[CP2K-user] [CP2K:13750] Re: H2 single molecule AIMD
Travis
polla... at gmail.com
Mon Aug 10 17:34:26 UTC 2020
Hi,
Have you tried setting a very small ANGVEL_TOL?
-T
On Monday, August 10, 2020 at 12:59:57 PM UTC-4 Lucas Lodeiro wrote:
> Hi Marcella,
> I try the MD with periodic and non periodic conditions. When ANGVEL_ZERO
> was applied for a non periodic cell, the simulation starts with zero
> angular velocity, but the numerical inaccuracies pumps some angular
> velocity at the first steps... and the molecule starts rotating.
> As you mention, for a diatomic molecule it is not possible to apply any
> constraint... in all cases it will be not physical.
> Is there a way to fix the rotational movement?
>
> El lun., 10 ago. 2020 a las 6:03, Marcella Iannuzzi (<ma... at gmail.com>)
> escribió:
>
>> 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!
>>>
>> --
>> 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 cp... at googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/aed754ac-07de-40c2-9114-4370f7af7b16n%40googlegroups.com
>> <https://groups.google.com/d/msgid/cp2k/aed754ac-07de-40c2-9114-4370f7af7b16n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200810/a0d316bc/attachment.htm>
More information about the CP2K-user
mailing list