[CP2K-user] [CP2K:17160] Re: Comparison between set initial temperature and temperature calculated from velocities

[松尾拓郎]

Hi Marcella,

Thank you for your reply.

I understand your intention of dividing by the correct number of DoF.

I found that when I calculated with (T_Si_1 + T_Si_2 + ... +T_Si_32 + T_O_1
+ T_O_2 + ... + T_O_64 + T_C_1 + T_C_2 + ... T_C_4)/100 times the ratio of
DoF (300/297), I was able to get the same temperature as the cp2k output.

I didn't consider the translational DoF of the cell which is 3.
It became clear that the number 300 was DoF including the translational DoF
of the cell and the number 297 = 300 - 3.

Thank you very much for your help!

Kind regards
Matsuo

2022年6月13日(月) 16:05 Marcella Iannuzzi <marci.akira at gmail.com>:

>
> No need to consider any cp2k section
> I suppose that to calculate the temperature you summed up the kinetic
> energies  and then divided by the number of degrees of freedom.
> The question is whether you divided by the correct number of DoF, i.e.,
> 297 according to the output you sent.
> Regards
> Marcella
>
>
> On Monday, June 13, 2022 at 3:41:45 AM UTC+2 mto wrote:
>
>> Marcella,
>>
>> Are you referring to the cp2k section ROTATIONAL_INFO
>> <https://manual.cp2k.org/cp2k-8_1-branch/CP2K_INPUT/MOTION/MD/PRINT/ROTATIONAL_INFO.html>
>>  ?
>> If so, I was afraid I didn't consider the section.
>>
>> Here is my simulation output on calculation of degrees of freedom.
>>
>>  DOF| Calculation of degrees of freedom
>>  DOF| Number of atoms
>>    100
>>  DOF| Number of intramolecular constraints                           0
>>  DOF| Number of intermolecular constraints                           0
>>  DOF| Invariants (translations + rotations)
>>  3
>>  DOF| Degrees of freedom
>>    297
>>
>> The number of the translational and rotational degrees of freedom seem to
>> be  3×(100-1) = 297, 0×(100-0) = 0.
>>
>> I calculated the temperature considering the number of translational
>> degrees of freedom (3) '1/2*m*v^2 = 3/2*kb*T'.
>> However I didn't consider the number of rotational degrees of freedom
>> because it seemed to be 0.
>>
>> Kind regards
>> Matsuo
>>
>> 2022年6月11日(土) 16:21 Marcella Iannuzzi <marci... at gmail.com>:
>>
>>> What about the translational and rotational degrees of freedom?
>>> Kind regards
>>> Marcella
>>>
>>> On Saturday, June 11, 2022 at 4:59:33 AM UTC+2 mto wrote:
>>>
>>>> Hi Marcella,
>>>>
>>>> Thank you for your response.
>>>>
>>>> Yes, I believe I have.
>>>> I calculated the temperature of the system by using the following
>>>> method.
>>>>
>>>>    1. Temperatures of each atom at 0th step were calculated with
>>>>    1/2*m*v^2 = 3/2*kb*T, here the value of 'm' is mass in atomic mass units
>>>>    (amu).
>>>>    mass: 28.0855 (Si), 15.9994 (O), 12.0107 (C)
>>>>    amu = 1.660538782E-27 kg
>>>>    mSi = amu*28.0855 kg, mO = amu*15.9994 kg, mC = amu*12.0107 kg
>>>>    v^2 = (vx^2 + vy^2 + vz^2)*10^10 (m/s)^2
>>>>    kb = 1.3806504E-23 m^2*kg*s^-2*K^-1
>>>>    2. 0th step temperature (T_all) is calculated
>>>>    I have 32 Si, 64 O and 4 C, so I calculated the temperature of each
>>>>    individual atom and determined the average T
>>>>    T_Si_k = mSi*v^2/(3*kb)
>>>>    T_O_k =  mO*v^2/(3*kb)
>>>>    T_C_k =  mC*v^2/(3*kb) (k represents the ID of the atom.)
>>>>    T_all = (T_Si_1 + T_Si_2 + ... +T_Si_32 + T_O_1 + T_O_2 + ... +
>>>>    T_O_64 + T_C_1 + T_C_2 + ... T_C_4) / (32 + 64 + 4)
>>>>
>>>> Is this what you were referring to when you suggested looking at the
>>>> degrees of freedom?
>>>>
>>>> Regards
>>>> Matsuo
>>>>
>>>> 2022年6月10日(金) 1:04 Marcella Iannuzzi <marci... at gmail.com>:
>>>>
>>>>>
>>>>> Hi
>>>>>
>>>>> Are you sure that you considered the correct number of degrees of
>>>>> freedom?
>>>>> Regards
>>>>> Marcella
>>>>>
>>>>>
>>>>> On Thursday, June 9, 2022 at 6:09:06 AM UTC+2 mto wrote:
>>>>>
>>>>>> Dear cp2k users,
>>>>>>
>>>>>> I wanted to conduct a comparison and performed ab initio molecular
>>>>>> dynamics (MD) simulations with an imposed initial temperature of 300 K. I
>>>>>> then calculated the temperature from the velocities at the 0th step, but
>>>>>> this value was 297K, which does not match with the temperature I set. I
>>>>>> calculated the latter temperature (297K) from '0step_velocities.xyz'
>>>>>> which is attached on this message. Both of them must be the same because
>>>>>> the 0th step velocities are determined by the initial temperature. (The
>>>>>> equation I used: 1/2m*v^2 = 3/2kb*T )
>>>>>> Does anyone know why there is a difference in temperatures?
>>>>>>
>>>>>> Thank you in advance,
>>>>>> Matsuo
>>>>>>
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