Some doubts about one-dimensional concentration distribution calculation

[BOWEN AI]

Dear Professor: 

    I used the 1D concentration distribution calculation you proposed in my simulation, but I encountered some confusion. My model is shown in the figure, the upper part is a liquid area, the middle part is a nanopore area, and the lower part is another liquid area.

In your article, you calculated the one-dimensional concentration distribution by dividing the area. However, in this model, the volume of the middle hole part and the liquid area is inconsistent, and a volume step phenomenon will occur. In this case, is the one-dimensional concentration distribution you proposed still applicable? I would be very grateful if you could answer my doubts in your busy schedule.

[Y. Wang]

Hi Bowen,

Thank you for trying the code.

Did you mean you want to calculate density distribution along the pore? If so, the code "almost" can do that in this way: you can define a cubic pillar as the atom selection area like shown in the picture, then calculate the density distribution along the cubic pillar, that could be used to represent the density distribution along the pore. But one thing that may affect the accuracy is the radical distribution in the pore, if the density distribution is nearly homogeneous in the pore, the cubic pillar method is accurate; otherwise it may not be that accurate. You can check the radical distribution by using the code, i.e., do a 2D density distribution on a slice of the pore.

Hope that helps you.

Best,

Yuxiang

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[BOWEN AI]

Thanks, Professor:

     I have also written a program by myself based on your idea. If I only count part of the hole area, the concentration distribution data obtained will fluctuate greatly, so I will try your code. Thank you very much for your reply. I wish you all the best. 

     I also attach the code I wrote myself.