<div dir="ltr"><div><div><div><div>Dear PWscf,<br><br></div>I calculated phonon frequencies in graphene with a vacancy. The graphene supercell consists of 8x8 graphene unit cells.<br></div>The total number of carbon atoms is 127.<br>
<br></div>First, I did vc-relax. I use Hexagonal Bravais-lattice (ibrav=4). I put graphene on xy plane and add 10A vaccum along z.<br></div>I let cell to relax on xy plane by setting cell_dofree = '2Dxy'. <br>
<div><div><div><div><br></div><div>After vc-relax, I get cellfm(1) and celldm(3) from CELL_PARAMETERS, and relaxed atom coordinates. I then shift the xyz<br></div><div>origin to sit on the second carbon atom. Then I did scf calculation.<br>
<br></div><div>After scf, I did phonon at gamma. It is surprise that I get 18 large negative frequencies,<br><br> omega( 1) = -37.586127 [THz] = -1253.738261 [cm-1]<br> omega( 2) = -37.463417 [THz] = -1249.645075 [cm-1]<br>
omega( 3) = -16.009128 [THz] = -534.007018 [cm-1]<br> omega( 4) = -15.142685 [THz] = -505.105600 [cm-1]<br> omega( 5) = -13.292746 [THz] = -443.398278 [cm-1]<br> omega( 6) = -12.913799 [THz] = -430.757972 [cm-1]<br>
omega( 7) = -12.044742 [THz] = -401.769344 [cm-1]<br> omega( 8) = -11.458667 [THz] = -382.219978 [cm-1]<br> omega( 9) = -11.159627 [THz] = -372.245096 [cm-1]<br> omega(10) = -10.124189 [THz] = -337.706588 [cm-1]<br>
omega(11) = -9.750365 [THz] = -325.237163 [cm-1]<br> omega(12) = -9.181481 [THz] = -306.261246 [cm-1]<br> omega(13) = -6.553153 [THz] = -218.589651 [cm-1]<br> omega(14) = -6.308569 [THz] = -210.431201 [cm-1]<br>
omega(15) = -5.502983 [THz] = -183.559752 [cm-1]<br> omega(16) = -4.371858 [THz] = -145.829499 [cm-1]<br> omega(17) = -4.365529 [THz] = -145.618374 [cm-1]<br> omega(18) = -4.313700 [THz] = -143.889531 [cm-1]<br>
omega(19) = 0.714302 [THz] = 23.826541 [cm-1]<br> omega(20) = 1.865588 [THz] = 62.229321 [cm-1]<br> omega(21) = 3.299527 [THz] = 110.060384 [cm-1]<br> omega(22) = 7.051360 [THz] = 235.208052 [cm-1]<br>
<br></div><div>I do not know what is the problems. Is it due to the shift of coordinate origin<br></div><div>after vc-relax? <br><br>In phonon input, i use ldisp=.true., and nq1=1,nq2=1,nq3=1. I think it is equivalent <br>
to gamma phonon calculation.<br></div><div><br></div><div>I paste below my vc-relax, scf, and phonon input files. I really appreciate<br></div><div>if anyone can help me to find out the problems.<br><br></div><div>Thanks,<br>
<br></div><div>Jie Jiang<br></div><div>Applied Physics<br></div><div>Yale University<br></div><div>New Haven<br></div><div><br><br><br></div><div>vc-relax input<br>===<br>&CONTROL<br> calculation = "vc-relax",<br>
prefix = "r"<br> pseudo_dir = "../../../../pseudo/",<br> outdir = "./tmp/",<br>/<br>&SYSTEM<br> ibrav = 4,<br> celldm(1) = 37.1824314600000,<br> nat = 127,<br>
ntyp = 1,<br> ecutwfc = 110.0,<br> occupations = "smearing",<br> smearing = "methfessel-paxton",<br> degauss = 0.01,<br>/<br>&ELECTRONS<br> conv_thr = 1.D-10,<br> mixing_beta = 0.5D0,<br>
/<br>&IONS<br> pot_extrapolation = "second_order",<br> wfc_extrapolation = "second_order",<br>/<br>&CELL<br>cell_dynamics = 'bfgs',<br>cell_factor = 1.5D0,<br>cell_dofree = '2Dxy',<br>
