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

[Travis]

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!
>>>
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>
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