[Pw_forum] electron-phonon calculations
Dear all,
I have relaxed the system I am working on with 8 points using shifted x and y
axes, namely :
K_POINTS {AUTOMATIC}
2 8 1 1 1 0
with a pressure =0.06 Kbars.
My aim is to do electron phonon calculations; however here, we need to use
unshifted axes with denser points; I used
K_POINTS {AUTOMATIC}
2 16 1 1 1 0
The pressure on the system in this case was 0.1 Kbars (shifting a bit from the
0.06 Kbars in the first case). My question is is it ok to do that and will the
forces have severe changes (I forgot to print the forces) or should I have
relaxed the system in the first place with unshifted axes?
Regards
Elie Moukaes
University of Nottingham
UK
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[Pw_forum] relaxation of the 60 C atom supercell
Dear all, I am still "fighting" with the 60 carbon atom system that I am trying to relax. I did a relaxation using 4 k-points and I got the system relaxed then I did an scf calculation with 25 points (for phonon calculations) and the total force is 0.099839. Does this mean that using 4 points is not enough? how many points do I have to consider as 25 points would really take a lot of time? Shall I relax for 10 k-points, the same as I was doing for an scf calculation? Can anyone advise me on that? Thanks again and sorry to disturb you with that many times. I am trying to avoid the negative frequencies that I obtained before totally relaxing the crystal. Elie MUniversity of Nottng7 2rduk -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110911/51adbb5d/attachment-0001.htm
[Pw_forum] results of vc-relax
Prof. Giannozzi, Thanks for the answer Elie > From: giannozz at democritos.it > Date: Sat, 10 Sep 2011 20:26:40 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] results of vc-relax > > > On Sep 10, 2011, at 18:37 , Elie Moujaes wrote: > > > I didnt quite understand this final step > > http://www.democritos.it/pipermail/pw_forum/2011-April/020154.html > > The problem mentioned at the end has been meanwhile solved > in v.4.3.2 > > P. > --- > Paolo Giannozzi, Dept of 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://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110910/d4a7c719/attachment.htm
[Pw_forum] results of vc-relax
Dear all, I have relaxed my 60 Carbon atom system using four k points . everything went ok but i could not understand the final steps of the calculation. I have reached a total force of 0.002024 and a pressure of 0.00 and then teh final positions of the atoms and unit cell were printed. After that a scf calculation started running but with old coordinates where the total force is 0.03 (Of course I will do an scf calculation later with higher points)! I didnt quite understand this final step. i will post the related output for you: convergence has been achieved in 7 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force =-0.00023166 -0.000228540. atom 2 type 1 force =-0.9534 -0.000276250. atom 3 type 1 force = 0.3632 -0.70340. atom 4 type 1 force =-0.7340 -0.000416370. atom 5 type 1 force = 0.00042431 -0.000213070. atom 6 type 1 force = 0.00018754 -0.000114560. atom 7 type 1 force =-0.00013707 -0.000222760. atom 8 type 1 force =-0.3971 -0.000206830. atom 9 type 1 force = 0.00010279 -0.000124220. atom 10 type 1 force = -0.00039366 -0.000103000. atom 11 type 1 force = 0.5799 -0.000158780. atom 12 type 1 force = -0.27020.32370. atom 13 type 1 force = 0.7204 -0.89130. atom 14 type 1 force = 0.000176160.36310. atom 15 type 1 force = -0.000142750.07480. atom 16 type 1 force = 0.7827 -0.94040. atom 17 type 1 force = -0.000231490.000168410. atom 18 type 1 force = -0.73410.000224880. atom 19 type 1 force = -0.19710.000117830. atom 20 type 1 force = -0.81790.000331610. atom 21 type 1 force = -0.09770.000226610. atom 22 type 1 force = 0.000120170.000137980. atom 23 type 1 force = 0.61710.000378560. atom 24 type 1 force = 0.000119890.000324990. atom 25 type 1 force = -0.000169560.000235280. atom 26 type 1 force = -0.000172830.000170270. atom 27 type 1 force = 0.000150450.000315820. atom 28 type 1 force = -0.98140.000217130. atom 29 type 1 force = 0.99810.000357320. atom 30 type 1 force = 0.000181500.000261850. atom 31 type 1 force = -0.000214480.000309530. atom 32 type 1 force = -0.83000.000129880. atom 33 type 1 force = 0.000139300.000451180. atom 34 type 1 force = -0.27600.37520. atom 35 type 1 force = -0.26600.000293320. atom 36 type 1 force = 0.000172020.45160. atom 37 type 1 force = -0.84250.000253240. atom 38 type 1 force = 0.14400.000160610. atom 39 type 1 force = -0.21970.000198800. atom 40 type 1 force = 0.05850.000146960. atom 41 type 1 force = 0.02350.000182580. atom 42 type 1 force = -0.2749 -0.25780. atom 43 type 1 force = 0.74040.05080. atom 44 type 1 force = -0.00018007 -0.000123890. atom 45 type 1 force = 0.58340.76200. atom 46 type 1 force = -0.000125510.05120. atom 47 type 1 force = 0.00017256 -0.37660. atom 48 type 1 force = -0.4018 -0.000206540. atom 49 type 1 force = -0.0882 -0.00014507 0. atom 50 type 1 force = 0.5372 -0.000332960. atom 51 type 1 force = 0.00011833 -0.000193270. atom 52 type 1 force = 0.0983 -0.000237360. atom 53 type 1 force =-0.6016 -0.000326030. atom 54 type 1 force = 0.00012524 -0.000362760. atom 55 type 1 force = -0.00013815 -0.000169260. atom 56 type 1 force = 0.8094 -0.000348270. atom 57 type 1 force = -0.4248 -0.000261220. atom 58 type 1 force =
[Pw_forum] problems with vc-relax
Thanks all for your suggestions,
I did a relaxation of the system with only the gamma point and it was amazingly
quick. It was done in 3 hours. The main reason to do the relaxation is because
I got negative frequencies while trying to execute ph.x which took a really
long time (12 days more or less). The reason for that I guess is the mechanical
instability of the system. This is why I want to make sure the system is
relaxed before performing ph.x again. I did start again relaxing the system
with 4 points now (still going on with oscillations in the total force). My scf
file for phonons is with 25 points and the one with scf calculations is with 10
points. Is there a quick way to know if the number of points is sufficient for
relation or not or is the only way to take the new coordinates do an scf
calculation with say 10 points in my case and check the total force?
Regards
Elie
> Date: Thu, 8 Sep 2011 23:58:13 -0400
> From: xijunw at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] problems with vc-relax
>
> Hi,
>
> You are right. Tests should be done. I was suggesting "start" from
> gamma k-points to make a quick relaxation. After this, relaxation with
> larger k-points could be followed if necessary.
>
> Regards,
> Xijun
>
> On Thu, Sep 8, 2011 at 7:35 PM, WF wrote:
> > Is it good enough to relax an arbitrary system with only gamma k-points? I
> > thought it is necessary to do some test with k-points as this effect change
> > from system to system. In my experience, more k-points is necessary for a
> > metal-like system, i.e. graphene.
> >
> > Best regards,
> >
> > Wu, F
> >
> >> Date: Thu, 8 Sep 2011 11:12:24 -0400
> >> From: xijunw at gmail.com
> >> To: pw_forum at pwscf.org
> >> Subject: Re: [Pw_forum] problems with vc-relax
> >>
> >> On Thu, Sep 8, 2011 at 10:26 AM, Elie Moujaes
> >> wrote:
> >> > Hello Xijun,
> >>
> >> Hello Elie,
> >>
> >> > I did not send the e-mail twice intentionally. There was a problem with
> > my
> >> > e-mail and it kept giving me an error about problems with Windows hotmai
> >> > hence why it was sent twice without me knowing except now when I opened
> > my
> >> > e-mail so I apologize for that. Also I wont include blank lines in the
> > input
> >> > file either. Back to my calculations, I have restarted the
> > calculations, it
> >> > went fine at first but then I got the error:
> >> > from scale_h: not enough memory allocated for radial FFT; try restarting
> >> > with a larger cell_factor.
> >>
> >> Check the manual for definition of cell_factor. The default value is
> >> 1.2, you could try a larger value.
> >>
> >> What's your new K_POINTS setting? Since you are relax the system, I
> >> suggest you start from:
> >>
> >> K_POINTS {gamma}
> >>
> >> This will far faster. and need far less memory.
> >>
> >> > Another simple question: I realized when I restarted everything that the
> >> > positions of the atoms were the initial ones even before starting the
> >> > relaxation process where as the k-points used were the NEW ones. Is that
> >> > normal? or should I have substituted the the C atoms positions by the
> > most
> >> > recent ones then restart again?
> >>
> >> Yes, restart again with NEW ATOMIC_POSITIONS and "restart_mode=
> > 'from_scratch' "
> >>
> >> Regards,
> >> - Xijun
> >>
> >> > Regards
> >> > Elie
> >> >
> >> >> Date: Wed, 7 Sep 2011 16:20:49 -0400
> >> >> From: xijunw at gmail.com
> >> >> To: pw_forum at pwscf.org
> >> >> Subject: Re: [Pw_forum] problems with vc-relax
> >> >>
> >> >> Hi, Elie,
> >> >>
> >> >> Please do not repeat sending the same message to the mail list. Also,
> >> >> people will be more happy to help you if you keep your mail neat by
> >> >> removing all the unnecessary blank lines in the input file.
> >> >>
> >> >> Regards,
> >> >> Xijun
> >> >>
> >> >> On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes
> >
> >> >> wrote:
> >> >> > Dear all,
> >> >> >
> >> >> >
> >> >> >
> >> >> > I am relaxing a 60 atom supercell (graphene grain boundary) to make
> > the
&g
[Pw_forum] problems with vc-relax
Thanks very much for your suggestions again. I did not know I can use K_POINTS
{gamma} (only one point) in the relaxation process as I used K_POINTS
{automatic} 7 7 1 in my relaxation process.
Regards
Elie
> Date: Thu, 8 Sep 2011 11:12:24 -0400
> From: xijunw at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] problems with vc-relax
>
> On Thu, Sep 8, 2011 at 10:26 AM, Elie Moujaes
> wrote:
> > Hello Xijun,
>
> Hello Elie,
>
> > I did not send the e-mail twice intentionally. There was a problem with my
> > e-mail and it kept giving me an error about problems with Windows hotmai
> > hence why it was sent twice without me knowing except now when I opened my
> > e-mail so I apologize for that. Also I wont include blank lines in the input
> > file either. Back to my calculations, I have restarted the calculations, it
> > went fine at first but then I got the error:
> > from scale_h: not enough memory allocated for radial FFT; try restarting
> > with a larger cell_factor.
>
> Check the manual for definition of cell_factor. The default value is
> 1.2, you could try a larger value.
>
> What's your new K_POINTS setting? Since you are relax the system, I
> suggest you start from:
>
> K_POINTS {gamma}
>
> This will far faster. and need far less memory.
>
> > Another simple question: I realized when I restarted everything that the
> > positions of the atoms were the initial ones even before starting the
> > relaxation process where as the k-points used were the NEW ones. Is that
> > normal? or should I have substituted the the C atoms positions by the most
> > recent ones then restart again?
>
> Yes, restart again with NEW ATOMIC_POSITIONS and "restart_mode=
> 'from_scratch' "
>
> Regards,
> - Xijun
>
> > Regards
> > Elie
> >
> >> Date: Wed, 7 Sep 2011 16:20:49 -0400
> >> From: xijunw at gmail.com
> >> To: pw_forum at pwscf.org
> >> Subject: Re: [Pw_forum] problems with vc-relax
> >>
> >> Hi, Elie,
> >>
> >> Please do not repeat sending the same message to the mail list. Also,
> >> people will be more happy to help you if you keep your mail neat by
> >> removing all the unnecessary blank lines in the input file.
> >>
> >> Regards,
> >> Xijun
> >>
> >> On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes >> hotmail.co.uk>
> >> wrote:
> >> > Dear all,
> >> >
> >> >
> >> >
> >> > I am relaxing a 60 atom supercell (graphene grain boundary) to make the
> >> > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped
> >> > after
> >> > 4 days of execution and without reaching the desired force threshold.