/<br>CELL_PARAMETERS {alat}<br> 0.990791608000000 1.149000000000000E-006 0.000000000000000E+000<br> -0.495394809000000 0.858051261000000 0.000000000000000E+000<br> 0.000000000000000E+000 0.000000000000000E+000 0.488230895000000<br>
ATOMIC_SPECIES<br> C 12.0107 C.pz-vbc.UPF <br>ATOMIC_POSITIONS (bohr)<br>C 2.302993096 -1.329627620 0.000000357<br>C 0.000000000 0.000000000 0.000000000<br>C 0.000005525 2.659262769 0.000000162<br>
C -2.303512280 3.990772100 0.000000247<br>C -2.302102107 6.648781074 -0.000001394<br>C -4.601461335 7.977294495 -0.000000259<br>C -4.603697557 10.635976850 -0.000001849<br>
C -6.883119798 11.951997643 -0.000007847<br>C -6.988584635 14.594286018 -0.000012083<br>C -9.219212665 15.946999659 -0.000021785<br>C -9.275242192 18.555041992 -0.000011205<br>
C -11.510828808 19.967493325 -0.000006219<br>C -11.510823248 22.599514671 -0.000002940<br>C -13.812141620 23.930769000 -0.000000444<br>C -13.812995382 26.586328581 0.000000376<br>
C -16.115605712 27.914120812 0.000000688<br>C 6.909113358 -1.330240955 0.000000838<br>C 4.605190015 0.000641170 0.000000442<br>C 4.606205594 2.659396340 -0.000000157<br>
C 2.303147639 3.987881238 -0.000000028<br>C 2.302530331 6.648577995 -0.000001650<br>C 0.003057052 7.976175261 -0.000001078<br>C 0.000038241 10.636291447 -0.000001394<br>
C -2.300171427 11.963331863 -0.000000259<br>C -2.332541703 14.617087579 0.000000450<br>C -4.648562170 15.946759948 -0.000003096<br>C -4.632043287 18.595312914 -0.000002096<br>
C -6.933994055 19.905312372 -0.000004180<br>C -6.927515885 22.575863141 -0.000001617<br>C -9.209553912 23.930765533 -0.000001276<br>C -9.208692857 26.586313704 -0.000001395<br>
C -11.510863430 27.918976326 0.000000372<br>C 11.515263064 -1.329642430 0.000000503<br>C 9.213040030 0.000648709 -0.000001181<br>C 9.212019097 2.659395551 -0.000001487<br>
C 6.909119307 3.988971113 -0.000002267<br>C 6.909111662 6.648133900 -0.000000157<br>C 4.607077332 7.978391770 -0.000000028<br>C 4.606127303 10.637373285 0.000000162<br>
C 2.301243813 11.966517180 0.000000247<br>C 2.291005029 14.624693473 0.000000260<br>C -0.020806079 15.950567763 -0.000000842<br>C -0.013325891 18.608364481 -0.000001474<br>
C -2.317383242 19.931667411 -0.000001500<br>C -2.311371442 22.588698180 -0.000000093<br>C -4.616826207 23.911121728 0.000000239<br>C -4.609163202 26.576144230 -0.000000255<br>
C -6.906092724 27.914120348 0.000000293<br>C 16.121094313 -1.329548130 0.000000476<br>C 13.818246794 -0.000002747 0.000000510<br>C 13.818260354 2.659253132 0.000000503<br>
C 11.515079234 3.987884818 -0.000001181<br>C 11.515703839 6.648582299 0.000000838<br>C 9.211160756 7.978391002 0.000000442<br>C 9.212112545 10.637379117 0.000000357<br>
C 6.909121018 11.967009455 0.000000000<br>C 6.909137448 14.626101312 0.000000251<br>C 4.600672362 15.953351247 -0.000000050<br>C 4.602360204 18.611306698 0.000000493<br>
C 2.295292721 19.937879290 -0.000001710<br>C 2.298490363 22.596639760 0.000000521<br>C -0.005661715 23.923252818 0.000000038<br>C -0.000982215 26.584525808 0.000000525<br>
