Necromancing Narcoleptics

Names I have come up with for a band (if I ever get around to forming one):

Box of Donuts
Necromancing Narcoleptics
Brain Dead Chemists
Scientific Syphilis

For some reason I can't get anyone else to go along with any of them. The first is still my favorite (update: after watching the documentary on Netflix about killer whales in captivity, I no longer think it's funny to joke about dead baby whales, so if someone wants they can use the name, just know I will in no way support said band).

Have you ever wondered why Japan is do awesome? If not, you should have been pondering this question, and I will now pause for a moment to let you ponder it in solemn silence....if that moment wasn't long enough then pause again until you've had enough time (maybe watch a baseball game) and then come back for the answer. Part of the reason is that their dogs don't do their business like most dogs, no, their dogs leave ice cream treats of delight and joy.

Yes that is real and totally awesome!

To my grandma (and the two other people that look at this on occasion) it's okay if you don't understand what I'm talking about, no one really does including myself.

Symmetry, you think it's pretty cool and awesome, and in some regards it is, but in the long run it sucks. It sucks the life and soul out of you and will eventually want you to make everything around you completely unsymmetrical. This includes your own face (you remember how your mom would say, 'If you hold your face that way long enough it's going to stay like that forever...' that's where you obtained a real life lesson that you might need eventually) and that of loved ones as well. This they won't appreciate as much initially, but they will eventually learn to love you again. Symmetry is part of the problem with physics right now and why people are arguing about different models of how the world should be described. Personally I've been dealing with it on a much smaller scale and for problems that have far fewer effects on how we live and die. It still is a pain in the butt.

title looks an awful lot like tilde

Their are many words inn English that sound much like won wood expect other words to sound, butt they are spelled a bitt differently. Eye personally like them very much.

Things have been off the wall!! Okay, in the world of a scientists, which honestly isn't all that exciting, it has been wild and crazy. Yes, you might have guessed it, Target had bubble wrap on sale and we went nuts with it!! There was also a small, and I do mean small, conference I went to recently, and it was pretty good. I get nervous speaking in front of moderate to large groups, and I was sweating like a monstrosity of a pig when I gave my 15 minute presentation (no, they haven't figured out yet how awesome I am and have yet to invite me to be a speaker that gets to ramble on for upwards of 40 minutes, thus boring the crowd into a diabetic coma as you redundantly repeat yourself, replete with nonsensical chicanery and diabolical madness) and was shaking so bad I couldn't use the laser pointer (which was about the size of an ICBM) as I ended up pointing it all over the room at everything except my presentation-I think I blinded a few of the audience members, so we'll see if anyone comes after me for the damages. Probably the most frustrating thing about working in the sciences is knowing that while science is supposed to be based on fact and scientists, at least in the sciency part of their lives, are supposed to support things based on fact. This means they'll have to change their views if it turns out that they were wrong, say, 40 years earlier in their careers. This doesn't happen. Probably never will. Part of the reason is funding. Governments are stupid. If a scientists were to say to the governing body that hands out money, "Sorry, all this work I've been doing over the last several decades, while good and it has brought some insight, was not entirely correct and so now I need you to give me more money so I can pursue a different line of research that we believe to be correct...." they would never see even a penny from them EVER again. So we're somewhat forced, though I must admit, scientists are not the most humble group of people, to tell everyone that we're right, their wrong, the facts be damned! This also means that a lot of people are willfully ignorant to what other people are doing, either because they don't want to look in the literature, or simply because that's their prejudice and they don't like what someone else is doing, especially since it happens to be more correct than the idea they came up with.

Right now, one of the hot topics is multireference electronic structure methods. "Oh, we'll have to use multireference ________(insert your mothers face here) method to solve this problem" which shows an extreme lack of understanding and even thought put into what these problems are really even concerned with and what it takes to solve them properly. Gah!!! And people wonder why I'm already really grey. Okay, it's because of my jeans, but this isn't helping any either. Single excitations are NOT a measure of the multireference nature of the problem!!! Double and higher-order excitations are.

We're getting a mini donkey. I've always wanted my own little jackass, and now I'm going to get one.

