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mjohnson541
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add Li adsorption to test data
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‎rmgpy/data/test_data/thermo/groups/adsorptionLi.py‎

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#!/usr/bin/env python
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# encoding: utf-8
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name = "Surface Adsorption Corrections Lithium"
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shortDesc = "Li"
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longDesc = """
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Changes due to adsorbing on a Lithium electrode.
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Note: "-h" means "horizontal"
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Li enthalpy of formation 159.30 kJ/mol https://webbook.nist.gov/cgi/cbook.cgi?ID=C7439932&Units=SI&Mask=1#ref-2
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https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf
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LiF = 577
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LiH = 247
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LiO = 341
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LiOH = 427
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https://pubs.acs.org/doi/abs/10.1021/om950966x
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Li-CH3 = 190.37
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LiF
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4.329154975994253
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LiH
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0.9089463523933348
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LiO
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1.8831875966917782
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LiOH
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2.7745146925392903
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LiC
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0.3220178240463045
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"""
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entry(
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index = 0,
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label = "R*",
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group =
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"""
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1 R ux
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2 * X ux
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""",
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thermo = None,
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shortDesc = """Anything adsorbed anyhow.""",
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longDesc =
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"""
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R
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X
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***********
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This node should be empty, ensuring that one of the nodes below is used.
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The group could well be defined as:
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1 R ux
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2 * Xux
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but then it is identical with the R*vdW node, and the database tests
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do not like that. It should be OK, because things would check the
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tree in order, and if there *was* a bond it would match either
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R*bidentate or R*single_chemisorbed and thus not R*vdW.
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""",
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)
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entry(
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index = 1,
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label = "R*single_chemisorbed",
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group =
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"""
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1 * X u0 {2,S}
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2 R ux {1,S}
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""",
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thermo = ThermoData(
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Tdata = ([300,400,500,600,800,1000,1500],'K'),
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Cpdata = ([-0.07,1.05,1.77,2.43,2.8,3.08,3.39],'cal/(mol*K)'),
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H298 = (-2,'eV/molecule'),
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S298 = (-38.17,'cal/(mol*K)'),
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),
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shortDesc = """""",
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longDesc =
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"""
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""",
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)
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entry(
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index = 2,
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label = "C*",
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group =
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"""
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1 * X u0 {2,S}
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2 C ux {1,S}
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""",
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thermo = ThermoData(
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Tdata = ([300,400,500,600,800,1000,1500],'K'),
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Cpdata = ([-0.45,0.61,1.42,2.02,2.81,3.26,3.73],'cal/(mol*K)'),
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H298 = (-0.5,'eV/molecule'),
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S298 = (-32.73,'cal/(mol*K)'),
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),
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shortDesc = """""",
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longDesc =
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"""
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CR3
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|
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***********
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""",
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)
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entry(
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index = 3,
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label = "O*",
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group =
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"""
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1 * X u0 {2,S}
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2 O ux {1,S}
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""",
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thermo = ThermoData(
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Tdata = ([300,400,500,600,800,1000,1500],'K'),
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Cpdata = ([1.09,1.82,2.2,2.42,2.65,2.75,2.86],'cal/(mol*K)'),
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H298 = (-1.88,'eV/molecule'),
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S298 = (-33.89,'cal/(mol*K)'),
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),
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shortDesc = """Came from OH single-bonded on Pt(111)""",
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longDesc =
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"""
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R
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|
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O
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|
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***********
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""",
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)
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entry(
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index = 4,
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label = "F*",
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group =
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"""
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1 * X u0 {2,S}
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2 F ux {1,S}
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""",
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thermo = ThermoData(
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Tdata = ([300,400,500,600,800,1000,1500],'K'),
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Cpdata = ([1.09,1.82,2.2,2.42,2.65,2.75,2.86],'cal/(mol*K)'),
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H298 = (-4.33,'eV/molecule'),
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S298 = (-26,'cal/(mol*K)'),
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),
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shortDesc = """""",
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longDesc =
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"""
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F
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|
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***********
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""",
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)
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entry(
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index = 5,
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label = "H*",
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group =
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"""
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1 * X u0 {2,S}
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2 H ux {1,S}
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""",
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thermo = ThermoData(
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Tdata = ([300,400,500,600,800,1000,1500],'K'),
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Cpdata = ([1.09,1.82,2.2,2.42,2.65,2.75,2.86],'cal/(mol*K)'),
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H298 = (-0.9,'eV/molecule'),
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S298 = (-26,'cal/(mol*K)'),
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),
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shortDesc = """""",
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longDesc =
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"""
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H
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|
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***********
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""",
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)
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entry(
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index = 6,
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label = "OH*",
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group =
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"""
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1 * X u0 {2,S}
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2 O u0 {1,S} {3,S}
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3 H u0 {2,S}
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""",
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thermo = ThermoData(
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Tdata = ([300,400,500,600,800,1000,1500],'K'),
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Cpdata = ([1.09,1.82,2.2,2.42,2.65,2.75,2.86],'cal/(mol*K)'),
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H298 = (-2.77,'eV/molecule'),
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S298 = (-34,'cal/(mol*K)'),
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),
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shortDesc = """Came from OH single-bonded on Pt(111)""",
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longDesc =
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"""
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H
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|
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O
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|
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***********
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""",
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)
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entry(
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index = 7,
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label = "R*vdW",
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group =
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"""
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1 * X u0
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2 R u0
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""",
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thermo = ThermoData(
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Tdata = ([300,400,500,600,800,1000,1500],'K'),
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Cpdata = ([1.23,1.71,2,2.19,2.39,2.5,2.61],'cal/(mol*K)'),
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H298 = (-0.5,'eV/molecule'),
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S298 = (-20.48,'cal/(mol*K)'),
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),
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shortDesc = """Average of (CR4)*, (NR3)* and (OR2)* thermo.""",
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longDesc =
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"""
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""",
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metal = "Pt",
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facet = "111",
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)
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entry(
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index = 8,
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label = "O*vdW",
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group =
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"""
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1 * X u0 p0
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2 O u0 p2
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""",
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thermo = ThermoData(
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Tdata = ([300,400,500,600,800,1000,1500],'K'),
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Cpdata = ([0.71,1.22,1.49,1.65,1.81,1.9,1.98],'cal/(mol*K)'),
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H298 = (-0.8,'eV/molecule'),
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S298 = (-22.53,'cal/(mol*K)'),
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),
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shortDesc = """""",
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longDesc =
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"""
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""",
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)
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tree(
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"""
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L1: R*
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L2: R*single_chemisorbed
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L3: C*
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L3: O*
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L4: OH*
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L3: F*
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L3: H*
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L2: R*vdW
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L3: O*vdW
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"""
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)
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