update notebook, add description, change cutoff distance

python-module/ML_of_Forces/GP_custom_gen.py

@@ -402,7 +402,8 @@ def cov_sim_tries(a, b, sig): # SO(3) linear covariant kernel
     ri, rj = np.sqrt(ris), np.sqrt(rjs)
     
     # take only particles within the first shell
-    cut = 4.5
+    cut = 4.17
+
     a, b = a[ri<= cut], b[rj <= cut]
     ris, rjs = ris[ri<= cut], rjs[rj <= cut]
     ri, rj = ri[ri<= cut], rj[rj <= cut]
@@ -637,12 +638,12 @@ def cov_sim48(a, b, sig, theta): # O48 covariant kernel
     ris, rjs = ((a**2).sum(1)), ((b**2).sum(1))
     ri, rj = np.sqrt(ris), np.sqrt(rjs)
     # take only particles within the first shells
-    cut = 2.7#4.17
+    cut = 5 #2.7#4.17
     a, b = a[ri<= cut], b[rj <= cut]
     la, lb = len(a), len(b)
 
     simgij = np.array( [cdist(a, np.einsum('ik, jk -> ji', rten48[sym], b), 'sqeuclidean') for sym in np.arange(48)] )
-    simgij = np.exp(-simgij/(4*sig**2))
+    simgij = simgij # np.exp(-simgij/(4*sig**2))
     simg = np.einsum('gij -> g', simgij)/((2*(np.pi*sig*sig)**0.5)**D)
     # exp:np.exp((2*simg - 2)/(2*theta))
     # simsq: simg**2