./Job.out output for 1003: Bulk_VBiO4_opt
Status:
finished
[Sun Apr 06 19:32:18 SAST 2025] [MD] [warn] 'Starting MedeA Core 3.7.0'
MedeA version 3.7.0
#-------------------------------------------------------------------------------
# This calculation has 1 stage
#-------------------------------------------------------------------------------
Stage 1: VASP 6
#-------------------------------------------------------------------------------
# Running the calculation
#-------------------------------------------------------------------------------
Stage 1: VASP 6
Sucessfully opened MedeA database from /home/medea/MD/Databases/MedeA.db
VASP 6 CALCULATION PROTOCOL:
============================
1. Geometry optimization (atom positions, unit cell shape, unit cell volume)
Saved properties in this step: charge density, wave functions
2. Calculate superposed atomic charge densities for difference charge density
VASP parameters
===============
This is a calculation based on density functional theory and the GGA-PBE exchange-correlation functional for describing the interactions.
Van der Waals interactions are added by means of a forcefield (DFT+D3 approach of S. Grimme with Becke-Johnson-damping).
This is a spin-polarized magnetic calculation using 'normal' precision
and a default planewave cutoff energy of 400.000 eV.
The electronic iterations convergence is 1.00E-08 eV using the Fast (Davidson and RMM-DIIS) algorithm
and reciprocal space projection operators.
The requested k-spacing is 0.35 per Angstrom, which leads to a 5x5x3 mesh.
This corresponds to actual k-spacings of 0.245 x 0.245 x 0.181 per Angstrom.
The k-mesh is forced to have an odd number of points in each direction.
Using Gaussian smearing with a width of 0.05 eV.
Other non-default parameters:
Extrafine augmentation grid for accurate forces is TRUE
Extra input is LPLANE = .TRUE.
NCORE = 8
NPAR = 8
LSCALU = .FALSE.
NSIM = 4
(Pseudo, difference,
spin) charge density is TRUE
Wave functions is TRUE
==========================================
Using version 4.0 GGA-PBE / PAW potentials:
V sv PAW_PBE V_sv 02Aug2007
Bi d PAW_PBE Bi_d 06Sep2000
O PAW_PBE O 08Apr2002
There are 14 symmetry-unique k-points
The plane wave cutoff is 400.00 eV
VASP energy: -183.795189 eV for V4Bi4O16 cell
Non-dispersive: -178.152229 eV
Van der Waals: -5.642960 eV
Initial VASP energy: -183.718380 eV for V4Bi4O16 cell
Relaxation energy: -0.076809 eV gained after 9 optimization steps.
Electronic contributions:
Empirical Formula Cell
VBiO4 (VBiO4)4
----------------- -----------------
VASP Energy -45.948797 -183.795189 eV
= -4433.384 -17733.536 kJ/mol
Cell parameters:
Parameter Original change Final %
---------- ------------ ---------- ------------ -----
a 5.122106 -0.033919 5.088187 -0.7
b 5.122106 -0.033919 5.088187 -0.7
c 11.592129 -0.091803 11.500326 -0.8
alpha 90.000000 0.000000 90.000000 0.0
beta 90.000000 0.000000 90.000000 0.0
gamma 90.000000 0.000000 90.000000 0.0
Volume 304.130739 -6.391352 297.739386 -2.1
Density: 7.226 Mg/m^3
The pressure given below is exerted by the system according to its volume.
Positive pressure would cause expansion during full geometry optimization.
Pressure: -18.000 MPa
= -180.000 bar
XX YY ZZ YZ XZ XY
Stress: -20.295 -20.295 94.736 0.000 -0.000 -0.000 MPa
= -202.950 -202.950 947.360 0.000 -0.000 -0.000 bar
The stress tensor above is imposed on the system, i.e. negative values of diagonal components
would cause expansion of the corresponding lattice parameter upon full geometry optimization.
The pressure and stress include only electronic terms, i.e. the vibrational,
temperature and other terms are not included here.
Fractional Coordinates:
Atom Initial Coordinates Final Coordinates
----- -------- -------- -------- -------- -------- --------
V0 0.5000 0.5000 0.0000 0.5000 0.5000 0.0000
V1 0.5000 0.0000 0.2500 0.5000 0.0000 0.2500
V2 0.0000 0.0000 0.5000 0.0000 0.0000 0.5000
V3 0.0000 0.5000 0.7500 0.0000 0.5000 0.7500
Bi4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
Bi5 0.0000 0.5000 0.2500 0.0000 0.5000 0.2500
Bi6 0.5000 0.5000 0.5000 0.5000 0.5000 0.5000
Bi7 0.5000 0.0000 0.7500 0.5000 0.0000 0.7500
O8 0.1410 0.7500 0.4209 0.1415 0.7500 0.4197
O9 0.7500 0.1410 0.1709 0.7500 0.1415 0.1697
O10 0.2500 0.8590 0.1709 0.2500 0.8585 0.1697
O11 0.8590 0.2500 0.4209 0.8585 0.2500 0.4197
O12 0.6410 0.7500 0.3291 0.6415 0.7500 0.3303
O13 0.7500 0.6410 0.0791 0.7500 0.6415 0.0803
O14 0.3590 0.2500 0.3291 0.3585 0.2500 0.3303
