reading geometry (coordinates and cell parameters) from a restart file

Matt W MattWa... at gmail.com
Tue Nov 15 10:12:56 CET 2016


Hi,

you need to use the &EXT_RESTART 
<https://manual.cp2k.org/trunk/CP2K_INPUT/EXT_RESTART.html> section instead 
of trying to read the restart file in the topology section.

Something like

&EXT_RESTART
   RESTART_FILE_NAME umsm-nh2-1.restart
&END EXT_RESTART

should do. By default, it reads in all information from the restart file 
 (but your input file must still be valid, and define the topology 
correctly as this is processed before the external file). 

Matt

On Tuesday, November 15, 2016 at 8:35:52 AM UTC, David T wrote:
>
> Dear cp2krs
>
> I am optimising some molecules using GEO_OPT.
>
> is it possible read a geometry from a restart file? and the cell 
> parameters?
> I am trying but I cannot :-(
>
> concerning the geometry this is what I put in the input:
>
>     &TOPOLOGY
> !!    COORD_FILE_NAME umsm-nh2.xyz
> !!    COORD_FILE_FORMAT XYZ
>       COORD_FILE_NAME umsm-nh2-1.restart
>       COORD_FILE_FORMAT CP2K
>     &END
>
> and this is the error I had:
>
>
>  *******************************************************************************
>  *   
> ___                                                                       *
>  *  /   
> \                                                                      *
>  * 
> [ABORT]                                                                     
> *
>  *  \___/    A floating point type object was expected, found end of the 
> line, *
>  *    |         File: 'umsm-nh2-1.restart', Line: 1, Column: 1, Chunk: < 
> >     *
>  *  
> O/|                                                                        *
>  * /| 
> |                                                                        *
>  * / \                                          
> input/cp_parser_methods.F:1194 *
>
>  *******************************************************************************
>
>
> Concerning the cell parameters it is even worse:
>
> Input:
>     &CELL
> !!    ABC [angstrom] 41.868 41.880 17.564
> !!    ALPHA_BETA_GAMMA 90. 90. 120.
>     CELL_FILE_FORMAT CP2K
>     CELL_FILE_NAME umsm-nh2-1.restart
>       SYMMETRY NONE
>     &END CELL
>
> error:
> forrtl: severe (59): list-directed I/O syntax error, unit -5, file 
> Internal List-Directed Read
>
> However in the restart file I can see the information are present:
>
> [tiana at deneb1 tmp]$ grep -A3  COORD umsm-nh2-1.restart
>
>      &COORD
> Zn    7.0975619283291929E+00    1.7345103848396320E+01    
> 1.3189045443483327E+01
> Zn    1.3818777106160974E+01    1.8926557862281943E+01    
> 4.4217589353253608E+00
> Zn    2.3603220884596876E+00    3.3736335046100855E+01    
> 1.3189876918006378E+01
> --
>      &END COORD
>
> and 
>
> [tiana at deneb1 tmp]$ grep CELL umsm-nh2-1.restart 
>    RUN_TYPE  CELL_OPT
>    &CELL_OPT
>      TYPE  DIRECT_CELL_OPT
>    &END CELL_OPT
>      &CELL
>        MULTIPLE_UNIT_CELL  1 1 1
>      &END CELL
>
> Any idea of/how can I parse that file?
>
> Cheers
> Davide
>
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