From 655e8ded2d9181b6313dd4b510616876ad9f216f Mon Sep 17 00:00:00 2001
From: Matt Johnson <mjohnson541@gmail.com>
Date: Tue, 9 May 2023 16:07:19 -0700
Subject: [PATCH] add Li adsorption to test data

---
 .../test_data/thermo/groups/adsorptionLi.py   | 261 ++++++++++++++++++
 1 file changed, 261 insertions(+)
 create mode 100644 rmgpy/data/test_data/thermo/groups/adsorptionLi.py

diff --git a/rmgpy/data/test_data/thermo/groups/adsorptionLi.py b/rmgpy/data/test_data/thermo/groups/adsorptionLi.py
new file mode 100644
index 00000000000..d9a933994b3
--- /dev/null
+++ b/rmgpy/data/test_data/thermo/groups/adsorptionLi.py
@@ -0,0 +1,261 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface Adsorption Corrections Lithium"
+shortDesc = "Li"
+longDesc = """
+Changes due to adsorbing on a Lithium electrode.
+Note: "-h" means "horizontal"
+
+Li enthalpy of formation 159.30 kJ/mol https://webbook.nist.gov/cgi/cbook.cgi?ID=C7439932&Units=SI&Mask=1#ref-2
+
+https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf
+LiF = 577
+LiH = 247
+LiO = 341
+LiOH = 427
+
+https://pubs.acs.org/doi/abs/10.1021/om950966x
+Li-CH3 = 190.37
+
+LiF
+4.329154975994253
+LiH
+0.9089463523933348
+LiO
+1.8831875966917782
+LiOH
+2.7745146925392903
+LiC
+0.3220178240463045
+"""
+
+entry(
+    index = 0,
+    label = "R*",
+    group = 
+"""
+1   R ux
+2 * X ux
+""",
+    thermo = None,
+    shortDesc = """Anything adsorbed anyhow.""",
+    longDesc = 
+"""
+R
+   X
+***********
+This node should be empty, ensuring that one of the nodes below is used.
+
+
+The group could well be defined as:
+
+    1 R ux
+    2 * Xux
+
+but then it is identical with the R*vdW node, and the database tests
+do not like that. It should be OK, because things would check the
+tree in order, and if there *was* a bond it would match either
+R*bidentate or R*single_chemisorbed and thus not R*vdW.
+""",
+)
+
+entry(
+    index = 1,
+    label = "R*single_chemisorbed",
+    group = 
+"""
+1 * X u0 {2,S}
+2   R ux {1,S}
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([-0.07,1.05,1.77,2.43,2.8,3.08,3.39],'cal/(mol*K)'),
+        H298 = (-2,'eV/molecule'),
+        S298 = (-38.17,'cal/(mol*K)'),
+    ),
+    shortDesc = """""",
+    longDesc = 
+"""
+
+""",
+)
+
+entry(
+    index = 2,
+    label = "C*",
+    group = 
+"""
+1 * X u0 {2,S}
+2   C ux {1,S}
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([-0.45,0.61,1.42,2.02,2.81,3.26,3.73],'cal/(mol*K)'),
+        H298 = (-0.5,'eV/molecule'),
+        S298 = (-32.73,'cal/(mol*K)'),
+    ),
+    shortDesc = """""",
+    longDesc = 
+"""
+   CR3
+   |
+***********
+""",
+)
+
+entry(
+    index = 3,
+    label = "O*",
+    group = 
+"""
+1 * X u0 {2,S}
+2   O ux {1,S}
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([1.09,1.82,2.2,2.42,2.65,2.75,2.86],'cal/(mol*K)'),
+        H298 = (-1.88,'eV/molecule'),
+        S298 = (-33.89,'cal/(mol*K)'),
+    ),
+    shortDesc = """Came from OH single-bonded on Pt(111)""",
+    longDesc = 
+"""
+   R
+   |
+   O
+   |
+***********
+""",
+)
+
+entry(
+    index = 4,
+    label = "F*",
+    group = 
+"""
+1 * X u0 {2,S}
+2   F ux {1,S}
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([1.09,1.82,2.2,2.42,2.65,2.75,2.86],'cal/(mol*K)'),
+        H298 = (-4.33,'eV/molecule'),
+        S298 = (-26,'cal/(mol*K)'),
+    ),
+    shortDesc = """""",
+    longDesc = 
+"""
+   F
+   |
+***********
+""",
+
+)
+
+entry(
+    index = 5,
+    label = "H*",
+    group = 
+"""
+1 * X u0 {2,S}
+2   H ux {1,S}
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([1.09,1.82,2.2,2.42,2.65,2.75,2.86],'cal/(mol*K)'),
+        H298 = (-0.9,'eV/molecule'),
+        S298 = (-26,'cal/(mol*K)'),
+    ),
+    shortDesc = """""",
+    longDesc = 
+"""
+   H
+   |
+***********
+""",
+)
+
+entry(
+    index = 6,
+    label = "OH*",
+    group = 
+"""
+1 * X u0 {2,S}
+2   O u0 {1,S} {3,S}
+3   H u0 {2,S}
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([1.09,1.82,2.2,2.42,2.65,2.75,2.86],'cal/(mol*K)'),
+        H298 = (-2.77,'eV/molecule'),
+        S298 = (-34,'cal/(mol*K)'),
+    ),
+    shortDesc = """Came from OH single-bonded on Pt(111)""",
+    longDesc = 
+"""
+   H
+   |
+   O
+   |
+***********
+""",
+)
+
+entry(
+    index = 7,
+    label = "R*vdW",
+    group = 
+"""
+1 * X u0
+2   R u0
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([1.23,1.71,2,2.19,2.39,2.5,2.61],'cal/(mol*K)'),
+        H298 = (-0.5,'eV/molecule'),
+        S298 = (-20.48,'cal/(mol*K)'),
+    ),
+    shortDesc = """Average of (CR4)*, (NR3)* and (OR2)* thermo.""",
+    longDesc = 
+"""
+
+""",
+    metal = "Pt",
+    facet = "111",
+)
+
+entry(
+    index = 8,
+    label = "O*vdW",
+    group = 
+"""
+1 * X u0 p0
+2   O u0 p2
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([0.71,1.22,1.49,1.65,1.81,1.9,1.98],'cal/(mol*K)'),
+        H298 = (-0.8,'eV/molecule'),
+        S298 = (-22.53,'cal/(mol*K)'),
+    ),
+    shortDesc = """""",
+    longDesc = 
+"""
+""",
+)
+
+tree(
+"""
+L1: R*
+    L2: R*single_chemisorbed
+        L3: C*
+        L3: O*
+            L4: OH*
+        L3: F*
+        L3: H*
+    L2: R*vdW
+        L3: O*vdW
+"""
+)
+