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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 12 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= -3.523143659974
   SCF=   2  NormRD=  0.567253699744  Uele= -4.405605131921
   SCF=   3  NormRD=  0.103433490729  Uele= -3.982266241934
   SCF=   4  NormRD=  0.024234990593  Uele= -3.906896836134
   SCF=   5  NormRD=  0.011006215697  Uele= -3.893084558820
   SCF=   6  NormRD=  0.006494145332  Uele= -3.890357113476
   SCF=   7  NormRD=  0.002722267527  Uele= -3.891669816209
   SCF=   8  NormRD=  0.000000672350  Uele= -3.889285164733
   SCF=   9  NormRD=  0.000000402419  Uele= -3.889285102456
   SCF=  10  NormRD=  0.000000346348  Uele= -3.889285101128
   SCF=  11  NormRD=  0.000000515395  Uele= -3.889285101063
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.         -3.889285101063

  Ukin.          5.533754016241
  UH0.         -14.855520072374
  UH1.           0.041395625260
  Una.          -5.040583803800
  Unl.          -0.134640939010
  Uxc0.         -1.564720823137
  Uxc1.         -1.564720823137
  Ucore.         9.551521413583
  Uhub.          0.000000000000
  Ucs.           0.000000000000
  Uzs.           0.000000000000
  Uzo.           0.000000000000
  Uef.           0.000000000000
  UvdW           0.000000000000
  Utot.         -8.033515406373

  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  -0.69897190537228  -0.69897190537228
          2  -0.41522646150979  -0.41522646150979
          3  -0.41522645534084  -0.41522645534084
          4  -0.41521772830844  -0.41521772830844
          5   0.21218282298348   0.21218282298348
          6   0.21218282358344   0.21218282358344
          7   0.21227055734372   0.21227055734372
          8   0.24742493684297   0.24742493684297

***********************************************************
***********************************************************
                   Mulliken populations                    
***********************************************************
***********************************************************

  Total spin S =  0.000000000000

                    Up spin      Down spin     Sum           Diff
      1    C      2.509755704  2.509755704   5.019511408   0.000000000
      2    H      0.372561098  0.372561098   0.745122197   0.000000000
      3    H      0.372561019  0.372561019   0.745122038   0.000000000
      4    H      0.372561127  0.372561127   0.745122254   0.000000000
      5    H      0.372561051  0.372561051   0.745122102   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    0.681752967  0.681752967   1.363505935   0.000000000
   sum over m      0.681752967  0.681752967   1.363505935   0.000000000
   sum over m+mul  0.681752967  0.681752967   1.363505935   0.000000000
  px          0    0.609349992  0.609349992   1.218699985   0.000000000
  py          0    0.609302752  0.609302752   1.218605504   0.000000000
  pz          0    0.609349993  0.609349993   1.218699985   0.000000000
   sum over m      1.828002737  1.828002737   3.656005474   0.000000000
   sum over m+mul  1.828002737  1.828002737   3.656005474   0.000000000

    2    H          Up spin      Down spin     Sum           Diff
            multiple
  s           0    0.372561098  0.372561098   0.745122197   0.000000000
   sum over m      0.372561098  0.372561098   0.745122197   0.000000000
   sum over m+mul  0.372561098  0.372561098   0.745122197   0.000000000

    3    H          Up spin      Down spin     Sum           Diff
            multiple
  s           0    0.372561019  0.372561019   0.745122038   0.000000000
   sum over m      0.372561019  0.372561019   0.745122038   0.000000000
   sum over m+mul  0.372561019  0.372561019   0.745122038   0.000000000

    4    H          Up spin      Down spin     Sum           Diff
            multiple
  s           0    0.372561127  0.372561127   0.745122254   0.000000000
   sum over m      0.372561127  0.372561127   0.745122254   0.000000000
   sum over m+mul  0.372561127  0.372561127   0.745122254   0.000000000

    5    H          Up spin      Down spin     Sum           Diff
            multiple
  s           0    0.372561051  0.372561051   0.745122102   0.000000000
   sum over m      0.372561051  0.372561051   0.745122102   0.000000000
   sum over m+mul  0.372561051  0.372561051   0.745122102   0.000000000

***********************************************************
***********************************************************
                    Dipole moment (Debye)                  
***********************************************************
***********************************************************

 Absolute D        0.00000071

                      Dx                Dy                Dz
 Total              0.00000046        0.00000000       -0.00000054
 Core               0.00000000        0.00000000        0.00000000
 Electron           0.00000046        0.00000000       -0.00000054
 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   0.000000000327 -0.000...
    2     H    -0.88998  -0.62931   0.00000  -0.064883705001 -0.045...
    3     H     0.00000   0.62931  -0.88998   0.000000043463  0.045...
    4     H     0.00000   0.62931   0.88998   0.000000045939  0.045...
    5     H     0.88998  -0.62931   0.00000   0.064883635459 -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.        11.725

                               Min_ID   Min_Time       Max_ID   Max_Time
   Total Computational Time =     0       11.725          0       11.725
   readfile                 =     0        8.987          0        8.987
   truncation               =     0        0.155          0        0.155
   MD_pac                   =     0        0.000          0        0.000
   OutData                  =     0        0.452          0        0.452
   DFT                      =     0        2.130          0        2.130

*** In DFT ***

   Set_OLP_Kin              =     0        0.127          0        0.127
   Set_Nonlocal             =     0        0.104          0        0.104
   Set_ProExpn_VNA          =     0        0.132          0        0.132
   Set_Hamiltonian          =     0        0.741          0        0.741
   Poisson                  =     0        0.351          0        0.351
   Diagonalization          =     0        0.004          0        0.004
   Mixing_DM                =     0        0.000          0        0.000
   Force                    =     0        0.200          0        0.200
   Total_Energy             =     0        0.296          0        0.296
   Set_Aden_Grid            =     0        0.022          0        0.022
   Set_Orbitals_Grid        =     0        0.026          0        0.026
   Set_Density_Grid         =     0        0.120          0        0.120
   RestartFileDFT           =     0        0.003          0        0.003
   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 Molekel [60] and XCrySDen [61]. The visualization will be illustrated in the latter section.


next up previous contents index
Next: Automatic running test Up: User's manual of OpenMX Previous: Tips for installation   Contents   Index
t-ozaki 2013-05-22