update notebook part 1

.gitignore

@@ -36,3 +36,6 @@ syntax: glob
 #emacs TAGS
 TAGS
 
+.idea
+notebook/FF-fit_adam.bkr
+notebook/FF-fit_aldo.bkr

read_lammps_data.py

@@ -17,18 +17,46 @@ class TimeStep(object):
         import ase
 
         atoms = ase.atoms.Atoms(
-            'Si',
-            positions=self.confs,
+            'Si'*len(self.confs),
+            positions=np.asarray(self.confs, dtype=np.float),
             cell=[self.xhi-self.xlo, self.yhi-self.xlo,self.zhi-self.zlo],
             pbc=[1, 1, 1],
         )
 
-        N = 207
-        num_lines = sum(1 for line in open('disloiron.xyz'))
-        steps = 100  # num_lines/(N+2)
+
+        # N = 207
+        # num_lines = sum(1 for line in open('disloiron.xyz'))
+        # steps = 100  # num_lines/(N+2)
+
+        N = len(self.confs)
 
         r_cut = 5  # 3.5  4.4
 
+        cutoffs = np.ones(len(atoms)) * r_cut / 2.
+        nl = NeighborList(cutoffs, skin=0., sorted=False, self_interaction=False,
+                          bothways=True)
+        nl.build(atoms)
+
+
+        confs=[]
+
+        cell = atoms.get_cell()
+
+        indices, offsets = nl.get_neighbors(0)
+        offsets = np.dot(offsets, cell)
+        conf = np.zeros((len(indices), 3))
+
+        for i, (a2, offset) in enumerate(zip(indices, offsets)):
+            d = atoms.positions[a2] + offset - atoms.positions[0]
+            conf[i] = d
+        confs.append(conf)
+
+
+
+        print(confs)
+
+
+
 
         cutoffs = np.ones(N) * r_cut / 2.
         print(cutoffs)
@@ -160,6 +188,9 @@ if __name__ == '__main__':
 
     filename='data-lammps/Silic_300/Si_300_dump.atom'
 
+
+
+
     with ReadLammpsDumpFile(filename) as file:
 
         for timestep in file: