fixing a few legacy networkx commands. Fixes #28

peteboyd · Dec 13, 2019 · 1065ff3 · 1065ff3
1 parent 51af69c
commit 1065ff3
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Showing 2 changed files with 17 additions and 17 deletions.
diff --git a/lammps_interface/lammps_main.py b/lammps_interface/lammps_main.py
@@ -101,13 +101,13 @@ def unique_atoms(self, g):
             if data['force_field_type'] is None:
                 if data['h_bond_donor']:
                     # add neighbors to signify type of hbond donor
-                    label = (data['element'], data['h_bond_donor'], molid, tuple(sorted([g.node[j]['element'] for j in g.neighbors(node)])))
+                    label = (data['element'], data['h_bond_donor'], molid, tuple(sorted([g.nodes[j]['element'] for j in g.neighbors(node)])))
                 else:
                     label = (data['element'], data['h_bond_donor'], molid)
             else:
                 if data['h_bond_donor']:
                     # add neighbors to signify type of hbond donor
-                    label = (data['force_field_type'], data['h_bond_donor'], molid, tuple(sorted([g.node[j]['element'] for j in g.neighbors(node)])))
+                    label = (data['force_field_type'], data['h_bond_donor'], molid, tuple(sorted([g.nodes[j]['element'] for j in g.neighbors(node)])))
                 else:
                     label = (data['force_field_type'], data['h_bond_donor'], molid)
 
@@ -447,7 +447,7 @@ def assign_force_fields(self):
             # prompt for ForceField?
             rep = self.subgraphs[self.molecule_types[mtype][0]]
             #response = input("Would you like to apply a new force field to molecule type %i with atoms (%s)? [y/n]: "%
-            #        (mtype, ", ".join([rep.node[j]['element'] for j in rep.nodes()])))
+            #        (mtype, ", ".join([rep.nodes[j]['element'] for j in rep.nodes()])))
             #ff = self.options.force_field
             #if response.lower() in ['y','yes']:
             #    ff = input("Please enter the name of the force field: ")
@@ -459,7 +459,7 @@ def assign_force_fields(self):
             ff = self.options.mol_ff
             if ff is None:
                 ff = self.options.force_field
-                atoms = ", ".join([rep.node[j]['element'] for j in rep.nodes()])
+                atoms = ", ".join([rep.nodes[j]['element'] for j in rep.nodes()])
                 print("WARNING: Molecule %s with atoms (%s) will be using the %s force field as no "%(mtype,atoms,ff)+
                       " value was set for molecules. To prevent this warning "+
                       "set --molecule-ff=[some force field] on the command line.")
@@ -531,7 +531,7 @@ def compute_simulation_size(self):
                 # prompt for replication of this molecule in the supercell.
                 rep = self.subgraphs[self.molecule_types[mtype][0]]
                 response = input("Would you like to replicate molceule %i with atoms (%s) in the supercell? [y/n]: "%
-                        (mtype, ", ".join([rep.node[j]['element'] for j in rep.nodes()])))
+                        (mtype, ", ".join([rep.nodes[j]['element'] for j in rep.nodes()])))
                 if response in ['y', 'Y', 'yes']:
                     for m in self.molecule_types[mtype]:
                         self.subgraphs[m].build_supercell(supercell, self.cell, track_molecule=True, molecule_len=molcount)

diff --git a/lammps_interface/structure_data.py b/lammps_interface/structure_data.py
@@ -1162,7 +1162,7 @@ def detect_clusters(self, num_neighbors, tol, type='Inorganic', general_metal=Fa
                             # found cluster
                             # update the 'hybridization' data
                             for i,j in clique:
-                                self.nodes[i]['special_flag'] = cluster.node[j]['special_flag']
+                                self.nodes[i]['special_flag'] = cluster.nodes[j]['special_flag']
                             cluster_found = True
                             print("Found %s"%(name))
                             store_sbus.setdefault(name, []).append([i for (i,j) in clique])
@@ -1281,13 +1281,13 @@ def build_supercell(self, sc, lattice, track_molecule=False, molecule_len=0, red
 
