[CP2K:613] Re: How do I generate PSF ?
Jack Shultz
jackyg... at gmail.com
Mon Jan 21 03:35:27 UTC 2008
On Jan 20, 2008 9:15 PM, Teodoro Laino <teodor... at gmail.com> wrote:
>
> Hi Jack,
>
> If I run that input file that's what I get:
>
>
> ************* ******** ***********
> ************* **********************
> **** **** **** ***********
> ******** **** ******* ****
> ******* **** ******* ****
> **** **** **** ****
> **** **** ********** ****
> **** **** ******** ****
> FRONTIERS IN SIMULATION TECHNOLOGY
>
> C.J. Mundy, S. Balasubramanian,
> Ken Bagchi, J. Hutter, Ari Seitsonen
> IFW Kuo, T. Laino, J. VandeVondele
> Version 0.31415
>
>
>
>
> EWALD| Summation is done
> by: EWALD
> EWALD| Alpha parameter
> [ ANGSTROM^-1] 0.3600
> EWALD| Real Space Cutoff
> [ ANGSTROM] 9.3720
> EWALD| G-space max. Miller index 29
> 29 29
>
> GENERATE| Preliminary Number of Bonds
> generated: 6
> GENERATE| Achieved consistency in connectivity generation.
> GENERATE| Number of Bonds
> generated: 6
> GENERATE| Preliminary Number of Bends
> generated: 4
> GENERATE| Number of Bends
> generated: 4
> GENERATE| Number of UB
> generated: 4
> GENERATE| Preliminary Number of Torsions
> generated: 2
> GENERATE| Number of Torsions
> generated: 2
> GENERATE| Number of Impropers
> generated: 0
> GENERATE| Number of 1-4 interactions
> generated: 2
>
>
> *
> *** ERROR in force_field_control ***
> *
>
>
> *** force field file missing ***
>
>
> ===== Routine Calling Stack =====
>
> 4 force_field_control
> 3 fist_init
> 2 fist_create_force_env
> 1 CP2K
> CP2K| Abnormal program termination, stopped by process number 0
> Aborted
> ------------------------------------------------------------------------
> --------------------------------
>
> CP2K has generated the proper topology. CP2K does not hang (at least
> the g95 compiled version)
> but gives an error because you didn't provide any parameter file (the
> line PARM_FILE_NAME in the input is empty).
> I just put a more strict control on this variable.. updating and
> recompiling you should be able to
> get the same error I get and CP2K should not hang anymore.
>
> Anyway, are you sure that you want to simulate this reaction
> using a classical FF? The ones we support are *mainly* non-reactive
> (yet!).
Do I understand you correctly, there are no FORCEFIELDs I can use that
support reactions currently?
>
>
> Moreover, If you should use the 2H2O+O2.xyz, as a standard xyz file
> asking cp2k to generate a topology,
> you may get in serious trouble since what it should be an hydrogen
> bond between two water molecules
> is only 1.04 Angstrom long.. i.e. that hydrogen is at the same
> distance between the two oxygens.
>
So I did not displace the water molecules appropriately? I only tried to
seperate them by 2 angstroms along the x-axis...maybe I should move them 1
angstrom along the y-axis as well? Should that help?
>
> Cheers
> Teo
>
> On 21 Jan 2008, at 00:16, Jack Shultz wrote:
>
> > ../../../exe/Cygwin-i686-g95/cp2k.sopt -i 2H2O2_CI-NEB.inp > out.txt
> >
> > Hope this helps. Here is what I've done with my rudimentary knowledge.
> >
> > >
> > jshultz at HYDROGEN has created process
> > number 0 1048
> >
> > **** **** ****** ** PROGRAM STARTED AT
> > 20080120 180252.000
> > ***** ** *** *** ** PROGRAM STARTED
> > ON HYDROGEN
> > ** **** ****** PROGRAM STARTED
> > BY jshultz
> > ***** ** ** ** ** PROGRAM PROCESS
> > ID 1048
> > **** ** ******* ** PROGRAM STARTED IN /usr/src/cp2k/tests/
> > NEB/regtest-1
> >
> > CP2K| version string: CP2K version 2.0.0
> > (development version)
> > CP2K| is freely available from http://
> > cp2k.berlios.de/
> > CP2K| Program compiled at Mon Jan 14
> > 22:38:57 EST 2008
> > CP2K| Program compiled
> > on HYDROGEN
> > CP2K| Program compiled for
> > Cygwin-i686-g95
> > CP2K| Last CVS entry xray_diffraction.F/1.18/Thu Jan 3
> > 23:07:09 2008
> > CP2K| Input file name
> > 2H2O2_CI-NEB.inp
> >
> > GLOBAL| Force Environment
> > number 1
> > GLOBAL| Basis set file
> > name BASIS_SET
> > GLOBAL| Potential file
> > name POTENTIAL
> > GLOBAL| MM Potential file name
> > MM_POTENTIAL
> > GLOBAL| Coordinate file
> > name 2H2O.pdb
> > GLOBAL| Method
> > name CP2K
> > GLOBAL| Project
> > name GLYGLY
> > GLOBAL| Preferred FFT
> > library FFTW3
> > GLOBAL| Run type
> > WAVEFUNCTION_OPTIMIZATION
> > GLOBAL| All-to-all communication in single
> > precision F
> > GLOBAL| FFTs using library dependent
> > lengths F
> > GLOBAL| Global print
> > level 1
> > GLOBAL| Total number of message passing
> > processes 1
> > GLOBAL| Number of threads for this
> > process 1
> > GLOBAL| This output is from
> > process 0
> >
> > WARNING : FFT library FFTW3 is not available Trying FFTSG as a
> > default
> >
> >
> > ************* ******** ***********
> > ************* **********************
> > **** **** **** ***********
> > ******** **** ******* ****
> > ******* **** ******* ****
> > **** **** **** ****
> > **** **** ********** ****
> > **** **** ******** ****
> > FRONTIERS IN SIMULATION TECHNOLOGY
> >
> > C.J. Mundy, S. Balasubramanian,
> > Ken Bagchi, J. Hutter, Ari Seitsonen
> > IFW Kuo, T. Laino, J. VandeVondele
> > Version 0.31415
> >
> >
> >
> >
> > EWALD| Summation is done
> > by: EWALD
> > EWALD| Alpha parameter
> > [ ANGSTROM^-1] 0.3600
> > EWALD| Real Space Cutoff
> > [ ANGSTROM] 9.3720
> > EWALD| G-space max. Miller index 29
> > 29 29
> >
> > GENERATE| Preliminary Number of Bonds
> > generated: 6
> > GENERATE| Achieved consistency in connectivity generation.
> > GENERATE| Number of Bonds
> > generated: 6
> > GENERATE| Preliminary Number of Bends
> > generated: 4
> > GENERATE| Number of Bends
> > generated: 4
> > GENERATE| Number of UB
> > generated: 4
> > GENERATE| Preliminary Number of Torsions
> > generated: 2
> > GENERATE| Number of Torsions
> > generated: 2
> > GENERATE| Number of Impropers
> > generated: 0
> > GENERATE| Number of 1-4 interactions
> > generated: 2<2H2O2_CI-
> > NEB.inp><2H2O.pdb><2H2O+O2.xyz><2H2O.xyz>
>
>
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20080120/fad3f591/attachment.htm>
More information about the CP2K-user
mailing list