[Pw_forum] Tiwisted bilayer graphene scf calculation
Dear All
I prepared following scf file for twisted bilayer graphene I tried to used
this article phys.rev.b 86,125414 theoretical study of twist bilayer
graphene.
but I do not know when I check the position of atoms in xcrysden every
thing becomes mix up that I prepare in angstrom however in my program that
I produced the position of atoms it seems everything ok. I will appreciate
you help me. Thanks .
This is my scf file:
&control
prefix='bitw',
calculation='scf',
restart_mode='from_scratch',
pseudo_dir = './pseudo/',
outdir='./tmp/'
/
&system
ibrav= 0,
nat=76,
ntyp= 1,
occupations='smearing',
smearing='methfessel-paxton',
degauss =0.02
ecutwfc = 40,
ecutrho = 720,
nbnd = 20,
/
&electrons
conv_thr = 1.0d-10,
mixing_mode = 'plain',
mixing_beta = 0.7,
diagonalization = 'cg',
/
CELL_PARAMETERS{angstrom}
10.8000 1.2471 0
4.3200 9.9766 0
0.0 0.0 6.7
ATOMIC_SPECIES
C 12.0107 C.pz-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C 0 0 0
C 2.16 1.247 0
C 3.6 1.247 0
C 6.48 1.247 0
C 7.92 1.247 0
C 1.44 2.494 0
C 4.32 2.494 0
C 5.76 2.494 0
C 8.64 2.494 0
C 10.08 2.494 0
C 2.16 3.741 0
C 3.6 3.741 0
C 6.48 3.741 0
C 7.92 3.741 0
C 10.8 3.741 0
C 4.32 4.988 0
C 5.76 4.988 0
C 8.64 4.988 0
C 10.08 4.988 0
C 3.6 6.235 0
C 6.48 6.235 0
C 7.92 6.235 0
C 10.9 6.235 0
C 12.24 6.235 0
C 4.32 7.482 0
C 5.76 7.482 0
C 8.64 7.482 0
C 10.08 7.482 0
C 12.96 7.482 0
C 6.48 8.730
C 7.92 8.730
C 10.8 8.730
C 12.24 8.730
C 5.76 9.977 0
C 8.64 9.977 0
C 10.08 9.977 0
C 12.96 9.977 0
C 14.4 9.977 0
C 0 0 6.7
C 1.402 3.281 6.7
C 4.206 0.9843 6.7
C 5.609 1.312 6.7
C 8.413 1.969 6.7
C 9.815 2.297 6.7
C 1.819 1.706 6.7
C 3.221 2.035 6.7
C 6.025 2.691 6.7
C 7.428 3.019 6.7
C 10.23 3.675 6.7
C 11.63 4.003 6.7
C 3.638 3.413 6.7
C 5.04 3.771 6.7
C 7.844 4.397 6.7
C 9.247 4.725 6.7
C 12.05 5.381 6.7
C 2.653 4.463 6.7
C 5.457 5.119 6.7
C 6.859 5.447 6.7
C 9.664 6.104 6.7
C 11.07 6.432 6.7
C 3.07 5.841 6.7
C 4.472 6.169 6.7
C 7.276 6.826 6.7
C 8.678 7.154 6.7
C 11.48 7.816.7
C 12.88 8.138 6.7
C 4.889 7.548 6.7
C 6.291 7.876 6.7
C 9.095 8.532 6.7
C 10.5 8.866.7
C 13.3 9.516 6.7
C 3.904 8.598 6.7
C 6.708 9.254 6.7
C 8.11 9.582 6.7
C 10.91 10.24 6.7
C 12.32 10.57 6.7
K_POINTS automatic
8 8 1 0 0 0
Best Regard
Pourya Ayria
PhD student of Tohoku university Japan
[Pw_forum] phonon calculation
Yes, of course. On Fri, Feb 21, 2014 at 7:52 PM, yelena wrote: > Hello! > > I was using ph.x to calculate phonons at gamma point. I got dynamical > matrix for gamma and atomic displacement, mode symmetry... > I was wondering if this all is possible to get for any other point (K, > M...)? > Best, > Jelena Pesic > PhD Student, > Center for Solid State Physic and New Materials, > Institute of Physics, Belgrade, Serbia > ___ > 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
[Pw_forum] phonon calculation
Hello, Yes, you can get the phonons, eigenvectors, dynamical matrices for any point. Symmetries are only for Gamma. Thank you __ Iyad Al-Qasir, PhD Assistant Professor Department of Nuclear Engineering University of Sharjah Sharjah, UAE On Fri, Feb 21, 2014 at 3:52 PM, yelena wrote: > Hello! > > I was using ph.x to calculate phonons at gamma point. I got dynamical > matrix for gamma and atomic displacement, mode symmetry... > I was wondering if this all is possible to get for any other point (K, > M...)? > Best, > Jelena Pesic > PhD Student, > Center for Solid State Physic and New Materials, > Institute of Physics, Belgrade, Serbia > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140221/bcd778c6/attachment.html
[Pw_forum] Charge density with and without the electric field
Dear Hadi Arefi, Thank you so much for your kind help. I found your reply very helpful. On 21 February 2014 20:03, Hadi Arefi wrote: > Dear Mudit, > > > > I couldn't find a 'charge density difference plot' in supplementary > information but I assume they just calculated the charge density for those > two structures that you mentioned, and subtracted from each other. The > result can be plotted as a distribution of charge in 3D (2D) or you can add > up the values to get a number for different regions [but again I think > total number is still zero]. > > > > Please have a closer look in the pp.x input file [plot_num, nfile, weight > ...] to see how you can do this. Also there are many similar issues from the > past if you search the forum. > > > > Best, > > > > Hadi. > > > > *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] > *On > Behalf Of *Mudit Dixit > *Sent:* 21 February 2014 13:28 > *To:* PWSCF Forum > *Subject:* Re: [Pw_forum] Charge density with and without the electric > field > > > > Dear Hadi Arefi, > > Thanks for the quick response. > > In the second point I meant that in the paper" > http://www.nature.com/nature/journal/v488/n7413/full/nature11340.html"; > authors have calculated induced charge as > > > > ?(G111,E=X)-?