The h Bar

12:02 AM

@DanielSank he's just being polite

@DanielSank doing

@DanielSank We know that pretty much you are the only person who can answer these questions, so isn't it better that we just discuss it here?

DanielSank

12:40 AM

@TanMath when I say "just ask", I mean don't waste time saying "can I ask about blah blah".

vzn

yesterday, by DanielSank

Just ASK THE F------ QUESTION.

Bernardo Meurer

Any C ninjas around?

TanMath

1 hour ago, by TanMath

is it true that these excitons are just oding diffusion?

@vzn have you seen anything regarding quantum walks and quantum computation?

vzn

@TanMath in some abstract sense all optimization problems are equivalent. some of this is related to the NP class. in practice the "conversion efficiency" can be a factor. the Vattay/ Kauffman ideas are about utilizing "light harvesting processes" for quantum computation. apparently they have sketched out some of the math. sounds like ~½-way plausible idea but but havent heard of anyone building on this direction "yet".

TanMath

@vzn in their method, would you just encode the site energy for F(1) in chromophore 1, all the way to F(7)?

Because when they said "function values" it wasn't very clear...

vzn

12:51 AM

← ninja, PERIOD :P

@TanMath need to look at the paper in more detail what pg are you talking about? (iiuc) they are noting that the general eqn for the FMO complex "looks" like an optimization problem. these types of eqns generally "optimize" for something like "least energy levels" aka something like "principle of least action"

TanMath

Another problem I think is that finding the optimum of a function with only 7 values is useless... same with finding the shortest path of a graph with seven nodes... so clearly, bigger protein-pigment complexes would need to be used...

vzn

@TanMath what is a "quantum walk"? dont think have heard that

TanMath

"For the simplicity let this function have only discrete values from 0 to K. If we are able to
map the values of this function to the electrostatic site energies of the chromophores Hnn = 0fn and we
5
deploy reaction centers near to them trapping the excitons with some rate κ and can access the current at
each reaction center it will be proportional with the probability to find the exciton on the chromophore
$jn ∼ \kappa \rho_{nn}$." - Vattay and Kauffman

@vzn a quantum random walk to be specific

Quantum walk

In quantum computing, quantum walks are the quantum analogue of classical random walks. Analogous to the classical random walk, where the walker's current state is described by a probability distribution over positions, the walker in a quantum walk is in a superposition of positions. Like classical random walks, there are two types of quantum walks: discrete-time quantum walks and continuous-time quantum walks. == Motivation == Quantum walks are motivated by the widespread use of classical random walks in the design of randomized algorithms, and are part of several quantum algorithms. For some...

vzn

@TanMath that sounds like "brownian motion"?

ok

@TanMath there might be some rough connection between "quantum random walks" and adiabatic QM computing eg explored by dwave....

TanMath

they say that the dynamics of the fmo complex is similar to a quantum walk... I think they call it a directed quantum walk

vzn

12:59 AM

ok

TanMath

@DanielSank did you see the questions i had posted on physics.SE? are they too dumb?

vzn

ref [6] Mohseni et al has more on "Environment-assisted quantum walks in photosynthetic energy transfer"

TanMath

@vzn I read that paper... it is quite complicated... but I got the gist of it... says nothing about quantum computation

vzn

V&K p4-5 is where they sketch how to map the computation problem onto chromophores. the idea seems to be to put multiple reaction chambers near different chromophores as the energy measuring devices. and maybe to control the initial energy in the chromophores? and the interactions between them? and then the exciton "samples" this energy field quantum mechanically aka "in parallel" and arrives at a destination reaction chamber, and apparently its destination encodes the problem solution...?

TanMath

1:18 AM

@vzn I thought they randomly select the coupling constants (which determine the interactions between the chromophores)... they talk about the requirements needed for measurement...

vzn

2nd thought maybe their idea is 1 reaction chamber per chromophore.

TanMath

@vzn yep!

vzn

"If we are able to map the values of this ('optimization target') function to the electrostatic site energies of the chromophores H_nm..."

this notation is confusing because is the n in f_n the same as the n in H_nm?

ok eqn (1) n ranges 1...N where N is the # of chromophore sites.

what is m? maybe the 2nd chromophore of an n,m pair where m also ranges 1...N?