> >> > The
> >> > following output was obtained :
> >> >
> >> >
> >> >
> >> > 1st relaxation process:
> >> >
> >> >
> >> >
> >> > Total force 0.091 Pressure =- 114.1 kbar
> >> >
> >> >
> >> >
> >> > 2nd relaxation process:
> >> >
> >> >
> >> >
> >> > total force 0.1 Pressure = -55 kbar
> >> >
> >> >
> >> >
> >> > (new enthalpy < old enthalpy)
> >> >
> >> >
> >> >
> >> > 3rd process:
> >> >
> >> >
> >> >
> >> > total force = 0.058 pressure = -11 kbar
> >> >
> >> >
> >> >
> >> > Then in the 4th process, calculations stopped. Here are the last few
> >> > lines
> >> > of the output:
> >> >
> >> >
> >> >
> >> > iteration # 2 ecut=36.75 Ry beta=0.30
> >> > Davidson diagonalization with overlap
> >> > c_bands: 5 eigenvalues not converged
> >> > c_bands: 1 eigenvalues not converged
> >> > c_bands: 3 eigenvalues not converged
> >> > c_bands: 1 eigenvalues not converged
> >> > c_bands: 4 eigenvalues not converged
> >> > c_bands: 4 eigenvalues not converged
> >> > c_bands: 4 eigenvalues not converged
> >> > c_bands: 4 eigenvalues not converged
> >> > c_bands: 5 eigenvalues not converged
> >> > c_bands: 5 eigenvalues not converged
> >> > c_bands: 2 eigenvalues not converged
> >> > c_bands: 2 eigenv
[Pw_forum] problems with vc-relax
Hello Xijun, I did not send the e-mail twice intentionally. There was a problem with my e-mail and it kept giving me an error about problems with Windows hotmai hence why it was sent twice without me knowing except now when I opened my e-mail so I apologize for that. Also I wont include blank lines in the input file either. Back to my calculations, I have restarted the calculations, it went fine at first but then I got the error: from scale_h: not enough memory allocated for radial FFT; try restarting with a larger cell_factor. Another simple question: I realized when I restarted everything that the positions of the atoms were the initial ones even before starting the relaxation process where as the k-points used were the NEW ones. Is that normal? or should I have substituted the the C atoms positions by the most recent ones then restart again? Regards Elie > Date: Wed, 7 Sep 2011 16:20:49 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > Hi, Elie, > > Please do not repeat sending the same message to the mail list. Also, > people will be more happy to help you if you keep your mail neat by > removing all the unnecessary blank lines in the input file. > > Regards, > Xijun > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > > > > > 1st relaxation process: > > > > > > > > Total force 0.091 Pressure =- 114.1 kbar > > > > > > > > 2nd relaxation process: > > > > > > > > total force 0.1 Pressure = -55 kbar > > > > > > > > (new enthalpy < old enthalpy) > > > > > > > > 3rd process: > > > > > > > > total force = 0.058 pressure = -11 kbar > > > > > > > > Then in the 4th process, calculations stopped. Here are the last few lines > > of the output: > > > > > > > > iteration # 2 ecut=36.75 Ry beta=0.30 > > Davidson diagonalization with overlap > > c_bands: 5 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 3 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 4 eigenvalues not converged > > c_bands: 4 eigenvalues not converged > > c_bands: 4 eigenvalues not converged > > c_bands: 4 eigenvalues not converged > > c_bands: 5 eigenvalues not converged > > c_bands: 5 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > ethr = 2.90E-04, avg # of iterations = 17.6 > > > > negative rho (up, down): 0.132E-01 0.000E+00 > > > > total cpu time spent up to now is 382283.13 secs > > > > total energy =-676.77947904 Ry > > Harris-Foulkes estimate =-676.82846513 Ry > > estimated scf accuracy< 0.17363554 Ry > > > > iteration # 3 ecut=36.75 Ry beta=0.30 > > Davidson diagonalization with overlap > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 3 eigenvalues not converged > > > > > > > > The input of the vc-relax is: > > > > > > > > &control > > > > prefix='GBphonon', > > > > calculation='vc-relax', > > > > restart_mode='from_scratch', > > > > tstress=.true., > > > > tprnfor=.true, > > > > pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', > > > > outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', > > > > > > > > / > > > > &system > > > > ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, > > occupations='smearing', smearing='mp',degauss=0.01 > > > > / > > > > &electrons > > > > conv_thr=1.D-6, > > > > mixing_beta=0.3D0, > > > > diago_david_ndim=2, > > > > > > > > / > > > > > > > >
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/38d4a09f/attachment.htm
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/9b2202ec/attachment.htm
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/5f7d5890/attachment-0001.htm
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/5d06481e/attachment.htm
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/d18c2aa9/attachment.htm
[Pw_forum] problems in vc relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate =-676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0 .. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie Moujaes University of Nott University Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/eccff488/attachment-0001.htm
[Pw_forum] problems with vc-relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate =-676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0 .. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie Moujaes University of Nott University Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/17335ac0/attachment-0001.htm
[Pw_forum] problems with vc-relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0.. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/467de01e/attachment.htm
[Pw_forum] problems with vc-relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0.. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/df4a8543/attachment-0001.htm
[Pw_forum] problems with vc-relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0.. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/eec0853b/attachment.htm
[Pw_forum] cannot allocate memory error
Thanks a lot for the reply ..I was trying to gain some time as I am running other programs on the server at Uni. I guess I will have to do things step by step Thanks again Elie > From: ttduyle at gmail.com > Date: Sat, 3 Sep 2011 11:30:00 -0400 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] cannot allocate memory error > > On Sat, Sep 3, 2011 at 11:23 AM, Elie Moujaes > wrote: > > Dear all, > > I am having a problem when I am running a scf calculation for a 72-atom > > supercell of Carbon grain boundaries. The calculations start and then after > > a few minutes stop with the following error: > > Operating system error: Cannot allocate memory > > operating system error: cannot allocate memory > > out of memory > > Can anyone tell me what is going on? I am not sure if it is really a memory > > problem or something else? > Yes. It said that. Your system is quite large for running on a > personal desktop. Check output to see how much memory you need for > this system. > -- > Duy Le > PhD Candidate > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > ___ > 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/20110903/f4e56844/attachment-0001.htm
[Pw_forum] cannot allocate memory error
Dear all, I am having a problem when I am running a scf calculation for a 72-atom supercell of Carbon grain boundaries. The calculations start and then after a few minutes stop with the following error: Traceback: not available, compile with -ftrace=frame or -ftrace=fullOperating system error: Cannot allocate memory Memory allocation failed on my desktop at work. I have the espresso-4.2 there. On my laptop at home (where I have downloaded the latest espresso-4.3.2 version). Now I am getting the error : operating system error: cannot allocate memoryout of memory Can anyone tell me what is going on? I am not sure if it is really a memory problem or something else? Thanks Elie MoujaesUniversity of NottinghamNG7 2RDUK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110903/f915da4d/attachment.htm
[Pw_forum] total force and number of k-points
Professor Giannozzi, Thanks a lot for your reply. Elie > From: giannozz at democritos.it > Date: Fri, 2 Sep 2011 22:55:25 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] total force and number of k-points > > > On Sep 2, 2011, at 15:54 , Elie Moujaes wrote: > > > I have a simple question: does the total force acting > > on a system depend on the number of k-points used? > > not sure what you mean by "total force", but forces on > atoms depend upon the number of k-points, for sure > > > That is in my scf calculation I am using a grid of 4x4x1 > > for my system whereas the grid must be denser if phonon > > calculations are taking place I am using 8x8x1. Do I get > > different total force acting on the system and does it mean > > I have to relax the crystal twice one for an scf calculation > > and another for a phonon calculation? > > in principle a system should be relaxed for the same set of > parameters (cutoff, k-points) that are used in the subsequent > phonon calculation. The difference might be small enough to > be negligible, but this is something that should be checked. > > P. > --- > Paolo Giannozzi, Dept of 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://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110903/fce43158/attachment.htm
[Pw_forum] total force and number of k-points
Dear all, I have a simple question: does the total force acting on a system depend on the number of k-points used? That is in my scf calculation I am using a grid of 4x4x1 for my system whereas the grid must be denser if phonon calculations are taking place I am using 8x8x1. Do I get different total force acting on the system and does it mean I have to relax the crystal twice one for an scf calculation and another for a phonon calculation? Thanks Elie MoujawsUniversity of NottsUniversity ParkNG7 2RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110902/a53b37fd/attachment.htm
[Pw_forum] units of q-vectors when performing the ph.x command
dear all, a simple question: what are the units of the q vectors we assign in the ph.in file? is it cartesian or in terms of 2 pi/a? N.B: In my bands file, the points are define in terms of the reciprocal lattice vectors b. Thanks Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110826/5a4d60b9/attachment.htm
[Pw_forum] usage of recover=.true. (solved)
Guys, Thanks a lot for your help. I just checked the output file now and the calculations are running normally. I am at mode 139. Thanks once again for all the suggestions Elie -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/8374aa8f/attachment-0001.htm
[Pw_forum] usage of recover=.true.
Thank you.I hope it works as I definitely do not want to lose the 105 modes..It took 7 days to do that. But how to re execute the ph.x command..I tried doing the usual:/..././ph.x GB60.phG.out but it exited. Is there another way to restart the command? Thanks againElie Date: Mon, 22 Aug 2011 22:21:25 +0800 From: flux_ra...@163.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK ___ 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/20110822/a3c78cb1/attachment.htm
[Pw_forum] usage of recover=.true.
Thanks a lot for the answer. The problem is I started calculating the phonons at the Gamma point. In my system there are 180 modes and something went wrong with the server so it stopped at the 106.I am doing the 180 in one go! Is there a way to save the 106 ones already done! or u suggest that I calculate each one of them in a separate fie and use recover=.true.? ThanksElie From: c...@sissa.it Date: Mon, 22 Aug 2011 16:17:17 +0200 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. Dear Elie, In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: Variable: recover Type: LOGICAL Default:.false. Description:If .true. restart from an interrupted run. So set it to false in your first run and true in the second and the following runs. HTH,Changru On 22 Aug, 2011, at 16:06, Elie Moujaes wrote:Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- ___ 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/20110822/d55d7b8b/attachment.htm
[Pw_forum] usage of recover=.true.
Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/72337054/attachment.htm
[Pw_forum] usage of recover=.true.
Dear all, I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? Thanks Elie MoujaesUniversity of NottinghamNG7 2RDUK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110819/4572e0ad/attachment.htm
[Pw_forum] phonon calculations for a system of 60 atoms
Hello all, i am doing a phonon calculation for a system of 60 carbon atoms. I have two small questions: (1) what is the safe value that I can set to tr2_ph and get good results? I am doing the calculations for a tr2_ph=1.0D-10 but it is taking a long timee and I have got like 180 modes of irreducible representations. (2) I am doing phonon calculations at special points (Gamma, M, X) separately. Is there a way to collect these to get the phonon band dispersion later? Thanks Elie Mouaesuniversity of NottinghamNottinghamNG7 2RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/f7435f5f/attachment.htm
[Pw_forum] electronic DOS for a GB system of 60 atoms
Dear Lars, Thanks very much for your help. Elie Date: Tue, 2 Aug 2011 22:35:16 +0200 From: jenaparad...@googlemail.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] electronic DOS for a GB system of 60 atoms Dear Elie, it looks like you have way too few k-points for your nscf calculation. For a well converged DOS it isnecessary to have sufficient dense k-grid. By increasing the number of k-points you'll see, that the DOS will be much smoother, because up to know the 'waves' in your DOS doesn't seem to be physical, I think they are artificial and a result of a low k-sampling. If the grid is dense enough and your DOS doesn't change anymore you can also decrease the smearing and improve the behaviour of your spectra close to the gap. Hope that helps Lars 2011/8/2 Elie Moujaes Dear all, I am trying to reproduce calculations done on the electronic DOS of a 60 carbon system. I have got that the DOS is around 0.2 at the Fermi level whereas the calculations done previously got that it is exactly zero. In addition their curve seems sharper than mine. I used degauss=0.01 in nscf and scf calculations. the grid for scf was 4 4 1 whilst it was 9 9 1 for nscf. You will find attached the ps file of the DOS. Can anyone advise me on that? ThanksElie Moujaes University of NottinghamNG7 2RDUK ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Lars Matthes Institut f?r Festk?rpertheorie und -optik Friedrich-Schiller-Universit?t Jena Max-Wien-Platz 1 07743 Jena Germany Phone: +49.3641.947163 Mail: Lars.Matthes at uni-jena.de ___ 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/20110802/c32d7703/attachment.htm
[Pw_forum] electronic DOS for a GB system of 60 atoms
Dear all,I am trying to reproduce calculations done on the electronic DOS of a 60 carbon system. I have got that the DOS is around 0.2 at the Fermi level whereas the calculations done previously got that it is exactly zero. In addition their curve seems sharper than mine. I used degauss=0.01 in nscf and scf calculations. the grid for scf was 4 4 1 whilst it was 9 9 1 for nscf. You will find attached the ps file of the DOS. Can anyone advise me on that?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/74686d85/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: GBm.dos.ps Type: application/postscript Size: 42117 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110802/74686d85/attachment-0001.ps
[Pw_forum] DOS of a 60 carbon grain boundary system
Dear all, I am trying to reproduce calculations done on the electronic DOS of a 60 carbon system. I have got that the DOS is around 0.2 at the Fermi level whereas the calculations done previously got that it is exactly zero. In addition their curve seems sharper than mine. I used degauss=0.01 in nscf and scf calculations. the grid for scf was 4 4 1 whilst it was 9 9 1 for nscf. You will find attached the ps file of the DOS. Can anyone advise me on that? Thanks Eie Moukaes University of NottinghamNG7 2RDUK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110730/e24d7e41/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: GBm.dos.ps Type: application/postscript Size: 42117 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110730/e24d7e41/attachment-0001.ps
[Pw_forum] simple question about plotband.x
Dear all, I am doing calculations on grain boundaries of graphene. When I use plotband.x and restrict the limit of the energies between say -2.1 and 2.1 eV , The produced curve has limits between -2.7 and 1.8. Why is that the case? This is also affecting the graph in the sense that when I set the fermi energy as a reference , the dashed line at the zero is lower than the actual Fermi energy where bands intersect..See graph attached (in the graph the point 0.0 is lower than 0.3299 where the bands intersect). Howvere the general band structure is correct. How can I solve this problem Thanks Elias MoukaesUniversity of NottsUKNG7 2RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110715/1b2feb8d/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: GB60.ps Type: application/postscript Size: 35077 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110715/1b2feb8d/attachment-0001.ps
[Pw_forum] Grain boundary Scf calculations stopping
