[Pw_forum] multiple ph.x runs with same outdir

[Sridhar Sadasivam]

Hello,
I'm splitting a phonon calculation with many q-pts into multiple
independent calculations using the start_q, last_q options (basically
manual image parallelization). Is it necessary that these runs have
separate 'outdir'? The wavefunctions from scf occupy a lot of memory and
I'd prefer not to copy them separately for each of the phonon calculations.
Is it possible to run these different phonon calculations with the same
'outdir'?

I guess the code creates a separate directory $prefix.q_$qpt for each of
the q-pts under $outdir/_ph0 directory -- so I believe that shouldn't be an
issue. However, the status_run.xml will be simultaneously written by
multiple jobs -- that may be a problem I guess?

Any thoughts will be appreciated.

Thanks,
Sridhar
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Re: [Pw_forum] EPW Superconductivity

[Sridhar Sadasivam]

Hello,

There is a separate mailing list for problems associated with EPW -
http://epwforum.uk/index.php
Please post there in the future as you're more likely to get an answer.

But in this case, I think there is no input variable called "epf_mem" in
EPW.

Best,
Sridhar
Argonne National Lab

On Thu, Jul 28, 2016 at 2:32 AM, Gargee Bhattacharyya <
bhattacharyya.gar...@gmail.com> wrote:

> Dear all,
>  I am trying to calculate *electron-phonon coupling strangth,
> anisotropic Elishberg spectral function , anisotrotic superconducting gap*
> using EPW as instructed from the site given below
>
> http://epw.org.uk/Main/About
>
> http://epw.org.uk/Documentation/Tutorial
>
> I am trying to run EPW on bulk FCC Lead. I shall be highly obliged if
> anyone help me to find my error. I have calculated using the following
> steps:
>
> mpirun -np 4 ../../../../bin/pw.x < scf.in > scf.out
> mpirun -np 4 ../../../../bin/ph.x < ph.in > ph.out
> python pp.py < pp.in
> mpirun -np 4 ../../../../bin/pw.x < scf_epw.in > scf_epw.out
> mpirun -np 4 ../../../../bin/pw.x -npool 4 < nscf_epw.in > nscf_epw.out
> mpirun -np 4 ../../../src/epw.x -npool 4 < epw.in > epw.out
>
> all the calculation were completed successfully except the last epw
> calculation
>
> *mpirun -np 4 ../../../src/epw.x -npool 4 < epw.in  >
> epw.out*
>
> It is showing error :
>
> Program EPW v.4.0.0 starts on 28Jul2016 at 10:27:15
>
>  This program is part of the open-source Quantum ESPRESSO suite
>  for quantum simulation of materials; please cite
>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>   URL http://www.quantum-espresso.org;,
>  in publications or presentations arising from this work. More details
> at
>  http://www.quantum-espresso.org/quote
>
>  Parallel version (MPI), running on 4 processors
>  R & G space division:  proc/nbgrp/npool/nimage =   4
>
>
>  
> %%
>  *Error in routine epw_readin (1):*
> * reading input_epw namelist*
>
>  
> %%
>
>  stopping ...
> --
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
>
> *My input file is :*
>
> 
>   prefix  = 'pb'
>   amass(1)= 207.2
>   outdir  = './'
>
>   elph= .true.
>   kmaps   = .false.
>   epbwrite= .true.
>   epbread = .false.
>
>   epf_mem = .true.
>   etf_mem = .true.
>
>   epwwrite= .true.
>   epwread = .false.
>
>   nbndsub =  4
>   nbndskip=  0
>
>   wannierize  = .true.
>   num_iter= 300
>   dis_win_max = 18
>   dis_froz_max= 8
>   proj(1) = 'Pb:sp3'
>
>   iverbosity  = 0
>
>   elinterp= .true.
>   phinterp= .true.
>
>   tshuffle2   = .true.
>   tphases = .false.
>
>   elecselfen  = .true.
>   phonselfen  = .true.
>   a2f = .true.
>
>   parallel_k  = .true.
>   parallel_q  = .false.
>
>   fsthick = 0.5
>   eptemp  = 0.045
>   degaussw= 0.045
>   degaussq= 0.05
>
>   dvscf_dir   = './save'
>   filukk  = './pb.ukk'
>
>   nk1 = 6
>   nk2 = 6
>   nk3 = 6
>
>   nq1 = 6
>   nq2 = 6
>   nq3 = 6
>
>   nqf1 = 4
>   nqf2 = 4
>   nqf3 = 4
>   nkf1 = 30
>   nkf2 = 30
>   nkf3 = 30
>  /
>   16 cartesian
> 0.000   0.000   0.000   0.0909090
>-0.167   0.167  -0.167   0.0909090
>-0.333   0.333  -0.333   0.0909090
> 0.500  -0.500   0.500   0.0909090
> 0.000   0.333   0.000   0.0909090
>-0.167   0.500  -0.167   0.0909090
> 0.667  -0.333   0.667   0.0909090
> 0.500  -0.167   0.500   0.0909090
> 0.333   0.000   0.333   0.0909090
> 0.000   0.667   0.000   0.0909090
> 0.833  -0.167   0.833   0.0909090
> 0.667   0.000   0.667   0.0909090
> 0.000  -1.000   0.000   0.0909090
> 0.667  -0.333   1.000   0.0909090
> 0.500  -0.167   0.833   0.0909090
>-0.333  -1.000   0.000   0.0909090
>
>
> --
> Yours sincerely
>
> Gargee Bhattacharyya
> ​PhD Pursuing
> Metallurgy Engineering & Materials Science
> IIT Indore ​
>
> M.Tech (VLSI Design & Microelectronics Technology)
> Department of ETCE
> Jadavpur University
>
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Re: [Pw_forum] Phonon Calculation

[Sridhar Sadasivam]

Hi Ericmoore,

The message "1 eigenvalues not converged" is typical and this message often
occurs during electronic bandstructure calculcation (which is the first
step of a phonon calculation). I don't think that is the reason why your
calculation may be stopping (someone correct me if I'm wrong). Could you
post more details on what exactly it prints just before the code stops?

Sridhar
Purdue University

On Fri, May 20, 2016 at 10:23 AM, Jossou, Ericmoore <
ericmoore.jos...@usask.ca> wrote:

> Dear All,
>
> I am running a phonon calculation but after 3-4 matdyn files the
> calculation stops. I noticed that the Ph.out contains the message below
> which perhaps is responsible:
>
>
>
> Band Structure Calculation
>
>  Davidson diagonalization with overlap
>
>  c_bands:  1 eigenvalues not converged
>
>  c_bands:  1 eigenvalues not converged
>
>  c_bands:  1 eigenvalues not converged
>
>  c_bands:  1 eigenvalues not converged
>
>
>
>  ethr =  1.92E-11,  avg # of iterations = 47.2
>
>
>
>  total cpu time spent up to now is 2828.2 secs
>
>
>
>  End of band structure calculation
>
>
>
>  Number of k-points >= 100: set verbosity='high' to print the bands.
>
>
>
>  the Fermi energy is11.3008 ev
>
>
>
> I do appreciate any help to resolve this problem.
>
>
>
> *Warm Regards,*
>
>
>
> *Ericmoore Elijah JOSSOU*
>
> *PhD Student,*
>
> *Department of Mechanical Engineering,*
>
> *University of Saskatchewan*
>
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Re: [Pw_forum] Resuming Electron-phonon calculations after calculation's unintentional end

[Sridhar Sadasivam]

You can set recover = .true. to restart the calculation.

Sridhar
Purdue University

On Sat, Apr 30, 2016 at 4:57 AM, Hüseyin Yasin Uzunok <
hyuzu...@sakarya.edu.tr> wrote:

> Dear All,
> While I was calculating dynamical matrices an accident has occured and i
> ended unintentionally at the 25th mode. So I need to resume  the
> calculation where it ended before, but i couldn't find it how. Could you
> help me to resume the calculation? My input file is mentioned below.
> Yours.
>
>
>
>
>
> cat > elph.in < el-phonons in  La
>  
>tr2_ph=1.0d-14,
>alpha_mix(1)=0.200,
>prefix='La'
>fildvscf='La.dv',
>trans=.true.,
>electron_phonon='interpolated',
>el_ph_sigma=0.002,
>el_ph_nsigma=10,
>amass(1)= 138.91,
>  outdir='$HOME/murx/La/'
>fildyn='La.dyn5'
>  /
> 0.250E+00  -0.500E+00   0.108648413733159E+00
>
>
> --
> ---
>
>
>
> *Arş. Gör. H. Yasin UZUNOK*
>
>
> *Sakarya Üniversitesi Fizik Bölümü*
> *tel:0.264.295 6192*
> --
>
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[Pw_forum] metal-semiconductor interface

[Sridhar Sadasivam]

Hello,

This is not exactly a question on QE but a general question on computing
electrostatic potential near a metal-semiconductor interface using DFT. I
would really appreciate thoughts from the QE community.