Bernardo Meurer

@JohnRennie I have finished the refactoring (for the most part)

vzn

TM not sure what you are referring to as "coupling constants"...

Bernardo Meurer

1:28 AM

My graphics struct works and all the rendering is being done successfully

TanMath

@vzn V_nm

the off-diagonal elements of the Hamiltonian

heather

@BernardoMeurer =D

nice

Bernardo Meurer

@heather I'll give you access to the repo so you can see my masterpiece

heather

okay

Bernardo Meurer

@heather I added you

heather

1:33 AM

just got an email

geesh, that's....awesome/crazy

Bernardo Meurer

@heather Switch to the struct branch

on the project01 folder, main.c

The main branch has my professor's shitty code

vzn

TM "the operators Vj describe the coupling of the system and the environment..." dont see V_nm

TanMath

yep...

heather

@BernardoMeurer lol

TanMath

you know, you can mention me if you want...

vzn

1:36 AM

@TanMath what?

TanMath

sorry... my notation is confusing...

and so is theirs! ;)

@vzn arxiv.org/pdf/0805.2741.pdf

page 2

Bernardo Meurer

@heather You can try running it, it should work

Alas the struct branch has no movements yet (give me 20 minutes and it will)

heather

@BernardoMeurer, crouton still doesn't work for me - i tried reinstalling it and the chromebook decided to get grumpy.

vzn

TM its an intriguing paper and seems like it might be a sort of adiabatic computation, but not sure right now... seems quite novel/ unprecedented... it seems adiabatic because they seem not to be trying to micromanage/ precisely control qubit transport...

Bernardo Meurer

@heather Hm? What happens?

TanMath

1:40 AM

@vzn do you have any suggestions on what I should look into?

vzn

> The Vmn are Coulomb couplings of the transition densities of the chro-
mophores...

TanMath

@vzn what's interesting is they say the current is simply $jn = κ<n|e^{−βH}|n>/Z$.

heather

@BernardoMeurer, oh, it would just give a blank screen, so i then switched the chromebook back into normal mode to get rid of it and try reinstall, and then switched back, and then the download had trouble so i had to delete it (can't remember quite what happened), and then i had to go do something so i left it for the moment

on top of that i was also having more than a few memory issues for some reason (on the computer)

TanMath

@vzn this constant determines the interactions between chromophores

vzn

TM V&K seems hard to follow, seems sketchy but experts would likely have much better understanding...

@TanMath V&K? where?

btw are you still undergrad? what is your major? biology or something like that?

TanMath

1:44 AM

@vzn i agree, but I liked the approach... nice and simple and interesting results

@vzn yep...

vzn

lol "nice and simple" yeah right o_O

it seems like probably a lot of grad students would struggle with the paper... o_O

TanMath

it is simple compare to other papers

vzn

think they need to explain better what they are controlling in the setup. presumably chromophore initial energies and their interactions/ couplings, but think its a bit unclear

TanMath

even for me it is pretty hard...

I don't follow the redfield stuff very well...

vzn

on reading it wonder if anyone is working with simulations in this area, it would be great to jump to that step...

Bernardo Meurer

1:48 AM

@heather I blame ubuntu

@dmckee I am loving C

Now that JR has taught me struct and typedef wizardry I have UNLIMITED POWER

vzn

honestly DS probably would understand the paper a lot better than either of us but hes not nec on spking terms with either of us :|

TanMath

whatever happened to MM?

@vzn yeah, it is really sad...

heather

@vzn that's not the case

vzn

@TanMath as the kids say these days "triggered"

heather

he simply wishes you to speak clearly and state the question, without extensive abbreviations, etc.

@vzn, you have received multiple comments asking you to rephrase and use complete sentences - this is for a reason.

2

@TanMath and @vzn, you both have been asked to simply state the question without bothering with "can I ask?" multiple times and you still do it.

vzn

1:53 AM

@heather not really interested in listening to the (multiple self appointed) Language Police of HBar Chat at moment :|

heather

it is frustrating for most involved.

