[ENH] Add Miedema's scale of electronegativity (#204)

* add miedema electronegativity

* update reference

* add docs on Miedema electronegativity

* add plots of eletronegativities

* add function for plotting en scales

alembic/versions/db2973cd13af_add_miedema_electronegativity_volume_.py

@@ -0,0 +1,31 @@
+"""add miedema electronegativity volume and density
+
+Revision ID: db2973cd13af
+Revises: abff1959e2ec
+Create Date: 2024-11-05 22:29:32.441355
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = 'db2973cd13af'
+down_revision = 'abff1959e2ec'
+branch_labels = None
+depends_on = None
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+
+    op.add_column("elements", sa.Column("en_miedema", sa.Float))
+    op.add_column("elements", sa.Column("miedema_molar_volume", sa.Float))
+    op.add_column("elements", sa.Column("miedema_electron_density", sa.Float))
+
+
+def downgrade():
+
+    with op.batch_alter_table("elements") as batch_op:
+        batch_op.drop_column("en_miedema")
+        batch_op.drop_column("miedema_molar_volume")
+        batch_op.drop_column("miedema_electron_density")

docs/source/data.rst

@@ -101,6 +101,8 @@ The following data are currently available:
 +-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
 | ``electrophilicity``                    | Parr's electrophilicity index                                        |                | computed     | :cite:`Parr1999`                               |
 +-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
+| ``en_miedema``                          | Miedema's scale of Electronegativity                                 | V              | stored       | :cite:`deboer1988cohesion,ZHANG201658`         |
++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
 | ``evaporation_heat``                    | Evaporation heat                                                     | kJ/mol         | stored       |                                                |
 +-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
 | ``fusion_heat``                         | Fusion heat                                                          | kJ/mol         | stored       |                                                |
@@ -147,6 +149,10 @@ The following data are currently available:
 +-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
 | ``metallic_radius``                     | Single-bond metallic radius                                          | pm             | stored       | :cite:`kyleandlaby`                            |
 +-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
+| ``miedema_electron_density``            | Electron density parameter from a model by Miedema                   |                | stored       | :cite:`deboer1988cohesion,ZHANG201658`         |
++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
+| ``miedema_molar_volume``                | Molar volume parameter from a model by Miedema                       | cm^3           | stored       | :cite:`deboer1988cohesion,ZHANG201658`         |
++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
 | ``molar_heat_capacity``                 | Molar heat capacity @ 25 C, 1 bar                                    | J/mol/K        | stored       | :cite:`haynes2014crc`                          |
 +-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+
 | ``molcas_gv_color``                     | Element color in MOCAS GV convention as HEX codes.                   |                | stored       | :cite:`molcas-colors`                          |

docs/source/electronegativity.rst

@@ -16,6 +16,7 @@ appropriate formulas. The following scales are stored:
 
 - :ref:`Allen <allen_en>`
 - :ref:`Ghosh <ghosh_en>`
+- :ref:`Miedema <miedema_en>`
 - :ref:`Pauling <pauling_en>`
 
 Moreover there are electronegativity scales that can be computed from their
@@ -61,6 +62,15 @@ Example::
     >>> Si.electronegativity('allen')
     11.33
 
+Graph
+-----
+
+.. image:: _static/img/en_allen.png
+   :width: 100%
+   :alt: Allen's electronegativity scale
+   :align: center
+
+
 .. _allred-rochow_en:
 
 Allred and Rochow
@@ -81,6 +91,14 @@ Example::
     >>> Si.electronegativity('allred-rochow')
     0.00028240190249702736
 
+Graph
+-----
+
+.. image:: _static/img/en_allred-rochow.png
+   :width: 100%
+   :alt: Allred and Rochow's electronegativity scale
+   :align: center
+
 .. _cottrell-sutton_en:
 
 Cottrell and Sutton
@@ -100,6 +118,14 @@ Example::
     >>> Si.electronegativity('cottrell-sutton')
     0.18099342720014772
 
+Graph
+-----
+
+.. image:: _static/img/en_cottrell-sutton.png
+   :width: 100%
+   :alt: Cottrell and Sutton's electronegativity scale
+   :align: center
+
 .. _ghosh_en:
 
 Ghosh
@@ -119,6 +145,13 @@ Example::
     >>> Si.en_ghosh
     0.178503
 
+Graph
+-----
+
+.. image:: _static/img/en_ghosh.png
+   :width: 100%
+   :alt: Ghosh's electronegativity scale
+   :align: center
 
 .. _gordy_en:
 
