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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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exact value of bin_width #146

Closed nasimanousheh closed 4 years ago

nasimanousheh commented 4 years ago

@kadupitiya and @jadhao NanoconfinementMd.cpp is updated. The correct value of bin_width is defined to calculate screening factor.

jadhao commented 4 years ago

@nasimanousheh does this affect calculation of ion density profile? Any effects should be noted in readme as instructions to choose proper parameters to recover known results.

nasimanousheh commented 4 years ago

@nasimanousheh does this affect calculation of ion density profile? Any effects should be noted in readme as instructions to choose proper parameters to recover known results.

@jadhao: it does not effect the density profiles. Creating "screen factor" profile happens after creating ion density.

In fact, the value of bin_with that we choose in input to define the density profiles (and screening factor) is not the exact value in our calculation. In our calculation, number_bins = lz/bin_width and because "number_bins" is integer, we should adjust the bin_width value according to number_bin to have a symmetry profile. So: bin_width = lz/number_bins;

I will explain and update "README.md" and update the examples (including screen factor profile) very soon.

jadhao commented 4 years ago

@nasimanousheh sounds good. approving