Test calculation

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 9 seconds by using 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 11 iterations within 1.0e-10 Hartree.

***********************************************************
***********************************************************
                  SCF history at MD= 1
***********************************************************
***********************************************************

   SCF=   1  NormRD=  1.000000000000  Uele= -3.523169099737
   SCF=   2  NormRD=  0.405885255370  Uele= -3.821653634211
   SCF=   3  NormRD=  0.353978312886  Uele= -4.025870411638
   SCF=   4  NormRD=  0.274975654611  Uele= -4.136402321036
   SCF=   5  NormRD=  0.049594489014  Uele= -3.933807675400
   SCF=   6  NormRD=  0.011397089683  Uele= -3.897749974768
   SCF=   7  NormRD=  0.001393372045  Uele= -3.889481762569
   SCF=   8  NormRD=  0.000009816453  Uele= -3.889316103737
   SCF=   9  NormRD=  0.000000420019  Uele= -3.889316051627
   SCF=  10  NormRD=  0.000000000625  Uele= -3.889316014196
   SCF=  11  NormRD=  0.000000000010  Uele= -3.889316014154
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.         -3.889316014154

  Ukin.          5.533759381319
  UH0.         -14.855519969177
  UH1.           0.041396138421
  Una.          -5.040606545160
  Unl.          -0.134650846424
  Uxc0.         -1.564720263875
  Uxc1.         -1.564720263875
  Ucore.         9.551521413583
  Uhub.          0.000000000000
  Ucs.           0.000000000000
  Uzs.           0.000000000000
  Uzo.           0.000000000000
  Uef.           0.000000000000
  UvdW           0.000000000000
  Utot.         -8.033540955189

  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  -0.69897506409889  -0.69897506409889
          2  -0.41523055770550  -0.41523055770550
          3  -0.41523055766184  -0.41523055766184
          4  -0.41522182761058  -0.41522182761058
          5   0.21221759601554   0.21221759601554
          6   0.21221759681275   0.21221759681275
          7   0.21230533061106   0.21230533061106
          8   0.24741918445314   0.24741918445314

***********************************************************
***********************************************************
                   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.         9.082

                               Min_ID   Min_Time       Max_ID   Max_Time
   Total Computational Time =     0        9.082          0        9.082
   readfile                 =     0        6.240          0        6.240
   truncation               =     0        0.000          0        0.000
   MD_pac                   =     0        0.000          0        0.000
   OutData                  =     0        0.571          0        0.571
   DFT                      =     0        2.089          0        2.089

*** In DFT ***

   Set_OLP_Kin              =     0        0.083          0        0.083
   Set_Nonlocal             =     0        0.082          0        0.082
   Set_ProExpn_VNA          =     0        0.147          0        0.147
   Set_Hamiltonian          =     0        0.689          0        0.689
   Poisson                  =     0        0.264          0        0.264
   Diagonalization          =     0        0.007          0        0.007
   Mixing_DM                =     0        0.000          0        0.000
   Force                    =     0        0.205          0        0.205
   Total_Energy             =     0        0.438          0        0.438
   Set_Aden_Grid            =     0        0.025          0        0.025
   Set_Orbitals_Grid        =     0        0.026          0        0.026
   Set_Density_Grid         =     0        0.118          0        0.118
   RestartFileDFT           =     0        0.002          0        0.002
   Mulliken_Charge          =     0        0.000          0        0.000
   FFT(2D)_Density          =     0        0.000          0        0.000
   Others                   =     0        0.003          0        0.003

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 [64], Molekel [65], and XCrySDen [66]. The visualization will be illustrated in the latter section.

2016-04-03