This is a collections of examples and tutorials to demonstrate how to use PyXtal

├── README.md
├── example_01_3D_VASP.py   
├── example_02_LJ_cluster.py
├── example_03_LJ_optalg.py
├── example_04_LJ_38.py
├── example_05_LJ_4D.py
├── example_06_C_2D_lammps.py
├── example_07_3D_ICE_lammps.py
└── tutorials_notebook
    ├── 01_atomic_crystals.ipynb
    └── 02_molecular_crystals.ipynb

Installation

Examples 06 and 07 require the installation of LAMMPS and GULP as follows

LAMMPS

download the most recent version of lammps (e.g., lammps-11Aug17) from http://lammps.sandia.gov/download.html

$ tar -xf lammps-stable.tar.gz
$ cd lammps-11Aug17/src
$ make yes-class2
$ make yes-kspace
$ make yes-manybody
$ make yes-molecule
$ make yes-python
$ make yes-rigid
$ make yes-user-misc
$ make mpi
$ make mpi mode=shlib

It works up to LAMMPS (3 Mar 2020) This should create the file liblammps_mpi.so in the src directory, as well as a soft link liblammps.so, which is what the Python wrapper will load by default. Then one just need to add the path of src to the .bashrc file as follows,

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/scratch/qzhu/soft/lammps/src #please modify the path if necessary

then in lammps/src

make install-python

GULP

Download GULP from http://gulp.curtin.edu.au/gulp/ After the installation, export the following environment variables

$ export PATH=/scratch/qzhu/pkgs/gulp-5.2/Src:$PATH
$ export GULP_LIB=/scratch/qzhu/pkgs/gulp-5.2/Libraries

Test

To test if it works correctly, run the following,

$ python test_installation.py 
PyXtal:  0.0.9
ase:  3.19.1
Using PyXtal to generate structure
Convert PyXtal structure to ASE
launch the LAMMPS calculator
-5.348217915131606
launch the GULP calculator
-5.34821791