[CP2K-user] [CP2K:18357] Re: Guided AIMD reaction, CONSTRAINT, RESTRAINT, METADYNAMICS

[Dobromir A Kalchevski]

Dear Marcella Iannuzzi,

Thank you for your reply.

Best Regards,
Dobromir

On Friday, January 20, 2023 at 2:21:37 PM UTC+2 Marcella Iannuzzi wrote:

> Dear Dobromir
>
> The TARGET is the initial value that is imposed to the variable, as it is 
> defined. 
> The TARGET_GROWTH is the rate of change of that target value, which in the 
> example you posted is ridiculously high:
>
> TARGET_GROWTH {Real}
> *Specifies the growth speed of the target value of the constrained 
> collective variable.*
>
> The constraint with the value determined by the growth rate will be 
> imposed, no matter which are the other forces in place.
> At least until the calculation does not converge anymore and everything 
> explodes.
>
> Nothing of this is a sampling in the NVT ensemble, anyway.
>
> If the goal is to sample the final state after the reaction has occurred, 
> just start a simulation from the configuration of the reacted molecule.
> If the goal is to find the reaction mechanism, there is no way out of 
> studying the free energy surface or, in simpler cases, the potential energy 
> surface. 
> An efficient way to find  the potential minimal energy pathway in  cases 
> like yours is in general the nudged elastic band approach.
>
> Regards
> Marcella
>
>
> On Thursday, January 19, 2023 at 9:42:15 PM UTC+1 Dobromir A Kalchevski 
> wrote:
>
>> Hello everyone!
>>
>> I want to make a molecule occasionally approach a surface and react with 
>> it in a NVT ensemble production run. I don't want it fixed in predetermined 
>> coordinates and I don't want it to fly away or to wait for too long of a 
>> trajectory.
>> For now I don't want to study the reaction's thermodynamics. 
>> Experimentally the reaction occurs.
>>
>> I tried the following approaches without success:
>>
>> I defined a COLVAR for the distance between one surface atom (Si) and the 
>> center atom (C) of the gas phase reagent molecule (methane)
>>
>>         &COLVAR
>>             &DISTANCE
>>                 AXIS XYZ                !DEF XYZ, ANY COMBINATION
>>                 ATOMS 50 81
>>             &END DISTANCE
>>         &END COLVAR
>>
>> and then I defined a CONSTRAINT
>>
>>     &CONSTRAINT
>>         &COLLECTIVE
>>             COLVAR 2
>>             INTERMOLECULAR
>>             TARGET [angstrom] 1.87
>>             TARGET_GROWTH [angstrom*fs^-1] 0.25
>>             TARGET_LIMIT [angstrom] 5.0
>>         &END COLLECTIVE
>>     &END CONSTRAINT
>>
>> The result is that both atoms get closer too quickly and the system gets 
>> an unphysical geometry - the Si kind of moves too far away from it's 
>> lattice and the C abandons its hydrogens. The remperature rises too quickly 
>> to unbelievable degrees, the calculation slows down and eventually the 
>> program dies.
>> My cell is defined just fine, with enough space for the gas reagent to 
>> move around. I use a XYZ PBC with space left in one dimension so it 
>> effectively becomes 2D. In that space is the reacting molecule.
>> I tried playing with TARGET_GROWTH with many values from 0.01 to 5.0 and 
>> the result is always the same.
>> In this group I read that the moment TARGET is set the atoms are also set 
>> at that distance, so I tried switching TARGET and TARGET_LIMIT, but even 
>> then the result is the same - wrong geometry, they get too close too 
>> quickly even with very low TARGET_GROWTH, too high temperature - program 
>> dies.
>> - Is this a bug, because it makes no sense as expected behavior ?
>>
>> I also tried using a RESTRAINT:
>>
>>     &CONSTRAINT
>>         &COLLECTIVE
>>             COLVAR 2
>>             INTERMOLECULAR
>>             TARGET [angstrom] 3.0
>>             &RESTRAINT
>>                 K [kcalmol] 1.0
>>             &END RESTRAINT
>>         &END COLLECTIVE
>>     &END CONSTRAINT
>>
>> with the COLVAR being a plane between 3 surface atoms:
>>
>>         &COLVAR
>>             &DISTANCE_POINT_PLANE
>>                 &POINT
>>                     TYPE GEO_CENTER
>>                     ATOMS 8
>>                 &END POINT
>>                 &POINT
>>                     TYPE GEO_CENTER
>>                     ATOMS 21
>>                 &END POINT
>>                 &POINT
>>                     TYPE GEO_CENTER
>>                     ATOMS 28
>>                 &END POINT
>>                 &POINT
>>                     TYPE GEO_CENTER
>>                     ATOMS 81
>>                 &END POINT
>>                 ATOMS_PLANE 1 2 3
>>                 ATOM_POINT 4
>>             &END DISTANCE_POINT_PLANE
>>         &END COLVAR
>>
>> and the gas phase reagent does not stop at the TARGET distance, instead 
>> it gets inserted into the Si lattice, pushing Si atoms away, inserting both 
>> C and H from the methane and one of the hydrogens flied far away. 
>> Temperature goes anomalously high, program slows down, dies. At least it 
>> took some time and steps to get to the wrong point.
>> - Why didn't the molecule stop at the surface, while experiencing the 
>> forces of the lattice atoms ?
>> - Why did it do beyond the TARGET distance ?
>> - Is this a bug ?
>>
>> Can I use metadynamics in any way to push the molecule towards the 
>> surface for a reaction to occur ? Once again, I'm not interested in 
>> studying the FES or the rest of the thermodynamics.
>>
>> I just need a way to get the gas phase reagent to occasionally get close 
>> enough for a reaction.
>>
>> I think the answers to those question can be very useful for many.
>>
>> I attach some pictures of the anomalous results. The first two are from 
>> the CONSTRAINT, the 3rd is from the RESTRAINT.
>>
>> Best Regards,
>> Dobromir
>>
>

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