(G111,E=0).They have also shown the charge > density difference plot in supporting information. I am unable > to understand how they have obtained the induced charge as a number. > > > > > > Thank you so much for your help. > > Regards, > > Mudit Dixit > > > > On 21 February 2014 18:27, Hadi Arefi wrote: > > Dear Mudit, > > > > > > >My questions are following: > > >1. How apply electric filed in 111 direction. > > > > You simply can redefine your lattice in the way that (111) direction lies > along one of the x, y or z direction, then apply the field along that > direction. > > > > >2. How > > > > ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid. > > > > Not quite sure what you mean but obviously the difference going to be an > array which you can plot using xcrysden. My understanding is that you did > not add external charge by applying electric field and the difference in > charge density will rises from charge reorganisation due to external field > (if there is any) unless you are interested in the local differences. Then > you have the 3D mesh and need to find your points and subtract the values > of equivalent points with and without applying field and then summation. > > > > HTH, > > > > > > Hadi Arefi > > PhD student > > Electronic theory&modeling group > > *Tyndall National Institute* > > University College Cork > > Lee Maltings > > Dyke Parade > > Cork, Ireland > > Tel: +353 21 234 6972 > > Email: *hadi.arefi at tyndall.ie * > > Website: http://www.tyndall.ie > > [image: cid:image001.jpg at 01CBEADB.24D1AE90] <http://www.tyndall.ie/> > > > > . > > > > > > *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] > *On > Behalf Of *Mudit Dixit > *Sent:* 20 February 2014 09:11 > *To:* pw_forum at pwscf.org > *Subject:* [Pw_forum] Charge density with and without the electric field > > > > Dear PW users, > > I am trying to calculate charge density difference (i.e. induced charge) > in presence of Electric Field(G111 direction) and absence of electric > filed. > > > > My questions are following: > > 1. How apply electric filed in 111 direction. > > 2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid. > > > > Thanks a lot for your help. > > > > > > Regards, > > Mudit > > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140221/d84619b1/attachment.html -- next part -- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 3084 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140221/d84619b1/attachment.jpg
[Pw_forum] Charge density with and without the electric field
Dear Hadi Arefi, ??Thanks for the quick response. In the second point I meant that in the paper" http://www.nature.com/nature/journal/v488/n7413/full/nature11340.html"; authors have calculated induced charge as ? ?(G111,E=X)-?(G111,E=0).They have also shown the charge density difference plot in supporting information. I am unable to understand how they have obtained the induced charge as a number. ?Thank you so much for your help. Regards, Mudit Dixit? On 21 February 2014 18:27, Hadi Arefi wrote: > Dear Mudit, > > > > > > >My questions are following: > > >1. How apply electric filed in 111 direction. > > > > You simply can redefine your lattice in the way that (111) direction lies > along one of the x, y or z direction, then apply the field along that > direction. > > > > >2. How > ?? > ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid. > > > > Not quite sure what you mean but obviously the difference going to be an > array which you can plot using xcrysden. My understanding is that you did > not add external charge by applying electric field and the difference in > charge density will rises from charge reorganisation due to external field > (if there is any) unless you are interested in the local differences. Then > you have the 3D mesh and need to find your points and subtract the values > of equivalent points with and without applying field and then summation. > > > > HTH, > > > > > > Hadi Arefi > > PhD student > > Electronic theory&modeling group > > *Tyndall National Institute* > > University College Cork > > Lee Maltings > > Dyke Parade > > Cork, Ireland > > Tel: +353 21 234 6972 > > Email: *hadi.arefi at tyndall.ie * > > Website: http://www.tyndall.ie > > [image: cid:image001.jpg at 01CBEADB.24D1AE90] <http://www.tyndall.ie/> > > > > . > > > > > > *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] > *On > Behalf Of *Mudit Dixit > *Sent:* 20 February 2014 09:11 > *To:* pw_forum at pwscf.org > *Subject:* [Pw_forum] Charge density with and without the electric field > > > > Dear PW users, > > I am trying to calculate charge density difference (i.e. induced charge) > in presence of Electric Field(G111 direction) and absence of electric > filed. > > > > My questions are following: > > 1. How apply electric filed in 111 direction. > > 2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid. > > > > Thanks a lot for your help. > > > > > > Regards, > > Mudit > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140221/ca53c769/attachment.html -- next part -- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 3084 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140221/ca53c769/attachment.jpg
[Pw_forum] phonon calculation
And I could get mode symmetry at any high-symmetry point? On 21 Feb 2014 15:03, xirainbow wrote: > Yes, of course. > > On Fri, Feb 21, 2014 at 7:52 PM, yelena wrote: >> Hello! >> >> I was using ph.x to calculate phonons at gamma point. I got >> dynamical >> matrix for gamma and atomic displacement, mode symmetry... >> I was wondering if this all is possible to get for any other point >> (K, >> M...)? >> Best, >> Jelena Pesic >> PhD Student, >> Center for Solid State Physic and New Materials, >> Institute of Physics, Belgrade, Serbia >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Rh2 Dimer Bond Length.
