Merge pull request #312 from pyiron/reference_data

Provide functions for reference data

.ci_support/environment-old.yml

@@ -2,17 +2,20 @@ channels:
 - conda-forge
 dependencies:
 - ase =3.22.1
+- dynaphopy =1.17.5
 - gpaw =20.1.0
+- iprpy-data =2023.07.25
+- jinja2 =2.11.3
+- lammps =2022.06.23
+- lxml =4.9.1
+- mendeleev =0.12.0
 - numpy =1.23.5
+- pandas =2.0.0
+- phonopy =2.20.0
+- pylammpsmpi =0.2.1
+- requests =2.24.0
 - scipy =1.11.1
+- seekpath =1.9.0
 - spglib =2.0.2
-- phonopy =2.20.0
 - structuretoolkit =0.0.10
-- seekpath =1.9.0
-- lammps =2022.06.23
-- pandas =1.5.3
-- pylammpsmpi =0.2.1
-- jinja2 =2.11.3
-- iprpy-data =2023.07.25
-- dynaphopy =1.17.5
 - tqdm =4.44.0

.ci_support/environment.yml

@@ -3,10 +3,14 @@ channels:
 dependencies:
 - ase =3.23.0
 - coverage
+- lxml =5.2.2
+- mendeleev =0.17.0
 - numpy =1.26.4
+- pandas =2.2.2
+- phonopy =2.26.6
+- requests =2.32.3
 - scipy =1.14.0
+- seekpath =2.1.0
 - spglib =2.5.0
-- phonopy =2.26.6
 - structuretoolkit =0.0.27
-- seekpath =2.1.0
 - tqdm =4.66.4

atomistics/referencedata/__init__.py

@@ -0,0 +1,21 @@
+from atomistics.referencedata.wikipedia import (
+    get_elastic_properties as get_elastic_properties_from_wikipedia,
+)
+
+try:
+    from atomistics.referencedata.mendeleev import (
+        get_chemical_information as get_chemical_information_from_mendeleev,
+    )
+    from atomistics.referencedata.wolframalpha import (
+        get_chemical_information as get_chemical_information_from_wolframalpha,
+    )
+except ImportError:
+    __all__ = []
+else:
+    __all__ = [
+        get_chemical_information_from_mendeleev,
+        get_chemical_information_from_wolframalpha,
+    ]
+
+
+__all__ += [get_elastic_properties_from_wikipedia]

