Coordination number CV

marci marc... at pci.uzh.ch
Wed Feb 20 23:07:37 CET 2013


Dear Martin, 

the coordination number as CV is defined from a set of atoms to another 
set, and it is normalized with respect to the number of atoms in the first 
set. Therefore it is not restricted to values between 0 and 1. 
kind regards
Marcella

On Wednesday, February 20, 2013 5:50:41 PM UTC+1, Martin wrote:
>
> Hi all,
>
> I am using coordination number as a collective variable in a metadynamics 
> simulation in CP2K.  I have read already that cp2k normalizes the 
> coordination number by the number of atoms thus it should always be between 
> 0 and 1.  I am concerned that there is a bug because I get values slightly 
> higher than 1 (e.g. 1.20021749) in my COLVAR.dat file as well as in my free 
> energy output.  Does anybody know why this might be happening?
>
> Thanks.
> Martin
>
> Here are the pertinent parts of my input file:
>
>  &GLOBAL
>    PREFERRED_FFT_LIBRARY  FFTSG
>    EXTENDED_FFT_LENGTHS  T
>    PRINT_LEVEL  MEDIUM
>    PROJECT_NAME GACTIN
>    RUN_TYPE  MD
>  &END GLOBAL
>  &MOTION
>    &MD
>      ENSEMBLE  NVT
>      STEPS  10000
>      TIMESTEP     4.9999999999999989E-01
>      STEP_START_VAL  10531
>      TIME_START_VAL     5.5554999999993852E+03
>      ECONS_START_VAL    -1.3825824210408957E+03
>      TEMPERATURE     3.1000000000000000E+02
>      COMVEL_TOL     1.0000000000000001E-05
>      &THERMOSTAT
>        TYPE  NOSE
>        &NOSE
>          TIMECON     9.9999999999999964E+00
>          &COORD
>               -1.9870307101421267E+00    1.5164403362900575E+02   
>  2.0651877984243871E+04
>          &END COORD
>          &VELOCITY
>               -2.6525573239549802E-06    1.6855266002596401E-03   
>  3.2669753771567196E-03
>          &END VELOCITY
>          &MASS
>                1.9734082808800943E+07    1.6778542540323039E+02   
>  1.6778542540323039E+02
>          &END MASS
>          &FORCE
>               -1.0987144495918850E-08   -5.0234551461375742E-06   
> -3.0100014648276899E-06
>          &END FORCE
>        &END NOSE
>      &END THERMOSTAT
>   &END MD
>   &FREE_ENERGY
>      METHOD  METADYN
>      &METADYN
>        TEMPERATURE     3.1000000000000000E+02
>        MIN_DISP     2.9999999999999999E-02
>        OLD_HILL_NUMBER  649
>        OLD_HILL_STEP  6925
>        TEMP_TOL     2.0000000000000003E+02
>        WW     1.9599999999999999E-03
>        DO_HILLS  T
>        DELTA_T     2.4000000000000000E+03
>        LAGRANGE  T
>        STEP_START_VAL  6931
>        NHILLS_START_VAL  649
>        COLVAR_AVG_TEMPERATURE_RESTART     3.4475790517869569E+02
>        &METAVAR
>          LAMBDA     2.0000000000000000E+00
>          MASS     4.9999999999999972E+01
>          SCALE     2.0000000000000000E-02
>          COLVAR  1
>        &END METAVAR
>        &METAVAR
>          LAMBDA     2.0000000000000000E+00
>          MASS     4.9999999999999972E+01
>          SCALE     2.0000000000000000E-02
>          COLVAR  2
>        &END METAVAR
>        &PRINT
>          &COLVAR  SILENT
>            FILENAME =COLVAR.dat
>            &EACH
>              MD  1
>            &END EACH
>          &END COLVAR
>          &HILLS  SILENT
>            FILENAME =HILLS.dat
>            &EACH
>              MD  1
>            &END EACH
>          &END HILLS
>        &END PRINT
>      &END METADYN
>    &END FREE_ENERGY
>  &END MOTION
>
> ....
>  &FORCE_EVAL
>    &SUBSYS
>    ....
>      &COLVAR
>        &COORDINATION
>          ATOMS_FROM  5871
>          ATOMS_TO  5870 5868 5869
>          R0     4.5000000000000000E+00
>        &END COORDINATION
>      &END COLVAR
>      &COLVAR
>        &COORDINATION
>          ATOMS_FROM  5871
>          ATOMS_TO  5876 5879 5882 5885 5888 5894 5897 5939 6533 \
>           10418 12167 15677 16733 19781 23543 23597 24299 24314 25400 \
>           29297 34814 39116 39695 44897 50948 53462 55361
>          R0     4.5000000000000000E+00
>        &END COORDINATION
>      &END COLVAR
>    ....
>    &END SUBSYS
>  &END FORCE_EVAL
>
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