{SPAM?} [CP2K:3010] Re: DFT-D

Matthias Krack matthia... at psi.ch
Fri Dec 17 09:56:58 CET 2010


Hi Teo,

you are right, I was mistaken, mixing Hockney and MT.

sorry,

Matthias

On Dec 17, 9:52 am, Teodoro Laino <teodor... at gmail.com> wrote:
> Hi Matthias,
>
> That's quite wrong - MT requires a box which must be AT LEAST double the size of the electronic density.
> Providing only 3-5 or 6 Angstrom more for each dimension will lead to wrong results. Or would work for molecule of maximum 10 Angstrom wide (in the direction in which you add that buffer).
>
> Other methods, not implemented in CP2K, like Hockney require that the density has to be zero at the
> edges of the box. This is not the case for MT: it is even more demanding.
>
> So if the molecule is 15 Angstrom in one dimension (I'm talking only about atomic distances) the minimum box will be 30 + some buffer (3-5 Angstrom) to keep into account the electronic density in that dimension.
>
> Also using an adaptive box can be quite dangerous in terms of convergence of results: if the molecule is flat one has to consider only the thickness of the electronic density and without knowing it a priori any number (3 or 5) can be absolutely arbitrary.
>
> Best,
> Teo
>
> On Dec 17, 2010, at 9:43 AM, Matthias Krack wrote:
>
> > Hi Joerg,
>
> > I don't know to which script you are referring. Anyhow, just take care
> > that there is at least a 3 Angstrom (better more, ie. 5 or 6 A)
> > distance between the atoms of your system and the box walls for
> > isolated system runs, e.g. the difference between the maximum and
> > minimum atomic x coordinate of your system plus 5 A will give you the
> > box edge length a (do the same for y and z to get b and c). The extra
> > space (vacuum portion) is needed, because decoupling methods like MT
> > require that the electron density is (almost) zero at the box walls.
> > Thus a flat molecule can be placed in an adapted flat box. Use a
> > visualization tool to check your setup. Note, for larger systems and
> > thus larger boxes (like 27 A**3) you will need proper computational
> > resources, i.e. a parallel computer with enough CPU cores and RAM to
> > keep the grids in memory. For your system you might need 32 CPU cores
> > or even more.
>
> > cheers,
>
> > Matthias
>
> > On Dec 16, 10:54 pm, Jörg Saßmannshausen <j.sassma... at ucl.ac.uk>
> > wrote:
> >> Hi Matthias,
>
> >> thanks for the reply.
> >> I was using the script from the workshop to get the box size. You are not
> >> aware of any bugs in that script which could lead to a wrong box size for
> >> rathe large but flat molecules?
>
> >> I will toy around with the grid size and see if I can get it going.
> >> Probably moving to a PBC calculation would not help with the problem at all I
> >> would guess, or?
>
> >> All the best from a rainy London
>
> >> Jörg
>
> >> On Dienstag 14 Dezember 2010 Matthias Krack wrote:
>
> >>> Hi Joerg,
>
> >>> your simulation box size seems to be about 27 Angstrom^3 and using a
> >>> cutoff 660 Ry for such a box will result in large grids and thus huge
> >>> memory allocations. Possibly, the extreme memory request is the reason
> >>> for abnormal program termination. You may check your grid sizes using
> >>>http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/PRINT/GRID_INFORM....
> >>> html to get an idea of what will be used.
> >>> Afaik, SAVE_MEM helps only for systems which are large due to the
> >>> number of atoms employed. This is not the case for your system and
> >>> thus there is no impact from this keyword.
