From b04a6f05df44f0d1170aa2638d56fb40b18236bd Mon Sep 17 00:00:00 2001 From: Lukasz Mentel Date: Fri, 31 May 2024 18:44:26 +0200 Subject: [PATCH] Create metadata table for stored properties (#156) * add metadata table * fix typos * fix typos * add metadata table with initial contents * add ParrPearson on hardness * update metadata schema and data * add documentation for PropertyMetadata class * update docstring * add propertymetadata to fetch tables * correct format * update units * render updated data docs * update isotope metadata * add isotope metadata to PropertyMetadata * docs * add PropertyMetadata to models.__all__ --- README.md | 4 +- ...7d745d77a7c1_add_propertymetadata_table.py | 41 ++ docs/source/api/mendeleev.cli.rst | 27 +- docs/source/api/mendeleev.ion.rst | 27 +- docs/source/api/mendeleev.models.rst | 2 + docs/source/api/models.rst | 9 + docs/source/data.rst | 485 +++++++++--------- docs/source/data_access.rst | 1 + docs/source/references.bib | 12 + mendeleev/elements.db | Bin 827392 -> 827392 bytes mendeleev/fetch.py | 1 + mendeleev/models.py | 54 +- 12 files changed, 379 insertions(+), 284 deletions(-) create mode 100644 alembic/versions/7d745d77a7c1_add_propertymetadata_table.py diff --git a/README.md b/README.md index 54d6f30..5cbcdc8 100644 --- a/README.md +++ b/README.md @@ -286,7 +286,7 @@ the `Element` object: >>> from mendeleev import element The `element` method accepts unique identifiers: atomic number, atomic -symbol or element\'s name in english. To retrieve the entries on Silicon +symbol or element\'s name in English. To retrieve the entries on Silicon by symbol type ``` {.sourceCode .python} @@ -340,7 +340,7 @@ following attributes per isotope The columns represent the attributes `atomic_number`, `mass`, `abundance` and `mass_number` respectively. -### Accesing data tables and the database +### Accessing data tables and the database [mendeleev](http://mendeleev.readthedocs.org) offers also methods for accessing whole tables of data, e.g. table with the data on all isotopes diff --git a/alembic/versions/7d745d77a7c1_add_propertymetadata_table.py b/alembic/versions/7d745d77a7c1_add_propertymetadata_table.py new file mode 100644 index 0000000..ca0791a --- /dev/null +++ b/alembic/versions/7d745d77a7c1_add_propertymetadata_table.py @@ -0,0 +1,41 @@ +"""add PropertyMetadata table + +Revision ID: 7d745d77a7c1 +Revises: 703682715347 +Create Date: 2024-05-21 13:11:24.427405 + +""" + +# revision identifiers, used by Alembic. +revision = '7d745d77a7c1' +down_revision = '703682715347' +branch_labels = None +depends_on = None + +from alembic import op +import sqlalchemy as sa + + +value_origin_enum = sa.Enum('STORED', 'COMPUTED', name='valueorigin') + +def upgrade(): + + op.create_table( + 'propertymetadata', + sa.Column('id', sa.Integer, primary_key=True, autoincrement=True), + sa.Column('table_name', sa.String, nullable=True), + sa.Column('column_name', sa.String, nullable=True), + sa.Column('class_name', sa.String, nullable=False), + sa.Column('attribute_name', sa.String, nullable=False), + sa.Column('category', sa.String, nullable=False), + sa.Column('value_origin', value_origin_enum, nullable=False), + sa.Column('description', sa.Text, nullable=False), + sa.Column('unit', sa.String, nullable=True), + sa.Column('annotations', sa.Text, nullable=True), + sa.Column('citation_keys', sa.String, nullable=True) + ) + + +def downgrade(): + op.drop_table('propertymetadata') + value_origin_enum.drop(op.get_bind()) \ No newline at end of file diff --git a/docs/source/api/mendeleev.cli.rst b/docs/source/api/mendeleev.cli.rst index caccff9..aceb604 100644 --- a/docs/source/api/mendeleev.cli.rst +++ b/docs/source/api/mendeleev.cli.rst @@ -1,29 +1,6 @@ mendeleev.cli ============= -.. automodule:: mendeleev.cli - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - clielement - - - - - - - - - - - - +.. currentmodule:: mendeleev +.. autodata:: cli \ No newline at end of file diff --git a/docs/source/api/mendeleev.ion.rst b/docs/source/api/mendeleev.ion.rst index 7ec6887..2dfca05 100644 --- a/docs/source/api/mendeleev.ion.rst +++ b/docs/source/api/mendeleev.ion.rst @@ -1,29 +1,6 @@ mendeleev.ion ============= -.. automodule:: mendeleev.ion - - - - - - - - - - - - .. rubric:: Classes - - .. autosummary:: - - Ion - - - - - - - - +.. currentmodule:: mendeleev +.. autodata:: ion \ No newline at end of file diff --git a/docs/source/api/mendeleev.models.rst b/docs/source/api/mendeleev.models.rst index 996b3df..b5d55f5 100644 --- a/docs/source/api/mendeleev.models.rst +++ b/docs/source/api/mendeleev.models.rst @@ -33,8 +33,10 @@ IsotopeDecayMode OxidationState PhaseTransition + PropertyMetadata ScreeningConstant Series + ValueOrigin diff --git a/docs/source/api/models.rst b/docs/source/api/models.rst index d65ffd6..0ba2fc9 100644 --- a/docs/source/api/models.rst +++ b/docs/source/api/models.rst @@ -95,6 +95,15 @@ OxidationState .. autoclass:: mendeleev.models.OxidationState :members: +.. _propertymetadata-class: + +PropertyMetadata +---------------- + +.. currentmodule:: mendeleev.models + +.. autoclass:: mendeleev.models.PropertyMetadata + :members: .. _econf-class: diff --git a/docs/source/data.rst b/docs/source/data.rst index ab77551..2e3898c 100644 --- a/docs/source/data.rst +++ b/docs/source/data.rst @@ -12,230 +12,251 @@ Elements The following data are currently available: -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| Name | Type | Comment | Unit | Data Source | -+===============================+=======+======================================================+===================+=====================================================+ -| abundance_crust | float | Abundance in the Earth's crust | mg/kg | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| abundance_sea | float | Abundance in the seas | mg/L | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| annotation | str | Annotations regarding the data | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| atomic_number | int | Atomic number | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| atomic_radius | float | Atomic radius | pm | :cite:`Slater1964` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| atomic_radius_rahm | float | Atomic radius by Rahm et al. | pm | :cite:`Rahm2016,Rahm2017` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| atomic_volume | float | Atomic volume | cm\ :sup:`3`/mol | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| atomic_weight | float | Atomic weight\ ([#f1]_) | | :cite:`Meija2016,iupac-weights` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| atomic_weight_uncertainty | float | Atomic weight uncertainty\ ([#f1]_) | | :cite:`Meija2016,iupac-weights` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| block | str | Block in periodic table | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| boiling_point | float | Boiling temperature | K | :cite:`haynes2016crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| c6 | float | C_6 dispersion coefficient in a.u. | a.u. | :cite:`Chu2004,Tang1976` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| c6_gb | float | C_6 dispersion coefficient in a.u. (Gould & Bučko) | a.u. | :cite:`Gould2016` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| cas | str | Chemical Abstracts Serice identifier | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| covalent_radius_bragg | float | Covalent radius by Bragg | pm | :cite:`Bragg1920` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| covalent_radius_cordero | float | Covalent radius by Cerdero et al.\ ([#f2]_) | pm | :cite:`Cordero2008` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| covalent_radius_pyykko | float | Single bond covalent radius by Pyykko et al. | pm | :cite:`Pyykko2009` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| covalent_radius_pyykko_double | float | Double bond covalent radius by Pyykko et al. | pm | :cite:`Pyykko2009a` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| covalent_radius_pyykko_triple | float | Triple bond covalent radius by Pyykko et al. | pm | :cite:`Pyykko2005` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| cpk_color | str | Element color in CPK convention | HEX | :cite:`wiki-cpk` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| critical_pressure | float | Critical pressure | MPa | :cite:`haynes2016crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| critical_temperature | float | Critical temperature | K | :cite:`haynes2016crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| density | float | Density at 295K\ ([#f10]_) | g/cm\ :sup:`3` | :cite:`haynes2014crc,enwiki:1039678864` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| description | str | Short description of the element | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| dipole_polarizability | float | Dipole polarizability | a.u. | :cite:`Schwerdtfeger2018` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| dipole_polarizability_unc | float | Dipole polarizability uncertainty | a.u. | :cite:`Schwerdtfeger2018` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| discoverers | str | The discoverers of the element | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| discovery_location | str | The location where the element was discovered | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| discovery_year | int | The year the element was discovered | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| electron_affinity | float | Electron affinity\ ([#f3]_) | eV | :cite:`haynes2014crc,Andersen2004` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| electrons | int | Number of electrons | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| electrophilicity | float | Electrophilicity index | eV | :cite:`Parr1999` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| en_allen | float | Allen's scale of electronegativity\ ([#f4]_) | eV | :cite:`Mann2000a,Mann2000` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| en_ghosh | float | Ghosh's scale of electronegativity | | :cite:`Ghosh2005` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| en_mulliken | float | Mulliken's scale of electronegativity | eV | :cite:`Mulliken1934` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| en_pauling | float | Pauling's scale of electronegativity | | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| econf | str | Ground state electron configuration | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| evaporation_heat | float | Evaporation heat | kJ/mol | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| fusion_heat | float | Fusion heat | kJ/mol | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| gas_basicity | float | Gas basicity | kJ/mol | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| geochemical_class | str | Geochemical classification | | :cite:`white2013geochemistry` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| glawe_number | int | Glawe's number (scale) | | :cite:`Glawe2016` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| goldschmidt_class | str | Goldschmidt classification | | :cite:`white2013geochemistry,wiki-goldschmidt` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| group | int | Group in periodic table | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| heat_of_formation | float | Heat of formation | kJ/mol | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| inchi | str | International Chemical Identifier | | :cite:`IUPAC-InChI` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| ionenergy | tuple | Ionization energies | eV | :cite:`NIST-ASD` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| ionic_radii | list | Ionic and crystal radii in pm\ ([#f9]_) | pm | :cite:`Shannon1976,Lundberg2016` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| is_monoisotopic | bool | Is the element monoisotopic | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| is_radioactive | bool | Is the element radioactive | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| isotopes | list | Isotopes | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| jmol_color | str | Element color in Jmol convention | HEX | :cite:`jmol-colors` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| lattice_constant | float | Lattice constant | Angstrom | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| lattice_structure | str | Lattice structure code | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| mass_number | int | Mass number (most abundant isotope) | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| melting_point | float | Melting temperature | K | :cite:`haynes2016crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| mendeleev_number | int | Mendeleev's number\ ([#f5]_) | | :cite:`Pettifor1984,Villars2004` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| metallic_radius | float | Single-bond metallic radius | pm | :cite:`kyleandlaby` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| metallic_radius_c12 | float | Metallic radius with 12 nearest neighbors | pm | :cite:`kyleandlaby` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| molar_heat_capacity | float | Molar heat capacity @ 25 C, 1 bar | J/(mol K) | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| molcas_gv_color | str | Element color in MOCAS GV convention | HEX | :cite:`molcas-colors` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| name | str | Name in English | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| name_origin | str | Origin of the name | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| neutrons | int | Number of neutrons (most abundant isotope) | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| oxistates | list | Commonly occurring oxidation states | | :cite:`enwiki:1102394064` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| nist_webbook_url | str | URL for the NIST Chemistry WebBook | | :cite:`NIST-CH-WB` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| oxistates | list | Oxidation states | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| period | int | Period in periodic table | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| pettifor_number | float | Pettifor scale | | :cite:`Pettifor1984` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| proton_affinity | float | Proton affinity | kJ/mol | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| protons | int | Number of protons | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| sconst | float | Nuclear charge screening constants\ ([#f6]_) | | :cite:`Clementi1963,Clementi1967` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| series | int | Index to chemical series | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| sources | str | Sources of the element | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| specific_heat_capacity | float | Specific heat capacity @ 25 C, 1 bar | J/(g K) | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| symbol | str | Chemical symbol | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| thermal_conductivity | float | Thermal conductivity @25 C | W/(m K) | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| triple_point_pressure | float | Triple point pressure | kPa | :cite:`haynes2016crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| triple_point_temperature | float | Triple point temperature | K | :cite:`haynes2016crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| uses | str | Applications of the element | | | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius | float | Van der Waals radius | pm | :cite:`haynes2014crc` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius_alvarez | float | Van der Waals radius according to Alvarez\ ([#f7]_) | pm | :cite:`Alvarez2013,Vogt2014` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius_batsanov | float | Van der Waals radius according to Batsanov | pm | :cite:`Batsanov2001` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius_bondi | float | Van der Waals radius according to Bondi | pm | :cite:`Bondi1964` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius_dreiding | float | Van der Waals radius from the DREIDING FF | pm | :cite:`Mayo1990` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius_mm3 | float | Van der Waals radius from the MM3 FF | pm | :cite:`Allinger1994` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius_rt | float | Van der Waals radius according to Rowland and Taylor | pm | :cite:`Rowland1996` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius_truhlar | float | Van der Waals radius according to Truhlar | pm | :cite:`Mantina2009` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ -| vdw_radius_uff | float | Van der Waals radius from the UFF | pm | :cite:`Rappe1992` | -+-------------------------------+-------+------------------------------------------------------+-------------------+-----------------------------------------------------+ ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| Attribute name | Description | Unit | Value origin | Citation keys | ++=========================================+======================================================================+================+==============+================================================+ +| ``abundance_crust`` | Abundance in the Earth's crust | mg/kg | stored | :cite:`haynes2014crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``abundance_sea`` | Abundance in the seas | mg/L | stored | :cite:`haynes2014crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``atomic_number`` | Atomic number | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``atomic_radius_rahm`` | Atomic radius by Rahm et al. | pm | stored | :cite:`Rahm2016,Rahm2017` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``atomic_radius`` | Atomic radius | pm | stored | :cite:`Slater1964` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``atomic_volume`` | Atomic volume | cm^3/mol | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``atomic_weight_uncertainty`` | Atomic weight uncertainty | Da | stored | :cite:`Meija2016,iupac-weights` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``atomic_weight`` | Relative atomic weight ([#f_atomic_weight]_) | Da | stored | :cite:`Meija2016,iupac-weights` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``block`` | Block in periodic table | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``boiling_point`` | Boiling point | K | stored | :cite:`haynes2016crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``c6_gb`` | C_6 dispersion coefficient according to Gould & Bučko | hartree/bohr^6 | stored | :cite:`Gould2016` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``c6`` | C_6 dispersion coefficient | hartree/bohr^6 | stored | :cite:`Chu2004,Tang1976` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``cas`` | Chemical Abstracts Serice identifier | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``covalent_radius_bragg`` | Covalent radius by Bragg | pm | stored | :cite:`Bragg1920` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``covalent_radius_cordero`` | Covalent radius by Cerdero et al. ([#f_covalent_radius_cordero]_) | pm | stored | :cite:`Cordero2008` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``covalent_radius_pyykko_double`` | Double bond covalent radius by Pyykko et al. | pm | stored | :cite:`Pyykko2009a` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``covalent_radius_pyykko_triple`` | Triple bond covalent radius by Pyykko et al. | pm | stored | :cite:`Pyykko2005` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``covalent_radius_pyykko`` | Single bond covalent radius by Pyykko et al. | pm | stored | :cite:`Pyykko2009` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``cpk_color`` | Element color in CPK convention ([#f_color]_) | | stored | :cite:`wiki-cpk` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``critical_pressure`` | Critical pressure | MPa | stored | :cite:`haynes2016crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``critical_temperature`` | Critical temperature | K | stored | :cite:`haynes2016crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``density`` | Density at 295K ([#f_density]_) | g/cm^3 | stored | :cite:`haynes2014crc,enwiki:1039678864` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``description`` | Short description of the element | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``dipole_polarizability_unc`` | Uncertainty of the dipole polarizability | bohr^3 | stored | :cite:`Schwerdtfeger2018` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``dipole_polarizability`` | Dipole polarizability | bohr^3 | stored | :cite:`Schwerdtfeger2018` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``discoverers`` | The discoverers of the element | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``discovery_location`` | The location where the element was discovered | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``discovery_year`` | The year the element was discovered | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``econf`` | Ground state electronic configuration | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electron_affinity`` | Electron affinity ([#f_electron_affinity]_) | eV | stored | :cite:`haynes2014crc,Andersen2004` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_allen`` | Allen's scale of electronegativity ([#f_electronegativity_allen]_) | eV | stored | :cite:`Mann2000a,Mann2000` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_allred_rochow`` | Allred and Rochow's scale of electronegativity | e^2/pm^2 | computed | :cite:`Allred1958` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_cottrell_sutton`` | Cottrell and Sutton's scale of electronegativity | e^0.5/pm^0.5 | computed | :cite:`Cottrell1951` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_ghosh`` | Ghosh's scale of electronegativity | 1/pm | stored | :cite:`Ghosh2005` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_gordy`` | Gordy's scale of electronegativity | e/pm | computed | :cite:`Gordy1946` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_li_xue`` | Li and Xue's scale of electronegativity | 1/pm | computed | :cite:`Li2006,Li2009` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_martynov_batsanov`` | Martynov and Batsanov's scale of electronegativity | eV^0.5 | computed | :cite:`Batsanov1982` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_mulliken`` | Mulliken's scale of electronegativity | eV | computed | :cite:`Mulliken1934` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_nagle`` | Nagle's scale of electronegativity | 1/bohr | computed | :cite:`Nagle1990` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_pauling`` | Pauling's scale of electronegativity | | stored | :cite:`haynes2014crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electronegativity_sanderson`` | Sanderson's scale of electronegativity | | computed | :cite:`Sanderson1951,Sanderson1952` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electrons`` | Number of electrons | | computed | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``electrophilicity`` | Parr's electrophilicity index | | computed | :cite:`Parr1999` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``evaporation_heat`` | Evaporation heat | kJ/mol | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``fusion_heat`` | Fusion heat | kJ/mol | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``gas_basicity`` | Gas basicity | kJ/mol | stored | :cite:`haynes2014crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``geochemical_class`` | Geochemical classification | | stored | :cite:`white2013geochemistry` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``glawe_number`` | Glawe's number (scale) | | stored | :cite:`Glawe2016` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``goldschmidt_class`` | Goldschmidt classification | | stored | :cite:`white2013geochemistry,wiki-goldschmidt` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``group`` | Group in the periodic table | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``hardness`` | Absolute hardness. Can also be calcualted for ions. | eV | computed | :cite:`ParrPearson1983` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``heat_of_formation`` | Heat of formation | kJ/mol | stored | :cite:`haynes2014crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``inchi`` | International Chemical Identifier | | computed | :cite:`IUPAC-InChI` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``ionenergy`` | See IonizationEnergy class documentation | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``ionic_radii`` | See IonicRadius class documentation | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``is_monoisotopic`` | Is the element monoisotopic | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``is_radioactive`` | Is the element radioactive | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``isotopes`` | See Isotope class documentation | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``jmol_color`` | Element color in Jmol convention ([#f_color]_) | | stored | :cite:`jmol-colors` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``lattice_constant`` | Lattice constant | angstrom | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``lattice_structure`` | Lattice structure code | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``mass_number`` | Mass number of the most abundant isotope | | computed | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``melting_point`` | Melting point | K | stored | :cite:`haynes2016crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``mendeleev_number`` | Mendeleev's number ([#f_mendeleev_number]_) | | stored | :cite:`Pettifor1984,Villars2004` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``metallic_radius_c12`` | Metallic radius with 12 nearest neighbors | pm | stored | :cite:`kyleandlaby` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``metallic_radius`` | Single-bond metallic radius | pm | stored | :cite:`kyleandlaby` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``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 ([#f_color]_) | | stored | :cite:`molcas-colors` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``name_origin`` | Origin of the name | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``name`` | Name in English | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``neutrons`` | Number of neutrons | | computed | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``nist_webbook_url`` | URL for the NIST Chemistry WebBook | | computed | :cite:`NIST-CH-WB` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``nvalence`` | Number of valence electrons | | computed | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``oxides`` | Possible oxides based on oxidation numbers | | computed | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``oxistates`` | See OxidationState class documentation | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``period`` | Period in periodic table | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``pettifor_number`` | Pettifor scale | | stored | :cite:`Pettifor1984` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``proton_affinity`` | Proton affinity | kJ/mol | stored | :cite:`haynes2014crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``protons`` | Number of protons | | computed | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``sconst`` | See ScreeningConstant class documentation | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``series`` | Series in the periodic table | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``softness`` | Absolute softness. Can also be calculated for ions. | 1/eV | computed | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``sources`` | Sources of the element | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``specific_heat_capacity`` | Specific heat capacity @ 25 C, 1 bar | J/g/K | stored | :cite:`haynes2014crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``symbol`` | Chemical symbol | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``thermal_conductivity`` | Thermal conductivity @25 C | W/m/K | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``triple_point_pressure`` | Presseure of the triple point | kPa | stored | :cite:`haynes2016crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``triple_point_temperature`` | Temperature of the triple point | K | stored | :cite:`haynes2016crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``uses`` | Main applications of the element | | stored | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius_alvarez`` | Van der Waals radius according to Alvarez ([#f_vdw_radius_alvarez]_) | pm | stored | :cite:`Alvarez2013,Vogt2014` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius_batsanov`` | Van der Waals radius according to Batsanov | pm | stored | :cite:`Batsanov2001` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius_bondi`` | Van der Waals radius according to Bondi | pm | stored | :cite:`Bondi1964` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius_dreiding`` | Van der Waals radius from the DREIDING FF | pm | stored | :cite:`Mayo1990` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius_mm3`` | Van der Waals radius from the MM3 FF | pm | stored | :cite:`Allinger1994` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius_rt`` | Van der Waals radius according to Rowland and Taylor | pm | stored | :cite:`Rowland1996` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius_truhlar`` | Van der Waals radius according to Truhlar | pm | stored | :cite:`Mantina2009` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius_uff`` | Van der Waals radius from the UFF | pm | stored | :cite:`Rappe1992` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``vdw_radius`` | Van der Waals radius | pm | stored | :cite:`haynes2014crc` | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ +| ``zeff`` | Effective nuclear charge | | computed | | ++-----------------------------------------+----------------------------------------------------------------------+----------------+--------------+------------------------------------------------+ + Isotopes ======== -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| Name | Type | Comment | Unit | Data Source | -+===============================+=======+======================================================+======================+=========================+ -| abundance | float | Relative Abundance | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| abundance_uncertainty | float | Uncertainty of relative abundance | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| atomic_number | int | Atomic number | | | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| decay_modes | obj | Decay modes with intensities | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| discovery_year | int | Year the isotope was discovered | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| g_factor | float | Nuclear g-factor | | :cite:`Stone2014` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| g_factor_uncertainty | float | Uncertainty of the nuclear g-factor | | :cite:`Stone2014` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| half_life | float | Half life of the isotope | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| half_life_uncertainty | float | Uncertainty of the half life | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| half_life_unit | str | Unit in which the half life is given | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| is_radioactive | bool | Is the isotope radioactive | | :cite:`iupac-masses` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| mass | float | Atomic mass | Da | :cite:`iupac-masses` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| mass_number | int | Mass number of the isotope | | :cite:`iupac-masses` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| mass_uncertainty | float | Uncertainty of the atomic mass | Da | :cite:`iupac-masses` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| parity | str | Parity, if present, it can be either `+` or `-` | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| quadrupole_moment | float | Nuclear electric quadrupole moment | b [100 fm\ :sup:`2`] | :cite:`Stone2013` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| quadrupole_moment_uncertainty | float | Nuclear electric quadrupole moment | b [100 fm\ :sup:`2`] | :cite:`Stone2013` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ -| spin | str | Nuclear spin quantum number | | :cite:`Kondev2021` | -+-------------------------------+-------+------------------------------------------------------+----------------------+-------------------------+ ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| Attribute name | Description | Unit | Value origin | Citation keys | ++===================================+=================================================+==========+==============+======================+ +| ``abundance_uncertainty`` | Uncertainty of relative abundance | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``abundance`` | Relative Abundance | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``atomic_number`` | Atomic number | | stored | | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``decay_modes`` | Decay modes with intensities | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``discovery_year`` | Year the isotope was discovered | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``g_factor_uncertainty`` | Uncertainty of the nuclear g-factor | | stored | :cite:`Stone2014` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``g_factor`` | Nuclear g-factor | | stored | :cite:`Stone2014` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``half_life_uncertainty`` | Uncertainty of the half life | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``half_life_unit`` | Unit in which the half life is given | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``half_life`` | Half life of the isotope | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``is_radioactive`` | Is the isotope radioactive | | stored | :cite:`iupac-masses` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``mass_number`` | Mass number of the isotope | | stored | :cite:`iupac-masses` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``mass_uncertainty`` | Uncertainty of the atomic mass | Da | stored | :cite:`iupac-masses` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``mass`` | Atomic mass | Da | stored | :cite:`iupac-masses` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``parity`` | Parity, if present, it can be either `+` or `-` | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``quadrupole_moment_uncertainty`` | Nuclear electric quadrupole moment | 100 fm^2 | stored | :cite:`Stone2013` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``quadrupole_moment`` | Nuclear electric quadrupole moment | 100 fm^2 | stored | :cite:`Stone2013` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ +| ``spin`` | Nuclear spin quantum number | | stored | :cite:`Kondev2021` | ++-----------------------------------+-------------------------------------------------+----------+--------------+----------------------+ Isotope Decay Modes @@ -318,7 +339,7 @@ for compatibility. The table below provides explanations of the symbols. .. rubric:: Data Footnotes -.. [#f1] **Atomic Weights** +.. [#f_atomic_weight] **Atomic Weights** Atomic weights and their uncertainties were retrieved mainly from ref. :cite:`iupac-weights`. For elements whose values were given as ranges the *conventional atomic weights* from @@ -329,13 +350,17 @@ for compatibility. The table below provides explanations of the symbols. In case of Tc and Pm relative weights of their isotopes were used, for Tc isotope 98, and for Pm isotope 145 were taken from `CIAAW `_. -.. [#f2] **Covalent Radius by Cordero et al.** +.. [#f_covalent_radius_cordero] **Covalent Radius by Cordero et al.** In order to have a more homogeneous data for covalent radii taken from ref. :cite:`Cordero2008` the values for 3 different valences for C, also the low and high spin values for Mn, Fe Co, were respectively averaged. -.. [#f3] **Electron affinity** +.. [#f_color] **colors** + + HEX codes for colors. + +.. [#f_electron_affinity] **Electron affinity** Electron affinities were taken from :cite:`haynes2014crc` for the elements for which the data was available. For He, Be, N, Ar and Xe affinities were @@ -348,15 +373,15 @@ for compatibility. The table below provides explanations of the symbols. - Electron affinity of cobalt was taken from :cite:`Chen2016a`. - Electron affinity of lead was taken from :cite:`Chen2016`. -.. [#f4] **Allen's configuration energies** +.. [#f_electronegativity_allen] **Allen's configuration energies** The values of configurational energies from refs. :cite:`Mann2000a` and :cite:`Mann2000` were taken as reported in eV without converting to Pauling units. -.. [#f5] **Mendeleev numbers** +.. [#f_mendeleev_number] **Mendeleev numbers** - Mendeleev numbers were mostly taken from :cite:`Villars2004` but the range + Mendeleev numbers were sourced from :cite:`Villars2004` but the range was extended to cover the whole periodic table following the prescription in the article of increasing the numbers going from top to bottom in each group and group by group from left to right in the periodic table. @@ -381,10 +406,10 @@ for compatibility. The table below provides explanations of the symbols. 