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Topics - DSarkar

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1
Hi,

I am trying to run multiple MD simulations at the same time on multiple nodes of our cluster. Could you please let me know how the license checking takes place when I run the simulation? Is the license checked at the beginning of execution of each python script, or does it check continually at some interval, or at the beginning of each module (such as Geometry Optimization, different Molecular Dynamics modules, etc.)? It would help me define the pbs script accordingly. In case it is checked only once before the start of a python file, do you think it may be possible for me to define some "clones" of the atkpython file and separately set the path to each license file corresponding to the particular node (I have obtained different academic license for each node)?

Regards,

Debarghya

2
General Questions / User Defined Tabulated Potential
« on: May 4, 2016, 05:47 »
Hi,

What is the starting radius of the user defined tabulated potential? Is it 0 by definition?

Regards,

Debarghya

3
General Questions / Non-equilibrium momentum exchange
« on: April 29, 2016, 19:18 »
Hi,

I am trying to simulate thermal transport in VNL using the non-equilibrium momentum exchange formalism, and had a few clarifications regarding that:
1. In the MD Analyzer, the temperature profile that is shown, is that the average temperature at each point between tmin and tmax?
2. How exactly is the heat rate reported at the end of the log file, calculated? Is it also an average heat rate over all the exchange processes in the simulation? Or is it also averaged over all the simulation steps (so that essentially higher the simulation steps, lower the heat rate)?
3. Do you have a suggestion for a "good" heat flux? Or could you suggest a method for determining it based on maybe material parameters?
4. In a paper http://www.tandfonline.com/doi/pdf/10.1080/0026897031000068578, which also uses the same formalism, it is stated that atoms at the interface are loosely bound by weak harmonic springs to avoid dissolution. Can that be done in VNL?
5. Does this simulation consider atomic vibrational energy, or is it only translational energy that is considered?
6. Any system, irrespective of whether it has an interface, would come to the same temperature throughout if allowed sufficient time to relax. So instead of calling temperature profile at equilibrium, I would prefer calling it temperature profile at steady state, where the heat exchange rate and the time of relaxation are consistently chosen. It seems, therefore, that the choice of this combination is very critical. Do you have any suggestion regarding this, or any rule of thumb to follow based on material used, cross-section area, etc.?
7. Do you have any suggestion about the length of the "Hot" and "Cold" regions? I believe this also has a bearing on the resultant heat flux, since a longer length would possibly give a broader distribution of velocities and therefore, higher flux--is that understanding correct? Apart from that, what else needs to be considered for these regions? Once again, could you give a good number of atoms that you think should be included in these regions?
8. Some papers have set the boundary condition as temperature, and have calculated the heat flux. Is there a way in VNL to do so, i.e. have thermostats connected to some of the atoms, and see the evolution?
9. If I am interested in changing the exchange rate over time, which cannot be currently done directly in VNL, is it possible to carry over the results of one momentum exchange simulation to another? I know I can carry over the bulk configuration and velocities, but at this point I am a bit confused if that should be sufficient for the next momentum exchange simulation I would be looking for. Do you think I need to read some other results from the previous simulation and use that for some calculation in the next momentum exchange step?
10. Any other general comments inspired by these questions are highly welcome.

As a note in case it helps, I am currently looking at a Si-Ge-Si system where the temperature is above the melting point of Ge but below that of Si. I highly appreciate your comments. I have greatly benefited from all your previous replies.

Regards,

Debarghya

4
General Questions / ZBL Potential
« on: April 19, 2016, 05:30 »
Hi,

I was trying to reproduce the results of this paper: http://www.tandfonline.com/doi/abs/10.1080/10420150.2013.792818#.VxWj-zArKhc. They have used a combination of Coulomb potential, Buckingham potential, and ZBL potential for the interactions. Referring to the tutorial http://docs.quantumwise.com/tutorials/combining_potentials.html, I have some fair idea of implementing the Coulomb and the Buckingham potentials. However, I have a few questions regarding the ZBL potential.
1. As per the description in http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.tersoffzblpotential.html, and looking through external references, I don't understand what bf and rf signify, and what values to put in for my structure.
2. How to set the outer cut-off radius (referred to as r_cut in the several other potential implementations)?
3. If I set the r_cut for ZBL and r_i for Buckingham, will the range of radii between them be automatically spline interpolated?
4. Any suggestion for the type of Coulomb interaction to use: DSF or SPME?
I greatly appreciate your useful replies.