I think that the problem is that if you push
pseudopotentials with nonlinear core correction
(the "-n-" letter in the pseudopotential name)
so close that they overlap, unpredictable
results may follow
P.
On Fri, 2014-02-21 at 11:52 +, Jack Davis wrote:
> Dear Forum,
>
> I am trying to calculate the bond length of a rhodium dimer in Quantum
> ESPRESSO. However, I am gaining an unnaturally short bond length of c.a. 1.2
> angstrom. I calculated this first as a relaxation, but then carried out scf
> steps with varying bond lengths (from about 1.0 to 3.0 angstroms) and it gave
> similar results. I found that this difference in energy was around 10 Ry
> lower than similar bond lengths. I have tried using different
> pseudopotentials (PBE, PBEsol and pz), reduced smearing and a higher cut off
> but they make little difference. I was wondering if there were any issues
> with my input, or if this is a result of an error in the calculation.
> Attached is my input file from one of the scf steps:
>
> &CONTROL
> calculation = "scf",
> prefix = "QE",
> pseudo_dir = "/gpfs/bb/nxf093/pseudo",
> etot_conv_thr= 1.0D-4,
> forc_conv_thr= 1.0D-3,
> disk_io = "none",
> nstep= 500,
> /
> &SYSTEM
> ibrav= 0,
> nat = 2,
> ntyp = 1,
> ecutwfc = 55.D0,
> occupations = "smearing",
> smearing = "fd",
> degauss = 0.020,
> tot_charge =0,
> /
> &ELECTRONS
> electron_maxstep = 5000,
> conv_thr = 1.D-5,
> mixing_beta = 0.6D0,
> mixing_mode = "local-TF"
> /
> &IONS
> /
> CELL_PARAMETERS {angstrom}
> 20.00 0.00 0.00
> 0.00 20.00 0.00
> 0.00 0.00 20.00
> ATOMIC_SPECIES
> Rh 102.91 Rh.pbe-spn-kjpaw_psl.0.2.3.UPF
> ATOMIC_POSITIONS {angstrom}
> Rh 0.00.00.0
> Rh 2.00.00.0
> K_POINTS {Gamma}
>
> Best Wishes,
> Niall Falconbridge & Jack Davis
>
> School of Chemistry
> University of Birmingham
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Calculation Precision on QE5.0.2-GPU
hi everyone:
It's my first time to use QE, and I meet some problems that I don't
know how to handle it.
*DESCRIPTION*
At first, I compile the QE5.0.2 without GPU. And I use pw.x to run my
relax.in(attach at the end), using the command:
*[PATH_TO_QE]/bin/pw.x -in relax.in <http://relax.in/>*
By this version, I can run relax.in to the end.
However, when I recompile QE with Nvidia GPU (QE-GPU-r216.tar.gz with
the QE-5.0.2_GPU-r216.patch, and I use CUDA5.5), I meet the one of the Frequent
errors during
execution<http://www.quantum-espresso.org/faq/frequent-errors-during-execution/>,
which is
*%%%*
*Error in routine electrons (1):*
*charge is wrong*
*%%%*
So I change the input file by comment some settings on SYSTEM modules.
*! occupations='smearing',smearing='gaussian',degauss=0.002,*
*! nspin=2*
And then I can run it on my gpu host, using my gpu card. For this
situation, I guess the "*gaussian **smearing" *may lost some precision on
GPU calculation. But I'm not sure that.
*QUESTION*
I feel confused of this situation. My question is
1, Is the GPU's precision not support for some of the QE workload? or
just some algorithms?
2, If it's just for the algorithms problem, which algorithm would be
affect during calculating on GPU version? How should I do when I want to
use GPU to accelera the QE-CPU version?
3, The last question is, what changes would happen to the final result
when I modify the parameter "*occupations" *and* "**smearing**"*? Just like
the PW/tests/check-pw.x.j, if I don't have the reference, How can I check
whether my result is true when I calculate for the new workload?
Thanks for everyone ! Maybe my chinglish would confuse you, but please
report it to me. Because I really want you help !
Thank you very much !
--
Tobin Chen
Sun Yat-Sen University <http://www.sysu.edu.cn/>, Guangdong, China.
*file relax.in <http://relax.in/>*
&control
calculation = 'vc-relax'
prefix='Na2Fe2As2O',
pseudo_dir
='/home/jin/projects/asc14/suanli/test2/workload1/workload2-upf'
outdir='./tmp'
etot_conv_thr = 1.0E-5 ,
forc_conv_thr = 1.0D-4
tprnfor=.TRUE.
disk_io='none'
/
&system
ibrav=7,
celldm(1) =7.691188393, celldm(3)=3.756265356,
nat=7, ntyp=5,
ecutwfc=40, ecutrho=480,
occupations='smearing',smearing='gaussian',degauss=0.002,
nspin=2
starting_magnetization(2)=0.125
starting_magnetization(3)=-0.125
! nbnd=35
! lda_plus_u=.TRUE.
