[Pw_forum] fix the position of a particular atom
Dear PWscf users and developer, I am computing the diffusion barrier in simple metal system. Can I fix the position of a (set of) particular atom during relaxation? which keyword are related to such input? Thanks regards Nay Lin Nanyang Technological University -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100107/859be2b5/attachment.htm
[Pw_forum] How to use plotrho.x to plot 2D graph?
Dear all, I run a pw.x calculation on my system. I wanted to plot the total potential profile vs z (length of the system). I use the post processing tool pp.x and follow the example05 as the following: &inputpp prefix = 'GphBN' outdir = '/pwscf/pwscftemp' filplot = 'totalpotential' plot_num= 1 / &plot nfile = 1 filepp(1) = 'totalpotential' weight(1) = 1.0 iflag = 2 output_format = 2 fileout = 'GphBN.rho.dat' e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, nx=40, ny=40 / --- I got 2 files as indicated above "totalpotential" and "GphBN.rho.dat" where the format of the output is 2 suitable for 2D plot with plotrho.x However, I do not know how to run plotrho.x since there is no details about it. What I found is the example05: --- GphBN.rho.dat GphBN.rho.ps n 0 0.09 6 -- (what does n? 0 0.09 6? stands for) I tried to run it for my calculation but it is giving error message : too many input argument. Does any one have an idea about how to run plotrho.x ? Or does any one have a suggestion to visualize totalpotentail vs z (2D) with other formats (except xcrysden). Thank you in advance for your help. Mohamed S Majdoub Mechanical Engineering University of Houston -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100107/01385748/attachment-0001.htm
[Pw_forum] [Fwd: openmpi problem]
Dear all, I just want to say that I solved my problem installed lam_runtime as root on my machine. Regards, Veronica Mensaje original Asunto: openmpi problem De: Ver?nica Muriel S?nchez Fecha: Jue, 7 de Enero de 2010, 4:56 pm Para: "PWSCF Forum" -- Dear all, My name is Veronica Sanchez, I am doing my PhD at University of Buenos Aires. I want to install the QE code to run it in parallel on my computer. To do this I installed the openmpi-1.4 version. I did the ./configure and the make install inside this directory. When I try to run with mpirun, I get the following error message: mpirun: symbol lookup error: mpirun: undefined symbol: orte_forward_job_control I didn?t find too much information about this error on the web. If anyone has an idea to solve this problem it would be a lot of help! Thanks! Veronica
[Pw_forum] openmpi problem
Dear all, My name is Veronica Sanchez, I am doing my PhD at University of Buenos Aires. I want to install the QE code to run it in parallel on my computer. To do this I installed the openmpi-1.4 version. I did the ./configure and the make install inside this directory. When I try to run with mpirun, I get the following error message: mpirun: symbol lookup error: mpirun: undefined symbol: orte_forward_job_control I didn?t find too much information about this error on the web. If anyone has an idea to solve this problem it would be a lot of help! Thanks! Veronica
[Pw_forum] ecut dependence of symmetry operations(?)
Dear Stefano,
Thanks for your reply. I had not initially realized that discussions in
the forum about symmetry and FFT grid are directly related to its ecut
dependence. I browsed through forum after getting replies, and now have
got some idea about it.
Sincerely,
Madhura.
> Madhura: this has been discussed zilliions of times in this forum, and has
> to do with the way symmetry operations are found out by the code. When the
> symmetry group of the system is non-symmorphic, only those fractional
> translations that are commensurate with the FFT grid are actually found.
> This may sound a bit cryptic, and I leave it as such on purpose. You will
> find much more about this issue by browsing the archives of this mailing
> list. Hope this helps - SB
>
> On Jan 5, 2010, at 12:24 PM, Madhura Marathe wrote:
>
>> Dear all,
>>
>> While performing convergence calculations w.r.t energy cut-off for a
>> bulk
>> system, I found that the number of symmetry operations detected by a
>> code
>> is different depending on the value of ecut. This is very surprising
>> because for the same system, the symmetries should not depend on the
>> ecut
>> value.
