problem with phonon calculations

Phonons, DFPT, electron-phonon, electric-field response, mechanical response…

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BAMGBOSE, M. K.
Posts: 87
Joined: Mon Jul 02, 2012 1:40 pm
Location: Department of Physics, Federal University of Agriculture Abeokuta, Nigeria.

problem with phonon calculations

Post by BAMGBOSE, M. K. » Mon Aug 06, 2012 2:20 pm

Someone please help me out. These are my input files,
# Crystalline CaB6 : computation of the phonon spectrum

ndtset 12
#Set 1 : ground state self-consistency

getwfk1 0 # Cancel default
kptopt1 1 # Automatic generation of k points, taking
# into account the symmetry
nqpt1 0 # Cancel default
tolvrs1 1.0d-18 # SCF stopping criterion (modify default)
rfphon1 0 # Cancel default

#Q vectors for all datasets

#Complete set of symmetry-inequivalent qpt chosen to be commensurate
# with kpt mesh so that only one set of GS wave functions is needed.
#Generated automatically by running GS calculation with kptopt=1,
# nshift=0, shiftk=0 0 0 (to include gamma) and taking output kpt set
# file as qpt set. Set nstep=1 so only one iteration runs.

nqpt 1 # One qpt for each dataset (only 0 or 1 allowed)
# This is the default for all datasets and must
# be explicitly turned off for dataset 1.

qpt2 0.00000000E+00 0.00000000E+00 0.00000000E+00
qpt3 0.00000000E+00 0.00000000E+00 0.00000000E+00
qpt4 2.50000000E-01 0.00000000E+00 0.00000000E+00
qpt5 5.00000000E-01 0.00000000E+00 0.00000000E+00
qpt6 2.50000000E-01 2.50000000E-01 0.00000000E+00
qpt7 5.00000000E-01 2.50000000E-01 0.00000000E+00
qpt8 5.00000000E-01 5.00000000E-01 0.00000000E+00
qpt9 2.50000000E-01 2.50000000E-01 2.50000000E-01
qpt10 5.00000000E-01 2.50000000E-01 2.50000000E-01
qpt11 5.00000000E-01 5.00000000E-01 2.50000000E-01
qpt12 5.00000000E-01 5.00000000E-01 5.00000000E-01

#Set 2 : Response function calculation of d/dk wave function

iscf2 -3 # Need this non-self-consistent option for d/dk
kptopt2 2 # Modify default to use time-reversal symmetry
rfphon2 0 # Cancel default
rfelfd2 2 # Calculate d/dk wave function only
tolwfr2 1.0d-22 # Use wave function residual criterion instead

#Set 3 : Response function calculation of Q=0 phonons and electric field pert.

getddk3 2 # d/dk wave functions from last dataset
kptopt3 2 # Modify default to use time-reversal symmetry
rfelfd3 3 # Electric-field perturbation response only

#Sets 4-12 : Finite-wave-vector phonon calculations (defaults for all datasets)

getwfk 1 # Use GS wave functions from dataset1
kptopt 3 # Need full k-point set for finite-Q response
rfphon 1 # Do phonon response
rfatpol 1 7 # Treat displacements of all atoms
rfdir 1 1 1 # Do all directions (symmetry will be used)
tolvrs 1.0d-8 # This default is active for sets 3-10

#########################################################################################################
#Data common to all datasets
nshiftk 1
shiftk 0.5 0.5 0.5
ngkpt 4 4 4 ! This is much too low : should be at least 24x24x24

acell 3*4.19
diemac 10.0
ecut 45.00 ! This is also too low
iscf 5
nstep 25
ixc 11
natom 7
ntypat 2
rprim 1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0


# Atomic positions
xred 0.00 0.00 0.00 #Ca1
0.50 0.50 0.20 #B2
0.50 0.50 -0.20 #B2
0.50 0.20 0.50 #B2
0.50 -0.20 0.50 #B2
0.20 0.50 0.50 #B2
0.80 0.50 0.50 #B2

nband 16

typat 1 2 2 2 2 2 2
znucl 20 5
# add to conserve old < 6.7.2 behavior for calculating forces at each SCF step
optforces 1
And
!Input file for the anaddb code. Analysis of the CaB6 DDB

!Flags
ifcflag 1 ! Interatomic force constant flag

!Wavevector grid number 1 (coarse grid, from DDB)
brav 1 ! Bravais Lattice : 1-S.C., 2-F.C., 3-B.C., 4-Hex.)
ngqpt 4 4 4 ! Monkhorst-Pack indices
nqshft 1 ! number of q-points in repeated basic q-cell
q1shft 3*0.0

!Effective charges
asr 1 ! Acoustic Sum Rule. 1 => imposed asymetrically
chneut 1 ! Charge neutrality requirement for effective charges.