! Hubbard_U(2)=6.0
/
&electrons
electron_maxstep=300
mixing_beta = 0.3
conv_thr = 1.0d-10
/
&ions
bfgs_ndim= 3,
ion_dynamics='bfgs'
pot_extrapolation = 'second_order' ,
wfc_extrapolation = 'second_order'
/
&CELL
cell_dynamics = 'bfgs'
/
ATOMIC_SPECIES
Na 22.99 Na.pw91-sp-van_ak.UPF
Fe1 55.845 Fe.pw91-sp-van_ak.UPF
Fe2 55.845 Fe.pw91-sp-van_ak.UPF
As 74.92 As.pw91-n-van.UPF
O 16.00 O.pw91-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
Na 0.00 0.00 4.7989032000
Na 0.00 0.0010.4890968000
Fe1 0.00-2.035000 7.644000
Fe2 2.035000 0.00 7.644000
As 0.00 0.00 1.8529056000
As 0.00 0.0013.4350944000
O 0.00 0.00 7.644000
K_POINTS {automatic}
4 4 4 1 1 1
npool=2
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[Pw_forum] Charge density with and without the electric field
Dear Mudit, I couldn?t find a ?charge density difference plot? in supplementary information but I assume they just calculated the charge density for those two structures that you mentioned, and subtracted from each other. The result can be plotted as a distribution of charge in 3D (2D) or you can add up the values to get a number for different regions [but again I think total number is still zero]. Please have a closer look in the pp.x input file [plot_num, nfile, weight ?] to see how you can do this. Also there are many similar issues from the past if you search the forum. Best, Hadi. From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of Mudit Dixit Sent: 21 February 2014 13:28 To: PWSCF Forum Subject: Re: [Pw_forum] Charge density with and without the electric field Dear Hadi Arefi, ??Thanks for the quick response. In the second point I meant that in the paper"http://www.nature.com/nature/journal/v488/n7413/full/nature11340.html"; authors have calculated induced charge as ? ?(G111,E=X)-?(G111,E=0).They have also shown the charge density difference plot in supporting information. I am unable to understand how they have obtained the induced charge as a number. ?Thank you so much for your help. Regards, Mudit Dixit? On 21 February 2014 18:27, Hadi Arefi mailto:hadi.arefi at tyndall.ie>> wrote: Dear Mudit, >My questions are following: >1. How apply electric filed in 111 direction. You simply can redefine your lattice in the way that (111) direction lies along one of the x, y or z direction, then apply the field along that direction. >2. How ?? ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid. Not quite sure what you mean but obviously the difference going to be an array which you can plot using xcrysden. My understanding is that you did not add external charge by applying electric field and the difference in charge density will rises from charge reorganisation due to external field (if there is any) unless you are interested in the local differences. Then you have the 3D mesh and need to find your points and subtract the values of equivalent points with and without applying field and then summation. HTH, Hadi Arefi PhD student Electronic theory&modeling group Tyndall National Institute University College Cork Lee Maltings Dyke Parade Cork, Ireland Tel: +353 21 234 6972 Email: hadi.arefi at tyndall.ie<mailto:hadi.arefi at tyndall.ie> Website: http://www.tyndall.ie<http://www.tyndall.ie/> [cid:image001.jpg at 01CBEADB.24D1AE90]<http://www.tyndall.ie/> . From: pw_forum-bounces at pwscf.org<mailto:pw_forum-bounces at pwscf.org> [mailto:pw_forum-bounces at pwscf.org<mailto:pw_forum-boun...@pwscf.org>] On Behalf Of Mudit Dixit Sent: 20 February 2014 09:11 To: pw_forum at pwscf.org<mailto:pw_forum at pwscf.org> Subject: [Pw_forum] Charge density with and without the electric field Dear PW users, I am trying to calculate charge density difference (i.e. induced charge) in presence of Electric Field(G111 direction) and absence of electric filed. My questions are following: 1. How apply electric filed in 111 direction. 2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid. Thanks a lot for your help. Regards, Mudit ___ Pw_forum mailing list Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org> http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140221/4951de3c/attachment.html -- next part -- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 3084 bytes Desc: image001.jpg Url : http://pwscf.org/pipermail/pw_forum/attachments/20140221/4951de3c/attachment.jpg
[Pw_forum] Rh2 Dimer Bond Length.
Dear Jack,
Why don't you try turning on the spin? Noble metal dimers tend to have
large magnetic moments. I recently ran a similar calculation which gave
about 2.2 A for the bond length and about 4 muB for magnetization.
Hope this helps.
Hande
On Fri, 21 Feb 2014, Jack Davis wrote:
> Dear Forum,
>
> I am trying to calculate the bond length of a rhodium dimer in Quantum
> ESPRESSO. However, I am gaining an unnaturally short bond length of c.a. 1.2
> angstrom. I calculated this first as a relaxation, but then carried out scf
> steps with varying bond lengths (from about 1.0 to 3.0 angstroms) and it gave
> similar results. I found that this difference in energy was around 10 Ry
> lower than similar bond lengths. I have tried using different
> pseudopotentials (PBE, PBEsol and pz), reduced smearing and a higher cut off
> but they make little difference. I was wondering if there were any issues
> with my input, or if this is a result of an error in the calculation.
