Phonons, DFPT, electron-phonon, electric-field response, mechanical response…
Moderators: mverstra, joaocarloscabreu
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roginovicci
- Posts: 75
- Joined: Thu Dec 02, 2010 10:36 pm
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by roginovicci » Tue Mar 15, 2011 10:20 pm
Hello, I'm trying to perform response function 2 calculations on GaN. I'm stack in the step 4. Here is input file for anadb program:
ganrf2_4.in
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!Input file for the anaddb code. Analysis of the AlAs DDB
!Flags
ifcflag 1 ! Interatomic force constant flag
!Wavevector grid number 1 (coarse grid, from DDB)
brav 4 ! Bravais Lattice : 1-S.C., 2-F.C., 3-B.C., 4-Hex.)
ngqpt 5 5 4 ! Monkhorst-Pack indices. Same as ngkpt?
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 0 ! Dipole-dipole interaction treatment
ifcana 1 ! Analysis of the IFCs
ifcout 12 ! Number of IFC's written in the output, per atom
natifc 1 ! Number of atoms in the cell for which ifc's are analysed
atifc 1 ! List of atoms
# This line added when defaults were changed (v5.3) to keep the previous, old behaviour
symdynmat 0
and here is ganrf2_4.files:
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ganrf2_4.in
ganrf2_4.out
ganrf2_3.ddb.out
ganrf2_4_band2eps
ganrf2_dummy1
ganrf2_dummy2
ganrf2_dummy3
and log file has such a wierd comments like:
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 1 3 1 3 187
and finally a have error:
symdm9 : ERROR -
Informations are missing in the DDB.
In blok 1 the following element is missing :
idir1,ipert1,idir2,ipert2= 1 3 1 3
Action : add the required information in the DDB,
or modify your input file.
Could you please give me any help please. I am stuck
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jzwanzig
- Posts: 504
- Joined: Mon Aug 17, 2009 9:25 am
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by jzwanzig » Wed Mar 16, 2011 11:35 am
You need to also post your abinit input file in addition to the anaddb input file.
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
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roginovicci
- Posts: 75
- Joined: Thu Dec 02, 2010 10:36 pm
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by roginovicci » Wed Mar 16, 2011 1:55 pm
Dear jzwanzig, Thank you for the reply. The input file is as follows:
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# Crystalline GaN : computation of the phonon spectrum
ndtset 17
#chksymbreak=0
#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 2.00000000E-01 0.00000000E+00 0.00000000E+00
qpt5 4.00000000E-01 0.00000000E+00 0.00000000E+00
qpt6 2.00000000E-01 2.00000000E-01 0.00000000E+00
qpt7 4.00000000E-01 2.00000000E-01 0.00000000E+00
qpt8 0.00000000E+00 0.00000000E+00 2.50000000E-01
qpt9 2.00000000E-01 0.00000000E+00 2.50000000E-01
qpt10 4.00000000E-01 0.00000000E+00 2.50000000E-01
qpt11 2.00000000E-01 2.00000000E-01 2.50000000E-01
qpt12 4.00000000E-01 2.00000000E-01 2.50000000E-01
qpt13 0.00000000E+00 0.00000000E+00 5.00000000E-01
qpt14 2.00000000E-01 0.00000000E+00 5.00000000E-01
qpt15 4.00000000E-01 0.00000000E+00 5.00000000E-01
qpt16 2.00000000E-01 2.00000000E-01 5.00000000E-01
qpt17 4.00000000E-01 2.00000000E-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 4-17 : 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 2 # Treat displacements of all atoms
rfdir 1 1 1 # Do all directions (symmetry will be used)
tolvrs 1.0d-12 # This default is active for sets 3-10
