Merge pull request #2 from eimrek/release/1.4.1

Release/1.4.1

example.ipynb

@@ -69,7 +69,7 @@
    },
    "outputs": [],
    "source": [
-    "mfh_model.report(num_orb=2, sts_h=3.0, sts_broad=0.04)"
+    "mfh_model.report(num_orb=2, sts_h=10.0, sts_broad=0.05)"
    ]
   },
   {

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="tb-mean-field-hubbard",
-    version="1.4.0",
+    version="1.4.1",
     author="Kristjan Eimre",
     author_email="[email protected]",
     description="Package to run tight-binding mean field hubbard calculations",

tb_mean_field_hubbard/__init__.py

@@ -1,3 +1,3 @@
 from .mfh import MeanFieldHubbardModel
 
-__version__ = "1.4.0"
+__version__ = "1.4.1"

tb_mean_field_hubbard/mfh.py

@@ -319,7 +319,7 @@ def _get_atoms_extent(self, atoms, edge_space):
         ymax = np.max(atoms.positions[:, 1]) + edge_space
         return xmin, xmax, ymin, ymax
 
-    def calc_orb_ldos_map(self, i_spin, i_orb, h=6.0, edge_space=5.0, dx=0.1, z_eff=1):
+    def calc_orb_map(self, i_spin, i_orb, h=10.0, edge_space=5.0, dx=0.1, z_eff=3.25):
 
         extent = self._get_atoms_extent(self.ase_geom, edge_space)
 
@@ -336,9 +336,9 @@ def calc_orb_ldos_map(self, i_spin, i_orb, h=6.0, edge_space=5.0, dx=0.1, z_eff=
             pz_orb = utils.carbon_2pz_slater(local_grid[0] - p[0], local_grid[1] - p[1], h, z_eff)
             orb_map[local_i[0]:local_i[1], local_i[2]:local_i[3]] += coef * pz_orb
 
-        return np.abs(orb_map)**2
+        return orb_map
 
-    def calc_sts_map(self, energy, broadening=0.05, h=6.0, edge_space=5.0, dx=0.1, z_eff=1):
+    def calc_sts_map(self, energy, broadening=0.05, h=10.0, edge_space=5.0, dx=0.1, z_eff=3.25):
 
         extent = self._get_atoms_extent(self.ase_geom, edge_space)
         # define grid
@@ -351,20 +351,20 @@ def calc_sts_map(self, energy, broadening=0.05, h=6.0, edge_space=5.0, dx=0.1, z
             for i_orb, evl in enumerate(self.evals[i_spin]):
                 if np.abs(energy - evl) <= 3.0 * broadening:
                     broad_coef = utils.gaussian(energy - evl, broadening)
-                    orb_ldos_map = self.calc_orb_ldos_map(i_spin, i_orb, h, edge_space, dx, z_eff)
+                    orb_ldos_map = np.abs(self.calc_orb_map(i_spin, i_orb, h, edge_space, dx, z_eff))**2
                     final_map += broad_coef * orb_ldos_map
         return final_map
 
     def plot_sts_map(self,
                      ax,
                      energy,
                      broadening=0.05,
-                     h=6.0,
+                     h=10.0,
                      edge_space=5.0,
                      dx=0.1,
                      title=None,
                      cmap='seismic',
-                     z_eff=1):
+                     z_eff=3.25):
 
         final_map = self.calc_sts_map(energy, broadening, h, edge_space, dx, z_eff)
 
@@ -374,7 +374,7 @@ def plot_sts_map(self,
         ax.axis('off')
         ax.set_title(title)
 
-    def report(self, num_orb=2, sts_h=3.5, sts_broad=0.05):
+    def report(self, num_orb=2, sts_h=10.0, sts_broad=0.05):
 
         print(f"multiplicity:       {self.multiplicity:12d}")
         print(f"abs. magnetization: {self.abs_mag:12.4f}")

tb_mean_field_hubbard/utils.py

@@ -215,23 +215,23 @@ def radial(r, n, l):
     return orbital
 
 
-def carbon_2pz_slater(x, y, z, z_eff=1):
+def carbon_2pz_slater(x, y, z, z_eff=3.25):
     """Carbon 2pz slater orbital
 
     z_eff determines the effective nuclear charge interacting with the pz orbital
-    Options:
+    Potential options:
 
     z_eff = 1
-        This corresponds to a hydrogen-like 2pz orbital
-        it matches best with DFT reference and is thus the default
+        This corresponds to a hydrogen-like 2pz orbital and in
+        some cases matches well with DFT reference
 
     z_eff = 3.136
-        Based on https://en.wikipedia.org/wiki/Effective_nuclear_charge
+        Value shown in https://en.wikipedia.org/wiki/Effective_nuclear_charge
 
     z_eff = 3.25
-        This is the value calculated by Slater's rules
-        https://en.wikipedia.org/wiki/Slater%27s_rules
-        This value matches with https://doi.org/10.1038/s41557-019-0316-8
+        This is the value calculated by Slater's rules (https://en.wikipedia.org/wiki/Slater%27s_rules)
+        This value is also used in https://doi.org/10.1038/s41557-019-0316-8
+        This is the default.
     
     """
     r_grid = np.sqrt(x**2 + y**2 + z**2)  # angstrom