DFT-D

Matt W mattwa... at gmail.com
Mon Dec 20 17:05:32 CET 2010


Hi Jörg,

It is definitely worth looking closely at the RS grids.  One (more)
technicality is that, by default the 2 highest RS grids are
distributed across the processors, thus total memory should conserved,
as it were and reduce per core with #procs.  Grids below this, I
think, are fully replicated across all processors, which might not be
a good thing for your big box - it will give a large memory term that
will not reduce with #procs.  This can be altered in the MGRID
section, but hard to say more without actually seeing data.

Best from rather grim London,

Matt

On Dec 17, 9:56 am, Jörg Saßmannshausen <j.sassma... at ucl.ac.uk>
wrote:
> Dear Theo and Matthias,
>
> many thanks for your replies.
>
> Yes, I remember from the tutorial that you need the 'right size of the box'
> and, as mentioned by Theo, should be at least double the size of the electron
> density. Fortunately, I should have access to a larger cluster over Christmas.
> Now, correct me if I am wrong, the memory of the whole calculation should be
> (fairly) the same, say 64 GB, regardless whether I run it hypothetically on
> one or 64 cores, right? I am aware of some overhead when I run things in
> parallel. The reason I am asking is, the IB cluster here has 4 cores per node
> with 8 GB or RAM, so I would need some rule of thumb to estimate the numbers
> of cores I would need.
> The reason behind all of that is that I need to do some testing to get the
> right hardware configuration for the new cluster we want to purchase.
> Obviously, I want enough memory (I am currently applying 3 GB per core for the
> Intel Nehalem) but I don't want to overkill it with memory. Hence all my
> testing.
>
> All the best from a cold London
>
> Jörg
>
> On Friday 17 December 2010 08:58:41 Teodoro Laino wrote:
>
> > Joerg,
>
> > the script you've been using should be the one we distributed at the CP2K
> > tutorial. It's strange that Matthias does not know anything about that
> > since he was tutor at that tutorial. Anyway: the script does exactly what
> > I said in the previous mail.
> > It takes the linear dimensions of the molecule (atomic distances) and sums
> > up a buffer 3-5 Angstrom. This will lead to converged results for
> > decouplers like MT.
> > Again in CP2K we do not have cheaper decoupler (you may try the others one
> > available like :
>
> > MULTIPOLE
>
> > WAVELET
>
> > )
> > Refer to the papers cited for each of these methods for constraints about
> > the box size: each of them is slightly different. For large molecules
> > WAVELET may be definitely much better. In fact for WAVELET is also enough
> > that the density is zero at the border of the box. But there are other
> > constraints : for non-periodic calculations we have implemented only cubic
> > boxes. So.. you see.. depends a lot.. for MT you can use an orthorhombic
> > (but larger in size).. for WAVELET a cubic although a bit smaller.
>
> > Up to you the final decision.
> > Teo
>
> > On Dec 16, 2010, at 10:54 PM, Jörg Saßmannshausen 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_INFORMATI
> > >> ON. 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
>
> ...
>
> read more »


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