Changed the sign of electrons in PCET families

This is to make them consistent with Li families
ssun30 · Sep 19, 2024 · 42e2f1c · 42e2f1c
1 parent e49f692
commit 42e2f1c
Show file tree

Hide file tree

Showing 10 changed files with 240 additions and 38 deletions.
diff --git a/input/kinetics/families/Surface_Proton_Electron_Reduction_Alpha/rules.py b/input/kinetics/families/Surface_Proton_Electron_Reduction_Alpha/rules.py
@@ -17,7 +17,7 @@
         Ea = (15, 'kJ/mol'), # activation energy at the reversible potential
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff
+        electrons = 1, # electron stochiometric coeff
     ),
     rank = 0,
     shortDesc = u"""Default""",

diff --git a/input/kinetics/families/Surface_Proton_Electron_Reduction_Alpha/training/reactions.py b/input/kinetics/families/Surface_Proton_Electron_Reduction_Alpha/training/reactions.py
@@ -20,7 +20,7 @@
 #         Ea = (0.61, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Tafel""",
@@ -42,7 +42,7 @@
         Ea = (0.44, 'eV/molecule'), # activation energy
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff 
+        electrons = 1, # electron stochiometric coeff 
     ),
     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
     longDesc = u"""Tafel""",
@@ -64,7 +64,7 @@
 #         Ea = (0.19, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -86,7 +86,7 @@
 #         Ea = (0.13, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -108,7 +108,7 @@
 #         Ea = (0.77, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Tafel""",
@@ -130,7 +130,7 @@
         Ea = (0.44, 'eV/molecule'), # activation energy
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff 
+        electrons = 1, # electron stochiometric coeff 
     ),
     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
     longDesc = u"""Tafel""",
@@ -152,7 +152,7 @@
 #         Ea = (0.59, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -174,7 +174,7 @@
 #         Ea = (0.53, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -196,7 +196,7 @@
 #         Ea = (0.62, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Tafel""",
@@ -218,7 +218,7 @@
         Ea = (0.37, 'eV/molecule'), # activation energy
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff 
+        electrons = 1, # electron stochiometric coeff 
     ),
     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
     longDesc = u"""Tafel""",
@@ -240,7 +240,7 @@
 #         Ea = (0.15, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2017.01.050""",
 #     longDesc = u"""
@@ -263,7 +263,7 @@
 #         Ea = (0.78, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Tafel""",
@@ -285,7 +285,7 @@
         Ea = (0.59, 'eV/molecule'), # activation energy
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff 
+        electrons = 1, # electron stochiometric coeff 
     ),
     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
     longDesc = u"""Tafel""",
@@ -307,7 +307,7 @@
 #         Ea = (0.17, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -329,7 +329,7 @@
 #         Ea = (0.09, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -351,7 +351,7 @@
 #         Ea = (1.20, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Tafel""",
@@ -373,7 +373,7 @@
         Ea = (0.97, 'eV/molecule'), # activation energy
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff 
+        electrons = 1, # electron stochiometric coeff 
     ),
     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
     longDesc = u"""Tafel""",
@@ -395,7 +395,7 @@
 #         Ea = (0.99, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -417,7 +417,7 @@
 #         Ea = (0.43, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -439,7 +439,7 @@
 #         Ea = (0.87, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Tafel""",
@@ -461,7 +461,7 @@
         Ea = (0.48, 'eV/molecule'), # activation energy
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff 
+        electrons = 1, # electron stochiometric coeff 
     ),
     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
     longDesc = u"""Tafel""",
@@ -483,7 +483,7 @@
 #         Ea = (0.06, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",
@@ -505,7 +505,7 @@
 #         Ea = (0.03, 'eV/molecule'), # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
 #     longDesc = u"""Heyrovsky""",

diff --git a/input/kinetics/families/Surface_Proton_Electron_Reduction_Alpha_vdW/rules.py b/input/kinetics/families/Surface_Proton_Electron_Reduction_Alpha_vdW/rules.py
@@ -17,7 +17,7 @@
         Ea = (15, 'kJ/mol'), # activation energy at the reversible potential
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff
+        electrons = 1, # electron stochiometric coeff
     ),
     rank = 0,
     shortDesc = u"""Default""",

