[gpaw-users] vdW-DF2
Duy Le
ttduyle at gmail.com
Tue Oct 5 16:47:46 CEST 2010
I don't know if anyone has any trick for the problem. I am surrendering to
it.
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.
"Men don't need hand to do things"
On Wed, Sep 29, 2010 at 5:41 PM, Duy Le <ttduyle at gmail.com> wrote:
> Hi,
> Sure. I am sending a tar file, which contains input file, and 3 output
> files corresponding to vdW-DF, revPBE, vdW-DF2.
> Thank you for your help.
> Best,
> Link to the file: http://physics.ucf.edu/~dle/vdW-DF2.problem.tar
>
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
> On Wed, Sep 29, 2010 at 5:26 PM, Duy Le <ttduyle at gmail.com> wrote:
>
>> Hi,
>> Sure. I am sending a tar file, which contains input file, and 3 output
>> files corresponding to vdW-DF, revPBE, vdW-DF2.
>> Thank you for your help.
>> Best,
>>
>> --------------------------------------------------
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>> On Wed, Sep 29, 2010 at 3:13 AM, Jess Wellendorff Pedersen <
>> printerfejl at gmail.com> wrote:
>>
>>> Hi Duy,
>>>
>>> could you send us a s ample of the text output?
>>>
>>> / Jess
>>>
>>> Duy Le wrote:
>>>
>>>> Dear all,
>>>>
>>>> Did any one try this system? Whatever I did- such as: change mixer
>>>> parameter, eigeinsolver- I could not get the scf converged. If anyone has
>>>> any tip, please let me know.
>>>>
>>>> Best regards,
>>>> Duy
>>>> --------------------------------------------------
>>>> Duy Le
>>>> PhD Student
>>>> Department of Physics
>>>> University of Central Florida.
>>>>
>>>> "Men don't need hand to do things"
>>>>
>>>>
>>>> On Thu, Sep 23, 2010 at 6:41 PM, Duy Le <ttduyle at gmail.com <mailto:
>>>> ttduyle at gmail.com>> wrote:
>>>>
>>>> Dear all,
>>>> Sorry for my belated response. I was trying do it myself first but
>>>> unfortunately I could not get any of them converged.
>>>> Below are the input (input.py) and structure (MOL.xsf). With this
>>>> input and structure, I have no problem with vdW-DF1 or revPBE or any
>>>> other DFT functional but I can not get vdW-DF2 converged. The "Error
>>>> in Wave Functions" was oscillating and it could not be smaller than
>>>> 1.0e-6.
>>>>
>>>> Best regards,
>>>> Duy
>>>>
>>>> Here are the inputs:
>>>> ~~~~ input.py
>>>> ##/usr/bin/env python
>>>> from ase import *
>>>> from ase.lattice.surface import *
>>>> from gpaw import GPAW
>>>> from gpaw.utilities.tools import cutoff2gridspacing,
>>>> gridspacing2cutoff
>>>> from gpaw.vdw import FFTVDWFunctional
>>>> from gpaw.poisson import PoissonSolver
>>>> vdw = FFTVDWFunctional(nspins=1,exchange='X_PW86-None',Zab=-1.887)
>>>> system=read('MOL.xsf')
>>>> d=0
>>>> output='MOL.'+str(d)+'.txt'
>>>> tmpfile='MOL.'+str(d)+'.gpw'
>>>> xsf='MOL.'+str(d)+'.xsf'
>>>>
>>>> k=1
>>>> ngx=96
>>>> ngy=96
>>>> ngz=112
>>>>
>>>>
>>>> calc=GPAW(kpts=(k,k,1),
>>>> xc=vdw,verbose=1,
>>>> gpts=(ngx,ngy,ngz),
>>>> convergence={'energy':0.0001,
>>>> 'density':1.e-4,
>>>> # 'eigenstates': 1.0e-6, # default 1.0e-9
>>>> 'band':'occupied'},
>>>> # eigensolver='cg',
>>>> # poissonsolver=PoissonSolver(nn=4, eps=1e-7),
>>>> txt=output)
>>>> system.set_calculator(calc)
>>>> Etot = system.get_potential_energy()
>>>>
>>>>
>>>> ~~~~ MOL.xsf
>>>> ANIMSTEPS 1
>>>> CRYSTAL
>>>> PRIMVEC 1
>>>> 17.14730299493188 0.00000000000000 0.00000000000000
>>>> 0.00000000000000 17.32500000000000 0.00000000000000
>>>> 0.00000000000000 0.00000000000000 19.80000000000000
>>>> PRIMCOORD 1
>>>> 15 1
>>>> 6 7.88929861131941 8.74279897333303 9.23519036609335
>>>> 6 9.29407452321463 8.66235256964292 9.22660802911678
>>>> 6 9.25953637200172 6.44054447324515 9.21345896750818
>>>> 6 7.19487577477512 7.50640945431773 9.23391747470668
>>>> 6 8.57448589108522 10.77139928082912 9.22321194485284
>>>> 7 10.03927789166028 7.54045396872909 9.21601308563562
>>>> 7 7.91048599589602 6.35523280726322 9.21957979402641
>>>> 7 7.45472256395586 10.06949990739891 9.23111842694947
>>>> 7 9.71946649561474 9.98338351912395 9.22313940828820
>>>> 7 5.83477936812194 7.43368881826066 9.24868794967438
>>>> 1 8.63391314599401 11.85291790879339 9.20920053359968
>>>> 1 10.68059547151664 10.30415787931885 9.19583460569330
>>>> 1 9.78701750033542 5.48653725614175 9.20204409378673
>>>> 1 5.38210093732843 6.53173729472345 9.20183809503345
>>>> 1 5.27897101044724 8.27578470491815 9.20575836661537
>>>>
>>>> --------------------------------------------------
>>>> Duy Le
>>>> PhD Student
>>>> Department of Physics
>>>> University of Central Florida.
