Merge pull request #1785 from ReactionMechanismGenerator/pdep_bugs

Several small Pdep bug fixes

arkane/common.py

@@ -297,9 +297,6 @@ def load_yaml(self, path, label=None, pdep=False):
             self.imaginary_frequency = ScalarQuantity()
             self.imaginary_frequency.make_object(data=freq_data, class_dict=class_dict)
 
-        if pdep and not self.is_ts and (self.transport_data is None or self.energy_transfer_model is None):
-            raise ValueError('Transport data and an energy transfer model must be given if pressure-dependent '
-                             'calculations are requested. Check file {0}'.format(path))
         if pdep and not self.is_ts and self.smiles is None and self.adjacency_list is None \
                 and self.inchi is None and self.molecular_weight is None:
             raise ValueError('The molecular weight was not specified, and a structure was not given so it could '

rmgpy/pdep/me.pyx

@@ -104,7 +104,7 @@ cpdef generate_full_me_matrix(network, bint products=True):
             if k_ij[i, j, n_grains - 1,0] > 0 or k_ij[j, i, n_grains - 1,0] > 0:
                 for r in range(n_grains):
                     for s in range(n_j):
-                        u, v = indices[i, r, s], v = indices[j,r,s]
+                        u, v = indices[i, r, s], indices[j, r, s]
                         if u > -1 and v > -1:
                             me_mat[u, v] = k_ij[j, i, r, s]
                             me_mat[u, u] -= k_ij[j, i, r, s]

rmgpy/pdep/network.py

@@ -75,8 +75,8 @@ class Network(object):
     `active_j_rotor`        ``True`` if the J-rotor is treated as active, ``False`` if treated as adiabatic
     `rmgmode`               ``True`` if in RMG mode, ``False`` otherwise
     ----------------------- ----------------------------------------------------
-    `eqRatios`              An array containing concentration of each isomer and reactant channel present at equilibrium
-    `coll_freq`              An array of the frequency of collision between
+    `eq_ratios`             An array containing concentration of each isomer and reactant channel present at equilibrium
+    `coll_freq`             An array of the frequency of collision between
     `Mcoll`                 Matrix of first-order rate coefficients for collisional population transfer between grains for each isomer
     `dens_states`           3D np array of stable configurations, number of grains, and number of J
     ======================= ====================================================
@@ -269,7 +269,7 @@ def calculate_rate_coefficients(self, Tlist, Plist, method, error_check=True):
                 K[t, p, :, :] = self.K
 
                 # Check that the k(T,P) values satisfy macroscopic equilibrium
-                eq_ratios = self.eqRatios
+                eq_ratios = self.eq_ratios
                 for i in range(n_isom + n_reac):
                     for j in range(i):
                         Keq0 = K[t, p, j, i] / K[t, p, i, j]
@@ -693,7 +693,7 @@ def calculate_microcanonical_rates(self):
                     rxn.network_kinetics.get_rate_coefficient(temperature)
 
             # Determine the expected value of the equilibrium constant (Kc)
-            Keq_expected = self.eqRatios[prod] / self.eqRatios[reac]
+            Keq_expected = self.eq_ratios[prod] / self.eq_ratios[reac]
 
             # Determine the actual values of k(T) and Keq
             C0 = 1e5 / (constants.R * temperature)
@@ -831,7 +831,7 @@ def calculate_equilibrium_ratios(self):
             if self.products[i].has_statmech() or self.products[i].has_thermo():
                 G = self.products[i].get_free_energy(temperature)
                 eq_ratios[n_isom + n_reac + i] = math.exp(-G / constants.R / temperature) * conc ** (len(self.products[i].species) - 1)
-        self.eqRatios = eq_ratios
+        self.eq_ratios = eq_ratios
         return eq_ratios / np.sum(eq_ratios)
 
     def calculate_collision_model(self):