Added new "Lookup Scaler" for plotting

catmap/analyze/mechanism.py

@@ -7,6 +7,9 @@
 except ImportError:
     print('Warning! graphviz not imported.')
 from itertools import chain, product
+import matplotlib as mpl
+mpl.rcParams['text.usetex'] = True
+import pylab as plt
 
 class MechanismAnalysis(MechanismPlot,ReactionModelWrapper,MapPlot):
     """

catmap/scalers/__init__.py

@@ -3,3 +3,4 @@
 from .thermodynamic_scaler import *
 from .concentration_scaler import *
 from .null_scaler import *
+from .lookup_scaler import *

catmap/scalers/lookup_scaler.py

@@ -0,0 +1,31 @@
+from .scaler_base import *
+
+class LookupScaler(ScalerBase):
+    """Scaler which looks up all available energies for a given surface."""
+
+    def get_electronic_energies(self,descriptors):
+
+        assert descriptors in self.surface_names, "Descriptor must be a surface name for LookupScaler."
+
+        surf_idx = self.surface_names.index(descriptors)
+        all_ads = self.adsorbate_names + self.transition_state_names
+
+        E_dict = {}
+        gas_names = list(self.gas_names)
+
+        for g in gas_names:
+            E_dict[g] = self.species_definitions[g]['formation_energy']
+
+        for sp in all_ads:
+            E = self.species_definitions[sp]['formation_energy'][surf_idx]
+            try:
+                E = float(E)
+                E_dict[sp] = E 
+            except ValueError: #if the energy doesn't exist for a given surface it is stored as '-'
+                pass
+
+        return E_dict
+
+    def get_rxn_parameters(self,descriptors):
+        Gs = self.get_free_energies(descriptors)
+        return [Gs[d] for d in self.adsorbate_names+self.transition_state_names]

requirements.txt

@@ -6,3 +6,4 @@ ase == 3.17 ; python_version < "3.5"
 ase ; python_version >= "3.5"
 graphviz
 tqdm
+pathlib