C -2.303681902 27.912056704 0.000000520<br>C 20.725777253 -1.324409636 0.000000525<br>C 18.424748247 0.006014964 0.000000520<br>C 18.428945418 2.670570198 -0.000000255<br>
C 16.121755667 3.990775079 0.000000293<br>C 16.120373568 6.648782233 -0.000001395<br>C 13.815164914 7.976182745 0.000000372<br>C 13.818209422 10.636304072 0.000000376<br>
C 11.516998772 11.966520621 0.000000688<br>C 11.527269729 14.624710884 0.000000474<br>C 9.217593156 15.953358113 0.000000398<br>C 9.215921791 18.611321236 0.000000143<br>
C 6.909127428 19.939428692 0.000000292<br>C 6.909143393 22.599224794 -0.000001609<br>C 4.605039542 23.928339241 0.000000164<br>C 4.606046805 26.588309792 0.000000280<br>
C 2.302586618 27.918208899 0.000000178<br>C 25.329135212 -1.321861903 0.000000521<br>C 23.028174883 0.010279424 0.000000038<br>C 23.031081920 2.674353563 -0.000000093<br>
C 20.733098467 4.009717806 0.000000239<br>C 20.734125167 6.678456684 -0.000001617<br>C 18.419722581 7.977302014 -0.000001276<br>C 18.421988661 10.635977853 -0.000002940<br>
C 16.118425725 11.963344484 -0.000000444<br>C 16.150832966 14.617092045 -0.000000782<br>C 13.839101621 15.950585238 -0.000000618<br>C 13.831615713 18.608383868 -0.000000285<br>
C 11.522999004 19.937898904 -0.000000332<br>C 11.519805456 22.596662128 -0.000001325<br>C 9.213240862 23.928353565 -0.000001404<br>C 9.212255090 26.588318515 -0.000001609<br>
C 6.909152607 27.919167382 0.000000164<br>C 29.932480852 -1.324398805 0.000000493<br>C 27.630097865 0.010287571 -0.000001710<br>C 27.627185840 2.674360964 -0.000001474<br>
C 25.329139528 4.008075319 -0.000001500<br>C 25.329130131 6.680800591 -0.000002096<br>C 23.043658254 8.019342328 -0.000004180<br>C 23.042406318 10.722150584 -0.000011205<br>
C 20.701390594 11.951993341 -0.000006219<br>C 20.806941045 14.594264007 -0.000010668<br>C 18.466860453 15.946772942 -0.000003806<br>C 18.450351909 18.595322022 -0.000002667<br>
C 16.135692435 19.931687041 -0.000002960<br>C 16.129671921 22.588721224 -0.000000285<br>C 13.823966088 23.923278046 -0.000000332<br>C 13.819281124 26.584547978 0.000000143<br>
C 11.515705465 27.918230392 0.000000292<br>C 34.537169624 -1.329517428 0.000000251<br>C 32.233501238 0.006040635 -0.000000050<br>C 32.229322639 2.670593730 0.000000260<br>
C 29.925172586 4.009737356 -0.000000842<br>C 29.924136170 6.678492848 0.000000450<br>C 27.614592204 8.019382847 -0.000003096<br>C 27.615861435 10.722231414 -0.000012083<br>
C 25.329059361 11.977648756 -0.000021785<br>C 23.037668400 15.946842114 -0.000025349<br>C 23.093675405 18.554991348 -0.000010668<br>C 20.752324331 19.905299743 -0.000003806<br>
C 20.745851705 22.575872454 -0.000000782<br>C 18.435143371 23.911137552 -0.000000618<br>C 18.427471979 26.576173499 0.000000474<br>C 16.121987757 27.912082095 0.000000398<br>
K_POINTS {automatic}<br> 3 3 1 0 0 0<br>===<br></div><div><br></div><div>scf input<br>====<br>&CONTROL<br> calculation = "scf",<br> prefix = "r"<br> pseudo_dir = "../../../../pseudo/",<br>
outdir = "./tmp/",<br> wf_collect = .true.<br>/<br>&SYSTEM<br> ibrav = 4,<br> celldm(1) = 36.840041055603187,<br> celldm(3) = 0.49276850051802218,<br> nat = 127,<br> ntyp = 1,<br>
