Two Quick Examples
Running SCF Calculation
A quick LCAO example
ABACUS is well known for its support of LCAO (Linear Combination of Atomic Orbital) basis set in calculating periodic condensed matter systems, so it’s a good choice to start from a LCAO example of self-consistent field (SCF) calculation. Here, FCC MgO has been chosen as a quick start example. The default name of a structure file in ABACUS is STRU. The STRU file for FCC MgO in a LCAO calculation is shown below:
#This is the atom file containing all the information
#about the lattice structure.
ATOMIC_SPECIES
Mg 24.305 Mg_ONCV_PBE-1.0.upf # element name, atomic mass, pseudopotential file
O 15.999 O_ONCV_PBE-1.0.upf
NUMERICAL_ORBITAL
Mg_gga_8au_100Ry_4s2p1d.orb
O_gga_8au_100Ry_2s2p1d.orb
LATTICE_CONSTANT
1.8897259886 # 1.8897259886 Bohr = 1.0 Angstrom
LATTICE_VECTORS
4.25648 0.00000 0.00000
0.00000 4.25648 0.00000
0.00000 0.00000 4.25648
ATOMIC_POSITIONS
Direct #Cartesian(Unit is LATTICE_CONSTANT)
Mg #Name of element
0.0 #Magnetic for this element.
4 #Number of atoms
0.0 0.0 0.0 0 0 0 #x,y,z, move_x, move_y, move_z
0.0 0.5 0.5 0 0 0 #x,y,z, move_x, move_y, move_z
0.5 0.0 0.5 0 0 0 #x,y,z, move_x, move_y, move_z
0.5 0.5 0.0 0 0 0 #x,y,z, move_x, move_y, move_z
O #Name of element
0.0 #Magnetic for this element.
4 #Number of atoms
0.5 0.0 0.0 0 0 0 #x,y,z, move_x, move_y, move_z
0.5 0.5 0.5 0 0 0 #x,y,z, move_x, move_y, move_z
0.0 0.0 0.5 0 0 0 #x,y,z, move_x, move_y, move_z
0.0 0.5 0.0 0 0 0 #x,y,z, move_x, move_y, move_z
Next, the INPUT file is required, which sets all key parameters to direct ABACUS how to calculte and what to output:
INPUT_PARAMETERS
suffix MgO
ntype 2
pseudo_dir ./
orbital_dir ./
ecutwfc 100 # Rydberg
scf_thr 1e-4 # Rydberg
basis_type lcao
calculation scf # this is the key parameter telling abacus to do a scf calculation
The pseudopotential files of Mg_ONCV_PBE-1.0.upf and O_ONCV_PBE-1.0.upf should be provided under the directory of pseudo_dir defined in INPUT (the default directory is “./”), and the orbital files Mg_gga_8au_100Ry_4s2p1d.orb and O_gga_8au_100Ry_2s2p1d.orb under the directory of orbital_dir also defined in INPUT (the default directory is “./”). The pseudopotential and orbital files can be downloaded from the ABACUS website.
The final mandatory input file is called KPT, which sets the reciprocal space k-mesh. Below is an example:
K_POINTS
0
Gamma
4 4 4 0 0 0
After all the above input files have been set, one should be able to run the first quick example. The simplest way is to use the command line, e.g.:
mpirun -np 2 abacus
The main output information is stored in the file OUT.MgO/running_scf.log, which starts with
WELCOME TO ABACUS v3.2
'Atomic-orbital Based Ab-initio Computation at UStc'
Website: http://abacus.ustc.edu.cn/
Version: Parallel, in development
Processor Number is 2
Start Time is Mon Oct 24 01:47:54 2022
------------------------------------------------------------------------------------
READING GENERAL INFORMATION
global_out_dir = OUT.MgO/
global_in_card = INPUT
pseudo_dir =
orbital_dir =
DRANK = 1
DSIZE = 2
DCOLOR = 1
GRANK = 1
GSIZE = 1
The esolver type has been set to : ksdft_lcao
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
| |
| Reading atom information in unitcell: |
| From the input file and the structure file we know the number of |
| different elments in this unitcell, then we list the detail |
| information for each element, especially the zeta and polar atomic |
| orbital number for each element. The total atom number is counted. |
| We calculate the nearest atom distance for each atom and show the |
| Cartesian and Direct coordinates for each atom. We list the file |
| address for atomic orbitals. The volume and the lattice vectors |
| in real and reciprocal space is also shown. |
| |
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
......
