[CP2K-user] [CP2K:18354] Guided AIMD reaction, CONSTRAINT, RESTRAINT, METADYNAMICS

[Dobromir A Kalchevski]

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

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/24dd6704-1c10-4a20-a64d-9fb1ba3f9812n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230119/d851859b/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot from 2023-01-19 13-47-42.png
Type: image/png
Size: 28476 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230119/d851859b/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot from 2023-01-19 13-29-49.png
Type: image/png
Size: 62995 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230119/d851859b/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot from 2023-01-19 15-27-03.png
Type: image/png
Size: 127177 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230119/d851859b/attachment-0005.png>