Update on university work, problem is solved!

University work is going well, this morning I solved a problem that had come up yesterday when I tried to put the particles in the structure I wanted. It looks like it’s solved, anyhow! It always makes me feel good when I’ve solved a problem (and really frustrated when I can’t seem to solve it!). The problem was that upon moving, the particles overlapped each other, but only certain particles did this. It turns out, because of the way the periodic boundaries work, that some spheres coded in where actually the exact same sphere, but drawn twice. Stay with me for a moment. The particles are all in a simulation box. Periodic boundaries mean that all around this box, there are exact copies of this box (this is called minimum image convention). Periodic boundaries means that when a particle exits the box in one direction, it enters the box again from the opposite reaction. So the spheres I had at the corners of the box, actually were the same ones but the program draws them just like the coordinates I gave it. The solution was to remove certain ‘duplicate’ spheres, it took me some time to figure out which one’s which though and by trial and error but mostly logical thinking, I managed to remove the right ones (although there are various ways it could be done, it doesn’t matter which of the duplicate ones I remove, as long as there’s one of each kind). I don’t know if it makes sense, anyhow I’m glad I solved the problem!

Now I’ll have to prepare files for simulations and run several simulations (at different pressures) to find out what happens to the structure depending on the pressure (and other variables, but they stay constant). Aside from that, there is my thesis to continue writing on. There are several more parts that my professor wants more content on (and I think she is right), so I’ll have to read some more books and articles, among other things. Most of the parts to be added have to do with the theory of molecular simulations. Of course the part with the results of my simulations is and will be a work in progress until all simulations have completed and I’ve interpreted their data.

Pretty soon now some more results from the simulations with the volume changing slower, will be there (I mean the simulations will be done). I’m not sure what they’ll be, it could be that the volume is still changing too rapidly (I believe I made the chance of it to occur 25% once the volume move has been chosen, instead of 100%. The chance to randomly choose the volume move is equal to the amount of units in the box plus one I believe. With units I mean either big spheres or a tetramer (a tetramer consists of four smaller particles and is considered one unit).

Hopefully I’ll have some other posts up in a while on a few games and book stuff! I do feel like writing about certain things, anyhow.

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