!Interatomic force constant info
dipdip 1 ! Dipole-dipole interaction treatment

!Phonon band structure output for band2eps - See note near end for
! dealing with gamma LO-TO splitting issue.
eivec 4

!Wavevector list number 1 (Reduced coordinates and normalization factor)
nph1l 51 ! number of phonons in list 1

qph1l 0.000 0.000 0.000 1.0 !(gamma point)
0.000 0.050 0.000 1.0
0.000 0.100 0.000 1.0
0.000 0.150 0.000 1.0
0.000 0.200 0.000 1.0
0.000 0.250 0.000 1.0
0.000 0.300 0.000 1.0
0.000 0.350 0.000 1.0
0.000 0.400 0.000 1.0
0.000 0.450 0.000 1.0
0.000 0.500 0.000 1.0 !(X point)
0.050 0.050 0.000 1.0
0.100 0.100 0.000 1.0
0.150 0.150 0.000 1.0
0.200 0.200 0.000 1.0
0.250 0.250 0.000 1.0
0.300 0.300 0.000 1.0
0.350 0.350 0.000 1.0
0.400 0.400 0.000 1.0
0.450 0.450 0.000 1.0
0.500 0.500 0.000 1.0 !(M point)
0.450 0.450 0.000 1.0
0.400 0.400 0.000 1.0
0.350 0.350 0.000 1.0
0.300 0.300 0.000 1.0
0.250 0.250 0.000 1.0
0.200 0.200 0.000 1.0
0.150 0.150 0.000 1.0
0.100 0.100 0.000 1.0
0.050 0.050 0.000 1.0
0.000 0.000 0.000 1.0 !(GAMMA point)
0.050 0.050 0.050 1.0
0.100 0.100 0.100 1.0
0.150 0.150 0.150 1.0
0.200 0.200 0.200 1.0
0.250 0.250 0.250 1.0
0.300 0.300 0.300 1.0
0.350 0.350 0.350 1.0
0.400 0.400 0.400 1.0
0.450 0.450 0.450 1.0
0.500 0.500 0.500 1.0 !(R point)
0.450 0.500 0.450 1.0
0.400 0.500 0.400 1.0
0.350 0.500 0.350 1.0
0.300 0.500 0.300 1.0
0.250 0.500 0.250 1.0
0.200 0.500 0.200 1.0
0.150 0.500 0.150 1.0
0.100 0.500 0.100 1.0
0.050 0.500 0.050 1.0
0.000 0.500 0.000 1.0 !(X point)
!Wavevector list number 2 (Cartesian directions for non-analytic gamma phonons)

!The output for this calculation must be cut-and-pasted into the
! t59_out.freq file to be used as band2eps input to get proper LO-TO
! splitting at gamma. Note that gamma occurrs twice.

nph2l 1 ! number of directions in list 2

qph2l 1.0 0.0 0.0 0.0
# This line added when defaults were changed (v5.3) to keep the previous, old behaviour
symdynmat 0
Now my frequency file has 21 columns, but the in the abinit example has 6 columns. Someone should please correct my input files. Thanks.
M. K. Bamgbose (PhD),
Condensed Matter Physics.

User avatar
jzwanzig
Posts: 504
Joined: Mon Aug 17, 2009 9:25 am

Re: problem with phonon calculations

Post by jzwanzig » Mon Aug 06, 2012 2:31 pm

Why should the files be the same? the material you are studying is different from the material in the tutorial. Specifically, tutorial is AlAs, so 2 atoms and 6 modes, while you have 7 atoms and 21 modes.
Josef W. Zwanziger
Professor, Department of Chemistry
Canada Research Chair in NMR Studies of Materials
Dalhousie University
Halifax, NS B3H 4J3 Canada
jzwanzig@gmail.com

BAMGBOSE, M. K.
Posts: 87
Joined: Mon Jul 02, 2012 1:40 pm
Location: Department of Physics, Federal University of Agriculture Abeokuta, Nigeria.

