From 1689be10a67243cd1231f9601e708141e7f2d1d7 Mon Sep 17 00:00:00 2001
From: davidfarinajr <farina.d@northeastern.edu>
Date: Fri, 22 Jan 2021 20:59:42 -0500
Subject: [PATCH] added method and test for changing reference potential for
 surfaceChargeTransfer

---
 rmgpy/kinetics/surface.pxd    |  2 ++
 rmgpy/kinetics/surface.pyx    | 11 +++++++++++
 rmgpy/kinetics/surfaceTest.py | 22 +++++++++++++++++++++-
 3 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/rmgpy/kinetics/surface.pxd b/rmgpy/kinetics/surface.pxd
index 6f96bbfdbf..07068f66af 100644
--- a/rmgpy/kinetics/surface.pxd
+++ b/rmgpy/kinetics/surface.pxd
@@ -91,6 +91,8 @@ cdef class SurfaceChargeTransfer(KineticsModel):
 
     cpdef change_t0(self, double T0)
 
+    cpdef change_v0(self, double V0)
+
     cpdef fit_to_data(self, np.ndarray Tlist, np.ndarray klist, str kunits, double T0=?, np.ndarray weights=?, bint three_params=?)
 
     cpdef bint is_identical_to(self, KineticsModel other_kinetics) except -2
diff --git a/rmgpy/kinetics/surface.pyx b/rmgpy/kinetics/surface.pyx
index f9a58776dd..2778944d92 100644
--- a/rmgpy/kinetics/surface.pyx
+++ b/rmgpy/kinetics/surface.pyx
@@ -684,6 +684,17 @@ cdef class SurfaceChargeTransfer(KineticsModel):
         self._A.value_si /= (self._T0.value_si / T0) ** self._n.value_si
         self._T0.value_si = T0
 
+    cpdef change_v0(self, double V0):
+        """
+        Changes the reference potential to `V0` in volts, and adjusts the
+        activation energy `Ea` accordingly.
+        """
+
+        if self._ne.value > 0:
+            self._Ea.value_si = self.get_activation_energy_from_potential(V0, non_negative=False)
+
+        self._V0.value_si = V0
+
     cpdef fit_to_data(self, np.ndarray Tlist, np.ndarray klist, str kunits, double T0=1,
                       np.ndarray weights=None, bint three_params=False):
         """
diff --git a/rmgpy/kinetics/surfaceTest.py b/rmgpy/kinetics/surfaceTest.py
index dcc68e6c85..2f9bc70031 100644
--- a/rmgpy/kinetics/surfaceTest.py
+++ b/rmgpy/kinetics/surfaceTest.py
@@ -587,7 +587,6 @@ def test_get_activation_energy_from_potential(self):
             Ea = self.surfchargerxn_reduction.get_activation_energy_from_potential(V, False)
             self.assertAlmostEqual(self.surfchargerxn_oxidation.Ea.value_si, Ea, 6)
 
-
     def test_get_rate_coefficient(self):
         """
         Test that the SurfaceChargeTransfer.to_surface_arrhenius method works
@@ -612,6 +611,27 @@ def test_get_rate_coefficient(self):
                 self.assertAlmostEqual(k_oxidation,self.surfchargerxn_oxidation.get_rate_coefficient(T,V))
                 self.assertAlmostEqual(k_reduction,self.surfchargerxn_reduction.get_rate_coefficient(T,V))
 
+    def test_change_v0(self):
+        
+        V0 = self.surfchargerxn_oxidation.V0.value_si
+        ne = self.surfchargerxn_oxidation.ne.value
+        for V in (V0 + 1, V0, V0 - 1, V0):
+            delta = V - self.surfchargerxn_oxidation.V0.value_si
+            V_i = self.surfchargerxn_oxidation.V0.value_si
+            Ea_i = self.surfchargerxn_oxidation.Ea.value_si
+            self.surfchargerxn_oxidation.change_v0(V)
+            self.assertEqual(self.surfchargerxn_oxidation.V0.value_si, V_i + delta)
+            self.assertAlmostEqual(self.surfchargerxn_oxidation.Ea.value_si, Ea_i - (ne * constants.F * delta), 6)
+
+        V0 = self.surfchargerxn_reduction.V0.value_si
+        ne = self.surfchargerxn_reduction.ne.value
+        for V in (V0 + 1, V0, V0 - 1, V0):
+            delta = V - self.surfchargerxn_reduction.V0.value_si
+            V_i = self.surfchargerxn_reduction.V0.value_si
+            Ea_i = self.surfchargerxn_reduction.Ea.value_si
+            self.surfchargerxn_reduction.change_v0(V)
+            self.assertEqual(self.surfchargerxn_reduction.V0.value_si, V_i + delta)
+            self.assertAlmostEqual(self.surfchargerxn_reduction.Ea.value_si, Ea_i, 6)
 
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
\ No newline at end of file