'Murder the government' -NOFX

I have a feeling

You ever get that feeling that someone is watching you? Not just that they are watching you, but that they are intensely watching you with ill intent, and they are much much closer than you would care to venture. I usually imagine they are beneath my bed, or if my eyes are closed, that they are standing next to my bed, watching and waiting for me to open my eyes and look at them. I rarely open my eyes if I wake up and it's not light out. That is unless I have to use the restroom really really REALLY REALLY REALLY REALLY bad. Otherwise, the 'ol bladder can expand its horizons and forget about getting relief while it's still dark because I will not be moving or opening my eyes till then. If I do have to get up, it's very quickly and I refuse to look in any mirrors. You know that in mirrors you'll see things that otherwise you couldn't see like ghosts and spirits that want to do you harm. I don't like mirrors at night.

Things have been progressing nicely. Sorry I have been silent for a little while. I can still play some mean pinball though.

I've started to do, what I like to think of as becoming more mature, and have come to some realizations. One of which is, I've been eating too much meat lately. Growing up is overrated, just ask the dead.

String searches in a hay stack, that's pretty much what I've been up to lately. Kind of boring, but still a good time on a lonely weekday night, not that I'm ever lonely.

Is the world really that dumb?

I ask this question, because in my mind anyway, there's no way I'm really that smart.

I've decided I can't pay too close attention to world news because it just makes me upset, and I'm trying to be a better person and when I run into people being stupid, I have a tendency to let them know they're being stupid and why. It never really goes that well.

On the other hand, I'm always amazed at how stupid I can be sometimes. I had a math teacher in high school (seriously, I only had one for all three years, and no I did not repeat the same class over and over till he passed me out of pity, at least not that I'm willing to admit to) that forbid the words 'dumb' and 'stupid' to be said in his class. We came up with what we thought were clever ways to get around this by discovering words like torpid, insipid, etc. If you did happen to say either stupid or dumb in his class he would go over to this dusty chalk board, cover a section with chalk, erase it with an even older and dustier eraser and he would then take aim and chuck it at you. Most students just sat there cringing waiting for the eraser to pelt them and cover them with chalk dust. I quickly figured out that I didn't have to sit still for him and could ever deflect the eraser. I didn't always win these matches, but I did become quite skilled at eraser blocking. I also learned a good amount of math and that's where my love of mathy things started was from that teacher who took the time to explain derivatives and calculus to a poor confused teenager.

There are few things more maddening than projection operators. Sure they sound all cuddly and friendly and like they'll be really easy to work with and make your life soooo much easier. They are none of the above and they definitely don't make your life easier, at least until you finally figure them out and can get a good handle on them. Sure they're just matrices and blah blah blah, but what if it's not a matrix, but it's a TENSOR??? What then smarty pants? Tensors kill people, or they at least have the capacity to kill people, if we ever get a spaceship that can leave our solar system and happens to fly just a little too close to a black hole. That's right, they'll end up being forced tot watch the movie Event Horizon. Sure, it's got the guy from Jurassic Park in it (I am a child of the 80's and 90's) and he still is wicked awesome in that movie, but the only thing that could have made that movie worse was if Pauly Shore had shown up. Actually that would have made it down right terrifying and put it squarely in the jaws of the horror movie genre. Tensors, they will kill you in the end. That's been the last bit of my conundrumming lately. My ears are pounding and my head aches from it. It's not as hard as I thought it was, and was making it, now I just have to make sure I don't mess up the coding....c'est la guerr.

If all of the rain drops were lemon drops and gum drops

We'd all have teeth like the British, that's what would happen. Unless of course they were sugar free lemon drops and gum drops, in which case, our teeth might be okay. Did you know that drinking diet drinks actually increases your chances of contracting type II diabetes? That's right, but cutting our sugar from your diet, you're actually making things worse, but only because you're replacing it with something else, that in all actuality is still a sugar, just one your body doesn't process the same way. I always laugh when something is 'sugar free' but contains glucose, sucralose, wood, etc. because they're all just sugars. The main difference between sugars and alcohol? More OH groups. I like sugar.

You know how you're working on a project and you get all excited and happy because you think you're done after all that labor, pain, sweat, blood, and vomit, and you know it wasn't all yours? That's the worse part, and you can't even remember where the extra bodily fluids came from or who they belong to. After all of that you find out....you're not done. You're far from done. In fact you're so far from being done you feel like you've been undone, and very dumb. I am currently riding the small bus. I need to try and figure out how to project the eigenvectors on specific subspaces of the problem I'm working with. It sounds simple. It sounds so simple you should be able to have a first grader do it. I'm sure the first grader could sit down and whip the problem out in a matter of minutes. Being a graduate student, it's going to take me considerably longer. Stupid first graders. I knew there was a reason I didn't like them. Some times life is good. Other times, it comes up and when you're not looking smashes you upside the head and then jumps up and down on your special place all while laughing like a mad man at your pain and anguish.