atomistics/referencedata/mendeleev.py

@@ -0,0 +1,114 @@
+from mendeleev.fetch import fetch_table
+
+
+def get_chemical_information(chemical_symbol: str) -> dict:
+    """
+    Get information of a given chemical element
+
+    Args:
+        chemical_symbol: Chemical Element like Au for Gold
+
+    Returns:
+        dict: Dictionary with the following keys
+            abundance_crust: Abundance in the Earth’s crust in mg/kg
+            abundance_sea: Abundance in the seas in mg/L
+            atomic_number: Atomic number
+            atomic_radius_rahm: Atomic radius by Rahm et al. in pm
+            atomic_radius: Atomic radius in pm
+            atomic_volume: Atomic volume in cm^3/mol
+            atomic_weight_uncertainty: Atomic weight uncertainty in Da
+            atomic_weight: Relative atomic weight in Da
+            block: Block in periodic table
+            boiling_point: Boiling point in K
+            c6_gb: C_6 dispersion coefficient according to Gould & Bučko in hartree/bohr^6
+            c6: C_6 dispersion coefficient in hartree/bohr^6
+            cas: Chemical Abstracts Serice identifier
+            covalent_radius_bragg: Covalent radius by Bragg in pm
+            covalent_radius_cordero: Covalent radius by Cerdero et al. in pm
+            covalent_radius_pyykko_double: Double bond covalent radius by Pyykko et al. in pm
+            covalent_radius_pyykko_triple: Triple bond covalent radius by Pyykko et al. in pm
+            covalent_radius_pyykko: Single bond covalent radius by Pyykko et al. in pm
+            cpk_color: Element color in CPK convention
+            critical_pressure: Critical pressure in MPa
+            critical_temperature: Critical temperature in K
+            density: Density at 295K in g/cm^3
+            description: Short description of the element
+            dipole_polarizability_unc: Uncertainty of the dipole polarizability in bohr^3
+            dipole_polarizability: Dipole polarizability in bohr^3
+            discoverers: The discoverers of the element
+            discovery_location: The location where the element was discovered
+            discovery_year: The year the element was discovered
+            econf: Ground state electronic configuration
+            electron_affinity: Electron affinity in eV
+            electronegativity_allen: Allen’s scale of electronegativity in eV
+            electronegativity_allred_rochow: Allred and Rochow’s scale of electronegativity in e^2/pm^2
+            electronegativity_cottrell_sutton: Cottrell and Sutton’s scale of electronegativity in e^0.5/pm^0.5
+            electronegativity_ghosh: Ghosh’s scale of electronegativity in 1/pm
+            electronegativity_gordy: Gordy’s scale of electronegativity in e/pm
+            electronegativity_li_xue: Li and Xue’s scale of electronegativity in 1/pm
+            electronegativity_martynov_batsanov: Martynov and Batsanov’s scale of electronegativity in eV^0.5
+            electronegativity_mulliken: Mulliken’s scale of electronegativity in eV
+            electronegativity_nagle: Nagle’s scale of electronegativity in 1/bohr
+            electronegativity_pauling: Pauling’s scale of electronegativity
+            electronegativity_sanderson: Sanderson’s scale of electronegativity
+            electrons: Number of electrons
+            electrophilicity: Parr’s electrophilicity index
+            evaporation_heat: Evaporation heat in kJ/mol
+            fusion_heat: Fusion heat in kJ/mol
+            gas_basicity: Gas basicity in kJ/mol
+            geochemical_class: Geochemical classification
+            glawe_number: Glawe’s number (scale)
+            goldschmidt_class: Goldschmidt classification
+            group: Group in the periodic table
+            hardness: Absolute hardness. Can also be calcualted for ions. in eV
+            heat_of_formation: Heat of formation in kJ/mol
+            inchi: International Chemical Identifier
+            ionenergy: See IonizationEnergy class documentation
+            ionic_radii: See IonicRadius class documentation
+            is_monoisotopic: Is the element monoisotopic
+            is_radioactive: Is the element radioactive
+            isotopes: See Isotope class documentation
+            jmol_color: Element color in Jmol convention
+            lattice_constant: Lattice constant
+            lattice_structure: Lattice structure code
+            mass_number: Mass number of the most abundant isotope
+            melting_point: Melting point in K
+            mendeleev_number: Mendeleev’s number
+            metallic_radius_c12: Metallic radius with 12 nearest neighbors in pm
+            metallic_radius: Single-bond metallic radius in pm
+            molar_heat_capacity: Molar heat capacity @ 25 C, 1 bar in J/mol/K
+            molcas_gv_color: Element color in MOCAS GV convention
+            name_origin: Origin of the name
+            name: Name in English
+            neutrons: Number of neutrons
+            nist_webbook_url: URL for the NIST Chemistry WebBook
+            nvalence: Number of valence electrons
+            oxides: Possible oxides based on oxidation numbers
+            oxistates: See OxidationState class documentation
+            period: Period in periodic table
+            pettifor_number: Pettifor scale
+            proton_affinity: Proton affinity in kJ/mol
+            protons: Number of protons
+            sconst: See ScreeningConstant class documentation
+            series: Series in the periodic table
+            softness: Absolute softness. Can also be calculated for ions. in 1/eV
+            sources: Sources of the element
+            specific_heat_capacity: Specific heat capacity @ 25 C, 1 bar in J/g/K
+            symbol: Chemical symbol
+            thermal_conductivity: Thermal conductivity @25 C in W/m/K
+            triple_point_pressure: Presseure of the triple point in kPa
+            triple_point_temperature: Temperature of the triple point in K
+            uses: Main applications of the element
+            vdw_radius_alvarez: Van der Waals radius according to Alvarez in pm
+            vdw_radius_batsanov: Van der Waals radius according to Batsanov in pm
+            vdw_radius_bondi: Van der Waals radius according to Bondi in pm
+            vdw_radius_dreiding: Van der Waals radius from the DREIDING FF in pm
+            vdw_radius_mm3: Van der Waals radius from the MM3 FF in pm
+            vdw_radius_rt: Van der Waals radius according to Rowland and Taylor in pm
+            vdw_radius_truhlar: Van der Waals radius according to Truhlar in pm
+            vdw_radius_uff: Van der Waals radius from the UFF in pm
+            vdw_radius: Van der Waals radius in pm
+            zeff: Effective nuclear charge
+    """
+    df = fetch_table("elements")
+    return df[df.symbol == chemical_symbol].squeeze(axis=0).to_dict()

atomistics/referencedata/wikipedia.py

@@ -0,0 +1,40 @@
+import pandas
+
+
+def get_elastic_properties(chemical_symbol: str) -> dict:
+    """
+    Looks up elastic properties for a given chemical symbol from the Wikipedia: https://en.wikipedia.org/wiki/Elastic_properties_of_the_elements_(data_page)
+    sourced from webelements.com.
+
+    Args:
+        chemical_symbol (str): Chemical symbol of the element.
+
+    Returns:
+        dict: Dictionary with the following keys
+            youngs_modulus: Young's modulus (or Young modulus) in GPa is a mechanical property of solid materials that
+                            measures the tensile or compressive stiffness when the force is applied lengthwise.
+            poissons_ratio: In materials science and solid mechanics, Poisson's ratio ν (nu) is a measure of the Poisson
+                            effect, the deformation (expansion or contraction) of a material in directions perpendicular
+                            to the specific direction of loading.
+            bulk_modulus: The bulk modulus (K or B or k) in GPa of a substance is a measure of the resistance of a
+                          substance to bulk compression.
+            shear_modulus: In materials science, shear modulus or modulus of rigidity in GPa, denoted by G, or sometimes
+                           S or μ, is a measure of the elastic shear stiffness of a material and is defined as the ratio
+                           of shear stress to the shear strain.
+    """
+    property_lst = [
+        "youngs_modulus",
+        "poissons_ratio",
+        "bulk_modulus",
+        "shear_modulus",
+    ]
+    df_lst = pandas.read_html(
+        "https://en.wikipedia.org/wiki/Elastic_properties_of_the_elements_(data_page)"
+    )
+    property_dict = {}
+    for i, p in enumerate(property_lst):
+        df_tmp = df_lst[i]
+        property_dict[p] = float(
+            df_tmp[df_tmp.symbol == chemical_symbol].squeeze(axis=0).to_dict()["WEL[1]"]
+        )
+    return property_dict