@vzn i am simply explaining the situation, i am not commenting either way. please don't say DS is "not on speaking terms" with either of you, because that isn't true.

also, phrases like that frustrate people - we're not trying to be rude, just help you out.

vzn

@heather lol maybe you havent read the recent transcript

heather

@vzn, I have, and I still maintain this viewpoint.

dmckee

@BernardoMeurer Well, I like it too. A good mixture between exposing the internals but giving you good enough tools to actually get some stuff done.

vzn

@heather whatever my pov is DS is out of line

TanMath

1:55 AM

@heather to be accurate, he said this twice... and I thought he wanted me to ask on physics.SE

just a misunderstanding...

heather

@vzn he is not.

@TanMath indeed, that's all i'm pointing out =)

dmckee

But at a certain scale those tools begin to feel a little deficient.

vzn

@heather since you insist & say so it must be true right? maybe if you visited my own qm computing lab you might see things differently :P

TanMath

@heather he doesn't want to talk to me for other reasons...

Bernardo Meurer

@dmckee Yeah, well, it's certainly a bit too verbose, but it works well

TanMath

1:57 AM

@heather i also think he shouldn't be cursing...

yesterday, by DanielSank

Just ASK THE F------ QUESTION.

heather

::shrugs:: did you read the surrounding transcript?

Balarka Sen

well technically he didn't curse :P

heather

ah.

okay, maybe he was frustrated =/

@TanMath, can you trust me when I say that DS is not like that most of the time? That's the first time I've seen something quite like that.

TanMath

ok...

vzn

← SHRUGS HARDER

TanMath

2:00 AM

I had a misunderstanding... Now reading the transcript, I realize what @DanielSank meant...

Bernardo Meurer

@vzn I shrugged so hard once I dislocated my shoulder

TanMath

wat??

heather

@TanMath it can also be hard - is english your first language? (curious)

@vzn okay, that's going a bit far

TanMath

why does everybody ask this?

heather

i'm just curious

TanMath

2:01 AM

am i really that bad with english??

heather

no, lol, there are just many people from around the world in this chat

that's why i was wondering.

vzn

@heather lol so then substitute whatever word you want so its the distance you prefer :P

TanMath

ok.. I was born in America and have only lived in America... English is my first language!

heather

@vzn how about the distance where we don't insult people because we have a personal grudge against them

(or we don't insult people period)

TanMath

@vzn don't call him that... he is the only one who can help us out in this subject...

vzn

2:02 AM

@heather yeah lets see everyone follow that in here good luck with that :)

heather

@TanMath yeah, you don't have bad english or anything - does everyone seriously ask you that?

TanMath

@vzn at this rate, DS will never talk to you

@heather probably 3rd or 4th time...

I think twice in this chat

heather

@vzn just because someone else murders people, do you do it? no.

TanMath

^

heather

@TanMath huh, wow - sorry about that =)

TanMath

2:04 AM

its ok...

Balarka Sen

i am sure you have better things to do than this meta-conversation about a comment Daniel Sank made

h bar spends hella time on meta-discussions

TanMath

i dont see why that is a problem

just because it is a physics chat doesn't mean we talk physics...

Balarka Sen

it's just tedious. whatever

TanMath

have you been to other chats?

Balarka Sen

I am from the math chat.

heather

2:06 AM

the math chat doesn't do this as much, yep!

Balarka Sen

It's fine not talking physics; I talk math and philosophy here with a bunch of other people. Some talk about food and music. Some about JEE. I just think meta-babbles are super tedious. If you don't think this that's fine.

TanMath

well if you have been to the PPCG chat or chem chat is much worse

Bernardo Meurer

@BalarkaSen Do you want to discuss which license is more Free GPL or BSD?

Balarka Sen

@Bernardo Maybe, if I knew what those are? :P

Bernardo Meurer

@BalarkaSen The answer is GPL, that's all you need to know

now, repeat after me:

"There is no system but GNU and Linux is one of it's kernels"

Balarka Sen

2:10 AM

"There is no system but GNU and Linux is one of it's kernels"

2

Bernardo Meurer

Very good

Welcome to the Church of Emacs

stallman.org/saint.html

Balarka Sen

i'm ok with my windows man

vzn

@heather since you ask, do sometimes feel like murdering some ppl, but its generally a bit rare feeling for me :P

@TanMath and hes always sooo helpful isnt he?

Bernardo Meurer

@BalarkaSen Proprietary malware

Balarka Sen

's okizay

TanMath

2:18 AM

@vzn stop with your sarcasm...

vzn

@BalarkaSen is it interesting to you? do you understand it? do you still have any interest in number theory?

