[Pw_forum] 18 negative frequencies

Jie Jiang jiejiangnc at gmail.com
Mon Apr 7 17:08:40 CEST 2014


Dear PWscf,

I calculated phonon frequencies in graphene with a vacancy. The graphene
supercell consists of 8x8 graphene unit cells.
The total number of carbon atoms is 127.

First, I did vc-relax. I use Hexagonal Bravais-lattice (ibrav=4). I put
graphene on xy plane and add  10A vaccum along z.
I let cell to relax on xy plane by setting  cell_dofree   = '2Dxy'.

After vc-relax, I get cellfm(1) and celldm(3) from CELL_PARAMETERS, and
relaxed atom coordinates. I then shift the xyz
origin to sit on the second carbon atom. Then I did scf calculation.

After scf, I did phonon at gamma. It is surprise that I get 18 large
negative frequencies,

      omega( 1) =     -37.586127 [THz] =   -1253.738261 [cm-1]
     omega( 2) =     -37.463417 [THz] =   -1249.645075 [cm-1]
     omega( 3) =     -16.009128 [THz] =    -534.007018 [cm-1]
     omega( 4) =     -15.142685 [THz] =    -505.105600 [cm-1]
     omega( 5) =     -13.292746 [THz] =    -443.398278 [cm-1]
     omega( 6) =     -12.913799 [THz] =    -430.757972 [cm-1]
     omega( 7) =     -12.044742 [THz] =    -401.769344 [cm-1]
     omega( 8) =     -11.458667 [THz] =    -382.219978 [cm-1]
     omega( 9) =     -11.159627 [THz] =    -372.245096 [cm-1]
     omega(10) =     -10.124189 [THz] =    -337.706588 [cm-1]
     omega(11) =      -9.750365 [THz] =    -325.237163 [cm-1]
     omega(12) =      -9.181481 [THz] =    -306.261246 [cm-1]
     omega(13) =      -6.553153 [THz] =    -218.589651 [cm-1]
     omega(14) =      -6.308569 [THz] =    -210.431201 [cm-1]
     omega(15) =      -5.502983 [THz] =    -183.559752 [cm-1]
     omega(16) =      -4.371858 [THz] =    -145.829499 [cm-1]
     omega(17) =      -4.365529 [THz] =    -145.618374 [cm-1]
     omega(18) =      -4.313700 [THz] =    -143.889531 [cm-1]
     omega(19) =       0.714302 [THz] =      23.826541 [cm-1]
     omega(20) =       1.865588 [THz] =      62.229321 [cm-1]
     omega(21) =       3.299527 [THz] =     110.060384 [cm-1]
     omega(22) =       7.051360 [THz] =     235.208052 [cm-1]

I do not know what is the problems. Is it due to the shift of coordinate
origin
after vc-relax?

In phonon input, i use ldisp=.true., and nq1=1,nq2=1,nq3=1. I think it is
equivalent
to gamma phonon calculation.

I paste below my vc-relax, scf, and phonon input files.  I really appreciate
if anyone can help me to find out the problems.

