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If the installation is completed normally, please move to the directory 'work' and perform the program 'openmx' using an input file 'Methane.dat' which can be found in the directory 'work' as follows:
% mpirun -np 1 openmx Methane.dat > met.std &
Or if you use the MPI/OpenMP version:
% mpirun -np 1 openmx Methane.dat -nt 1 > met.std &
The test input file 'Methane.dat' is for performing the SCF calculation of a methane molecule with a fixed structure (No MD). The calculation is performed in only about 5 seconds by using a single core on a 2.6 GHz Xeon machine, although it is dependent on a computer. When the calculation is completed normally, 11 files and one directory
met.std standard output of the SCF calculation
met.out input file and standard output
met.xyz final geometrical structure
met.ene values computed at every MD step
met.md geometrical structures at every MD step
met.md2 geometrical structure of the final MD step
met.cif cif file of the initial structure for Material Studio
met.tden.cube total electron density in the Gaussian cube format
met.v0.cube Kohn-Sham potential in the Gaussian cube format
met.vhart.cube Hartree potential in the Gaussian cube format
met.dden.cube difference electron density measured from atomic density
met_rst/ directory storing restart files
are output to the directory 'work'.
The output data to a standard output is stored to the file 'met.std'
which is helpful to know the computational flow of the SCF procedure.
The file 'met.out' includes computed results such as the total
energy, forces, the Kohn-Sham eigenvalues, Mulliken charges, the convergence
history for the SCF calculation, and analyzed computational time.
A part of the file 'met.out' is shown below. It is found that
the eigenvalues energy converges by 14 iterations
within 1.0e-10 Hartree.
***********************************************************
***********************************************************
SCF history at MD= 1
***********************************************************
***********************************************************
SCF= 1 NormRD= 1.000000000000 Uele= -3.523169099731
SCF= 2 NormRD= 0.181517404404 Uele= -3.686855123738
SCF= 3 NormRD= 0.449067381009 Uele= -4.193062144919
SCF= 4 NormRD= 0.541215648203 Uele= -4.381387140154
SCF= 5 NormRD= 0.509921689399 Uele= -4.352426233337
SCF= 6 NormRD= 0.004026023243 Uele= -3.886371199720
SCF= 7 NormRD= 0.000838640096 Uele= -3.889312346884
SCF= 8 NormRD= 0.000420666755 Uele= -3.889396659132
SCF= 9 NormRD= 0.000241013350 Uele= -3.889362708861
SCF= 10 NormRD= 0.000573725679 Uele= -3.889427222948
SCF= 11 NormRD= 0.000000150516 Uele= -3.889316043314
SCF= 12 NormRD= 0.000000001917 Uele= -3.889316014533
SCF= 13 NormRD= 0.000000000005 Uele= -3.889316014156
SCF= 14 NormRD= 0.000000000001 Uele= -3.889316014146
Also, the total energy, chemical potential, Kohn-Sham eigenvalues,
the Mulliken charges, dipole moment, forces, fractional coordinate,
and analysis of computational time are output in 'met.out' as follows:
*******************************************************
Total energy (Hartree) at MD = 1
*******************************************************
Uele. -3.889316014146
Ukin. 5.533759381370
UH0. -14.855519969177
UH1. 0.041396138425
Una. -5.040606545149
Unl. -0.134650846490
Uxc0. -1.564720263874
Uxc1. -1.564720263874
Ucore. 9.551521413583
Uhub. 0.000000000000
Ucs. 0.000000000000
Uzs. 0.000000000000
Uzo. 0.000000000000
Uef. 0.000000000000
UvdW 0.000000000000
Uch 0.000000000000
Utot. -8.033540955187
Note:
Utot = Ukin+UH0+UH1+Una+Unl+Uxc0+Uxc1+Ucore+Uhub+Ucs+Uzs+Uzo+Uef+UvdW
Uene: band energy
Ukin: kinetic energy
UH0: electric part of screened Coulomb energy
UH1: difference electron-electron Coulomb energy
Una: neutral atom potential energy
Unl: non-local potential energy
Uxc0: exchange-correlation energy for alpha spin
Uxc1: exchange-correlation energy for beta spin
Ucore: core-core Coulomb energy
Uhub: DFT+U energy
Ucs: constraint energy for spin orientation
Uzs: Zeeman term for spin magnetic moment
Uzo: Zeeman term for orbital magnetic moment
Uef: electric energy by electric field
UvdW: semi-empirical vdW energy
(see also PRB 72, 045121(2005) for the energy contributions)
Chemical potential (Hartree) 0.000000000000
***********************************************************
***********************************************************
Eigenvalues (Hartree) for SCF KS-eq.
