CO molecule

In this example, how to run a self-consistent field (SCF) calculation of a molecule is described. A CO molecule is placed in a rectangular box of the cell edges of 6, 4, and 4 Bohrs with the cutoff energies of 30.25 and 400 Ry for the wave functions and the augmentation charge, respectively. The Brillouin zone is sampled with the Gamma [(0,0,0)] point.

  • Input file (nfinp_1)
         0     0     0     0     0     0 : I_CTRL(1:6) (DUMMY)
      5.50 20.00     2     2     2       : GMAX GMAXP NTYP NATM NATM2
         1     0                         : NUM_SPACE_GROUP TYPE_BRAVIS_LATTICE
      6.00  4.00  4.00 90.00 90.00 90.00 : A B C ALPHA BETA GAMMA
         1     1     1     1     1     1 : N1 N2 N3 M1 M2 M3
         1     0                         : NCORD, NINV
      0.00  0.00  0.00     1     1     1 : CPS(1,1:3) IWEI IMDTYP ITYP
      2.20  0.00  0.00     1     1     2 : CPS(1,1:3) IWEI IMDTYP ITYP
         6  0.15 12.01     3     1  0.d0 : IATOMN ALFA AMION ILOC IVAN
         8  0.15 16.00     3     1  0.d0 : IATOMN ALFA AMION ILOC IVAN
         0     0     0     0     0       : ICOND INIPOS INIVEL ININOS INIACC
         0     1                         : IPRE IPRI
       200   200     0    57200.00     0 : NMD1 NMD2 ITER_LAST CPUMAX IFSTOP
         3     1                         : WAY_MIX MIX_WHAT
         0     8   0.8                   : STARTING_MIXING KBXMIX ALPHA 
      0.60  0.50  0.60  0.70  1.00       : DTIM1 DTIM2 DTIM3 DTIM4 DTIM_LAST
     30.00     2     1    0.10D-08       : DTIO IMDALG IEXPL EDELTA
     0.001    0.10D+02     0             : WIDTH FORCCR ISTRESS
    ggapbe     1                         : XCTYPE NSPIN
      1.00                               : DESTM
       102                               : NBZTYP
         0     0     0                   : NKX  NKY  NKZ  (DUMMY)
         0     0     0                   : NKX2 NKY2 NKZ2 (DUMMY)
         8                               : NEG
         1                               : NEXTST
         0                               : (DUMMY)
         2                               : IMSD
         0                               : EVALUATE_EKO_DIFF
         0                               : NPDOSAO
         0   0.0                         : SM_N DOPPING
  • Execution (interactive mode)
     $ mpirun -np 6 ./STATE < nfinp_1 > nfout_1
  • Execution (batch mode)
    $ qsub qsub.sh
  • Job script (qsub.sh)
    #$ -S /bin/sh
    #$ -cwd
    #$ -pe fillup 6
    #$ -N CO
    
    #disable OPENMP parallelism
    export OMP_NUM_THREADS=1
    
    # execuable of the STATE code
    ln -fs ../../src/STATE .
    
    # pseudopotential data
    ln -fs ../../gncpp/pot.C_pbe1 fort.37
    ln -fs ../../gncpp/pot.O_pbe1 fort.38
     
    # launch STATE
    $ mpirun -np $NSLOTS ./STATE < nfinp_1 > nfout_1
  • A part of output file (nfout_1) When the program STATE starts, following greeting is printed:
     ***********************************************************************
     *                                                                     *
     *                                                                     *
     *                                                                     *
     *              ******  ********    **    ******** ********            *
     *             ******** ********   ****   ******** ********            *
     *             **          **     **  **     **    **                  *
     *              ***        **    ********    **    ******              *
     *                ***      **   **********   **    ******              *
     *                  **     **  **        **  **    **                  *
     *             ********    ** **          ** **    ********            *
     *              ******     ** VERSION 5.6.5  **    ********            *
     *                               RICS-AIST                             *
     *                           OSAKA UNIVERSITY                          *
     *                                                                     *
     ***********************************************************************
    