Dear All, I am running scf calculations for a 72 Carbon atom grain boundary system. I had problems in the convergence in the past with the c_bands error erupting and the program stopping. The calculations have been stopping i guess due to the lack of enough memory so I tried several things like reducing ecutwfc to 30 but had to put a value of ecutrho equal to 200 to ensure a small negative charge density. I have also used diago_david_ndim=2. The calculations are still stopping (they stopped at the 10th iteration now) and am still getting some messages from c_bands; Here is a part of the input. Can anyone please advise me of what to change to make the calculations work because the system is already large (288 electrons) and takes scf calculations a few days to be done. Thank You Elie MoujaesUniversity of NottinghamNG7 2RDUK control prefix='GBdensity', calculation='scf', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo', / &system ibrav= 0, celldm(1) =1.889725989, nat=72, ntyp= 1, ecutwfc =30.0, ecutrho = 200.D0, nosym=.true.,occupations='smearing', smearing='mv', degauss=0.01 / &electrons conv_thr=1.D-4, mixing_beta=0.3D0,mixing_mode='local-TF'diago_david_ndim=2, / CELL_PARAMETERS (alat) 29.41660 0.0 0.0 0.0 6.60990 0.0 0.0 0.0 33.0 ATOMIC_SPECIES C 12.0107 C.pz-rrjus.UPF ATOMIC_POSITIONS (angstrom) C -17.267939 -5.262892 -0.02 C -17.658134 -3.893047 -0.02 C -16.648186 -2.8921450.00 C -16.979016 -1.481403 -0.01 C -15.822497 -7.1886510.03 C -15.974769 -5.7580110.01 C -14.931838 -4.783788 -0.02 C -15.260133 -3.372206 -0.03 C -14.164353 -2.443247 -0.01 C -14.448789 -1.0380330.01 C -13.357280 -6.694629 -0.03 C -13.589274 -5.266428 -0.06 C -12.507820 -4.324210 -0.03 C -12.797007 -2.912572 -0.03 C -11.713425 -1.9675540.02 C -11.996028 -0.5540490.01 C -10.908497 -6.218111 -0.01 C -11.153648 -4.7983950.00 C -10.348701 -2.4390650.02 C -10.066097 -3.852576 -0.01 C -9.265132 -1.494029 -0.01 C -9.554319 -0.0823940.00 C -8.472857 -5.750083 -0.02 C -8.704854 -4.3218880.01 C -7.613348 -3.3685920.01 C -7.897799 -1.963373 -0.03 C -6.802030 -1.0344150.00 C -7.1302880.377174 -0.02 C -6.239632 -3.827864 -0.01 C -6.087349 -5.2584890.02 C -5.083140 -2.9252030.00 C -5.413953 -1.5144630.00 C -4.403993 -0.5135660.02 C -4.7941340.8562880.02 C -3.676893 -4.887701 -0.01 C -3.676919 -3.479951 -0.03 C -2.270708 -2.925222 -0.02 C -2.949816 -0.513582 -0.02 C -1.939871 -1.5144810.01 . . K_POINTS automatic 4 4 1 0 0 0 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110610/40591a62/attachment-0001.htm
[Pw_forum] c_bands : eigenvalues not converged
Dear All, I am still running a band structure calculation on a 72 Carbon atom system but it is taking a bit too long and till now the results are: negative rho (up, down) = 0.0406, 0 Band Structure Calculation: Davidson Diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 1 eigenvalue not converged and is still running for like 6 days. The system is very similar to graphene and its DOS should be similar. I gathered that there might be something wrong with my input..Please can anyone help me on that? The input is: control prefix='GBdensity', calculation='bands', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo', / &system ibrav= 0, celldm(1) =1.889725989, nat=72, ntyp= 1, ecutwfc =32.0, ecutrho = 160.D0, nosym=.true.,occupations='smearing', smearing='mp', degauss=0.01 / &electrons conv_thr=1.D-4, mixing_beta=0.1D0, / CELL_PARAMETERS (alat) 29.41660 0.0 0.0 0.0 6.60990 0.0 0.0 0.0 33.0 ATOMIC_SPECIES C 12.0107 C.pz-rrjus.UPF ATOMIC_POSITIONS (angstrom) C -17.267939 -5.262892 -0.02 C -17.658134 -3.893047 -0.02 C -16.648186 -2.8921450.00 C -16.979016 -1.481403 -0.01 C -15.822497 -7.1886510.03 C -15.974769 -5.7580110.01 C -14.931838 -4.783788 -0.02 C -15.260133 -3.372206 -0.03 C -14.164353 -2.443247 -0.01 C -14.448789 -1.0380330.01 C -13.357280 -6.694629 -0.03 C -13.589274 -5.266428 -0.06 C -12.507820 -4.324210 -0.03 C -12.797007 -2.912572 -0.03 C -11.713425 -1.9675540.02 C -11.996028 -0.5540490.01 C -10.908497 -6.218111 -0.01 C -11.153648 -4.7983950.00 C -10.348701 -2.4390650.02 C -10.066097 -3.852576 -0.01 C -9.265132 -1.494029 -0.01 C -9.554319 -0.0823940.00 C -8.472857 -5.750083 -0.02 C -8.704854 -4.3218880.01 C -7.613348 -3.3685920.01 C -7.897799 -1.963373 -0.03 C -6.802030 -1.0344150.00 C -7.1302880.377174 -0.02 C -6.239632 -3.827864 -0.01 C -6.087349 -5.2584890.02 C -5.083140 -2.9252030.00 C -5.413953 -1.5144630.00 C -4.403993 -0.5135660.02 C -4.7941340.8562880.02 C -3.676893 -4.887701 -0.01 C -3.676919 -3.479951 -0.03 C -2.270708 -2.925222 -0.02 C -2.949816 -0.513582 -0.02 C -1.939871 -1.5144810.01 . . K_POINTS crystal_b 5 0.0 0.0 0.0 12 0.0 0.5 0.0 12 0.5 0.02160 0.0 12 0.38540 0.5 0.0 12 0.0 0.0 0.0 12 Regards Elie Moujaes University of Nottingham Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/f0fa5036/attachment-0001.htm
[Pw_forum] Fortan compiler cannot create executables
I am really thankful for your help. I renamed it and now it displayed : checking for g95.g95 but it stopped with another error: Configure: WARNING: In the future, Auticonfig will not detect cross-tools whose name does not start with the host triplet. If you think this configuration is useful to you, please write to autoconf at gnu.org. Checking for Fortran compiler default output filename...Configure: error: Fortran compiler cannot create executables Elie From: ttdu...@gmail.com Date: Sun, 17 Apr 2011 21:23:36 -0400 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Fortan compiler cannot create executables Rename or make an sanple link i686-pc-linux-gnu-g95 to g95 and try. QE looks for g95 file, you don't have it.-- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Sun, Apr 17, 2011 at 9:16 PM, Elie Moujaes wrote: Dear Duy Le, Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and is in the bin folder in g95-install. Adding this to the path i.e : /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin produces the same error : checking for g95...no Elie > Date: Sun, 17 Apr 2011 20:55:58 -0400 > From: ttduyle at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Fortan compiler cannot create executables > > You just need to identify CORRECTLY the PATH of g95 excutable, not the > source code PATH > > On Sunday, April 17, 2011, Elie Moujaes wrote: > > > > > > > > > > > > Dear Masoud, > > > > I have tried setenv but it did not really work. Initially, my PATH was: > > /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and > > the new path is: > > > > /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install > > > > but when I ./configure again, I still get checking for g95..noso I am > > not sure what is still going wrong > > > > ELie > > > > Date: Sun, 17 Apr 2011 09:26:17 +0430 > > From: masoudnahali at gmail.com > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] Fortan compiler cannot create executables > > > >Dear Elie > > > > Using csh/tcsh you should try "setenv" instead of "export". > > > > > > > > > > Elie on Sun, 17 Apr 2011 00:31:35 wrote: > > > > Unfortunately, my CSH shell does not support the EXPORT command. > > Best Wishes > > > > > > Masoud > > -- > > Masoud Nahali, Ph. D Student > > Sharif University of Technology > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > -- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ___ 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/20110418/675c6eaa/attachment.htm
[Pw_forum] Fortan compiler cannot create executables
Dear Duy Le, Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and is in the bin folder in g95-install. Adding this to the path i.e : /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin produces the same error : checking for g95...no Elie > Date: Sun, 17 Apr 2011 20:55:58 -0400 > From: ttduyle at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Fortan compiler cannot create executables > > You just need to identify CORRECTLY the PATH of g95 excutable, not the > source code PATH > > On Sunday, April 17, 2011, Elie Moujaes wrote: > > > > > > > > > > > > Dear Masoud, > > > > I have tried setenv but it did not really work. Initially, my PATH was: > > /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and > > the new path is: > > > > /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install > > > > but when I ./configure again, I still get checking for g95..noso I am > > not sure what is still going wrong > > > > ELie > > > > Date: Sun, 17 Apr 2011 09:26:17 +0430 > > From: masoudnahali at gmail.com > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] Fortan compiler cannot create executables > > > >Dear Elie > > > > Using csh/tcsh you should try "setenv" instead of "export". > > > > > > > > > > Elie on Sun, 17 Apr 2011 00:31:35 wrote: > > > > Unfortunately, my CSH shell does not support the EXPORT command. > > Best Wishes > > > > > > Masoud > > -- > > Masoud Nahali, Ph. D Student > > Sharif University of Technology > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > -- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > ___ > 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/20110418/63f8dec0/attachment.htm
[Pw_forum] Fortan compiler cannot create executables
Dear Masoud, I have tried setenv but it did not really work. Initially, my PATH was: /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and the new path is: /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install but when I ./configure again, I still get checking for g95..noso I am not sure what is still going wrong ELie Date: Sun, 17 Apr 2011 09:26:17 +0430 From: masoudnah...@gmail.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Fortan compiler cannot create executables Dear Elie Using csh/tcsh you should try "setenv" instead of "export". Elie on Sun, 17 Apr 2011 00:31:35 wrote: Unfortunately, my CSH shell does not support the EXPORT command. Best Wishes Masoud -- Masoud Nahali, Ph. D Student Sharif University of Technology ___ 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/20110418/86dd6b8f/attachment.htm
[Pw_forum] Fortan compiler cannot create executables
Dear Masoud, thanks very much for your help. I knew that I need to change the path but i did not know how so thanks for thr info. Unfortunately, my CSH shell does not support the EXPORT command so whenever I use it it outputs : Export: command not found. I do not have a /bin because this is running on my network account..I even tried before to use ln -s to copy stuff but permission was denied. is there any other command you are aware of for a csh/sh shell (other than export I mean)? Thank you ELie Date: Sat, 16 Apr 2011 14:11:00 +0430 From: masoudnah...@gmail.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Fortan compiler cannot create executables Dear Elie Try "export PATH=$PATH:/path/to/your/directory/where/g95/installed" then update your database (updatedb command) and restart your computer. Also, you can copy g95 binary files from where you have installed the g95 to /bin.You should examine "g95" or "gfortran" commands in your linux console before trying to compile the QE. I hope it helps. Best Wishes Masoud -- Masoud Nahali, Ph. D Student Sharif University of Technology On Sat, Apr 16, 2011 at 11:57 AM, Elie Moujaes wrote : Hello everyone, I am trying to re-install quantum espresso-4.3 on the University's LINUX interface (because of a recent crash and I lost most of my files). when I "sudo ./configure ", It is giving an error stating that : checking building system type... x86_64-unknown-linux-gnu checking architecture... x86_64 checking for ifort.. no checking for pgf90... no checking for pathf95.. no checking for sunf95.. no checking for openf95... no checking for gfortran... no checking for g95... no checking for f90... no checking for Fortran compiler default output... configure: error: Fortran compiler cannot create executables See `config.log' for more details. I have already installed g95. I really don't know why this error is coming. Please can anyone help. Thanks Elie Moujaes University of Nottingham Nottingham NG7 2RD ___ 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/20110417/6ff6bc69/attachment-0001.htm
[Pw_forum] Fortan compiler cannot create executables
Hello everyone, I am trying to re-install quantum espresso-4.3 on the University's LINUX interface (because of a recent crash and I lost most of my files). when I "sudo ./configure ", It is giving an error stating that : checking building system type... x86_64-unknown-linux-gnu checking architecture... x86_64 checking for ifort.. no checking for pgf90... no checking for pathf95.. no checking for sunf95.. no checking for openf95... no checking for gfortran... no checking for g95... no checking for f90... no checking for Fortran compiler default output... configure: error: Fortran compiler cannot create executables See `config.log' for more details. I have already installed g95. I really don't know why this error is coming. Please can anyone help. Thanks Elie Moujaes University of Nottingham Nottingham NG7 2RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110416/499497f7/attachment.htm
[Pw_forum] band structure of a 60 Carbon atom system
Dear all, I am trying to get the band structure of a 60 Carbon atom system. i have done the scf calculations and the band structure calculation. I am comparing my results to other ones. I have realised that in my calculations even after setting the Fermi energy to zero, Two of the bands that are supposed to cross at the zero level in others calculations crossed below the zero reference in my calculations. The shape of the curves are similar though. I am trying to figure out the origin of this difference. Could anyone tell me what might be going wrong? Is this a pseudopotential related problem? Thanks Elie Moujaes University of nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110214/024f0309/attachment.htm
[Pw_forum] Fortran Runtime error: bad real number in item 1 of list input
Guys, I am sorry to bother you with my electron phonon calculations again. I am trying to do my calculations for a different system of bilayer graphene but I get errors like: At line 356 of file q2r.f90 (Unit 51 "a2Fq2r.51") Traceback: not available, compile with -ftrace=frame or -ftrace=full Fortran Runtime error: bad real number in item 1 of list input when running q2r.x and At line 1659 of file matdyn.f90 (Unit 51 "a2Fmatdyn.61") Traceback: not available, compile with -ftrace=frame or -ftrace=full Fortran Runtime error: End of File when running matdyn.x I do not know what is going on. I tried the same calculations with a smaller grid before and everything went fine Regards Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110209/81944919/attachment.htm
[Pw_forum] error ephsum using ph.x
Dera Prof. Isaev, Thanks a lot for the info. I have read the example which is I guess Example 7 in the guide but did not quite understand it.Anyhow will look out other examples . regards Elie Date: Mon, 7 Feb 2011 08:09:21 -0800 From: eyvaz_is...@yahoo.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] error ephsum using ph.x Dear Elie, >from elphsum : error # 2 > q is not a vector in the dense grid That means k-points set used in the first scf step and what you specified in elph.in file are incompatible, i.e. nq1,nq2,nq3 are not divisors of that numbers used to generate dense k-points set. Regarding lambda.x, I guess, there was an example file (an input file) where an explanation was done. If you can not find it (please search before) then contact me. Besides, all info calculated via lambda.x can now be obtained using matdyn.x Bests, Eyvaz. --- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From: Elie Moujaes To: pw_forum at pwscf.org Sent: Mon, February 7, 2011 4:51:07 PM Subject: [Pw_forum] error ephsum using ph.x Dear all, (1) First of all sorry to bombard you with a lot of questions but I am trying to perform the electron phonon calculation of monolayer graphene and I am facing some problems. when performing the ph.x command, after some time, I get an error: from elphsum : error # 2 q is not a vector in the dense grid %% stopping ... This is when trying to do calculations for one particular point. my input file is the following: Electron-Phonon interaction for monolayer graphene &inputph tr2_ph=1.0d-14, prefix='elphmonograph', fildvscf='mgraphdv', amass(1)=12.0107, outdir='/tmp/results_MOUJAES/', fildyn='elphmgraph.dyn', elph=.true., trans=.true., ldisp=.true. nq1=8, nq2=8, nq3=1 / I have tried with lesser points like say nq1=2, nq2=2, nq3=1 and I did not get such an error. (2) My second question is about lambda.x .I have read the example in the QE package but have not really understood it fully. Can anyone briefly explain to me or just point out where there is more explanation about this executable..I fully understtod what it does though.. Regards and thanks for your time Elie Moujaes University of Nottingham NG7 2RD UK ___ 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/20110207/f0fed174/attachment-0001.htm
[Pw_forum] error ephsum using ph.x
Dear all, (1) First of all sorry to bombard you with a lot of questions but I am trying to perform the electron phonon calculation of monolayer graphene and I am facing some problems. when performing the ph.x command, after some time, I get an error: from elphsum : error # 2 q is not a vector in the dense grid %% stopping ... This is when trying to do calculations for one particular point. my input file is the following: Electron-Phonon interaction for monolayer graphene &inputph tr2_ph=1.0d-14, prefix='elphmonograph', fildvscf='mgraphdv', amass(1)=12.0107, outdir='/tmp/results_MOUJAES/', fildyn='elphmgraph.dyn', elph=.true., trans=.true., ldisp=.true. nq1=8, nq2=8, nq3=1 / I have tried with lesser points like say nq1=2, nq2=2, nq3=1 and I did not get such an error. (2) My second question is about lambda.x .I have read the example in the QE package but have not really understood it fully. Can anyone briefly explain to me or just point out where there is more explanation about this executable..I fully understtod what it does though.. Regards and thanks for your time Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/bba46afb/attachment.htm
[Pw_forum] problems with q2r.x executable
Prof. Giannozzi, Thanks very much for your reply. I just repeated the calculations and it worked quite well. Regards Elie Moujaes University of Nottingham NG7 2RD UK > From: giannozz at democritos.it > Date: Fri, 4 Feb 2011 22:14:33 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with q2r.x executable > > > On Feb 4, 2011, at 14:38 , Elie Moujaes wrote: > > > the first three which should be .51, .52 and .53 files > > are all produced with the same name a2Fq2r and they > > appear as WORD files whilst the others are ok. > > you need to go into the code where it opens those files > and see what happens. There is no way anybody else > can find an explanation for such an unlikely event without > looking more closely. > > P. > --- > Paolo Giannozzi, Dept of 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://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110207/011ee552/attachment-0001.htm
[Pw_forum] problems with q2r.x executable
When I execute ph.x , amongst the other files I get (.dyn0, .dyn1,..), I get
those a2Fq2r files. it is strange that the first three which should be .51, .52
and .53 files are all produced with the same name a2Fq2r and they appear as
WORD files whilst the others are ok. I have also tried deleting everything from
the .tmp folder but in vain. ph.x still produces the same strain of files so
that when i execute q2r.x, the code complains that a2Fq2r.51 is missing!