>>
>> For Ecut = 20, 25, 40, 50 and 55 Ry, the output says -
>> "24 Sym.Ops. (with inversion)";
>> whereas for ecut = 30, 35, 45 and 60 Ry, the output is -
>> "12 Sym.Ops. (no inversion)"
>>
>> I have performed the same calculations using versions 4.0.4 and 4.1 with
>> the same results.
>> The input file is as follows -
>> *
>> &control
>>calculation = 'scf'
>>verbosity = 'high'
>>restart_mode = 'from_scratch',
>>prefix = 'RuGGA',
>>tstress=.true.
>>tprnfor=.true.
>>pseudo_dir = '/home/madhura-data/pseudo/',
>>outdir = '/home/madhura-data/tmp/'
>> /
>> &system
>>ibrav = 4, celldm(1) = 5.1831, celldm(3) = 1.584,
>>nat = 2, ntyp = 1,
>>ecutwfc = 20, ecutrho = 160, # ecutrho =
>> 8*ecutwfc
>>occupations='smearing', smearing='mp',degauss=0.05
>>nbnd = 20
>> /
>> &electrons
>>diagonalization = 'david', mixing_mode = 'plain',
>>mixing_beta = 0.7, conv_thr = 1.0d-12
>> /
>> ATOMIC_SPECIES
>> Ru 101.07 Ru.pbe-n-van.UPF
>> ATOMIC_POSITIONS {crystal}
>> Ru 0.00 0.00 0.00
>> Ru 0.6667 0. 0.50
>> K_POINTS automatic
>> 8 8 8 0 0 0
>> *
>>
>> Can anybody explain what is happening? Or do I need to file a bug
>> report?
>> Because except for this problem, energies and stress values seem to be
>> converging.
>>
>> Thanks and regards,
>> Madhura.
>>
>> --
>> Madhura Marathe,
>> PhD student, TSU,
>> JNCASR, Bangalore.
>> India.
>> Phone No: +91-80-22082835
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> ---
> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) /
> stefanobaroni (skype)
>
> La morale est une logique de l'action comme la logique est une morale de
> la pens?e - Jean Piaget
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Madhura Marathe,
PhD student, TSU,
JNCASR, Bangalore.
India.
Phone No: +91-80-22082835
[Pw_forum] Number of bands in bands_FS
Dear all (especially dear Eyvaz Isaev), why it is not possible to read in more than 8 bands using bands_FS? The program bands_FS reads the pre-calculated bandstructure for a given k-mesh (kvecs_FS). Lets say I have chosen 18 (everything higher than 8) bands for this calculation. Than the program bands_FS interrupts in the post process with the following error message: forrtl: severe (59): list-directed I/O syntax error, unit 5, file stdin Image PCRoutine LineSource bands_FS.x 0804B894 MAIN__ 327 bands_FS.f90 so I have tried to decrypt the code, but I didn't get inside. Clearly it something wrong with the parameter nlines, which changes if nbands > 8 - but I don't get it. Has anyone an idea what's going wrong? Thanks a lot... Nicki - Nicki Frank Hinsche, Dipl. Phys. Institut f?r Physik - Theoretische Physik, Martin-Luther-Universit?t Halle-Wittenberg, Von-Seckendorff-Platz 1, Raum 1.07 D-06120 Halle/Saale, Germany Tel.: ++49 345 5525460 -
[Pw_forum] Let's connect on LinkedIn
LinkedIn I'd like to add you to my professional network on LinkedIn. - Devis Di Tommaso Confirm that you know Devis Di Tommaso https://www.linkedin.com/e/isd/977273650/h39Z4CJA/ Every day, millions of professionals like Devis Di Tommaso use LinkedIn to connect with colleagues, find experts, and explore opportunities. -- (c) 2009, LinkedIn Corporation -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100107/322a1e08/attachment.htm
[Pw_forum] Error: bfgs history already reset at previous step
Dear friend, It might be a bug for QE 4.0.3. I recalculated it in QE 4.1.2. The convergence is much better. thank you for reading best vega On 1/7/2010 13:26, mohnish pandey wrote: > Dear Vega, >Try reducing "trust_radius_min". I faced the same > problem once and I did the same thing and it worked. Normally this > happens near the convergence... > HAPPY COMPUTING, > MOHNISH, > > On Wed, Jan 6, 2010 at 9:11 AM, vega lew <mailto:quantumdft at gmail.com>> wrote: > > Dear all, > I used to calculate the structure and the energy of Pt dimers > (two Pt atoms) in a large supercell. I have tested various > structure in triplet, which is most stable state for single Pt atom. > But the code report