Merge branch 'brucefan1983:master' into master

Author: psn417

README.md

@@ -24,13 +24,13 @@ This software is distributed under the GNU General Public License (GPL) version
 * When the compilation finishes, two executables, `gpumd` and `nep`, will be generated in the `src` directory. 
 
 ## Run GPUMD
-* Go to the directory of an example and type one of the following commands:
+* Go to the directory of an example in the [examples directory](examples) and type one of the following commands:
   * `path/to/gpumd`
   * `path/to/nep`
 
-## Colab tutorial
+## Tutorials
 * We provide a [Colab Tutorial](https://colab.research.google.com/drive/1QnXAveZgzwut4Mvldsw-r2I0EWIsj1KA?usp=sharing) to show the workflow of the construction of a NEP model and its application in large-scale atomistic simulations for PbTe system. This will run entirely on Google's cloud virtual machine.
-* You can also check other offline tutorials in the examples.
+* We also provide many tutorials and examples in the [GPUMD-Tutorials repository](https://github.com/brucefan1983/GPUMD-Tutorials).
 
 ## Manual
 * For users and developers:

doc/gpumd/input_parameters/compute_dos.rst

@@ -63,8 +63,3 @@ This means that you
 Caveats
 -------
 This keyword cannot be used in the same run as the :ref:`compute_sdc keyword <kw_compute_sdc>`.
-
-
-Related tutorial
-----------------
-The use of this keyword is illustrated in the :ref:`tutorial on the density of states <tutorials>`.

doc/gpumd/input_parameters/compute_hac.rst

@@ -49,8 +49,3 @@ Example 2
 
 This is similar to the above example but with one expection:
 The :term:`HAC`/:term:`RTC` data will be averaged for every 10 data before outputing, generating :math:`10^4` rows of data in the output file.
-
-Related tutorial
-----------------
-
-The use of the :attr:`compute_hac` keyword is illustrated in the tutorial on :ref:`thermal transport from EMD simulations <tutorials>`.

doc/gpumd/input_parameters/compute_hnemd.rst

@@ -57,8 +57,3 @@ Example 2
    compute_hnemd 1000 0 0.00001 0
 
 This is similar to the above example, but the external driving force is applied along the :math:`y` direction.
-
-Related tutorial
-----------------
-
-The use of the :attr:`compute_hnemd` keyword is illustrated in :ref:`the tutorial on calculating the thermal conductivity via HNEMD simulations <tutorials>`.

doc/gpumd/input_parameters/compute_shc.rst

@@ -97,9 +97,3 @@ Caveats
 This computation can be memory consuming.
 
 If you want to use the in-out decomposition for 2D materials, you need to make the basal plane in the :math:`xy` directions.
-
-
-Related tutorial
-----------------
-
-The use of this keyword is illustrated in the tutorial on the :ref:`thermal transport from NEMD and HNEMD simulations <tutorials>`.

doc/gpumd/input_parameters/deform.rst

@@ -10,7 +10,7 @@ This keyword is used to deform the simulation box, which can be used to do tensi
 Syntax
 ------
 
-The :attr:`deform` keyord requires 4 parameters::
+The :attr:`deform` keyword requires 4 parameters::
 
   deform <A_per_step> <deform_x> <deform_y> <deform_z>
 

doc/gpumd/input_parameters/fix.rst

@@ -16,10 +16,6 @@ The full command reads::
 
 Here, the :attr:`group_label` refers to the grouping method 0 defined in the :ref:`simulation model file <model_xyz>`.
 
-Example
--------
-The use of this keyword is illustrated in the :ref:`tutorial on thermal transport from NEMD and HNEMD simulations <tutorials>`.
-
 Caveats
 -------
 This keyword is not propagating, which means that it only affects the simulation within the run it belongs to.

doc/gpumd/input_parameters/index.rst

@@ -19,6 +19,7 @@ Below you can find a listing of keywords for the ``run.in`` input file.
    dftd3
    change_box
    deform
+   move
    ensemble
    ensemble_standard
    ensemble_mttk

doc/gpumd/input_parameters/move.rst

@@ -0,0 +1,39 @@
+.. _kw_move:
+.. index::
+   single: move (keyword in run.in)
+
+:attr:`move`
+============
+
+This keyword is used to move part of the system with a constant velocity.
+
+Syntax
+------
+
+The :attr:`move` keyword requires 4 parameters::
+
+  move <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.
+
+
+Example
+-------
+
+One can first equilibrate the system and then move one group of atoms and at the same time fix another group of atoms::
+
+  # equilibration stage
+  ensemble npt_scr 300 300 100 0 0 0 100 100 100 1000
+  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
+  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.

doc/index.rst

@@ -14,7 +14,6 @@ In addition to :ref:`several empirical interatomic potentials <potentials>`, it
    installation
    theory/index
    potentials/index
-   tutorials/index
 
 .. toctree::
    :maxdepth: 2