Investigate the correct algorithms for the simulation

TechnionYP5779 / SimuMole

Computer simulation method that displays the physical movements of atoms and molecules.

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Investigate the correct algorithms for the simulation #8

Closed HadadIdan closed 5 years ago

HadadIdan commented 5 years ago

(Requires contact with Client)

ghost commented 5 years ago

according to this diagram , I think we can find every thing we need in https://udel.edu/~arthij/MD.pdf

ghost commented 5 years ago

https://embnet.vital-it.ch/MD_tutorial/pages/MD.Part1.html

shorter

HadadIdan commented 5 years ago

The issue was to investigate it, and to write a wiki about it, summarizing it. Here is what you did: This is were the picture is from: http://lmgtfy.com/?t=i&q=algorithm+for+molecular+dynamics This is where your second source is from: http://www.letmegooglethat.com/?q=algorithm+for+molecular+dynamics Number 3 from the top in the search (in my browser) The only thing you did was to give us 2 sources. It doesn't help us because someone will have to read and summarize them (if they are even relevant), which was your original task. :/

ghost commented 5 years ago

there you can find the formulas to calculate the velocity,tempature,location and etc as mention in the diagram

OrYasso commented 5 years ago

Hey, I think what Idan means is: Yeah, we can find these functions there (we need to verify that all necessary functions are there), but we want them in one place in our wiki, where we can see them without the need of scrolling an article to see them and reading the info there to know which one is referencing to which algorithm.

EyalFaygen commented 5 years ago

@elizabethyeshaayahu320 thats awesome but the point of the research is that you will tell us whats the right algorithm we need based on the data you extracted from the file the client gave us. the proper way to close this issue is to write a wiki page we can all read that should contain:

specify what algorithm we should use (a closed algorithm that we can start implement, i.e in shouldn't contain words like "some function of" )
state why you choose this algorithm so we can properly present it to the client for approval
what resources you used to determine what is the correct algorithm

all of this needs to be done before we can start implementing the algorithm and start working on the simulation

ghost commented 5 years ago

Two question to ask our client tomorrow:

does she knows the formula for calculating the potential energy?
is it OK to assume zero velocity in the beginning?

OrYasso commented 5 years ago

@elizabethyeshaayahu320 Hey, add the questions you want to ask in the wiki here.

ghost commented 5 years ago

did it . thanks

HadadIdan commented 5 years ago

Closed since we are going in a new direction as decided in this group meeting