[CP2K-user] [CP2K:17135] Re: Comparison between set initial temperature and temperature calculated from velocities
松尾拓郎
22w1045k at shinshu-u.ac.jp
Mon Jun 13 01:41:34 UTC 2022
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.akira 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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