unique_vacancies(num = 15, Lx = model.Lx, Ly = model.Ly, basis = model.states_uc, seed = rng_seed)
+    vacncies = strawberrypy.utils.unique_vacancies(num = 15, Lx = model.Lx, Ly = model.Ly, basis = atoms_uc, seed = rng_seed)
     model.add_vacancies(vacancies_list = vacancies)
 
 .. note::
@@ -146,7 +146,7 @@ Output: ``In the pristine KM model (w = 0): SPSCN = -0.0024642975185114. In the
 
 Topological periodic heterostructure
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-As an example, we report here the code used to generate Fig. 3 of Ref. `Baù-Marrazzo(2023) <https://arxiv.org/abs/2310.15783>`_.
+As an example, we report here the code used to generate Fig. 3 of Ref. `Baù-Marrazzo(2023) <https://doi.org/10.1103/PhysRevB.109.014206>`_.
 
 .. code:: python
 
@@ -176,4 +176,4 @@ As an example, we report here the code used to generate Fig. 3 of Ref. `Baù-Mar
 
 .. image:: _static/media/heterostructure_pbclcm.png
    :width: 150%
-   :alt: PBC local Chern marker produced with the code above
+   :alt: PBC local Chern marker produced with the code above

pyproject.toml

@@ -31,8 +31,8 @@ repository = "https://github.com/strawberrypy-developers/strawberrypy.git"
 documentation = "http://strawberrypy.readthedocs.io/"
 
 [project.optional-dependencies]
-devs = ["sphinx==6.2.1",
-        "sphinx-copybutton==0.5.2",
-        "sphinxawesome-theme==5.0.1",
-        "sphinx_book_theme==1.0.1",
-        ]
+devs = ["sphinx",
+        "sphinx-copybutton",
+        "sphinxawesome-theme",
+        "sphinx_book_theme",
+        ]

strawberrypy/classes.py

@@ -326,6 +326,7 @@ def add_vacancies(self, vacancies_list):
         self.hamiltonian = ham
         self.sz = sz
         self.n_occ = int(nocc)
+        self.n_orb = int(norbs)
         self.disordered = True
         self.cart_positions = cart_pos.T
 

strawberrypy/finite_model.py

@@ -140,7 +140,7 @@ def local_chern_marker(self, direction : int = None, start : int = 0, return_pro
             raise NotImplementedError("The local Chern marker is not yet implemented for dimensionality different than 2.")
 
         if input_projector is None:
-            # Eigenvectors at \Gamma
+            # Eigenvectors of the Hamiltonian
             eigenvals, eigenvecs = la.eigh(self.hamiltonian)
 
             # Evaluate the chemical potential
@@ -216,9 +216,9 @@ def localization_marker(self, direction : int = None, start : int = 0, return_pr
         Returns
         --------
             lattice_loc :
-                Local Chern marker evaluated on the whole lattice if :python:`direction == None`.
+                Localization marker evaluated on the whole lattice if :python:`direction == None`.
             loc_direction :
-                Local Chern marker evaluated along :python:`direction` starting from :python:`start`.
+                Localization marker evaluated along :python:`direction` starting from :python:`start`.
             gs_projector :
                 Ground state projector, returned if :python:`return_projector == True`.
 
@@ -236,12 +236,12 @@ def localization_marker(self, direction : int = None, start : int = 0, return_pr
 
         if direction is not None:
             if direction == 0:
-                if start not in range(self.Ly): raise RuntimeError("Invalid start parameter (must be within [0, ny_sites - 1]).")
+                if start not in range(self.Ly): raise RuntimeError("Invalid start parameter (must be within [0, self.Ly - 1]).")
             else:
-                if start not in range(self.Lx): raise RuntimeError("Invalid start parameter (must be within [0, nx_sites - 1]).")
+                if start not in range(self.Lx): raise RuntimeError("Invalid start parameter (must be within [0, self.Lx - 1]).")
 
         if input_projector is None:
-            # Eigenvectors at \Gamma
+            # Eigenvectors of the Hamiltonian
             _, eigenvecs = la.eigh(self.hamiltonian)
 
             # Build the ground state projector

strawberrypy/supercell.py

@@ -330,7 +330,7 @@ def single_point_spin_chern(self, spin : str = 'down', formula : str = 'both', r
 
     def pbc_local_chern_marker(self, direction : int = None, start : int = 0, return_projector : bool = False, input_projector = None, formula : str = "symmetric", macroscopic_average : bool = False, cutoff : float = 0.8, smearing_temperature : float = 0, fermidirac_cutoff : float = 0.1):
         r"""
-        Evaluate the local Chern marker provided in Ref. `Baù-Marrazzo (2023) <https://arxiv.org/abs/2310.15783>`_ on the whole supercell if :python:`direction == None`. If ``direction`` is not :python:`None` evaluates the PBC local Chern marker along :python:`direction` starting from :python:`start`. Allowed directions are ``0`` (meaning along :math:`\mathbf{a}_1`), and ``1`` (meaning along :math:`\mathbf{a}_2`).
+        Evaluate the local Chern marker provided in Ref. `Baù-Marrazzo (2023) <https://doi.org/10.1103/PhysRevB.109.014206>`_ on the whole supercell if :python:`direction == None`. If ``direction`` is not :python:`None` evaluates the PBC local Chern marker along :python:`direction` starting from :python:`start`. Allowed directions are ``0`` (meaning along :math:`\mathbf{a}_1`), and ``1`` (meaning along :math:`\mathbf{a}_2`).
         
         Parameters
         ----------

strawberrypy/utils.py

@@ -140,6 +140,7 @@ def unique_vacancies(num : int, Lx : int, Ly : int, basis : int, seed : int = No
 
         # If this is a new entry store it
         if not trial_index in indexes:
+            indexes.append(trial_index)
             unique_list.append(trial)
 
     return unique_list

tests/check/lcm_vacancies.check

@@ -1,118 +1,118 @@
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