There exists a lot of DFT papers that plot the electrostatic potential near
a metal-semiconductor interface and use it to obtain the Schottky barrier
height. Here's one such example where the authors work with a RhSi (metal)
- Si interface:
http://scitation.aip.org/content/aip/journal/jap/112/9/10.1063/1.4761994 You
will notice from Figure 3 in that paper that the average electrostatic
potential (average over each sinusoidal oscillation) becomes constant in
the semiconductor within a small length (~ 5 Angstrom) away from the
interface. I have seen this in many other papers and in my own
calculations.

However, for an undoped semiconductor (no screening), the potential is not
expected to become constant for at least a few tens of nm away from the
interface (example:
http://www.nextnano.de/nextnano3/tutorial/1Dtutorial_Schottky_barrier.htm
 ).

I'm trying to understand why DFT predicts a very small screening length
even for undoped semiconductors. I am wondering if this is a DFT limitation
and thought someone might have some idea on this? I would really appreciate
any thoughts.

Thank you!
Sridhar
Purdue University
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Re: [Pw_forum] Negative frequencies in phonon calculation

[Sridhar Sadasivam]

I have restarted phonon calculations in the past with no issues. However, I
haven't tried this with the latest versions -- I think I was using espresso
5.1.

Sridhar
Purdue University

On Tue, Jan 12, 2016 at 5:56 AM, Paolo Giannozzi 
wrote:

> Hard to say. If you get for the same system different results from a
> standard calculation and from one that was interrupted and restarted, yes,
> there is a problem. Otherwise ... there may still be a problem that shows
> up only under some circumstances.
>
> Paolo
>
> On Tue, Jan 12, 2016 at 11:20 AM, Cameron Foss  wrote:
>
>> Hello all,
>>
>> Recently I have experienced negative frequencies from a phonon
>> calculation that had been restarted after an unplanned interruption. The
>> calculation is for Transition Metal Dichalcogenide MoSe2 and WSe2. Is it
>> possible for negative frequencies to come from numerical errors from
>> restarting the calculation?
>>
>> Regards,
>> Cameron
>>
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>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
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Re: [Pw_forum] i-v characteristics

[Sridhar Sadasivam]

Yes, pwcond would be ideal for this. But is it possible to simulate
electron transport in doped graphene (or doped materials in general) using
pwcond? To include the dopant atoms explicitly, would require very large
unit cells I believe. Is there a better way to do it in pwcond?

Thanks,
Sridhar
Purdue University

On Wed, Nov 25, 2015 at 3:29 AM, Karim Elgammal  wrote:

> I believe that pwcond code in espresso, can do the job.
> I myself, wants to do the same for graphene properly as well.
> you can check the documentation here, it is based on Landauer-Buttiker
> formula: http://iramis.cea.fr/Pisp/alexander.smogunov/PWCOND/pwcond.html
> and here is the input file parameters:
> http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PWCOND.html
>
> Karim Elgammal
> PhD student
> Materials- and Nanophysics
> KTH
> Sweden
>
>
>
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Re: [Pw_forum] Geometry (Structural) Optimization

[Sridhar Sadasivam]

Hi Amir,
The calculation for geometry optimization does not require data from any
previous scf runs - It is a separate calculation. You need to use the same
pw.x program that you use for scf. But just change the calculation
parameter in  namelist to 'relax' or 'vc-relax'. Apart from that,
your input file is quite similar to that for scf.
Sridhar
Purdue University

On Wed, Oct 21, 2015 at 7:51 PM, Mofrad, Amir Mehdi (MU-Student) <
am...@mail.missouri.edu> wrote:

> Hi all,
>
>
>   I have done an SCF calculation on a silicon unit cell and I want to do a
> structural (geometry) optimization next. The documentation for this purpose
> was not that helpful and I have a couple of questions, for instance should
> I use the data generated from the scf calculation or should I define a
> thoroughly different input file for this calculation? What is the command
> to do so? Is it the same as pw.x or something else?   Any help would be
> appreciated.
>
>
> Thank you,
>
>
> Amir
>
>
>
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Re: [Pw_forum] imaginary frequency at extended Q point

[Sridhar Sadasivam]

Try reducing the tr2_ph parameter. 1D-11 is too high. I have had similar
problems in the past and it was solved by reducing tr2_ph. I would suggest
trying 1D-13 or 1D-14.
-Sridhar
Purdue University

On Mon, Oct 19, 2015 at 9:36 PM, 潭影空人心 <774729...@qq.com> wrote:

> Dear all,
>I used nq1 = 2, nq2 = 2, nq3 = 2 and nq1 = 4, nq2 = 4, nq3 = 4
> ,respectively, to do a phonon calculation. There is no imaginary
> frequency at the calculated Q points, but after calculations of Q2R and
> MATDYN, imaginary frequencies appear near GAMMA point(not GAMMA point).
>
> My settings are as follows:
> 1.lattice relaxation under pressure:
> 
> calculation   = 'vc-relax'
>
> restart_mode  = 'from_scratch'
> prefix= 'cras'
>
> pseudo_dir= '/data1/tan1/software/espresso-5.1/pseudo/'
> outdir= './tempdir/'
> etot_conv_thr = 1.0D-6
> forc_conv_thr = 1.0D-4
> tstress   = .true.
> tprnfor   = .true.
>
> /
> 
> ibrav = 8
> A = 5.58
> B = 3.36
> C = 6.17
> nat   = 8
> ntyp  = 4
> ecutwfc   = 120
> occupations   = 'smearing'
> smearing  = 'methfessel-paxton'
> degauss   = 0.04
> nspin = 2
> starting_magnetization(1) = -1
> starting_magnetization(2) = 1
> starting_magnetization(3) = 0
> starting_magnetization(4) = 0
> /
> 
> electron_maxstep  = 100
> conv_thr  = 1.0d-6
> mixing_beta   = 0.7
>
> /
> 
> ion_dynamics = 'bfgs'
> /
> 
>press = 1500
>cell_dynamics = 'bfgs'
>press_conv_thr= 0.1
>cell_factor   = 2.5d0
> /
> ATOMIC_SPECIES
>Cr1   51.9961   Cr.pz-hgh.UPF
>Cr2   51.9961   Cr.pz-hgh.UPF
>As1   74.9216   As.pz-hgh.UPF
>As2   74.9216   As.pz-hgh.UPF
> ATOMIC_POSITIONS (crystal)
> Cr1   0.012000  0.25  0.201000  1 0 1
> Cr2   0.988000  0.75  0.799000  1 0 1
> Cr2   0.512000  0.25  0.299000  1 0 1
> Cr1   0.488000  0.75  0.701000  1 0 1
> As1   0.195000  0.25  0.582000  1 0 1
> As2   0.805000  0.75  0.418000  1 0 1
> As2   0.695000  0.25  0.918000  1 0 1
> As1   0.305000  0.75  0.082000  1 0 1
> K_POINTS {automatic}
>
> 6 8 6 0 0 0
>
>
> 2.interior coordination relaxation:
> All is the same as above, but "ecutwfc = 50"
> 3.self-consistent iteration for phonon calculation:
>  calculation = 'scf' restart_mode = 'from_scratch' prefix = 'cras'
> pseudo_dir = '/data1/tan1/software/espresso-5.1/pseudo/' outdir =
> './tempdir/' tstress = .true. tprnfor = .true. /  ibrav = 0
> celldm(1) = 10.54467182 nat = 8 ntyp = 4 ecutwfc = 50 occupations =
> 'smearing' smearing = 'methfessel-paxton' degauss = 0.05 nspin = 2
> starting_magnetization(1) = -1 starting_magnetization(2) = 1
> starting_magnetization(3) = 0 starting_magnetization(4) = 0 / 
> electron_maxstep = 200 conv_thr = 1.0d-10 mixing_beta = 0.7 /
> ATOMIC_SPECIES Cr1 51.9961 Cr.pz-hgh.UPF Cr2 51.9961 Cr.pz-hgh.UPF As1
> 74.9216 As.pz-hgh.UPF As2 74.9216 As.pz-hgh.UPF CELL_PARAMETERS (alat=
> 10.54467182) 0.9146 0. 0. 0. 0.4765 0. 0. 0. 0.9628
> ATOMIC_POSITIONS (crystal) Cr1 0.0104 0.2500 0.1827 Cr2 0.9896 0.7500
> 0.8173 Cr2 0.5104 0.2500 0.3173 Cr1 0.4896 0.7500 0.6827 As1 0.1833 0.2500
> 0.5616 As2 0.8167 0.7500 0.4384 As2 0.6833 0.2500 0.9384 As1 0.3167 0.7500
> 0.0616 K_POINTS {automatic} 6 8 6 0 0 0
> 4.self-consistent iteration for electron-phonon coupling:
> All is the same as phonon calculation but k-mesh 12 16 12,and in addition
> to "la2F = .true.".
> 5.phonon calculation:
>  tr2_ph = 1.0d-11 prefix = 'cras' fildvscf = 'crasdv' amass(1) =
> 51.9961 amass(2) = 51.9961 amass(3) = 74.9216 amass(4) = 74.9216 outdir =
> './tempdir/', fildyn = 'cras.dyn', electron_phonon='interpolated'
> el_ph_sigma = 0.005, el_ph_nsigma = 10, trans = .true. ldisp = .true.
> alpha_mix(1) = 0.5 recover =.true. nq1 = 2 nq2 = 2 nq3 = 2 /
> 6.q2r:
>  zasr='crystal', fildyn='cras.dyn', flfrc='cras222.fc', la2F=.true. /
> 7. asr='crystal',
> amass(1)=51.9961,amass(2)=51.9961,amass(3)=74.9216,amass(4)=74.9216,
> flfrc='cras222.fc', flfrq='cras.freq', q_in_band_form=.true.,
> la2F=.true.,dos=.false. / 8 0.00 0.00 0.00 50 0.50 0.00
> 0.00 50 0.50 0.785906 0.00 50 0.00 0.00 0.00 50
> 0.00 0.00 0.456275 50 0.50 0.00 0.456275 50 0.50
> 0.785906 0.456275 50 0.00 0.00 0.456275 1
>
> I am eagerly hoping someone can help me.
>
> Thank you.
>
>
> tanlin
>
> 2015.10.20
>
>
> ___
> 

