improve readme

Author: Han Wang

README.md

@@ -102,6 +102,14 @@ source $tensorflow_venv/bin/activate
 pip install --upgrade pip
 pip install --upgrade tensorflow==1.14.0
 ```
+It is notice that everytime a new shell is started and one wants to use `DeePMD-kit`, the virtual environment should be activated by 
+```bash
+source $tensorflow_venv/bin/activate
+```
+if one wants to skip out of the virtual environment, he/she can do
+```bash
+deactivate
+```
 If one has multiple python interpreters named like python3.x, it can be specified by, for example
 ```bash
 virtualenv -p python3.7 $tensorflow_venv
@@ -483,7 +491,7 @@ Running an MD simulation with LAMMPS is simpler. In the LAMMPS input file, one n
 pair_style     deepmd graph.pb
 pair_coeff     
 ```
-where `graph.pb` is the file name of the frozen model. The `pair_coeff` should be left blank. It should be noted that LAMMPS counts atom types starting from 1, therefore, all LAMMPS atom type will be firstly subtracted by 1, and then passed into the DeePMD-kit engine to compute the interactions. A detailed documentation of this pair style is [here](doc/lammps-pair-style-deepmd.md).
+where `graph.pb` is the file name of the frozen model. The `pair_coeff` should be left blank. It should be noted that LAMMPS counts atom types starting from 1, therefore, all LAMMPS atom type will be firstly subtracted by 1, and then passed into the DeePMD-kit engine to compute the interactions. [A detailed documentation of this pair style is available.](doc/lammps-pair-style-deepmd.md).
 
 ### Long-range interaction
 The reciprocal space part of the long-range interaction can be calculated by LAMMPS command `kspace_style`. To use it with DeePMD-kit, one writes 

doc/lammps-pair-style-deepmd.md

@@ -35,13 +35,13 @@ This pair style takes the deep potential defined in a model file that usually ha
 
 The model deviation evalulate the consistency of the force predictions from multiple models. By default, only the maximal, minimal and averge model deviations are output. If the key `atomic` is set, then the model deviation of force prediction of each atom will be output.
 
-By default, the model deviation is output in absolute value. If the keyword `relative` is set, then the relative model deviation will be output, which is defined by
+By default, the model deviation is output in absolute value. If the keyword `relative` is set, then the relative model deviation will be output. The relative model deviation of the force on atom `i` is defined by
 ```math
-         |Df|
-Ef = -------------
-      |f| + level
+           |Df_i|
+Ef_i = -------------
+       |f_i| + level
 ```
-where `Df` is the model deviation of a force, `|f|` is the norm of the force and `level` is provided as the parameter of the keyword `relative`.
+where `Df_i` is the absolute model deviation of the force on atom `i`, `|f_i|` is the norm of the the force and `level` is provided as the parameter of the keyword `relative`.
 
 
 ## Restrictions
@@ -50,6 +50,8 @@ where `Df` is the model deviation of a force, `|f|` is the norm of the force and
 
 - The `atom_style` of the system should be `atomic`.
 
+- When using the `atomic` key word of `deepmd` is set, one should not use this pair style with MPI parallelization.
+
 
 [DP]:https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.143001
 [DP-SE]:https://arxiv.org/abs/1805.09003