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softmaterialslab / nanoconfinement-md

This code allows users to simulate ions confined between material surfaces that are nanometers apart, and extract the associated ionic structure.
Apache License 2.0
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changed to get a concise, effective outlog; suppressed file writing t… #51

Closed jadhao closed 6 years ago

jadhao commented 6 years ago

…hat is not needed in rappture; minimum steps needs to be 20000 to enable proper equilibration

kadupitiya commented 6 years ago

@jadhao : everything looks fine. Did you change the file name "initial_configuration.dat"? So if user ran a simulation with steps less than 10,000, production will not happen. Is that okay. We may want to change the min steps in tool.xml as well.

smarru commented 6 years ago

@jadhao I just built your fork in my workspace https://github.com/jadhao/nanoconfinement-md/, it runs fine but the plots are empty. I will look more closely what changed.

jadhao commented 6 years ago

@kadupitiya yes I did change the file name And yes, we must set 20,000 as the minimum. 10,000 is the default hit eqm for steps < 100,000. This is because system does not reach equilibrium before 10,000 for all the params.

jadhao commented 6 years ago

@smarru 20,000 is the minimum number of time steps; we should not go lower than this. the code was remade to reflect that. so the wrapper may need a change in the min S. then it should work.

jadhao commented 6 years ago

@kadupitiya @smarru please change min steps in wrapper etc. to 20000

kadupitiya commented 6 years ago

@jadhao Okay. I am doing the +/- combined plot. So I will add min step 20000 to tool.xml. Can you merge this so I can pull the latest version?

jadhao commented 6 years ago

verified by team

smarru commented 6 years ago

@jadhao sorry missed that. Changing the minimum to 20,000 worked. + 1 for these changes.