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Offline Jyotirmoy Deb

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Phonon DOS
« on: August 26, 2020, 19:16 »
Could you please tell me how to  get the projected phonondos using quantumATK?  Actually I have a 2D carbon material in which three different coordination of Carbon atom is present and I want to investigate the contribution in the phonon dos for each type of carbon atom.

Thanking you in advance.
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Offline Troels-Markussen

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Re: Phonon DOS
« Reply #1 on: August 27, 2020, 10:42 »
Hi,
We currently don't have an analysis object for calculating projected phonon density of states. However, I have previously shared a script that you can hopefully use. See the attachment here:
https://forum.quantumatk.com/index.php?topic=6427.msg27005#new

Regards,
Troels
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Offline Jyotirmoy Deb

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Thermodynamic stability
« Reply #2 on: August 28, 2020, 22:05 »
Thank you very much sir for your kind reply.

I want to check thermodynamic stability of a 2D material at 300 K and 1000 K. I have run the simulation and obtained the required plot. But I am facing one problem, though I am perfoming the simulation using NVTNoseHoover  thermostat but in the temperature vs time step plot it is observed that huge fluctuation in temperature is there w.r.t reserviour temperature. Could you please tell me how to overcome this? I have attached the input for your reference.
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Offline Julian Schneider

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Re: Phonon DOS
« Reply #3 on: September 2, 2020, 10:05 »
Hi,

these fluctuations are not uncommon for Nose-Hoover-like thermostats, especially for small systems like yours. One could try to increase the thermostat timescale or the Nose-Hoover chain length (in script), but this would probably only decrease the fluctuations a bit and with DFT-MD it is probably not so easy to run a few test simulations.

If it is only about the stability of the system at the given temperature, then you could use NVT-Berendsen instead. This should give a much more constant temperature than Nose-Hoover.
Berendsen is a bit more approximate in how exactly the canonical ensemble is reproduced, but just for qualitatively checking the thermal stability it should be ok.

Best,
Julian
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Offline Jyotirmoy Deb

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Re: Phonon DOS
« Reply #4 on: September 2, 2020, 10:52 »
Thank you sir for your reply.
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Offline Jyotirmoy Deb

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MD Simulation
« Reply #5 on: September 4, 2020, 18:40 »
I was running a AIMD simulation using quantumATK for 10000 steps with a time step of 1fs using NooseHover thermostat. But unfortunately the calculation was terminated after 7000 steps. Kindly suggest me how to restart the calculation from there.   
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Offline Jyotirmoy Deb

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Re: Phonon DOS
« Reply #6 on: September 4, 2020, 18:52 »
Sir As per your suggestion I have modified the script for my system and get the plot for phonon dos. Kindly noote that my system comsists of 26 C atoms with different coordination (2, 3 and 4) and I want to get the phonon dos for these three different coordination. Kindly suggest me how to modify the script. I have attached input and output for your reference.  In my system the atom index 4, 5 is for 4 cordinated C atom,  atom index 0, 1, 2, 3 is for 3 cordinated C atom, atom index 6-25 is for 2 cordinated C atom.
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Offline Troels-Markussen

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Re: Phonon DOS
« Reply #7 on: September 11, 2020, 12:01 »
Hi,

I don't understand what you need more. Your script seems right, plotting the differently coordinated C atoms in different colors, and there are no errors in the log. So what excactly is the problem?

Regards,
Troels
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