[Pw_forum] problem with saw like potential calculation on Graphene BN system

mohamed sabri majdoub majdoub at gmail.com
Fri Dec 25 05:14:06 CET 2009


Dear PWSCF users,

I want to plot the electric potential difference between 2 configurations of
Graphene on BN system. One in the presence of sawlike potential and one
without.
The calculation without saw like potential did converge. Here a snapshot of
the end of the output :
----------------------------------------------------------------------------------------
 the Fermi energy is     0.5431 ev

!    total energy              =  -876.50130984 Ry
     Harris-Foulkes estimate   =  -876.50131070 Ry
     estimated scf accuracy    <     0.00000098 Ry

     The total energy is the sum of the following terms:

     one-electron contribution =-11420.47672354 Ry
     hartree contribution      =  5787.16715122 Ry
     xc contribution           =  -257.10494832 Ry
     ewald contribution        =  5013.91321080 Ry
     smearing contrib. (-TS)   =     0.00000000 Ry

     convergence has been achieved in   8 iterations

     Forces acting on atoms (Ry/au):

     atom   1 type  1   force =     0.00004991    0.00023487    0.00013847
     atom   2 type  1   force =    -0.00000850    0.00023513    0.00011854
     atom   3 type  1   force =     0.00004362   -0.00023146    0.00012581
     atom   4 type  1   force =     0.00004572    0.00006253    0.00014587
     atom   5 type  1   force =    -0.00004755    0.00008873   -0.00029256
     atom   6 type  1   force =    -0.00007509    0.00026086   -0.00026676
     atom   7 type  1   force =    -0.00001273    0.00026096   -0.00023962
     atom   8 type  1   force =     0.00009831   -0.00024159    0.00014046
     atom   9 type  1   force =     0.00011792   -0.00023203    0.00013144
     atom  10 type  1   force =     0.00016918   -0.00023359    0.00015208
     atom  11 type  1   force =     0.00015964   -0.00005540    0.00016279
     atom  12 type  1   force =     0.00000416    0.00023161    0.00013408
     atom  13 type  1   force =     0.00010353   -0.00005959    0.00014542
     atom  14 type  1   force =     0.00005981    0.00005922    0.00016221
     atom  15 type  1   force =     0.00006131    0.00022791    0.00015555
     atom  16 type  1   force =    -0.00003569   -0.00025848   -0.00024195
     atom  17 type  1   force =    -0.00001015    0.00025569   -0.00025872
     atom  18 type  1   force =    -0.00006646    0.00025363   -0.00028531
     atom  19 type  1   force =    -0.00004477    0.00008710   -0.00030934
     atom  20 type  1   force =    -0.00009101   -0.00027172   -0.00027002
     atom  21 type  1   force =    -0.00014921   -0.00025552   -0.00025789
     atom  22 type  1   force =    -0.00020251   -0.00026290   -0.00028407
     atom  23 type  1   force =    -0.00007504   -0.00008404   -0.00029430
     atom  24 type  1   force =    -0.00016627   -0.00008191   -0.00031347
     atom  25 type  2   force =     0.00051603   -0.00031111    0.00031922
     atom  26 type  2   force =     0.00066795    0.00017652    0.00031399
     atom  27 type  2   force =     0.00052005   -0.00017951    0.00026165
     atom  28 type  2   force =     0.00007573    0.00032942    0.00032267
     atom  29 type  2   force =     0.00020909   -0.00017517    0.00031074
