[CP2K:3495] Re: CI BAND calculation

Nikita Vakula vakul... at gmail.com
Fri Sep 16 11:53:07 CEST 2011


Thanks for your reply. I used 120 procs.
Best regards,
Nikita

2011/9/16 Teodoro Laino <teodor... at gmail.com>

> just replied. Another info: how many procs did you use in your submission ?
>
> On Sep 16, 2011, at 8:05 AM, Nikita wrote:
>
> > Hello, Teo!
> > Thanks for your prompt reply!
> >
> >> concerning the input.
> >> When I write NPROC_REP 4 and NUMBER_OF_REPLICA 5, the program
> > writes
> >> that the number of images is 5 and the number of replicas is 30
> > (?!?)
> >    That's not possible. Please attach the corresponding output...
> >
> >> I'm trying to do CI NEB calculation but have a few questions
> > I sent the output on your email (there's no option to attach files in
> > google groups)
> >
> >
> *******************************************************************************
> >
> >
> *******************************************************************************
> >
> > **
> > **
> > **  ########     ###    ##    ## ########    Nudged Elastic Band
> > Method      **
> > **  ##     ##   ## ##   ###   ## ##     ##   String
> > Method                   **
> > **  ##     ##  ##   ##  ####  ## ##
> > ##                                   **
> > **  ########  ##     ## ## ## ## ##     ##   Number of
> > Images :            5 **
> > **  ##     ## ######### ##  #### ##     ##   Number of
> > Replicas:          30 **
> > **  ##     ## ##     ## ##   ### ##     ##   Number of Procs/
> > Rep:          4 **
> > **  ########  ##     ## ##    ##
> > ########                                    **
> > **                                           T. Laino
> > 2009-2010             **
> >
> >
> *******************************************************************************
> >
> >
> *******************************************************************************
> >
> >
> >> (the number of processors used in calculation was 120).
> >> And the second question is how to set coordinates of images
> > correctly?
> >> I mean if I have 5 images with xyz files 1.xyz, 2.xyz, 3.xyz,
> > 4.xyz,
> >> 5.xyz: where the first and the last xyz correspond to optimized
> >> initial and final configurations, consequently, and 2,3,4
> > correspond
> >> to some intermidiate configurations, what should I write in
> > &coord
> >> section and in &replica?
> >    please refer to the regtest: you can find this information in
> > them..
> >
> > I looked at this example and that's not clear what to write in coord
> > section and replica section. In this input in coord section I wrote
> > the initial configuration (the file start.xyz), and in replica section
> > I wrote coordinates of all configurations (initial, final and
> > intermediate). Am I right?
> >
> > Best regards,
> > Nikita
> >
> > On Sep 15, 11:05 am, Teodoro Laino <teodor... at gmail.com> wrote:
> >> On Sep 15, 2011, at 9:02 AM, Nikita wrote:
> >>
> >>> Dear CP2K users and developers,
> >>
> >>> I'm trying to do CI NEB calculation but have a few questions
> >>> concerning the input.
> >>> When I write NPROC_REP 4 and NUMBER_OF_REPLICA 5, the program writes
> >>> that the number of images is 5 and the number of replicas is 30 (?!?)
> >>
> >> That's not possible. Please attach the corresponding output...
> >>
> >>> (the number of processors used in calculation was 120).
> >>> And the second question is how to set coordinates of images correctly?
> >>> I mean if I have 5 images with xyz files 1.xyz, 2.xyz, 3.xyz, 4.xyz,
