Merge pull request brucefan1983#1418 from duanzaixu/gitpr

Update deform syntax

Author: brucefan1983

doc/gpumd/input_parameters/deform.rst

@@ -10,7 +10,9 @@ This keyword is used to deform the simulation box, which can be used to do tensi
 Syntax
 ------
 
-The :attr:`deform` keyword requires 4 parameters::
+The :attr:`deform` keyword supports two forms.
+
+**4-parameter form** ::
 
   deform <A_per_step> <deform_x> <deform_y> <deform_z>
 
@@ -20,11 +22,22 @@ This gives a strain rate of :math:`10^{8}` s :math:`^{-1}` if the time step is 1
 The second parameter :attr:`deform_x` can be 0 or 1, where 0 means do not deform the :math:`x` direction and 1 means deform the :math:`x` direction.
 The last two parameters have similar meanings for the :math:`y` and :math:`z` directions.
 
+In this form, the same deformation rate is applied to all directions that are flagged as deformed.
+
+**6-parameter form** ::
+
+  deform <A_per_step_x> <A_per_step_y> <A_per_step_z> <deform_x> <deform_y> <deform_z>
+
+Here, :attr:`A_per_step_x`, :attr:`A_per_step_y`, :attr:`A_per_step_z` specify the increment (or decrement) of the box length in the x, y, and z directions per simulation step, respectively. The unit is Ångstrom/step. For example, if the box length in the x-direction is initially 100 Å and :attr:`A_per_step_x` is set to :math:`10^{-5}` Å/step, then after :math:`10^{6}` steps, the box length will change by 10%. With a time step of 1 fs, this corresponds to a strain rate of :math:`10^{8}` s :math:`^{-1}`. Use :attr:`deform_x`, :attr:`deform_y`, :attr:`deform_z` to enable or disable deformation in each direction. A value of `1` enables deformation, while `0` disables it. For a direction where deformation is disabled, the box length remains constant throughout the simulation.
+
+This form allows independent deformation rates in the x, y, and z directions.
 
 Example
 -------
 
-For uniaxial tensile test, one can first equilibrate the system and then deform the box::
+For uniaxial tensile test, one can first equilibrate the system and then deform the box.
+
+**Using the 4-parameter form**::
 
   # equilibration stage
   ensemble npt_scr 300 300 100 0 0 0 100 100 100 1000
@@ -35,6 +48,19 @@ For uniaxial tensile test, one can first equilibrate the system and then deform
   deform 0.00001 1 0 0
   run 1000000
 
+**Using the 6-parameter form**::
+
+  # equilibration stage
+  ensemble npt_scr 300 300 100 0 0 0 100 100 100 1000
+  run 1000000
+
+  # production stage
+  ensemble npt_scr 300 300 100 0 0 0 100 100 100 1000
+  deform 0.00001 0 0 1 0 0
+  run 1000000
+
+Both examples achieve the same deformation (x-direction stretched at 0.00001 Å/step).
+
 Caveats
 -------
 * Currently, one must use the NPT ensemble when using this keyword.
@@ -43,3 +69,4 @@ Caveats
   one can set the elastic constant for that direction to be larger than 2000 GPa.
 * In the equilibration stage, it is also recommended to use the NPT ensemble to obtain the zero strain state before applying the deformation.
 * One must control the three pressure components independently when using this keyword.
+* The 6-parameter form is more flexible and is recommended for new input files.