[CP2K-user] H2 single molecule AIMD

Lucas Lodeiro eluni... at gmail.com
Sun Aug 9 20:29:20 UTC 2020

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:
                                 Number of Intramolecular constraints:
                                 Number of Intermolecular constraints:
                                  Invariants(translation + rotations):
                                                   Degrees of freedom:

 Restraints Information
                                  Number of Intramolecular restraints:
                                  Number of Intermolecular restraints:
 ************************** Velocities initialization
 Initial Temperature
 COM velocity:                       NaN                 NaN
 COM position:            5.669178398657      5.669178398657
 Angular velocity:                   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?

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