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Ab initio Calculations Using Vasp Code

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How to perform a standard calculation for a single oxygen atom in a box

Abderrahmane REGGAD 11:28


Input

POSCAR

O atom in a box
 1.0          ! universal scaling parameters
 8.0 0.0 0.0  ! lattice vector  a(1)
 0.0 8.0 0.0  ! lattice vector  a(2)
 0.0 0.0 8.0  ! lattice vector  a(3)
1             ! number of atoms
cart          ! positions in cartesian coordinates
 0 0 0
 

We are using a POSCAR file with a single atom. Sufficiently large lattice parameters are selected so that no (significant) interactions between atoms in neighbouring cells is present.

 INCAR

 SYSTEM = O atom in a box
 ISMEAR = 0  ! Gaussian smearing

 KPOINTS

Gamma-point only
 0
Monkhorst Pack
 1 1 1
 0 0 0

 For atoms or molecules a single k point is sufficient. When more k points are used only the interaction between atoms (which should be zero) is described more accurately.

POTCAR 

Download the pseudopotential file from this link Oatom.tgz

Calculation

/O-atom_scf> vasp_gam

 

Stdout 

 vasp.5.4.1 05Feb16 (build Mar 10 2022 19:01:08) gamma-only                     
  
 POSCAR found :  1 types and       1 ions
 LDA part: xc-table for Pade appr. of Perdew
 POSCAR, INCAR and KPOINTS ok, starting setup
 WARNING: small aliasing (wrap around) errors must be expected
 FFT: planning ...
 WAVECAR not read
 entering main loop
       N       E                     dE             d eps       ncg     rms          rms(c)
DAV:   1     0.401551970622E+02    0.40155E+02   -0.11086E+03    14   0.324E+02
DAV:   2     0.215084107566E+02   -0.18647E+02   -0.18376E+02    28   0.312E+01
DAV:   3     0.949309188805E+00   -0.20559E+02   -0.20463E+02    21   0.690E+01
DAV:   4    -0.301708029401E+00   -0.12510E+01   -0.11406E+01    14   0.208E+01
DAV:   5    -0.313224606489E+00   -0.11517E-01   -0.11489E-01    14   0.216E+00    0.296E-01
DAV:   6    -0.314529039707E+00   -0.13044E-02   -0.66941E-03    28   0.570E-01    0.138E-01
DAV:   7    -0.314614061799E+00   -0.85022E-04   -0.56234E-05    14   0.976E-02
   1 F= -.31461406E+00 E0= -.16035174E+00  d E =-.308525E+00
 writing wavefunctions

 

The example output (stdout) for the O atom was obtained using VASP version 5.4.1. The initial charge corresponds to the charge of isolated overlapping atoms (POTCAR file). For the first 4 steps the charge remains fixed, then the charge is updated (rms(c) column)

Short explanation of the symbols in the OSZICAR and stdout file:

N iteration count
E total energy
dE change of total energy
d eps change of the eigenvalues (fixed potential)
ncg number of optimisation steps {\mathrm {H}}\psi
rms total residual vector \sum _{{nk}}w_{{k}}f_{{nk}}({\mathrm {H}}-\epsilon _{{nk}})\psi _{{nk}}
rms(c) charge density residual vector

OUTCAR

The individual parts of the OUTCAR file are separated by lines. 

----------------------------------------------------------

The OUTCAR file is divided into the following parts:

  • Nearest neighbor distances and analysis of symmetry
  • Verbose job information
  • Information on lattice, k points and positions
  • Information on the basis set (number of plane waves)
  • Non-local pseudo potential information
  • Information for each electronic step (one line in OSZICAR)
  • Timing and energy information

  

   POTLOK:  cpu time    0.0878: real time    0.0877
   SETDIJ:  cpu time    0.0015: real time    0.0014
    EDDAV:  cpu time    0.0267: real time    0.0434
      DOS:  cpu time    0.0001: real time    0.0001
   --------------------------------------------
     LOOP:  cpu time    0.1165: real time    0.1346
   
eigenvalue-minimisations :    16
total energy-change (2. order) : 0.3844697E+02  (-0.9672571E+02)
number of electron       6.0000000 magnetization
augmentation part        6.0000000 magnetization
    
Free energy of the ion-electron system (eV)      
 ---------------------------------------------------
 alpha Z        PSCENC =         0.27135287
 Ewald energy   TEWEN  =       -91.92708002
 -Hartree energ DENC   =      -281.84385691
 -exchange      EXHF   =         0.00000000
 -V(xc)+E(xc)   XCENC  =        26.11948841
 PAW double counting   =       245.99840262     -247.84808825
 entropy T*S    EENTRO =        -0.08636665
 eigenvalues    EBANDS =       -44.50008162
 atomic energy  EATOM  =       432.26319604
 Solvation  Ediel_sol  =         0.00000000
 ---------------------------------------------------
 free energy    TOTEN  =        38.44696648 eV
    
 energy without entropy =       38.53333313  energy(sigma->0) =       38.49014980

    Information on the Eigenvalues

E-fermi :  -8.8431     XC(G=0):  -0.8043     alpha+bet : -0.1463
k-point     1 :       0.0000    0.0000    0.0000
band No.  band energies     occupation
1     -23.8439      2.00000
2      -8.9040      1.33333
3      -8.9040      1.33333
4      -8.9040      1.33333
5      -0.4676      0.00000
6       1.8633      0.00000
7       1.8633      0.00000
8       1.8633      0.00000

