[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

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.
>       LIST                   1 2
> 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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