Re: [Pw_forum] quantum espresso latest version installation

[Sridhar Sadasivam]

Sorry please ignore this message. I was supposed to send this to the local
cluster administrators :)
Sridhar

On Wed, Oct 14, 2015 at 10:45 AM, Sridhar Sadasivam <ssad...@purdue.edu>
wrote:

> Hello,
> I am a regular user of quantum espresso on the RCAC clusters. I am writing
> to request the installation of the latest version (QE 5.2.1) and make it
> available as a module. The latest package is available in this link:
> http://qe-forge.org/gf/project/q-e/frs/?action=FrsReleaseBrowse_package_id=18
> Thanks,
> Sridhar
>
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[Pw_forum] quantum espresso latest version installation

[Sridhar Sadasivam]

Hello,
I am a regular user of quantum espresso on the RCAC clusters. I am writing
to request the installation of the latest version (QE 5.2.1) and make it
available as a module. The latest package is available in this link:
http://qe-forge.org/gf/project/q-e/frs/?action=FrsReleaseBrowse_package_id=18
Thanks,
Sridhar
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Re: [Pw_forum] Question on pseudopotential

[Sridhar Sadasivam]

Thanks so much, Mostafa!
-Sridhar

On Tue, Aug 25, 2015 at 5:43 PM, Mostafa Youssef  wrote:

> Hi Sridhar,
>
> Of course you can do this mix. Please have a look at:
>
> http://www.quantum-espresso.org/faq/pseudopotentials/#2.3
>
>
> M. Y.
> MIT
>
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[Pw_forum] Question on pseudopotential

[Sridhar Sadasivam]

Hello espresso users

I am working with a cobalt silicide material. I am thinking of using
Co.pbe-nd-rrkjus.UPF for Co along with Si.pbe-n-rrkjus_psl.0.1.UPF for Si.
Although both are PBE ultrasoft pseudopotentials, the pseudopotential for
Co was generated using the QE PP library while that for Si was generated
using the PS library. Is it okay to use these pseudopotentials (with
different origins) together in one calculation?

Thanks,
Sridhar
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Re: [Pw_forum] Is the phonon line-width gamma positive for a instable mode with negative freqency?

[Sridhar Sadasivam]

Dear Ding-Fu,
As Nicki pointed out, omega(q,v) is imaginary for unstable modes. So
omega^2 is negative and hence lambda is negative.

If you look at the definition of electron-phonon matrix element g, it
contains a sqrt(omega(q,v)) in the denominator. Thus |g|^2 contains
omega(q,v) in the denominator. And this omega(q,v) cancels with the other
omega(q,v) in the formula for gamma. I think this is the reason, that gamma
is still positive for unstable modes.

Sridhar
Graduate Student
Purdue University

On Thu, Feb 12, 2015 at 8:46 AM, Dingfu Shao  wrote:

> Dear Ion,
>
>   Thanks for your reply.  Now I understand it.
>
> Best regards,
>
> Yours Ding-Fu Shao
>
>
> 2015-02-12 15:44 GMT+08:00 Ion Errea :
>
>>  Dear Ding-Fu,
>>
>> Considering that the g contains a omega(q,v)^-1/2, gamma(q,v) is
>> independent of the phonon frequency and, thus, always positive.
>>
>> On the contrary, calculating lambda for a mode with imaginary frequencies
>> makes no sense, as the crystal is unstable in the harmonic approximation.
>>
>> Bests,
>>
>> Ion Errea
>>
>> Donostia International Physics Center (DIPC),
>> Manuel de Lardizabal Pasealekua 4,
>> 20018 Donostia-San Sebastián, Basque Country, Spain
>>
>> Email:  ion.er...@ehu.eus
>> Tel:+34 943 01 54 23
>> Fax:+34 943 01 56 00
>> Web:http://ionerrea.wordpress.com/
>>
>> 12/02/15 02:54(e)an, Dingfu Shao igorleak idatzi zuen:
>>
>>  Dear QE developers and users,
>>
>>When calculating the electron-phonon coupling, the phonon
>> line-width gamma is defined as
>> gamma(q,v) = 2 * pi * omega(q,v) * sum( |g|^2) * delta(E_q) *
>> delta(E_(k+q)).  (1)
>>
>>  And the electron-phonon coupling strength for mode v at q is
>>
>>  lambda(q,v) = gamma(q,v) / (pi * h * N(E_F) * (omega(q,v))^2)
>> (2).
>>
>>  (See
>> http://www.quantum-espresso.org/wp-content/uploads/Doc/ph_user_guide/node12.html
>> )
>>
>>  Accoding to these definitions, it seems that the  phonon line-width
>> gamma(q,v), electron-phonon coupling strength  lambda(q,v) must be BOTH
>> negative when a instable mode with negetive frequency omega(q,v) is
>> calculated.
>>
>>  However, I checked the electron phonon coupling I calculated before, I
>> found with a  negetive omega(q,v), there are negative lambda(q,v) and
>> positive gamma(q,v). I found some similar report, for example, PHYSICAL
>> REVIEW B 86, 155125 (2012), in which the positive gammas were calculated
>> for the instable mode.
>>
>>  That  realy puzzles me. Can anybody explain it?
>>
>>  Thanks a lot!
>>
>>  Best regards,
>>  yours
>>  Ding-Fu Shao
>>
>>
>>
>>
>>
>>
>> --
>>
>>
>> *Ding-Fu Shao, Ph.D *
>>
>> *Institute of Solid State Physics*
>>
>> *Chinese Academy of Sciences*
>>
>> *P. O. Box 1129*
>>
>> *Hefei 230031*
>>
>> *Anhui Province*
>>
>> *P. R. China*
>>
>>
>>
>>
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>>
>>
>>
>
>
> --
>
>
> *Ding-Fu Shao, Ph.D *
>
> *Institute of Solid State Physics*
>
> *Chinese Academy of Sciences*
>
> *P. O. Box 1129*
>
> *Hefei 230031*
>
> *Anhui Province*
>
> *P. R. China*
>
> *Email: dingfu.s...@gmail.com *
>
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Re: [Pw_forum] difference in output from dynmat.x and matdyn.x

[Sridhar Sadasivam]

Dear Lorenzo,
I apologize for getting back so late on this. I had posted a reply but
looks like the email bounced back due to some size restriction on the
attachment. But to answer your question, I did not find a negative
frequency anywhere else in the q-point grid. I am attaching my scf, ph, q2r
and matdyn input files. I am facing the same problem with another crystal
structure of SiO2 as well (cristobalite). I feel like I am making some
mistake in the input files that is probably important for polar materials.