Thanks,

Jie Jiang
Applied Physics
Yale University
New Haven



vc-relax input
===
&CONTROL
  calculation  = "vc-relax",
  prefix       = "r"
  pseudo_dir   = "../../../../pseudo/",
  outdir       = "./tmp/",
/
&SYSTEM
  ibrav     = 4,
  celldm(1) = 37.1824314600000,
  nat       = 127,
  ntyp      = 1,
  ecutwfc   = 110.0,
  occupations = "smearing",
  smearing    = "methfessel-paxton",
  degauss     = 0.01,
/
&ELECTRONS
  conv_thr    = 1.D-10,
  mixing_beta = 0.5D0,
/
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
&CELL
cell_dynamics = 'bfgs',
cell_factor   = 1.5D0,
cell_dofree   = '2Dxy',
/
CELL_PARAMETERS {alat}
  0.990791608000000       1.149000000000000E-006  0.000000000000000E+000
 -0.495394809000000       0.858051261000000       0.000000000000000E+000
  0.000000000000000E+000  0.000000000000000E+000  0.488230895000000
ATOMIC_SPECIES
 C     12.0107     C.pz-vbc.UPF
ATOMIC_POSITIONS (bohr)
C         2.302993096        -1.329627620         0.000000357
C         0.000000000         0.000000000         0.000000000
C         0.000005525         2.659262769         0.000000162
C        -2.303512280         3.990772100         0.000000247
C        -2.302102107         6.648781074        -0.000001394
C        -4.601461335         7.977294495        -0.000000259
C        -4.603697557        10.635976850        -0.000001849
C        -6.883119798        11.951997643        -0.000007847
C        -6.988584635        14.594286018        -0.000012083
C        -9.219212665        15.946999659        -0.000021785
C        -9.275242192        18.555041992        -0.000011205
C       -11.510828808        19.967493325        -0.000006219
C       -11.510823248        22.599514671        -0.000002940
C       -13.812141620        23.930769000        -0.000000444
C       -13.812995382        26.586328581         0.000000376
C       -16.115605712        27.914120812         0.000000688
C         6.909113358        -1.330240955         0.000000838
C         4.605190015         0.000641170         0.000000442
C         4.606205594         2.659396340        -0.000000157
C         2.303147639         3.987881238        -0.000000028
C         2.302530331         6.648577995        -0.000001650
C         0.003057052         7.976175261        -0.000001078
C         0.000038241        10.636291447        -0.000001394
C        -2.300171427        11.963331863        -0.000000259
C        -2.332541703        14.617087579         0.000000450
C        -4.648562170        15.946759948        -0.000003096
C        -4.632043287        18.595312914        -0.000002096
C        -6.933994055        19.905312372        -0.000004180
C        -6.927515885        22.575863141        -0.000001617
C        -9.209553912        23.930765533        -0.000001276
C        -9.208692857        26.586313704        -0.000001395
C       -11.510863430        27.918976326         0.000000372
C        11.515263064        -1.329642430         0.000000503
C         9.213040030         0.000648709        -0.000001181
C         9.212019097         2.659395551        -0.000001487
C         6.909119307         3.988971113        -0.000002267
C         6.909111662         6.648133900        -0.000000157
C         4.607077332         7.978391770        -0.000000028
C         4.606127303        10.637373285         0.000000162
C         2.301243813        11.966517180         0.000000247
C         2.291005029        14.624693473         0.000000260
C        -0.020806079        15.950567763        -0.000000842
C        -0.013325891        18.608364481        -0.000001474
C        -2.317383242        19.931667411        -0.000001500
C        -2.311371442        22.588698180        -0.000000093
C        -4.616826207        23.911121728         0.000000239
C        -4.609163202        26.576144230        -0.000000255
C        -6.906092724        27.914120348         0.000000293
C        16.121094313        -1.329548130         0.000000476
C        13.818246794        -0.000002747         0.000000510
C        13.818260354         2.659253132         0.000000503
C        11.515079234         3.987884818        -0.000001181
C        11.515703839         6.648582299         0.000000838
C         9.211160756         7.978391002         0.000000442
C         9.212112545        10.637379117         0.000000357
C         6.909121018        11.967009455         0.000000000
