[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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