# tolvrs 1.0d-15 set this for precise calculations
#Common input variables
# Definition of the unit cell
acell 6.0383566806E+00 6.0383566806E+00 9.8430892710E+00
angdeg 90.000 90.000 120.000
spgroup 186
# Definition of the atom
ntypat 2 # Two types of atoms
znucl 31 7 # Ga and N atomic numbers of the
natom 4 # There are four atoms in a cell
typat 1 1 2 2 # Type 1 is Ga, type 2 is N
xred
3.3333333333E-01 6.6666666667E-01 0.0000000000
6.6666666667E-01 3.3333333333E-01 5.0000000000E-01
3.3333333333E-01 6.6666666667E-01 3.7662692182E-01
6.6666666667E-01 3.3333333333E-01 8.7662692182E-01
## Definition of XC functional and planewave basis set
ixc 11 # Teter XC functional
ecut 35 # Kinetic energy cut-off (in Ha)
ecutsm 0.5
dilatmx 1.05
# Definition of the k-point grid
# kptopt 1
shiftk 0.0 0.0 0.5
ngkpt 5 5 4
nshiftk 1
# Parameters of the SCF cycles
iscf 7 # Pulay mixing (default for norm-conserving PSP)
nstep 100
The qpt vector list i got using the following input file:
Code: Select all
# Definition of the unit cell
acell 6.0383566806E+00 6.0383566806E+00 9.8430892710E+00
angdeg 90.000 90.000 120.000
spgroup 186
# Definition of the atom
ntypat 2 # Two types of atoms
znucl 31 7 # Ga and N atomic numbers of the
natom 4 # There are four atoms in a cell
typat 1 1 2 2 # Type 1 is Ga, type 2 is N
xred
1/3 2/3 0.0
2/3 1/3 0.5
1/3 2/3 3.7662692182E-01
2/3 1/3 8.7662692182E-01
#Gives the number of band, explicitely (do not take the default)
nband 8 # Explicit number of valence bands
## Definition of XC functional and planewave basis set
ixc 11 # Teter XC functional
ecut 35 # Kinetic energy cut-off (in Ha)
ecutsm 0.5
dilatmx 1.05
# Definition of the k-point grid
kptopt 1
shiftk 0.0 0.0 0.0
ngkpt 5 5 4
nshiftk 1
iscf 7 # Pulay mixing (default for norm-conserving PSP)
tolvrs 1.0d-15
nstep 1 # Maximal number of SCF cycles
nline 1 # Maximal number of SCF cycles
The last gave me output file with the following set:
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...skip...
-outvars: echo values of variables after computation --------
acell 6.0383566806E+00 6.0383566806E+00 9.8430892710E+00 Bohr
amu 6.97230000E+01 1.40067400E+01
dilatmx 1.05000000E+00
ecut 3.50000000E+01 Hartree
ecutsm 5.00000000E-01 Hartree
etotal -3.5989390043E+00
fcart 0.0000000000E+00 3.2954119707E-27 -4.8086547231E-02
0.0000000000E+00 -9.8862359121E-27 -4.8086547231E-02
0.0000000000E+00 -3.2954119707E-27 4.8086547231E-02
0.0000000000E+00 9.8862359121E-27 4.8086547231E-02
istwfk 2 0 0 0 0 0 0 0 0 0
4 0 0 0 0
ixc 11
kpt 0.00000000E+00 0.00000000E+00 0.00000000E+00
2.00000000E-01 0.00000000E+00 0.00000000E+00
4.00000000E-01 0.00000000E+00 0.00000000E+00
2.00000000E-01 2.00000000E-01 0.00000000E+00
4.00000000E-01 2.00000000E-01 0.00000000E+00
0.00000000E+00 0.00000000E+00 2.50000000E-01
2.00000000E-01 0.00000000E+00 2.50000000E-01
4.00000000E-01 0.00000000E+00 2.50000000E-01
2.00000000E-01 2.00000000E-01 2.50000000E-01
4.00000000E-01 2.00000000E-01 2.50000000E-01
0.00000000E+00 0.00000000E+00 5.00000000E-01
2.00000000E-01 0.00000000E+00 5.00000000E-01
4.00000000E-01 0.00000000E+00 5.00000000E-01
2.00000000E-01 2.00000000E-01 5.00000000E-01
4.00000000E-01 2.00000000E-01 5.00000000E-01
kptrlen 3.01917834E+01
kptrlatt 5 0 0 0 5 0 0 0 4
nband 8
ngfft 36 36 60
nkpt 15
nline 1
nstep 1
nsym 12
ntypat 2
occ 2.000000 2.000000 2.000000 2.000000 2.000000 2.000000
2.000000 2.000000
rprim 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00
-5.0000000000E-01 8.6602540378E-01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 1.0000000000E+00
...skip...
Thanks in advance!