 

  • Information on stress tensor 
The O atom (Example: Oatom)
FORCE on cell =-STRESS in cart. coord.  units (eV):
Direction    XX          YY          ZZ          XY          YZ          ZX
--------------------------------------------------------------------------------------
Alpha Z     0.27135     0.27135     0.27135
Ewald     -30.64236   -30.64236   -30.64236     0.00000     0.00000     0.00000
Hartree    93.90244    93.90244    93.90244    -0.00000    -0.00000    -0.00000
E(xc)     -27.93035   -27.93035   -27.93035    -0.00000    -0.00000    -0.00000
Local    -147.86211  -147.86211  -147.86211     0.00000     0.00000     0.00000
n-local   -20.54942   -20.54942   -20.54942    -0.00000    -0.00000    -0.00000
augment     5.55366     5.55366     5.55366     0.00000    -0.00000     0.00000
Kinetic   126.50998   126.50998   126.50997    -0.00000     0.00000    -0.00000
Fock        0.00000     0.00000     0.00000     0.00000     0.00000     0.00000
-------------------------------------------------------------------------------------
Total      -0.74681    -0.74681    -0.74681     0.00000    -0.00000    -0.00000
in kB      -2.33695    -2.33695    -2.33695     0.00000    -0.00000    -0.00000
external pressure =       -2.34 kB  Pullay stress =        0.00 kB

 

  • Information on the energy 
The O atom (Example: Oatom)
FORCE on cell =-STRESS in cart. coord.  units (eV):
Direction    XX          YY          ZZ          XY          YZ          ZX
--------------------------------------------------------------------------------------
Alpha Z     0.27135     0.27135     0.27135
Ewald     -30.64236   -30.64236   -30.64236     0.00000     0.00000     0.00000
Hartree    93.90244    93.90244    93.90244    -0.00000    -0.00000    -0.00000
E(xc)     -27.93035   -27.93035   -27.93035    -0.00000    -0.00000    -0.00000
Local    -147.86211  -147.86211  -147.86211     0.00000     0.00000     0.00000
n-local   -20.54942   -20.54942   -20.54942    -0.00000    -0.00000    -0.00000
augment     5.55366     5.55366     5.55366     0.00000    -0.00000     0.00000
Kinetic   126.50998   126.50998   126.50997    -0.00000     0.00000    -0.00000
Fock        0.00000     0.00000     0.00000     0.00000     0.00000     0.00000
-------------------------------------------------------------------------------------
Total      -0.74681    -0.74681    -0.74681     0.00000    -0.00000    -0.00000
in kB      -2.33695    -2.33695    -2.33695     0.00000    -0.00000    -0.00000
external pressure =       -2.34 kB  Pullay stress =        0.00 kB

 

  • Information on the energy 
FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV)
---------------------------------------------------
free  energy   TOTEN  =        -0.31463722 eV
energy  without entropy=       -0.00611258  energy(sigma->0) =       -0.16037490

 

The relevant energy for molecules and atoms is energy without entropy. 

energy  without entropy=     -0.00611258  energy(sigma->0) =     -0.16037490

Three degenerate p orbitals are occupied by 2/3 electrons causing an unphysical electronic entropy 

entropy T*S    EENTRO =      -0.30852464

 

A tiny value of SIGMA=0.01 would reduce the entropy but might slow convergence (default is SIGMA=0.2). SIGMA controls the electronic temperature, which is not a very meaningful quantity for molecules and atoms.

The total energy is found to be essentially zero. VASP subtracts from any calculated energy the energy of the atom in the configuration for which the pseudo potential was generated. All pseudo potentials were generated using non spin-polarized reference atoms. 

 

Restart of the calculation

When VASP is restarted the WAVECAR file is read and the run is continued from the previous wave functions (converging rapidly).

 

 vasp.5.4.1 05Feb16 (build Mar 10 2022 19:01:08) gamma-only                                                                                                                                    
                                                                                                                                                                                               
 POSCAR found :  1 types and       1 ions                                                                                                                                                      
 LDA part: xc-table for Pade appr. of Perdew                                                                                                                                                   
 found WAVECAR, reading the header                                                                                                                                                             
 POSCAR, INCAR and KPOINTS ok, starting setup                                                                                                                                                  
 WARNING: small aliasing (wrap around) errors must be expected                                                                                                                                 
 FFT: planning ...                                                                                                                                                                             
 reading WAVECAR                                                                                                                                                                               
 the WAVECAR file was read successfully
 initial charge from wavefunction
 entering main loop
       N       E                     dE             d eps       ncg     rms          rms(c)
DAV:   1    -0.314677534760E+00   -0.31468E+00   -0.38264E-05    14   0.694E-02    0.274E-03
DAV:   2    -0.314677196981E+00    0.33778E-06   -0.63151E-07    28   0.612E-03
   1 F= -.31467720E+00 E0= -.16041488E+00  d E =-.308525E+00
 writing wavefunctions

 


 

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