> Attached is my input file from one of the scf steps:
>
> &CONTROL
> calculation = "scf",
> prefix = "QE",
> pseudo_dir = "/gpfs/bb/nxf093/pseudo",
> etot_conv_thr= 1.0D-4,
> forc_conv_thr= 1.0D-3,
> disk_io = "none",
> nstep= 500,
> /
> &SYSTEM
> ibrav= 0,
> nat = 2,
> ntyp = 1,
> ecutwfc = 55.D0,
> occupations = "smearing",
> smearing = "fd",
> degauss = 0.020,
> tot_charge =0,
> /
> &ELECTRONS
> electron_maxstep = 5000,
> conv_thr = 1.D-5,
> mixing_beta = 0.6D0,
> mixing_mode = "local-TF"
> /
> &IONS
> /
> CELL_PARAMETERS {angstrom}
> 20.00 0.00 0.00
> 0.00 20.00 0.00
> 0.00 0.00 20.00
> ATOMIC_SPECIES
> Rh 102.91 Rh.pbe-spn-kjpaw_psl.0.2.3.UPF
> ATOMIC_POSITIONS {angstrom}
> Rh 0.00.00.0
> Rh 2.00.00.0
> K_POINTS {Gamma}
>
> Best Wishes,
> Niall Falconbridge & Jack Davis
>
> School of Chemistry
> University of Birmingham
>
>
>
--
Hande Toffoli
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande
[Pw_forum] Charge density with and without the electric field
Dear Mudit, >My questions are following: >1. How apply electric filed in 111 direction. You simply can redefine your lattice in the way that (111) direction lies along one of the x, y or z direction, then apply the field along that direction. >2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid. Not quite sure what you mean but obviously the difference going to be an array which you can plot using xcrysden. My understanding is that you did not add external charge by applying electric field and the difference in charge density will rises from charge reorganisation due to external field (if there is any) unless you are interested in the local differences. Then you have the 3D mesh and need to find your points and subtract the values of equivalent points with and without applying field and then summation. HTH, Hadi Arefi PhD student Electronic theory&modeling group Tyndall National Institute University College Cork Lee Maltings Dyke Parade Cork, Ireland Tel: +353 21 234 6972 Email: hadi.arefi at tyndall.ie<mailto:hadi.arefi at tyndall.ie> Website: http://www.tyndall.ie<http://www.tyndall.ie/> [cid:image001.jpg at 01CBEADB.24D1AE90]<http://www.tyndall.ie/> . From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of Mudit Dixit Sent: 20 February 2014 09:11 To: pw_forum at pwscf.org Subject: [Pw_forum] Charge density with and without the electric field Dear PW users, I am trying to calculate charge density difference (i.e. induced charge) in presence of Electric Field(G111 direction) and absence of electric filed. My questions are following: 1. How apply electric filed in 111 direction. 2. How ?(G111,E=X)-?(G111,E=0) give a number not an array on FFT grid. Thanks a lot for your help. Regards, Mudit -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140221/7c7790ba/attachment.html -- next part -- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 3084 bytes Desc: image001.jpg Url : http://pwscf.org/pipermail/pw_forum/attachments/20140221/7c7790ba/attachment.jpg
[Pw_forum] phonon calculation
Hello! I was using ph.x to calculate phonons at gamma point. I got dynamical matrix for gamma and atomic displacement, mode symmetry... I was wondering if this all is possible to get for any other point (K, M...)? Best, Jelena Pesic PhD Student, Center for Solid State Physic and New Materials, Institute of Physics, Belgrade, Serbia
[Pw_forum] Help: pwscf band structure does not agree with published result
In your results there are 26 electrons, 13 bands below the gap. Apart from the 6 deep states, there are 7 bands in the region a few eV under the top of the valence band. In the published results, I count 14 bands in the same region. Either published bands are spin-split, or you aren't comparing bands for the same system P. On Tue, 2014-02-18 at 00:00 -0600, life related wrote: > Hi Pwscfer, > > > I am trying to calculate band structure of WSe2 with pwscf and > compare with published result from paper "Electronic Band Structures > of Molybdenum and Tungsten Dichalcogenides by the GW > Approach"(http://pubs.acs.org/doi/abs/10.1021/jp300079d) > which use wien2k. > > > I can not figure out what need to be done to make the band structure > of WSe2. I have uploaded the inputs & outputs into public google drive > https://drive.google.com/folderview?id=0B3c9yvnT6BoBSG1MT2pZNV9uS00&usp=sharing > > , which is different from bands of WSe2 as shown in the link: > http://pubs.acs.org/action/showImage?doi=10.1021% > 2Fjp300079d&iName=master.img-003.jpg&type=master > > > pwscf relax input: > &control > calculation='relax', > restart_mode='from_scratch', > prefix='SL_MoS2', > tstress = .false., > tprnfor = .false., > nstep = 300, > etot_conv_thr = 1.0d-6, > forc_conv_thr = 4.0d-4, > pseudo_dir = './', > outdir='./', > > > / > &system > ibrav = 4, celldm(1) = 6.202080695, celldm(3) = 3.9488117, nat= 3, > ntyp= 2, > ecutwfc = 60.0, > ecutrho = 550.0, > occupations = 'smearing' > degauss = 1.0d-4, > nbnd = 30 > / > &electrons > diagonalization='david' > mixing_mode = 'local-TF' > mixing_beta = 0.5 > conv_thr = 1.0d-7 > electron_maxstep = 200 > diago_david_ndim = 8 > > > / > &ions > ion_dynamics='bfgs' > / > ATOMIC_SPECIES > W183.84000 W.pbe-nsp-van.bin > Se 78.96000 Se.pbe-n-rrkjus_psl.0.2.UPF > > > ATOMIC_POSITIONS (angstrom) > > > W 0.001.8948643.24 > Se 1.6410000.9474324.910544 > Se 1.6410000.9474321.569456 > > > K_POINTS automatic > 24 24 1 0 0 0 > > > Thanks for your comments and help! > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Calculation Precision on QE5.0.2-GPU
hi everyone:
It's my first time to use QE, and I meet some problems that I don't
know how to handle it.