errors after a few bfgs steps like this: > > %% > task # 0 > from bfgs : error # 1 > bfgs history already reset at previous step > > %% > I wondering how to deal with this situation. > my input files is shown as follows, > &CONTROL > calculation = 'relax' , > restart_mode = 'from_scratch' , > outdir = '/tmp/' , > wfcdir = '/tmp/' , > pseudo_dir = '/home/vega/espresso/pseudo/' , > disk_io = 'none' , >nstep = 1000 , > / > &SYSTEM >ibrav = 8, >celldm(1) =24.8624, >celldm(2) = 0.8520, >celldm(3) = 1.6964, > nat = 2, > ntyp = 1, >nosym = .true. , >ecutwfc = 30, >ecutrho = 300, > occupations = 'smearing', > degauss = 0.007, > nspin = 2, >multiplicity = 3, > / > &ELECTRONS > mixing_mode ='local-TF', > mixing_beta = 0.4, > > / > &IONS > ion_dynamics = 'bfgs' , > / > ATOMIC_SPECIES > Pt 195.08 Pt.pw91-n-van.UPF > ATOMIC_POSITIONS crystal > Pt 0.540794031 0.322983976 0.495002098 > Pt 0.500777594 0.548429786 0.493029885 > K_POINTS gamma > the input parameters might not very suitable for the calculation > of Pt dimers itself. But the parameters should be consistent with > the previous calculation, which is composed of two Pt atoms on > certain surface slab model. > So could any one give me some suggestions? > Thank you for reading > vega > > -- > > == > Vega Lew ( weijia liu) > Graduate student > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > ** > Email: vegalew at gmail.com <mailto:vegalew at gmail.com> > Office: Room A705, Technical Innovation Building, Xinmofan Road > 5#, Nanjing, Jiangsu, China > > ** > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org> > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Mohnish Pandey > Y6927262,4th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR > 09235721300 > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100107/7dd52750/attachment-0001.htm
[Pw_forum] Error: bfgs history already reset at previous step
Dear Vega, Try reducing "trust_radius_min". I faced the same problem once and I did the same thing and it worked. Normally this happens near the convergence... HAPPY COMPUTING, MOHNISH, On Wed, Jan 6, 2010 at 9:11 AM, vega lew wrote: > Dear all, > > I used to calculate the structure and the energy of Pt dimers (two Pt > atoms) in a large supercell. I have tested various structure in triplet, > which is most stable state for single Pt atom. > But the code report errors after a few bfgs steps like this: > > > %% > task # 0 > from bfgs : error # 1 > bfgs history already reset at previous step > > > %% > I wondering how to deal with this situation. > > my input files is shown as follows, > > &CONTROL > calculation = 'relax' > , > restart_mode = 'from_scratch' > , > outdir = '/tmp/' , > wfcdir = '/tmp/' > , > pseudo_dir = '/home/vega/espresso/pseudo/' > , > disk_io = 'none' > , >nstep = 1000 > , > / > > &SYSTEM > >ibrav = > 8, >celldm(1) =24.8624, >celldm(2) = 0.8520, >celldm(3) = 1.6964, > nat = > 2, > ntyp = > 1, >nosym = .true. > , >ecutwfc = 30, >ecutrho = 300, > occupations = 'smearing', > degauss = 0.007, > nspin = 2, >multiplicity = 3, > / > > &ELECTRONS > > mixing_mode ='local-TF', > mixing_beta = > 0.4, > > / > > &IONS > > ion_dynamics = 'bfgs' > , > / > > > ATOMIC_SPECIES > Pt 195.08 > Pt.pw91-n-van.UPF > ATOMIC_POSITIONS crystal > Pt 0.540794031 0.322983976 0.495002098 > Pt 0.500777594 0.548429786 0.493029885 > K_POINTS gamma > > the input parameters might not very suitable for the calculation of Pt > dimers itself. But the parameters should be consistent with the previous > calculation, which is composed of two Pt atoms on certain surface slab > model. > > So could any one give me some suggestions? > > Thank you for reading > > vega > > -- > > == > Vega Lew ( weijia liu) > Graduate student > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > ** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ** > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100107/7d67608c/attachment.htm
[Pw_forum] ecut dependence of symmetry operations(?)