ecutwfc = 110.0,<br> occupations = "smearing",<br> smearing = "methfessel-paxton",<br> degauss = 0.01,<br>/<br>&ELECTRONS<br> conv_thr = 1.D-10,<br> mixing_beta = 0.5D0,<br>/<br>
ATOMIC_SPECIES<br> C 12.0107 C.pz-vbc.UPF <br>ATOMIC_POSITIONS (bohr)<br>C 2.302993096 -1.329627620 0.000000357<br>C 0.000000000 0.000000000 0.000000000<br>C 0.000005525 2.659262769 0.000000162<br>
C -2.303512280 3.990772100 0.000000247<br>C -2.302102107 6.648781074 -0.000001394<br>C -4.601461335 7.977294495 -0.000000259<br>C -4.603697557 10.635976850 -0.000001849<br>
C -6.883119798 11.951997643 -0.000007847<br>C -6.988584635 14.594286018 -0.000012083<br>C -9.219212665 15.946999659 -0.000021785<br>C -9.275242192 18.555041992 -0.000011205<br>
C -11.510828808 19.967493325 -0.000006219<br>C -11.510823248 22.599514671 -0.000002940<br>C -13.812141620 23.930769000 -0.000000444<br>C -13.812995382 26.586328581 0.000000376<br>
C -16.115605712 27.914120812 0.000000688<br>C 6.909113358 -1.330240955 0.000000838<br>C 4.605190015 0.000641170 0.000000442<br>C 4.606205594 2.659396340 -0.000000157<br>
C 2.303147639 3.987881238 -0.000000028<br>C 2.302530331 6.648577995 -0.000001650<br>C 0.003057052 7.976175261 -0.000001078<br>C 0.000038241 10.636291447 -0.000001394<br>
C -2.300171427 11.963331863 -0.000000259<br>C -2.332541703 14.617087579 0.000000450<br>C -4.648562170 15.946759948 -0.000003096<br>C -4.632043287 18.595312914 -0.000002096<br>
C -6.933994055 19.905312372 -0.000004180<br>C -6.927515885 22.575863141 -0.000001617<br>C -9.209553912 23.930765533 -0.000001276<br>C -9.208692857 26.586313704 -0.000001395<br>
C -11.510863430 27.918976326 0.000000372<br>C 11.515263064 -1.329642430 0.000000503<br>C 9.213040030 0.000648709 -0.000001181<br>C 9.212019097 2.659395551 -0.000001487<br>
C 6.909119307 3.988971113 -0.000002267<br>C 6.909111662 6.648133900 -0.000000157<br>C 4.607077332 7.978391770 -0.000000028<br>C 4.606127303 10.637373285 0.000000162<br>
C 2.301243813 11.966517180 0.000000247<br>C 2.291005029 14.624693473 0.000000260<br>C -0.020806079 15.950567763 -0.000000842<br>C -0.013325891 18.608364481 -0.000001474<br>
C -2.317383242 19.931667411 -0.000001500<br>C -2.311371442 22.588698180 -0.000000093<br>C -4.616826207 23.911121728 0.000000239<br>C -4.609163202 26.576144230 -0.000000255<br>
C -6.906092724 27.914120348 0.000000293<br>C 16.121094313 -1.329548130 0.000000476<br>C 13.818246794 -0.000002747 0.000000510<br>C 13.818260354 2.659253132 0.000000503<br>
C 11.515079234 3.987884818 -0.000001181<br>C 11.515703839 6.648582299 0.000000838<br>C 9.211160756 7.978391002 0.000000442<br>C 9.212112545 10.637379117 0.000000357<br>
C 6.909121018 11.967009455 0.000000000<br>C 6.909137448 14.626101312 0.000000251<br>C 4.600672362 15.953351247 -0.000000050<br>C 4.602360204 18.611306698 0.000000493<br>
C 2.295292721 19.937879290 -0.000001710<br>C 2.298490363 22.596639760 0.000000521<br>C -0.005661715 23.923252818 0.000000038<br>C -0.000982215 26.584525808 0.000000525<br>
