ASE is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
Webpage: http://wiki.fysik.dtu.dk/ase
- Python_ 3.9 or later
- NumPy_ (base N-dimensional array package)
- SciPy_ (library for scientific computing)
- Matplotlib_ (2D Plotting)
Optional:
git clone https://gitlab.com/1041176461/ase-abacus.git cd ase-abacus pip install .
ABACUS supports two types of basis sets: PW, LCAO. The path of pseudopotential and numerical orbital files can be set throught the environment variables ABACUS_PP_PATH and ABACUS_ORBITAL_PATH, respectively, e.g.:
PP=${HOME}/pseudopotentials
ORB=${HOME}/orbitals
export ABACUS_PP_PATH=${PP}
export ABACUS_ORBITAL_PATH=${ORB}
For PW calculations, only ABACUS_PP_PATH is needed. For LCAO calculations, both ABACUS_PP_PATH and ABACUS_ORBITAL_PATH should be set.
In order to run a calculation, you have to ensure that at least the following parameters are specified, either in the initialization or as environment variables:
| keyword | description |
|---|---|
pp |
dict of pseudopotentials for involved elememts,
such as pp={'Al':'Al_ONCV_PBE-1.0.upf',...}. |
pseudo_dir |
directory where the pseudopotential are located,
Can also be specified with the ABACUS_PP_PATH
environment variable. Default: pseudo_dir=./. |
basis |
dict of orbital files for involved elememts, such as
basis={'Al':'Al_gga_10au_100Ry_4s4p1d.orb'}.
It must be set if you want to do LCAO
calculations. But for pw calculations, it can be omitted. |
basis_dir |
directory where the orbital files are located,
Can also be specified with the ABACUS_ORBITAL_PATH
environment variable. Default: basis_dir=./. |
xc |
which exchange-correlation functional is used.
An alternative way to set this parameter is via
seting dft_functional which is an ABACUS
parameter used to specify exchange-correlation
functional |
kpts |
1. a tuple (or list) of 3 integers kpts=(int, int, int),
it is interpreted as the dimensions of a Monkhorst-Pack
grid, when kmode is Gamma or MP. It is
interpreted as k-points, when kmode is Direct,
Cartesian or Line, and knumber should also
be set in these modes to denote the number of k-points.
Some other parameters for k-grid settings:
including koffset and kspacing.
2. dict, Parameters of cell.bandpath and
ase.calculators.calculator.kpts2sizeandoffsets are
supported to be keys of the dictionary parameters['kpts'],
and k-points will be generated by ASE. |
For more information on pseudopotentials and numerical orbitals, please visit ABACUS. The elaboration of input parameters can be found here.
The input parameters can be set like:
calc = Abacus(profile=profile, ntype=1, ecutwfc=100, scf_nmax=100, smearing_method='gaussian', smearing_sigma=0.01, basis_type='pw', ks_solver='cg', calculation='scf' pp=pp, basis=basis, kpts=kpts)
The command to run jobs can be set by specifying AbacusProfile:
# load ASE-ABACUS
from ase.calculators.abacus import AbacusProfile
# for OpenMP setting
import os
os.environ("OMP_NUM_THREADS") = 16
# for ABACUS Profile
abacus = '/usr/local/bin/abacus'
profile = AbacusProfile(argv=f'mpirun -n 2 {abacus}') # directly the command for running ABACUS
in which abacus sets the absolute path of the abacus executable. One can also export abacus to $PATH and use it.
After molecular dynamics calculations, the log file 'running_md.log' can be read. If the 'STRU_MD_*' files are not continuous (e.g. 'STRU_MD_0', 'STRU_MD_5', 'STRU_MD_10'...), the index parameter of read should be as a slice object. For example, when using the command read('running_md.log', index=slice(0, 15, 5), format='abacus-out') to parse 'running_md.log', 'STRU_MD_0', 'STRU_MD_5' and 'STRU_MD_10' will be read.
The 'MD_dump' file is also supported to be read-in by read('MD_dump', format='abacus-md')'
SPAP (Structure Prototype Analysis Package) is written by Dr. Chuanxun Su to analyze symmetry and compare similarity of large amount of atomic structures. The coordination characterization function (CCF) is used to measure structural similarity. An unique and advanced clustering method is developed to automatically classify structures into groups.
If you use this program and method in your research, please read and cite the publication:
Su C, Lv J, Li Q, Wang H, Zhang L, Wang Y, Ma Y. Construction of crystal structure prototype database: methods and applications. J Phys Condens Matter. 2017 Apr 26;29(16):165901.
and you should install it first with command pip install spap.