TanMath

Apart from MM, he is the only other person who helped me...

Balarka Sen

@vzn Yes, somewhat, yes.

vzn

@TanMath lol reminds me of stockholm syndrome :P

@BalarkaSen so what is a better thing to do? maybe something other than SE chat? :P

Balarka Sen

Not talking meta.

Logging off the SE chat is also an option.

vzn

2:21 AM

@BalarkaSen thx for narrowing it down! :P

Balarka Sen

No problem.

Sir Cumference

Is it worth the trouble to learn 3D modeling?

vzn

(man think theres someone really sensitive in here, better split before the hammer really comes down) o_O

heather

what are you talking about @vzn

@SirCumference depends

DanielSank

Hi, everybody.

heather

2:24 AM

@DanielSank hello

Bernardo Meurer

@Riker Go away cat

Shoo

no cat here

Balarka Sen

You did the better thing, @vzn. Congrats.

DanielSank

Yo @TanMath what question did you want me to look at?

Link plz.

TanMath

0

Q: What is thermal relaxation?

In open quantum systems, we model a process known as thermal relaxation. What is this process? Why is it that only the Redfield equation models this process, and the Lindblad equation doesn't (does it have to do with the secular approximation)? Is it possible to add a Lindblad superoperator to mo...

open-quantum-systems

1

Q: Is recombination and quantum dissipation the same?

I have been reading two articles on the quantum transport of the FMO complex (https://arxiv.org/abs/1311.4688, https://arxiv.org/abs/0807.0929). In these papers, each model different processes occuring that affect the quantum transport of the excitons in the FMO complex. In the first article they...

quantum-mechanics open-quantum-systems

Bernardo Meurer

@DanielSank Can you try and run my code see if it doesn't explode your house?

TanMath

2:26 AM

@BernardoMeurer lol

DanielSank

@BernardoMeurer What code?

Bernardo Meurer

@DanielSank My project

DanielSank

@BernardoMeurer 2048?

I'm on my work laptop, so no.

Bernardo Meurer

::nods::

That goddamn work laptop :P

DanielSank

You might try to steal trade secrets.

TanMath

2:27 AM

@BernardoMeurer you are working on 2048? i love that game...

I know there's a udacity course on building a 2048

Bernardo Meurer

@TanMath It's my mid-semester project for CS-101 yeah

in C99 with SDL

TanMath

@BernardoMeurer what's c99

Bernardo Meurer

the 1999 standard of the C programming language

TanMath

what?

that's like teaching people pascal in the 21st century!

DanielSank

@BernardoMeurer I feel like I should try to do that to learn some basic stuff.

Bernardo, be my teacher.

Bernardo Meurer

2:29 AM

@TanMath Are you stupid or misinformed?

TanMath

@BernardoMeurer nvm, I take back my comment...

I am misinformed

Bernardo Meurer

@DanielSank I can teach you C if you want, there's a lot of cool stuff to do

TanMath

at least it is not as bad as learning XHTML...

Bernardo Meurer

@TanMath C has high performance, and it's really expandable. You can control memory with a lot of precision. I'm a computer engineer, that's what I need

TanMath

I once had to learn XHTML, and half the stuff isn't in HTML5 anymore...

@BernardoMeurer I learnt C++, didn't like very much... i think I will stick to python and matlab

Bernardo Meurer

2:31 AM

C++ is nice, but C is the OG

DanielSank

@BernardoMeurer I'd rather do C++ and avoid the crazy bits.

Basically, C with classes.

Bernardo Meurer

@DanielSank Fair enough, C++ is really easy actually

TanMath

kinda weird...

dmckee

@DanielSank And namespaces.

Gotta love those namespaces/

DanielSank

@dmckee my god yes.

Bernardo Meurer

2:32 AM

At least I never had much trouble with it once I learned to leave my C past behind

TanMath

in python to print its just print "hello world"

DanielSank

I can't wait for C to get modules.

Bernardo Meurer

@dmckee I refuse to use namespaces

Or rather

TanMath

in c++ it is something like stdout << "hello world"

DanielSank

@TanMath Yeah, so, that's not really a great case for comparing C and Python.

They're good for completely different things.

Bernardo Meurer

2:33 AM

to do that using namespace std bullcrap

Never ever do that

dmckee

@BernardoMeurer I've personally written projects more than 50k LOC and 30 source files.

