[CP2K-user] H2 single molecule AIMD
Marcella Iannuzzi
marci... at gmail.com
Mon Aug 10 10:03:05 UTC 2020
The translational and rotational degrees of freedom are subtracted, hence
fixing 4 more degrees of freedom by constraints you end up with a negative
number of DoF, which is obviously not physical.
Are you using PBC? The ANGVEL_ZERO keyword is ignored with PBC
Regards
Marcella
On Sunday, August 9, 2020 at 10:26:49 PM UTC+2 Lucas Lodeiro wrote:
> Hi all!
>
> I am exploring single molecule AIMD (H2 in this case) for different
> purposes. The main problem that I face is temperature/rotational modes. I
> try to run a AIMD using NVE and NVT ensembles, but there are some problems.
> For an NVE ensemble, the system starts rotating with a conserved angular
> moment, even if I set equal to zero the total angular moment... This disrupt
> the linear movement of H2 bond oscillation. The rotation couples with the
> bond and generates a fake two frequency oscillator. If, after the AIMD, I
> correct the trajectory to a zero total angular moment for all frames
> (simple for diatomic homonuclear molecule, but not so easy for polyatomic
> molecules), the oscillator recovers the single frequency motion.
> For an NVT ensemble, the thermalization is so hard for few atoms... and
> the system is very bad behaved.
>
> Now I try an NVE ensemble with constrain MD, fixing the Y and Z position
> of both atoms, and put the bond along the X direction.
>
> &CONSTRAINT
> &FIXED_ATOMS
> COMPONENTS_TO_FIX YZ
> LIST 1 2
> &END FIXED_ATOMS
> &END CONSTRAINT
>
> I think with it, I force the MD to evolve only over the X axis... but the
> initial step gives me a NaN temperature and kinetic energy, no matter
> what initial temperature I use. I attach both files.
>
> The output file prints:
> Calculation of degrees of freedom
> Number of atoms:
> 2
> Number of Intramolecular constraints:
> 4
> Number of Intermolecular constraints:
> 0
> Invariants(translation + rotations):
> 5
> Degrees of freedom:
> -3
>
>
> Restraints Information
> Number of Intramolecular restraints:
> 0
> Number of Intermolecular restraints:
> 0
> ************************** Velocities initialization
> **************************
> Initial Temperature
> NaN K
> COM velocity: NaN NaN
> NaN
> COM position: 5.669178398657 5.669178398657
> 5.669178398657
> Angular velocity: NaN NaN
> NaN
>
> *******************************************************************************
>
> It seems, the degrees of freedom is: 3N - constrains - invariants...
> Is there a way to force the MD only along one axis to avoid rotation?
>
> Regards!
>
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