I would really appreciate it if someone could look into it. Thanks!
Sridhar
Purdue University

On Mon, Nov 17, 2014 at 2:34 AM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

>  Dear Sridhar,
> normally the sum rules imposed by matdyn are enough to set the acoustic
> bands at gamma to exactly zero. If this is not the case, it normally means
> that you have some negative frequency somewhere else in the q-point grid.
> Please check the other matdyn files to see if this is the case: the
> frequencies are at the end of the file.
>
> kind regards
>
>
>
> On 17/11/14 02:03, Sridhar Sadasivam wrote:
>
> Dear Stefano,
>
>  Thanks for your reply. Here are the frequencies at gamma point when I
> set zasr and asr to 'simple'
>-12.8981  -12.8981   -4.5998  142.6073  168.0267  168.0267
>   249.0588  249.0588  340.4760  344.4668  379.2589  379.2589
>   417.0274  417.0274  429.6273  457.2113  657.8050  657.8050
>   746.0641  755.8553  755.8553 1032.5200 1032.5200 1037.0491
>  1048.5362 1136.7760 1136.7760
>
>  Thanks,
> Sridhar
>
> On Sun, Nov 16, 2014 at 5:25 AM, stefano de gironcoli <degir...@sissa.it>
> wrote:
>
>>  dear Sridhar Sadasivam
>>   can you try to set zasr and asr to 'simple' in the q2r+matdyn case
>> and report the results ?
>>   thanks
>> stefano
>>
>>
>>
>> On 11/15/2014 11:49 PM, Sridhar Sadasivam wrote:
>>
>>  Dear espresso users and developers,
>>
>>  I am trying to obtain the phonon dispersion of alpha-quartz (SiO2)
>> which has a 9 atom unit cell. I ran ph.x on a 3 x 3 x 3 q-point grid. I am
>> seeing some strange behavior where there seems to be a difference in the
>> frequencies output from dynmat.x and matdyn.x. I will explain my problem
>> below.
>>
>>  I diagonalized the dynamical matrix at the gamma point using dynmat.x
>> with acoustic sum rule set to crsytal. Since SiO2 is a polar material,
>> LO-TO splitting will need to be considered at the gamma point but I am
>> ignoring it currently (I did not specify any direction for LO-TO splitting
>> in the dynmat.x input). This gave me the following 27 frequencies (in
>> cm^-1) at the gamma point: (0,0,0, 152.24, 175.57, 175.57, 256.32, 256.32,
>> 341.09, 354.41, 376.86, 376.86, 419.01, 419.01, 435.37, 455.70, 659.12,
>> 659.12, 744.54, 754.62, 1034.38, 1034.38, 1040.20, 1051.12, 1139.60,
>> 1139.60)
>>
>>  I also used q2r.x (with zasr = 'crystal') to obtain the force constants
>> and then used matdyn.x (with asr = 'crystal') to obtain the frequencies at
>> the gamma point. However with matdyn.x, I obtain the following frequencies
>> at the gamma point: (-29.4088,-22.2535,-22.2535,152.2412,175.8141,175.8141,
>> 256.3373, 256.3373, 341.0892, 355.4227, 376.0495 , 376.0495, 418.6344,
>> 418.6344, 435.3710, 453.6862, 659.7607, 659.7607, 746.4843, 754.8867,
>> 754.8867, 1034.1751, 1034.1751, 1039.7590, 1051.1207, 1139.8191, 1139.8191)
>>
>>  Could someone please explain why I am getting imaginary frequencies
>> from matdyn.x while dynmat.x gives real frequencies at the same q-point
>> (gamma in this case)?
>>
>>  Thanks,
>> Sridhar
>> Purdue University
>>
>>
>>
>>  ___
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>>
>>
>>
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>
>
>
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>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> +33 (0)1 44 275 084 / skype: paulatzhttp://www-int.impmc.upmc.fr/~paulatto/
> 23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
>
>
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SiO2.in
Description: Binary data


matdyn.in.freq
Description: Binary data


q2r.in
Description: Binary data


ph_1.in
Description: Binary data
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Re: [Pw_forum] difference in output from dynmat.x and matdyn.x

[Sridhar Sadasivam]

Dear Stefano,

Thanks for your reply. Here are the frequencies at gamma point when I set
zasr and asr to 'simple'
  -12.8981  -12.8981   -4.5998  142.6073  168.0267  168.0267
  249.0588  249.0588  340.4760  344.4668  379.2589  379.2589
  417.0274  417.0274  429.6273  457.2113  657.8050  657.8050
  746.0641  755.8553  755.8553 1032.5200 1032.5200 1037.0491
 1048.5362 1136.7760 1136.7760

Thanks,
Sridhar

On Sun, Nov 16, 2014 at 5:25 AM, stefano de gironcoli <degir...@sissa.it>
wrote:

>  dear Sridhar Sadasivam
>   can you try to set zasr and asr to 'simple' in the q2r+matdyn case
> and report the results ?
>   thanks
> stefano
>
>
>
> On 11/15/2014 11:49 PM, Sridhar Sadasivam wrote:
>
> Dear espresso users and developers,
>
>  I am trying to obtain the phonon dispersion of alpha-quartz (SiO2) which
> has a 9 atom unit cell. I ran ph.x on a 3 x 3 x 3 q-point grid. I am seeing
> some strange behavior where there seems to be a difference in the
> frequencies output from dynmat.x and matdyn.x. I will explain my problem
> below.
>
>  I diagonalized the dynamical matrix at the gamma point using dynmat.x
> with acoustic sum rule set to crsytal. Since SiO2 is a polar material,
> LO-TO splitting will need to be considered at the gamma point but I am
> ignoring it currently (I did not specify any direction for LO-TO splitting
> in the dynmat.x input). This gave me the following 27 frequencies (in
> cm^-1) at the gamma point: (0,0,0, 152.24, 175.57, 175.57, 256.32, 256.32,
> 341.09, 354.41, 376.86, 376.86, 419.01, 419.01, 435.37, 455.70, 659.12,
> 659.12, 744.54, 754.62, 1034.38, 1034.38, 1040.20, 1051.12, 1139.60,
> 1139.60)
>
>  I also used q2r.x (with zasr = 'crystal') to obtain the force constants
> and then used matdyn.x (with asr = 'crystal') to obtain the frequencies at
> the gamma point. However with matdyn.x, I obtain the following frequencies
> at the gamma point: (-29.4088,-22.2535,-22.2535,152.2412,175.8141,175.8141,
> 256.3373, 256.3373, 341.0892, 355.4227, 376.0495 , 376.0495, 418.6344,
> 418.6344, 435.3710, 453.6862, 659.7607, 659.7607, 746.4843, 754.8867,
> 754.8867, 1034.1751, 1034.1751, 1039.7590, 1051.1207, 1139.8191, 1139.8191)
>
>  Could someone please explain why I am getting imaginary frequencies from
> matdyn.x while dynmat.x gives real frequencies at the same q-point (gamma
> in this case)?
>
>  Thanks,
> Sridhar
> Purdue University
>
>
>
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[Pw_forum] difference in output from dynmat.x and matdyn.x

[Sridhar Sadasivam]

Dear espresso users and developers,

I am trying to obtain the phonon dispersion of alpha-quartz (SiO2) which
has a 9 atom unit cell. I ran ph.x on a 3 x 3 x 3 q-point grid. I am seeing
some strange behavior where there seems to be a difference in the
frequencies output from dynmat.x and matdyn.x. I will explain my problem
below.

