Fixing a bond in DFT

[Pankaj Mishra]

Dear Andreas, Ari and Marco

Your suggestion is helpful. But i still i am missing one point. 
Suppose i am fixing  for larger system (suppose 32 water molecules), then 
how can i fix the  distance between oxygen and hydrogen of water. I mean do 
i need to define bond for each bonded atom pair separately for distance in  
COLVAR ? Is there some way to define molecule? For DFT calculation, i am 
just using atom ID (O or H) and its positions in random order. 
I hope for some suggestion. 

Thank you so much 


On Thursday, 13 November 2014 13:47:30 UTC+1, Andreas Funk wrote:
>
> Dear Wei,
>
> The first thing I see in your input is that you specify one colvar in 
> SUBSYS, but in MOTION you call two colvars. This cannot work. As it is only 
> one bond you specify as colvar, you should work with one colvar in the 
> CONSTRAINT section. Then you should keep it "fixed" like this in section 
> MOTION:
>
> &CONSTRAINT
>   &COLLECTIVE
>     COLVAR 1
>     INTERMOLECULAR
>     TARGET 2.399706
>     &RESTRAINT
>       K 1.0
>     &END RESTRAINT
>   &END COLLECTIVE
> &END CONSTRAINT
>
> Please keep in mind that the distance you want it to be fixed (TARGET) is 
> in bohrs, not angstroms. You need to experiment a little with the force 
> constant for the restraint. Check it in your runs if it is sufficient to 
> keep the bond length fixed within your desired accuracy. In principle, it 
> should do the job. I have used this kind of constraint successfully for 
> both, geometry optimizations and MD.
>
> Best regards
>
> Andreas
>
>
> Am Donnerstag, 13. November 2014 12:31:24 UTC+1 schrieb Wei:
>>
>> Dear Pankaj, Ari and Marco,
>>
>> I'd also like to fix a bond during a MD (DFT) run (not the absolute 
>> atomic positions). I tried to specify CP2K_INPUT / MOTION / CONSTRAINT / 
>> COLLECTIVE and CP2K_INPUT / FORCE_EVAL / SUBSYS / COLVAR by following an 
>> expample from regtest /Fist/regtest-12/water_3_dist_2.inp.
>>
>> However, the calculation always crashes with an error:
>>
>>  *
>>  *** 12:16:30 ERRORL2 in topology_input:read_constraints_section 
>> processor  ***
>>  ***      0  err=-300  condition FAILED at line 
>> 561                         ***
>>  *
>>
>>  ===== Routine Calling Stack =====
>>
>>             3 topology_control
>>             2 quickstep_create_force_env
>>             1 CP2K
>>  CP2K| condition FAILED at line 561
>>  CP2K| Abnormal program termination, stopped by process number 0
>>
>>
>> Could you please give me some hint on this issue? I put my input file 
>> below. Thanks in advance!
>>
>> Best Regards
>>
>> Wei
>>
>> input 
>>
>> &FORCE_EVAL
>>   METHOD QUICKSTEP
>>   &DFT
>>     BASIS_SET_FILE_NAME ./GST.qbs
>>     POTENTIAL_FILE_NAME ./GTH_POTENTIALS
>>     &MGRID
>>       CUTOFF 300
>>     &END MGRID
>>     &QS
>>       EPS_DEFAULT 1.0e-12
>>       EXTRAPOLATION ASPC
>>       EXTRAPOLATION_ORDER 0
>>       MAP_CONSISTENT
>>     &END QS
>>     &SCF
>>       EPS_SCF 1.0e-7
>>       MAX_SCF 40
>>       MAX_SCF_HIST 2
>>       &OT ON
>>         MINIMIZER DIIS
>>         PRECONDITIONER FULL_KINETIC
>>         ENERGY_GAP 0.002
>>         STEPSIZE 0.0875
>>       &END OT
>>       &OUTER_SCF ON
>>         MAX_SCF 800
>>         EPS_SCF 1.0e-7
>>       &END OUTER_SCF
>>       SCF_GUESS RANDOM
>> #     SCF_GUESS HISTORY_RESTART
>>     &END SCF
>>     &XC
>>       &XC_FUNCTIONAL PBE
>>       &END XC_FUNCTIONAL
>>     &END XC
>>   &END DFT
>>   &SUBSYS
>>     &CELL
>>       ABC   18.62463  18.62463  18.62463
>>     &END CELL
>>     &COORD
>>  Ge 10.0 10.0 10.0  bond
>>  Te 13.0 10.0 10.0  bond
>>     &END COORD
>>     &COLVAR
>>       &DISTANCE
>>         ATOMS 1 2
>>       &END DISTANCE
>>     &END COLVAR
>>     &KIND Ge
>>       BASIS_SET DZVP-MOLOPT-SR-GTH-q4
>>       POTENTIAL GTH-PBE-q4
>>     &END KIND
>>     &KIND Te
>>       BASIS_SET DZVP-MOLOPT-SR-GTH-q6
>>       POTENTIAL GTH-PBE-q6
>>     &END KIND
>>   &END SUBSYS
>> &END FORCE_EVAL
>> &GLOBAL
>>   PREFERRED_FFT_LIBRARY FFTW
>>   PRINT_LEVEL LOW
>>   PROJECT GeTe.md
>>   RUN_TYPE MD
>> &END GLOBAL
>>
>> &MOTION
>>   &MD
>>     ENSEMBLE LANGEVIN
>>     STEPS    20
>>     TEMPERATURE  1100
>>     TIMESTEP 2.0
>>     &LANGEVIN
>>       GAMMA 4.0E-3
>>       NOISY_GAMMA 3.5E-5
>>     &END LANGEVIN
>>   &END MD
>>   &CONSTRAINT
>>     &COLLECTIVE
>>       MOLNAME  bond
>>       COLVAR 1
>>     &END COLLECTIVE
>>     &COLLECTIVE
>>       MOLNAME  bond
>>       COLVAR 2
>>     &END COLLECTIVE
>>   &END CONSTRAINT
>> &END MOTION
>>
>>>
>>>>
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