     atom  30 type  2   force =     0.00004563    0.00020570    0.00026529
     atom  31 type  2   force =    -0.00030754   -0.00020609   -0.00000963
     atom  32 type  2   force =    -0.00045660    0.00016711    0.00003189
     atom  33 type  2   force =    -0.00030679   -0.00035495    0.00003254
     atom  34 type  2   force =     0.00046005    0.00018799    0.00031787
     atom  35 type  2   force =     0.00031926   -0.00032862    0.00031348
     atom  36 type  2   force =    -0.00050536   -0.00019000   -0.00000976
     atom  37 type  2   force =     0.00029818   -0.00018842    0.00025352
     atom  38 type  2   force =    -0.00007132    0.00034273    0.00002266
     atom  39 type  2   force =    -0.00021836   -0.00016861    0.00002478
     atom  40 type  2   force =    -0.00004970    0.00020543   -0.00000631
     atom  41 type  2   force =    -0.00068094    0.00015822    0.00002829
     atom  42 type  2   force =    -0.00059726    0.00032077    0.00003622
     atom  43 type  2   force =    -0.00075121   -0.00017896    0.00002988
     atom  44 type  2   force =    -0.00061187    0.00020308   -0.00000938
     atom  45 type  2   force =     0.00061125    0.00019187    0.00025788
     atom  46 type  2   force =    -0.00052473   -0.00032891    0.00002424
     atom  47 type  2   force =     0.00059689    0.00030997    0.00032171
     atom  48 type  2   force =     0.00074993   -0.00018601    0.00031044
     atom  49 type  3   force =    -0.00021629    0.00013637   -0.00002211
     atom  50 type  3   force =    -0.00012927   -0.00004552   -0.00003957
     atom  51 type  3   force =    -0.00014022   -0.00007112   -0.00014479
     atom  52 type  3   force =     0.00003567   -0.00002637   -0.00004582
     atom  53 type  3   force =     0.00001837   -0.00001681   -0.00013369
     atom  54 type  3   force =     0.00014761    0.00017594   -0.00012332
     atom  55 type  3   force =     0.00008922    0.00003087   -0.00005261
     atom  56 type  3   force =     0.00006341    0.00001675   -0.00016291
     atom  57 type  3   force =     0.00019014   -0.00019338   -0.00013489
     atom  58 type  3   force =     0.00025998    0.00019164   -0.00013950
     atom  59 type  3   force =     0.00012773   -0.00000666   -0.00014741
     atom  60 type  3   force =     0.00016931   -0.00001882   -0.00003757
     atom  61 type  3   force =     0.00007519   -0.00019259   -0.00010957
     atom  62 type  3   force =    -0.00005198    0.00001843   -0.00013946
     atom  63 type  3   force =    -0.00003895    0.00002506   -0.00004626
     atom  64 type  3   force =     0.00005318    0.00007782   -0.00012175
     atom  65 type  3   force =     0.00004722    0.00005668   -0.00005446
     atom  66 type  3   force =    -0.00004209   -0.00013570   -0.00006567
     atom  67 type  3   force =    -0.00008733    0.00007755   -0.00012696
     atom  68 type  3   force =    -0.00008666    0.00005408   -0.00003186
     atom  69 type  3   force =    -0.00017176   -0.00013583   -0.00004644
     atom  70 type  3   force =    -0.00014236    0.00012217   -0.00005216
     atom  71 type  3   force =    -0.00004416   -0.00005654   -0.00005829
     atom  72 type  3   force =    -0.00004246   -0.00007653   -0.00012550