DanielSank

You're not going to write git in python, for example.

TanMath

@DanielSank true...

dmckee

I've worked on projects near 2 MLOC.

Bernardo Meurer

@dmckee Yeah, I meant the using directive for namespaces

bad wording on my part

TanMath

2:33 AM

I guess i never had any use for C++, except for arduino

arduino has a similar language to C++

Bernardo Meurer

@TanMath Arduino is C

C99 with some library additions to be precise

dmckee

@BernardoMeurer OK. That's fair.

TanMath

@BernardoMeurer really? i always thought it was like C++

well now i know

@DanielSank so i assume my question is better with the change?

DanielSank

@TanMath your thermal relaxation question looks good. Unfortunately, I don't know the answer.

TanMath

ok... and what about the dissipation/recombination one?

DanielSank

2:35 AM

@BernardoMeurer Is that like from std import *?

Bernardo Meurer

@DanielSank Yes, pretty much

It makes a mess

It's bad for your health

using namespace std is for people who are not using their brain ;^)

DanielSank

lol

TanMath

@DanielSank so I saw your comment, but I am not sure I should include the entire redfield and lindblad model from the question...

Can I just say page numbers?

where the important info is?

DanielSank

@TanMath You can do whatever you want, but I would say more detail is better.

The reader cannot read your mind, and I doubt most users are going to go pull up the paper just for the sake of answering a PSE question.

I mostly answer questions that I can figure out pretty quickly, or that require calculation that I actually feel excited to do.

I don't think I've ever bothered to go read articles to answer a PSE question. It's just way too much work.

0celouvsky

@heather what?

TanMath

2:42 AM

ok... I will put in more detail, it will take me some time to do so...

0celouvsky

that statement is missing a lot of context

DanielSank

@0celouvsky Then read more context.

TanMath

^

@DanielSank thanks!

now, for the fmo complex, if the excitons are diffusing, what makes that so special?

0celouvsky

@DanielSank I mean the murder one

I didn't read any other context

I wouldn't murder just because other people are doing it

but there might be a good reason, who knows

Bernardo Meurer

@dmckee Are you still there?

dmckee

2:44 AM

Sorta.

DanielSank

^ LIES

TanMath

@0celouvsky he/she is meaning that if someone insults somebody, you shouldn't do it... please read the convo

Bernardo Meurer

@dmckee Quick one, in my struct I have a memebr var like this unsigned int *cells;

dmckee

Yeah...

0celouvsky

who was instulted???

Bernardo Meurer

2:46 AM

And now I want an array of those cells, so I added another member unsigned int **history;

TanMath

@0celouvsky please read the convo

0celouvsky

link?

Bernardo Meurer

When I instantiate my struct and intialize everything I allocate cells like this

self->size = size;
    self->bytesize = self->size * self->size * sizeof(unsigned int);

    self->cells = (unsigned int *) calloc(self->size * self->size, sizeof(unsigned int));
    if (self->cells == NULL) catchError("Board allocation failed.", "");

0celouvsky

DS is out of line??

Bernardo Meurer

And then I allocate history accordingly like such

self->history = (unsigned int **) calloc(UNDO_DEPTH, self->bytesize);
if(self->history == NULL) catchError("History allocation failed.","");

Is this correct?

DanielSank

2:47 AM

@0celouvsky lolwut?

0celouvsky

@DanielSank vzn said you're out a line

DanielSank

@0celouvsky Y U always ask questions about transcript instead of reading transcript?

TanMath

@0celouvsky thanks for the gossip...

0celouvsky

in the end I refuse to agree with someone who can't type properly

@DanielSank I am reading

DanielSank

@0celouvsky I suggested that he "ASK THE FUCKING QUESTION". I didn't think that was out of line, to be honest.

0celouvsky

2:47 AM

But I must have missed some earlier controversy

Bernardo Meurer

Can't we all just rejoice on the fact that there is no system but GNU and Linux is one of it's kernels and chill?

DanielSank

But Windows...

TanMath

@DanielSank i prefer that this language not be used... is that fine?

0celouvsky

@BernardoMeurer if you can't take the heat then get out the streets

Bernardo Meurer

@DanielSank That's just malware

DanielSank

2:48 AM

@TanMath Yep.