    PROGRAM STATE STARTED AT: Feb 13  7:23:59 2019
    When the calculation converges, total energy and its components are printed:
                                       TOTAL CHARGE DENSITY =      9.9999966
    
                         TOTAL ENERGY AND ITS COMPONENTS 
                      TOTAL ENERGY     =         -22.21942426 A.U.
                       FREE ENERGY     =         -22.21942426 A.U.
                    KINETIC ENERGY     =           9.92110961 A.U.
                    HARTREE ENERGY     =           5.12119509 A.U.
                         XC ENERGY     =          -5.89585261 A.U.
                      LOCAL ENERGY     =         -20.23157826 A.U.
                   NONLOCAL ENERGY     =           6.73684719 A.U.
                      EWALD ENERGY     =         -17.87114528 A.U.
                         PC ENERGY     =           0.00000000 A.U.
                   ENTROPIC ENERGY     =           0.00000000 A.U.
    
                                             FERMI ENERGY =       0.43248245
    followed by the eigenvalues and occupations
     NKP=    1  NGP=       287  K=(  0.00000  0.00000  0.00000)  WKP= 1.0000
                                  EIGEN VALUE 
     -0.65555 -0.09532 -0.04691  0.20279  0.20279  0.58836  0.58836  0.79516
                                   OCCUPATION 
      1.00000  1.00000  1.00000  1.00000  1.00000  0.00000  0.00000  0.00000
    and forces acting on atoms
        ATOM              COORDINATES                        FORCES
    MD:   1
    MD:     1  C    0.000000    0.000000    0.000000   0.01851  0.00000 -0.00000
    MD:     2  O    2.200000    0.000000    0.000000  -0.01858  0.00000 -0.00000
    Convergence of the total energy can be monitored by using grep as
    grep ETOT: nfout_1
    ETOT:   1    -16.71058056  0.1671E+02  0.8965E-01
    ETOT:   2    -20.04069483  0.3330E+01  0.6387E-01
    ETOT:   3    -21.45761599  0.1417E+01  0.6830E-01
    ETOT:   4    -22.15338988  0.6958E+00  0.2822E-01
    ETOT:   5    -22.21588778  0.6250E-01  0.7654E-02
    ETOT:   6    -22.21907373  0.3186E-02  0.1845E-02
    ETOT:   7    -22.21941896  0.3452E-03  0.4914E-03
    ETOT:   8    -22.21942378  0.4822E-05  0.1031E-03
    ETOT:   9    -22.21942425  0.4641E-06  0.1578E-04
    ETOT:  10    -22.21942426  0.9876E-08  0.4861E-05
    ETOT:  11    -22.21942426  0.2909E-09  0.2236E-05
    ETOT:  12    -22.21942425  0.6225E-09  0.3018E-05
    ETOT:  13    -22.21942426  0.9965E-09  0.7976E-06
    Finally, the following ascii art is printed
    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
                               _______________________
         __________   _______/______v______v______v___]
        D          | |                                 |
        D   A A    | | Congratulations!                |  C( > < )D
      --  =(^.^)=  | |  The calculation has converged. |    = o =
     |     @@@@@   | |                                 |    (    )~
     /--=O=-+-=O=---+--=O=--+--==O==--+--==O==--+--=O=-+--=O=---=O=-/
      
      
    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
    If SCF does NOT converge, following ascii art is printed.
     Sorry!                                           < < <  
       The calculation has not converged.            < < <   
                                                       < < <  
                                                ___________________
       @ @                                     |                   |
        *    ***                               |                   |XXX
        *   *   *   *                          |   Have a break!   |   X
         ***     ***  ...                      |                   |   X
                                               |                   |   X
                                               |                   |XXX
                   @@                          |___________________|
                    ***** ...                [_______________________]
    In such a case, check the input parameters, in particular, the mixing parameter, and restart the calculation.
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Last-modified: 2019-11-28 (木) 21:45:34 (12d)