diff --git a/deepmd/descriptor/se_a.py b/deepmd/descriptor/se_a.py
index 3b5d1d0922..60de701886 100644
--- a/deepmd/descriptor/se_a.py
+++ b/deepmd/descriptor/se_a.py
@@ -586,6 +586,7 @@ def _filter_lower(
                              [ 0, start_index* 4],
                              [-1, incrs_index* 4] )
         shape_i = inputs_i.get_shape().as_list()
+        natom = tf.shape(inputs_i)[0]
         # with (natom x nei_type_i) x 4
         inputs_reshape = tf.reshape(inputs_i, [-1, 4])
         # with (natom x nei_type_i) x 1
@@ -603,7 +604,7 @@ def _filter_lower(
             net = 'filter_-1_net_' + str(type_i)
           else:
             net = 'filter_' + str(type_input) + '_net_' + str(type_i)
-          return op_module.tabulate_fusion(self.table.data[net].astype(self.filter_np_precision), info, xyz_scatter, tf.reshape(inputs_i, [-1, shape_i[1]//4, 4]), last_layer_size = outputs_size[-1])  
+          return op_module.tabulate_fusion(self.table.data[net].astype(self.filter_np_precision), info, xyz_scatter, tf.reshape(inputs_i, [natom, shape_i[1]//4, 4]), last_layer_size = outputs_size[-1])  
         else:
           if (not is_exclude):
               xyz_scatter = embedding_net(
@@ -620,11 +621,16 @@ def _filter_lower(
                   uniform_seed = self.uniform_seed)
               if (not self.uniform_seed) and (self.seed is not None): self.seed += self.seed_shift
           else:
-            w = tf.zeros((outputs_size[0], outputs_size[-1]), dtype=GLOBAL_TF_FLOAT_PRECISION)
-            xyz_scatter = tf.matmul(xyz_scatter, w)
+            # we can safely return the final xyz_scatter filled with zero directly
+            return tf.cast(tf.fill((natom, 4, outputs_size[-1]), 0.), GLOBAL_TF_FLOAT_PRECISION)
           # natom x nei_type_i x out_size
           xyz_scatter = tf.reshape(xyz_scatter, (-1, shape_i[1]//4, outputs_size[-1]))  
-          return tf.matmul(tf.reshape(inputs_i, [-1, shape_i[1]//4, 4]), xyz_scatter, transpose_a = True)
+          # When using tf.reshape(inputs_i, [-1, shape_i[1]//4, 4]) below
+          # [588 24] -> [588 6 4] correct
+          # but if sel is zero
+          # [588 0] -> [147 0 4] incorrect; the correct one is [588 0 4]
+          # So we need to explicitly assign the shape to tf.shape(inputs_i)[0] instead of -1
+          return tf.matmul(tf.reshape(inputs_i, [natom, shape_i[1]//4, 4]), xyz_scatter, transpose_a = True)
 
 
     def _filter(
@@ -644,6 +650,18 @@ def _filter(
         shape = inputs.get_shape().as_list()
         outputs_size = [1] + self.filter_neuron
         outputs_size_2 = self.n_axis_neuron
+        all_excluded = all([(type_input, type_i) in self.exclude_types for type_i in range(self.ntypes)])
+        if all_excluded:
+            # all types are excluded so result and qmat should be zeros
+            # we can safaly return a zero matrix...
+            # See also https://stackoverflow.com/a/34725458/9567349
+            # result: natom x outputs_size x outputs_size_2
+            # qmat: natom x outputs_size x 3
+            natom = tf.shape(inputs)[0]
+            result = tf.cast(tf.fill((natom, outputs_size_2, outputs_size[-1]), 0.), GLOBAL_TF_FLOAT_PRECISION)
+            qmat = tf.cast(tf.fill((natom, outputs_size[-1], 3), 0.), GLOBAL_TF_FLOAT_PRECISION)
+            return result, qmat
+            
         with tf.variable_scope(name, reuse=reuse):
           start_index = 0
           type_i = 0
@@ -665,7 +683,8 @@ def _filter(
                       suffix = "_"+str(type_i))
                   if type_i == 0:
                       xyz_scatter_1 = ret
-                  else:
+                  elif (type_input, type_i) not in self.exclude_types:
+                      # add zero is meaningless; skip
                       xyz_scatter_1+= ret
                   start_index += self.sel_a[type_i]
           else :
diff --git a/deepmd/descriptor/se_r.py b/deepmd/descriptor/se_r.py
index 40bbc21593..f362302f11 100644
--- a/deepmd/descriptor/se_r.py
+++ b/deepmd/descriptor/se_r.py
@@ -478,11 +478,11 @@ def _filter_r(self,
                                                 trainable = trainable, 
                                                 uniform_seed = self.uniform_seed)
                     if (not self.uniform_seed) and (self.seed is not None): self.seed += self.seed_shift
+                    # natom x nei_type_i x out_size
+                    xyz_scatter = tf.reshape(xyz_scatter, (-1, shape_i[1], outputs_size[-1]))
                 else:
-                    w = tf.zeros((outputs_size[0], outputs_size[-1]), dtype=GLOBAL_TF_FLOAT_PRECISION)
-                    xyz_scatter = tf.matmul(xyz_scatter, w)
-                # natom x nei_type_i x out_size
-                xyz_scatter = tf.reshape(xyz_scatter, (-1, shape_i[1], outputs_size[-1]))
+                    natom = tf.shape(inputs)[0]
+                    xyz_scatter = tf.cast(tf.fill((natom, shape_i[1], outputs_size[-1]), 0.), GLOBAL_TF_FLOAT_PRECISION)
                 xyz_scatter_total.append(xyz_scatter)
 
             # natom x nei x outputs_size