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 19 seconds by using a 2.8 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.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_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 ten iterations
within 1.0e-8 Hartree of the eigenvalues energy.
***********************************************************
***********************************************************
SCF history at MD= 1
***********************************************************
***********************************************************
SCF= 1 NormRD= 1.000000000000 Uele= -3.799184452246
SCF= 2 NormRD= 0.294505017736 Uele= -3.180922853695
SCF= 3 NormRD= 0.088735677892 Uele= -3.371991788328
SCF= 4 NormRD= 0.021096020042 Uele= -3.435330322070
SCF= 5 NormRD= 0.006019683784 Uele= -3.449516147408
SCF= 6 NormRD= 0.000784960310 Uele= -3.452522027174
SCF= 7 NormRD= 0.000002401488 Uele= -3.453266301971
SCF= 8 NormRD= 0.000000599833 Uele= -3.453266643608
SCF= 9 NormRD= 0.000000184742 Uele= -3.453266654138
SCF= 10 NormRD= 0.000000562332 Uele= -3.453266655628
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. -3.453266655628
Ukin. 5.824571448666
UH0. -14.517598384684
UH1. 0.012112580595
Una. -6.365977496421
Unl. 0.681047544610
Uxc0. -1.609135574068
Uxc1. -1.609135574068
Ucore. 9.551521413583
Uhub. 0.000000000000
Ucs. 0.000000000000
Uzs. 0.000000000000
Uzo. 0.000000000000
Uef. 0.000000000000
Utot. -8.032594041787
Note:
Utot = Ukin+UH0+UH1+Una+Unl+Uxc0+Uxc1+Ucore+Uhub+Ucs+Uzs+Uzo+Uef
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
(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 -0.64275532805563 -0.64275532805563
2 -0.36132252595285 -0.36132252595285
3 -0.36127775831387 -0.36127775831387
4 -0.36127771549143 -0.36127771549143
5 0.26426269019400 0.26426269019400
6 0.26445588063823 0.26445588063823
7 0.26445588290286 0.26445588290286
8 0.31938640324811 0.31938640324811
***********************************************************
***********************************************************
Mulliken populations
***********************************************************
***********************************************************
Total spin S = 0.000000000000
Up spin Down spin Sum Diff
1 C 2.363735209 2.363735209 4.727470417 0.000000000
2 H 0.409066202 0.409066202 0.818132405 0.000000000
3 H 0.409066194 0.409066194 0.818132388 0.000000000
4 H 0.409066200 0.409066200 0.818132400 0.000000000
5 H 0.409066195 0.409066195 0.818132389 0.000000000
Decomposed Mulliken populations
1 C Up spin Down spin Sum Diff
multiple
s 0 0.598003833 0.598003833 1.196007665 0.000000000
sum over m 0.598003833 0.598003833 1.196007665 0.000000000
sum over m+mul 0.598003833 0.598003833 1.196007665 0.000000000
px 0 0.588514078 0.588514078 1.177028156 0.000000000
py 0 0.588703212 0.588703212 1.177406425 0.000000000
pz 0 0.588514085 0.588514085 1.177028171 0.000000000
sum over m 1.765731376 1.765731376 3.531462752 0.000000000
sum over m+mul 1.765731376 1.765731376 3.531462752 0.000000000
2 H Up spin Down spin Sum Diff
multiple
s 0 0.409066202 0.409066202 0.818132405 0.000000000
sum over m 0.409066202 0.409066202 0.818132405 0.000000000
sum over m+mul 0.409066202 0.409066202 0.818132405 0.000000000
3 H Up spin Down spin Sum Diff
multiple
s 0 0.409066194 0.409066194 0.818132388 0.000000000
sum over m 0.409066194 0.409066194 0.818132388 0.000000000
sum over m+mul 0.409066194 0.409066194 0.818132388 0.000000000
4 H Up spin Down spin Sum Diff
multiple
s 0 0.409066200 0.409066200 0.818132400 0.000000000
sum over m 0.409066200 0.409066200 0.818132400 0.000000000
sum over m+mul 0.409066200 0.409066200 0.818132400 0.000000000
5 H Up spin Down spin Sum Diff
multiple
s 0 0.409066195 0.409066195 0.818132389 0.000000000
sum over m 0.409066195 0.409066195 0.818132389 0.000000000
sum over m+mul 0.409066195 0.409066195 0.818132389 0.000000000
***********************************************************
***********************************************************
Dipole moment (Debye)
***********************************************************
***********************************************************
Absolute D 0.00000009
Dx Dy Dz
Total 0.00000004 0.00000005 -0.00000007
Core 0.00000000 0.00000000 0.00000000
Electron 0.00000004 0.00000005 -0.00000007
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 -0.000000037541 0.000...
2 H -0.88998 -0.62931 0.00000 -0.048431334064 -0.034...
3 H 0.00000 0.62931 -0.88998 0.000000053600 0.034...
4 H 0.00000 0.62931 0.88998 -0.000000012054 0.034...
5 H 0.88998 -0.62931 0.00000 0.048431331537 -0.034...
coordinates.forces>
***********************************************************
***********************************************************
Fractional coordinates of the final structure
***********************************************************
***********************************************************
1 C 0.00000000000000 0.00000000000000 0.00000000000000
2 H 0.86968043640398 0.89633135611159 0.00000000000000
3 H 0.00000000000000 0.10366864388841 0.86968043640398
4 H 0.00000000000000 0.10366864388841 0.13031956359602
5 H 0.13031956359602 0.89633135611159 0.00000000000000
***********************************************************
***********************************************************
Computational Time (second)
***********************************************************
***********************************************************
Elapsed.Time. 18.554
Min_ID Min_Time Max_ID Max_Time
Total Computational Time = 0 18.554 0 18.554
readfile = 0 16.096 0 16.096
truncation = 0 0.728 0 0.728
MD_pac = 0 0.010 0 0.010
DFT = 0 1.376 0 1.376
*** In DFT ***
Set_OLP_Kin = 0 0.119 0 0.119
Set_Nonlocal = 0 0.198 0 0.198
Set_Hamiltonian = 0 0.087 0 0.087
Poisson = 0 0.118 0 0.118
Diagonalization = 0 0.023 0 0.023
Mixing_DM = 0 0.002 0 0.002
Force = 0 0.288 0 0.288
Total_Energy = 0 0.111 0 0.111
Set_Aden_Grid = 0 0.027 0 0.027
Set_Orbitals_Grid = 0 0.111 0 0.111
Set_Density_Grid = 0 0.053 0 0.053
Others = 0 0.237 0 0.237
The files, met.tden.cube, met.v0.cube, met.vhart.cube, are the total electron density, the Kohn-Sham potential, and the Hartree potential, 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 gOpenMol [48], Molekel [49], and XCrysDen [50]. The visualization will be illustrated in the latter section.