*DESCRIPTION*
At first, I compile the QE5.0.2 without GPU. And I use pw.x to run my
relax.in(attach at the end), using the command:
*[PATH_TO_QE]/bin/pw.x -in relax.in <http://relax.in>*
By this version, I can run relax.in to the end.
However, when I recompile QE with Nvidia GPU (QE-GPU-r216.tar.gz with
the QE-5.0.2_GPU-r216.patch, and I use CUDA5.5), I meet the one of the Frequent
errors during
execution<http://www.quantum-espresso.org/faq/frequent-errors-during-execution/>,
which is
*%%%*
*Error in routine electrons (1):*
*charge is wrong*
*%%%*
So I change the input file by comment some settings on SYSTEM modules.
*! occupations='smearing',smearing='gaussian',degauss=0.002,*
*! nspin=2*
And then I can run it on my gpu host, using my gpu card. For this
situation, I guess the "*gaussian **smearing" *may lost some precision on
GPU calculation. But I'm not sure that.
*QUESTION*
I feel confused of this situation. My question is
1, Is the GPU's precision not support for some of the QE workload? or
just some algorithms?
2, If it's just for the algorithms problem, which algorithm would be
affect during calculating on GPU version? How should I do when I want to
use GPU to accelera the QE-CPU version?
3, The last question is, what changes would happen to the final result
when I modify the parameter "*occupations" *and* "**smearing**"*? Just like
the PW/tests/check-pw.x.j, if I don't have the reference, How can I check
whether my result is true when I calculate for the new workload?
Thanks for everyone ! Maybe my chinglish would confuse you, but please
report it to me. Because I really want you help !
Thank you very much !
--
Tobin Chen
Sun Yat-Sen University <http://www.sysu.edu.cn/>, Guangdong, China.
*file relax.in <http://relax.in>*
&control
calculation = 'vc-relax'
prefix='Na2Fe2As2O',
pseudo_dir
='/home/jin/projects/asc14/suanli/test2/workload1/workload2-upf'
outdir='./tmp'
etot_conv_thr = 1.0E-5 ,
forc_conv_thr = 1.0D-4
tprnfor=.TRUE.
disk_io='none'
/
&system
ibrav=7,
celldm(1) =7.691188393, celldm(3)=3.756265356,
nat=7, ntyp=5,
ecutwfc=40, ecutrho=480,
occupations='smearing',smearing='gaussian',degauss=0.002,
nspin=2
starting_magnetization(2)=0.125
starting_magnetization(3)=-0.125
! nbnd=35
! lda_plus_u=.TRUE.
! Hubbard_U(2)=6.0
/
&electrons
electron_maxstep=300
mixing_beta = 0.3
conv_thr = 1.0d-10
/
&ions
bfgs_ndim= 3,
ion_dynamics='bfgs'
pot_extrapolation = 'second_order' ,
wfc_extrapolation = 'second_order'
/
&CELL
cell_dynamics = 'bfgs'
/
ATOMIC_SPECIES
Na 22.99 Na.pw91-sp-van_ak.UPF
Fe1 55.845 Fe.pw91-sp-van_ak.UPF
Fe2 55.845 Fe.pw91-sp-van_ak.UPF
As 74.92 As.pw91-n-van.UPF
O 16.00 O.pw91-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
Na 0.00 0.00 4.7989032000
Na 0.00 0.0010.4890968000
Fe1 0.00-2.035000 7.644000
Fe2 2.035000 0.00 7.644000
As 0.00 0.00 1.8529056000
As 0.00 0.0013.4350944000
O 0.00 0.00 7.644000
K_POINTS {automatic}
4 4 4 1 1 1
npool=2
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[Pw_forum] Rh2 Dimer Bond Length.