@@ -140,6 +173,14 @@ Example::
     >>> Si.electronegativity('gordy')
     0.03275862068965517
 
+Graph
+-----
+
+.. image:: _static/img/en_gordy.png
+   :width: 100%
+   :alt: Gordy's electronegativity scale
+   :align: center
+
 .. _li_xue_en:
 
 Li and Xue
@@ -186,6 +227,47 @@ Example::
     >>> Si.electronegativity(scale='martynov-batsanov')
     5.0777041564076963
 
+Graph
+-----
+
+.. image:: _static/img/en_martynov-batsanov.png
+   :width: 100%
+   :alt: Martynov and Batsanov's electronegativity scale
+   :align: center
+
+.. _miedema_en:
+
+Miedema
+=======
+
+Miedema et. al. :cite:`deboer1988cohesion,ZHANG201658` devised a semi-empirical 
+theory that could predict formation enthalpies and other
+basic properties of various alloys. It is based on estimating quantitatively the enthalpy
+(energy) effects when bringing dissimilar elements into
+contact, which will change the electron density at the so-called
+Wigner-Seitz cell boundary, and would tend to shift their electron densities
+due to an electronegativity difference.
+
+The enthalpy can be estimated with three critical parameters,
+i.e. the electronegativity difference :math:`\Delta\phi` (defined as :math:`\phi_A - \phi_B`),
+the electron-density discontinuity :math:`\Delta n^{1/3}_{WS}`, which is the difference in the
+:math:`n_{WS}` - the electron density based on the volume of Wigner-Seitz atomic cells :math:`V_{m}`. 
+
+Atomic electronegativities :math:`\phi` are empirical parameters in this model and are tabulated in ``mendeleev``. 
+
+Example::
+
+    >>> Si.en_miedema
+    4.7
+
+Graph
+-----
+
+.. image:: _static/img/en_miedema.png
+   :width: 100%
+   :alt: Miedema's electronegativity scale
+   :align: center
+
 .. _mulliken_en:
 
 Mulliken
@@ -205,6 +287,14 @@ Example::
     >>> Si.electronegativity('mulliken')
     4.0758415
 
+Graph
+-----
+
+.. image:: _static/img/en_mulliken.png
+   :width: 100%
+   :alt: Mulliken's electronegativity scale
+   :align: center
+
 .. _nagle_en:
 
 Nagle
@@ -221,6 +311,14 @@ Example::
     >>> Si.electronegativity('nagle')
     0.47505611644667534
 
+Graph
+-----
+
+.. image:: _static/img/en_nagle.png
+   :width: 100%
+   :alt: Nagle's electronegativity scale
+   :align: center
+
 .. _pauling_en:
 
 Pauling
@@ -243,6 +341,14 @@ Example::
     >>> Si.electronegativity('pauling')
     1.9
 
+Graph
+-----
+
+.. image:: _static/img/en_pauling.png
+   :width: 100%
+   :alt: Pauling's electronegativity scale
+   :align: center
+
 .. _sanderson_en:
 
 Sanderson
@@ -266,6 +372,14 @@ Example::
     >>> Si.electronegativity()
     0.3468157872145231
 
+Graph
+-----
+
+.. image:: _static/img/en_sanderson.png
+   :width: 100%
+   :alt: Sanderson's electronegativity scale
+   :align: center
+
 
 Fetching all electronegativities
 ================================

docs/source/references.bib

@@ -880,4 +880,22 @@ @misc{ionization_energies
   howpublished = {{NIST Atomic Spectra Database (ver. 5.11), [Online]. Available: {\tt{https://physics.nist.gov/asd}} [2024, August 17]. National Institute of Standards and Technology, Gaithersburg, MD.}},
   year         = {2023},
   note         = {Accessed: 2015-04-13}
+}
+@article{ZHANG201658,
+  title   = {Miedema Calculator: A thermodynamic platform for predicting formation enthalpies of alloys within framework of Miedema’s Theory},
+  journal = {Computer Physics Communications},
+  volume  = {209},
+  pages   = {58-69},
+  year    = {2016},
+  issn    = {0010-4655},
+  doi     = {https://doi.org/10.1016/j.cpc.2016.08.013},
+  url     = {https://www.sciencedirect.com/science/article/pii/S0010465516302430},
+  author  = {R.F. Zhang and S.H. Zhang and Z.J. He and J. Jing and S.H. Sheng}
+}
+@book{deboer1988cohesion,
+  title     = {Cohesion in metals. Transition metal alloys},
+  author    = {De Boer, Frank R and Mattens, W and Boom, R and Miedema, AR and Niessen, AK},
+  place     = {Netherlands},
+  publisher = {North-Holland},
+  year      = {1988}
 }