Regards
Elie
> From: giannozz at democritos.it
> Date: Fri, 4 Feb 2011 08:55:57 +0100
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] problems with q2r.x executable
>
>
> On Feb 4, 2011, at 1:38 , Elie Moujaes wrote:
>
> > The problem is the {a2Fq2r.51, a2Fq2r.52, a2Fq2r.53} are all appearing
> > as a2Fq2r
>
> what do you mean? I have never heard that file X "appears" as Y
>
> P.
> ---
> Paolo Giannozzi, Dept of 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://www.democritos.it/mailman/listinfo/pw_forum
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[Pw_forum] problems with q2r.x executable
Dear all,
I am having problems with the ph.x command in the calculation of the
electron-phonon coefficients for graphene. Some of the files produced are of
the type a2Fq2r. In my case there are 10 of these a2Fq2r.51, a2Fq2r.52,
a2Fq2r.53, a2Fq2r.54, a2Fq2r.55, a2Fq2r.56, a2Fq2r.57, a2Fq2r.58, a2Fq2r.59,
a2Fq2r.60. The problem is the {a2Fq2r.51, a2Fq2r.52, a2Fq2r.53} are all
appearing as a2Fq2r so that when the q2r.x executable is applied, it complains
that the files .51, .52 and ,53 are missing. Can anyone point out what the
problem might be?
Thanks
Elie Moujaes
University of Nottingham
NG72RD
UK
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[Pw_forum] computing electron phonon coefficients
One more question regarding the electron-phonon implementation in QE. Is it possible to plot the band structure and the DOS including the electron phonon interaction in the calculations? Regards Elie Moujaes University of Nottingham NOttingham NG7 2RD UK > From: giannozz at democritos.it > Date: Thu, 3 Feb 2011 07:38:58 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] computing electron phonon coefficients > > > On Feb 2, 2011, at 19:40 , Elie Moujaes wrote: > > > I am trying to compute the electron phonon coefficients for > > monolayer graphene (using the options elph=.true. and trans=.true.) > > in the ph.in file. I am using Espresso-4.2. The ph.x executable is > > stopping after some time with the message: > > > > At line 378 of file elphon.f90 (Unit 40 "/tmp/results-MOUJAES/ > > elphomonograph.a2Fsave") > > Traceback is not availabe, compile with -ftrace=frame or -ftrace=full > > Fortran runtime error : End of file > > before running the electron-phonon calculation, you have to run a non- > scf calculation > with an option (la2f or something like this) that produces the > required file (the one > that is missing here) > > P. > --- > Paolo Giannozzi, Dept of 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://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110203/4ae7566d/attachment.htm
[Pw_forum] computing electron phonon coefficients
Dear Prof. Giannozzi, Thanks very much for your reply. Regards Elie > From: giannozz at democritos.it > Date: Thu, 3 Feb 2011 07:38:58 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] computing electron phonon coefficients > > > On Feb 2, 2011, at 19:40 , Elie Moujaes wrote: > > > I am trying to compute the electron phonon coefficients for > > monolayer graphene (using the options elph=.true. and trans=.true.) > > in the ph.in file. I am using Espresso-4.2. The ph.x executable is > > stopping after some time with the message: > > > > At line 378 of file elphon.f90 (Unit 40 "/tmp/results-MOUJAES/ > > elphomonograph.a2Fsave") > > Traceback is not availabe, compile with -ftrace=frame or -ftrace=full > > Fortran runtime error : End of file > > before running the electron-phonon calculation, you have to run a non- > scf calculation > with an option (la2f or something like this) that produces the > required file (the one > that is missing here) > > P. > --- > Paolo Giannozzi, Dept of 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://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110203/261f814d/attachment.htm
[Pw_forum] computing electron phonon coefficients
Dear all , I am trying to compute the electron phonon coefficients for monolayer graphene (using the options elph=.true. and trans=.true.) in the ph.in file. I am using Espresso-4.2. The ph.x executable is stopping after some time with the message: At line 378 of file elphon.f90 (Unit 40 "/tmp/results-MOUJAES/elphomonograph.a2Fsave") Traceback is not availabe, compile with -ftrace=frame or -ftrace=full Fortran runtime error : End of file Can anyone tell me how to fix this problem ? Regards Elie Moujaes University of nottingham NottinghamNG7 2RD uk -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110202/202debc6/attachment.htm
[Pw_forum] 60 atom Grain boundary... (Elie Moujaes)
Thank you very much for your help. I have just got some few more questions: (1) is changing the mesh in the DOS program means decreasing DeltaE? (2) Concerning the convergence against smearing, does this mean that one has to decrease degauss (mine is degauss=0.01) to get better results? You will find below a part of the bands input file. &control prefix='GBdensity', calculation='bands', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =40.0, ecutrho = 160.D0, occupations='smearing', smearing='mp', degauss=0.01 / &electrons conv_thr=1.D-5, mixing_beta=0.1D0, / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 -0.000547177 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0 C -10.331417950 -2.543878336 0.0 C -8.972994221 -3.016349126 0.0 C -8.181174559 -0.722870888 0.0 C -9.522448653 -6.774832629 0.0 C -9.676361200 -5.364937582 0.0 C -8.645931928 -4.406311082 0.0 .. ... Thanks again Elie Moujaes University of Nottingham NG7 2RD UK Date: Wed, 26 Jan 2011 01:42:39 +0900 From: adadadad3...@gmail.com To: pw_forum at pwscf.org CC: dekura at sci.ehime-u.ac.jp Subject: Re: [Pw_forum] 60 atom Grain boundary... (Elie Moujaes) Dear Elie Moujaes Do you mean that your calculated Fermi-energy in C60 system is not located at which the DOS becomes zero even though you got the reasonable band structure. If so, I recommend a check for the convergence of Fermi-energy. For example, please check the energy convergence against (1) increase of the number of k-points in nscf calculation, after you confirm that the KS energy spectrum is converged sufficiently in SCF calculation (and also should check the convergence against the smearing width) (2) change in the mesh in DOS calculation. May be you will get more reliable and better result. Hope this helps. Best Regards. Haruhiko Dekura Haruhiko Dekura Postdoctoral Fellow Senior Research Fellow Center, Ehime University, 2?5 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan = Dear all, I am trying to get the band structure and the DOS of a Grain boundary system of 60 atoms. (1) The band structure seems ok but when I am trying to set the Fermi energy to be the reference (i.e at 0) where two bands cross, it is not working i.e. I am still getting that the two bands still cross at a negative value (my Fermi energy is -0.098eV). Why is this happening? (2) The DOS of the system is not zero at zero energy (maybe this is a consequence of 1) and it is a bit wiggly as well (see graph attached) Thanks in advance Regards Elie Moujaes University of Nottingham NG7 2RD UK ___ 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/20110125/fae4cadc/attachment-0001.htm
[Pw_forum] 60 atom Grain boundary...
Dear all, I am trying to get the band structure and the DOS of a Grain boundary system of 60 atoms. (1) The band structure seems ok but when I am trying to set the Fermi energy to be the reference (i.e at 0) where two bands cross, it is not working i.e. I am still getting that the two bands still cross at a negative value (my Fermi energy is -0.098eV). Why is this happening? (2) The DOS of the system is not zero at zero energy (maybe this is a consequence of 1) and it is a bit wiggly as well (see graph attached) Thanks in advance Regards Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110125/f6213af7/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: GB60DOS.ps Type: application/octet-stream Size: 124076 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110125/f6213af7/attachment-0001.obj
[Pw_forum] Bilayer graphene subject to an electric field
Dear Prof. Eyvaz, Thanks a lot for the information. Everything is solved now.. Elie Date: Tue, 14 Dec 2010 13:40:59 -0800 From: eyvaz_is...@yahoo.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Bilayer graphene subject to an electric field Hi, A couple of comments that might be useful. 1. As you use an US pseudopotential, reduce ecutwfc down to ~30Ry. I do not see any reason for such kind of high cutoff energy, unless you performed some tests and proved that 60Ry is better. Besides, for the same reason (US PsP), you should use more ecutrho (8-12 times of ecutwfc). By default ecutrho=4*ecutwfc (why so, think about) and this works for norm-conserving PsPs. As a reference see N.Mounet and N. Marzari, Phys. Rev. B 71, 205214 (2005), where they used ecutoff=40Ry for graphene and other C-based structures. 2. I have noticed that the job started to converge when I used smaller efield_cart(3)=0.05, after 49 iteration I had estimated scf accuracy< 0.7068 Ry but then my notebook turned off due to a heating problem, I suggest. As I just tried to test the problem I used only 2x2x1 k-points set, and mixing_beta(1)=0.05. But when I used efield_cart(3)=0.005 (with mixing coefficient 0.1) the job finished after 11 iterations. Hope this helps. Bests, Eyvaz. --- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From: Elie Moujaes To: pw_forum at pwscf.org Sent: Mon, December 13, 2010 1:57:36 PM Subject: [Pw_forum] Bilayer graphene subject to an electric field Dear all, I am trying to get the band structure of bilayer graphene under the effect of an external electric field. I have done the scf calculations without the inclusion of an electric field , then again did teh scf calculation with an electric field included in the z-direction (of value 0.1 Ry). However the convergence is not achieved and it stopped after 100 iterations giving the following message: total cpu time spent up to now is 83435.11 secs total energy = -52.83248336 Ry Harris-Foulkes estimate = -45.80937450 Ry estimated scf accuracy< 0.00524127 Ry End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping You will find below the inout file for the scf calculation when an electric field is applied: &control prefix='bielgraphene', calculation='scf', restart_mode='from_scratch', lelfield = .true., nberrycyc= 1, pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 60.D0,occupations='smearing',smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-5, mixing_mode='local-TF' mixing_beta=0.1D0 efield_cart(1) = 0.000, efield_cart(2) = 0.000, efield_cart(3) = 0.10, / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.00 0.00 0.257692 C 0.33 -0.3 0.00 C -0.33 0.3 0.257692 K_POINTS automatic 25 25 1 0 0 0 Thanks Elie Moujaes University of Nottingham NG7 2RD UK ___ 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/20101217/733d6536/attachment-0001.htm
[Pw_forum] Bilayer graphene subject to an electric field
Dear all, I am trying to get the band structure of bilayer graphene under the effect of an external electric field. I have done the scf calculations without the inclusion of an electric field , then again did teh scf calculation with an electric field included in the z-direction (of value 0.1 Ry). However the convergence is not achieved and it stopped after 100 iterations giving the following message: total cpu time spent up to now is 83435.11 secs total energy = -52.83248336 Ry Harris-Foulkes estimate = -45.80937450 Ry estimated scf accuracy< 0.00524127 Ry End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping You will find below the inout file for the scf calculation when an electric field is applied: &control prefix='bielgraphene', calculation='scf', restart_mode='from_scratch', lelfield = .true., nberrycyc= 1, pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 60.D0,occupations='smearing',smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-5, mixing_mode='local-TF' mixing_beta=0.1D0 efield_cart(1) = 0.000, efield_cart(2) = 0.000, efield_cart(3) = 0.10, / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.00 0.00 0.257692 C 0.33 -0.3 0.00 C -0.33 0.3 0.257692 K_POINTS automatic 25 25 1 0 0 0 Thanks Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101213/4850afb4/attachment.htm
[Pw_forum] gdir value
Dear all, I am doing some band structure calculations in graphene under the effect of the electric field. I need to specify gdir which in this case refers to the direction of the electric field. If my electric field is in the z-direction, does it mean that gdir = 3? Thanks Elie Moujaes University of Nottingham UK NG7 2 RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101209/fc5d89bd/attachment.htm
[Pw_forum] pw2wannier error
Dear all, I am applying the pw2wannier90.x executable to bilayer graphene but I am getting the very famous error: Checking info from wannier.nnkp file Something wrong! rlatt(i,j) = 4.536660026280493 at(i,j)= 5.33041005 I am using the version v3.2.3 of wannier90 so the precision to which the lattice vectors are written should be fine. The strange thing is that the values are not that close to each other. You will find attcahed the scf and the win files. Regards Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101130/1060b576/attachment.htm -- next part -- An embedded and charset-unspecified text was scrubbed... Name: tbbigraph.scf.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20101130/1060b576/attachment.txt -- next part -- An embedded and charset-unspecified text was scrubbed... Name: bigraphtb.win Url: http://www.democritos.it/pipermail/pw_forum/attachments/20101130/1060b576/attachment.asc
[Pw_forum] wannier90.x missing
Thanks very much...I missed that..sorry :) Thank you Regards > Date: Mon, 29 Nov 2010 18:22:20 +0100 > From: giannozz at democritos.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] wannier90.x missing > > re-run configure > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > ___ > 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/20101129/46dccb4c/attachment.htm
[Pw_forum] wannier90.x missing
Thanks again for ur help. I redownloaded the whole .tar file for wannier and untarred it and when I tried the command make wannier, I got an error : entering directory 'espresso-4.2//wannier90-1.2/src' ifort -O2 -c constants.f90 make [1] ifort command not found mak[1] *** [constants.o] error 127 make[1] leaving directory 'espresso-4.2//wannier90-1.2/src' make: *** [wannier] error 2 presumably related to the compiler (ifort which I dont have). I am using a cygwin interface to execute LIUNX commands. I guess the solution is to change the compiler command but from where? sorry for my limited knowledge about UNIX regards Elie Moujaes From: sclau...@sissa.it Date: Mon, 29 Nov 2010 17:00:32 +0100 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] wannier90.x missing I suppose that you must first download the wannier90 plugin from the qe-forge website http://qe-forge.org/frs/?group_id=10 put it in the right place and the retry. GS Il giorno 29/nov/2010, alle ore 16.41, Elie Moujaes ha scritto: Thanks for the reply.. I have tried make w90 before yes but it stopped giving me an error: cp: cannot create regular file `.../wannier90-1.2/make.sys` : no such file or directory make[1]: *** w90 error 1 make[1]: /espresso-4.2/plugins Regards Elie Moujaes From: sclau...@sissa.it Date: Mon, 29 Nov 2010 15:12:17 +0100 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] wannier90.x missing Have you tried with the following? make w90 BTW, if you simply type make, you'll get a list of all possible targets and what will be built for each of them GS Il giorno 29/nov/2010, alle ore 14.32, Elie Moujaes ha scritto: Dear all, I am using the wannier functions to get the band structure in bilayer graphene. in expresso-4.2, I found all the executables (pw2wannier90.x, wannier_plot.x, etc..) except the wannier90.x executable that I need. I downloaded the folder W90 from the QE site and I found the the wannier90.f90 program. I tried to form the executable by tping: g95 wannier.f90 -o wannier but I got some errors. Is it possible to let me know where I can find the executable or how to form it given that I have the .f90 file. Regards Elie Moujaes University of Nottingham NG7 2RD UK ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne ___ 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/20101129/649d663d/attachment.htm
[Pw_forum] wannier90.x missing
Thanks for the reply.. I have tried make w90 before yes but it stopped giving me an error: cp: cannot create regular file `.../wannier90-1.2/make.sys` : no such file or directory make[1]: *** w90 error 1 make[1]: /espresso-4.2/plugins Regards Elie Moujaes From: sclau...@sissa.it Date: Mon, 29 Nov 2010 15:12:17 +0100 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] wannier90.x missing Have you tried with the following? make w90 BTW, if you simply type make, you'll get a list of all possible targets and what will be built for each of them GS Il giorno 29/nov/2010, alle ore 14.32, Elie Moujaes ha scritto: Dear all, I am using the wannier functions to get the band structure in bilayer graphene. in expresso-4.2, I found all the executables (pw2wannier90.x, wannier_plot.x, etc..) except the wannier90.x executable that I need. I downloaded the folder W90 from the QE site and I found the the wannier90.f90 program. I tried to form the executable by tping: g95 wannier.f90 -o wannier but I got some errors. Is it possible to let me know where I can find the executable or how to form it given that I have the .f90 file. Regards Elie Moujaes University of Nottingham NG7 2RD UK ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne ___ 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/20101129/6ec512c2/attachment.htm
[Pw_forum] wannier90.x missing
Dear all, I am using the wannier functions to get the band structure in bilayer graphene. in expresso-4.2, I found all the executables (pw2wannier90.x, wannier_plot.x, etc..) except the wannier90.x executable that I need. I downloaded the folder W90 from the QE site and I found the the wannier90.f90 program. I tried to form the executable by tping: g95 wannier.f90 -o wannier but I got some errors. Is it possible to let me know where I can find the executable or how to form it given that I have the .f90 file. Regards Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101129/d9f5a935/attachment.htm
[Pw_forum] band structure of a 60 atom grain boundary
Dear all, I am trying to get the band structure of a 60-atom GB of graphene. The result is ok except that two of the bands should touch at some point and they are not touching. Could that be a probvlem in the convergence or in the set degauss value? Thanks Regards Elie Moujaes University of Nottingham NG7 2RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101124/1c39ea6e/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: GB60.bands.ps Type: application/postscript Size: 36709 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101124/1c39ea6e/attachment-0001.ps
[Pw_forum] Brillouin Zone for my supercell
Thank you all for the information. I will be having a look at XCrysDen and looking at other books as well... Regards Elie > Date: Thu, 28 Oct 2010 21:05:50 +0300 > From: ismotochi at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Brillouin Zone for my supercell > > Hi Elie, You can find the information you want on high symmetry points > by working in Xcrysden. > > Motochi Isaac > Moi University- Kenya > ___ > 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/20101028/dfa22635/attachment.htm
[Pw_forum] Brillouin Zone for my supercell
Dear All, I am working with a supercell of 60 Carbon atoms. I am trying to do scf and band structure calculations. Is there anything in QE that is used to draw the Brillouin zone for my supercell as I need to find the coordinates of the points that are intercepts with the walls of the Brillouin zone or maybe find coordinates of high symmetry points in the BZ? How can I get such information? Regards Elie Moujaes University of Nottingham BG7 2RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101028/e163be36/attachment.htm
[Pw_forum] Bilayer graphene with an electric field applied
Dear Professor Paulatto, thanks for bringing this up. Indeed, I was plotting the band energies of the regukar k grid instead. Everything seems right now.. Regards Elie > To: pw_forum at pwscf.org > Date: Thu, 30 Sep 2010 17:46:39 +0200 > From: Lorenzo.Paulatto at impmc.upmc.fr > Subject: Re: [Pw_forum] Bilayer graphene with an electric field applied > > In data 30 settembre 2010 alle ore 15:30:01, Elie Moujaes > ha scritto: > > The thing is there are no problems in the DOS calculations; only in the > > band structure. > > Are you sure you did a proper band plot along a path in the Brillouin zone > (like example01) and not just plot of the band energies of the regular > grid of k-points? > > regards > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > ___ > 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/20101001/87cc26fe/attachment.htm
[Pw_forum] Bilayer graphene with an electric field applied
Dear Gabriele,
I have tried the tefield but i am getting the same messy results again.. The
thing is there are no problems in the DOS calculations; only in the band
structure. I have increased the E field in the new calculation to 0.1 instead
of the 0.001 old value. I am attaching a very small part of the results as a
tif file because of the attachment limitations in the forum. When you have
time, please let me know what you think...