O15 0.2500 0.3590 0.0791 0.2500 0.3585 0.0803
O16 0.6410 0.2500 0.9209 0.6415 0.2500 0.9197
O17 0.2500 0.6410 0.6709 0.2500 0.6415 0.6697
O18 0.7500 0.3590 0.6709 0.7500 0.3585 0.6697
O19 0.3590 0.7500 0.9209 0.3585 0.7500 0.9197
O20 0.1410 0.2500 0.8291 0.1415 0.2500 0.8303
O21 0.2500 0.1410 0.5791 0.2500 0.1415 0.5803
O22 0.8590 0.7500 0.8291 0.8585 0.7500 0.8303
O23 0.7500 0.8590 0.5791 0.7500 0.8585 0.5803
Analytic Derivatives:
Atom Derivatives fractional Derivatives Cartesian (eV/Ang)
----- -------- -------- -------- -------- -------- --------
V0 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000
V1 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000
V2 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000
V3 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000
Bi4 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000
Bi5 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000
Bi6 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000
Bi7 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000
O8 0.0018 0.0016 0.0010 0.0095 0.0080 0.0112 maximum gradient = 0.0167
O9 -0.0016 0.0018 0.0010 -0.0080 0.0095 0.0112
O10 0.0016 -0.0018 0.0010 0.0080 -0.0095 0.0112
O11 -0.0018 -0.0016 0.0010 -0.0095 -0.0080 0.0112
O12 0.0018 0.0016 -0.0010 0.0095 0.0080 -0.0112
O13 -0.0016 0.0018 -0.0010 -0.0080 0.0095 -0.0112
O14 -0.0018 -0.0016 -0.0010 -0.0095 -0.0080 -0.0112
O15 0.0016 -0.0018 -0.0010 0.0080 -0.0095 -0.0112
O16 0.0018 0.0016 0.0010 0.0095 0.0080 0.0112
O17 -0.0016 0.0018 0.0010 -0.0080 0.0095 0.0112
O18 0.0016 -0.0018 0.0010 0.0080 -0.0095 0.0112
O19 -0.0018 -0.0016 0.0010 -0.0095 -0.0080 0.0112
O20 0.0018 0.0016 -0.0010 0.0095 0.0080 -0.0112
O21 -0.0016 0.0018 -0.0010 -0.0080 0.0095 -0.0112
O22 -0.0018 -0.0016 -0.0010 -0.0095 -0.0080 -0.0112
O23 0.0016 -0.0018 -0.0010 0.0080 -0.0095 -0.0112
Atomic partial charges (electron charges):
Atom s p d total
----- -------- -------- -------- --------
V0 2.358 6.520 3.231 12.109
V1 2.358 6.520 3.231 12.109
V2 2.358 6.520 3.231 12.109
V3 2.358 6.520 3.231 12.109
Bi4 1.583 0.707 9.967 12.256
Bi5 1.583 0.707 9.967 12.256
Bi6 1.583 0.707 9.967 12.256
Bi7 1.583 0.707 9.967 12.256
O8 1.278 2.819 0.005 4.102
O9 1.277 2.825 0.005 4.107
O10 1.277 2.824 0.005 4.106
O11 1.278 2.820 0.005 4.103
O12 1.278 2.820 0.005 4.103
O13 1.277 2.824 0.005 4.106
O14 1.278 2.819 0.005 4.102
O15 1.277 2.825 0.005 4.107
O16 1.278 2.819 0.005 4.102
O17 1.277 2.825 0.005 4.107
O18 1.277 2.824 0.005 4.106
O19 1.278 2.820 0.005 4.103
O20 1.278 2.820 0.005 4.103
O21 1.277 2.824 0.005 4.106
O22 1.278 2.819 0.005 4.102
O23 1.277 2.825 0.005 4.107
Total magnetic moment: 0.0000 Bohr magnetons
Atomic partial magnetic moments (Bohr magnetons):
Atom s p d total
----- -------- -------- -------- --------
V0 0.000 -0.000 0.000 -0.000
V1 0.000 -0.000 0.000 -0.000
V2 0.000 -0.000 0.000 -0.000
V3 0.000 -0.000 0.000 -0.000
Bi4 -0.000 0.000 -0.000 -0.000
Bi5 -0.000 0.000 -0.000 -0.000
Bi6 -0.000 0.000 -0.000 -0.000
Bi7 -0.000 0.000 -0.000 -0.000
O8 0.000 0.000 -0.000 0.000
O9 0.000 0.000 -0.000 0.000
O10 0.000 0.000 -0.000 0.000
O11 0.000 0.000 -0.000 0.000
O12 0.000 0.000 -0.000 0.000
O13 0.000 0.000 -0.000 0.000
O14 0.000 0.000 -0.000 0.000
O15 0.000 0.000 -0.000 0.000
O16 0.000 0.000 -0.000 0.000
O17 0.000 0.000 -0.000 0.000
O18 0.000 0.000 -0.000 0.000
O19 0.000 0.000 -0.000 0.000
O20 0.000 0.000 -0.000 0.000
O21 0.000 0.000 -0.000 0.000
O22 0.000 0.000 -0.000 0.000
O23 0.000 0.000 -0.000 0.000
Analysis of the electronic structure:
The system is a magnetic semiconductor with an indirect gap of 2.129 eV.
The valence band (spin 2, #104) maximum is located near (-0.40 0.20 0.00), at -0.400 eV with respect to the Fermi level.
The conduction band (spin 1, #105) minimum is located near (0.40 0.00 0.00), at 1.729 eV with respect to the Fermi level.
The center of the gap is located at 0.664244 eV with respect to the Fermi level.
The Fermi energy is used as the zero of the energy scale.
SUPERPOSITION OF ATOMIC CHARGE DENSITIES
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!!!! ERROR !!!!
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Error with the charge density handling: One of the files was truncated or not readable
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Job completed on Sun 06 April 2025 at 19:59:45 SAST after 1634 s (0:27:14)
Entire job completed on Sun 06 April 2025 at 19:59:46 SAST after 1635 s (0:27:15)
and running 2 tasks.