Dear Forum,
I am trying to calculate the bond length of a rhodium dimer in Quantum
ESPRESSO. However, I am gaining an unnaturally short bond length of c.a. 1.2
angstrom. I calculated this first as a relaxation, but then carried out scf
steps with varying bond lengths (from about 1.0 to 3.0 angstroms) and it gave
similar results. I found that this difference in energy was around 10 Ry lower
than similar bond lengths. I have tried using different pseudopotentials (PBE,
PBEsol and pz), reduced smearing and a higher cut off but they make little
difference. I was wondering if there were any issues with my input, or if this
is a result of an error in the calculation. Attached is my input file from one
of the scf steps:
&CONTROL
calculation = "scf",
prefix = "QE",
pseudo_dir = "/gpfs/bb/nxf093/pseudo",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
disk_io = "none",
nstep= 500,
/
&SYSTEM
ibrav= 0,
nat = 2,
ntyp = 1,
ecutwfc = 55.D0,
occupations = "smearing",
smearing = "fd",
degauss = 0.020,
tot_charge =0,
/
&ELECTRONS
electron_maxstep = 5000,
conv_thr = 1.D-5,
mixing_beta = 0.6D0,
mixing_mode = "local-TF"
/
&IONS
/
CELL_PARAMETERS {angstrom}
20.00 0.00 0.00
0.00 20.00 0.00
0.00 0.00 20.00
ATOMIC_SPECIES
Rh 102.91 Rh.pbe-spn-kjpaw_psl.0.2.3.UPF
ATOMIC_POSITIONS {angstrom}
Rh 0.00.00.0
Rh 2.00.00.0
K_POINTS {Gamma}
Best Wishes,
Niall Falconbridge & Jack Davis
School of Chemistry
University of Birmingham
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[Pw_forum] Band Structure calculation
Thank you very much for the reply. Jamil. From: stefano de gironcoli To: pw_forum at pwscf.org Sent: Thursday, 20 February 2014, 16:59 Subject: Re: [Pw_forum] Band Structure calculation it's what typically happens in a metal... Please provide your affilaition. stefano %--- Stefano de Gironcoli - SISSA & DEMOCRITOS iOn 02/20/2014 03:48 PM, MISSAOUI Jamil wrote: Hi, >In my calculation of band structure I found that the number of electrons in >some points K (occupation numbers) exceeds the total number of electrons of my >system. can it happen? >Best regard. >Jamil. > > > > > >___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140221/2ce03bbf/attachment.html
[Pw_forum] igk files
On 02/21/2014 09:45 AM, Caloma Trumica wrote:
> Dear all,
>
> What data are stored in *.igk{n} files? Also, which f90 code controls
> the output of the igk files.
>
\psi_k(r) = exp(-i r.k) \sum_G u_G exp( -i G.r)
= \sum_G u_G exp( -i (G+k).r)
The G vectors are sorted on the FFT grid in a regular order, i.e. in
unit of reciprocal lattice vectors
G_1 = (0,0,0)
G_2=(0,0,1)
..
G_nx=(0,0,nx-1)
G_nx+1=(0,1,0)
...
G_nx*ny*nz=(nz-1,ny-1,nx-1)
Note that this set of point form a box with the same shape as the
reciprocal lattice unit cell (but much larger).
However, the condition on the cutoff selects a sphere of valid G
points, such as |G+k|^2 < ecutwfc.
The file igk (one for each k point) contains the list of G vector such
that |G+k|^2 < ecutwfc, sorted in order of increasing |G+k|
The list is generated by ./PW/src/gk_sort.f90 and written just afterward
in hinit0.f90 (and in many otehr palces in other codes)
HTH
cheers
> Thanks a lot.
>
--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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[Pw_forum] regarding born-effective charge
> On Thu, 2014-02-20 at 09:19 +0530, himanshu at iopb.res.in wrote: > >> I tried to perform Born-effective charge calculation >> according to the procedure given in example10 of >> Example Directory > > in the newer version of QE, it is in example 04 > >> I first did scf calculation by displacing 0.05Angstrom one >> of the atom along x-axis and then did nscf calculation with >> options lberry=.true.,gdr=1 and nppstr=70. >> >> but i am getting NAN value > > I am not sure I did exactly the same as what you did, > but I don't get any NaN Thanks for the reply I run the example files BP.in and chg.in both are working fine but when i repeat the same exercise with my sample GeSe in that output file I am getting NAN values. I am attaching my input files for scf and nscf calulations. I am thankful if any QE user point out missing terms in my input files. Thanks and regards Himanshu I.O.P. Bhubaneswer > P. > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > 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 > -- next part -- A non-text attachment was scrubbed... Name: input_scf_gese0.0ge_x-0.05.in Type: application/octet-stream Size: 1591 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140221/6cdc2e5c/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: input_nscf_gese0.0ge_x-0.05.in Type: application/octet-stream Size: 1624 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140221/6cdc2e5c/attachment-0001.obj
[Pw_forum] Calculation Precision on QE5.0.2-GPU
Dear Tobin,
you problem is not new, other people (in China) pointed to me about it. So the
issue you see it is 99% due to a possible bug in ADDUSDENS. I have been able to
reproduce it locally on my cluster. Please ad the flag
"-D__DISABLE_CUDA_ADDUSDENS" to make.sys, it will make the issue disappear. I
am investigating during these days to find a fix and I will commit it as fast
as I can.
The ML list for QE-GPU is q-e-gpgpu at qe-forge.org Please send there any
queries concerning the package, I rarely follow what is posted on the main
PWscf mailing-list.
Good luck for the competition
F
On Feb 21, 2014, at 3:56 AM, Tobin Chen wrote:
> hi everyone:
> It's my first time to use QE, and I meet some problems that I don't know
> how to handle it.
> DESCRIPTION
> At first, I compile the QE5.0.2 without GPU. And I use pw.x to run my
> relax.in(attach at the end), using the command:
> [PATH_TO_QE]/bin/pw.x -in relax.in
> By this version, I can run relax.in to the end.
> However, when I recompile QE with Nvidia GPU (QE-GPU-r216.tar.gz with the
> QE-5.0.2_GPU-r216.patch, and I use CUDA5.5), I meet the one of the Frequent
> errors during execution, which is
> %%%
> Error in routine electrons (1):
> charge is wrong
> %%%
> So I change the input file by comment some settings on SYSTEM modules.