> >>> 5.xyz: where the first and the last xyz correspond to optimized
> >>> initial and final configurations, consequently, and 2,3,4 correspond
> >>> to some intermidiate configurations, what should I write in &coord
> >>> section and in &replica?
> >>
> >> please refer to the regtest: you can find this information in them..
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>> Below is an example of my input (in coord section I wrote coordinates
> >>> from 1.xyz, and in replica section I wrote the other coordinates)
> >>> Best regards,
> >>> Nikita
> >>
> >>> &GLOBAL
> >>>  PROJECT butadiene
> >>>  PRINT_LEVEL medium
> >>>  RUN_TYPE BAND
> >>>  WALLTIME -1
> >>> &END GLOBAL
> >>
> >>> &FORCE_EVAL
> >>>  METHOD QUICKSTEP
> >>>  &DFT
> >>>    UKS .true.
> >>>    BASIS_SET_FILE_NAME ./BASIS_MOLOPT
> >>>    POTENTIAL_FILE_NAME ./POTENTIAL
> >>>    CHARGE 0
> >>>    MULTIPLICITY 1
> >>>   &QS
> >>>       EPS_DEFAULT 1.0E-12
> >>>       MAP_CONSISTENT
> >>>       EXTRAPOLATION PS
> >>>       EXTRAPOLATION_ORDER 2
> >>>     &END QS
> >>>     &SCF
> >>>       SCF_GUESS ATOMIC
> >>>       EPS_SCF 1.0E-7
> >>>       MAX_SCF 40
> >>>       &OUTER_SCF
> >>>          EPS_SCF 1.0E-7
> >>>          MAX_SCF 20
> >>>       &END
> >>>       &OT
> >>>          MINIMIZER CG
> >>>          PRECONDITIONER FULL_ALL
> >>>          ENERGY_GAP 0.001
> >>>       &END
> >>>     &END SCF
> >>>    &XC
> >>>      &XC_FUNCTIONAL PBE
> >>>      &END XC_FUNCTIONAL
> >>>    &END XC
> >>>  &END DFT
> >>>  &SUBSYS
> >>>    &CELL
> >>>       A     15.0000    0.00000000    0.00000000
> >>>       B      0.00000000   15.000    0.00000000
> >>>       C      0.00000000    0.00000000   15.0000
> >>>      ALPHA_BETA_GAMMA 90.0 90.0 90.0
> >>>      PERIODIC XY
> >>>    &END CELL
> >>>    &COORD
> >>> C        0.000000008     -1.548391596     -0.517468642
> >>> C       -0.000000012     -0.733564930      0.551479348
> >>> H        0.000000018     -1.165377516     -1.539680765
> >>> H        0.000000030     -2.631675687     -0.399525215
> >>> H       -0.000000011     -1.194051595      1.543703106
> >>> C        0.000000004      0.733564889      0.551479100
> >>> C        0.000000063      1.548391456     -0.517468532
> >>> H       -0.000000009      1.194051658      1.543703205
> >>> H       -0.000000020      2.631675808     -0.399525172
> >>> H       -0.000000010      1.165377544     -1.539680891
> >>>    &END COORD
> >>>    &KIND H
> >>>      BASIS_SET DZVP-MOLOPT-GTH-q1
> >>>      POTENTIAL GTH-PBE-q1
> >>>    &END
> >>>    &KIND C
> >>>      BASIS_SET DZVP-MOLOPT-GTH-q4
> >>>      POTENTIAL GTH-PBE-q4
> >>>    &END
> >>>  &END SUBSYS
> >>> &END FORCE_EVAL
> >>
> >>> &MOTION
> >>>  &PRINT
> >>>    &VELOCITIES OFF
> >>>    &END
> >>>  &END
> >>>  &BAND
> >>>    NPROC_REP 4
> >>>    BAND_TYPE CI-NEB
> >>>    NUMBER_OF_REPLICA 5
> >>>    K_SPRING 0.05
> >>>    ROTATE_FRAMES T
> >>>    &CI_NEB
> >>>       NSTEPS_IT  5
> >>>    &END
> >>>    &OPTIMIZE_BAND
> >>>      &DIIS
> >>>       MAX_STEPS 200
> >>>       MAX_SD_STEPS 10
> >>>      &END
> >>>    &END
> >>>    &REPLICA
> >>>      COORD_FILE_NAME  ./start.xyz
> >>>    &END
> >>>    &REPLICA
> >>>      COORD_FILE_NAME  ./1.xyz
> >>>    &END
> >>>    &REPLICA
> >>>      COORD_FILE_NAME  ./2.xyz
> >>>    &END
> >>>    &REPLICA
> >>>      COORD_FILE_NAME  ./3.xyz
> >>>    &END
> >>>    &REPLICA
> >>>      COORD_FILE_NAME  ./finish.xyz
> >>>    &END
> >>>    &PROGRAM_RUN_INFO
> >>>    &END
> >>>    &CONVERGENCE_INFO
> >>>    &END
> >>>  &END BAND
> >>> &END MOTION
> >>
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