C -2.303681902 27.912056704 0.000000520<br>C 20.725777253 -1.324409636 0.000000525<br>C 18.424748247 0.006014964 0.000000520<br>C 18.428945418 2.670570198 -0.000000255<br>
C 16.121755667 3.990775079 0.000000293<br>C 16.120373568 6.648782233 -0.000001395<br>C 13.815164914 7.976182745 0.000000372<br>C 13.818209422 10.636304072 0.000000376<br>
C 11.516998772 11.966520621 0.000000688<br>C 11.527269729 14.624710884 0.000000474<br>C 9.217593156 15.953358113 0.000000398<br>C 9.215921791 18.611321236 0.000000143<br>
C 6.909127428 19.939428692 0.000000292<br>C 6.909143393 22.599224794 -0.000001609<br>C 4.605039542 23.928339241 0.000000164<br>C 4.606046805 26.588309792 0.000000280<br>
C 2.302586618 27.918208899 0.000000178<br>C 25.329135212 -1.321861903 0.000000521<br>C 23.028174883 0.010279424 0.000000038<br>C 23.031081920 2.674353563 -0.000000093<br>
C 20.733098467 4.009717806 0.000000239<br>C 20.734125167 6.678456684 -0.000001617<br>C 18.419722581 7.977302014 -0.000001276<br>C 18.421988661 10.635977853 -0.000002940<br>
C 16.118425725 11.963344484 -0.000000444<br>C 16.150832966 14.617092045 -0.000000782<br>C 13.839101621 15.950585238 -0.000000618<br>C 13.831615713 18.608383868 -0.000000285<br>
C 11.522999004 19.937898904 -0.000000332<br>C 11.519805456 22.596662128 -0.000001325<br>C 9.213240862 23.928353565 -0.000001404<br>C 9.212255090 26.588318515 -0.000001609<br>
C 6.909152607 27.919167382 0.000000164<br>C 29.932480852 -1.324398805 0.000000493<br>C 27.630097865 0.010287571 -0.000001710<br>C 27.627185840 2.674360964 -0.000001474<br>
C 25.329139528 4.008075319 -0.000001500<br>C 25.329130131 6.680800591 -0.000002096<br>C 23.043658254 8.019342328 -0.000004180<br>C 23.042406318 10.722150584 -0.000011205<br>
C 20.701390594 11.951993341 -0.000006219<br>C 20.806941045 14.594264007 -0.000010668<br>C 18.466860453 15.946772942 -0.000003806<br>C 18.450351909 18.595322022 -0.000002667<br>
C 16.135692435 19.931687041 -0.000002960<br>C 16.129671921 22.588721224 -0.000000285<br>C 13.823966088 23.923278046 -0.000000332<br>C 13.819281124 26.584547978 0.000000143<br>
C 11.515705465 27.918230392 0.000000292<br>C 34.537169624 -1.329517428 0.000000251<br>C 32.233501238 0.006040635 -0.000000050<br>C 32.229322639 2.670593730 0.000000260<br>
C 29.925172586 4.009737356 -0.000000842<br>C 29.924136170 6.678492848 0.000000450<br>C 27.614592204 8.019382847 -0.000003096<br>C 27.615861435 10.722231414 -0.000012083<br>
C 25.329059361 11.977648756 -0.000021785<br>C 23.037668400 15.946842114 -0.000025349<br>C 23.093675405 18.554991348 -0.000010668<br>C 20.752324331 19.905299743 -0.000003806<br>
C 20.745851705 22.575872454 -0.000000782<br>C 18.435143371 23.911137552 -0.000000618<br>C 18.427471979 26.576173499 0.000000474<br>C 16.121987757 27.912082095 0.000000398<br>
K_POINTS {automatic}<br> 3 3 1 0 0 0<br>====<br><br></div><div>phonon input<br>===<br>phonons on a grid<br>&inputph<br>prefix='r'<br>amass(1)=12.0107<br>ldisp=.true.<br>fildyn='dyn',<br>nq1=1,<br>nq2=1,<br>
nq3=1,<br>tr2_ph=1.0d-12,<br>outdir='./tmp'<br>/<br>====<br></div><div><br></div><div><br><br><br> <br></div><div><br><br></div><div> <br><br><br></div></div></div></div></div>