Where the buffalo chips roam

There are few things more satisfying than finally getting a project to work. Eating the unborn is one of them, unless they're raw, then that's just gross and wrong.

And now for something completely the same, but different:

Apparently when you solve a non-Hermitian eigenvalue problem, and especially when there are degeneracies in the eigenvalues, it turns into a really ugly mess. I don't really understand too much of it yet, but I'm starting to look at locating conical intersections and the seams that are defined by the g- and h-vectors using coupled cluster theory. You would think that because coupled cluster methods do such an amazing job at describing the many-electron wave function that they would also do a kick butt job for finding conical intersections/seams, more particularly, those methods that are able to handle quasi- and near degeneracies of electronic states. In some cases it seems to be true, and they work really well, but in others, not so much. This is a new area for me, so I'm looking forward to digging into this a little more and learning something new.

I learned something else that was new to me today. The stairs next to my office will not take me to the sub-basement floor, but rather to a mysterious floor beneath the sub-basement that is locked up tighter than a nunnery on valentines day, but looks very interesting (mostly because I can't go in there). If curiosity killed the cat, I'm in trouble, but then so are most scientists and elementary school kids (amazing what we have in common with them).

Good posture is bad for your gas mileage

It's true, especially if you ride a scooter. I have a scooter that I ride to work when it's not too cold (when it's 50 degrees, in stupid units, outside and you're riding on a scooter at 25-30 mph it feels like it's about 20 degrees-again, in stupid units) and I love it, for the most part. True, my lawn mower has more horsepower than my scooter, and going uphill is a bit of a challenge, but you can't really beat 100 miles/gallon and mostly free parking in most places here. If I want to get really good gas mileage though, I have to hunch myself forward on my scooter and try to make myself more aerodynamic. If I sit up straight, like I've been taught since I was a kid, it will not only make me go slower, but it also kills my gas mileage and I only get about 90 miles/gallon. I know, I know, that's still pretty good, but it just goes to show that what they teach you as a child isn't always correct...all the time.

I GOT IT WORKING!!!!!!!

For those who read these short blurbs, thank you first of all (I'm a bit surprised people look at this, honestly, so seriously, thank you), and secondly, you'll know what I'm talking about (maybe).

It came down to units and then to using a numerically stable algorithm to diagonalize the matrix, otherwise I was getting complex eigenvalues, which was a bad thing for what I am testing this on. It amazes me how two algorithms, which in the end are supposed to give you the exact same solutions, and which to the unlearned computer science person (i.e., me) don't really appear to have any significant differences. The timings are about the same, they both put the matrix into the same form before diagonalizing it, etc. etc. etc. But there are some huge differences when you compare the results. The first, which is not numerically stable, can give large variations in the results just from small changes in the input, and when you're doing something like numerical differentiation, there's always going to be small variations in the inputs you give the program. A lesson learned...and probably forgotten before I get to something like this again.

My heart will go on...beating even after I'm dead because you'll be breaking my ribs and making it pump

For more reasons than one, it's a shame the titanic sunk.

Numerical noise. Who would have thought that it would be such a big deal? Not me, that's for sure. There seems to be some funky (and not in a good Parliament/P-Funk kind of way either) things going on with my project I've been working on. I'm getting some small imaginary eigenvalues. They should all be real, and the fact that they're small and imaginary says that it's not a huge problem but that there's some noise coming from somewhere in my program. I think I'm going to dig into the diagonalization routine tomorrow and see if that might be the issue. I hope it is...it probably isn't though. That seems to be an immutable physical law: whatever you hope it might be, it won't be that, in fact it's going to be the very thing you don't know about right now but if you did know about it right now you'd be offering your soul in exchange for it to not be that thing. I think I might be in purgatory. Anyone else here dead, or not really sure they're alive anyway?