Regards,

Debarghya

5
Hi,

As described in several tutorials, we can extract the position and velocity of atoms in an ensemble from any time point in a simulation run by opening the "xyz.nc" file using the Movie Tool, and sending the configuration to the required module (builder, script generator, etc.). While this is a very convenient method for many applications, for relatively large system and/or simulation sizes, this method is quite time consuming. So I was wondering if it is possible to do either of the following:
1. Extract the bulk structure using some script at any time step without opening the "xyz.nc" file in the Movie Tool.
2. Open the file in the Movie Tool and run some script to select the bulk structure at, say the time step currently selected there, and send it to one of the modules.
Any suggestion/advice is highly appreciated.

Regards,

Debarghya

6
Hi,

I am trying to simulate the interfacial thermal resistance at Si-Ge interfaces, and was following the tutorial on the Si(100) and Si(110) interface using MD. I have attached a file describing the geometry I am currently looking at. From the NPT stabilization of this and similar other previous simulations, it seems to me that the structure is not fully relaxed. In the NPT simulation, there appears to be large destabilizing force at the beginning, which results in weird situations like a wavy character throughout the Si-Ge-Si structure, premature melting at localized regions, etc. In this simulation I set the maximum number of steps in Geometry Optimization as 100000 (maximum possible in VNL), but it ran for 14 fs, and went onto the NPT step. Could you please help me setup the proper relaxation method for this kind of interface? Is there a suitable tutorial or other resource that you can possibly point me to, so that I can get a better hold on the geometry optimization methods? Thanks a lot, I really appreciate your help.

Regards,

Debarghya


7
General Questions / Resource reqirement
« on: March 25, 2016, 00:06 »
Hi,

Is there a way to estimate the time required to finish a simulation given the computation resources for a certain simulation setup? It would be helpful for me to estimate the time required as I am running on a common queued cluster, so that I can request resources optimally.

Regards,

Debarghya


8
General Questions / Error message for NPT Si-Ge-Si heating
« on: March 24, 2016, 08:29 »
Hi,

I am trying to make a stabilized Si-Ge-Si interface at 1200K. I designed two simulations (one of them is attached because of size constraint in attachments): one where the bulk structure was initialized to 0K, and another where initial velocities were initialized to 1200K (Maxwell-Boltzmann). Both are placed in an NPT Berendsen with high thermal coupling constant 50000 fs for slow heating, and set to run for 1 nm at 1fs step size. Both simulations get prematurely terminated: the first one shows some movie for 60 fs, whereas the second one does not display any movie at all, with an error message. The error message from the log files for both are also attached. Could you please let me know where I am going wrong in my methods?

Regards,

Debarghya

9
General Questions / Boundary conditions
« on: March 23, 2016, 07:28 »
Hi,

How do I know if periodic boundary conditions are applied to my simulation structure? And how would I change the boundary conditions?

Regards,

Debarghya

10
Hi,

I am trying to parallelize an MD simulation with a Trial license on our cluster, and am facing the error message "No access to tty". What should I append in my job submission script that you feel would help alleviate this?

Regards,

Debarghya

11
Hi,

I was wondering if it is possible to parallelize a job on multiple nodes with different Academic licenses installed on each node. If so, how may it be done? Also, my cluster nodes each have 2 processors with 8 cores each. While running the job, if I change the machine settings to Multiprocess, choose No. of processors=2, Enable threading, enable auto-threading, it would take longer than if I run on a single core.  How can I check the actual resources that I used? I appreciate your replies very much.

Regards,

Debarghya

12
General Questions / EMT Calculator has no parameter
« on: March 7, 2016, 01:38 »
I was trying to simulate a Si-Ge interface for some MD modeling. The potential chosen was Tersoff-SiGe-1989. There was a message saying that the EMT calculator has no parameters for Ge. What does this mean? How may that affect my simulation? Is there a way around? I was trying to find the interfacial thermal resistance between Si and Ge, and was following the methodology described in the VNL tutorials for interface between Si(100) and Si(110).

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