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Messages - DSarkar

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16
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

17
Thank you.

18
General Questions and Answers / 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

19
Okay thanks for the clarification.

20
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

21
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

22
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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