Frequently Asked Questions
General Questions
1. What are the merits of ABACUS in respect of functionality, performance, and/or accuracy?
Users are referred to the introduction of features of ABACUS in the feature list.
Installation
Setting up jobs
1. Why pseudopotential files must be provided in LCAO calculation?
The pseudopotentials are used to approximate the potential of nuclear and core electrons, while the numerical orbitals are basis sets used to expand the Hamiltonian. So both pseudopotential and numerical orbital files are needed in LCAO calculation.
2. What is the correlation between pseudopotential and numerical orbital files?
The numerical orbital files are generated for a specific pseudopotential. So the right numerical orbital files must be chosen for a specific pseudopotential. We suggest users choose numerical orbital files and the corresponding pseudopotential files from the ABACUS website because their accuracy has been tested. However, interesting users may also generate their own numerical orbitals for a specific type of pseudopential by using the tools provided in the abacus-develop/tools directory.
3. How to set ecutwfc in LCAO calculation? Must it be 100 Ry for a numerical orbital file like Cu_lda_7.0au_100Ry_2s2p2d?
It is recommended to set ecutwfc to the value that the numerical orbital file suggests, but it is not a must. The ecutwfc value only affects the number of FFT grids.
4. Does ABACUS support LCAO calculations accounting for external electric field effects?
Yes, users are referred to documentation on external electric field.
5. Can ABACUS calculate non-periodic systems, such as ionic liquids?
Non-periodic systems such as liquid systems can be calculated by using supercell and gamma-only calculation.
6. How to perform spin-orbital coupling (SOC) calculations in ABACUS?
Apart from setting relavant keys (lspinorb to 1) in the INPUT file, SOC calculations can only be performed with fully-relativistic pseudopotentials. Users are suggested to download fully-relativistic versions of SG15_ONCV pseudopotential files from a website. The numerical orbital files generated from the corresponding scalar-relativistic pseudoptential files by ABACUS (here) can be used in collaboration with the fully-relativistic pseudopotentials.
7. How to restart jobs in abacus?
For restarting SCF calculations, users are referred to the documentation about continuation of job. For restarting MD calculations, please see md_restart.
8. Can DeePKS model be used for structural optimization calculation? What parameters need to be modified or called?
If you train the DeePKS model with force labels, then the DeePKS model can provide force calculation with the same accuracy as your target method, and can thus be used for structural optimization. To do that, you just need to train the model with force label enabled.
Failed jobs
1. Why my calculation is pend by using mpirun?
This is usually caused by overloading of CPUs’ memory without specifying thread numbers. Setting export OMP_NUM_TREANDS=1 will solve this problem, or one can use the command like OMP_NUM_THREADS=1 mpirun -n 8 abacus to rerun failed jobs.
2. My relaxation failed. How to deal with it?
This is usually caused by the difficulty in converging charge density. Reducing charge mixing coefficient (mixing_beta) might help. For large systems up to hundreds of atoms, it is suggested to choose the Kerker mixing method by setting parameter “mixing_gg0” as “1.5”.
Sometimes, loose convergence threshold of charge density (parameter “scf_thr”) will cause atomic forces not correctly enough, please set it at most “1e-7” for relaxation calculation.
Miscellaneous
1. How to visualize charge density file?
The output file SPIN1_CHG.cube can be visualized by using VESTA.
2. How to change cif file directly to STRU file?
One way to change from cif to STRU is to use the ASE-ABACUS interface. An example of the converting script is provided below:
from ase.io import read, write
from pathlib import Path
cs_dir = './'
cs_cif = Path(cs_dir, 'SiO.cif')
cs_atoms = read(cs_cif, format='cif')
cs_stru = Path(cs_dir, 'STRU')
pp = {'Si':'Si.upf','O':'O.upf'}
basis = {'Si':'Si.orb','O':'O.orb'}
write(cs_stru, cs_atoms, format='abacus', pp=pp, basis=basis)
3. What is the convergence criterion for the SCF process in ABACUS?
ABACUS applies the density difference between two SCF steps (labeled as DRHO in the screen output) as the convergence criterion, which is considered as a more robust choice compared with the energy difference. DRHO is calculated via DRHO = |rho(G)-rho_previous(G)|^2. Note that the energy difference between two SCF steps (labed as EDIFF) is also printed out in the screen output.