>
> >>> cheers,
>
> >>> Matthias
>
> >>> On Dec 13, 11:54 pm, Jörg Saßmannshausen <j.sassma... at ucl.ac.uk>
>
> >>> wrote:
> >>>> Dear Juerg,
>
> >>>> ok, I am now playing around with the DFT-D in cp2k.
> >>>> I am currently trying to ascertain how much memory we would require for
> >>>> the work we are planning to do and for the new cluster. Hence, these are
> >>>> test runs of the right size of molecule but not with a really good
> >>>> optimised structure (i.e. not optimised with DFT-D).
>
> >>>> I have tried both the DFT-D2 and DFT-D3 option and I got 2 problems:
> >>>> a) the test molecule needs about > 48 GB of RAM, which is significant. Is
> >>>> there any way to get that into a more handable size? I have tried the
> >>>> SAVE_MEM in GLOBAL but that did not really had any effect it seems.
> >>>> Following Matthias' suggestion some time ago, I am using a cutoff of 660,
> >>>> which was working well for different molecules in the past.
>
> >>>> b) I get the following error for the DFT-D2 frequency calculation:
>
> >>>> [ ... ]
> >>>>  REPLICA| layout of the replica grid, number of groups                  
> >>>>       2
> >>>>  REPLICA| layout of the replica grid, size of each group                
> >>>>       1
> >>>>  REPLICA| MPI process to grid (group,rank) correspondence:
> >>>>   (   0 :    0,   0)  (   1 :    1,   0)
>
> >>>>  VIB| Vibrational Analysis Info
>
> >>>>   Pair potential vdW calculation
> >>>>   Dispersion potential type: DFTD2
> >>>>   Scaling parameter (s6)   1.00000000000000000
> >>>>   Exponential prefactor     20.000000000000000
> >>>>   Total vdW energy [au]     : -6.37708902660472643E-002
> >>>>   Total vdW energy [kcal]   :  -40.016837470249470
>
> >>>>   Dispersion Forces
> >>>>   Atom   Kind                            Forces
> >>>> [ ... ]
> >>>>  |G| =   5.08859983571732719E-002
>
> >>>>  Stress Tensor (dispersion)
> >>>>  -0.911187517690E-03 -0.491992126627E-02  0.140501262854E-01
> >>>>  -0.491992126627E-02  0.134365275526E-01  0.179254944339E-02
> >>>>   0.140501262854E-01  0.179254944339E-02 -0.155716224075E-01
> >>>>    Tr(P)/3 :   -1.01542745750825042E-003
>
> >>>>  CP2K| condition FAILED at line 253
> >>>>  CP2K| Abnormal program termination, stopped by process number 1
> >>>>  CP2K| condition FAILED at line 253
> >>>>  CP2K| Abnormal program termination, stopped by process number 0
>
> >>>> For the DFT-D3 calculation I get this error:
> >>>> [ ... ]
>
> >>>> |G| =   1.19763995420629592E-002
>
> >>>>  Stress Tensor (dispersion)
> >>>>  -0.525748742588E-02 -0.260638877285E-02  0.799232865409E-02
> >>>>  -0.260638877285E-02 -0.433023621108E-03  0.181088946886E-02
> >>>>   0.799232865409E-02  0.181088946886E-02 -0.929520614835E-02
> >>>>    Tr(P)/3 :   -4.99523906511300034E-003
>
> >>>>  CP2K| condition FAILED at line 236
> >>>>  CP2K| Abnormal program termination, stopped by process number 0
>
> >>>> It appears to me I am doing something wrong. I basically have copied and
> >>>> pasted your section into the force_eval.inc file.
> >>>> Can you or somebody be so kind and point me in the right direction? It is
> >>>> possible to do the frequency calculation with DFT-D or am I wrong here?
>
> >>>> I have attached the input files dft-d-D2.inp, force_eval-D2.inc and
> >>>> subsys.inc.
>
> >>>> All the best from London
>
> >>>> Jörg
>
> >>>> On Montag 22 November 2010 hut... at pci.uzh.ch wrote:
> >>>>> Hi
>
> >>>>> here is an example for the Grimme D2 method
> >>>>>       &vdW_POTENTIAL
> >>>>>          DISPERSION_FUNCTIONAL PAIR_POTENTIAL