Madhura: this has been discussed zilliions of times in this forum, and has to
do with the way symmetry operations are found out by the code. When the
symmetry group of the system is non-symmorphic, only those fractional
translations that are commensurate with the FFT grid are actually found. This
may sound a bit cryptic, and I leave it as such on purpose. You will find much
more about this issue by browsing the archives of this mailing list. Hope this
helps - SB
On Jan 5, 2010, at 12:24 PM, Madhura Marathe wrote:
> Dear all,
>
> While performing convergence calculations w.r.t energy cut-off for a bulk
> system, I found that the number of symmetry operations detected by a code
> is different depending on the value of ecut. This is very surprising
> because for the same system, the symmetries should not depend on the ecut
> value.
>
> For Ecut = 20, 25, 40, 50 and 55 Ry, the output says -
> "24 Sym.Ops. (with inversion)";
> whereas for ecut = 30, 35, 45 and 60 Ry, the output is -
> "12 Sym.Ops. (no inversion)"
>
> I have performed the same calculations using versions 4.0.4 and 4.1 with
> the same results.
> The input file is as follows -
> *
> &control
>calculation = 'scf'
>verbosity = 'high'
>restart_mode = 'from_scratch',
>prefix = 'RuGGA',
>tstress=.true.
>tprnfor=.true.
>pseudo_dir = '/home/madhura-data/pseudo/',
>outdir = '/home/madhura-data/tmp/'
> /
> &system
>ibrav = 4, celldm(1) = 5.1831, celldm(3) = 1.584,
>nat = 2, ntyp = 1,
>ecutwfc = 20, ecutrho = 160, # ecutrho = 8*ecutwfc
>occupations='smearing', smearing='mp',degauss=0.05
>nbnd = 20
> /
> &electrons
>diagonalization = 'david', mixing_mode = 'plain',
>mixing_beta = 0.7, conv_thr = 1.0d-12
> /
> ATOMIC_SPECIES
> Ru 101.07 Ru.pbe-n-van.UPF
> ATOMIC_POSITIONS {crystal}
> Ru 0.00 0.00 0.00
> Ru 0.6667 0. 0.50
> K_POINTS automatic
> 8 8 8 0 0 0
> *
>
> Can anybody explain what is happening? Or do I need to file a bug report?
> Because except for this problem, energies and stress values seem to be
> converging.
>
> Thanks and regards,
> Madhura.
>
> --
> Madhura Marathe,
> PhD student, TSU,
> JNCASR, Bangalore.
> India.