Thank you
Elie
Date: Wed, 29 Sep 2010 09:55:03 +0200
From: sclau...@sissa.it
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Bilayer graphene with an electric field applied
Dear Elje,
since you are dealing with a slab geometry and you want to apply the field
along the direction perpendicular to the surface, why don't you use the
sawtooth potential (tefield=.TRUE. instead of lefield=.TRUE.) to generate the E
field?
On 09/28/2010 10:41 PM, Elie Moujaes wrote:
Dear all,
I
I am trying to get the band structure of graphene under the effect of an
electric field. The problem is that the result at the end is very messy and
jiggly. I repeated the calculations many times but I still get the same result.
I first performed a scf calculation without the electric field followed by a
scf calculation with an electric field and then the band calculation.
Do you have some evidence that your "messy and jiggly" band structure is wrong?
Are you sure that you are visualizing it in the correct way?
HTH
GS
SCF with electric field
&control
prefix='bi elgraphene',
calculation='scf',
restart_mode='from_scratch',
lelfield = .true.,
pseudo_dir = '/espresso-4.2/pseudo/',
outdir='/tmp/results_MOUJAES/'
/
&system
ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1,
ecutwfc = 110.D0,occupations='smearing',smearing='methfessel-paxton',
degauss=0.01
/
&electrons
conv_thr=1.D-10,
mixing_mode='plain'
efield_cart(1) = 0.0,
efield_cart(2) = 0.0,
efield_cart(3) = 0.001,
startingwfc = 'random'
/
ATOMIC_SPECIES
C 12.0107 C.pz-vbc.UPF
ATOMIC_POSITIONS crystal
C 0.00 0.00 0.00
C 0.00 0.00 0.257692
C 0.33 -0.3 0.00
C -0.33 0.3 0.257692
K_POINTS automatic
38 38 1 0 0 0
I noticed that part of the bands calculation output had a problem with the
convergence of one of thh eigenavalues as some of the input looked like:
per-process dynamical memory:30.2 Mb
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
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
Please can anyone suggest me of what could have gone wrong...
Thanks
Elie Moujaes
University of Nottingham
NG7 2RD
UK
___
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Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne
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[Pw_forum] Bilayer graphene with an electric field applied
Thanks very much for your help. I will use the sawtooth potential and see what
happens. I will have another look on the band structure as well because I have
done the DOS calculations and the graph seems pretty ok..
Regards
Elie
Date: Wed, 29 Sep 2010 09:55:03 +0200
From: sclau...@sissa.it
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Bilayer graphene with an electric field applied
Dear Elje,
since you are dealing with a slab geometry and you want to apply the field
along the direction perpendicular to the surface, why don't you use the
sawtooth potential (tefield=.TRUE. instead of lefield=.TRUE.) to generate the E
field?
On 09/28/2010 10:41 PM, Elie Moujaes wrote:
Dear all,
I
I am trying to get the band structure of graphene under the effect of an
electric field. The problem is that the result at the end is very messy and
jiggly. I repeated the calculations many times but I still get the same result.
I first performed a scf calculation without the electric field followed by a
scf calculation with an electric field and then the band calculation.
Do you have some evidence that your "messy and jiggly" band structure is wrong?
Are you sure that you are visualizing it in the correct way?
HTH
GS
SCF with electric field
&control
prefix='bi elgraphene',
calculation='scf',
restart_mode='from_scratch',
lelfield = .true.,
pseudo_dir = '/espresso-4.2/pseudo/',
outdir='/tmp/results_MOUJAES/'
/
&system
ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1,
ecutwfc = 110.D0,occupations='smearing',smearing='methfessel-paxton',
degauss=0.01
/
&electrons
conv_thr=1.D-10,
mixing_mode='plain'
efield_cart(1) = 0.0,
efield_cart(2) = 0.0,
efield_cart(3) = 0.001,
startingwfc = 'random'
/
ATOMIC_SPECIES
C 12.0107 C.pz-vbc.UPF
ATOMIC_POSITIONS crystal
C 0.00 0.00 0.00
C 0.00 0.00 0.257692
C 0.33 -0.3 0.00
C -0.33 0.3 0.257692
K_POINTS automatic
38 38 1 0 0 0
I noticed that part of the bands calculation output had a problem with the
convergence of one of thh eigenavalues as some of the input looked like:
per-process dynamical memory:30.2 Mb
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
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 1 eigenvalues not converged
Please can anyone suggest me of what could have gone wrong...
Thanks
Elie Moujaes
University of Nottingham
NG7 2RD
UK
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[Pw_forum] Bilayer graphene with an electric field applied
Dear all, I I am trying to get the band structure of graphene under the effect of an electric field. The problem is that the result at the end is very messy and jiggly. I repeated the calculations many times but I still get the same result. I first performed a scf calculation without the electric field followed by a scf calculation with an electric field and then the band calculation. SCF with no electric field: control prefix='bi elgraphene', calculation='scf', restart_mode='from_scratch', lelfield = .true., pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 110.D0,occupations='smearing', smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-10, mixing_mode='plain' efield_cart(1) = 0.0, efield_cart(2) = 0.0, efield_cart(3) = 0.0, startingwfc = 'random' / ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.00 0.00 0.257692 C 0.33 -0.3 0.00 C -0.33 0.3 0.257692 K_POINTS automatic 38 38 1 0 0 0 SCF with electric field &control prefix='bi elgraphene', calculation='scf', restart_mode='from_scratch', lelfield = .true., pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 110.D0,occupations='smearing',smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-10, mixing_mode='plain' efield_cart(1) = 0.0, efield_cart(2) = 0.0, efield_cart(3) = 0.001, startingwfc = 'random' / ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.00 0.00 0.257692 C 0.33 -0.3 0.00 C -0.33 0.3 0.257692 K_POINTS automatic 38 38 1 0 0 0 I noticed that part of the bands calculation output had a problem with the convergence of one of thh eigenavalues as some of the input looked like: per-process dynamical memory:30.2 Mb 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 c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged Please can anyone suggest me of what could have gone wrong... Thanks Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100928/68755545/attachment-0001.htm
[Pw_forum] quantum capacitance
Dear all, I am interested in extracting the quantum capacitance of gated bilayer graphene system (system under the effect of an external electric field inclusing the resulting screening effects)that I am working on. Is there a possibility to do so using quantum espresso (maybe from the calculation of the bandstructure). Thanks Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100917/02b635dc/attachment.htm
[Pw_forum] non existent or non writable directory
Dear Profs Gianozzi and Sitamtze, Thanks for the help. It was easy. I just missed a subdirectory but strangely enough I have not realised that before..Sorry. Thanks for the help Elie Moujaes University of Nottingham NG7 2RD uk From: elie.mouj...@hotmail.co.uk To: pw_forum at pwscf.org Date: Mon, 13 Sep 2010 13:38:30 +0100 Subject: [Pw_forum] non existent or non writable directory Dear all, I have a small problem. I was trying to run a scf calculation for my system and I used the same outdir I usually use in my calculations but then after a few seconds the program stopped with an error: from outdir: error # 1 /exp/home/caiapo/./Moujaes-Results/ non existent or non writable I made another directory and when I re-ran the calculation i got the same problem (although that new directory is empty).. How can I resolve this? ___ 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/20100913/d0c6b59b/attachment.htm
[Pw_forum] non existent or non writable directory
Dear all, I have a small problem. I was trying to run a scf calculation for my system and I used the same outdir I usually use in my calculations but then after a few seconds the program stopped with an error: from outdir: error # 1 /exp/home/caiapo/./Moujaes-Results/ non existent or non writable I made another directory and when I re-ran the calculation i got the same problem (although that new directory is empty).. How can I resolve this? -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100913/69bafdbd/attachment.htm
[Pw_forum] Bilayer graphene with electric field applied (revisited)
Dear all, I am still having problems with the convergence concerning a system of bilayer graphene under the effect of an electric field. The band structure graph is very jiggy. Below you will find the calculation= `bands` input and part of this output will also be shown. Please can anyone advise me on that. Thanks very much. I used all types of pseudopotentials with the correct ecutrho and ecutwfc. Elie Moujaes University of Nottingham NG7 2RD UK INPUT: &control prefix='bi elgraphene', calculation='bands', restart_mode='from_scratch', lelfield = .true., pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 37.D0,ecutrho = 147.D0, occupations='smearing',london =.true., smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-5, mixing_beta=0.3D0, mixing_mode='local-TF' efield_cart(1) = 0.0, efield_cart(2) = 0.0, efield_cart(3) = 0.001, startingwfc = 'random' / ATOMIC_SPECIES C 12.0107 C.lda-paw_kj.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.00 0.00 0.257692 C 0.33 -0.3 0.00 C -0.33 0.3 0.257692 K_POINTS automatic 130 130 1 0 0 0 PART OF THE OUTPUT: The potential is recalculated from file : /tmp/results_MOUJAES/bi elgraphene.save/charge-density.dat negative rho (up, down): 0.637E-05 0.000E+00 Starting wfc are random total cpu time spent up to now is 1233.06 secs per-process dynamical memory:17.2 Mb 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 c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged .. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100910/8a8df98b/attachment.htm
[Pw_forum] vc-relax applied to my 60 atom supercell
Dear all, Coming back to my problem of the 60 atom supercell system I am trying to relax. I required a threshold on the force of 1 x 10^-2 and a pressure of 0. The last calculation gave a total force of 0.06 and a Pressure of -1.43. The next calculation started but it stopped at iteration #4. What does that mean? Does it mean that the system cannot be relaxed further? You will find that part of the output below.. Thanks for your help Elie Moujaes University of Nottingham NG7 2RD UK convergence has been achieved in 10 iterations Forces acting on atoms (Ry/au): negative rho (up, down): 0.919E-03 0.000E+00 atom 1 type 1 force = 0.009440170.000125920. atom 2 type 1 force =-0.00488708 -0.002131130. atom 3 type 1 force = 0.006640770.004640420. atom 4 type 1 force = 0.00096759 -0.004586710. atom 5 type 1 force = 0.01002253 -0.013082390. atom 6 type 1 force = 0.00799961 -0.002387240. . . . . . . . . . . Total force = 0.061991 Total SCF correction = 0.001951 entering subroutine stress ... negative rho (up, down): 0.919E-03 0.000E+00 total stress (Ry/bohr**3) (kbar) P= -1.43 -0.0390 0.0845 0. -0.57 1.24 0.00 0.0845 -0.2347 0. 1.24 -3.45 0.00 0. 0. -0.0185 0.00 0.00 -0.27 number of scf cycles= 14 number of bfgs steps= 11 enthalpy old= -1068.3030395302 Ry enthalpy new= -1068.3098378481 Ry CASE: enthalpy_new < enthalpy_old new trust radius= 0.2403077890 bohr new conv_thr= 0.015904 Ry new unit-cell volume = 9735.83760 a.u.^3 ( 1442.70227 Ang^3 ) CELL_PARAMETERS (alat) 24.058294126 -0.002192356 0.0 -0.001341739 6.509292054 0.0 0.0 0.0 9.212515550 ATOMIC_POSITIONS (angstrom) C -11.335280905 -3.515203132 0.0 C -10.657767548 -1.149649613 0.0 C -12.033031163 -7.107759788 0.0 C -12.031326615 -5.724096322 0.0 C -10.944247190 -4.869160124 0.0 C -10.338808038 -2.534974709 0.0 C -8.985760316 -3.012717974 0.0 C -8.192434693 -0.717181304 0.0 C -9.526336004 -6.767499680 0.0 C -9.682866449 -5.356879517 0.0 C -8.653891794 -4.400804217 0.0 C -7.911461714 -2.099192195 0.0 C -6.578108913 -2.564323810 0.0 C -5.806387518 -0.245896701 0.0 C -7.125796276 -6.285858068 0.0 C -7.349229181 -4.878790195 0.0 C -6.284145613 -3.951282991 0.0 C -5.517574956 -1.633184889 0.0 C -4.178728834 -2.099522550 0.0 C -3.424138062 0.202618721 0.0 C -4.737058424 -5.828536905 0.0 C -4.961882542 -4.420577505 0.0 C -3.892737039 -3.482790455 0.0 C -3.097430525 -1.187683989 0.0 C -1.730699233 -1.658846422 0.0 C -1.110502040 0.680446865 0.0 C -2.384811748 -5.350149373 0.0 C -2.546600674 -3.937650826 0.0 C -1.403364997 -3.046551554 0.0 C -0.715541301 -0.676400470 0.0 C0.713170432 -0.676470962 0.0 C1.105099243 0.680029519 0.0 C -0.000673053 -4.977164160 0.0 C -0.000879723 -3.593109373 0.0 C1.38538 -3.046541966 0.0 C1.726158571 -1.659274114 0.0 C3.088907501 -1.187830369 0.0 C3.413577242 0.201583523 0.0 C2.380884236 -5.349818198 0.0 C2.540180472 -3.938378442 0.0 C3.883120559 -3.483612146 0.0 C4.167810371 -2.100500424 0.0 C5.503697730 -1.632252402 0.0 C5.791361812 -0.246027847 0.0 C4.726465742 -5.828725203 0.0 C4.951407014 -4.420956882 0.0 C6.271404898 -3.950299333 0.0 C6.560859752 -2.564412490 0.0 C7.893877259 -2.094718931 0.0 C8.175441759 -0.716749156 0.0 C7.113957767 -6.283092448 0.0 C7.335009264 -4.876554488 0.0 C8.641907380 -4.398668976 0.0 C8.967995800 -3.009028351 0.0 C 10.37945 -2.532973131 0.0 C 10.649883277 -1.152489915 0.0 C9.516365619 -6.770006826 0.0 C9.671733891 -5.358446
[Pw_forum] STOP ERROR reading file header