     Total force =     0.003351     Total SCF correction =     0.002631
     SCF correction compared to forces is too large, reduce conv_thr

     bfgs converged in  13 scf cycles and   9 bfgs steps

     End of BFGS Geometry Optimization

     Final energy   =    -876.5013098370 Ry

CELL_PARAMETERS (alat)
   8.519800000   0.000000000   0.000000000
   0.000000000   7.376000000   0.000000000
   0.000000000   0.000000000  22.612000000

ATOMIC_POSITIONS (angstrom)
B        0.709950650   8.606569870  11.178365426
B        0.710024516  11.065188378  11.178196366
B        2.839938440   7.377781874  11.178319218
B        0.710003828   6.148025709  11.178218236
B        6.389924656   6.147964138   8.062298249
B        6.390045708   8.606511929   8.062245112
B        6.389941890  11.065116918   8.062198735
B        2.839865957   9.836415504  11.178333535
B        7.099785762   7.377773800  11.178462669
B        7.099706769   9.836400737  11.178246106
B        7.099765193  12.294941516  11.178080685
B        4.969848766  11.065215568  11.178307441
B        2.839916149  12.294955434  11.178236791
B        4.969832821   6.148051719  11.178244158
B        4.969772362   8.606593646  11.178348415
B        4.260019659   7.377879436   8.062200371
B        2.130114662  11.065151536   8.062160115
B        2.130210597   8.606534945   8.062244345
B        2.130093260   6.147990069   8.062272651
B        4.260115164   9.836500060   8.062243629
B        0.000180549   7.377867664   8.062111429
B        0.000292205   9.836490209   8.062287258
B        4.260009665  12.295042075   8.062285335
B        0.000162547  12.295032239   8.062347953
C        2.129922912   6.148297792  14.677832647
C        2.129898772   8.606705408  14.677897532
C        2.129914411  11.065574848  14.677963367
C        0.000068718  12.294705904  14.677868648
C        0.000053160   9.836298362  14.677932899
C        0.000073932   7.377414454  14.677964666
C        0.710227438  11.065590534  14.678750754
C        0.710251453   8.606714593  14.678702525
C        0.710221997   6.148318211  14.678645264
C        6.389834558   8.606693656  14.677924270
C        6.389852550   6.148292755  14.677908278
C        4.970160509  11.065589647  14.678773294
C        6.389855501  11.065564265  14.678043187
C        7.100003923  12.294682839  14.678727191
C        7.100037940   9.836278772  14.678753690
C        7.100008554   7.377395526  14.678751306
C        4.970190603   8.606726322  14.678729152
C        2.840223138  12.294698795  14.678638311
C        2.840251568   9.836294701  14.678705275
C        2.840237809   7.377407509  14.678730745
C        4.259849922   7.377427143  14.677992752
C        4.970158608   6.148316286  14.678700531
C        4.259855357  12.294715913  14.677865997
C        4.259828430   9.836309885  14.677925676
N        0.000002933  12.294522833  11.177753922
N       -0.000114976   9.836059259  11.178044619
N       -0.000089035   7.377375641  11.178758586
N        2.840197587   7.377329909   8.060087341
N        2.840244711   9.836019456   8.060785586
N        2.840070287  12.294499078   8.060835649
N        4.970091529  11.065685303   8.060080269
N        4.970143219   8.607015481   8.060979848
N        4.969965790   6.148541676   8.060878366
N        7.099915340  12.294465358   8.060960245
N        7.100108356   9.835990065   8.060871705
N        7.100041209   7.377303136   8.060015919
N        0.710167780   6.148535741   8.060734949
N        0.710348552   8.607004732   8.060847766
N        0.710306279  11.065688042   8.060132335
N        6.389651783  11.065583541  11.178411967
N        6.389636917   8.606910547  11.178226850
N        6.389756113   6.148451575  11.178145965
N        2.129867804  11.065590918  11.178559562
N        2.129852170   8.606920005  11.178062941
N        2.129961474   6.148457117  11.178029406
N        4.259863960  12.294553821  11.178043095
N        4.259744575   9.836088605  11.178207224
N        4.259762106   7.377399069  11.178563700



     Writing output data file GphBN.save

     PWSCF        :     0d   21h55m CPU time,        1d    0h16m wall time

     init_run     :  1392.70s CPU
     electrons    : 77427.55s CPU (      13 calls,5955.966 s avg)
     update_pot   :     5.78s CPU (      12 calls,   0.481 s avg)
     forces       :    56.54s CPU (      13 calls,   4.349 s avg)

     Called by init_run:
     wfcinit      :  1387.88s CPU
     potinit      :     0.11s CPU

     Called by electrons:
     c_bands      : 73400.15s CPU (     131 calls, 560.307 s avg)
     sum_band     :  3619.03s CPU (     131 calls,  27.626 s avg)
     v_of_rho     :     1.66s CPU (     144 calls,   0.012 s avg)
     mix_rho      :   374.82s CPU (     131 calls,   2.861 s avg)

     Called by c_bands:
     init_us_2    :    16.43s CPU (   13800 calls,   0.001 s avg)
     cegterg      : 73387.98s CPU (    6550 calls,  11.204 s avg)

     Called by *egterg:
     h_psi        : 33317.15s CPU (   28811 calls,   1.156 s avg)
     g_psi        :    12.33s CPU (   22211 calls,   0.001 s avg)
     cdiaghg      : 36250.93s CPU (   28161 calls,   1.287 s avg)