mendeleev/fetch.py

@@ -107,6 +107,7 @@ def fetch_electronegativities(scales: List[str] = None) -> pd.DataFrame:
         Element.en_pauling.label("Pauling"),
         Element.en_allen.label("Allen"),
         Element.en_ghosh.label("Ghosh"),
+        Element.en_miedema.label("Miedema"),
     ).order_by("atomic_number")
     df = pd.read_sql_query(query.statement.compile(dialect=sqlite.dialect()), engine)
 

mendeleev/models.py

@@ -96,6 +96,10 @@ class Element(Base):
         electron_affinity (float): Electron affinity in eV
         electrophilicity (float): Parr's electrophilicity index
         econf (str): Ground state electron configuration
+        en_allen (float): ELectronegativity by Allen
+        en_ghosh (float): Electronegativity by Ghosh
+        en_miedema (float): Electronegativity by Miedema
+        en_pauling (float): Electronegativity by Pauling
         evaporation_heat (float): Evaporation heat in kJ/mol
         fusion_heat (float): Fusion heat in kJ/mol
         gas_basicity (float): Gas basicity
@@ -144,8 +148,7 @@ class Element(Base):
         vdw_radius_uff (float): Van der Waals radius from the UFF in pm
         vdw_radius_mm3 (float): Van der Waals radius from MM3 in pm
         oxistates (list): Oxidation states
-        ionenergies (dict): Ionization energies in eV parsed from
-            http://physics.nist.gov/cgi-bin/ASD/ie.pl on April 13, 2015
+        ionenergies (dict): Ionization energies in eV
     """
 
     __tablename__ = "elements"
@@ -179,6 +182,7 @@ class Element(Base):
     electron_affinity = Column(Float)
     en_allen = Column(Float)
     en_ghosh = Column(Float)
+    en_miedema = Column(Float)
     en_pauling = Column(Float)
     econf = Column("electronic_configuration", String)
     evaporation_heat = Column(Float)
@@ -198,6 +202,8 @@ class Element(Base):
     mendeleev_number = Column(Integer)
     metallic_radius = Column(Float)
     metallic_radius_c12 = Column(Float)
+    miedema_molar_volume = Column(Float)
+    miedema_electron_density = Column(Float)
     molar_heat_capacity = Column(Float)
     molcas_gv_color = Column(String)
     name = Column(String)
@@ -518,6 +524,7 @@ def electronegativity_scales(self, name: str = None) -> Union[Callable, List[str
             "gordy": self.electronegativity_gordy,
             "li-xue": self.electronegativity_li_xue,
             "martynov-batsanov": self.electronegativity_martynov_batsanov,
+            "miedema": self.en_miedema,
             "mulliken": self.electronegativity_mulliken,
             "nagle": self.electronegativity_nagle,
             "pauling": self.electronegativity_pauling,
@@ -1248,7 +1255,7 @@ class ScatteringFactor(Base):
 
     .. math::
 
-        \mu_a = 2 \cdot r_0 \cdot \lambda \cdot f_2
+        \\mu_a = 2 \cdot r_0 \cdot \lambda \cdot f_2
 
     where :math:`r_0` is the classical electron radius, and :math:`\lambda` is the wavelength.
 

mendeleev/vis/plotly.py

@@ -1,5 +1,6 @@
 import pandas as pd
 import plotly.graph_objects as go
+import plotly.express as px
 from plotly.graph_objs.layout import Shape, Annotation
 from pandas.api.types import is_float_dtype
 
@@ -162,3 +163,29 @@ def periodic_table_plotly(
     )
 
     return fig
+
+
+def plot_scale(data: pd.DataFrame, scale: str):
+    """Plot an electronegativity scale
+
+    Args:
+        data: DataFrame with the electronegativity data, obtained from :func:`fetch.fetch_electronegativities`
+        scale: Electronegativity scale to plot
+    """
+    fig = px.scatter(
+        data,
+        y=scale,
+        template="plotly_white",
+        height=600,
+        width=1400,
+        text="symbol",
+        title=f"{scale}'s Electronegativity",
+    )
+    fig.update_traces(
+        textposition="top center",
+        textfont={"size": 10},
+        marker={"size": 8, "color": "#0081a7"},
+    )
+    fig.update_layout(font={"size": 12})
+    fig.update_xaxes(title_text="Atomic Number", zeroline=False, range=[0, 119])
+    return fig