[Pw_forum] problems with vc-relax
Elie Moujaes
elie.moujaes at hotmail.co.uk
Fri Sep 9 17:00:01 CEST 2011
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 <windbellklbh at gmail.com> 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
> >> <elie.moujaes at hotmail.co.uk> 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
> > <elie.moujaes at 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 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 0.000000000
> >> >> >
> >> >> > 0.000000000 6.503051170 0.000000000
> >> >> >
> >> >> > 0.000000000 0.000000000 8.470514812
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > ATOMIC_SPECIES
> >> >> >
> >> >> > C 12.0107 C.blyp-mt.UPF
> >> >> >
> >> >> >
> >> >> >
> >> >> > ATOMIC_POSITIONS (angstrom)
> >> >> >
> >> >> > C -11.330758616 -3.527803203 0.000000000
> >> >> >
> >> >> > C -10.659793092 -1.160339161 0.000000000
> >> >> >
> >> >> > C -12.039843315 -7.112619698 0.000000000
> >> >> >
> >> >> > C -12.041158182 -5.732701936 0.000000000
> >> >> >
> >> >> > C -10.941089654 -4.881442842 0.000000000
> >> >> >
> >> >> > ......
> >> >> >
> >> >> >
> >> >> >
> >> >> > 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
> >> >> >
> >> >> >
> >> >> >
> >> >> > _______________________________________________
> >> >> > Pw_forum mailing list
> >> >> > Pw_forum at pwscf.org
> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Dept. of Chem and Biochem, Concordia University
> >> >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (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
> >> >
> >> > _______________________________________________
> >> > Pw_forum mailing list
> >> > Pw_forum at pwscf.org
> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dept. of Chem and Biochem, Concordia University
> >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (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
> >
> > -----------------------------------------------------------
> > Wu, F
> > College of Chemistry and Molecular Engineering, Peking University
> > ----------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Dept. of Chem and Biochem, Concordia University
> 7141 Sherbrooke Ouest, Montreal, QC, Canada (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
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