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jzwanzig
- Posts: 504
- Joined: Mon Aug 17, 2009 9:25 am
Post
by jzwanzig » Wed Mar 16, 2011 2:02 pm
I think the problem is that you should have rfatpol 1 4, not 1 2--you have 4 atoms in the cell, all should be treated, I think that's why anaddb complains about missing perturbations. Note that rfatpol refers to atoms, not to types of atoms--
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
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roginovicci
- Posts: 75
- Joined: Thu Dec 02, 2010 10:36 pm
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by roginovicci » Wed Mar 16, 2011 11:47 pm
Dear jzwanzig! My best wishes to you and to all your family! I appreciated a lot! It work like a charm! But I still having trouble plot phonon band structures
Here is my ganrf2_5.in file which i run with the following input to anaddb:
ganrf2_5.in
ganrf2_5.out
ganrf2_3.ddb.out
ganrf2_5_band2eps
ganrf2_dummy1
ganrf2_dummy2
ganrf2_dummy3
Code: Select all
!Input file for the anaddb code. Analysis of the GaN DDB
!Flags
ifcflag 1 ! Interatomic force constant flag
!Wavevector grid number 1 (coarse grid, from DDB)
brav 4 ! Bravais Lattice : 1-S.C., 2-F.C., 3-B.C., 4-Hex.)
ngqpt 5 5 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 0 ! 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 29 ! number of phonons in list 1
qph1l 0.0000 0.0000 0.0000 1.0 !(gamma point)
0.2500 0.2500 0.0000 3.0
0.5000 0.5000 0.0000 3.0
0.7500 0.7500 0.0000 3.0
1.0000 1.0000 0.0000 3.0 !(K point)
1.1250 0.7500 0.0000 3.0
1.2500 0.5000 0.0000 3.0
1.3750 0.2500 0.0000 3.0
1.5000 0.0000 0.0000 3.0 !(M point)
1.8750 0.7500 0.7500 3.0
2.2500 1.5000 1.5000 3.0
2.6250 2.2500 2.2500 3.0
3.0000 3.0000 3.0000 3.0 !(gamma point)
2.2500 2.2500 2.6250 3.0
1.5000 1.5000 2.2500 3.0
0.7500 0.7500 1.8750 3.0
0.0000 0.0000 1.5000 3.0 !(A point)
0.2500 0.2500 1.5000 3.0
0.5000 0.5000 1.5000 3.0
0.7500 0.7500 1.5000 3.0
1.0000 1.0000 1.5000 3.0 !(H point)
1.1250 0.7500 1.5000 3.0
1.2500 0.5000 1.5000 3.0
1.3750 0.2500 1.5000 3.0
1.5000 0.0000 1.5000 3.0 !(L point)
0.7500 0.0000 1.5000 3.0
0.5000 0.0000 1.5000 3.0
0.2500 0.0000 1.5000 3.0
0.0000 0.0000 1.5000 3.0 !(A point)
I have two main output files
ganrf2_5.out_B2EPS.displ ganrf2_5.out_B2EPS.freq
which I try to use with band2eps by ganrf2_6.in
Code: Select all
#Input file for 'band2eps.' This data layout must be used, line-by-line.
#number of atoms in a cell :
4
#minimum value, maximum value and number of tics of the vertical axe :
0.0 400.0 8
#Units : 1 for cm-1, 2 for THz :
1
#Number of lines :
7
#Description of the points in q space : Actually label is wrong
gamma K X gamma L X W L
#Number of q points for each line :
4 4 4 4 4 4 4
#Scale factor for each line :
1.06066017 0.35355339 1.0 0.86602540 0.86602540 0.5 0.70710678
#COLOR DEFINITION :
#put 1 in place of the atom you want to be colored in
#red
0 0
#green
0 0
#blue
0 0
but band2eps goes to sigfault
Should I rise Number of q points for each line ?
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jzwanzig
- Posts: 504
- Joined: Mon Aug 17, 2009 9:25 am
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by jzwanzig » Thu Mar 17, 2011 11:26 am
As I recall, in the band2eps input file, in the color definition lines you need a red input for each atom, a green for each atom, and so forth. So instead of lines like "0 0" which would be for 2 atoms, you now need "0 0 0 0" for example. I've made that mistake too, and was always slightly puzzled why the program crashes with a dramatic segfault rather than just a more normal complaint. But I've never taken the time to read the code and/or fix up the input parser.
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
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roginovicci
- Posts: 75
- Joined: Thu Dec 02, 2010 10:36 pm
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by roginovicci » Thu Mar 17, 2011 2:08 pm
God bless you! Many thanks in advance!!! I was just thinking that it is not only one parameter I have to change having 4 atoms in the cell. Shame on me I couldn't made it myself. Once more thank you very much, and sorry for my dummy questions.