Clowns are evil

It's amazing what Pennywise (not the clown) can do to help motivate you. Come to think of it, if Pennywise the clown was after me I'd have TONS of motivation to get done whatever I was doing to get as far away from him as possible. Can Pennywise be called 'him'? Technically Pennywise is an 'it'. I know, terrible puns, but I'm sure laughing. =D

If you ever do anything with numerical derivatives there's only one piece of advice I have for you: DON'T!!! Okay, that's not entirely truthful. You should if you need them. If you do need them, just watch your units. I know, I know, it's science, of course you're supposed to be careful of units, blah blah blah. What we're told in classes and what is done in practice is usually never the same in most cases. Kind of like the scientific method. Ha! The only thing the scientific method has been good for is to disprove something that lots of people have latched onto as true (did you hear that the main scientist saying drinking red wine is good for you faked almost all of his data?), and never has been used to find new discoveries.Scientists really do a piss poor job of informing the outside community as to what it is we really do. With numerical derivatives though, you need to make sure that the units you use for your input are also the same units you use to compute the derivative, conversions and everything else as well, otherwise you'll end up with garbage. That was one problem I was having. I can now reproduce the same results from another program I know works and generate the same matrix. The only problem now is that when I attempt to diagonalize the matrix to get the eigenvalues and eigenvectors I'm getting junk. The really disturbing part is that I'm using the diagonalization routines in BLAS. I have to be passing it the wrong information, or getting back the wrong info at some point.

You would hope that science would be more interesting than what it seems like from the few posts I've put on here so far. Well, not for me. This is exciting. It's frustrating as all get out when it's not working, but once you get it working, there are few things more satisfying in this life. Punk concerts are one of those few things.

One, ah ha ha ha ha ha....!@#(!&@$!!

It's all about counting. At least that's the latest thing I've been able to come up with for the problem I've been having with generating a matrix which I need to diagonalize. For an n-dimensional problem I need to generate (n**2 +1)-points. I just figured out today that the (n+1)th and (2n+1)th are not being generated properly. Every time. What I've decided I'm going to do is beat my brains out against the wall and finger paint with whatever it is that comes out. I think my office could use a nice mural on the back wall of some children frolicking in a field of red and orange and brown.

I'm watching two old men chase each other on TV right now. One of them needs oxygen, but he took it off to run faster, and the other one stopped chasing the other to get his oxygen tank and then hobbled after him. It was pretty funny, probably more funny than it came across.

Once I finish finger painting with my brain matter, I will sit down and try to fix my code and then head out to find the wizard of Oz since I'll need a new brain. This one seems a bit used and abused, and after the runin with the wall I'm going to have, I'm not sure it will really be good for too much more, even a paper weight. Brains probably wouldn't make the best paper weight anyway, get them all soggy and such. Brains. I'm sad zombies have become so mainstream and trendy. Thank goodness we still have all kinds of other nasty horrorishness that is too much for most mainstream media be able to stomach (i.e., The Loved Ones and A Serbian Film). Lovegood is also a safe fall back that is not easily moved over to film, especially if you put the stipulation on that it needs to be done well. Scientists aren't known for speaking good English. Usually we do a pretty piss pore/pour/poor job and sometimes it's even on a porpoise.

Gah! I don't care if I do use Fortran to code, C/C++/C#/Java/BLorganite/Hulfgurftunfrter are all the same in that they will all make you want to throw your computer out the window eventually and murder someone you've never met (you could even say that the various compilers of these languages fall under the same umbrella of murderous thoughts and intentions).

Home is where the cart is

Have you stopped and realized just how cool shopping carts are? They're also freakin' huge in the USA (possibly in other countries too) it's all psychololology and realizing that if someone has an empty cart they will want to fill it, even if it's with nothing but cheap useless stuff that will end up costing the shopper the GDP of smaller countries. Stinking librariatians and their free market disvaluation of the dollar. =D

So I'm back at home after two weeks aboard another country, and while I'm happy to be back, I must say it's been a bit hard for me to jump back into things (I think I'm still a little jet lagged). I've been trying and all that it's led to is anger, frustration, the purchase of a super nasty energy drink, which is consequently fueling this post as I just ended up getting garbage for something that should have been easy and definitely should not be giving me crap answers. I need to buy a smart monkey I can train to code what I need that way when there's a mistake I can berate the monkey instead of wanting to slam my head through the wall. I'm starting to realize why Microsoft usually releases software that isn't debugged properly, it would be bad for morale if it was debugged properly. That's a nice piece of reverse psychosis for you. Thank you Master Gates for saving many a headache and anger induced depressive episodes of programs by shifting all of that onto the users.