> >>>>>          &PAIR_POTENTIAL
> >>>>>             TYPE DFTD2
> >>>>>             R_CUTOFF 15.0
> >>>>>             SCALING 1.0
> >>>>>          &END PAIR_POTENTIAL
> >>>>>       &END vdW_POTENTIAL
>
> >>>>> The SCALING parameter refers to the s6 term in this method.
> >>>>> Default values for some functionals are available in the
> >>>>> code through
> >>>>>              REFERENCE_FUNCTIONAL BLYP
>
> >>>>> This is an example for the new D3 method
> >>>>>          DISPERSION_FUNCTIONAL PAIR_POTENTIAL
> >>>>>          &PAIR_POTENTIAL
> >>>>>             TYPE DFTD3
> >>>>>             REFERENCE_FUNCTIONAL BLYP
> >>>>>             CALCULATE_C9_TERM .TRUE.
> >>>>>             PARAMETER_FILE_NAME dftd3.dat
> >>>>>             R_CUTOFF 15.0
> >>>>>          &END PAIR_POTENTIAL
> >>>>>       &END vdW_POTENTIAL
>
> >>>>> With VERBOSE_OUTPUT TRUE you can get all kinds of detailed
> >>>>> energy contributions.
>
> >>>>> regards
>
> >>>>> Juerg Hutter
>
> >>>>> --------------------------------------------------------------
> >>>>> Juerg Hutter                       Phone : ++41 44 635 4491
> >>>>> Physical Chemistry Institute   FAX   : ++41 44 635 6838
> >>>>> University of Zurich               E-mail:  hut... at pci.uzh.ch
> >>>>> Winterthurerstrasse 190
> >>>>> CH-8057 Zurich, Switzerland
> >>>>> ---------------------------------------------------------------
>
> >>>>> -----cp... at googlegroups.com wrote: -----
>
> >>>>> To: cp2k <cp... at googlegroups.com>
> >>>>> From: Jörg Saßmannshausen <j.sassma... at ucl.ac.uk>
> >>>>> Sent by: cp... at googlegroups.com
> >>>>> Date: 11/21/2010 11:23AM
> >>>>> Subject: [CP2K:2928] DFT-D
>
> >>>>> Dear all
>
> >>>>> admittingly, my skills in cp2k are a bit rusty.
> >>>>> I wanted to look into the DFT-D option of cp2k, specially how the
> >>>>> second derivatives calculation are performing on rather large
> >>>>> molecules.
>
> >>>>>> From the manual I takt it one can do DFT-D calculations so I thought I
> >>>>>> am
>
> >>>>> using the water example and play around with that. I decided, mainly
> >>>>> for speed reasons, to go with the BP functional and compare that MD run
> >>>>> with one where DFT-D is switched on, i.e. BP-D.
> >>>>> However, I am not sure whether I done the setup correctly, so I thought
> >>>>> I might as well print out whether or not dispension is actually switch
> >>>>> on. Playing around with various option in
> >>>>> __ROOT__%FORCE_EVAL%DFT%PRINT%DFT_CONTROL_PARAMETERS
> >>>>> where somehow unsuccesful in this respect. Would somebody just briefly
> >>>>> comment on whether my input file (attached below) is correct and how to
> >>>>> print out the DFT parameters?
> >>>>> I have omitted the coordination section to save some space.
>
> >>>>> All the best from London!
>
> >>>>> Jörg
>
> >>>>> Input file:
> >>>>> &FORCE_EVAL
> >>>>>   METHOD QS
> >>>>>   &DFT
> >>>>>     BASIS_SET_FILE_NAME ../BASIS_SET
> >>>>>     POTENTIAL_FILE_NAME ../POTENTIAL
> >>>>>     &MGRID
> >>>>>       CUTOFF 280
> >>>>>     &END MGRID
> >>>>>     &QS
> >>>>>       EPS_DEFAULT 1.0E-12
> >>>>>       WF_INTERPOLATION PS
> >>>>>       EXTRAPOLATION_ORDER 3
> >>>>>     &END QS
> >>>>>     &SCF
> >>>>>       SCF_GUESS ATOMIC
> >>>>>       &OT ON
> >>>>>         MINIMIZER DIIS
> >>>>>       &END OT
> >>>>>     # SCF_GUESS        RESTART
> >>>>>     # EPS_SCF      1.0E-7
> >>>>>       &PRINT
> >>>>>         &RESTART OFF
> >>>>>         &END
> >>>>>       &END
> >>>>>     &END SCF
>
> ...
>
> read more »


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