C         6.909137448        14.626101312         0.000000251
C         4.600672362        15.953351247        -0.000000050
C         4.602360204        18.611306698         0.000000493
C         2.295292721        19.937879290        -0.000001710
C         2.298490363        22.596639760         0.000000521
C        -0.005661715        23.923252818         0.000000038
C        -0.000982215        26.584525808         0.000000525
C        -2.303681902        27.912056704         0.000000520
C        20.725777253        -1.324409636         0.000000525
C        18.424748247         0.006014964         0.000000520
C        18.428945418         2.670570198        -0.000000255
C        16.121755667         3.990775079         0.000000293
C        16.120373568         6.648782233        -0.000001395
C        13.815164914         7.976182745         0.000000372
C        13.818209422        10.636304072         0.000000376
C        11.516998772        11.966520621         0.000000688
C        11.527269729        14.624710884         0.000000474
C         9.217593156        15.953358113         0.000000398
C         9.215921791        18.611321236         0.000000143
C         6.909127428        19.939428692         0.000000292
C         6.909143393        22.599224794        -0.000001609
C         4.605039542        23.928339241         0.000000164
C         4.606046805        26.588309792         0.000000280
C         2.302586618        27.918208899         0.000000178
C        25.329135212        -1.321861903         0.000000521
C        23.028174883         0.010279424         0.000000038
C        23.031081920         2.674353563        -0.000000093
C        20.733098467         4.009717806         0.000000239
C        20.734125167         6.678456684        -0.000001617
C        18.419722581         7.977302014        -0.000001276
C        18.421988661        10.635977853        -0.000002940
C        16.118425725        11.963344484        -0.000000444
C        16.150832966        14.617092045        -0.000000782
C        13.839101621        15.950585238        -0.000000618
C        13.831615713        18.608383868        -0.000000285
C        11.522999004        19.937898904        -0.000000332
C        11.519805456        22.596662128        -0.000001325
C         9.213240862        23.928353565        -0.000001404
C         9.212255090        26.588318515        -0.000001609
C         6.909152607        27.919167382         0.000000164
C        29.932480852        -1.324398805         0.000000493
C        27.630097865         0.010287571        -0.000001710
C        27.627185840         2.674360964        -0.000001474
C        25.329139528         4.008075319        -0.000001500
C        25.329130131         6.680800591        -0.000002096
C        23.043658254         8.019342328        -0.000004180
C        23.042406318        10.722150584        -0.000011205
C        20.701390594        11.951993341        -0.000006219
C        20.806941045        14.594264007        -0.000010668
C        18.466860453        15.946772942        -0.000003806
C        18.450351909        18.595322022        -0.000002667
C        16.135692435        19.931687041        -0.000002960
C        16.129671921        22.588721224        -0.000000285
C        13.823966088        23.923278046        -0.000000332
C        13.819281124        26.584547978         0.000000143
C        11.515705465        27.918230392         0.000000292
C        34.537169624        -1.329517428         0.000000251
C        32.233501238         0.006040635        -0.000000050
C        32.229322639         2.670593730         0.000000260
C        29.925172586         4.009737356        -0.000000842
C        29.924136170         6.678492848         0.000000450
C        27.614592204         8.019382847        -0.000003096
C        27.615861435        10.722231414        -0.000012083
C        25.329059361        11.977648756        -0.000021785
C        23.037668400        15.946842114        -0.000025349
C        23.093675405        18.554991348        -0.000010668
C        20.752324331        19.905299743        -0.000003806
C        20.745851705        22.575872454        -0.000000782
C        18.435143371        23.911137552        -0.000000618
C        18.427471979        26.576173499         0.000000474
C        16.121987757        27.912082095         0.000000398
K_POINTS {automatic}
 3 3 1 0 0 0
===

