Add thermo and kinetics data for electrocatalytic CO2 reduction

input/kinetics/families/recommended.py

@@ -116,7 +116,7 @@
     'Surface_Adsorption_Bidentate',
     'Surface_Bidentate_Dissociation',
     'Surface_Monodentate_to_Bidentate',
-    'Surface_Dissociation_to_Bidentate', 
+    'Surface_Dissociation_to_Bidentate',
     'Surface_vdW_to_Bidentate',
     'Surface_Adsorption_Dissociative_Double',
     'Surface_Abstraction_Beta',
@@ -170,3 +170,24 @@
     'Li_Abstraction',
     'R_Addition_MultipleBond_Disprop',
 }
+
+# CO2RR families
+surface_CO2 = {
+    'Surface_Adsorption_Single',
+    'Surface_Adsorption_vdW',
+    'Surface_Adsorption_Dissociative',
+    'Surface_Dissociation',
+    'Surface_Abstraction',
+    'Surface_EleyRideal_Addition_Multiple_Bond',
+    'Surface_Migration',
+    'Surface_Dissociation_Double_vdW',
+    'Surface_Addition_Single_vdW',
+    'Surface_Dissociation_vdW',
+    'Surface_Abstraction_vdW',
+    'Surface_Dissociation_Beta',
+    'Surface_Adsorption_Bidentate',
+    'Surface_Bidentate_Dissociation',
+    'Surface_vdW_to_Bidentate',
+    'Surface_Abstraction_Single_vdW',
+    'Surface_Adsorption_Dissociative_Double',
+}

input/kinetics/libraries/CO2RR_DFT_Ag111/dictionary.txt

@@ -0,0 +1,81 @@
+
+X
+1 X u0 p0 c0
+
+proton
+1 H u0 p0 c+1
+
+e
+1 e u0 p0 c-1
+
+H2O
+1 O u0 p2 c0 {2,S} {3,S}
+2 H u0 p0 c0 {1,S}
+3 H u0 p0 c0 {1,S}
+
+CO2X
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,D}
+3 O u0 p2 c0 {2,D}
+4 X u0 p0 c0
+
+CO2HX
+1 O u0 p2 c0 {3,S} {4,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {5,S}
+4 H u0 p0 c0 {1,S}
+5 X u0 p0 c0 {3,S}
+
+CHO2X
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 H u0 p0 c0 {3,S}
+5 X u0 p0 c0 {1,S}
+
+OCX
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,D}
+3 X u0 p0 c0 {2,D}
+
+HCOOHX
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 H u0 p0 c0 {3,S}
+5 H u0 p0 c0 {1,S}
+6 X u0 p0 c0
+
+CHOX
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,S} {4,S}
+3 H u0 p0 c0 {2,S}
+4 X u0 p0 c0 {2,S}
+
+XCHOH
+1 O u0 p2 c0 {2,S} {4,S}
+2 C u0 p0 c0 {1,S} {3,S} {5,D}
+3 H u0 p0 c0 {2,S}
+4 H u0 p0 c0 {1,S}
+5 X u0 p0 c0 {2,S}
+
+CH2OX
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,S} {4,S}
+3 H u0 p0 c0 {2,S}
+4 H u0 p0 c0 {2,S}
+5 X u0 p0 c0
+
+XCH2OH
+1 O u0 p2 c0 {2,S} {3,S}
+2 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S}
+3 H u0 p0 c0 {1,S}
+4 H u0 p0 c0 {2,S}
+5 H u0 p0 c0 {2,S}
+6 X u0 p0 c0 {2,S}
+
+XCH2
+1 H u0 p0 c0 {2,S}
+2 C u0 p0 c0 {1,S} {3,S} {4,D}
+3 H u0 p0 c0 {2,S}
+4 X u0 p0 c0 {2,D}

input/kinetics/libraries/CO2RR_DFT_Ag111/reactions.py

@@ -0,0 +1,181 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "CO2RR_DFT_Ag111"
+shortDesc = u"Calculated by Manish Kumar Kothakonda at Northeastern University"
+longDesc = u"""
+Place holder for long description
+"""
+
+
+entry(
+    index = 1,
+    label = "CO2X + proton <=> CO2HX",
+    degeneracy = 1,
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.62, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (0.75, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 2,
+    label = "CO2X + proton <=> CHO2X",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.46, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (1.25, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 3,
+    label = "CO2HX + proton <=> OCX + H2O",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.36, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (0.25, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 4,
+    label = "CO2HX + proton <=> HCOOHX",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.62, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (2.40, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 5,
+    label = "CHO2X + proton <=> HCOOHX",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.12, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (2.64, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 6,
+    label = "OCX + proton <=> CHOX",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.49, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (0.45, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 7,
+    label = "CHOX + proton <=> XCHOH",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.71, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (2.14, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 8,
+    label = "CHOX + proton <=> CH2OX",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.36, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (2.60, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 9,
+    label = "XCH2OH + proton <=> XCH2 + H2O",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.19, # charge transfer coeff
+        A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (0.79, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)