> Phone No: +91-80-22082835
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni
(skype)
La morale est une logique de l'action comme la logique est une morale de la
pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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[Pw_forum] Pw_forum Digest, Vol 31, Issue 2
starting point. > > --- On Wed, 12/30/09, Zhen Huang wrote: > > > ph.x calculation generated files alas.dynX where X goes from > > 0 to 8. In the file alas.dyn0 it gives the k points.. Seems > > in the other dynX files for example .dyn1 it gives force > > constants of q=(0.0, 0.0, 0.0)? and .dyn2 gives force > > constants of q=(-0.25?? 0.25? -0.25) > > This is correct. 4x4x4 set of q-points gives 8 q-points for which dynamical > matrices have to be calculated. These q-points are written in dyn0 file. > Files dyn1 - dyn8 are dynamical matrices. > > > What is the T matrix? and Matrix 1 and 2 labeled below. > > There is no T-matrix at all, "T" means .true., i.e. AlAs, in fact, is > semi-conducting. > > Next 3x3 matrix is the macroscopic dielectric constants matrix. > > "Matrix 1" and "Matrix 2" contain effective Born charges for Al (atom 1) and > As (atom 2). > > For metals you find "F" (.false.) and no dielectric matrix and Born effective > charges. > > > Also, the questions are what is 4 4 4 representing the the force > > constants information part labeled below,? what does the 1 1 1 1 mean > on > > the second line and also what is the meaning of the index? > > 2?? 1?? 1? -6.26636620736E-03 (for example), I assume -6.266e-03 is > > the force constants but what is 2 1 1. > > You asked this question before. Please have a look at > > http://www.democritos.it/pipermail/pw_forum/2008-September/010099.html > > The only correction is that R=(i-1)*a + (j-1)*b + (k-1)*c (thanks Stefano > d.G). > > > If the forth column is the force constants why it is different from > > Ph.x calcualtion's output. > > Please do not mix dynamical matrix with IFC. The first one is in q-space, and > the second one is in R-space. > > > One more question, if I want to look at the force constants > > between a unit cell and its closest nearest neibhor unit > > cell do I look at the dynX output with k=(0, -1, 0), (-1, 0, > > 0) and such and second nearest unit cells will be in dynX of > > k=(0, -.5, 0), (-.5, 0, 0)? > > This is unclear what do you mean as IFC is for atoms, but not for unit cells. > Just keep in mind in the Linear Response theory all calculations are > performed inside the unit cell. To calculate the IFC range see a formula for > R given above. > > Bests, > Eyvaz. > > --- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > > > > > > > -- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 31, Issue 2 > *** > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100107/6ae45d31/attachment-0001.htm
[Pw_forum] Number of bands in bands_FS
Dear Niki, In fact, there is no limitation for bands to read, as far as I remember. Program stops if one tries to read more than the number of KS-bands. Please send me your output files to see a possible reason. Bests, Eyvaz. --- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 1/7/10, Nicki Frank Hinsche wrote: > From: Nicki Frank Hinsche > Subject: [Pw_forum] Number of bands in bands_FS > To: pw_forum at pwscf.org > Date: Thursday, January 7, 2010, 4:56 PM > Dear all (especially dear Eyvaz > Isaev), > > why it is not possible to read in more than 8 bands using > bands_FS?? > The program bands_FS reads the pre-calculated bandstructure > for a? > given k-mesh (kvecs_FS). Lets say I have chosen 18 > (everything higher? > than 8) bands for this calculation. Than the program > bands_FS? > interrupts in the post process with the following error > message: > > forrtl: severe (59): list-directed I/O syntax error, unit > 5, file stdin > Image? ? ? ? ? ? ? > ? ? ? ? ? > ???PC? ? ? ? > Routine? ? ? ? ? ? ? > ? ? > Line? ? ? ? Source > bands_FS.x? ? ? > ???0804B894? MAIN__? ? ? > ? ? ? ? ???327? > bands_FS.f90 > > > so I have tried to decrypt the code, but I didn't get > inside. Clearly? > it something wrong with the parameter nlines, which changes > if nbands? > > 8 - but I don't get it. > > Has anyone an idea what's going wrong? > > Thanks a lot... > Nicki > > > - > Nicki Frank Hinsche, Dipl. Phys. > Institut f?r Physik - Theoretische Physik, > Martin-Luther-Universit?t Halle-Wittenberg, > Von-Seckendorff-Platz 1, Raum 1.07 > D-06120 Halle/Saale, Germany > Tel.: ++49 345 5525460 > - > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
