modify the documentation

Author: luowh35

doc/gpumd/input_parameters/fix.rst

@@ -9,13 +9,28 @@ This keyword can be used to fix (freeze) a group of atoms
 
 Syntax
 ------
-This keyword requires a single parameter which is the label of the group in which the atoms are to be fixed (velocities and forces are always set to zero such that the atoms in the group do not move).
+This keyword accepts 1 or 2 parameters.
+The atoms in the specified group will be fixed (velocities and forces are always set to zero such that the atoms do not move).
 The full command reads::
 
   fix <group_label>
+  fix <grouping_method> <group_label>
 
-Here, the :attr:`group_label` refers to the grouping method 0 defined in the :ref:`simulation model file <model_xyz>`.
+- If only :attr:`group_label` is given, grouping method 0 is used by default.
+- If :attr:`grouping_method` is also specified, the given grouping method defined in the :ref:`simulation model file <model_xyz>` will be used.
+
+Example
+-------
+
+Fix group 0 using the default grouping method 0::
+
+  fix 0
+
+Fix group 2 using grouping method 1::
+
+  fix 1 2
 
 Caveats
 -------
-This keyword is not propagating, which means that it only affects the simulation within the run it belongs to.
+* This keyword is not propagating, which means that it only affects the simulation within the run it belongs to.
+* When both :attr:`fix` and :ref:`move <kw_move>` are used, they must use the same grouping method.

doc/gpumd/input_parameters/move.rst

@@ -10,12 +10,15 @@ This keyword is used to move part of the system with a constant velocity.
 Syntax
 ------
 
-The :attr:`move` keyword requires 4 parameters::
+The :attr:`move` keyword accepts 4 or 5 parameters::
 
   move <moving_group_id> <velocity_x> <velocity_y> <velocity_z>
+  move <grouping_method> <moving_group_id> <velocity_x> <velocity_y> <velocity_z>
 
-Here, :attr:`moving_group_id` specifies the group id for the moving part, which should be defined in the grouping method 0.
-The next three parameters specify the moving velocity vector, in units of Ångstrom/fs.
+- If only :attr:`moving_group_id` and velocities are given, grouping method 0 is used by default.
+- If :attr:`grouping_method` is also specified, the given grouping method defined in the :ref:`simulation model file <model_xyz>` will be used.
+
+The last three parameters specify the moving velocity vector, in units of Ångstrom/fs.
 
 
 Example
@@ -28,12 +31,19 @@ One can first equilibrate the system and then move one group of atoms and at the
   run 1000000
 
   # production stage
-  ensemble nvt_scr 300 300 100
-  fix  0            # fix atoms in group 0
-  move 1 0.001 0 0  # move atoms in group 1, with a speed of 0.001 Ångstrom/fs in the x direction
+  ensemble nvt_ber 300 300 100
+  fix  0            # fix atoms in group 0 (default grouping method 0)
+  move 1 0.001 0 0  # move atoms in group 1 (default grouping method 0)
+  run  1000000
+
+Using a specific grouping method::
+
+  ensemble nvt_ber 300 300 100
+  fix  1 0            # fix group 0 in grouping method 1
+  move 1 1 0.001 0 0  # move group 1 in grouping method 1
   run  1000000
 
 Caveats
 -------
-* One cannot use NPT when using this keyword.
-* Currently, the moving group must be defined in the grouping method 0. This might be extended in a future version.
+* One cannot use NPT when using this keyword. Only ``nvt_ber``, ``nvt_nhc``, ``nvt_bdp``, and ``heat_lan`` ensembles are supported.
+* When both :ref:`fix <kw_fix>` and :attr:`move` are used, they must use the same grouping method.