Thanks all for your help. It was a silly question from my part. I apologize. Reagrds Elie A M From: elie.mouj...@hotmail.co.uk To: pw_forum at pwscf.org Subject: STOP ERROR reading file header Date: Fri, 30 Jul 2010 14:35:46 +0100 Dear All, I am doing calculations for the band structure of bilayer graphene in the presence of an electric field. I reached the stage where the .DAT file was produced. However when i executed the plotband.x common using /espresso-4.2/bin/plotband.x and input"ed" the .DAT I got the error: STOP ERROR reading file header. When I checked the .DAT file I realized that the header is strange as it contains four stars () and looked like that: &plot nbnd= 12, nks= / 0.00 0.00 0.00 -18.176 -18.014 -6.915 -5.899 -1.571 -1.571 -1.546 -1.546 4.547 5.693 6.616 9.569 0.00 0.010497 0.00 -18.174 -18.012 -6.913 -5.896 -1.579 -1.576 -1.554 -1.550 4.550 5.696 6.619 9.571 0.00 0.020995 0.00 -18.168 -18.006 -6.905 -5.889 -1.603 -1.589 -1.578 -1.564 4.558 5.704 6.626 9.578 0.00 0.031492 0.00 -18.158 -17.997 -6.893 -5.878 -1.643 -1.611 -1.618 -1.586 4.571 5.717 6.639 9.589 0.00 0.041989 0.00 ... I tried to re-execute the bands.x command several times but in vain as the 4 stars re-appeared everytime. Does anyone know why is this occuring and how to treat it? Thanks Elie A. M. School of physics and astronomy University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100730/ad66141b/attachment.htm
[Pw_forum] STOP ERROR reading file header
Dear All, I am doing calculations for the band structure of bilayer graphene in the presence of an electric field. I reached the stage where the .DAT file was produced. However when i executed the plotband.x common using /espresso-4.2/bin/plotband.x and input"ed" the .DAT I got the error: STOP ERROR reading file header. When I checked the .DAT file I realized that the header is strange as it contains four stars () and looked like that: &plot nbnd= 12, nks= / 0.00 0.00 0.00 -18.176 -18.014 -6.915 -5.899 -1.571 -1.571 -1.546 -1.546 4.547 5.693 6.616 9.569 0.00 0.010497 0.00 -18.174 -18.012 -6.913 -5.896 -1.579 -1.576 -1.554 -1.550 4.550 5.696 6.619 9.571 0.00 0.020995 0.00 -18.168 -18.006 -6.905 -5.889 -1.603 -1.589 -1.578 -1.564 4.558 5.704 6.626 9.578 0.00 0.031492 0.00 -18.158 -17.997 -6.893 -5.878 -1.643 -1.611 -1.618 -1.586 4.571 5.717 6.639 9.589 0.00 0.041989 0.00 ... I tried to re-execute the bands.x command several times but in vain as the 4 stars re-appeared everytime. Does anyone know why is this occuring and how to treat it? Thanks Elie A. M. School of physics and astronomy University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100730/28f916e5/attachment.htm
[Pw_forum] c_bands: eigenvalues not converged ina bilayer graphene calculations with an electric field
Thanks for Professors Eyvaz and Paulo's suggestions and for their time. Regards Date: Mon, 19 Jul 2010 12:15:10 -0700 From: eyvaz_is...@yahoo.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] c_bands: eigenvalues not converged ina bilayer graphene calculations with an electric field Dear Elie, Have you read a discussion tree about this message in the forum, or even simpler - User Guide? > ecutwfc = 60.D0 > C 12.0 C.pz-rrkjus.UPF You vast time with such kind unusually high cutoff energy with US-type pseudopotential for which is ecutwfc typically is about 25-30Ry. Besides, you should add "ecutrho", 8-10 times of ecutwfc. For more information please see User Guide in your QE distribution directory. >smearing='XYZ' Is it really used in your calculations? Bests, Eyvaz. --- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01 / &electrons conv_thr=1.D-8, mixing_beta=0.1D0, mixing_mode='local-TF' efield_cart(1) = 0.0, efield_cart(2) = 0.0, efield_cart(3) = 0.00275021, / ATOMIC_SPECIES C 12.0 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.00 0.00 0.257692 C 0.33 -0.3 0.00 C -0.33 0.3 0.257692 K_POINTS automatic 20 20 1 0 0 0 Many thanks again.. Get a new e-mail account with Hotmail - Free. Sign-up now. _ http://clk.atdmt.com/UKM/go/19780/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100719/9b2ce78b/attachment.htm
[Pw_forum] c_bands: eigenvalues not converged ina bilayer graphene calculations with an electric field
I am trying to obtain the DOS (electronic) for a bilayer graphene when a homogeneous electric field is applied but the scf convergence is not being achieved and a lot of messages "c_bands: eigenvalues not converged" are displayed. I checked my input..I cannot see anything wrong..My conv_thresh is small enough..I will display my input and the output will be attached (i stopped the compilation at some point): thanks Elie Moujaes University of Nottingham NG7 2RD UK The scf input is: &control prefix='bi graphene', calculation='scf', restart_mode='from_scratch', lelfield = .true., pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1, ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01 / &electrons conv_thr=1.D-8, mixing_beta=0.1D0, mixing_mode='local-TF' efield_cart(1) = 0.0, efield_cart(2) = 0.0, efield_cart(3) = 0.00275021, / ATOMIC_SPECIES C 12.0 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.00 0.00 0.257692 C 0.33 -0.3 0.00 C -0.33 0.3 0.257692 K_POINTS automatic 20 20 1 0 0 0 Many thanks again.. _ http://clk.atdmt.com/UKM/go/19780/direct/01/ Do you have a story that started on Hotmail? Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100719/fe834cdd/attachment-0001.htm -- next part -- An embedded and charset-unspecified text was scrubbed... Name: bigraphdos-el.scf.out Url: http://www.democritos.it/pipermail/pw_forum/attachments/20100719/fe834cdd/attachment.asc
[Pw_forum] Negative pressure during vc-relax
Dear Profs Gionazzi and Kucukbenli,
Thanks very much for your suggestions. I will be revising my input and work
accordingly.
reagrds
Elie Moujaes
University of Nottingham
NG7 2RD
UK
> Date: Mon, 12 Jul 2010 15:48:55 +0200
> From: giannozz at democritos.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Negative pressure during vc-relax
>
> Paolo Giannozzi wrote:
>
> >> As you can see I have used a convergence threshold for electrons of the
> >> order of 10^-2
> >
> > way too small
>
> I meant: too big, you should use something like the
> default (10^{-6})
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
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[Pw_forum] Negative pressure during vc-relax
Dear All, I am trying to vc-relax a supercell made of 60 Carbon atoms. I have realized that during the iterations, the pressure is getting more negative. For example: Total Force Pressure (kbar) 3.042645-179.66 1.543265-189.02 0.871984-193.18 0.686871-194.73 0.537735-195.49 0.421031-195.96 0.366043-196.10 Is that due to the choice of the pseudopotential, the convergence thresholds or maybe both? I will post a part of the input. Thanks in advance. &control prefix='GB mgraphene', calculation='vc-relax', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', etot_conv_thr = 1.0D-2, forc_conv_thr = 1.0D-2, tstress = .true., tprnfor = .true., / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =30.0, ecutrho = 120.D0, occupations='smearing', smearing='mp', degauss=0.01 / &electrons conv_thr=1.D-2, mixing_beta=0.7D0, diagonalization='david' / &ions ion_dynamics = 'bfgs', / &cell cell_dynamics = 'damp-w', / CELL_PARAMETERS hexagonal 24.52769 0.0 0.0 0.03 6.614491 0.0 0.00 0.00 10. ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS angstrom C -11.737980-3.561278 0.00 C -11.057718-1.211571 0.00 C -12.45-7.189838 0.00 C -12.45-5.773759 0.00 C -11.329191-4.926800 0.00 C -10.692399-2.603942 0.00 ... As you can see I have used a convergence threshold for electrons of the order of 10^-2 (maybe it should be 10^-5??). The convergence on the forces is 10^-2 which I think is fine. the reason for putting such convergence thresholds is to gain a bit of time especially that i do not think one needs to go further down (than 10^-2 forces wise). Maybe also I am using an inconveninet pseudopotential..Any suggestions... Elie Moujaes University of Nottingham Nottingham NG7 2RD UK _ http://clk.atdmt.com/UKM/go/19780/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100712/d0c48caa/attachment.htm
[Pw_forum] vc-relax of a 60 atom supercell
Dear all, I am trying to relax a 60 atom supercell of graphene using vc-relax. (1) I want the relaxation to be with respect to both atomic coordinates and supercell vectors, Is vc-relax the correct calculation to use. (2) I used a vc relax to my superstructure but the programm stopped at the 9th iteration (well it did not stop literally but the calculations ended with no 9th iterations and no converged results along with errors related to the c_bands): Initial potential from superposition of free atoms Check: negative starting charge= -1.223428 starting charge 239.99756, renormalised to 240.0 negative rho (up, down): 0.122E+01 0.000E+00 Starting wfc are 240 atomic wfcs total cpu time spent up to now is 11871.45 secs per-process dynamical memory: 384.3 Mb Self-consistent Calculation iteration # 1 ecut=10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 6.7 negative rho (up, down): 0.117E+01 0.000E+00 total cpu time spent up to now is 47489.34 secs total energy =-643.54940490 Ry Harris-Foulkes estimate =-643.62010992 Ry estimated scf accuracy< 4.23960826 Ry iteration # 2 ecut=10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.77E-03, avg # of iterations = 2.2 negative rho (up, down): 0.109E+00 0.000E+00 total cpu time spent up to now is 64468.90 secs total energy =-642.58636317 Ry Harris-Foulkes estimate =-643.55371202 Ry estimated scf accuracy< 3.93330724 Ry iteration # 3 ecut=10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 1.64E-03, avg # of iterations = 2.0 negative rho (up, down): 0.148E+00 0.000E+00 total cpu time spent up to now is 85947.86 secs total energy =-642.70459925 Ry Harris-Foulkes estimate =-642.70343771 Ry estimated scf accuracy< 0.07850650 Ry iteration # 4 ecut=10.00 Ry beta=0.05 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 c_bands: 1 eigenvalues not converged ethr = 3.27E-05, avg # of iterations = 12.4 negative rho (up, down): 0.151E+00 0.000E+00 total cpu time spent up to now is 112929.09 secs total energy =-642.71219905 Ry Harris-Foulkes estimate =-642.71283310 Ry estimated scf accuracy< 0.06999785 Ry iteration # 5 ecut=10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 2.92E-05, avg # of iterations = 1.1 negative rho (up, down): 0.349E+00 0.000E+00 total cpu time spent up to now is 135493.02 secs total energy =-642.68724348 Ry Harris-Foulkes estimate =-642.71241729 Ry estimated scf accuracy< 0.06752485 Ry iteration # 6 ecut=10.00 Ry beta=0.05 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged ethr = 2.81E-05, avg # of iterations = 8.8 negative rho (up, down): 0.397E+00 0.000E+00 total cpu time spent up to now is 167131.43 secs total energy =-642.68305797 Ry Harris-Foulkes estimate =-642.69027767 Ry estimated scf accuracy< 0.02138677 Ry iteration # 7 ecut=10.00 Ry beta=0.05 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged ethr = 8.91E-06, avg # of iterations = 9.6 negative rho (up, down): 0.375E+00 0.000E+00 total cpu time spent up to now is 195521.38 secs total energy =-642.68507799 Ry Harris-Foulkes estimate =-642.68373726 Ry estimated scf accuracy< 0.01412971 Ry iteration # 8 ecut=10.00 Ry beta=0.05 Davidson diagonalization with overlap ethr = 5.89E-06, avg # of iterations = 1.2 negative rho (up, down): 0.241E+00 0.000E+00 total cpu time spent up to now is 217886.22 secs total energy =-642.68307655 Ry Harris-Foulkes estimate =-642.68513864 Ry estimated scf accuracy< 0.01367803 Ry iteration # 9 ecut=10.00 Ry beta=0.05 The input file is: &control prefix='GB mgraphene', calculation='vc-relax', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/Moujaes-Results/', tstress = .true., tprnfor = .true., disk_io = 'low' / &system
[Pw_forum] error while compiling the start_q, last_q, start_irr and last_irr technique
