How to understand the keywords atoms_from and atoms_to in the colvars??
ning.zh... at gmail.com
ning.zh... at gmail.com
Wed Sep 9 09:31:17 UTC 2015
Dear Marcella,
Thanks you for your reply. I have understand now.
* &COLVAR*
* &COORDINATION*
* ATOMS_FROM 1*
* ATOMS_TO 2 3*
* R_0 2.3*
* &END COORDINATION*
I can understand the section above that the "number" of atoms of type 2 *and
type 3* that are within a given radius (2.3) from atoms of type 1, in
average, right??
Furthermore, the output results included a file "***-COLVAR.metadynLog",
* 0.00000000 1.61674 0.00000 0.00000 0.00000
0.00000*
* 0.50000000 1.61884 0.00000 0.00000 0.00000
0.00000*
* 1.00000000 1.61648 0.00000 0.00000 0.00100
0.00000*
* 1.50000000 1.60987 -0.01564 0.00000 0.00095
0.00000*
* 2.00000000 1.59765 -0.03022 0.00000 0.00164
0.00000*
* 2.50000000 1.57905 -0.04642 0.00000 0.00082
0.00000*
* 3.00000000 1.55352 -0.01078 0.00000 0.00109
0.00000*
* 3.50000000 1.52892 -0.02935 0.00000 0.00047
0.00000*
* 4.00000000 1.50514 -0.00649 0.00000 0.00105
0.00000*
* 4.50000000 1.48856 -0.03022 0.00000 0.00071
0.00000*
* 5.00000000 1.47702 -0.02630 0.00000 0.00137
0.00000*
* 0.00000000 1.61674 0.00000 0.00000 0.00000
0.00000*
* 0.50000000 1.61884 0.00000 0.00000 0.00000
0.00000*
* 1.00000000 1.61648 0.00000 0.00000 0.00100
0.00000*
* 1.50000000 1.60987 -0.01564 0.00000 0.00095
0.00000*
* 2.00000000 1.59765 -0.03022 0.00000 0.00164
0.00000*
* 2.50000000 1.57905 -0.04642 0.00000 0.00082
0.00000*
* 3.00000000 1.55352 -0.01078 0.00000 0.00109
0.00000*
* 3.50000000 1.52892 -0.02935 0.00000 0.00047
0.00000*
* 4.00000000 1.50514 -0.00649 0.00000 0.00105
0.00000*
* 4.50000000 1.48856 -0.03022 0.00000 0.00071
0.00000*
* 5.00000000 1.47702 -0.02630 0.00000 0.00137
0.00000*
*......*
and a file "***-HILLS.metadynLog"
* 1.0 1.61648 0.02000 0.00100*
* 2.0 1.59765 0.02000 0.00100*
* 3.0 1.55352 0.02000 0.00100*
* 4.0 1.50514 0.02000 0.00100*
* 5.0 1.47702 0.02000 0.00100*
* 1.0 1.61648 0.02000 0.00100*
* 2.0 1.59765 0.02000 0.00100*
* 3.0 1.55352 0.02000 0.00100*
* 4.0 1.50514 0.02000 0.00100*
* 5.0 1.47702 0.02000 0.00100*
* 6.0 1.47374 0.02000 0.00100*
* 7.0 1.49936 0.02000 0.00100*
* 8.0 1.57313 0.02000 0.00100*
* 9.0 1.64781 0.02000 0.00100*
* 10.0 1.69384 0.02000 0.00100*
* 11.0 1.68170 0.02000 0.00100*
* 12.0 1.61092 0.02000 0.00100*
* 13.0 1.51437 0.02000 0.00100*
* 14.0 1.44559 0.02000 0.00100*
* 15.0 1.39573 0.02000 0.00100*
* 16.0 1.40930 0.02000 0.00100*
* 17.0 1.48566 0.02000 0.00100*
* 18.0 1.58976 0.02000 0.00100*
* 19.0 1.68096 0.02000 0.00100*
* 20.0 1.72275 0.02000 0.00100*
* 21.0 1.70510 0.02000 0.00100*
* 22.0 1.62193 0.02000 0.00100*
* 23.0 1.50355 0.02000 0.00100*
* 24.0 1.40440 0.02000 0.00100*
*.......*
But I don't understand what does every column stand for? Would you help me?
How can I get the figure of FES VS CV?
Thanks.
Ning
在 2015年9月8日星期二 UTC+8下午3:22:25，Marcella Iannuzzi写道：
>
> Dear .....
>
> Every COLVAR has different keywords depending on its functional definition.
> In the specific case, the coordination is defined as the "number" of atoms
> of type 2 that are within a given radius from atoms of type 1, in average.
> Regards
> Marcella
>
> On Monday, September 7, 2015 at 1:02:24 PM UTC+2, ning.... at gmail.com
> wrote:
>>
>> I am newer for the cp2k. I am studying the metadynamics method. I noted
>> that colvars section in the input files includes the keywords atoms_from
>> and atoms_to. I don't understand what does it mean? what does the R_0 stand
>> for?? For example, see the bold text
>>
>> &FORCE_EVAL
>> METHOD Quickstep
>> &DFT
>> BASIS_SET_FILE_NAME BASIS_SET
>> POTENTIAL_FILE_NAME POTENTIAL
>> &MGRID
>> CUTOFF 200
>> &END MGRID
>> &QS
>> &END QS
>> &SCF
>> SCF_GUESS ATOMIC
>> &END SCF
>> &XC
>> &XC_FUNCTIONAL Pade
>> &END XC_FUNCTIONAL
>> &END XC
>> &END DFT
>> &SUBSYS
>> &CELL
>> ABC 5.0 5.0 5.0
>> &END CELL
>> &COORD
>> O 0.000000 0.000000 -0.065587
>> H 0.000000 -0.757136 0.520545
>> H 0.000000 0.757136 0.520545
>> &END COORD
>> &KIND H
>> BASIS_SET DZVP-GTH-PADE
>> POTENTIAL GTH-PADE-q1
>> &END KIND
>> &KIND O
>> BASIS_SET DZVP-GTH-PADE
>> POTENTIAL GTH-PADE-q6
>> &END KIND
>> * &COLVAR*
>> * &COORDINATION*
>> * ATOMS_FROM 1*
>> * ATOMS_TO 2 3*
>> * R_0 2.3*
>> * &END COORDINATION*
>> &END COLVAR
>> &END SUBSYS
>> &END FORCE_EVAL
>> &GLOBAL
>> PROJECT H2O-meta_coord
>> RUN_TYPE MD
>> PRINT_LEVEL LOW
>> &END GLOBAL
>> &MOTION
>> &MD
>> ENSEMBLE NVT
>> STEPS 10000
>> TIMESTEP 0.5
>> TEMPERATURE 300.0
>> &THERMOSTAT
>> &NOSE
>> LENGTH 3
>> YOSHIDA 3
>> TIMECON 100.0
>> MTS 2
>> &END NOSE
>> &END
>> &END MD
>> &FREE_ENERGY
>> &METADYN
>> DO_HILLS
>> NT_HILLS 2
>> WW 1.0e-3
>> &METAVAR
>> SCALE 0.02
>> COLVAR 1
>> &END METAVAR
>> &PRINT
>> &COLVAR
>> COMMON_ITERATION_LEVELS 3
>> &END
>> &HILLS
>> COMMON_ITERATION_LEVELS 3
>> &END
>> &END
>> &END METADYN
>> &END
>> &END MOTION
>>
>> Any provides are welcome.
>>
>>
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