             # keep track of original index value from the unit cell.
             for i in range(1, totatomlen+1):
-                graph_image.node[unit_node_ids[i-1]+offset]['image'] = unit_node_ids[i-1]
+                graph_image.nodes[unit_node_ids[i-1]+offset]['image'] = unit_node_ids[i-1]
             if track_molecule:
                 self.molecule_images.append(graph_image.nodes())
                 graph_image.molecule_id = orig_copy.molecule_id + mol_offset
             # update cartesian coordinates for each node in the image
             for node in graph_image.nodes():
-                data = graph_image.node[node] 
+                data = graph_image.nodes[node] 
                 n_orig = data['image']
                 if track_molecule:
                     data['molid'] = graph_image.molecule_id
@@ -1353,8 +1353,8 @@ def build_supercell(self, sc, lattice, track_molecule=False, molecule_len=0, red
                 n1,n2 = graph_image.sorted_edge_dict[(v1,v2)]
                 # flag boundary crossings, and determine updated nodes.
                 # check symmetry flags if they need to be updated,
-                n1_data = graph_image.node[n1]
-                n2_data = graph_image.node[n2]
+                n1_data = graph_image.nodes[n1]
+                n2_data = graph_image.nodes[n2]
                 try:
                     n1_orig = n1_data['image']
                     n2_orig = n2_data['image']
@@ -1454,7 +1454,7 @@ def build_supercell(self, sc, lattice, track_molecule=False, molecule_len=0, red
                 union_graphs.append(graph_image)
         for G in union_graphs:
             for node in G.nodes():
-                data = G.node[node]
+                data = G.nodes[node]
                 self.add_node(node, **data)
            #once nodes are added, add edges.
         for G in union_graphs:
@@ -1649,8 +1649,8 @@ def write_CIF(graph, cell):
         sym = data['symflag']
 
 
-        label1 = "%s%i"%(graph.node[n1]['element'], n1)
-        label2 = "%s%i"%(graph.node[n2]['element'], n2)
+        label1 = "%s%i"%(graph.nodes[n1]['element'], n1)
+        label2 = "%s%i"%(graph.nodes[n2]['element'], n2)
         c.add_data("bonds", _geom_bond_atom_site_label_1=
                                     CIF.geom_bond_atom_site_label_1(label1))
         c.add_data("bonds", _geom_bond_atom_site_label_2=
@@ -1831,8 +1831,8 @@ def write_RASPA_CIF(graph, cell,classifier=0):
     #    sym = data['symflag']
 
 
-    #    label1 = "%s%i"%(graph.node[n1]['element'], n1)
-    #    label2 = "%s%i"%(graph.node[n2]['element'], n2)
+    #    label1 = "%s%i"%(graph.nodes[n1]['element'], n1)
+    #    label2 = "%s%i"%(graph.nodes[n2]['element'], n2)
     #    c.add_data("bonds", _geom_bond_atom_site_label_1=
     #                                CIF.geom_bond_atom_site_label_1(label1))
     #    c.add_data("bonds", _geom_bond_atom_site_label_2=
@@ -1879,7 +1879,7 @@ def write_RASPA_sim_files(lammps_sim,classifier=0):
 
             if(int(data['image']) > max_image):
                 max_image = int(data['image'])
-            #keys.append(lammps_sim.graph.node[n]['force_field_type'])
+            #keys.append(lammps_sim.graph.nodes[n]['force_field_type'])
 
     elif(classifier == 1):
         for node, data in sorted(lammps_sim.graph.nodes_iter2(data=True)):
@@ -1890,7 +1890,7 @@ def write_RASPA_sim_files(lammps_sim,classifier=0):
 
             if(int(data['image']) > max_image):
                 max_image = int(data['image'])
-            #keys.append(lammps_sim.graph.node[n]['force_field_type'])
+            #keys.append(lammps_sim.graph.nodes[n]['force_field_type'])
 
     print(max_image)
     for i in range(len(data_list)):