Graph-kernel function factory.

src/soap/soapy/lagraph.py

@@ -627,8 +627,11 @@ class ParticleGraph(object):
                 types_global=options_descriptor['type_list'])
             ix = adaptor.adapt(spectrum)
             dim = ix.shape[1]
-            assert ix.shape[0] == n_atoms
             P = ix
+            if options_soap.get('kernel.adaptor') in [ 'global-generic', 'global-specific' ]:
+                pass
+            else:
+                assert P.shape[0] == n_atoms 
         elif descriptor_type == 'soap-quippy':
             atoms_quippy = datasets.gdb.convert_ase2quippy_atomslist([atoms])[0]
             # Read options
@@ -671,7 +674,10 @@ class ParticleGraph(object):
                 #print z, z_idx
             P = np.array(ix)
             dim = P.shape[1]
-            assert P.shape[0] == n_atoms
+            if options_soap.get('kernel.adaptor') in [ 'global-generic', 'global-specific' ]:
+                pass
+            else:
+                assert P.shape[0] == n_atoms 
             #print P.dot(P.T)
         elif descriptor_type == 'npy_load':
             folder = options_descriptor["folder"]

src/soap/soapy/lamatch.py

@@ -3,6 +3,22 @@ import numpy.linalg as la
 import soap
 import permanent as perm
 import kernel as kern
+import lagraph
+
+def compare_graphs_average(g1, g2, options):
+    P1 = g1.P
+    P1_avg = np.average(g1.P, axis=0)
+    P1_avg = P1_avg / np.dot(P1_avg, P1_avg)**0.5
+    P2 = g2.P
+    P2_avg = np.average(g2.P, axis=0)
+    P2_avg = P2_avg / np.dot(P2_avg, P2_avg)**0.5
+    print P1.shape, P2.shape, P1_avg.shape, P2_avg.shape
+    return np.dot(P1_avg, P2_avg)
+
+def compare_graphs_global(g1, g2, options):
+    assert g1.P.shape[0] == 1 # Global descriptor computed?
+    assert g2.P.shape[0] == 1 # Global descriptor computed?
+    return np.dot(g1.P[0], g2.P[0])
 
 def compare_graphs_rematch(g1, g2, options):
     if options['graph']['hierarchical']:
@@ -134,3 +150,10 @@ def optimize_rematch(graphs, options, write_out=False, log=None, verbose=False):
     options['lamatch']['gamma'] = merits[-1][0]
     return
 
+GraphKernelFactory = {
+'rematch' : compare_graphs_rematch,
+'average': compare_graphs_average,
+'global': compare_graphs_global,
+'laplacian': lagraph.compare_graphs_laplacian_kernelized
+}
+