a437991e12a334b40b082fdc8b1b6dcf4a68021f,deepchem/models/tensorgraph/layers.py,NeighborList,get_cells_for_atoms,#NeighborList#Any#Any#,965

Before Change

    tiled_coords = tf.reshape(
        tf.tile(coords, (1, n_cells)), (n_cells * N, ndim))
    // List of N tensors of shape (n_cells, 1)
    tiled_coords = tf.split(tiled_coords, N)

    // Lists of length N 
    coords_rel = [
        tf.to_float(coords) - tf.to_float(cells)
        for (coords, cells) in zip(tiled_coords, tiled_cells)
    ]
    coords_norm = [tf.reduce_sum(rel**2, axis=1) for rel in coords_rel]

    // Lists of length n_cells
    // Get indices of k atoms closest to each cell point
    closest_inds = [tf.nn.top_k(-norm, k=1)[1] for norm in coords_norm]

    // TODO(rbharath): tf.stack for tf 1.0
    return tf.stack(closest_inds)

  def _get_num_nbrs(self):
    Get number of neighbors in current dimensionality space.
    ndim = self.ndim

After Change

    // Shape (N_atoms*n_cells, 1) after tile
    tiled_coords = tf.reshape(
        tf.tile(coords, (1, n_cells)), (n_cells * N_atoms, ndim))
    coords_vec = tf.reduce_sum((tiled_coords-tiled_cells)**2, axis=1)
    coords_norm = tf.reshape(coords_vec, (N_atoms, n_cells))

    closest_inds = tf.nn.top_k(-coords_norm,k=1)[1]
    return closest_inds

  def _get_num_nbrs(self):
    Get number of neighbors in current dimensionality space.
    ndim = self.ndim

Instances