     Called by h_psi:
     add_vuspsi   :   233.57s CPU (   28811 calls,   0.008 s avg)

     General routines
     calbec       :   412.35s CPU (   29461 calls,   0.014 s avg)
     cft3s        : 36152.87s CPU ( 6702434 calls,   0.005 s avg)
     davcio       :     1.12s CPU (   20350 calls,   0.000 s avg)

     Parallel routines
     fft_scatter  : 26097.00s CPU ( 6702434 calls,   0.004 s avg)
---------------------------------------------------------------------------------------------------------------------------------

For the second simulation in the presence of sawlike potential I had to add
the corresponding keyword to the same input file without changing the cutoff
energy,...
Here is the input :

-----------------------------------------------------------------------------------------------------------------------------------

 &control
             title = 'GphBNcapa'
       calculation = 'relax'
            outdir = '/pwscf/pwscftemp/GphBN'
            prefix = 'GphBN'
        pseudo_dir = '/pwscf/input/Gph-BN/pseudopot-C-B-N'
          tprnfor  = .t.
      restart_mode = 'from_scratch'
           tefield = .true.
          dipfield = .true.


 /
 &system
             ibrav = 0,
         celldm(1) = 1.8897261
               nat = 72,
              ntyp = 3,
           ecutwfc = 30.0
       occupations = 'smearing'
          smearing = 'gaussian'
           degauss = 0.003675
              edir = 3            ! This is the direction of applied field
              eamp = 0.002  ! Amplitude of e-field-should be small
           emaxpos = 0.9
            eopreg = 0.2

 /
 &electrons
    mixing_mode = 'local-TF'
    mixing_beta = 0.05
    diagonalization = 'david'
    conv_thr = 1.D-5
 /
 &ions
  trust_radius_ini = 0.10

 /
 &cell

ATOMIC_SPECIES
 B    10.81100   B.pz-vbc.UPF
 C    12.01070   C.pz-vbc.UPF
 N    14.00674   N.pz-vbc.UPF
ATOMIC_POSITIONS angstrom
 B         0.710000        8.607000       11.306000
 B         0.710000       11.066000       11.306000
 B         2.840000        7.377000       11.306000
 B         0.710000        6.148000       11.306000
 B         6.390000        6.148000        8.000000
 B         6.390000        8.607000        8.000000
 B         6.390000       11.066000        8.000000
 B         2.840000        9.836000       11.306000
 B         7.100000        7.377000       11.306000
 B         7.100000        9.836000       11.306000
 B         7.100000       12.295000       11.306000
 B         4.970000       11.066000       11.306000
 B         2.840000       12.295000       11.306000
 B         4.970000        6.148000       11.306000
 B         4.970000        8.607000       11.306000
 B         4.260000        7.377000        8.000000
 B         2.130000       11.066000        8.000000
 B         2.130000        8.607000        8.000000
 B         2.130000        6.148000        8.000000
 B         4.260000        9.836000        8.000000
 B         0.000000        7.377000        8.000000
 B         0.000000        9.836000        8.000000
 B         4.260000       12.295000        8.000000
 B         0.000000       12.295000        8.000000
 C         2.130000        6.148000       14.612000
 C         2.130000        8.607000       14.612000
 C         2.130000       11.066000       14.612000
 C         0.000000       12.295000       14.612000
 C         0.000000        9.836000       14.612000
 C         0.000000        7.377000       14.612000
 C         0.710000       11.066000       14.612000
 C         0.710000        8.607000       14.612000
 C         0.710000        6.148000       14.612000
 C         6.390000        8.607000       14.612000
 C         6.390000        6.148000       14.612000
 C         4.970000       11.066000       14.612000
 C         6.390000       11.066000       14.612000
 C         7.100000       12.295000       14.612000
 C         7.100000        9.836000       14.612000
 C         7.100000        7.377000       14.612000
 C         4.970000        8.607000       14.612000
 C         2.840000       12.295000       14.612000
 C         2.840000        9.836000       14.612000
 C         2.840000        7.377000       14.612000
 C         4.260000        7.377000       14.612000
 C         4.970000        6.148000       14.612000
 C         4.260000       12.295000       14.612000
 C         4.260000        9.836000       14.612000
 N         0.000000       12.295000       11.306000
 N         0.000000        9.836000       11.306000
 N         0.000000        7.377000       11.306000
 N         2.840000        7.377000        8.000000
 N         2.840000        9.836000        8.000000
 N         2.840000       12.295000        8.000000
 N         4.970000       11.066000        8.000000
 N         4.970000        8.607000        8.000000
 N         4.970000        6.148000        8.000000
 N         7.100000       12.295000        8.000000
 N         7.100000        9.836000        8.000000
 N         7.100000        7.377000        8.000000
 N         0.710000        6.148000        8.000000
 N         0.710000        8.607000        8.000000
 N         0.710000       11.066000        8.000000
 N         6.390000       11.066000       11.306000
 N         6.390000        8.607000       11.306000
 N         6.390000        6.148000       11.306000
 N         2.130000       11.066000       11.306000
 N         2.130000        8.607000       11.306000
 N         2.130000        6.148000       11.306000
 N         4.260000       12.295000       11.306000
 N         4.260000        9.836000       11.306000
 N         4.260000        7.377000       11.306000
K_POINTS automatic
10 10 1 1 1 0
CELL_PARAMETERS
8.51980 0.00000 0.00000
0.00000 7.37600 0.00000
0.00000 0.00000 22.6120
-------------------------------------------------------------------------------------------------------------------------------------------

