Fixed adsorbate-adsorbate interaction + backward python 2.7 compatibility

catmap/analyze/analysis_base.py

@@ -11,7 +11,7 @@
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 
 plt = catmap.plt
-pickle= catmap.pickle
+pickle = catmap.pickle
 np = catmap.np
 spline = catmap.spline
 mtransforms = catmap.mtransforms

catmap/model.py

@@ -10,7 +10,6 @@
 import re
 from .data import regular_expressions
 string2symbols = catmap.string2symbols
-pickle = catmap.pickle
 plt = catmap.plt
 
 
@@ -278,19 +277,20 @@ def Axb_solver(A, b):
             for attr in dir(self):
                 if (not attr.startswith('_') and
                         not callable(getattr(self, attr)) and
-                        attr not in self._classes):
+                        attr not in self._classes and
+                        not inspect.ismodule(getattr(self,attr))):
                     if (len(repr(getattr(self, attr))) >
                             self._max_log_line_length):
                         # Line is too long for logfile -> put into pickle
                         self._pickle_attrs.append(attr)
             pickled_data = {}
             for attr in self._pickle_attrs:
                 pickled_data[attr] = getattr(self, attr)
-            try:
-                pickle.dump(pickled_data, open(self.data_file, 'w'))
-            except:
+            if sys.version_info[0]<3:
+                catmap.pickle.dump(pickled_data, open(self.data_file, 'w'))
+            else:
                 # Fallback workaround for Py3
-                pickle.dump(pickled_data, open(self.data_file, 'wb'))
+                catmap.pickle.dump(pickled_data, open(self.data_file, 'wb',2))
 
             # Make logfile
             log_txt = self._log_imports
@@ -380,8 +380,8 @@ def load(self, setup_file): #
 
         globs = {}
         locs = defaults
-
-        exec(compile(open(setup_file, 'r').read(), '<string>', 'exec'), globs, locs)
+        
+        exec(compile(open(setup_file, 'rb').read(), '<string>', 'exec'), globs, locs)
         for var in locs.keys():
             if var in self._classes:
                 #black magic to auto-import classes
@@ -437,9 +437,9 @@ def load_data_file(self, overwrite=False):
         """
         if os.path.exists(self.data_file):
             try:
-                pickled_data = pickle.load(open(self.data_file, 'r'))
+                pickled_data = catmap.pickle.load(open(self.data_file, 'r'))
             except:
-                pickled_data = pickle.load(open(self.data_file, 'rb'))
+                pickled_data = catmap.pickle.load(open(self.data_file, 'rb'))
             for attr in pickled_data:
                 if not overwrite:
                     if getattr(self, attr, None) is None:  # Don't over-write
@@ -1155,7 +1155,9 @@ def _header(self,exclude_outputs=[],re_parse=False):
         for attr in dir(self):
             if (not attr.startswith('_') and
                     not callable(getattr(self,attr)) and
-                    attr not in self._classes):
+                    attr not in self._classes and
+                    not inspect.ismodule(getattr(self,attr))):
+                print(attr)
                 val = repr(getattr(self,attr))
                 new_line = ''
                 if attr not in self._pickle_attrs:

catmap/thermodynamics/first_order_interactions.py

@@ -270,7 +270,8 @@ def sync_with_species_defs(fitting_info,surf_id):
                     if cvg_Ed_Eint_i not in required_params_dict[reqd]:
                         required_params_dict[reqd] += [cvg_Ed_Eint_i]
 
-            for key in required_params_dict.keys():
+            for key in list(required_params_dict.keys()):
+                print(key)
                 keylist = eval(key)
                 cvgs = required_params_dict[key]
                 if len(keylist) == 1:
@@ -332,7 +333,7 @@ def sync_with_species_defs(fitting_info,surf_id):
 
             for key in cross_keys_3:
                 params = eval(key)
-                params = [pi for pi in params if pi not in fitting_info.keys()+user_inputs]
+                params = [pi for pi in params if pi not in list(fitting_info.keys())+user_inputs]
                 assert len(params) <= 1 #if not then something is very weird.
                 if params:
                     param = params[0]