Re: problem with phonon calculations

Post by BAMGBOSE, M. K. » Mon Aug 06, 2012 8:22 pm

Prof thanks alot, but kindly put me through how to plot this 21 modes from my frequency file. This is my frequency file.
-0.157111E-01 -0.157111E-01 -0.157111E-01 -0.836286E-07 -0.472495E-07 -0.253775E-07 0.342045E-02 0.342053E-02 0.342061E-02 0.556215E-02 0.556215E-02 0.556216E-02 0.146676E-01 0.146676E-01 0.146676E-01 0.185817E-01 0.185818E-01 0.185818E-01 0.215100E-01 0.215100E-01 0.304675E-01
-0.156244E-01 -0.157188E-01 -0.156244E-01 -0.419487E-03 0.982914E-03 -0.419501E-03 0.358787E-02 0.337438E-02 0.337446E-02 0.544018E-02 0.562115E-02 0.544020E-02 0.147010E-01 0.146181E-01 0.147010E-01 0.184305E-01 0.185660E-01 0.185660E-01 0.216974E-01 0.215125E-01 0.304420E-01
-0.153784E-01 -0.157430E-01 -0.153784E-01 -0.101300E-02 0.188626E-02 -0.101303E-02 0.376432E-02 0.321201E-02 0.321209E-02 0.512510E-02 0.578152E-02 0.512511E-02 0.147824E-01 0.144780E-01 0.147824E-01 0.179784E-01 0.185212E-01 0.185212E-01 0.221610E-01 0.215155E-01 0.303656E-01
-0.150127E-01 -0.157856E-01 -0.150127E-01 -0.196812E-02 0.258740E-02 -0.196816E-02 0.415740E-02 0.292293E-02 0.292301E-02 0.477620E-02 0.600155E-02 0.477621E-02 0.148676E-01 0.142715E-01 0.148676E-01 0.173878E-01 0.184551E-01 0.184551E-01 0.227563E-01 0.215081E-01 0.302388E-01
-0.145844E-01 -0.158479E-01 -0.145845E-01 -0.326660E-02 0.300954E-02 -0.326664E-02 0.482002E-02 0.268076E-02 0.268085E-02 0.455488E-02 0.623237E-02 0.455489E-02 0.149109E-01 0.140321E-01 0.149109E-01 0.167257E-01 0.183782E-01 0.183782E-01 0.233991E-01 0.214775E-01 0.300632E-01
-0.141569E-01 -0.159282E-01 -0.141569E-01 -0.459224E-02 0.325326E-02 -0.459228E-02 0.563150E-02 0.259660E-02 0.259669E-02 0.446468E-02 0.643391E-02 0.446468E-02 0.148852E-01 0.137953E-01 0.148852E-01 0.160216E-01 0.183029E-01 0.183029E-01 0.240434E-01 0.214159E-01 0.298432E-01
-0.137843E-01 -0.160199E-01 -0.137843E-01 -0.576796E-02 0.341877E-02 -0.576800E-02 0.647087E-02 0.259875E-02 0.259884E-02 0.444581E-02 0.658338E-02 0.444582E-02 0.147899E-01 0.135901E-01 0.147899E-01 0.152967E-01 0.182401E-01 0.182401E-01 0.246586E-01 0.213248E-01 0.295872E-01
-0.134994E-01 -0.161125E-01 -0.134994E-01 -0.674410E-02 0.354150E-02 -0.674413E-02 0.727428E-02 0.263038E-02 0.263048E-02 0.445758E-02 0.667645E-02 0.445759E-02 0.146491E-01 0.134333E-01 0.146491E-01 0.145802E-01 0.181964E-01 0.181964E-01 0.252175E-01 0.212171E-01 0.293109E-01
-0.133099E-01 -0.161923E-01 -0.133099E-01 -0.748584E-02 0.362966E-02 -0.748587E-02 0.798423E-02 0.266642E-02 0.266652E-02 0.447748E-02 0.672331E-02 0.447750E-02 0.145030E-01 0.133287E-01 0.145030E-01 0.139251E-01 0.181719E-01 0.181719E-01 0.256873E-01 0.211142E-01 0.290426E-01
-0.132055E-01 -0.162466E-01 -0.132055E-01 -0.795375E-02 0.368345E-02 -0.795378E-02 0.850853E-02 0.269365E-02 0.269375E-02 0.449332E-02 0.674106E-02 0.449333E-02 0.143939E-01 0.132709E-01 0.143939E-01 0.134294E-01 0.181614E-01 0.181614E-01 0.260178E-01 0.210398E-01 0.288323E-01