I think I'm going to have to gut the program and start over. There's that !(@&#!@$)!!!!! ghost in the program that I can't find and definitely does not want to be found. Maybe if I just scrap what I have so far and start over things might go better? Rome was great the second time around, so why shouldn't it work for me? Granted, I wasn't raised by wolves, nor do I have a brother, but I think if I start over now we might avoid the more unsightly things like vivisection and such. Tom Waits has a great song about the Roman empire.

Another day another squalor

Squalor, now there's a fun word you don't get to hear or use everyday, unless you're one of those amazingly obnoxious people that somehow can work all kinds of superfluous words into your loquacious allegories for the rest of us to listen to and wonder just what the hell you're even talking about. I don't really use big words very often, unless I'm trying to be spiffy, but people still don't understand what I'm talking about most of the time anyway. I've learned that's it's just better to shut up most of the time. That's the problem with the internet, that and governments are trying to regulate it, is that you can quite as a mouse-other than the tap-tap-tap of your keyboard-and still be noisy as all get out. This is how I know I'm getting old...I don't bounce like I used to when I fall off of really tall things.

So a continuation of what I was having problems with yesterday: it's still not working. I've narrowed some other things down and the good news is the more complex part of my code is working just fine, in fact it's spot on. The portion that feeds the complex part the data, you know where you're just adding and subtracting numbers, maybe multiplying by something every once in awhile, things you used to do in say kindergarten, or if you were a late bloomer like me, 10th grade, that's where the problems are. Good 'ol Achtung and his Razor. With so many people borrowing/stealing his razor for their own use, he probably hasn't shaved in close to a long time, and can probably rival Santa Claus in most crackhead-looking-old-guy-with-a-beard contest. I bet Santa was a pirate before he got hooked up with his current gig. Maybe that's his punishment for being such an evil and wicked pirate, he now has to eat cookies and other assorted treats that he knows kids have handled, licked, taken bites out of, and who knows what else with their hands covered in all kinds of kid goo and other fun things. Ugh, makes me no longer want to be a pirate. It's 4am back home and I'm up and working on something that makes me want to bash out the brains of small creatures very slowly, starting of course with my own. This feels like one of those bad dreams where you're trying to undo your pants because you really really REALLY need to use the restroom, but you can't...I should get back to work.

Introduction and stuff

For starters, yes I am insane and yes I am a quantum chemist. No, there is no direct (proven) correlation between the two. I have had major head trama before in my life (true story) but they say I was like this before my accident. As a quantum chemist I've been compared to the Dark Side, Nikita Khrushchev, the pied piper, and Trent Reznor, all of which I am very proud (due to the context in which I was compared, not because I like all of them by any means).

This is a place for me to air my different thoughts about what I'm working on and perhaps share something humorous (or even useful, heaven forbid) with someone else. If you happen to read this and there's something where you say "Gee Wally, that sounds like a great idea!" Much like in the TV show, I cannot be held responsible for any damages that may occur to you if you try it. I also make no claims to originality of the content here, and most likely I have stolen it from somewhere else along the way, I just don't remember, otherwise I'd give a reference.

I'm working on writing a routine to form the Hessian matrix and then diagonalize it to get the eigenvalues and eigenvectors. Simple enough, right? Oh no. I have no clue what's going on right now. Sometimes it works, other times it doesn't, other times I think my code is going to peel itself off my screen and come attack me for butchering it so much and so many times over. So far this was for problems larger than I was willing to do by hand. The smallest matrix that is still a real example is a six by six (that's 720 terms in your final expression before you simplify, and it's a sixth degree polynomial equations you will have to find the roots of) and I'm not that bored, even if I have nothing else to do right now. So I made up a toy problem and created a 3x3 matrix, diagonalized it by hand and got the eigenvalues. I then plugged it into my program and ran it and low and behold I got the correct eigenvalues. Okay, so my diagonalization routine is working. Perhaps the problem is in my routine that generates the Hessian. Pray for my soul as I go back into the dark....

UPDATE: Okay, so I'm closer to a solution. The results I'm getting are consistently about 60-90 wave numbers too low from what they should be. Now to figure out just where this error is coming from, and back into the abyss (I like that word, it just looks ominous and full of foreboding, I don't really remember much about the movie other than I confused it with Cocoon until I was about 17 years old, hmm, maybe it wasn't that good of a movie after all)  once again...