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:
% ./openmx Methane.dat > met.std &
If you use the MPI version:
% 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 22 seconds by using a 3.0 GHz Xeon machine, although it is dependent on a computer. When the calculation is completed normally, 12 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.memory0 analysis for used memory
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 calculation flow of 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 13 iterations
within 1.0e-10 Hartree of the eigenvalues energy.
***********************************************************
***********************************************************
SCF history at MD= 1
***********************************************************
***********************************************************
SCF= 1 NormRD= 1.000000000000 Uele= -3.522970720671
SCF= 2 NormRD= 0.567552960632 Uele= -4.406035918480
SCF= 3 NormRD= 0.103577047970 Uele= -3.982563880836
SCF= 4 NormRD= 0.024276527366 Uele= -3.907106698719
SCF= 5 NormRD= 0.011021213879 Uele= -3.893269738272
SCF= 6 NormRD= 0.006502298545 Uele= -3.890536263821
SCF= 7 NormRD= 0.002725952874 Uele= -3.891850244497
SCF= 8 NormRD= 0.000001084476 Uele= -3.889462477079
SCF= 9 NormRD= 0.000000811511 Uele= -3.889462413487
SCF= 10 NormRD= 0.000000192017 Uele= -3.889462411048
SCF= 11 NormRD= 0.000000419250 Uele= -3.889462409739
SCF= 12 NormRD= 0.000000097337 Uele= -3.889462410321
SCF= 13 NormRD= 0.000000728612 Uele= -3.889462410280
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. -3.889462410280
Ukin. 5.533459858548
UH0. -14.855515938622
UH1. 0.041430604622
Una. -5.040519980550
Unl. -0.134510930915
Uxc0. -1.564740249909
Uxc1. -1.564740249909
Ucore. 9.551521413583
Uhub. 0.000000000000
Ucs. 0.000000000000
Uzs. 0.000000000000
Uzo. 0.000000000000
Uef. 0.000000000000
UvdW 0.000000000000
Utot. -8.033615473149
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: LDA+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 -0.69898787792675 -0.69898787792675
2 -0.41525019565153 -0.41525019565153
3 -0.41525017036741 -0.41525017036741
4 -0.41524296119431 -0.41524296119431
5 0.21215435713251 0.21215435713251
6 0.21215435834358 0.21215435834358
7 0.21222566949123 0.21222566949123
8 0.24738715427497 0.24738715427497
***********************************************************
***********************************************************
Mulliken populations
***********************************************************
***********************************************************
Total spin S = 0.000000000000
Up spin Down spin Sum Diff
1 C 2.509482918 2.509482918 5.018965836 0.000000000
2 H 0.372629308 0.372629308 0.745258615 0.000000000
3 H 0.372629233 0.372629233 0.745258466 0.000000000
4 H 0.372629248 0.372629248 0.745258495 0.000000000
5 H 0.372629294 0.372629294 0.745258587 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 0.681687651 0.681687651 1.363375301 0.000000000
sum over m 0.681687651 0.681687651 1.363375301 0.000000000
sum over m+mul 0.681687651 0.681687651 1.363375301 0.000000000
px 0 0.609277923 0.609277923 1.218555847 0.000000000
py 0 0.609239357 0.609239357 1.218478715 0.000000000
pz 0 0.609277987 0.609277987 1.218555974 0.000000000
sum over m 1.827795267 1.827795267 3.655590535 0.000000000
sum over m+mul 1.827795267 1.827795267 3.655590535 0.000000000
2 H Up spin Down spin Sum Diff
multiple
s 0 0.372629308 0.372629308 0.745258615 0.000000000
sum over m 0.372629308 0.372629308 0.745258615 0.000000000
sum over m+mul 0.372629308 0.372629308 0.745258615 0.000000000
3 H Up spin Down spin Sum Diff
multiple
s 0 0.372629233 0.372629233 0.745258466 0.000000000
sum over m 0.372629233 0.372629233 0.745258466 0.000000000
sum over m+mul 0.372629233 0.372629233 0.745258466 0.000000000
4 H Up spin Down spin Sum Diff
multiple
s 0 0.372629248 0.372629248 0.745258495 0.000000000
sum over m 0.372629248 0.372629248 0.745258495 0.000000000
sum over m+mul 0.372629248 0.372629248 0.745258495 0.000000000
5 H Up spin Down spin Sum Diff
multiple
s 0 0.372629294 0.372629294 0.745258587 0.000000000
sum over m 0.372629294 0.372629294 0.745258587 0.000000000
sum over m+mul 0.372629294 0.372629294 0.745258587 0.000000000
***********************************************************
***********************************************************
Dipole moment (Debye)
***********************************************************
***********************************************************
Absolute D 0.00000039
Dx Dy Dz
Total 0.00000005 0.00000038 -0.00000008
Core 0.00000000 0.00000000 0.00000000
Electron 0.00000005 0.00000038 -0.00000008
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 -0.000003225748 -0.000...
2 H -0.88998 -0.62931 0.00000 -0.064919423417 -0.045...
3 H 0.00000 0.62931 -0.88998 -0.000000146241 0.045...
4 H 0.00000 0.62931 0.88998 -0.000000062326 0.045...
5 H 0.88998 -0.62931 0.00000 0.064930353276 -0.045...
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. 22.157
Min_ID Min_Time Max_ID Max_Time
Total Computational Time = 0 22.157 0 22.157
readfile = 0 13.029 0 13.029
truncation = 0 1.442 0 1.442
MD_pac = 0 0.004 0 0.004
DFT = 0 6.527 0 6.527
*** In DFT ***
Set_OLP_Kin = 0 0.332 0 0.332
Set_Nonlocal = 0 0.439 0 0.439
Set_Hamiltonian = 0 1.887 0 1.887
Poisson = 0 0.820 0 0.820
Diagonalization = 0 0.031 0 0.031
Mixing_DM = 0 0.002 0 0.002
Force = 0 0.572 0 0.572
Total_Energy = 0 1.749 0 1.749
Set_Aden_Grid = 0 0.052 0 0.052
Set_Orbitals_Grid = 0 0.233 0 0.233
Set_Density_Grid = 0 0.160 0 0.160
Others = 0 0.251 0 0.251
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 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 Molekel [55] and XCrySDen [56]. The visualization will be illustrated in the latter section.