4f and 4f' in :cite:`Clementi1967`. The value corresponding to 4f were used since according to the authors these are the dominant ones. -.. [#f7] **van der Waals radii according to Alvarez** +.. [#f_vdw_radius_alvarez] **van der Waals radii according to Alvarez** The bulk of the radii data was taken from Ref. :cite:`Alvarez2013`, but the - radii for noble gasses were update according to the values in Ref. + radii for noble gasses were updated according to the values in Ref. :cite:`Vogt2014`. .. [#f9] **Ionic radii for Actinoid (III) ions** @@ -393,7 +418,7 @@ for compatibility. The table below provides explanations of the symbols. from :cite:`Lundberg2016`. In addition ``crystal_radius`` values were computed by adding 14 pm to the ``ionic_radius`` values according to :cite:`Shannon1976`. -.. [#f10] **Densities** +.. [#f_density] **Densities** Density values for solids and liquids are always in units of grams per cubic centimeter and can be assumed to refer to temperatures near room temperature @@ -403,7 +428,7 @@ for compatibility. The table below provides explanations of the symbols. Original values for gasses are converted from g/L to g/cm\ :sup:`3`. For elements where several allotropes exist, the density corresponding to the - most abundand are reported (for full list refer to :cite:`haynes2014crc`), namely: + most abundant are reported (for full list refer to :cite:`haynes2014crc`), namely: - Antimony (gray) - Berkelium (α form) diff --git a/docs/source/data_access.rst b/docs/source/data_access.rst index 6d17269..c011507 100644 --- a/docs/source/data_access.rst +++ b/docs/source/data_access.rst @@ -38,6 +38,7 @@ tables are available: - :ref:`oxidationstates ` - :ref:`screeningconstants ` - :ref:`series ` +- :ref:`propertymetadata ` .. autofunction:: fetch_table diff --git a/docs/source/references.bib b/docs/source/references.bib index 2a2b732..532f00e 100644 --- a/docs/source/references.bib +++ b/docs/source/references.bib @@ -845,3 +845,15 @@ @book{haynes2016crc edition = {97th}, pages = {2704} } +@article{ParrPearson1983, + author = {Parr, Robert G. and Pearson, Ralph G.}, + title = {Absolute hardness: companion parameter to absolute electronegativity}, + journal = {Journal of the American Chemical Society}, + volume = {105}, + number = {26}, + pages = {7512-7516}, + year = {1983}, + doi = {10.1021/ja00364a005}, + url = {https://doi.org/10.1021/ja00364a005}, + eprint = {https://doi.org/10.1021/ja00364a005} +} diff --git a/mendeleev/elements.db b/mendeleev/elements.db index 030e2a04a6be6246f31f4a6935523882e024c321..f47af339b708d1fca81afa9d7abab2d46ffc42d0 100644 GIT binary patch delta 18741 zcmbtce{37qeLs@2t*CYq*|C)i%lbUmv7P7_MO!xQxQ;BziXux^B-u{t#MF^Ik!O*2 z%pED2S=I~P%P;Bckpu<|AYti+O zbzS%Qz8}Xsijo~n0Li;|@4nyfd++`6fQ1AN5zdLDSzw zK04dcc~|TYaUXf)#@07F51{pOEE}1vqUjqIG|!aqHC@E**K@df;c3pU1SDn8fdttV-i#>}ztwf&&MNV}3{gIw6J$-$V-#%Q`vn8YA*cHR6*2_j! z&+Apa^}c&_ZhT~6Tw549b!J>^eR};%yW$>$ld<%&p`9O@8+~YGu2<{2EoYZ%WovD7 zNq5~)t2T3XL7O>u<_x{1SF4VhtyPWnyX5q$QLvr5MCOG6tmvhhk+B`KU|O=rfujdQ zee#BzbIeNBv@LC6{83;JP*AhXs(g`AWLb7qr@k)h%*JN&mdvtIcdvhD$2)KQ?>9O( zzufWo|7^Ky8yIMFrF~%9m0DWgBd!+>Vd0KP+vVOkN6>rS<}-_=-eU|ueSP+u)x 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zF{2dGQa%5z?Vo1+w_?e5B`^Prl7uPKrkShyTzUp~%XToe!KkULyC&%BBzJh;e3KsB t7$u4jWm7feg#(N~5A3I+by|(AK%!u#3!ba8wC%=a(#TdgMz*r__zr!2=u7|r diff --git a/mendeleev/fetch.py b/mendeleev/fetch.py index 1307ea2..5ccf7fa 100644 --- a/mendeleev/fetch.py +++ b/mendeleev/fetch.py @@ -54,6 +54,7 @@ def fetch_table(table: str, **kwargs) -> pd.DataFrame: "isotopes", "oxidationstates", "phasetransitions", + "propertymetadata", "screeningconstants", "series", } diff --git a/mendeleev/models.py b/mendeleev/models.py index 89646c7..2ba10e0 100644 --- a/mendeleev/models.py +++ b/mendeleev/models.py @@ -1,14 +1,15 @@ # -*- coding: utf-8 -*- -"""module specifying the database models""" +"""module defining the database models""" from typing import Any, Callable, Dict, List, Tuple, Union from operator import attrgetter +import enum import math import urllib.parse import numpy as np -from sqlalchemy import Column, Boolean, Integer, String, Float, ForeignKey +from sqlalchemy import Column, Boolean, Integer, String, Float, ForeignKey, Text, Enum from sqlalchemy.orm import declarative_base, relationship, reconstructor from sqlalchemy.ext.associationproxy import association_proxy from sqlalchemy.ext.hybrid import hybrid_property, hybrid_method @@ -34,6 +35,7 @@ "IonicRadius", "OxidationState", "Isotope", + "PropertyMetadata", "Series", "ScreeningConstant", ] @@ -731,6 +733,54 @@ def __repr__(self) -> str: ) +class ValueOrigin(enum.Enum): + "Options for the origin of the property value." + + STORED = "stored" + COMPUTED = "computed" + + +class PropertyMetadata(Base): + """Metadata for properties of elements and isotopes. + + Args: + annotations (str): Additional information about the property. + attribute_name (str): Name of the attribute of the ORM class. + category (str): Category of the property. + citation_keys (str): Comma separated list of citation keys. See references.bib for full bibliography. + class_name (str): Name of the ORM class. + column_name (str): Name of the column in the database. + description (str): Description of the property. + table_name (str): Name of the table in the database. + unit (str): Unit of the property. + value_origin (ValueOrigin): Origin of the value, either stored or computed. + """ + + __tablename__ = "propertymetadata" + + id = Column(Integer, primary_key=True) + annotations = Column(Text) + attribute_name = Column(String, nullable=False) + category = Column(String) + citation_keys = Column(String) + class_name = Column(String, nullable=False) + column_name = Column(String, nullable=True) + description = Column(Text, nullable=False) + table_name = Column(String, nullable=True) + unit = Column(String) + value_origin = Column(Enum(ValueOrigin), nullable=False) + + def __repr__(self) -> str: + return "%s(\n%s)" % ( + self.__class__.__name__, + " ".join( + "\t%s=%r,\n" % (key, getattr(self, key)) + for key in sorted(self.__dict__.keys()) + if not key.startswith("_") + ), + ) + + def fetch_attrs_for_group(attrs: List[str], group: int = 18) -> Tuple[List[Any]]: """ A convenience function for getting a specified attribute for all