> ! occupations='smearing',smearing='gaussian',degauss=0.002,
> ! nspin=2
> And then I can run it on my gpu host, using my gpu card. For this
> situation, I guess the "gaussian smearing" may lost some precision on GPU
> calculation. But I'm not sure that.
>
> QUESTION
> I feel confused of this situation. My question is
> 1, Is the GPU's precision not support for some of the QE workload? or
> just some algorithms?
> 2, If it's just for the algorithms problem, which algorithm would be
> affect during calculating on GPU version? How should I do when I want to use
> GPU to accelera the QE-CPU version?
> 3, The last question is, what changes would happen to the final result
> when I modify the parameter "occupations" and "smearing"? Just like the
> PW/tests/check-pw.x.j, if I don't have the reference, How can I check whether
> my result is true when I calculate for the new workload?
>
> Thanks for everyone ! Maybe my chinglish would confuse you, but please
> report it to me. Because I really want you help !
> Thank you very much !
>
> --
> Tobin Chen
> Sun Yat-Sen University, Guangdong, China.
>
> file relax.in
> &control
>calculation = 'vc-relax'
>prefix='Na2Fe2As2O',
>pseudo_dir ='/home/jin/projects/asc14/suanli/test2/workload1/workload2-upf'
>outdir='./tmp'
> etot_conv_thr = 1.0E-5 ,
> forc_conv_thr = 1.0D-4
>tprnfor=.TRUE.
>disk_io='none'
> /
> &system
>ibrav=7,
>celldm(1) =7.691188393, celldm(3)=3.756265356,
>nat=7, ntyp=5,
>ecutwfc=40, ecutrho=480,
>occupations='smearing',smearing='gaussian',degauss=0.002,
>nspin=2
>starting_magnetization(2)=0.125
>starting_magnetization(3)=-0.125
> ! nbnd=35
> ! lda_plus_u=.TRUE.
> ! Hubbard_U(2)=6.0
> /
> &electrons
>electron_maxstep=300
>mixing_beta = 0.3
>conv_thr = 1.0d-10
> /
> &ions
> bfgs_ndim= 3,
> ion_dynamics='bfgs'
> pot_extrapolation = 'second_order' ,
> wfc_extrapolation = 'second_order'
> /
> &CELL
> cell_dynamics = 'bfgs'
> /
> ATOMIC_SPECIES
> Na 22.99 Na.pw91-sp-van_ak.UPF
> Fe1 55.845 Fe.pw91-sp-van_ak.UPF
> Fe2 55.845 Fe.pw91-sp-van_ak.UPF
> As 74.92 As.pw91-n-van.UPF
> O 16.00 O.pw91-van_ak.UPF
> ATOMIC_POSITIONS {angstrom}
> Na 0.00 0.00 4.7989032000
> Na 0.00 0.0010.4890968000
> Fe1 0.00-2.035000 7.644000
> Fe2 2.035000 0.00 7.644000
> As 0.00 0.00 1.8529056000
> As 0.00 0.0013.4350944000
> O 0.00 0.00 7.644000
> K_POINTS {automatic}
> 4 4 4 1 1 1
> npool=2
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Mr. Filippo SPIGA, M.Sc.
http://www.linkedin.com/in/filippospiga ~ skype: filippo.spiga
?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert
*
Disclaimer: "Please note this message and any attachments are CONFIDENTIAL and
may be privileged or otherwise protected from disclosure. The contents are not
to be disclosed to anyone other than the addressee. Unauthorized recipients are
requested to preserve this confidentiality and to advise the sender immediately
of any error in transmission."
[Pw_forum] Summer school
Dear PWSCF users, You may or may not know that PWSCF contains a built-in interface to CASINO - the Cambridge quantum Monte Carlo code. To cut a long story short -- and exaggerating only slightly -- this in principle allows you to take any system where PWSCF gets the answer wrong, and get it right instead. :-) As this is normally thought to be a useful trick, the authors of CASINO (Neil Drummond, Pablo Lopez Rios, and I) run a quantum Monte Carlo summer school for you every August in the Apuan Alps Centre for Physics in Tuscany, Italy. This year's school - "Quantum Monte Carlo and the CASINO program XI" - will take place from the 2nd to the 10th August. The summer school is also intended as a social occasion, where you can meet like-minded friends, future collaborators, and even wives and husbands (as has happened on multiple occasions in the past). You may also try your hand at hill walking and caving, eating nice food in Tuscan mountain restaurants, and similar enjoyable activities. More details are available from this website: http://vallico.net/casinoqmc/summer-schools/ So, if you want to come to Tuscany next summmer, learn how to use a very useful feature of quantum Espresso, and possibly get married, you are very welcome to apply. Best wishes, Mike Towler PS: We also run a full international QMC conference the week before the summer school which usually attracts around 50 people, so if you already know what you're doing, you might like to come to that instead. See here: http://vallico.net/casinoqmc/conferencesworkshops/ ++ |Dr. Mike Towler (mdt26 at cam.ac.uk) Theory of Condensed Matter (Rm 513)| | Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK | ! ** and University College London * ! |Tel. +44-(0)1223-746644 Mob. +44-(0)7432 491113 Fax. +44-(0)1223-337356| +--: www.tcm.phy.cam.ac.uk/~mdt26 :--+
[Pw_forum] igk files
Dear all,
What data are stored in *.igk{n} files? Also, which f90 code controls the
output of the igk files.
Thanks a lot.
Andy.
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