[gpaw-users] Full optimization in plane wave mode
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Mon Nov 12 13:32:18 CET 2012
On 11/08/12 12:06, Janne Hirvi wrote:
>
> Hi,
>
> I believe that I am using at least a quite new version of GPAW
> (0.9rev9473). The installation of the
>
> latest version to the FGI (Finnish Grid Infrastructure) only due to
> this problem may not be possible
>
> at least as quickly as I would need.
>
what about ASE, could changes like
https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/atoms.py?rev=2614
affect you?
>
> Moreover, during this morning I have learned something new about the
> stress in GPAW plane wave
>
> calculations (this is the first time I am using PW mode), which just
> confuses me:
>
> 1) Optimization by scanning through different cubic cell sizes gives a
> unit cell dimension of 7.28Å
>
> (cut-off = 400eV), but there is a positive stress in all three
> directions (0.016462). The sign of the stress
>
> components actually changes with a cell dimension of 6.96Å (for which
> energy is much higher), which
>
> corresponds to full optimization with UnitCellFilter. Any ideas why
> this kind of difference?
>
> 2) I am not yet sure if everything is just due to too small energy
> cut-off, but based on calculations for
>
> the tetragonal structure discussed below, stress values seems to be
> highly dependent on used cut-off
>
> value. Moreover, with a high cut-off value (800eV) energies behaved
> much more nicely (previously
>
> reported large fluctuations were related steps where cell size changed
> drastically), and a better
>
> correspondence to the results of other programs was achieved.
>
> 3) Moreover, based on some test calculations with VASP, I was
> wondering if I should actually define
>
> PW(cell=...) to be able to use same plane waves during the whole
> optimization instead of regenerating
>
> those for each cell size again and again?
>
i would try that if latest versions don't fix the problem.
Fixing number of planewaves is in fact used in the gpaw/ase command line
mode,
during calculation of EOS. I don't know what others programs do for cell
optimizations.
>
> 4) There is correlation between energy cut-off and grid spacing - if
> energy cut-off is increased grid spacing
>
> should decrease. Even with PW mode certain parts of the calculation
> are performed by taking benefit from
>
> the automatically generated grid. I suppose I shouldn't change this
> grid spacing?
>
reducing this automatic grid spacing may be necessary for very skewed cells:
https://listserv.fysik.dtu.dk/pipermail/gpaw-developers/2012-May/002870.html
Marcin
>
> Best regards,
>
> Janne
>
> *From:*Marcin Dulak [mailto:Marcin.Dulak at fysik.dtu.dk]
> *Sent:* Thursday, November 08, 2012 12:02 AM
> *To:* Janne Hirvi
> *Cc:* Vladislav Ivanistsev; Jón Steinar Garðarsson Mýrdal;
> gpaw-users at listserv.fysik.dtu.dk
> *Subject:* Re: [gpaw-users] Full optimization in plane wave mode
>
> On 11/07/12 15:03, Janne Hirvi wrote:
>
> Hi,
>
> I believe that full optimization with UnitCellFilter has been
> implemented only for plane wave mode (not for finite difference
> mode)?
>
> However, I will try to increase the cut-off energy (which
> basically corresponds to decrease in grid spacing for finite
> difference mode)
>
> and check what happens, even though these energy changes seems to
> be quite large.
>
> i would first verify the calculations with the latest ASE/GPAW.
> I heard rumors that at some point (just before Jens Jørgens leave)
> there were problems with stresses. You could maybe also limit the
> optimization to stress only
> with StrainFilter. If the problem persists attach the full script.
>
> Best regards,
>
> Marcin
>
>
> Regards,
>
> Janne
>
> *From:*Vladislav Ivanistsev [mailto:olunet at gmail.com]
> *Sent:* Wednesday, November 07, 2012 3:45 PM
> *To:* Jón Steinar Garðarsson Mýrdal
> *Cc:* Janne Hirvi; gpaw-users at listserv.fysik.dtu.dk
> <mailto:gpaw-users at listserv.fysik.dtu.dk>
> *Subject:* Re: [gpaw-users] Full optimization in plane wave mode
>
> I've also experienced similar problem with grid spacing. What is the
> lowest h value one can safely use. Is h=12 suitable?
