add electrocatLithermo library

input/thermo/libraries/electrocatLiThermo.py

@@ -0,0 +1,188 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "electrocatLiThermo"
+shortDesc = u"Ions and Li absorbates"
+longDesc = u"""
+Some surface species adsorbed on Pt(111),
+Mostly calculated by Katrin Blondal at Brown University around 2018,
+based on DFT calculations by Jelena Jelic at KIT.
+Note: "-h" means "horizontal".
+"""
+
+
+entry(
+    index = 1,
+    label = "vacant",
+    molecule =
+"""
+1 X  u0 p0 c0
+""",
+    thermo = NASA(
+        polynomials = [
+            NASAPolynomial(coeffs=[
+             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+             0.000000000E+00,   0.000000000E+00,   0.000000000E+00], Tmin=(298.0,'K'), Tmax=(1000.0, 'K')),
+            NASAPolynomial(coeffs=[
+             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+             0.000000000E+00,   0.000000000E+00,   0.000000000E+00], Tmin=(1000.0,'K'), Tmax=(3000.0, 'K')),
+        ],
+        Tmin = (298.0, 'K'),
+        Tmax = (3000.0, 'K'),
+    ),
+    metal = "Li",
+    facet = "111",
+)
+
+entry(
+    index = 2,
+    label = "electron",
+    molecule =
+"""
+1 e u0 p0 c-1
+""",
+    thermo = NASA(
+        polynomials = [
+            NASAPolynomial(coeffs=[
+             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+             0.000000000E+00,   0.000000000E+00,   0.000000000E+00], Tmin=(298.0,'K'), Tmax=(1000.0, 'K')),
+            NASAPolynomial(coeffs=[
+             0.000000000E+00,   0.000000000E+00,   0.000000000E+00,   0.000000000E+00,
+             0.000000000E+00,   0.000000000E+00,   0.000000000E+00], Tmin=(1000.0,'K'), Tmax=(3000.0, 'K')),
+        ],
+        Tmin = (298.0, 'K'),
+        Tmax = (3000.0, 'K'),
+    ),
+)
+
+entry(
+    index = 3,
+    label = "proton",
+    molecule =
+"""
+1 H u0 p0 c+1
+""",
+    thermo = ThermoData(
+        Tdata=([300,400,500,600,800,1000,1500],'K'),
+        Cpdata=([3.4475,3.4875,3.497,3.5045,3.5405,3.6095,3.86],'cal/(mol*K)'),
+        H298=(0,'kcal/mol'), S298=(15.6165,'cal/(mol*K)','+|-',0.0007),
+        comment = '1/2 free energy of H2(g)')
+)
+
+entry(
+    index = 4,
+    label = "H3O",
+    molecule =
+"""
+1 H u0 p0 c0 {3,S}
+2 H u0 p0 c0 {3,S}
+3 O u0 p2 c0 {1,S} {2,S}
+4 H u0 p0 c+1
+""",
+    thermo = ThermoData(Tdata=([300,400,500,600,800,1000,1500],'K'),
+        Cpdata=([11.4855,11.6675,11.876,12.1285,12.7355,13.3755,14.879],'cal/(mol*K)'),
+        H298=(-57.797,'kcal/mol'), S298=(60.7005,'cal/(mol*K)','+|-',0.0007),
+        comment="""1/2 free energy of H2(g) + H2O(g)""")
+)
+
+entry(
+    index = 5,
+    label = "H2O",
+    molecule =
+"""
+1 O u0 p2 c0 {2,S} {3,S}
+2 H u0 p0 c0 {1,S}
+3 H u0 p0 c0 {1,S}
+""",
+    thermo = ThermoData(
+        Tdata = ([300,400,500,600,800,1000,1500],'K'),
+        Cpdata = ([8.038,8.18,8.379,8.624,9.195,9.766,11.019],'cal/(mol*K)'),
+        H298 = (-57.797,'kcal/mol'),
+        S298 = (45.084,'cal/(mol*K)'),
+    ),
+    shortDesc = u"""""",
+    longDesc =
+u"""
+H298: ATcT version 1.110
+level of theory energy: CCSD(T)F12A/cc-pVQZ-F12//CCSD(T)/cc-pVQZ
+level of theory frequency: B3LYP/6-311++g(d,p)//B3LYP/6-311++g(d,p)
+""",
+)
+
+# entry(
+#     index = 6,
+#     label = "Li_ion",
+#     molecule =
+# """
+# 1 Li u0 p0 c+1
+# """,
+#     thermo = ThermoData(
+#         Tdata = ([300,400,500,600,800,1000,1500],'K'),
+#         Cpdata = ([0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0],'cal/(mol*K)'),
+#         H298 = (420.0,'kJ/mol'),
+#         S298 = (0.0,'cal/(mol*K)'),
+#     ),
+#     shortDesc = u"""""",
+#     longDesc =
+# u"""
+# # COSMOtherm calculations at tzvpd-fine:
+# # dSsolv: -20.51 cal/(mol*K)
+# # dGsolv: -93.26409698 kcal/mol
+# # dHsolv: -99.379 kcal/mol
+# dGgas: 0.0 + 420 kJ/mol (ionization energy)
+# """,
+# )
+
+# entry(
+#     index = 4,
+#     label = "CO2X",
+#     molecule =
+# """
+# 1 C u0 p0 {2,D} {3,D}
+# 2 O u0 p2 {1,D}
+# 3 O u0 p2 {1,D}
+# 4 X u0 p0
+# """,
+#     thermo = ThermoData(
+#         Tdata = ([300,400,500,600,800,1000,1500],'K'),
+#         Cpdata = ([8.869,9.845,10.626,11.264,12.229,12.898,13.822],'cal/(mol*K)'),
+#         H298 = (-98,'kcal/mol'),
+#         S298 = (28.54,'cal/(mol*K)'),
+#     ),
+#     shortDesc = u"""""",
+#     longDesc =
+# u"""
+
+# """,
+#     metal = "Pt",
+#     facet = "111",
+# )
+
+# entry(
+#     index = 6,
+#     label = "O=CX-CX=O",
+#     molecule =
+# """
+# 1 C u0 p0 c0 {2,S} {3,D} {5,S}
+# 2 C u0 p0 c0 {1,S} {4,D} {6,S}
+# 3 O u0 p2 c0 {1,D}
+# 4 O u0 p2 c0 {2,D}
+# 5 X u0 p0 c0 {1,S}
+# 6 X u0 p0 c0 {2,S}
+# """,
+#     thermo = ThermoData(
+#         Tdata = ([300,400,500,600,800,1000,1500],'K'),
+#         Cpdata = ([15.24,17.52,19.03,20.13,21.6,22.53,23.69],'cal/(mol*K)'),
+#         H298 = (-17.02,'kcal/mol'),
+#         S298 = (49.17,'cal/(mol*K)'),
+#     ),
+#     shortDesc = u"""""",
+#     longDesc =
+# u"""
+# OCCO from primary thermo library + Thermo group additivity estimation: adsorptionPt111(C-*R2C-*R2)
+
+# instead of OCCO(S)
+# """,
+#     metal = "Pt",
+#     facet = "111",
+# )