However, as calculation are running I noticed that they are not converging
properly. Too many eigenvalues are not converging. I might be wrong but this
is the output at the current step of the calculation:

-------------------------------------------------------------------------------------------------------------------------------------------
     iteration # 20     ecut=    30.00 Ry     beta=0.05
     Davidson diagonalization with overlap
     ethr =  1.00E-02,  avg # of iterations =  5.1

     negative rho (up, down):  0.590E+03 0.000E+00
     Computed dipoles :
       electron  22.15751  -1.62036**********
       ion     1932.056005018.71955  82.04264
       total   1909.898495020.339906342.69519
        Dipole field [a.u.]:          8.3119

     total cpu time spent up to now is  84515.55 secs

     total energy              = 85279.52921091 Ry
     Harris-Foulkes estimate   = 85603.57307858 Ry
     estimated scf accuracy    <  5376.92087915 Ry

     iteration # 21     ecut=    30.00 Ry     beta=0.05
     Davidson diagonalization with overlap
     ethr =  1.00E-02,  avg # of iterations =  5.1

     negative rho (up, down):  0.528E+03 0.000E+00
     Computed dipoles :
       electron  25.23753  -1.17788**********
       ion     1932.056005018.71955  82.04264
       total   1906.818475019.897436406.06262
        Dipole field [a.u.]:          8.3949

     total cpu time spent up to now is  85450.41 secs

     total energy              = 93168.49098676 Ry
     Harris-Foulkes estimate   = 86319.02586649 Ry
     estimated scf accuracy    <  4531.24319133 Ry

     iteration # 22     ecut=    30.00 Ry     beta=0.05
     Davidson diagonalization with overlap
     ethr =  1.00E-02,  avg # of iterations =  1.0

     negative rho (up, down):  0.381E+03 0.000E+00
     Computed dipoles :
       electron   1.09245  -0.07341**********
       ion     1932.056005018.71955  82.04264
       total   1930.963555018.792966652.29113
        Dipole field [a.u.]:          8.7176

     total cpu time spent up to now is  85733.13 secs

     total energy              = 99660.57900635 Ry
     Harris-Foulkes estimate   = 97379.26494465 Ry
     estimated scf accuracy    <  3775.34065180 Ry

     iteration # 23     ecut=    30.00 Ry     beta=0.05
     Davidson diagonalization with overlap
     c_bands: 23 eigenvalues not converged
     c_bands: 13 eigenvalues not converged
     ethr =  1.00E-02,  avg # of iterations = 11.7

     negative rho (up, down):  0.496E+03 0.000E+00
     Computed dipoles :
       electron -13.76337   0.04670**********
       ion     1932.056005018.71955  82.04264
       total   1945.819375018.672856746.79870
        Dipole field [a.u.]:          8.8414

