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

David T amazing... at gmail.com
Tue Nov 15 10:53:46 CET 2016


It worked :-)

Thanks

On Tuesday, 15 November 2016 10:12:56 UTC+1, Matt W wrote:
>
> 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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