scf input
====
&CONTROL
  calculation  = "scf",
  prefix       = "r"
  pseudo_dir   = "../../../../pseudo/",
  outdir       = "./tmp/",
  wf_collect    = .true.
/
&SYSTEM
  ibrav     = 4,
  celldm(1) = 36.840041055603187,
  celldm(3) = 0.49276850051802218,
  nat       = 127,
  ntyp      = 1,
  ecutwfc   = 110.0,
  occupations = "smearing",
  smearing    = "methfessel-paxton",
  degauss     = 0.01,
/
&ELECTRONS
  conv_thr    = 1.D-10,
  mixing_beta = 0.5D0,
/
ATOMIC_SPECIES
 C     12.0107     C.pz-vbc.UPF
ATOMIC_POSITIONS (bohr)
C         2.302993096        -1.329627620         0.000000357
C         0.000000000         0.000000000         0.000000000
C         0.000005525         2.659262769         0.000000162
C        -2.303512280         3.990772100         0.000000247
C        -2.302102107         6.648781074        -0.000001394
C        -4.601461335         7.977294495        -0.000000259
C        -4.603697557        10.635976850        -0.000001849
C        -6.883119798        11.951997643        -0.000007847
C        -6.988584635        14.594286018        -0.000012083
C        -9.219212665        15.946999659        -0.000021785
C        -9.275242192        18.555041992        -0.000011205
C       -11.510828808        19.967493325        -0.000006219
C       -11.510823248        22.599514671        -0.000002940
C       -13.812141620        23.930769000        -0.000000444
C       -13.812995382        26.586328581         0.000000376
C       -16.115605712        27.914120812         0.000000688
C         6.909113358        -1.330240955         0.000000838
C         4.605190015         0.000641170         0.000000442
C         4.606205594         2.659396340        -0.000000157
C         2.303147639         3.987881238        -0.000000028
C         2.302530331         6.648577995        -0.000001650
C         0.003057052         7.976175261        -0.000001078
C         0.000038241        10.636291447        -0.000001394
C        -2.300171427        11.963331863        -0.000000259
C        -2.332541703        14.617087579         0.000000450
C        -4.648562170        15.946759948        -0.000003096
C        -4.632043287        18.595312914        -0.000002096
C        -6.933994055        19.905312372        -0.000004180
C        -6.927515885        22.575863141        -0.000001617
C        -9.209553912        23.930765533        -0.000001276
C        -9.208692857        26.586313704        -0.000001395
C       -11.510863430        27.918976326         0.000000372
C        11.515263064        -1.329642430         0.000000503
C         9.213040030         0.000648709        -0.000001181
C         9.212019097         2.659395551        -0.000001487
C         6.909119307         3.988971113        -0.000002267
C         6.909111662         6.648133900        -0.000000157
C         4.607077332         7.978391770        -0.000000028
C         4.606127303        10.637373285         0.000000162
C         2.301243813        11.966517180         0.000000247
C         2.291005029        14.624693473         0.000000260
C        -0.020806079        15.950567763        -0.000000842
C        -0.013325891        18.608364481        -0.000001474
C        -2.317383242        19.931667411        -0.000001500
C        -2.311371442        22.588698180        -0.000000093
C        -4.616826207        23.911121728         0.000000239
C        -4.609163202        26.576144230        -0.000000255
C        -6.906092724        27.914120348         0.000000293
C        16.121094313        -1.329548130         0.000000476
C        13.818246794        -0.000002747         0.000000510
C        13.818260354         2.659253132         0.000000503
C        11.515079234         3.987884818        -0.000001181
C        11.515703839         6.648582299         0.000000838
C         9.211160756         7.978391002         0.000000442
C         9.212112545        10.637379117         0.000000357
C         6.909121018        11.967009455         0.000000000
C         6.909137448        14.626101312         0.000000251
C         4.600672362        15.953351247        -0.000000050
C         4.602360204        18.611306698         0.000000493
C         2.295292721        19.937879290        -0.000001710
C         2.298490363        22.596639760         0.000000521
C        -0.005661715        23.923252818         0.000000038
C        -0.000982215        26.584525808         0.000000525
C        -2.303681902        27.912056704         0.000000520
C        20.725777253        -1.324409636         0.000000525
C        18.424748247         0.006014964         0.000000520
C        18.428945418         2.670570198        -0.000000255
C        16.121755667         3.990775079         0.000000293
C        16.120373568         6.648782233        -0.000001395
C        13.815164914         7.976182745         0.000000372
C        13.818209422        10.636304072         0.000000376
C        11.516998772        11.966520621         0.000000688
C        11.527269729        14.624710884         0.000000474
C         9.217593156        15.953358113         0.000000398
C         9.215921791        18.611321236         0.000000143
C         6.909127428        19.939428692         0.000000292
C         6.909143393        22.599224794        -0.000001609
C         4.605039542        23.928339241         0.000000164
C         4.606046805        26.588309792         0.000000280
C         2.302586618        27.918208899         0.000000178
C        25.329135212        -1.321861903         0.000000521
C        23.028174883         0.010279424         0.000000038
C        23.031081920         2.674353563        -0.000000093
C        20.733098467         4.009717806         0.000000239
C        20.734125167         6.678456684        -0.000001617
C        18.419722581         7.977302014        -0.000001276
C        18.421988661        10.635977853        -0.000002940
C        16.118425725        11.963344484        -0.000000444
C        16.150832966        14.617092045        -0.000000782
C        13.839101621        15.950585238        -0.000000618
C        13.831615713        18.608383868        -0.000000285
C        11.522999004        19.937898904        -0.000000332
C        11.519805456        22.596662128        -0.000001325
C         9.213240862        23.928353565        -0.000001404
C         9.212255090        26.588318515        -0.000001609
C         6.909152607        27.919167382         0.000000164
C        29.932480852        -1.324398805         0.000000493
C        27.630097865         0.010287571        -0.000001710
C        27.627185840         2.674360964        -0.000001474
C        25.329139528         4.008075319        -0.000001500
C        25.329130131         6.680800591        -0.000002096
C        23.043658254         8.019342328        -0.000004180
C        23.042406318        10.722150584        -0.000011205
C        20.701390594        11.951993341        -0.000006219
C        20.806941045        14.594264007        -0.000010668
C        18.466860453        15.946772942        -0.000003806
C        18.450351909        18.595322022        -0.000002667
C        16.135692435        19.931687041        -0.000002960
C        16.129671921        22.588721224        -0.000000285
C        13.823966088        23.923278046        -0.000000332
C        13.819281124        26.584547978         0.000000143
C        11.515705465        27.918230392         0.000000292
C        34.537169624        -1.329517428         0.000000251
C        32.233501238         0.006040635        -0.000000050
C        32.229322639         2.670593730         0.000000260
C        29.925172586         4.009737356        -0.000000842
C        29.924136170         6.678492848         0.000000450
C        27.614592204         8.019382847        -0.000003096
C        27.615861435        10.722231414        -0.000012083
C        25.329059361        11.977648756        -0.000021785
C        23.037668400        15.946842114        -0.000025349
C        23.093675405        18.554991348        -0.000010668
C        20.752324331        19.905299743        -0.000003806
C        20.745851705        22.575872454        -0.000000782
C        18.435143371        23.911137552        -0.000000618
C        18.427471979        26.576173499         0.000000474
C        16.121987757        27.912082095         0.000000398
K_POINTS {automatic}
 3 3 1 0 0 0
====

phonon input
===
phonons on a grid
&inputph
prefix='r'
amass(1)=12.0107
ldisp=.true.
fildyn='dyn',
nq1=1,
nq2=1,
nq3=1,
tr2_ph=1.0d-12,
outdir='./tmp'
/
====
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