Dear Andrea, Thanks very much for the information. In fact, when I am running the ph2.in file (for q=2), it runs normally and doesnt give any error except that the output does not have a dynamical matrix i.e. the output looks like: Program PHONON v.4.2 starts on 2Jun2010 at 17:44:23 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "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/wiki/index.php/Citing_Quantum-ESPRESSO Ultrasoft (Vanderbilt) Pseudopotentials Starting q 2 larger than total number of q points 10 or of last q 1 PHONON : 7.04s CPU time,7.83s WALL time INITIALIZATION: init_vloc: 0.02s CPU 0.02s WALL ( 1 calls) init_us_1: 0.02s CPU 0.02s WALL ( 1 calls) DYNAMICAL MATRIX: General routines cft3 : 0.03s CPU 0.03s WALL ( 3 calls) so it is empty underneath DYNAMICAL MATRIX. The only way i was able to get rid of the recover error is to omit recover=.true. in the ph.in program but I guess this is essential. I will also post the scf calculation below: &control prefix='phmonog', calculation='scf', restart_mode='from_scratch', pseudo_dir = '/espresso-4.2/pseudo/', outdir='/tmp/results_MOUJAES/' verbosity='high' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=5.0, nat=2, ntyp= 1, ecutwfc = 110.D0,occupations='smearing', smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr=1.D-10, diagonalization='david', mixing_mode='plain' / ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.33 -0.3 0.00 K_POINTS automatic 26 26 1 0 0 0 ANY SUGGESTIONS? Thank you Elie Moujaes University fo Nootingham NG7 2RD UK > Date: Fri, 4 Jun 2010 21:15:04 +0200 > From: dalcorso at sissa.it > To: pw_forum at pwscf.org > CC: dalcorso at sissa.it > Subject: [Pw_forum] error while compiling the start_q, last_q, start_irr and > last_irr technique > > I am still using the start_q, last_q, start_irr and last_irr technique > (from GRID example) to calculate the phonon dispersion in graphene. > Everything is ok until I run ph.x for the first q (q=1 the Gamma > point). The input is: > > > > Phonon dispersion for monolayer graphene > > &inputph > > tr2_ph=1.0d-13, > > prefix='phmonog', > > ldisp=.true., > > nq1=8, nq2=8, nq3=1 > > start_q=1, > > last_q=1, > > start_irr=1, > > last_irr=4, > > recover=.true., > > amass(1)=12.0107, > > outdir='/tmp/results_MOUJAES/q1', > > fildyn='mgraph881.dyn', > > / > > No errors in running ph.x but teh output is a bit strange like : > > > > > Program PHONON v.4.2 starts on 4Jun2010 at 14:35:33 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please acknowledge > "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/wiki/index.php/Citing_Quantum-ESPRESSO > > Ultrasoft (Vanderbilt) Pseudopotentials > Starting q 2 larger than total number of q points 10 or of last q 1 > > This error depends on the fact that the recover procedure is confused > because the code was doing the second q point when it was interrupted > and > now you are trying to recover (you have recover=.true.) but ask to calculate > only q point 1. You are not allowed to change start_q and last_q > before finishing a calculation. Probably this part should be more > robust for these kind of problems, but at the moment it is not, sorry. > > When you try again and change q point to 2, the recover files are now > a mess and you get an error from the library routine that reads > the recovering files. > > At this point the only solution is to remove the outdir/_ph* files and > start again. If you have already the dynamical matrices of all q points > but the first you can simply calculate the gamma point starting from scratch. > > If the problem is still present after cleaning the outdir dire
[Pw_forum] error while compiling the start_q, last_q, start_irr and last_irr technique
Dear all, I am still using the start_q, last_q, start_irr and last_irr technique (from GRID example) to calculate the phonon dispersion in graphene. Everything is ok until I run ph.x for the first q (q=1 the Gamma point). The input is: Phonon dispersion for monolayer graphene &inputph tr2_ph=1.0d-13, prefix='phmonog', ldisp=.true., nq1=8, nq2=8, nq3=1 start_q=1, last_q=1, start_irr=1, last_irr=4, recover=.true., amass(1)=12.0107, outdir='/tmp/results_MOUJAES/q1', fildyn='mgraph881.dyn', / No errors in running ph.x but teh output is a bit strange like : Program PHONON v.4.2 starts on 4Jun2010 at 14:35:33 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "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/wiki/index.php/Citing_Quantum-ESPRESSO Ultrasoft (Vanderbilt) Pseudopotentials Starting q 2 larger than total number of q points 10 or of last q 1 PHONON : 7.10s CPU time,7.91s WALL time INITIALIZATION: init_vloc: 0.01s CPU 0.02s WALL ( 1 calls) init_us_1: 0.02s CPU 0.02s WALL ( 1 calls) DYNAMICAL MATRIX: General routines cft3 : 0.02s CPU 0.02s WALL ( 3 calls) when I run q=2 (next point with 6 irr representations) with input: Phonon dispersion for monolayer graphene &inputph tr2_ph=1.0d-13, prefix='phmonog', ldisp=.true., nq1=8, nq2=8, nq3=1 start_q=2, last_q=2, start_irr=1, last_irr=6, recover=.true., amass(1)=12.0107, outdir='/tmp/results_MOUJAES/q2', fildyn='mgraph881.dyn', / I get a strange error on the screen (not output file which contains no results): WARNING : THERE ARE PENDING ERRORS PENDING ERROR (ierr=1) ERROR IN: iotk_open_read (iotk_files.spp:487) PENDING ERROR (ierr =2) UNRECOVERABLE Not sure what all this means. Thanks in adavance for any suffestion... _ http://clk.atdmt.com/UKM/go/19780/direct/01/ Do you have a story that started on Hotmail? Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100604/771c296d/attachment-0001.htm
[Pw_forum] error 208, reading namelist cell
Thanks very much..That was a stupid mistake to do. Regards Elie From: sclau...@sissa.it To: pw_forum at pwscf.org Date: Fri, 4 Jun 2010 15:34:45 +0200 Subject: Re: [Pw_forum] error 208, reading namelist cell Dear Elie, the / should go at the end of each namelist, not at the beginning. The F90 standard prescribes that a namelist named, for instance, TEST, can be accessed with &TEST ... / or &TEST ... &END The namelist "cell" has not been closed in your example. HTH GS Il giorno 04/giu/10, alle ore 15:25, Elie Moujaes ha scritto: Dear All, I am trying to relax a system using vc-relax and I am getting the following error:
[Pw_forum] error 208, reading namelist cell
Dear All, I am trying to relax a system using vc-relax and I am getting the following error:
[Pw_forum] start_q, last_q, start_irr, last_irr
Dear Eyvaz and Jeff, Thank you very much for your help. The reason I am doing this is that I am still trying to get the phonon dispersion but using other this new technique implemented in version 4.2 of QE. Everything is going well except that for q-0 (the Gamma point), I am getting an error from davcio : error #20 error while reading from file The strange thing is that only for this point, I obtain such an error...I guess another guy posted that error earlier with the title Phonon calculations on the Grid. His name is shining star. Jeff, thanks for your suggestion as well. Actually i am still looking at the phono dispersion as a whole but found this technqieu which merges all files at the end and takes less time (I hope!). Regards Elie Moujaes University of Nottingham NG7 2RD UK > Date: Tue, 1 Jun 2010 15:39:07 -0700 > From: eyvaz_isaev at yahoo.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] start_q, last_q, start_irr, last_irr > > Dear Elie, > > --- On Wed, 6/2/10, Elie Moujaes wrote: > >I am trying to get the phonon dispersion of graphene by taking each q on > >>its own and performing the necessary operations (i.e using start_q, > >>last_q, start_irr, last_irr) then merging the points all together . Can > >>anyone please explain to me more about these parameters. > > I never used start_irr, last_irr, but I use actively start_q and last_q > parameters. After you get all dynX (including dyn0) files, just collect them > in a directory and run q2r.x. > > start_q - q-point from which ph.x starts, last_q - up to this q-point from > the list of q-points written in dyn0-file. I.e. if you have 12 q-points > according to dyn0-file, then you can choose any combination, start_q=1, > last_q=1 (usually this one is the Gamma point), or start_q=9, last_q=12 > (calculate phonons for q-points from 9th to 12th), or any other combination > you like (sure, last_q >= start_q). > > The same meaning for start_irr and last_irr, but for irreducible > representations. > > >I read the INPUT_PH and the examples in GRID but did not actually > >>understand what these mean..I got that irr is irreducible representation > >>but how can one set these each time one runs the calculation for a q. > > Specify in ph.in files the next lines: > > * > start_q=M > last_q=N > start_irr=I1 > last_irr=I2 > > If M=N, only irreducible representations (IrRep) in the range I1 - I2 will be > calculated for a given (defined by M) q-point. By default, all IrRep will be > calculated. > > So easy! > > Bests, > Eyvaz. > > --- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > 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 _ http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100602/bc22e50f/attachment-0001.htm
[Pw_forum] start_q, last_q, start_irr, last_irr
Dear all, I am trying to get the phonon dispersion of graphene by taking each q on its own and performing the necessary operations (i.e using start_q, last_q, start_irr, last_irr) then merging the points all together . Can anyone please explain to me more about these parameters. I read the INPUT_PH and the examples in GRID but did not actually understand what these mean..I got that irr is irreducible representation but how can one set these each time one runs the calculation for a q. Thanks ina dvance Elie Moujaes University of nottingham NG7 2RD Nottingham _ http://clk.atdmt.com/UKM/go/195013117/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100601/f2adf684/attachment-0001.htm
[Pw_forum] jagged phonon dispersion in graphene
Dear Prof. Isaev, Thanks very much for the information. I downloaded the attachment from one of the e-mails in the forum as a .BIN file. I am not sure though how to use it. Is it possible to explain me a bit more about this utility and how it can be used. I could not find it within the QE 4.2 package. This is why i downloaded it from forum. Many thanks Elie Mouajes University of nottingham NF7 2RD UK Date: Thu, 13 May 2010 06:31:39 -0700 From: eyvaz_is...@yahoo.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] jagged phonon dispersion in graphene Dear Elie, Have you tried PlotPhon utility from QE 4.2? Any troubles, please contact me. 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 isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 5/12/10, Elie Moujaes wrote: From: Elie Moujaes Subject: [Pw_forum] jagged phonon dispersion in graphene To: pw_forum at pwscf.org Date: Wednesday, May 12, 2010, 7:37 PM Dear all, Hope you are all doing fine. I am computing the phono dispersion in graphene. I am using 1000 points in the matdyn.in file and I used an 8x 8 x 1 grid but I get a jagged dispersion spectrum. I tried even using a 16 x16 x1 grid but almost got the same jagged results..I am not sure why this happening. You will find attached the ps graph of the dispersion. Below are all the input files. Thanks for your help in advance. SCF calculation: control prefix='phmonog', calculation='scf', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01, nelec=8 / &electrons conv_thr=1.D-8, mixing_beta=0.1D0, mixing_mode='local-TF' / ATOMIC_SPECIES C 12.0 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 1 1 1 C 0.33 -0.3 0.00 1 1 1 K_POINTS automatic 25 25 1 0 0 0 Ph.in file: Phonon dispersion for monographene &inputph tr2_ph=1.0d-12, prefix='phmonog', ldisp=.true., lnscf=.true., nq1=16, nq2=16, nq3=1 amass(1)=12.00, outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', fildyn='phmgraphene.dyn', / q2r file: &input fildyn = 'phmgraphene.dyn', zasr = 'crystal' , flfrc = 'mgraph16160.fc' / matdyn.in file : &input asr = 'crystal', amass(1) = 12.00 , flfrc = 'mgraph16160.fc', flfrq = 'mgraph16160.freq', / 1000 0. 0. 0. 1.00e-03 0. 0. 0.1000 1.00e-03 0. 0. 0.2000 1.00e-03 0. 0. 0.3000 1.00e-03 0. 0. 0.4000 1.00e-03 0. 0. 0.5000 1.00e-03 0. 0. 0.6000 1.00e-03 0. 0. 0.7000 1.00e-03 . Get a new e-mail account with Hotmail - Free. Sign-up now. -Inline Attachment Follows- ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _ http://clk.atdmt.com/UKM/go/19780/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100513/05eac753/attachment.htm
[Pw_forum] jagged phonon dispersion in graphene
Dear all, Hope you are all doing fine. I am computing the phono dispersion in graphene. I am using 1000 points in the matdyn.in file and I used an 8x 8 x 1 grid but I get a jagged dispersion spectrum. I tried even using a 16 x16 x1 grid but almost got the same jagged results..I am not sure why this happening. You will find attached the ps graph of the dispersion. Below are all the input files. Thanks for your help in advance. SCF calculation: control prefix='phmonog', calculation='scf', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/' / &system ibrav= 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01, nelec=8 / &electrons conv_thr=1.D-8, mixing_beta=0.1D0, mixing_mode='local-TF' / ATOMIC_SPECIES C 12.0 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 1 1 1 C 0.33 -0.3 0.00 1 1 1 K_POINTS automatic 25 25 1 0 0 0 Ph.in file: Phonon dispersion for monographene &inputph tr2_ph=1.0d-12, prefix='phmonog', ldisp=.true., lnscf=.true., nq1=16, nq2=16, nq3=1 amass(1)=12.00, outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', fildyn='phmgraphene.dyn', / q2r file: &input fildyn = 'phmgraphene.dyn', zasr = 'crystal' , flfrc = 'mgraph16160.fc' / matdyn.in file : &input asr = 'crystal', amass(1) = 12.00 , flfrc = 'mgraph16160.fc', flfrq = 'mgraph16160.freq', / 1000 0. 0. 0. 1.00e-03 0. 0. 0.1000 1.00e-03 0. 0. 0.2000 1.00e-03 0. 0. 0.3000 1.00e-03 0. 0. 0.4000 1.00e-03 0. 0. 0.5000 1.00e-03 0. 0. 0.6000 1.00e-03 0. 0. 0.7000 1.00e-03 . _ http://clk.atdmt.com/UKM/go/195013117/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100512/813fecad/attachment.htm -- next part -- A non-text attachment was scrubbed... Name: mgraph16160.bands.ps Type: application/postscript Size: 19751 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100512/813fecad/attachment-0001.ps
[Pw_forum] pw.x: command not found
Dear PWSCF users, I have downloaded the latest version of espresso (espresso-4.1.3) and I have placed that on the server (as I am working on the server for more space). The system's configuration is x86_64. The configuration ends with a success..However when I compile each package alone (say PW, or PP, pr PH) using make...I get a warning-at the end- of the type: "Clock skew detected : your build maybe incomplete"..All commands pw.x, pp.x and ph.x are in the bin folder but when i try to compile: /espresso-4.1.3/bin/pw.xfilename.out I get : "pw.x :command not found".. I do not really understand the source of this error Is it related to the above warning? Thank you Elie Moujaes University of Nottingham NG7 2RD UK _ http://clk.atdmt.com/UKM/go/19780/direct/01/ Do you have a story that started on Hotmail? Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100413/d758b8e1/attachment.htm
[Pw_forum] Traceback not available error!