I diagonalized the dynamical matrix at the gamma point using dynmat.x with
acoustic sum rule set to crsytal. Since SiO2 is a polar material, LO-TO
splitting will need to be considered at the gamma point but I am ignoring
it currently (I did not specify any direction for LO-TO splitting in the
dynmat.x input). This gave me the following 27 frequencies (in cm^-1) at
the gamma point: (0,0,0, 152.24, 175.57, 175.57, 256.32, 256.32, 341.09,
354.41, 376.86, 376.86, 419.01, 419.01, 435.37, 455.70, 659.12, 659.12,
744.54, 754.62, 1034.38, 1034.38, 1040.20, 1051.12, 1139.60, 1139.60)

I also used q2r.x (with zasr = 'crystal') to obtain the force constants and
then used matdyn.x (with asr = 'crystal') to obtain the frequencies at the
gamma point. However with matdyn.x, I obtain the following frequencies at
the gamma point: (-29.4088,-22.2535,-22.2535,152.2412,175.8141,175.8141,
256.3373, 256.3373, 341.0892, 355.4227, 376.0495 , 376.0495, 418.6344,
418.6344, 435.3710, 453.6862, 659.7607, 659.7607, 746.4843, 754.8867,
754.8867, 1034.1751, 1034.1751, 1039.7590, 1051.1207, 1139.8191, 1139.8191)

Could someone please explain why I am getting imaginary frequencies from
matdyn.x while dynmat.x gives real frequencies at the same q-point (gamma
in this case)?

Thanks,
Sridhar
Purdue University
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Re: [Pw_forum] wrong representation

[Sridhar Sadasivam]

>From release notes:
Fixed in 5.0.3 version:
[...]
   * PHonon: restart with convt=.true. was not working with PAW
   * PHonon: in matdyn.x, displacement patterns were no longer correct
 if eigenvectors of the dynamical matrix were also written to file
   * PHonon: compatibility with files produced by previous releases
 was broken if pools were used
   * VERY NASTY PHonon bug: symmetry Sq=-q+G introduced in v.5.0.2
 could lead to bad phonons in some cases and has been disabled
   * PHonon: effective charges eu + PAW were not accurate with pools;
 effective charges eu + US PP + spin-orbit nonmagnetic were not
 working in parallel.

Seems like 5.0.2 has some nasty bug in the phonon module. I don't know if
this is the problem but I would suggest trying out the latest version 5.1
or at least 5.0.3.
Sridhar
Graduate Student
Purdue University

On Sun, Oct 19, 2014 at 5:41 AM, Alwaleed Adllan 
wrote:

> Dear quantum espresso users
>
> I am running Phonon calculation for BaF2 324 atoms simple cubic
>  supercell. I got the following  error
>"Error in routine set_irr_sym_new (8122):
>   wrong representation"
>  using quantum espresso-5.0.2
>
>  the same calculation is running for scf without any error
>  Regards
>
> Alwaleed Ahmed Adllan
>
>
> *Technical Operations Manager Sudan Center for HPC and Grid Computing *
> *Africa City of Technology*
>
>
>
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[Pw_forum] elphon.f90

[Sridhar Sadasivam]

Dear espresso users and developers,

I have a couple of clarifications regarding the implementation of
electron-phonon coupling in elphon.f90. I am not sure if I am understanding
things correctly, so I would really appreciate some help.

1. After the call to elphon.f90, I believe el_ph_mat (ibnd,jbnd,k,disp)
contains the electron-phonon matrix element for coupling between an
electron of wavevector k in band 'ibnd' to an electron of wavevector k+q in
band 'jbnd' due to the displacement pattern given by disp. The displacement
patterns are given by the perturbations stored in the data-file.q.xml
files. Is my understanding correct?

2. I would like to obtain the matrix elements for coupling corresponding to
a particular phonon eigenmode, say u_{q,nu}, where nu is the mode number.
To do this, I think I would just need to do a linear combination of the
coupling matrix elements for the various displacement patterns (contained
in el_ph_mat) where the coefficients of the linear combination are the same
coefficients needed to express the phonon eigenvector in terms of the
displacement patterns stored in data-file.q.xml file. Is this correct?

Thanks in advance.
Sridhar
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[Pw_forum] Electron-phonon coupling code

[Sridhar Sadasivam]

Dear espresso users and developers,

I am trying to read through the electron-phonon coupling code and have a
few questions.

1. From phq_readin.f90
  SELECT CASE( trim( electron_phonon ) )
  CASE( 'simple' )
 elph=.true.
 elph_mat=.false.
 elph_simple=.true.
  CASE( 'Wannier' )
 elph=.true.
 elph_mat=.true.
 elph_simple=.false.
 auxdvscf=trim(fildvscf)
  CASE( 'interpolated' )
 elph=.true.
 elph_mat=.false.
 elph_simple=.false.
  CASE DEFAULT
 elph=.false.
 elph_mat=.false.
 elph_simple=.false.
  END SELECT

What does the case electron_phonon = 'Wannier' correspond to? I see from
phonon.f90 that the code would call ep_matrix_element_wannier.f90 if
elph_mat = .true. but this does not seem to be explained anywhere in the
documentation (
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PH.html#idp74656
)? Is this similar to an external program EPW which performs Wannier
interpolation from coarse to fine k-point grids.

2. From phonon.f90

   IF ( elph_mat ) then
  call ep_matrix_element_wannier()
   ELSE
  CALL elphon()
   END IF

elph_mat = .false. for both electron_phonon = 'simple' and electron_phonon
= 'interpolated'. So I guess elphon.f90 is invoked in both simple and
interpolated cases. Also in elphon.f90, there is no mention of the variable
'elph_simple'. It looks to me that both simple and interpolated cases would
lead to the same code being run. Where exactly is there a difference
between these two cases?

Thanks so much in advance!
Sridhar
Graduate Student
Purdue University
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[Pw_forum] problem with espresso 4.0.3

[Sridhar Sadasivam]

Dear espresso users and developers,

First of all, I apologize for requesting help with a very old version, but
I am forced to use espresso 4.0.3 as EPW is not compatible with any of the
newer versions. I tried running a simple silicon scf calculation with
espresso 4.0.3 but the code stops with the error that charge is wrong. I
have attached the input and output files. Newer versions (4.3.2, 5.0.3)
work fine with the same input file.

I obtain similar error with a simple aluminum scf calculation as well.

I would really appreciate any help or hints about what could be the
problem. Thanks,
Sridhar
Graduate Student
Purdue University
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[Pw_forum] Non-orthogonal modes with dynmat.x at gamma point

[Sridhar Sadasivam]

If you are talking about the vectors printed in the matdyn.modes file, then
yes they are not orthogonal as those are actually eigendisplacements and
not the eigenvectors of the dynamical matrix. But if you multiply the
eigendisplacements of each atom by the square root of the corresponding
atomic mass, then the resulting eigenvectors will be orthogonal.

Hope that helps.
Sridhar


On Wed, Aug 27, 2014 at 8:53 PM, Florian Altvater 
wrote:

> Hi,
> I calculated the phonons for an isolated naphthalene molecule as well as
> naphthalene crystal at q = (0,0,0). After diagonalizing the dynamical
> matrix with dynmat.x and enforcing the appropriate acoustic sum rule -
> "zero-dim" and "crystal" respectively - I get 6 and 3 acoustic modes
> with frequencies of 0 cm^-1. So far so good.
>
> If I use the displacements printed to dynmat.out (filout) and calculate
> the various scalar products of the modes, i.e. c_ij = m_i . m_j, I find
> that they are normalized but not orthogonal (c_ij != 0 for some i != j).
> Some of the overlaps c_ij are as high as 0.75, so it is not just
> numerical noise. By trying to find more information in the source files,
> I discovered that matdyn.x prints two files, flvec and fleig, where
> flvec prints non-orthogonal normalized vectors. So I thought that this
> could be the issue, as it is not clearly stated if dynmat prints
> eigenvectors or normalized modes like flvec. However, multiplying with
> the masses didn't help either.
>
> Is dynmat.x not printing eigenvectors? If it is/should, what could be
> the problem here? How would I debug the problem?
>
> Thanks so much for you help!
> Flo
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[Pw_forum] problem in plotting fermi surface using xcrysden for 2D material

[Sridhar Sadasivam]

It may be related to this:
http://www.democritos.it/pipermail/xcrysden/2009-May/000634.html
Try increasing the number of k-points along the non-periodic direction to 3.
Sridhar


On Thu, Jul 3, 2014 at 3:44 AM, Anjali Singh 
wrote:

> Hello Everyone,
>
> I am getting problem in plotting fermi surface for 2D material.
> The particular band which is overlapping with fermi level.
> when I am trying to plot it, xcrysden is getting crashed.
>
> Can somebody help me?
>
> --
> With Thanks and Regards
> Anjali Singh
>
>
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[Pw_forum] calculation of lifetime due to anharmonic phonon–phonon interaction with QE software

[Sridhar Sadasivam]

QE does not directly calculate phonon lifetimes but it is possible to
calculate the third-order anharmonic force constants from which you can
derive lifetime. d3.x is the program that is used to calculate third-order
force constants.
Sridhar
Purdue University


On Tue, Jun 17, 2014 at 10:44 PM, JAONA RANDRIANALISOA <
jaona.randrianalisoa at univ-reims.fr> wrote:

> Dear All,
>
> I am new user of Quantum Espresso software and my research focus
> concerns mainly thermal properties of materials (more particularly
> silicon nanostructures).
>
> I would like to know if it is possible to calculate "the lifetime due to
> anharmonic phonon?phonon interaction" with
> arbitrary wavevectors with QE package v5.1.
>
> Best regards,
>
> Jaona Randriaalisoa, Assistant Professor
> Universit? de Reims Champagne-Ardenne
>
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> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] Reg: q is not a vector in the dense grid.

