Installation and execution

Installation AMP²

System requirements

AMP² supports Python 2.7 and 3. Currently, the package is not compatible with lower version than 2.7. AMP² is utilizes Python modules in the following with link to each site.

• numpy [https://www.numpy.org]
• scipy [https://www.scipy.org]
• spglib [https://atztogo.github.io/spglib]
• PyYAML [https://pypi.org/project/PyYAML]

These modules should be pre-installed. In addition, AMP² needs gnuplot supporting ‘pngcairo’ and ‘pdfcairo’ to draw various figures.

Installation

To use AMP², please download the file from https://github.com/MDIL-SNU/AMP2 under the working directory.

Essential setting

Setting of configuration file

AMP² uses YAML style configuration file. All setting parameters used in AMP² can be controlled in “config.yaml”. Before using AMP², proper pathes and mpi program command should be set to be suitable for your system. Following commands are the essential directories and programs to be set.

Directory:
  submit:
  src:
  pot_path_gga:
  pot_path_lda:
Program:
  vasp_std:
  vasp_gam:
  vasp_ncl:
  gnuplot:
  mpi_command:

Details for the commands are in Configuration.

Execution AMP²

You can execute AMP² using Python command as following.

python [src_path]/main.py [path for configuration file] [path for nodefile] [the number of cores]

• [src_path] is the path for directory of source codes for AMP².
• [path for configuration file] is the path for configuration file (config.yaml).
• [path for nodefile] is used to record the information of computing nodes such as PBS_nodefile in Portable Batch System (PBS) and HOSTNAME in Sun Grid Engine (SGE). In the PBS system, we recommand to use the command, “echo $PBS_nodefile > nodefile”. Also, users can save an arbitrary text by writing in the nodefile.
• [the number of cores] is the number of cores to be used in parallel computing.

For the convenience, we provide the shell script file (run.sh) as following.

echo 'node information' > nodefile
NPROC=16       # The number of cores for parallel computing

### set path of config.yaml ###
conf=./config.yaml
###############################

### Do not change #############
src_path=`grep 'src_path' $conf | tr -s ' ' | cut -d " " -f 3`
###############################

python $src_path/main.py $conf nodefile $NPROC >& stdout.x

Before execution, you need to modify ‘node information’, NPROC and conf. Then, you can execute AMP² using shell script as following.

sh run.sh

The shell script file can be easily integrated with job scheduler program such as PBS.