[CP2K-user] [CP2K:13750] Re: H2 single molecule AIMD

Lucas Lodeiro eluni... at gmail.com
Mon Aug 10 17:02:24 UTC 2020

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 (<marci... at gmail.com>)

> 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.
>>       COMPONENTS_TO_FIX      YZ
>>       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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