> Ph.D. Vladislav Ivanistsev
>
> On Wed, Nov 7, 2012 at 1:33 PM, Jón Steinar Garðarsson Mýrdal
> <jsmy at dtu.dk <mailto:jsmy at dtu.dk>> wrote:
>
> Hi Janne
>
> When you change the shape or size of your super cell then the grid
> sampling will change and this can lead to a change in energy.
> Therefore it is important to run calculations where you perform cell
> optimization with extra small grid spacing.
> I would try lowering the value of h you are using.
>
> Mvh.
> Jón Steinar Garðarsson Mýrdal
> Ph.d Student
> DTU Energy Conversion
> -------------------------------------------
> Technical University of Denmark
> Department of Energy Conversion and Storage
> Frederiksborgvej 399
> Building 775
> 4000 Roskilde
> Direct +45 46775818
> jsmy at dtu.dk <mailto:jsmy at dtu.dk>
> http://www.dtu.dk
>
> ________________________________________
> From: gpaw-users-bounces at listserv.fysik.dtu.dk
> <mailto:gpaw-users-bounces at listserv.fysik.dtu.dk>
> [gpaw-users-bounces at listserv.fysik.dtu.dk
> <mailto:gpaw-users-bounces at listserv.fysik.dtu.dk>] On Behalf Of Janne
> Hirvi [janne.hirvi at uef.fi <mailto:janne.hirvi at uef.fi>]
> Sent: Wednesday, November 07, 2012 2:01 PM
> To: gpaw-users at listserv.fysik.dtu.dk
> <mailto:gpaw-users at listserv.fysik.dtu.dk>
> Subject: [gpaw-users] Full optimization in plane wave mode
>
>
> Dear GPAW-users,
>
> I tried to perform "full" optimization (in orthogonal cell) for silica
> structure using plane wave mode.
>
> The script was something like this
>
> -----
> mixerown=Mixer(beta=0.1, nmaxold=5, weight=50.0)
> calc=GPAW(mode=PW(400), xc='PBE', kpts=(4,4,4), mixer=mixerown,
> txt=name+'.txt')
> Bulk.set_calculator(calc)
>
> ucf=UnitCellFilter(Bulk,mask=[1,1,1,0,0,0])
> relax=BFGS(ucf)
> traj=PickleTrajectory(name+'.traj','w',Bulk)
> relax.attach(traj)
> relax.run(fmax=0.03)
> ----
>
> The corresponding calculation converged (stress and forces are small),
> but the energies for each step
>
> Zero Kelvin: -188.134359 (Step 1)
> Zero Kelvin: -187.264322
> Zero Kelvin: -187.394858
> Zero Kelvin: -187.853520
> Zero Kelvin: -187.879200
> Zero Kelvin: -188.081472
> Zero Kelvin: -188.048312
> Zero Kelvin: -188.051650
> Zero Kelvin: -188.081487
> Zero Kelvin: -188.096408 (Step 10)
> Zero Kelvin: -188.091418
> Zero Kelvin: -188.113318
> Zero Kelvin: -188.122375
> Zero Kelvin: -188.072067
> Zero Kelvin: -188.123096
> Zero Kelvin: -188.125491
> Zero Kelvin: -188.097103
> Zero Kelvin: -188.125748
> Zero Kelvin: -188.125478
> Zero Kelvin: -188.130157 (Step 20)
> Zero Kelvin: -188.146106
> Zero Kelvin: -188.122699
> Zero Kelvin: -188.065573
> Zero Kelvin: -188.071948
> Zero Kelvin: -188.033935
> Zero Kelvin: -187.960727
> Zero Kelvin: -187.975459
> Zero Kelvin: -187.954870
> Zero Kelvin: -187.941968
> Zero Kelvin: -187.914349 (Step 30)
> Zero Kelvin: -187.912083
> Zero Kelvin: -187.911463
> Zero Kelvin: -187.909650 (Step 33)
>
> behave quite strangely. The energy minimum has been reached around 20
> steps (only slightly smaller than that
> for the initial guess) and the final energy is quite notably higher.
>
> Do you know if this is related to large changes in cell dimensions
> when using plane wave mode or what might
> be the reason for this?
>
> Best regards,
>
> Janne Hirvi
>
> -----
> Janne Hirvi
> PhD (Physical Chemistry), Researcher
> University of Eastern Finland, Department of Chemistry
> P.O.Box 111, 80101 Joensuu, FINLAND
> Tel: +358 50 4422594 & +358 50 3474223
>
>
>
>
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>
>
>
--
***********************************
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk
***********************************
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