{SPAM?} [CP2K:2994] Re: DFT-D
Jörg Saßmannshausen
j.sassma... at ucl.ac.uk
Thu Dec 16 21:54:13 UTC 2010
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_INFORMATION.
>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
> > > &XC
> > > &XC_FUNCTIONAL BP
> > > &END XC_FUNCTIONAL
> > > &VDW_POTENTIAL
> > > &PAIR_POTENTIAL
> > > Type Grimme
> > > &end PAIR_POTENTIAL
> > > # POTENTIAL_TYPE DISPERSION_FUNCTIONAL
> > > &END VDW_POTENTIAL
> > > &END XC
> > > &print
> > > &DFT_CONTROL_PARAMETERS high
> > > &end DFT_CONTROL_PARAMETERS
> > > &end print
> > > &END DFT
> > > &SUBSYS
> > > &CELL
> > > ABC 9.8528 9.8528 9.8528
> > > &END CELL
> > > # 32 H2O (TIP5P,1bar,300K) a = 9.8528
> > > &COORD
> > > [ ... ]
> > > &END COORD
> > > &KIND H
> > > BASIS_SET TZV2P-GTH
> > > POTENTIAL GTH-PADE-q1
> > > &END KIND
> > > &KIND O
> > > BASIS_SET TZV2P-GTH
> > > POTENTIAL GTH-PADE-q6
> > > &END KIND
> > > &END SUBSYS
> > > &END FORCE_EVAL
> > > &GLOBAL
> > > PROJECT H2O-32-vdw
> > > RUN_TYPE MD
> > > PRINT_LEVEL low
> > > &TIMINGS
> > > THRESHOLD 0.000001
> > > &END
> > > &END GLOBAL
> > > &MOTION
> > > &MD
> > > ENSEMBLE NVE
> > > STEPS 300
> > > TIMESTEP 0.5
> > > TEMPERATURE 300.0
> > > &END MD
> > > &END MOTION
> > >
> > > --
> > > *************************************************************
> > > Jörg Saßmannshausen
> > > University College London
> > > Department of Chemistry
> > > Gordon Street
> > > London
> > > WC1H 0AJ
> > >
> > > email: j.sassma... at ucl.ac.uk
> > > web:http://sassy.formativ.net
> > >
> > > Please avoid sending me Word or PowerPoint attachments.
> > > Seehttp://www.gnu.org/philosophy/no-word-attachments.html
> > >
> > > --
> > > You received this message because you are subscribed to the Google
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> >
> > --
> > *************************************************************
> > Jörg Saßmannshausen
> > University College London
> > Department of Chemistry
> > Gordon Street
> > London
> > WC1H 0AJ
> >
> > email: j.sassma... at ucl.ac.uk
> > web:http://sassy.formativ.net
> >
> > Please avoid sending me Word or PowerPoint attachments.
> > Seehttp://www.gnu.org/philosophy/no-word-attachments.html
> >
> > dft-d-D2.inp
> > < 1KViewDownload
> >
> > subsys.inc
> > 4KViewDownload
> >
> > force_eval-D2.inc
> > 1KViewDownload
--
*************************************************************
Jörg Saßmannshausen
University College London
Department of Chemistry
Gordon Street
London
WC1H 0AJ
email: j.sassma... at ucl.ac.uk
web: http://sassy.formativ.net
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
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