[Sridhar Sadasivam]

If you want to compute electron-phonon interaction for a phonon of
wavevector q, you will need electron wavefunctions at k and k+q. Thus your
grid for scf should always be a multiple of your q-point grid for phonon
calculations. Since 8 is a multiple of 2 and 4 but not 6, you are getting
this error. Hope that helps.
Sridhar
Purdue University


On Sun, Jun 1, 2014 at 9:36 AM, Peram sreenivasa reddy <
peramsreenivas at gmail.com> wrote:

> Dear Pwscf,
>
>
> In my phonon calculations i got some error.
>
> For nq1=2, nq2=2, nq3=2 and nq1=4, nq2=4, nq3=4 i did not get any errors.
>
> But for nq1=6, nq2=6, nq3=6 grid i got the bellow error.
>
> Diagonalizing the dynamical matrix
>
>  q = (   -0.16667   0.16667  -0.16667 )
>
>  **
>  omega( 1) =   1.218152 [THz] =  40.633179 [cm-1]
>  omega( 2) =   1.218152 [THz] =  40.633179 [cm-1]
>  omega( 3) =   2.760322 [THz] =  92.074433 [cm-1]
>  omega( 4) =   3.157206 [THz] = 105.313054 [cm-1]
>  omega( 5) =   3.157206 [THz] = 105.313054 [cm-1]
>  omega( 6) =   3.160843 [THz] = 105.434373 [cm-1]
>  omega( 7) =   6.119555 [THz] = 204.126381 [cm-1]
>  omega( 8) =   6.129602 [THz] = 204.461528 [cm-1]
>  omega( 9) =   6.129602 [THz] = 204.461528 [cm-1]
>  omega(10) =   9.495441 [THz] = 316.733825 [cm-1]
>  omega(11) =   9.521102 [THz] = 317.589790 [cm-1]
>  omega(12) =   9.521102 [THz] = 317.589790 [cm-1]
>  **
>
>  Mode symmetry, C_3v (3m)   point group:
>
>  omega(  1 -  2) = 40.6  [cm-1]   --> EL_3
>  omega(  3 -  3) = 92.1  [cm-1]   --> A_1  L_1
>  omega(  4 -  5) =105.3  [cm-1]   --> EL_3
>  omega(  6 -  6) =105.4  [cm-1]   --> A_1  L_1
>  omega(  7 -  7) =204.1  [cm-1]   --> A_1  L_1
>  omega(  8 -  9) =204.5  [cm-1]   --> EL_3
>  omega( 10 - 10) =316.7  [cm-1]   --> A_1  L_1
>  omega( 11 - 12) =317.6  [cm-1]   --> EL_3
>
>  **
>  electron-phonon interaction  ...
>
>
>
>  
> %%
>  from elphsum : error # 3
>  q is not a vector in the dense grid
>
>  
> %%
>
>  stopping ...
>
>
>  
> %%
>  from elphsum : error # 3
>  q is not a vector in the dense grid
>
>  
> %%
>
> This error came after completing my first q point.
>
>
> Is this q grid is correct for the given k points mesh?
>
> Is it better to increase it to nq1=8, nq2=8, nq3=8. ?
>
> Thank you very much in advance.
>
>
>
>
>
>
>
> --
> *P.V.SREENIVASA REDDY*
>
> *Research ScholarDepartment of Physics *
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] How to add supercell to QE i/p file

[Sridhar Sadasivam]

I usually just write a small code to generate supercells. Knowing the
primitive lattice vectors and basis atoms (2 for graphene), it is very easy
to write a small code that can be used to generate a NxN supercell. You can
then also visualize in XCrysden to make sure that you have generated the
structure correctly.

You can use XCrysden to get the k-point path as well. Just remember that
the k-point path obtained from XCrysden is in crystal units.
Sridhar


On Thu, May 29, 2014 at 5:01 AM, siddheshwar chopra wrote:

> Dear users,
> Somebody please help me in making my first i/p file in QE for graphene. I
> want to find band gap of a 4x4x1 supercell of graphene..
> Also how do we  find k point path? Please help...
>
> Regards,
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] Real space force constants file

[Sridhar Sadasivam]

Thanks so much Prof. Giannozzi. I apologize for repeating the question.
Sridhar


On Wed, May 28, 2014 at 1:31 AM, Paolo Giannozzi
wrote:

> I just added point 7.7 of the FAQs, since this question is asked
> more often than not: http://www.quantum-espresso.org/faq/phonons/#7.7
>
> P.
>
> On Tue, 2014-05-27 at 09:20 +0530, Sridhar Sadasivam wrote:
> > Dear QE users and developers,
> >
> >
> > I am trying to use the real space force constants file obtained from
> > q2r.x to do some other calculations outside of QE. For this purpose, I
> > am trying to understand the format of the force constants file. I am
> > attaching a sample force constants file obtained by performing ph.x
> > and q2r.x on bulk silicon with a 4 x 4 x 4 q-mesh.
> >
> >
> > In the 22nd line in the file, it says 1 1 1 1. I believe the first two
> > 1's denote the x-direction and the last two 1's denote atom numbers
> > within the two-atom unit cell of silicon. After this it loops over all
> > 64 different combinations of indices in a 4 x 4 x 4 mesh and lists the
> > force constants in the 4th column. What do these 64 different
> > combinations mean? Do they denote unit cells?
> >
> >
> > For instance, let's take the first line: 1 1 1 2.6997. 2.6997 is the
> > force constant between which atoms?
> >
> >
> > Thanks for your help!
> > Sridhar
> > Purdue University
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] Real space force constants file

[Sridhar Sadasivam]

Dear QE users and developers,

I am trying to use the real space force constants file obtained from q2r.x
to do some other calculations outside of QE. For this purpose, I am trying
to understand the format of the force constants file. I am attaching a
sample force constants file obtained by performing ph.x and q2r.x on bulk
silicon with a 4 x 4 x 4 q-mesh.

In the 22nd line in the file, it says 1 1 1 1. I believe the first two 1's
denote the x-direction and the last two 1's denote atom numbers within the
two-atom unit cell of silicon. After this it loops over all 64 different
combinations of indices in a 4 x 4 x 4 mesh and lists the force constants
in the 4th column. What do these 64 different combinations mean? Do they
denote unit cells?

For instance, let's take the first line: 1 1 1 2.6997. 2.6997 is the force
constant between which atoms?

Thanks for your help!
Sridhar
Purdue University
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[Pw_forum] Factor M in electron-phonon coupling matrix element

[Sridhar Sadasivam]

Prof. Giannozzi,

Thanks for your reply. Yes I also think the formula is valid only for
single-atom unit cells.

I checked Ziman's textbook and it looks like there needs to be a summation
over the atoms in the unit cell for a multi-atom cell. Can I assume that QE
(5.0.3) implements the correct formula for multi-atom unit cell although
the formula given in the user guide is only valid for a single atom cell?