diff --git a/input/kinetics/families/Surface_Proton_Electron_Reduction_Alpha_vdW/training/reactions.py b/input/kinetics/families/Surface_Proton_Electron_Reduction_Alpha_vdW/training/reactions.py
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Surface_Proton_Electron_Reduction_Alpha/training"
+shortDesc = u"Reaction kinetics used to generate rate rules"
+longDesc = u"""
+Put kinetic parameters for specific reactions in this file to use as a
+training set for generating rate rules to populate this kinetics family.
+"""
+
+# entry(
+#     index = 1,
+#     label = "CH3X + H <=> CH4X",
+#     degeneracy = 1,
+#     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 = (0.51, 'V'), # reference potential
+#         Ea = (0.89, 'eV/molecule'), # activation energy
+#         Tmin = (200, 'K'),
+#         Tmax = (3000, 'K'),
+#         electrons = 1, # electron stochiometric coeff 
+#     ),
+#     shortDesc = u"""https://doi.org/10.1016/j.cattod.2017.01.050""",
+#     longDesc = u"""
+# """,
+#     metal = "Pt",
+#     facet = "111",
+#     site = "",
+#     rank = 5,
+# )
+
+entry(
+    index = 1,
+    label = "CH3X + H <=> CH4X",
+    degeneracy = 1,
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.23, # 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 = (-0.5, 'V'), # reference potential
+        Ea = (0.53, 'eV/molecule'), # activation energy
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff 
+    ),
+    shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
+    longDesc = u"""
+""",
+    metal = "Pt",
+    facet = "111",
+    site = "",
+    rank = 5,
+)
+
+# entry(
+#     index = 2,
+#     label = "HOX + H <=> H2OX",
+#     degeneracy = 1,
+#     kinetics = SurfaceChargeTransfer(
+#         alpha = 0.07, # 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 = (0.39, 'V'), # reference potential
+#         Ea = (0.14, 'eV/molecule'), # activation energy
+#         Tmin = (200, 'K'),
+#         Tmax = (3000, 'K'),
+#         electrons = 1, # electron stochiometric coeff 
+#     ),
+#     shortDesc = u"""https://doi.org/10.1016/j.cattod.2017.01.050""",
+#     longDesc = u"""
+# """,
+#     metal = "Pt",
+#     facet = "111",
+#     site = "",
+#     rank = 5,
+# )
+
+entry(
+    index = 2,
+    label = "HOX + H <=> H2OX",
+    degeneracy = 1,
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.11, # 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 = (-0.5, 'V'), # reference potential
+        Ea = (0.12, 'eV/molecule'), # activation energy
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff 
+    ),
+    shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
+    longDesc = u"""
+""",
+    metal = "Pt",
+    facet = "111",
+    site = "",
+    rank = 5,
+)
+
+entry(
+    index = 3,
+    label = "NH2X + H <=> NH3X",
+    degeneracy = 1,
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.35, # 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 = (-0.5, 'V'), # reference potential
+        Ea = (0.23, 'eV/molecule'), # activation energy
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff 
+    ),
+    shortDesc = u"""https://doi.org/10.1016/j.cattod.2018.03.048""",
+    longDesc = u"""
+""",
+    metal = "Pt",
+    facet = "111",
+    site = "",
+    rank = 5,
+)
+
diff --git a/input/kinetics/families/Surface_Proton_Electron_Reduction_Beta/rules.py b/input/kinetics/families/Surface_Proton_Electron_Reduction_Beta/rules.py
@@ -18,7 +18,7 @@
         Ea = (50, 'kJ/mol'), # activation energy at the reversible potential
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
-        electrons = -1, # electron stochiometric coeff
+        electrons = 1, # electron stochiometric coeff
     ),
     rank = 0,
     shortDesc = u"""Default""",

diff --git a/input/kinetics/families/Surface_Proton_Electron_Reduction_Beta/training/reactions.py b/input/kinetics/families/Surface_Proton_Electron_Reduction_Beta/training/reactions.py
@@ -20,7 +20,7 @@
 #         Ea = (40, 'kJ/mol') # activation energy
 #         Tmin = (200, 'K'),
 #         Tmax = (3000, 'K'),
-#         electrons = -1, # electron stochiometric coeff 
+#         electrons = 1, # electron stochiometric coeff 
 #     ),
 #     shortDesc = u"""Default""",
 #     longDesc = u"""