-0.131727E-01 -0.162658E-01 -0.131727E-01 -0.811420E-02 0.370158E-02 -0.811422E-02 0.871041E-02 0.270375E-02 0.270385E-02 0.449917E-02 0.674496E-02 0.449919E-02 0.143537E-01 0.132527E-01 0.143537E-01 0.132362E-01 0.181588E-01 0.181588E-01 0.261408E-01 0.210127E-01 0.287491E-01
-0.156605E-01 -0.156039E-01 -0.155391E-01 0.147333E-01 0.347039E-02 0.146693E-01 0.105782E-02 0.349153E-02 0.333612E-02 0.531453E-02 0.556680E-02 0.543323E-02 -0.592356E-03 0.146322E-01 0.686267E-03 0.182704E-01 0.185496E-01 0.185378E-01 0.217786E-01 0.216104E-01 0.304164E-01
-0.155402E-01 -0.152792E-01 -0.150650E-01 0.148878E-01 0.358107E-02 0.146372E-01 0.191539E-02 0.325280E-02 0.312885E-02 0.458480E-02 0.557184E-02 0.517799E-02 -0.139563E-02 0.145402E-01 0.124057E-02 0.175286E-01 0.184538E-01 0.183395E-01 0.223772E-01 0.218773E-01 0.302622E-01
-0.154086E-01 -0.147433E-01 -0.143940E-01 0.150708E-01 0.362593E-02 0.145428E-01 0.136286E-02 0.292714E-02 0.293637E-02 0.309961E-02 0.561154E-02 0.526150E-02 -0.250210E-02 0.144433E-01 0.152414E-02 0.165669E-01 0.183046E-01 0.180631E-01 0.230628E-01 0.222483E-01 0.300050E-01
-0.152805E-01 -0.140589E-01 -0.136460E-01 0.152908E-01 0.350016E-02 0.144679E-01 -0.308631E-02 0.303294E-02 0.285624E-02 -0.298531E-02 0.577583E-02 0.583691E-02 -0.378633E-02 0.144275E-01 0.124584E-02 0.154645E-01 0.181312E-01 0.177399E-01 0.237315E-01 0.226835E-01 0.296512E-01
-0.151156E-01 -0.133904E-01 -0.129153E-01 0.155904E-01 0.335574E-02 0.145390E-01 -0.489057E-02 0.309429E-02 0.287092E-02 -0.620152E-02 0.605309E-02 0.653815E-02 -0.502328E-02 0.145439E-01 -0.152334E-02 0.142649E-01 0.179701E-01 0.173920E-01 0.243423E-01 0.231707E-01 0.292159E-01
-0.148970E-01 -0.129682E-01 -0.122615E-01 0.159522E-01 0.331018E-02 0.147665E-01 -0.614249E-02 0.314912E-02 0.294639E-02 -0.884262E-02 0.637881E-02 0.714599E-02 -0.603084E-02 0.147473E-01 -0.314942E-02 0.130188E-01 0.178317E-01 0.170489E-01 0.248750E-01 0.237100E-01 0.287194E-01
-0.146951E-01 -0.129236E-01 -0.116983E-01 0.162791E-01 0.330732E-02 0.150327E-01 -0.701196E-02 0.321287E-02 0.305238E-02 -0.109934E-01 0.675443E-02 0.760520E-02 -0.677345E-02 0.149571E-01 -0.465579E-02 0.117858E-01 0.176803E-01 0.167591E-01 0.253147E-01 0.242985E-01 0.281811E-01
-0.146198E-01 -0.131557E-01 -0.111786E-01 0.163847E-01 0.331136E-02 0.152212E-01 -0.760423E-02 0.326957E-02 0.315711E-02 -0.125105E-01 0.721622E-02 0.792174E-02 -0.732406E-02 0.151320E-01 -0.615336E-02 0.106311E-01 0.174783E-01 0.166595E-01 0.256455E-01 0.249210E-01 0.276158E-01
-0.147062E-01 -0.134306E-01 -0.106515E-01 0.162867E-01 0.331540E-02 0.153035E-01 -0.796446E-02 0.330534E-02 0.323207E-02 -0.133220E-01 0.776610E-02 0.810918E-02 -0.769826E-02 0.152645E-01 -0.746513E-02 0.963745E-02 0.172632E-01 0.167313E-01 0.258520E-01 0.255365E-01 0.270488E-01