If ABAUCS finishes successfully, the total energy will be output in OUT.MgO/running_scf.log:
--------------------------------------------
!FINAL_ETOT_IS -7663.897267807250 eV
--------------------------------------------
A quick PW example
In order to run a SCF calculation with PW (Plane Wave) basis set, one has only to change the tag basis_type from lcao to pw in the INPUT file, and no longer needs to provide orbital files under NUMERICAL_ORBITAL in the STRU file.
The INPUT file follows as:
INPUT_PARAMETERS
suffix MgO
ntype 2
pseudo_dir ./
ecutwfc 100 # Rydberg
scf_thr 1e-4 # Rydberg
basis_type pw # changes the type of basis set
calculation scf # this is the key parameter telling abacus to do a scf calculation
And the STRU file will be:
#This is the atom file containing all the information
#about the lattice structure.
ATOMIC_SPECIES
Mg 24.305 Mg_ONCV_PBE-1.0.upf # element name, atomic mass, pseudopotential file
O 15.999 O_ONCV_PBE-1.0.upf
LATTICE_CONSTANT
1.8897259886 # 1.8897259886 Bohr = 1.0 Angstrom
LATTICE_VECTORS
4.25648 0.00000 0.00000
0.00000 4.25648 0.00000
0.00000 0.00000 4.25648
ATOMIC_POSITIONS
Direct #Cartesian(Unit is LATTICE_CONSTANT)
Mg #Name of element
0.0 #Magnetic for this element.
4 #Number of atoms
0.0 0.0 0.0 0 0 0 #x,y,z, move_x, move_y, move_z
0.0 0.5 0.5 0 0 0 #x,y,z, move_x, move_y, move_z
0.5 0.0 0.5 0 0 0 #x,y,z, move_x, move_y, move_z
0.5 0.5 0.0 0 0 0 #x,y,z, move_x, move_y, move_z
O #Name of element
0.0 #Magnetic for this element.
4 #Number of atoms
0.5 0.0 0.0 0 0 0 #x,y,z, move_x, move_y, move_z
0.5 0.5 0.5 0 0 0 #x,y,z, move_x, move_y, move_z
0.0 0.0 0.5 0 0 0 #x,y,z, move_x, move_y, move_z
0.0 0.5 0.0 0 0 0 #x,y,z, move_x, move_y, move_z
Use the same pseudopotential and KPT files as the above LCAO example. The final total energy will be output:
--------------------------------------------
!FINAL_ETOT_IS -7665.688319476949 eV
--------------------------------------------
Running Geometry Optimization
In order to run a full geometry optimization in ABACUS, the tag calculation in INPUT should be set to cell-relax. In addition, the convergence criteria for atomics force and cell stress can be set through the tags force_thr_ev and stress_thr, respectively. The maximum number of ionc steps is controlled by relax_nmax.
A quick LCAO example
The INPUT is provided as follows:
INPUT_PARAMETERS
suffix MgO
ntype 2
nelec 0.0
pseudo_dir ./
orbital_dir ./
ecutwfc 100 # Rydberg
scf_thr 1e-4 # Rydberg
basis_type lcao
calculation cell-relax # this is the key parameter telling abacus to do a optimization calculation
force_thr_ev 0.01 # the threshold of the force convergence, in unit of eV/Angstrom
stress_thr 5 # the threshold of the stress convergence, in unit of kBar
relax_nmax 100 # the maximal number of ionic iteration steps
out_stru 1
Use the same KPT, STRU, pseudopotential, and orbital files as in the above SCF-LCAO example. The final optimized structure can be found in STRU_NOW.cif and OUT.MgO/running_cell-relax.log.
A quick PW example
The INPUT is provided as follows:
INPUT_PARAMETERS
suffix MgO
ntype 2
nelec 0.0
pseudo_dir ./
ecutwfc 100 # Rydberg
scf_thr 1e-4 # Rydberg
basis_type pw
calculation cell-relax # this is the key parameter telling abacus to do a optimization calculation
force_thr_ev 0.01 # the threshold of the force convergence, in unit of eV/Angstrom
stress_thr 5 # the threshold of the stress convergence, in unit of kBar
relax_nmax 100 # the maximal number of ionic iteration steps
out_stru 1
Use the same KPT, STRU, and pseudopotential files as in the above SCF-PW examples. The final optimized structure can be found in STRU_NOW.cif and OUT.MgO/running_cell-relax.log.