[CP2K:612] Re: How do I generate PSF ?

[Teodoro Laino]

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!).

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.

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>