Thank you. Problem was sorted. Regards Elie > From: giannozz at democritos.it > Date: Tue, 6 Apr 2010 17:54:49 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Traceback not available error! > > > On Apr 6, 2010, at 16:48 , Elie Moujaes wrote: > > > Fortran runtime error: End of File > > this is the error: you are trying to read past the > end of file. > --- > Paolo Giannozzi, Dept of Physics, University of 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://www.democritos.it/mailman/listinfo/pw_forum _ http://clk.atdmt.com/UKM/go/19780/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100407/bf5c6294/attachment.htm
[Pw_forum] Traceback not available error!
Dear all, I am sorry to disturb you each now and then. I am at the last step of calculating the phonon dispresion spectrum for graphene mainly applying matdyn.x whne I got ther following error: At line 285 of file matdyn.f90 (Unit 5) Traceback not available, compile with -ftrace=frame or -ftrace=full Fortran runtime error: End of File Well, yes it is clear that something is wrong at line 285 of the fortran file code matdyn but i am not much of a fortran expert so even looking at the line 285 might not help much. My question is did anyone else got this specific error or is it just a problem with my compiler (which maybe is most certainly the case). Any suggestions of a solution or where I can find one.. P.S: I looked to several resources but I could not find any general solution to tackle the problem. Thanks Elie Moujaes University of Nottingham NG7 2RD Nottingham UK _ http://clk.atdmt.com/UKM/go/19780/direct/01/ Do you have a story that started on Hotmail? Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100406/68abd13f/attachment-0001.htm
[Pw_forum] ph.x taking a lot of time to run!
Thanks very much for the reply. It kind of made me relax. I knew that 8 points are not enough but I just wanted to check if I do get results or not after of course running q2r.x and matdyn.x later. Thank you again Elie > Date: Tue, 6 Apr 2010 12:45:17 +0800 > From: ouuing at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] ph.x taking a lot of time to run! > > Generally, the dynamics calculation will cost a long time. so you need > much better claculation source. I think 8 points perhaps are not > enough. nq1=4,nq2=4,na3=4, perhaps more is better. > > best regards. > > On Tue, Apr 6, 2010 at 2:10 AM, Elie Moujaes > wrote: > > Dear PWSCF users, > > > > Hope you all had a happy Easter. I am running the ph.x code for graphene(and > > Thankfully no errors are encountered). it is just that it IS taking a really > > long time to produce the dynamical matrices on the q grid I specified which > > is: > > > > nq1= 2, nq2=2, nq3=2 (a total of 8 points).. It is taking like an our to > > produce the .dyn files for every q point. I do not think it should require > > that much time. Is there something I might be missing? > > > > > > Thank you > > > > Elie Moujaes > > University of Nottingham > > NG7 2RD > > UK > > > > > > Get a new e-mail account with Hotmail - Free. Sign-up now. > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > Hanyu Liu(???), > MS. > State key Laboratory of Superhard Materials, Jilin University, China > Email: liuhanyu08 at mails.jlu.edu.cn ouuing at gmail.com > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum _ http://clk.atdmt.com/UKM/go/19780/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100406/9eb9701e/attachment.htm
[Pw_forum] ph.x taking a lot of time to run!
Dear PWSCF users, Hope you all had a happy Easter. I am running the ph.x code for graphene(and Thankfully no errors are encountered). it is just that it IS taking a really long time to produce the dynamical matrices on the q grid I specified which is: nq1= 2, nq2=2, nq3=2 (a total of 8 points).. It is taking like an our to produce the .dyn files for every q point. I do not think it should require that much time. Is there something I might be missing? Thank you Elie Moujaes University of Nottingham NG7 2RD UK _ http://clk.atdmt.com/UKM/go/195013117/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100405/cc13d510/attachment.htm
[Pw_forum] phonon dispersion for graphene
Dear Prof. Gianozzi and all, Actually the "&" was there but I missed it when i copied the file. The missing title was the problem. This is sorted but when I started running the ph.x I got another error: Atomic displacements: There are 6 irreducible representations Representation 1 1 modes -A To be done Representation 2 1 modes -A To be done Representation 3 1 modes -A To be done Representation 4 1 modes -A To be done Representation 5 1 modes - To be done Representation 6 1 modes - To be done %% from davcio : error #20 error while reading from file Well, I found that some people on the forum have got such an error but with I/O error than "reading from file". The error probably means that something was wrong while reading the previous file...I ran a scf calculation (pw.x) followed by the ph.x. I would appreciate it if you can suggest how to fic this problem..I repeated the calculations several times but in vain.. Regards > From: giannozz at democritos.it > Date: Wed, 31 Mar 2010 21:30:58 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] phonon dispersion for graphene > > > On Mar 31, 2010, at 21:26 , Elie Moujaes wrote: > > > reading inputph namelist > > if the code says that your namelist is wrong: it is wrong. > > > inputph > > Missing: a title line; a & before inputph > --- > Paolo Giannozzi, Dept of Physics, University of 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://www.democritos.it/mailman/listinfo/pw_forum _ Send us your Hotmail stories and be featured in our newsletter http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100331/46eadfdd/attachment-0001.htm
[Pw_forum] phonon dispersion for graphene
Dear All, I worked through example 06 but i am still getting the error which again is: Program PHONONv.4.1.2 starts ... Today is 31Mar2010 at 16:15:30 Ultrasoft (Vanderbilt) Pseudopotentials %% from phq_readin : error # 1 reading inputph namelist %% stopping ... In Example 06 they do not provide X, gamma,...positions. This is the case when one wants to calculate the dispersion at one particular point where providing the nq1 x nq2 xnq3 is no more necessary..I do not know what is going wrong..Here is the input again: inputph tr2_ph=1.0d-14, prefix='ph mono graphene', ldisp=.true. nq1=7, nq2=7, nq3=7 amass(1)=12.0, outdir='/tmp/results_MOUJAES/', fildyn='phmgraphene.dyn' / thanks elie moujaes University of Nottingham NG7 2RD > From: giannozz at democritos.it > Date: Wed, 31 Mar 2010 19:52:37 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] phonon dispersion for graphene > > > On Mar 31, 2010, at 19:40 , Elie Moujaes wrote: > > > N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3 > > grid and I got the previous error. Any examples dealing with this? > > examples/example06 > > --- > Paolo Giannozzi, Dept of Physics, University of 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://www.democritos.it/mailman/listinfo/pw_forum _ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100331/c09f1f52/attachment.htm
[Pw_forum] phonon dispersion for graphene
Thanks very much for your reply. What if I want to plot the graph of frequency versus the wavevector K specifying the Gamma, K and M points..Can one do this in one go or does he have to calculate the frequencies for each of the points separately and then connect them. N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3 grid and I got the previous error. Any examples dealing with this? Thanks Elie Mouaes University of Nottingham NG7 2RD UK > Date: Wed, 31 Mar 2010 17:16:57 +0200 > From: nnlinh at sissa.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] phonon dispersion for graphene > > Your input file lacks the points where you want to calculate phonon > dispersion (Gamma, X, ...) > So, you should see in example02 for reference of phonon input file > > Good luck > Linh > > Elie Moujaes wrote: > > Sear PWSCF users, > > > > I am calculating the phonon dispersion for graphene. I did the scf > > calculations then when I am running the ph.x command, I always get the > > error: > > > > > > > > Program PHONON v.4.1.2 starts ... > > Today is 31Mar2010 at 12: 1:50 > > > > Ultrasoft (Vanderbilt) Pseudopotentials > > > > %% > > from phq_readin : error # 1 > > reading inputph namelist > > %% > > > > stopping ... > > > > > > > > > > which means that something is wrong in the input. But I could not fins > > any mistake in the input file...Can anyone please check it for me? My > > input is: > > > > > > > > > > > > > > > > &inputph > > > > tr2_ph=1.0d-14, > > > > prefix='ph mono graphene', > > > > ldisp=.true., > > > > nq1=28, nq2=28, nq3=1, > > > > amass(1)=12.0, > > > > outdir='/tmp/results_MOUJAES/', > > > > fildyn='phmgraphene.dyn' > > > > / > > > > > > > > Thanks > > > > > > > > Elie Moujaes > > > > University of Nottingham > > > > NG7 2RD > > > > UK > > > > > > > > > > > > > > > > Got a cool Hotmail story? Tell us now > > <http://clk.atdmt.com/UKM/go/195013117/direct/01/> > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > - > Nguyen Ngoc Linh, PhD Student > c/o: SISSA & CNR-INFM Democritos, > via Beirut 2-4, 34014 Trieste (Italy) > email: nnlinh at sissa.it > phone: +39 04 03787 319 > skype: ngoclinh84phys > - > "The physics is theoretical but the fun is real" > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum _ Tell us your greatest, weirdest and funniest Hotmail stories http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100331/0b3028eb/attachment.htm
[Pw_forum] phonon dispersion for graphene
Sear PWSCF users, I am calculating the phonon dispersion for graphene. I did the scf calculations then when I am running the ph.x command, I always get the error: Program PHONONv.4.1.2 starts ... Today is 31Mar2010 at 12: 1:50 Ultrasoft (Vanderbilt) Pseudopotentials %% from phq_readin : error # 1 reading inputph namelist %% stopping ... which means that something is wrong in the input. But I could not fins any mistake in the input file...Can anyone please check it for me? My input is: &inputph tr2_ph=1.0d-14, prefix='ph mono graphene', ldisp=.true., nq1=28, nq2=28, nq3=1, amass(1)=12.0, outdir='/tmp/results_MOUJAES/', fildyn='phmgraphene.dyn' / Thanks Elie Moujaes University of Nottingham NG7 2RD UK _ Got a cool Hotmail story? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100331/dd660ea6/attachment.htm
[Pw_forum] Input to calculate band structure of bi layer graphene
Dear all, I am trying to get the band structure of bi layer graphene but I am not quite sure about the input..I am using experimental values for a and c..Of course a= 2.46 A and c=6.7079 A. Also for bilayer graphene we have 4 atoms per unit cell..what is confusing me is the distance between the layers within one bilyaer primitive cell. I read that the distance between one layer and the other within the bi layer primitive cell is 0.5 c= 3.35 A. this means that the interaction between the upper layer of one bilayer primitive cell and the lower layer of the next one is also 0.5c because the whole distance is c. My question is shouldnt the distance within the same primitive cell be less than that between one end of a bilayer primitive cell and the other end of the next one because as far as I know (not sure if I have this as a misconception), Qunatum Espresso produces images of the main primitive cell and in my case the next image must be further away so that no interaction would happen between all layers which would then be a model for graphite. My input for atomic positions and a and c are as follows: celldm(1) =4.608737, celldm(3)=2.725459 / ATOMIC_SPECIES C 12.0 C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 C 0.00 0.00 0.50 C 0.33 -0.3 0.00 C -0.33 0.3 0.50 Hope someone can give me advise or suggestions on this matter.. Thank you Elie Moujaes University of Nottingham NG7 2RD UK _ Send us your Hotmail stories and be featured in our newsletter http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100329/99635758/attachment-0001.htm
[Pw_forum] graph of band structure of bi layer graphene
Thank you. Elie Regards > From: giannozz at democritos.it > Date: Thu, 25 Mar 2010 22:03:31 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] graph of band structure of bi layer graphene > > > On Mar 25, 2010, at 19:39 , Elie Moujaes wrote: > > > what does the negative rho means > > > http://www.quantum-espresso.org/user_guide/node61.html > > --- > Paolo Giannozzi, Dept of Physics, University of 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://www.democritos.it/mailman/listinfo/pw_forum _ Tell us your greatest, weirdest and funniest Hotmail stories http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100325/8c358cfc/attachment.htm
[Pw_forum] graph of band structure of bi layer graphene
Dear PWSCF users and developers, I am trying trying to find the band structure of bi layer graphene using pw package. Everything goes fine until i execute? /espresso-4.1.2/bin/bands.xbigraphene.bands.out then the output looks like: Program POST-PROC v.4.1.2 starts ... Today is 25Mar2010 at 15:13:13 file C.pz-rrkjus.UPF: wavefunction(s) 2S renormalized negative rho (up, down): 0.214E-04 0.000E+00 what does the negative rho means and why the up rho is not exactly zero? When the graph is plotted using plotband.x I get a fairly decent graph but at the left corner I get some vertical thick lines (appearing on the negative side whereas the graph looks ok). I need to know what is this rho related to and how to make it exactly zero. is it by choosing a convenient degauss value? Thanks Elie Moujaes University of Nottingham NG7 2RD Nottingham _ Tell us your greatest, weirdest and funniest Hotmail stories http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100325/866dab85/attachment.htm
[Pw_forum] band structure of bi layer graphene
Dear all, I am trying to obtain the band structure of graphene. to do that, I supposed that celldim(1) =4.608737, celldm(3)=4.53666 so that c is 4.53666 *aThe carbon atoms are chosen such that: ATOMIC_POSITIONS crystal C 0.00 0.00 0.00 1 1 1 C 0.00 0.00 0.20 1 1 1 C 0.33 -0.3 0.00 1 1 1 C -0.33 0.3 0.20 1 1 1 we have 4 carbon atoms in bilayer graphene and the primitive cell has a z direction of 0.2*c= 1/5 so that the primitive cell is 3D. Since QE is a 3D program, I thought that setting c= 4.5366 will produce an image of the primitive cell that is 4.53666*4.608737 Bohrs away from the original one so that no interaction happens( in the acse of which I will be modelling something similar to graphite). I got the results whioch are satisfactory but still need some amendments...I just want to know if this line of thought is correct and if someone can have a look at the graph because it is not entirely correct. Maybe I need to increase the number of points.. I am open to suggestions if any...You will find ps file attached Regards ELie moujaes University of Nottingham NG7 2RD UK _ Send us your Hotmail stories and be featured in our newsletter http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100325/b46e804b/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: bigraph.bands.ps Type: application/postscript Size: 55446 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100325/b46e804b/attachment-0001.ps
[Pw_forum] Tight Binding (TB) model up to n nearest neighbours
Dear all, I calculated the band structure of graphene using a TB model using the Wannier90 package. Results are pretty good. But I am interested in calculating the band structure using a semi empirical TB model where one can input the number of nearest neighbours like 3 nearest neighbours, 6 nearest neighbours , 3 next next nearest neighbours,.for graphene. Is there a package to do that in QE or does it need to be implemented. Would md (molecular dynamics) perform that? Regards Elie Moujaes University of Nottingham NG7 2RD Nottingham UK _ Do you have a story that started on Hotmail? Tell us now http://clk.atdmt.com/UKM/go/195013117/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100318/438a2cc9/attachment.htm
