# 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. 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 pseudo_dir ./ orbital_dir ./ ecutwfc 100 # Rydberg scf_thr 1e-6 # SCF criterion 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](http://abacus.ustc.edu.cn/pseudo/list.htm). 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.: ``` OMP_NUM_THREADS=1 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 pseudo_dir ./ ecutwfc 100 # Rydberg scf_thr 1e-6 # SCF criterion 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 nelec 0.0 pseudo_dir ./ orbital_dir ./ ecutwfc 100 # Rydberg scf_thr 1e-6 # SCF criterion 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 nelec 0.0 pseudo_dir ./ ecutwfc 100 # Rydberg scf_thr 1e-6 # SCF criterion 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 `STRU_ION_D` with different format.