O atom
Task
Performing a standard calculation for a single oxygen atom in a box. Getting to know the main input and output files of VASP.
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.
Calculation
stdout
running on 8 total cores distrk: each k-point on 8 cores, 1 groups distr: one band on 1 cores, 8 groups using from now: INCAR vasp.5.4.1 05Feb16 (build Aug 22 2016 16:46:23) complex POSCAR found : 1 types and 1 ions scaLAPACK will be used 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 0.384469664751E+02 0.38447E+02 -0.96726E+02 16 0.293E+02 DAV: 2 0.345965628955E+01 -0.34987E+02 -0.34942E+02 32 0.450E+01 DAV: 3 -0.244485866931E+00 -0.37041E+01 -0.34307E+01 16 0.308E+01 DAV: 4 -0.312557021227E+00 -0.68071E-01 -0.66914E-01 16 0.508E+00 DAV: 5 -0.313520305300E+00 -0.96328E-03 -0.96311E-03 32 0.506E-01 0.286E-01 DAV: 6 -0.314540466589E+00 -0.10202E-02 -0.17853E-03 16 0.332E-01 0.142E-01 DAV: 7 -0.314637222361E+00 -0.96756E-04 -0.22710E-04 16 0.134E-01 1 F= -.31463722E+00 E0= -.16037490E+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 rms total residual vector 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
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).
running on 8 total cores
distrk: each k-point on 8 cores, 1 groups
distr: one band on 1 cores, 8 groups
using from now: INCAR
vasp.5.4.1 05Feb16 (build Aug 22 2016 16:46:23) complex
POSCAR found : 1 types and 1 ions
scaLAPACK will be used
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 -0.314680766875E+00 -0.31468E+00 -0.83090E-05 16 0.564E-02 0.107E-02
DAV: 2 -0.314677281013E+00 0.34859E-05 -0.10030E-05 16 0.198E-02
1 F= -.31467728E+00 E0= -.16041496E+00 d E =-.308525E+00
writing wavefunctions
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