Thanks,
Sridhar


On Mon, May 19, 2014 at 1:57 AM, Paolo Giannozzi
wrote:

> M should be the nuclear mass, if I remember correctly (these
> formulas are valid for crystals with a single kind of atoms,
> if I remember correctly)
>
> P.
>
> On Sat, 2014-05-17 at 18:02 +0530, Sridhar Sadasivam wrote:
> > Dear QE users and developers,
> >
> >
> > I am writing to ask for a small clarification in the formula that
> > defines the electron-phonon coupling matrix element (Equation 1 in the
> > phonon user guide:
> > http://www.quantum-espresso.org/wp-content/uploads/Doc/ph_user_guide.pdf)
> >
> >
> > What is 'M' in Equation 1? Is it the total mass of the unit cell?
> >
> >
> > Thanks,
> > Sridhar
> > Purdue University
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Factor M in electron-phonon coupling matrix element

[Sridhar Sadasivam]

Dear QE users and developers,

I am writing to ask for a small clarification in the formula that defines
the electron-phonon coupling matrix element (Equation 1 in the phonon user
guide:
http://www.quantum-espresso.org/wp-content/uploads/Doc/ph_user_guide.pdf )

What is 'M' in Equation 1? Is it the total mass of the unit cell?

Thanks,
Sridhar
Purdue University
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[Pw_forum] About zero forces.

[Sridhar Sadasivam]

I think the forces are zero because of symmetry in the bulk. You should try
vc-relax.


On Wed, Apr 2, 2014 at 3:08 PM, Mutlu COLAKOGULLARI wrote:

> Hello People,
>
> I want to relax CoPt bulk material. It has face-centered tetragonal (tP4)
> structural type. The relaxation is always finisihing after 1 scf cycle and
> 0 bfgs step. The forces are always zero. I mean the system is not relaxing.
> I googled the problem and I tried something in input, nevertheless I failed
> for every try. What am I doing something wrong? Do you have any suggestion
> or comment or web page?
> I am using svn version with latest updates.
> Here is my input file:
>
>  
> calculation   = 'relax',
> restart_mode  = 'from_scratch',
> pseudo_dir= '/home/mutlusan/Desktop/CoPt/pseudos',
> outdir= '/home/mutlusan/Desktop/CoPt/outdir.CoPt',
> prefix= 'CoPt',
> tprnfor   = .true.
> tstress   = .true.
>  wf_collect= .true.
> !etot_conv_thr = 1.0D-12,
> !forc_conv_thr = 1.0D-11 ,
> nstep = 300  ,
>disk_io = 'low'
>  /
>  
>ibrav = 6,
>   celldm(1)= 7.182849031  !a=3.801 A
>   celldm(3)= 0.979479084  !c=3.723 A
> ntyp = 2,
>   nat = 4,
>   ecutwfc = 85,
>   ecutrho = 850,
>   occupations = 'smearing'
>  smearing = 'mv'
>   degauss = 0.01
>  nspin=2
>  starting_magnetization(1)=0.5
>  /
>  
> conv_thr = 1.0d-8,
> diagonalization  = 'david'
> diago_david_ndim = 8
> mixing_mode  = 'plain'
> mixing_beta  = 0.7
> mixing_ndim   = 8
>  /
>
>  
> !   upscale=100,
>   ion_dynamics  = "bfgs",
>   bfgs_ndim = 8
> /
> !CELL_PARAMETERS
> !  7.182849031   0.00   0.00
> !  0.00   7.182849031   0.00
> !  0.00   0.00   7.0355450393
> ATOMIC_SPECIES
>   Co58.9332  Co.pbe-sp-van.UPF
>   Pt   195.0800  Pt.pbe-n-van.UPF
> ATOMIC_POSITIONS (crystal)
> Co 0.00.00.0
> Co 0.50.50.0
> Pt 0.50.00.5
> Pt 0.00.50.5
>   K_POINTS automatic
> 8 8 8 1 1 1
>
> I have attached the output file.
>
> with my best wishes,
>
>  Mutlu.
> __
> Mutlu COLAKOGULLARI
> Phone : +90 (284) 235 1179 (ext: 1207)
> Address  :  Trakya University
>Sciences Faculty,  Department of Physics,
>Balkan Campus, (22100) Merkez - Edirne - TURKEY
> Home page: http://goo.gl/DNXfNC
> __
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] regarding thermal conductivity

[Sridhar Sadasivam]

Well, this is not very straightforward. This paper gives you an idea:
http://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.085204
Sridhar
Purdue University


On Wed, Mar 26, 2014 at 7:16 AM, xirainbow  wrote:

> Sorry, I do not think so.
>
> On Wed, Mar 26, 2014 at 1:07 AM, kulwinder kaur 
> wrote:
> >
> > hello QE user
> >
> > how can i find thermal conductivity using quantum espresso code?
> >
> >
> >
> >
> >
> > --
> > Regards
> > kulwinder kaur
> > physics department
> > panjab university chandigarh
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> --
> 
> Hui Wang
> School of physics, Henan University of Science and Technology, Henan, China
> ___
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[Pw_forum] electrostatic potential

[Sridhar Sadasivam]

I think V_bare means the potential due to the nuclei and V_hartree is the
potential due to electrons. The units of the potential are in Ry.
Sridhar
Purdue University


On Fri, Mar 21, 2014 at 10:00 PM, DELLACA' Valentina (CRF) <
valentina.dellaca at crf.it> wrote:

> Dear all,
>
> In my understanding, to plot the electrostatic potential of a crystal one
> needs to perform a post processing run with pp.x, with plot_num=11. I was
> wondering the exact meaning of the  V_bare  and  V_H potential, and in
> which units the results come out.
>
> Thanks a lot!
>
> Valentina
>
>
>
> Valentina Dellac?
> Group Materials Labs
> PA - Materials CAE Development & Virtual Analysis
>
>
>
> Centro Ricerche Fiat S.C.p.A.
> Sede legale e amministrativa: Strada Torino, 50
> 10043 Orbassano (TO), Italia
> Tel  +39 011 9083138
> Fax +39 011 9083666
>
> www.crf.it
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] a2Fq2r files - electron-phonon coupling

[Sridhar Sadasivam]

Dear Prof. Giannozzi,

Thanks for your reply. Yes the coupling matrix elements do not depend on
the broadening. I agree.

My problem is this: how to extract the raw electron-phonon matrix elements
from Quantum Espresso? I understand how to obtain related quantities such
as phonon line widths and Eliashberg function. But I would like to obtain
the raw matrix elements. Is this possible and has anyone done it before?

Thanks,
Sridhar



On Fri, Mar 14, 2014 at 3:33 PM, Paolo Giannozzi
wrote:

> On Fri, 2014-03-14 at 09:32 +0530, Sridhar Sadasivam wrote:
>
> > Prof. Giannozzi, you had answered that they contain the
> > electron-phonon coupling matrix elements [...] could you
> > please explain the format of these files?
>
> no: I don't want to hear about electron-phonon coefficients
>
> > I also don't understand why the coupling matrix elements would depend
> > on broadening values.
>
> why do you think that coupling matrix elements depend upon the
> broadening? they don't. Where do you see it?
>
> P.
>
> >  For example, if you look at the definition of the electron-phonon
> > coefficients in the link below (see Equation 1 in Appendix), it does
> > not have any delta functions. Only the line width (and the Eliashberg
> > function, lambda) have delta functions in them and hence would depend
> > on the choice of broadening parameter.
> >
> >
> > http://www.quantum-espresso.org/wp-content/uploads/Doc/ph_user_guide.pdf
> >
> >
> >
> > I am very confused and I would really appreciate any sort of help.
> > Thanks a lot,
> > Sridhar
> > Purdue University
> >
> >
> > On Thu, Mar 13, 2014 at 10:53 AM, Sridhar Sadasivam
> >  wrote:
> > Hello,
> >
> >
> > I have a question about electron-phonon coupling in Quantum
> > Espresso. When ph.x is run with electron-phonon coupling (la2F
> > = .true.), it outputs a series of files a2Fq2r.* (* = 51-60).
> > Could someone explain what exactly is contained in these
> > files? Do they contain the electron-phonon coupling matrix
> > elements?
> >
> >
> > I did not find much information on this in the documentation.
> > Thank you!
> > Sridhar
> > Purdue University
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
>  Paolo Giannozzi, Dept. Chemistry,
>  Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>  Phone +39-0432-558216, fax +39-0432-558222
>
> ___
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> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] a2Fq2r files - electron-phonon coupling

[Sridhar Sadasivam]

I found the same question already asked in this forum a few years back:
http://qe-forge.org/pipermail/pw_forum/2010-May/091560.html

Prof. Giannozzi, you had answered that they contain the electron-phonon
coupling matrix elements. But I still do not understand the format of these
files. I am actually interested in getting the raw coupling matrix elements
instead of the other outputs such as Eliashberg function or the lambda
values. So could you please explain the format of these files?