>>>>
>>>> "Men don't need hand to do things"
>>>>
>>>>
>>>>
>>>> On Fri, Sep 17, 2010 at 7:18 AM, Jess Wellendorff Pedersen
>>>> <printerfejl at gmail.com <mailto:printerfejl at gmail.com>> wrote:
>>>> > Hi Duy,
>>>> >
>>>> > The present GPAW approach to vdW-DF-2 calculations uses revPBE
>>>> setups. I
>>>> > have not myself experienced convergence problems with vdW-DF-2
>>>> this way.
>>>> > Convergence for the 148 G2-2 molecules is pretty much the same
>>>> as for
>>>> > vdW-DF-1, in my experience. Please provide a bit more info on your
>>>> > calculations, especially which kind of molecules.
>>>> >
>>>> > /Jess
>>>> >
>>>> > Duy Le wrote:
>>>> >>
>>>> >> Dear all,
>>>> >>
>>>> >> I noticed that it is hard to get a SCF converged with vdW-DF2 for
>>>> >> isolated molecules. In fact I could not get any of them
>>>> converged. I
>>>> >> have not seen this problem with older version of vdW-DF.
>>>> >>
>>>> >> There is no such problem in the case of a system containing
>>>> molecules
>>>> >> on metal surfaces.
>>>> >>
>>>> >> Best regards,
>>>> >> Duy
>>>> >>
>>>> >> ********** example of input ****************
>>>> >> #!/usr/bin/env python
>>>> >> from ase import *
>>>> >> from ase.io <http://ase.io> import *
>>>>
>>>> >> from ase.lattice.surface import *
>>>> >> from gpaw import GPAW, Mixer, FermiDirac
>>>> >> from gpaw.utilities.tools import cutoff2gridspacing,
>>>> gridspacing2cutoff
>>>> >> from gpaw.vdw import FFTVDWFunctional
>>>> >> ##vdw = FFTVDWFunctional(nspins=1,Nalpha=20, lambd=1.2,rcut=125.0,
>>>> >> Nr=2048,size=None)
>>>> >> vdw = FFTVDWFunctional(nspins=2,exchange='X_PW86-None',Zab=-1.887)
>>>> >> system = read('POSCAR')
>>>> >> system.set_pbc((1,1,1))
>>>> >> output='output.txt'
>>>> >> k=1
>>>> >> ngx=152
>>>> >> ngy=100
>>>> >> ngz=180
>>>> >> print ngx,ngy,ngz
>>>> >> mm = [0] * len(system)
>>>> >> mm[192-162]=-1.
>>>> >> mm[195-162]=1.
>>>> >> mm[196-162]=1.
>>>> >> system.set_initial_magnetic_moments(mm)
>>>> >>
>>>> >> calc=GPAW(kpts=(k,k,1),
>>>> >> # occupations=FermiDirac(0.1),
>>>> >> # mixer=Mixer(beta=0.05, nmaxold=3, weight=50.0),
>>>> >> xc=vdw,spinpol=True,
>>>> >> gpts=(ngx,ngy,ngz),
>>>> >> convergence={'energy':0.0001,
>>>> >> 'density':1.e-4,
>>>> >> 'band':'occupied'},
>>>> >> txt=output)
>>>> >> system.set_calculator(calc)
>>>> >> GGA_energy = system.get_potential_energy()
>>>> >>
>>>> >>
>>>> >>
>>>> >> --------------------------------------------------
>>>> >> Duy Le
>>>> >> PhD Student
>>>> >> Department of Physics
>>>> >> University of Central Florida.