TanMath

thanks...

Bernardo Meurer

@0celouvsky Stop quoting Yatchy

DanielSank

@TanMath No problem.

dmckee

It looks at first like the allocation of the basic cells is correct, but the allocation of the history is definitely incorrect.

Bernardo Meurer

@dmckee Yeah, I figured

How the heck do I do that

dmckee

2:49 AM

You're allocating a collection of pointers.

0celouvsky

@BernardoMeurer u're just jealous that he gets mo money than you, mo cars, mo women

DanielSank

However, @TanMath, I must say: if I become frustrated in our conversations, I will either 1) Just stop participating in the conversation or 2) Type out an expletive like the one above.

Balarka Sen

I ended at 512

dmckee

SO

DanielSank

I have gone way, way past what I would consider to be normal levels of patience with you in the past, and frankly I'm not interested in exercising that any more until we have some more productive exchanges.

dmckee

2:50 AM

self->history = (unsigned int **) calloc(UNDO_DEPTH, sizeof(int*));

Or something like that.

DanielSank

geddemit C is so horrible

ugh

0celouvsky

Roger Godement

Roger Godement (French: [ɡɔdmɑ̃]; October 1, 1921 – July 21, 2016) was a French mathematician, known for his work in functional analysis as well as his expository books. == Biography == Godement started as a student at the École normale supérieure in 1940, where he became a student of Henri Cartan. He started research into harmonic analysis on locally compact abelian groups, finding a number of major results; this work was in parallel but independent of similar investigations in the USSR and Japan. Work on the abstract theory of spherical functions published in 1952 proved very influentia...

DanielSank

It's so old.

0celouvsky

@DanielSank reminds me of ^

DanielSank

Apparently Firefox actually ships with stuff written in Rust nowadays!!!

dmckee

2:52 AM

Then you have a choice to either allocate space for each of those pointer to point to and later copy boards (clear but clunky), or to redirect those pointer to existing boards and then allocate new space for the new board (the idomatic K&R way).

Bernardo Meurer

@dmckee Why sizeof(int*) ? Mustn't I make the second argumment of calloc be the same size as cells?

TanMath

@DanielSank i understand... i realize that during the last convo we had, I had a misunderstanding of what you wanted me to do...

Bernardo Meurer

Wait, what?

TanMath

I totally understand your point of view...

dmckee

@BernardoMeurer No matter what anyone has told you arrays are not pointers and pointer are not arrays.

Bernardo Meurer

2:53 AM

@TanMath The real question is, do you understand pointers?

@dmckee I mean size in bytes

TanMath

@BernardoMeurer ??

dmckee

Your earlier line self->history = (unsigned int **) calloc(UNDO_DEPTH, self->bytesize); tells me that self->history is a pointer to a pointer to int.

In that line you point it at a collection which should be a collection of pointers to int.

Bernardo Meurer

Hmmm

dmckee

Then you have to figure out what those pointer should point at.

Bernardo Meurer

Maybe history should just be an array

The idea here is that I can save the state of cells up to UNDO_DEPTH times

TanMath

2:55 AM

so if the probability of finding an exciton on a chromophore is 1/N (N = number of chromophores), whats so directed about the quantum walk of FMo complex?:

dmckee

It'll save a lot on memory mangement if you are willing to accept a fixed history depth.

TanMath

arxiv.org/abs/1311.4688

also, me and vzn are not sure if this article is sketchy

dmckee

@BernardoMeurer Sure. You're naming is clear enough that I was assuming exactly the same thing.

Bernardo Meurer

So the way I want to do it is to have a history array that can hold up to UNDO_DEPTH copies of cells. Whenever I want to retrieve a copy I get the first entry of the array, if I want to add a more recent copy I shift the array to the right and insert the new copy on [0]

UNDO_DEPTH is a define way up there and is set to 25

dmckee

I have a drawing tool I use to teach pointer and to work out what is going on in complciated pointer situations (akin to the way that free body diagrams are used to teach and solve Newtonian physics).

It involves a lot of boxes and arrows and I'm not sure that I can explain it in chat.

But it is your responsibility to know where every pointer points, if those locations are legally addressable, and if so how much such memory is out there.

Bernardo Meurer

2:59 AM

I guess I can just calloc history with lots of space

Transcript for