I also don't understand why the coupling matrix elements would depend on
broadening values. For example, if you look at the definition of the
electron-phonon coefficients in the link below (see Equation 1 in
Appendix), it does not have any delta functions. Only the line width (and
the Eliashberg function, lambda) have delta functions in them and hence
would depend on the choice of broadening parameter.

http://www.quantum-espresso.org/wp-content/uploads/Doc/ph_user_guide.pdf

I am very confused and I would really appreciate any sort of help. Thanks a
lot,
Sridhar
Purdue University


On Thu, Mar 13, 2014 at 10:53 AM, Sridhar Sadasivam wrote:

> Hello,
>
> I have a question about electron-phonon coupling in Quantum Espresso. When
> ph.x is run with electron-phonon coupling (la2F = .true.), it outputs a
> series of files a2Fq2r.* (* = 51-60). Could someone explain what exactly is
> contained in these files? Do they contain the electron-phonon coupling
> matrix elements?
>
> I did not find much information on this in the documentation. Thank you!
> Sridhar
> Purdue University
>
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[Pw_forum] a2Fq2r files - electron-phonon coupling

[Sridhar Sadasivam]

Hello,

I have a question about electron-phonon coupling in Quantum Espresso. When
ph.x is run with electron-phonon coupling (la2F = .true.), it outputs a
series of files a2Fq2r.* (* = 51-60). Could someone explain what exactly is
contained in these files? Do they contain the electron-phonon coupling
matrix elements?

I did not find much information on this in the documentation. Thank you!
Sridhar
Purdue University
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[Pw_forum] Problems with interrupted electron-phonon coupling calculation

[Sridhar Sadasivam]

I just thought I will restate my question, in case it wasn't clear last
time. In the case of a phonon only calculation at a particular q point, it
is possible to run the phonon calculation for different irreps separately
and then copy the data-file.q.irr.xml files into a common place and then
run the phonon calculation again after setting recover = .true., to obtain
the dynamical matrix for that q point. This is essentially grid
parallelization.

I need do this for an electron-phonon calculation. Could someone help me
with what output files that I have to copy from the runs on different
irreps so that I can get the correct electron-phonon coupling results when
I run all irreps together after setting recover = .true.?

Thank you and I would really appreciate any help.
Sridhar
Graduate Student
Purdue University


On Fri, Mar 7, 2014 at 1:45 PM, Sridhar Sadasivam wrote:

> I am using espresso 5.0.3. Thanks,
> Sridhar
>
>
> On Fri, Mar 7, 2014 at 1:30 PM, Paolo Giannozzi  uniud.it>wrote:
>
>> Code version? P.
>>
>> On Thu, 2014-03-06 at 23:36 +0530, Sridhar Sadasivam wrote:
>> > Hello,
>> >
>> >
>> > I am working on an electron-phonon coupling calculation of a large
>> > system (30 atoms). At each q-point I will have 30 x 3 = 90 irreducible
>> > representations. This will take a lot of computer time and I expect
>> > that my calculation will be interrupted (due to max wall time
>> > limitations in the computing cluster I use). So I will need to restart
>> > the calculation many times.
>> >
>> >
>> > To test if everything runs fine, I tried to run an electron-phonon
>> > coupling calculation on a simple 1 atom system. For a particular
>> > q-point I had 2 irreducible representations and I interrupted my
>> > calculation after the self-consistent calculation for the 1st
>> > representation. I then restarted the calculation setting "recover
>> > = .true.". The calculation starts with the 2nd representation and
>> > seems to complete, but the electron-phonon linewidths are wrong, i.e.,
>> > the results don't match the results I get when I run without any
>> > interruption. The phonon frequencies are correct in the interrupted
>> > calculation but the electron-phonon results are not. For some reason,
>> > restarting an interrupted ph.x calculation does not give the correct
>> > results for electron-phonon coupling.
>> >
>> >
>> > Does anyone know how I can resolve this issue? This is crucial as I
>> > will not be able to run the large system (30 atoms) without having to
>> > restart many times.
>> >
>> >
>> > I would really appreciate if someone could help me out on this. Please
>> > let me know if my question isn't clear and I can attach output files
>> > as well.
>> > Regards,
>> > Sridhar
>> > Purdue University,
>> > USA
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > ___
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>> > http://pwscf.org/mailman/listinfo/pw_forum
>>
>> --
>>  Paolo Giannozzi, Dept. Chemistry,
>>  Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>  Phone +39-0432-558216, fax +39-0432-558222
>>
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>> Pw_forum mailing list
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[Pw_forum] Problems with interrupted electron-phonon coupling calculation

[Sridhar Sadasivam]

I am using espresso 5.0.3. Thanks,
Sridhar


On Fri, Mar 7, 2014 at 1:30 PM, Paolo Giannozzi wrote:

> Code version? P.
>
> On Thu, 2014-03-06 at 23:36 +0530, Sridhar Sadasivam wrote:
> > Hello,
> >
> >
> > I am working on an electron-phonon coupling calculation of a large
> > system (30 atoms). At each q-point I will have 30 x 3 = 90 irreducible
> > representations. This will take a lot of computer time and I expect
> > that my calculation will be interrupted (due to max wall time
> > limitations in the computing cluster I use). So I will need to restart
> > the calculation many times.
> >
> >
> > To test if everything runs fine, I tried to run an electron-phonon
> > coupling calculation on a simple 1 atom system. For a particular
> > q-point I had 2 irreducible representations and I interrupted my
> > calculation after the self-consistent calculation for the 1st
> > representation. I then restarted the calculation setting "recover
> > = .true.". The calculation starts with the 2nd representation and
> > seems to complete, but the electron-phonon linewidths are wrong, i.e.,
> > the results don't match the results I get when I run without any
> > interruption. The phonon frequencies are correct in the interrupted
> > calculation but the electron-phonon results are not. For some reason,
> > restarting an interrupted ph.x calculation does not give the correct
> > results for electron-phonon coupling.
> >
> >
> > Does anyone know how I can resolve this issue? This is crucial as I
> > will not be able to run the large system (30 atoms) without having to
> > restart many times.
> >
> >
> > I would really appreciate if someone could help me out on this. Please
> > let me know if my question isn't clear and I can attach output files
> > as well.
> > Regards,
> > Sridhar
> > Purdue University,
> > USA
> >
> >
> >
> >
> >
> >
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
>  Paolo Giannozzi, Dept. Chemistry,
>  Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>  Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Problems with interrupted electron-phonon coupling calculation

[Sridhar Sadasivam]

Hello,

I am working on an electron-phonon coupling calculation of a large system
(30 atoms). At each q-point I will have 30 x 3 = 90 irreducible
representations. This will take a lot of computer time and I expect that my
calculation will be interrupted (due to max wall time limitations in the
computing cluster I use). So I will need to restart the calculation many
times.

To test if everything runs fine, I tried to run an electron-phonon coupling
calculation on a simple 1 atom system. For a particular q-point I had 2
irreducible representations and I interrupted my calculation after the
self-consistent calculation for the 1st representation. I then restarted
the calculation setting "recover = .true.". The calculation starts with the
2nd representation and seems to complete, but the electron-phonon
linewidths are wrong, i.e., the results don't match the results I get when
I run without any interruption. The phonon frequencies are correct in the
interrupted calculation but the electron-phonon results are not. For some
reason, restarting an interrupted ph.x calculation does not give the
correct results for electron-phonon coupling.

Does anyone know how I can resolve this issue? This is crucial as I will
not be able to run the large system (30 atoms) without having to restart
many times.

I would really appreciate if someone could help me out on this. Please let
me know if my question isn't clear and I can attach output files as well.
Regards,
Sridhar
Purdue University,
USA
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[Pw_forum] Fixing atoms in vc-relax

[Sridhar Sadasivam]

Hello,

I am trying to fix some atoms in a vc-relax simulation, i.e., I want the
relative positions of these atoms to remain the same during vc-relaxation.
I specified 0 0 0 next to the atomic positions of these atoms. However
their relative positions do change. I have tried giving the coordinates of
these atoms in both crystal and angstrom units with no luck.

Their relative positions do remain constant in a relax simulation but not
in a vc-relax simulation. Does anyone know what might be the problem?

Thanks,
Sridhar
Purdue University,
West Lafayette, IN 47906
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