     total cpu time spent up to now is  87071.95 secs

     total energy              =102491.23930709 Ry
     Harris-Foulkes estimate   =101273.97736718 Ry
     estimated scf accuracy    <  2033.03849554 Ry

     iteration # 24     ecut=    30.00 Ry     beta=0.05
     Davidson diagonalization with overlap
     c_bands: 24 eigenvalues not converged
     c_bands: 17 eigenvalues not converged
     c_bands: 20 eigenvalues not converged
     c_bands: 13 eigenvalues not converged
     c_bands:  7 eigenvalues not converged
     c_bands: 15 eigenvalues not converged
     c_bands: 15 eigenvalues not converged
     c_bands: 16 eigenvalues not converged
     c_bands: 19 eigenvalues not converged
     c_bands: 25 eigenvalues not converged
     c_bands:  8 eigenvalues not converged
     c_bands: 15 eigenvalues not converged
     c_bands: 18 eigenvalues not converged
     c_bands: 23 eigenvalues not converged
     c_bands: 36 eigenvalues not converged
     c_bands:  9 eigenvalues not converged
     c_bands: 10 eigenvalues not converged
     c_bands: 20 eigenvalues not converged
     c_bands: 18 eigenvalues not converged
     c_bands: 21 eigenvalues not converged
     c_bands: 14 eigenvalues not converged
     c_bands: 17 eigenvalues not converged
     c_bands:  5 eigenvalues not converged
     c_bands: 22 eigenvalues not converged
     c_bands:  3 eigenvalues not converged
     c_bands: 14 eigenvalues not converged
     c_bands: 15 eigenvalues not converged
     c_bands: 23 eigenvalues not converged
     c_bands: 15 eigenvalues not converged
     c_bands: 21 eigenvalues not converged
     c_bands: 14 eigenvalues not converged
     c_bands: 12 eigenvalues not converged
     c_bands: 15 eigenvalues not converged
     c_bands: 19 eigenvalues not converged
     c_bands:  6 eigenvalues not converged
     c_bands: 16 eigenvalues not converged
     c_bands: 22 eigenvalues not converged
     c_bands: 21 eigenvalues not converged
     c_bands:  8 eigenvalues not converged
     c_bands: 20 eigenvalues not converged
     c_bands:  3 eigenvalues not converged
     c_bands: 14 eigenvalues not converged
     c_bands: 19 eigenvalues not converged
     c_bands: 29 eigenvalues not converged
     c_bands: 23 eigenvalues not converged
     c_bands: 20 eigenvalues not converged
     ethr =  1.00E-02,  avg # of iterations =106.4

     negative rho (up, down):  0.448E+03 0.000E+00
     Computed dipoles :
       electron -22.55060   0.08222**********
       ion     1932.056005018.71955  82.04264
       total   1954.606605018.637336715.54551
        Dipole field [a.u.]:          8.8005

     total cpu time spent up to now is  98870.22 secs

     total energy              = 88277.44897680 Ry
     Harris-Foulkes estimate   =101483.98218627 Ry
     estimated scf accuracy    <  3047.32661549 Ry

     iteration # 25     ecut=    30.00 Ry     beta=0.05
     Davidson diagonalization with overlap
     c_bands:  5 eigenvalues not converged
     c_bands:  5 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  4 eigenvalues not converged
     c_bands:  4 eigenvalues not converged
     c_bands:  3 eigenvalues not converged
     c_bands:  4 eigenvalues not converged

--------------------------------------------------------------------------------------------------------------

I might need to increase the ecutwfc value to reach convergence. But, if
this is right how can I compare the 2 calcualtions with and without sawlike
potential at different cutoff energies. Do you have any suggestions to reach
convergence in presence of the applied potential. I am planning to use the
postprocessing tool pp.x to extract the total potential and plot the
potential diffrence between the 2 configurations. I beleive I should use
plot_num=1 (total potential V_bare+V_H + V_xc). But, how about plot_num=12
(the electric field potential) is it the external potential or the total
electric response? Or do I need to add both potential 1+12?

Thank you in advance for your suggestions and help on this problem.

Regards,

Mohamed Sabri Majdoub

Department of Mechanical Engineering
University of Houston
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