Posts Tagged ‘simulations’

Simulation problems

June 30, 2012

It turned out something had gone wrong with my simulations. They had started, but not finished, even though the computer told me they were finished. Later, I found out the computers had been down last week. This meant I had to redo my simulations. While I was at it, I also improved the code for the simulations and made it write away a few more variables (to do with the equilibrisation of the system). In the end, I spent nearly all of my time working on the code and simulations, as opposed to working on what I planned to work on. Needless to say, I haven’t done what I planned (will do so next week). When things don’t go as planned, that is difficult for me. So the thing with the computers happening, wasn’t too brilliant. On a positive note though, the simulations have been improved so hopefully that will be useful.

Update on university work, problem is solved!

June 12, 2012

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.

Summarising post of the past few months

June 11, 2012

Wow, and again I wait a few months until I post here again! It’s terrible of me. Not that there are a lot of people who read this, to my knowledge (and pretty much all of those learn how I’m doing, elsewhere). So. I’m working on my master thesis and recently it has become clear that we’ll aim for the graduation of May/June 2013. We have also agreed on the work I will do and won’t do. It’s going relatively well I would say. There are still ups and downs, sometimes I run into problems, sometimes they’re easy to fix. I guess it’s all part of research. I’m currently working on the binary system, that is to say, a system with 2/3rds big spheres and 1/3rd tetramers (four spheres attached to each other). Here’s an image of a random, initial configuration.

Binary system initial random configuration

However it turned out that particles get stuck because the volume shrinks too rapidly compared to the particle movements and rotations. The single hard spheres did not get stuck, but these tetramers have a more awkward shape. So there were two options now, and I’m exploring both. First is to let the volume change less rapidly. This does mean that in order to get the same results, I will need to simulate longer. The second option is to let the particles start in the structure that we’re interested in (for the binary system that is the MgCu2 structure) and then see if/when it melts. So that’s what I’m working on at the moment. I will also need to recode the single hard spheres and the sole tetramer system to start in certain structures (fcc). Below an image of what the MgCu2 structure looks like.

A snapshot of the MgCu2 structure

I have more images but I don’t want to crowd this post with too many of them, so more of that later (if I remember XD). My project is going well I would say, so that’s nice.

Other than university, what am I up to? Well, I watch some tv now and then and I play a game now and then. I can’t do either of these things too often. I also read books, read quite a few of those since I last posted here. I should write some reviews or something!

I’ve played a little bit of Mass Effect 3 since I last posted here in February, I’ve played some Defender’s Quest and some Magical Diary. So not a lot really compared to the time frame, but that’s okay. Those last two I’ve only played in the past few weeks (Magical Diary has only been out for a bit and I didn’t know Defender’s Quest much before then) since I bought them, but Mass Effect 3 I’ve had since around launch day. All three of them, so far, are great games and I thoroughly enjoy my time with them.

Book wise, I have signed up for GoodReads, Shelfari and BookLikes. Maybe some day later I’ll post links to my profile(s).

Well, that’s enough of a summarising post I’d say. It’s probably best to talk about specific things in specific posts, I think, otherwise things get a bit cluttered.

How my master research is going

February 24, 2012

And again some months pass before I look at this blog again. This time my dad making a made me think back of mine. Since quite a bit of stuff happened today, and in fact over the past few months, I thought it was about time I wrote (another) update.

I’m still working on my master project. Things are going with ups and downs, now and then there is lots of progress in a short amount of time, at other times there are just problems that persist for a few weeks until I’ve figured out solutions (or sometimes, what exactly the problem is). I still don’t enjoy programming, though I do think I enjoy it a lot more than when I first started! My programming on tetramers and binary systems (single bigger spheres mixed with tetramers) is complete! Well aside from possible errors obviously, because you never know (I keep finding them!). The latest results finally look good though. I’m currently gathering data and making graphs for the equation of state for single hard spheres and tetramers (that’s two seperate systems). However the program I was using for it didn’t want to display the axis properly (certain points are meant to be closer together than others, yet the program keeps displaying them all within an equal distance from each other). I’m in the process of finding a different program that works and learning how to use it. I made the first steps today but I ran out of time since I had to go to a colloquiem. The colloquiem was interesting, it was about colloids and electronic ink, electrophoresis etc. It was tiring to stay at uni for a longer time but the subject was quite interesting so I guess you could say it was worth it.

On another note, there are more students in our room which upsets me a bit as it’s no longer as quiet and calm (aside from the heating, the copy machine, footsteps and typing sounds) as things used to be. It could be worse though, so far nobody has had long chats about unrelated things. This morning, someone (I assume he’s a student though he doesn’t look really young, but I could be mistaken) needed to work on my desk so I had to be relocated to a different desk. As I’m not so good in dealing with unexpected situations, it took me a while to get used to this new desk. I don’t know how long he’ll be working there for but I assume he’ll be there for the coming weeks at least.

I’m starting to be able to follow the work discussions better and better. Obviously there are theories that I haven’t heard of before but I can generally understand what people are trying to research and it’s getting more interesting than at first.

Another thing of my work is that sometimes there is more work to do than other times. If I’m stuck because of an error and I can’t find the error, at some point I stop looking and take a break. I find that difficult as I feel guilty sometimes when I work different hours than I should.

I’m not totally enjoying my project all the time, sometimes yes, but other times no. I tend to get stressed, especially on fridays (or thursday nights etc). But now that I think about it I do think I enjoy it more than at first. Perhaps that’s also because things are going well atm.

On a completely unrelated note: I am playing more video games! Lately I’ve been playing some hours of Skyrim, which so far is an awesome game. I do have most of the sounds muted, this helps me a lot.

Well it’s now time to cook so with that I end my post here, hopefully I’ll make another one soon!