-0.147876E-01 -0.135480E-01 -0.103329E-01 0.162432E-01 0.331713E-02 0.153213E-01 -0.808763E-02 0.331709E-02 0.325897E-02 -0.135480E-01 0.817178E-02 0.817176E-02 -0.783519E-02 0.153212E-01 -0.808764E-02 0.908055E-02 0.171625E-01 0.167576E-01 0.259223E-01 0.259223E-01 0.266822E-01
-0.147062E-01 -0.134306E-01 -0.106515E-01 0.162867E-01 0.331540E-02 0.153035E-01 -0.796446E-02 0.330534E-02 0.323207E-02 -0.133220E-01 0.810918E-02 0.776610E-02 -0.769826E-02 0.152645E-01 -0.746513E-02 0.963745E-02 0.172632E-01 0.167313E-01 0.258520E-01 0.255365E-01 0.270488E-01
-0.146198E-01 -0.131557E-01 -0.111786E-01 0.163847E-01 0.331136E-02 0.152212E-01 -0.760423E-02 0.326957E-02 0.315711E-02 -0.125105E-01 0.792174E-02 0.721622E-02 -0.732406E-02 0.151320E-01 -0.615336E-02 0.106311E-01 0.174783E-01 0.166595E-01 0.256455E-01 0.249210E-01 0.276158E-01
-0.146951E-01 -0.129236E-01 -0.116983E-01 0.162791E-01 0.330732E-02 0.150327E-01 -0.701196E-02 0.321287E-02 0.305238E-02 -0.109934E-01 0.760520E-02 0.675443E-02 -0.677345E-02 0.149571E-01 -0.465579E-02 0.117858E-01 0.176803E-01 0.167591E-01 0.253147E-01 0.242985E-01 0.281811E-01
-0.148970E-01 -0.129682E-01 -0.122615E-01 0.159522E-01 0.331018E-02 0.147665E-01 -0.614249E-02 0.314912E-02 0.294639E-02 -0.884262E-02 0.714599E-02 0.637881E-02 -0.603084E-02 0.147473E-01 -0.314942E-02 0.130188E-01 0.178317E-01 0.170489E-01 0.248750E-01 0.237100E-01 0.287194E-01
-0.151156E-01 -0.133904E-01 -0.129153E-01 0.155904E-01 0.335574E-02 0.145390E-01 -0.489057E-02 0.309429E-02 0.287092E-02 -0.620152E-02 0.653815E-02 0.605309E-02 -0.502328E-02 0.145439E-01 -0.152334E-02 0.142649E-01 0.179701E-01 0.173920E-01 0.243423E-01 0.231707E-01 0.292159E-01
-0.152805E-01 -0.140589E-01 -0.136460E-01 0.152908E-01 0.350016E-02 0.144679E-01 -0.308631E-02 0.303294E-02 0.285624E-02 -0.298531E-02 0.583691E-02 0.577583E-02 -0.378633E-02 0.144275E-01 0.124584E-02 0.154645E-01 0.181312E-01 0.177399E-01 0.237315E-01 0.226835E-01 0.296512E-01
-0.154086E-01 -0.147433E-01 -0.143940E-01 0.150708E-01 0.362593E-02 0.145428E-01 0.136286E-02 0.292714E-02 0.293637E-02 0.309961E-02 0.526150E-02 0.561154E-02 -0.250210E-02 0.144433E-01 0.152414E-02 0.165669E-01 0.183046E-01 0.180631E-01 0.230628E-01 0.222483E-01 0.300050E-01
-0.155402E-01 -0.152792E-01 -0.150650E-01 0.148878E-01 0.358107E-02 0.146372E-01 0.191539E-02 0.325280E-02 0.312885E-02 0.458480E-02 0.517799E-02 0.557184E-02 -0.139563E-02 0.145402E-01 0.124057E-02 0.175286E-01 0.184538E-01 0.183395E-01 0.223772E-01 0.218773E-01 0.302622E-01
-0.156605E-01 -0.156039E-01 -0.155391E-01 0.147333E-01 0.347039E-02 0.146693E-01 0.105782E-02 0.349153E-02 0.333612E-02 0.531453E-02 0.543323E-02 0.556680E-02 -0.592356E-03 0.146322E-01 0.686267E-03 0.182704E-01 0.185496E-01 0.185378E-01 0.217786E-01 0.216104E-01 0.304164E-01
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Thanks alot for your usual cooperation.
M. K. Bamgbose (PhD),
Condensed Matter Physics.

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