Improve Rule Generation

rmgpy/constants.pxd

@@ -25,4 +25,4 @@
 #                                                                             #
 ###############################################################################
 
-cdef double pi, Na, kB, R, h, hbar, c, e, m_e, m_p, m_n, amu, a0, E_h
+cdef double pi, Na, kB, R, h, hbar, c, e, m_e, m_p, m_n, amu, a0, E_h, F

rmgpy/constants.py

@@ -110,6 +110,9 @@
 #: :math:`\pi = 3.14159 \ldots`      
 pi = float(math.pi)
 
+#: Faradays Constant F in C/mol
+F = 96485.3321233100184
+
 ################################################################################
 
 # Cython does not automatically place module-level variables into the module
@@ -130,4 +133,5 @@
     'm_n': m_n,
     'm_p': m_p,
     'pi': pi,
+    'F': F
 })

rmgpy/data/base.py

@@ -42,6 +42,7 @@
 from rmgpy.data.reference import Reference, Article, Book, Thesis
 from rmgpy.exceptions import DatabaseError, InvalidAdjacencyListError
 from rmgpy.kinetics.uncertainties import RateUncertainty
+from rmgpy.kinetics.arrhenius import ArrheniusChargeTransfer, ArrheniusChargeTransferBM
 from rmgpy.molecule import Molecule, Group
 
 
@@ -228,6 +229,8 @@ def load(self, path, local_context=None, global_context=None):
         local_context['shortDesc'] = self.short_desc
         local_context['longDesc'] = self.long_desc
         local_context['RateUncertainty'] = RateUncertainty
+        local_context['ArrheniusChargeTransfer'] = ArrheniusChargeTransfer
+        local_context['ArrheniusChargeTransferBM'] = ArrheniusChargeTransferBM
         local_context['metal'] = self.metal
         local_context['site'] = self.site
         local_context['facet'] = self.facet

rmgpy/data/kinetics/database.py

@@ -48,7 +48,7 @@
 from rmgpy.molecule import Molecule, Group
 from rmgpy.reaction import Reaction, same_species_lists
 from rmgpy.species import Species
-
+from rmgpy.data.solvation import SoluteData
 
 ################################################################################
 
@@ -79,7 +79,8 @@ def __init__(self):
             'SurfaceArrhenius': SurfaceArrhenius,
             'SurfaceArrheniusBEP': SurfaceArrheniusBEP,
             'R': constants.R,
-            'ArrheniusBM': ArrheniusBM
+            'ArrheniusBM': ArrheniusBM,
+            'SoluteData': SoluteData,
         }
         self.global_context = {}
 

rmgpy/kinetics/__init__.py

@@ -29,7 +29,8 @@
 
 from rmgpy.kinetics.model import KineticsModel, PDepKineticsModel, TunnelingModel, \
                    get_rate_coefficient_units_from_reaction_order, get_reaction_order_from_rate_coefficient_units
-from rmgpy.kinetics.arrhenius import Arrhenius, ArrheniusEP, PDepArrhenius, MultiArrhenius, MultiPDepArrhenius, ArrheniusBM
+from rmgpy.kinetics.arrhenius import Arrhenius, ArrheniusEP, PDepArrhenius, MultiArrhenius, MultiPDepArrhenius, \
+                   ArrheniusBM, ArrheniusChargeTransfer, ArrheniusChargeTransferBM
 from rmgpy.kinetics.chebyshev import Chebyshev
 from rmgpy.kinetics.falloff import ThirdBody, Lindemann, Troe
 from rmgpy.kinetics.kineticsdata import KineticsData, PDepKineticsData

rmgpy/kinetics/arrhenius.pxd

@@ -128,4 +128,55 @@ cdef class MultiPDepArrhenius(PDepKineticsModel):
 
     cpdef bint is_identical_to(self, KineticsModel other_kinetics) except -2
 
+
+    cpdef change_rate(self, double factor)
+
+################################################################################
+cdef class ArrheniusChargeTransfer(KineticsModel):
+
+    cdef public ScalarQuantity _A
+    cdef public ScalarQuantity _n
+    cdef public ScalarQuantity _Ea
+    cdef public ScalarQuantity _T0
+    cdef public ScalarQuantity _V0
+    cdef public ScalarQuantity _alpha
+    cdef public ScalarQuantity _electrons
+
+    cpdef double get_activation_energy_from_potential(self, double V=?, bint non_negative=?)
+
+    cpdef double get_rate_coefficient(self, double T, double V=?) except -1
+
+    cpdef change_rate(self, double factor)
+
+    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
+
+
+################################################################################
+
+cdef class ArrheniusChargeTransferBM(KineticsModel):
+
+    cdef public ScalarQuantity _A
+    cdef public ScalarQuantity _n
+    cdef public ScalarQuantity _E0
+    cdef public ScalarQuantity _w0
+    cdef public ScalarQuantity _V0
+    cdef public ScalarQuantity _alpha
+    cdef public ScalarQuantity _electrons
+
+    cpdef change_v0(self, double V0)
+
+    cpdef double get_activation_energy(self, double dGrxn) except -1
+
+    cpdef double get_rate_coefficient_from_potential(self, double T, double V, double dGrxn) except -1
+
+    cpdef ArrheniusChargeTransfer to_arrhenius_charge_transfer(self, double dGrxn)
+
+    cpdef bint is_identical_to(self, KineticsModel other_kinetics) except -2
+
     cpdef change_rate(self, double factor)