>>>> >>
>>>> >> "Men don't need hand to do things"
>>>> >>
>>>> >>
>>>> >>
>>>> >> On Mon, Aug 23, 2010 at 10:20 AM, Duy Le <ttduyle at gmail.com
>>>> <mailto:ttduyle at gmail.com>> wrote:
>>>> >>
>>>> >>>
>>>> >>> This's great news! I am also waiting for this.
>>>> >>> Thanks.
>>>> >>> --------------------------------------------------
>>>> >>> Duy Le
>>>> >>> PhD Student
>>>> >>> Department of Physics
>>>> >>> University of Central Florida.
>>>> >>>
>>>> >>> "Men don't need hand to do things"
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> On Mon, Aug 23, 2010 at 5:32 AM, Jess Wellendorff Pedersen
>>>> >>> <printerfejl at gmail.com <mailto:printerfejl at gmail.com>> wrote:
>>>> >>>
>>>> >>>>
>>>> >>>> You're right, as compared to vdW-DF-1, the vdW-DF-2 is
>>>> supposed to give
>>>> >>>> better vdW energetics as well as better vdW binding distances.
>>>> >>>>
>>>> >>>> I will commit the code-changes within a few hours, drop you a
>>>> mail when
>>>> >>>> it's there. The changes are only to the Python-code
>>>> (gpaw/vdw.py) so no
>>>> >>>> recompilation of C/Fortran-code is needed for that particular
>>>> update in
>>>> >>>> itself.
>>>> >>>>
>>>> >>>> - Jess
>>>> >>>>
>>>> >>>> Michael F. Peintinger wrote:
>>>> >>>>
>>>> >>>>>
>>>> >>>>> I would like to use it. I calculate Molecular Crystals and thus
>>>> >>>>> van-der-Waals binding may be important. As I try to find
>>>> structures I
>>>> >>>>> would like to try it.
>>>> >>>>> At the summer school there was a talk by Bengt where he
>>>> showed, that
>>>> >>>>> the
>>>> >>>>> second version is a significant improvement!
>>>> >>>>>
>>>> >>>>> Regards
>>>> >>>>>
>>>> >>>>> Michael
>>>> >>>>>
>>>> >>>>>
>>>> >>>>> On Mon, 2010-08-23 at 11:19 +0200, Jess Wellendorff Pedersen
>>>> wrote:
>>>> >>>>>
>>>> >>>>>
>>>> >>>>>>
>>>> >>>>>> Hi Michael,
>>>> >>>>>>
>>>> >>>>>> no, it is not. However, if there is a general need for it,
>>>> I can
>>>> >>>>>> commit
>>>> >>>>>> my personal modification of the vdW-DF code to the GPAW
>>>> svn, such that
>>>> >>>>>> one can use vdW-DF-2 like this:
>>>> >>>>>> *****************
>>>> >>>>>> from gpaw.vdw import FFTVDWFunctional
>>>> >>>>>> vdw =
>>>> FFTVDWFunctional(nspins=2,exchange='X_PW86-None',Zab=-1.887)
>>>> >>>>>> calc = GPAW(......, xc=vdw,.......)
>>>> >>>>>> *******************
>>>> >>>>>> All one would then need to remember is to set the number of
>>>> spins
>>>> >>>>>> correctly, i.r. nspins=1 for spin-paired systems, and
>>>> nspins=2 for
>>>> >>>>>> spin-polarized systems.
>>>> >>>>>>
>>>> >>>>>> Regards,
>>>> >>>>>> Jess Wellendorff
>>>> >>>>>>
>>>> >>>>>> Michael F. Peintinger wrote:
>>>> >>>>>>
>>>> >>>>>>
>>>> >>>>>>>
>>>> >>>>>>> Hi all,
>>>> >>>>>>>
>>>> >>>>>>> is the functional vdW-DF2 already in the svn?
>>>> >>>>>>>
>>>> >>>>>>> Best regards,
>>>> >>>>>>>
>>>> >>>>>>>
>>>> >>>>>>> Michael
>>>> >>>>>>>
>>>> >>>>>>>
>>>> >>>>>>>
>>>> >>>>>>>
>>>> >>>>>
>>>> >>>>>
>>>> >>>>
>>>> >>>> _______________________________________________
>>>> >>>> gpaw-users mailing list
>>>> >>>> gpaw-users at listserv.fysik.dtu.dk
>>>> <mailto:gpaw-users at listserv.fysik.dtu.dk>
>>>>
>>>> >>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>> >>>>
>>>> >>>>
>>>> >
>>>>
>>>>
>>>>
>>
>
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