improve README.md of SIAB

Author: wszhang

tools/SIAB/README.md

@@ -1,40 +1,57 @@
 # SIAB Package Description
 
 
-(S)ystematically
-(I)mprovable
-(A)tomic orbital
-(B)asis generator based on spillage formula
+**S**ystematically
+
+**I**mprovable
+
+**A**tomic orbital
+
+**B**asis generator based on spillage formula
 
 
 # HOW TO USE SIAB
 
-The optimization can choose three minimization methods: 'Simulated Annealing', 'PyTorch Gradient' and 'PyTorch Gradient whit dpsi'. 
+The optimization can choose one of the three minimization methods:
+
+- Simulated Annealing (**SA**),
+- PyTorch Gradient (**PTG**),
+- PyTorch Gradient with dpsi (**PTG_dpsi**).
+
+The executable files for the three methods are:
+
+- ./SimulatedAnnealing/source/SIA_s.exe, 
+- ./PyTorchGradient/source/main.py, 
+- ../opt_orb_pytorch_dpsi/main.py, 
 
-The executable files for three methods are './SimulatedAnnealing/source/SIA_s.exe', './PyTorchGradient/source/main.py', '../opt_orb_pytorch_dpsi/main.py', respectively.
+respectively.
 
 
-##  (1) write input file
-Firstly, write the input file, such as "ORBITAL_INPUT_DZP" in example-directories, for script 'Generate_Orbital_AllInOne.sh'.
-Both approachs, 'PyTorch Gradient' and 'Simulated Annealing', work with one bash script and use the same input file.
-Please use the absolute path for each each file and directory.
+##  1. Write input file
 
+Firstly, write the input file, such as **ORBITAL_INPUT_DZP** in example-directories, for script **Generate_Orbital_AllInOne.sh**.
+All three approachs work with the same bash script and use the same input file.
+Please use **absolute path** for each file/directory in input file.
 
-##  (2) set up dependence env
-Then, we set up the dependence env for ABACUS and SIAB, such as:
+
+##  2. Set up dependence environment
+
+Secondly, we set up the dependence environment for ABACUS and SIAB, such as:
 
 ```bash
 $ module load hpcx/2.9.0/hpcx-intel-2019.update5 mkl/2019.update5 elpa/2019.05.002/hpcx-intel-2019.update5
 ```
-Especially for SIAB with 'PyTorch Gradient' approach, we need pytorch v1.1.0.
+
+Especially for SIAB with **PyTorch Gradient** approach, we need pytorch v1.1.0.
 
 
-### how to install pytorch:
+### How to install pytorch:
+
 Take the HanHai20@USTC system for example:
 
 ```bash
-$ module load gcc/7.5.0min      #:optional, larger version gcc may not be necessary.
-$ module load anaconda3
+$ module load gcc/7.5.0min      #optional, maybe unnecessary.
+$ module load anaconda3_nompi
 $ module list
 Currently Loaded Modulefiles:
   1) elpa/2019.05.002/hpcx-intel-2019.update5   4) hpcx/2.9.0/hpcx-intel-2019.update5         7) libxc/4.3.4/hpcx-intel-2019.update5
@@ -44,18 +61,19 @@ $ python3 -V
 Python 3.7.4
 
 $ conda create -n pytorch110 python=3.7
-$ source activate pytorch110  #or: conda activate pytorch110
+$ source activate pytorch110    #or: conda activate pytorch110
 $ conda install pytorch torchvision torchaudio cpuonly -c pytorch
-$ source deactivate  #or: conda deactivate
+$ source deactivate             #or: conda deactivate
 
 $ source activate pytorch110  #or: conda activate pytorch110
 $ pip3 install --user scipy numpy
 $ pip3 install --user torch_optimizer
 ```
 
 
-## (3) run generation
-Finally, 'cd' into an example folder, and run command like this:
+## 3. Run generation
+
+Finally, `cd` into an example folder, and run command like this:
 
 ```bash
 $ ../Generate_Orbital_AllInOne.sh ORBITAL_INPUT_DZP