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Re: [lammps-users] Issues with CNT Thermal Conductivity Calculations
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Re: [lammps-users] Issues with CNT Thermal Conductivity Calculations


From: Santosh Mogurampelly <vedhava@...24...>
Date: Wed, 6 Sep 2017 16:41:25 -0400

What do yuo exactly mean by postprocessing J0Jt.dat? Apart from adding x,y,z components found in columns 4,5,6, you are not supposed to postprocess J0Jt.dat. That file already contains processed HCACF. Add columns 4,5,6 and plot against column 2. column 2 is the TimeDelta and therefore if you have used the example I shared, the x-axis maximum limit is 40000*5*0.0002 = 40 ps but your figure indicates something suspicious. If you are not sure about what matters most in the J0Jt.dat, try using 'overwrite' in the ave/correlate fix.

Santosh.

On Wed, Sep 6, 2017 at 4:23 PM, Daksha, Chaitanya Mrityunjay <daksha@...2437...> wrote:

Dr. Mogurampelly,


Thank you for your response. I have tried implementing a longer correlation length (I used your correlation length value of 40,000). Now, my HCACF is decaying to zero; however, I am receiving spikes in the data cyclically, as shown below:




Do you know why this may be the case? Is there a problem in how I am post-processing the J0Jt.dat file? I am merely adding the values from column 4,5,6 for each timestep, then plotting them over time. Please let me know if there is something wrong in my method.


Thank you for your time,

Chad Daksha


From: Santosh Mogurampelly <vedhava@...24...>
Sent: Thursday, August 31, 2017 2:05:52 AM

To: Daksha, Chaitanya Mrityunjay
Cc: lammps-users@...396...sourceforge.net
Subject: Re: [lammps-users] Issues with CNT Thermal Conductivity Calculations
 

On Wed, Aug 30, 2017 at 4:26 PM, Daksha, Chaitanya Mrityunjay <daksha@...2437...> wrote:

Thank you for your response. If you don't mind, I have a few questions:


Would it be possible for you to provide any reference(s) for this subtraction? The sources I've looked through don't apply this subtraction, at least to the best of my knowledge. I have attached them for viewing purpose. But, please correct me if I am wrong.


Subtracting average quantity while calculating time correlation functions is a general requirement, not specific to HCACF, but may not make any difference in many cases. Specific to HCACF, you may want to see the definitions in Eq. 2 and 3 of https://journals.aps.org/prb/pdf/10.1103/PhysRevB.43.6573. However, when I tested on a different system using my code, I found no difference with and without subtracting the average energy. So lammps code must give you the same answer without the need of subtracting the average energy.

My suggestion in the previous reply was in fact based on an apparently wrong data you provided, in which the HCACF fluctuates around non-zero value even at long time. I suspect you wrongly interpreted J0Jt.dat output.

With sufficiently long enough correlation length of few picoseconds (attached input), I got the following HCACF with your input file. 

Regarding your other questions, (1) your HCACF was not decaying to zero because you possibly used a short correlation length of 0.0002*100*10 = 0.2 ps (despite generating a nanosecond long trj); (2) you can see that the attached HCACF decays to zero in about 2 ps and as a general rule of thumb, you must need at least 10 such correlations long trj to get a decent estimate of thermal conductivity.


Inline image 1


Also, if I wanted to implement the subtraction, could you suggest ways it may be possible in my script? I do not think it is possible to implement the subtraction prior to the 'compute flux' command, since it requires arguments that are also computes. Therefore, I would be unable to create variables for the new potential and kinetic energies, post subtraction.


Thank you once again,

Chad Daksha


From: Santosh Mogurampelly <vedhava@...24...>
Sent: Tuesday, August 29, 2017 4:39:08 PM
To: Daksha, Chaitanya Mrityunjay
Cc: lammps-users@...655....net
Subject: Re: [lammps-users] Issues with CNT Thermal Conductivity Calculations
 
You should subtract the average of total energy from particle's total energy for the HCACF to decay to zero.


On Tue, Aug 29, 2017 at 3:06 PM, Daksha, Chaitanya Mrityunjay <daksha@...2437...> wrote:

Dear LAMMPS Users,

 

I am trying to calculate the thermal conductivity of a (10,10) CNT that is 5 nm in length using the Green-Kubo formalism.  I modified the liquid Argon LAMMPS thermal conductivity example for CNT.  First, I equilibrated the CNT structure at 300K, and then I ran the simulation to get the heat flux, heat current auto correlation function (HCACF) and thermal conductivity. To plot the HCACF, I averaged columns 4, 5, and 6 in the ‘J0Jt.dat’ file for every 1000 timesteps (which is my dump interval). 

 

 

Currently I am having two problems -

  1. The HCACF does not decay to zero. I have tried running the simulation for up to 1200 ps, but the HCACF still did not decay to zero. 
  2. The thermal conductivity value I attain differs based on the correlation length parameter I use in the ‘fix ave/correlate’ command.  Should the conductivity be independent of correlation length? If not, then how should I determine the appropriate correlation length?

 

I checked the LAMMPS email archive, but I was not able to find anything specific to my issues. Attached is the LAMMPS script, as well as other input data files. There is also a graph of the HCACF over time attached.

 

I would appreciate any insights as to why the HCACF does not decay to zero. 

 

 

Thank you,

 

Chad Daksha

 



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--
********************************************************************************************************
Be Cool Be Happy

Post Doctoral Fellow; Office: SERC, 701C; +1-215-204-4221
Prof. Michael L. Klein group
Institute for Computational Molecular Science
Temple University
1925 N. 12th St
Philadelphia, PA 19122, USA
https://scholar.google.com/citations?user=UkqEItoAAAAJ&hl=en
*******************************************************************************************************



--
********************************************************************************************************
Be Cool Be Happy

Post Doctoral Fellow; Office: SERC, 701C; +1-215-204-4221
Prof. Michael L. Klein group
Institute for Computational Molecular Science
Temple University
1925 N. 12th St
Philadelphia, PA 19122, USA
https://scholar.google.com/citations?user=UkqEItoAAAAJ&hl=en
*******************************************************************************************************