***********************************************************
***********************************************************
Chemical Potential (Hartree) = 0.00000000000000
Number of States = 8.00000000000000
HOMO = 4
Eigenvalues
Up-spin Down-spin
1 -0.69897506408475 -0.69897506408475
2 -0.41523055776668 -0.41523055776668
3 -0.41523055768741 -0.41523055768741
4 -0.41522182758055 -0.41522182758055
5 0.21221759603691 0.21221759603691
6 0.21221759685634 0.21221759685634
7 0.21230533059490 0.21230533059490
8 0.24741918440773 0.24741918440773
***********************************************************
***********************************************************
Mulliken populations
***********************************************************
***********************************************************
Total spin moment (muB) 0.000000000
Up spin Down spin Sum Diff
1 C 2.509748760 2.509748760 5.019497520 0.000000000
2 H 0.372562810 0.372562810 0.745125620 0.000000000
3 H 0.372562810 0.372562810 0.745125620 0.000000000
4 H 0.372562810 0.372562810 0.745125620 0.000000000
5 H 0.372562810 0.372562810 0.745125620 0.000000000
Sum of MulP: up = 4.00000 down = 4.00000
total= 8.00000 ideal(neutral)= 8.00000
Decomposed Mulliken populations
1 C Up spin Down spin Sum Diff
multiple
s 0 0.681737894 0.681737894 1.363475787 0.000000000
sum over m 0.681737894 0.681737894 1.363475787 0.000000000
sum over m+mul 0.681737894 0.681737894 1.363475787 0.000000000
px 0 0.609352701 0.609352701 1.218705403 0.000000000
py 0 0.609305463 0.609305463 1.218610926 0.000000000
pz 0 0.609352702 0.609352702 1.218705404 0.000000000
sum over m 1.828010866 1.828010866 3.656021733 0.000000000
sum over m+mul 1.828010866 1.828010866 3.656021733 0.000000000
2 H Up spin Down spin Sum Diff
multiple
s 0 0.372562810 0.372562810 0.745125620 0.000000000
sum over m 0.372562810 0.372562810 0.745125620 0.000000000
sum over m+mul 0.372562810 0.372562810 0.745125620 0.000000000
3 H Up spin Down spin Sum Diff
multiple
s 0 0.372562810 0.372562810 0.745125620 0.000000000
sum over m 0.372562810 0.372562810 0.745125620 0.000000000
sum over m+mul 0.372562810 0.372562810 0.745125620 0.000000000
4 H Up spin Down spin Sum Diff
multiple
s 0 0.372562810 0.372562810 0.745125620 0.000000000
sum over m 0.372562810 0.372562810 0.745125620 0.000000000
sum over m+mul 0.372562810 0.372562810 0.745125620 0.000000000
5 H Up spin Down spin Sum Diff
multiple
s 0 0.372562810 0.372562810 0.745125620 0.000000000
sum over m 0.372562810 0.372562810 0.745125620 0.000000000
sum over m+mul 0.372562810 0.372562810 0.745125620 0.000000000
***********************************************************
***********************************************************
Dipole moment (Debye)
***********************************************************
***********************************************************
Absolute D 0.00000000
Dx Dy Dz
Total 0.00000000 0.00000000 0.00000000
Core 0.00000000 0.00000000 0.00000000
Electron 0.00000000 0.00000000 0.00000000
Back ground -0.00000000 -0.00000000 -0.00000000
***********************************************************
***********************************************************
xyz-coordinates (Ang) and forces (Hartree/Bohr)
***********************************************************
***********************************************************
<coordinates.forces
5
1 C 0.00000 0.00000 0.00000 0.000000000000 0.00...
2 H -0.88998 -0.62931 0.00000 -0.064890985127 -0.04...
3 H 0.00000 0.62931 -0.88998 0.000000000002 0.04...
4 H 0.00000 0.62931 0.88998 0.000000000002 0.04...
5 H 0.88998 -0.62931 0.00000 0.064890985122 -0.04...
coordinates.forces>
***********************************************************
***********************************************************
Fractional coordinates of the final structure
***********************************************************
***********************************************************
1 C 0.00000000000000 0.00000000000000 0.00000000000000
2 H 0.91100190000000 0.93706880000000 0.00000000000000
3 H 0.00000000000000 0.06293120000000 0.91100190000000
4 H 0.00000000000000 0.06293120000000 0.08899810000000
5 H 0.08899810000000 0.93706880000000 0.00000000000000
***********************************************************
***********************************************************
Computational Time (second)
***********************************************************
***********************************************************
Elapsed.Time. 4.600
Min_ID Min_Time Max_ID Max_Time
Total Computational Time = 0 4.600 0 4.600
readfile = 0 2.578 0 2.578
truncation = 0 0.146 0 0.146
MD_pac = 0 0.000 0 0.000
OutData = 0 0.283 0 0.283
DFT = 0 1.591 0 1.591
*** In DFT ***
Set_OLP_Kin = 0 0.052 0 0.052
Set_Nonlocal = 0 0.039 0 0.039
Set_ProExpn_VNA = 0 0.156 0 0.156
Set_Hamiltonian = 0 0.663 0 0.663
Poisson = 0 0.214 0 0.214
Diagonalization = 0 0.005 0 0.005
Mixing_DM = 0 0.000 0 0.000
Force = 0 0.039 0 0.039
Total_Energy = 0 0.256 0 0.256
Set_Aden_Grid = 0 0.019 0 0.019
Set_Orbitals_Grid = 0 0.015 0 0.015
Set_Density_Grid = 0 0.124 0 0.124
RestartFileDFT = 0 0.004 0 0.004
Mulliken_Charge = 0 0.000 0 0.000
FFT(2D)_Density = 0 0.000 0 0.000
Others = 0 0.005 0 0.005
The files 'met.tden.cube', 'met.v0.cube', 'met.vhart.cube', and 'met.dden.cube', are the total electron density, the Kohn-Sham potential, the Hartree potential, and the difference electron density taken from the superposition of atomic densities of constituent atoms, respectively, which are output in the Gaussian cube format. Since the Gaussian cube format is one of well used grid formats, you can visualize the files using free molecular modeling software such as VESTA [103], Molekel [104], and XCrySDen [105]. The visualization will be illustrated in the later section.