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If that isn't enough, explain what you're currently trying to do and we'll take it from there.
Other relevant info on pipes and production levels:
But what happens when i need to put 3 molecules into a reactor? I figured that the left side of the reactors were "input" areas and the pipes coming out were suppose to go to freighters.
So if you could just explain in steps what to do like "attach X to X and create the combination shown X."
Sorry if im being difficult, im trying to explain exactly what my problem is but my english skills are lacking.
Basic flow of a puzzle is this:
1) Look at raw materials, required final product, and how many reactors you have to work with.
2) Think of convenient intermediate steps that you can dedicate one reactor to.
For instance, if you need to make benzene (a ring of six carbon atoms with odd bonding), and your input is just single carbon atoms, it might be too complicated for a single reactor -- so try having one reactor create chains of three carbons, and then pass them to a second reactor that just joins them and adjusts the bonds. And so on.
3) Lay out the reactors, and join them with pipes.
4) Go into the reactors from beginning to end, and right click on the outputs you're using (they'll light up when you mouse over). Drag and drop the molecule you're hoping to deliver through each pipe. Make sure to position the atoms in the grid space and orientation you want it to show up in for the next one -- intermediate outputs will show up in the next reactor exactly where and how they were flushed. Some tasks make it more efficient to drop molecules in the far corner to put them closer to the middle in the next one for maneuvering room, some in the closest edge to loop faster or deconstruct a molecule more easily, etc.
5) Go through each reactor and construct a circuit to deliver each of the intermediate steps you wrote down.
6) Watch something inevitably break, and then fix it. Repeat until enough useful things start getting done that you have something to work from for step 7.
7) Adjust previous notes and reactors as you come up with ideas that'll make later ones easier or more efficient.
If you need a reactor to take more than two different things -- which does happen later, and there are really good reasons to do this sometimes -- you have to do some prep work with a previous reactor.
Molecules will pop out in the next reactor in whatever order they were pushed through. So if you have an H2O, break it apart, and output the oxygen in the upper left, followed by the hydrogens in the lower left and right, the next reactor will call them one at a time in exactly that order.
This is useful, for instance, to easily construct hydrocarbons by pre-placing a pair of hydrogen atoms one space apart. The next reactor only needs to input twice from that pipe, then grab the carbon and move it between them.
It's also good for passing a sequence of pieces you didn't quite have the space to handle in the previous reactor. If you need to mess with a complicated acid or something, you can break it into the chunks you need and output each one separately through the same pipe. The next reactor can take them one at a time and build the new molecule much more smoothly.
Near the end of the game, you often just flat-out need to output more stuff than you have pipes for. You wind up having to use output pipes to pass several different things at once, and it becomes a juggling act to do what you need to.
Spoiler alert and stuff, this does involve exhaustively solving a puzzle, albeit not one in the main game, and not one it'll take too long for people who are poking around Research Net to do anyway.
Okay, so this is what we have to work with:
http://steamcommunity.com/sharedfiles/filedetails/?id=116964584
Note the Assembly and Disassembly reactors; Assemblers only have one output and can only make bonds, and Disassemblers have only one input and can only destroy bonds. This means I have some restrictions on what happens when. Also note the Recycler in the bottom; that means I'll probably have leftover atoms I need to throw away. Here's how I react to this:
1) I need to break apart the hydrogen. It goes right into a Disassembler.
2) I need to break apart the cyanogen and throw away one of the carbons. It goes into another Disassembler, and one of the outputs goes to the Recycler.
3) I need to combine everything back to make cyanamide at the end. So I feed the remaining outputs into an Assembler.
http://steamcommunity.com/sharedfiles/filedetails/?id=116964678
Next, I go into the cyanogen reactor and write out the outputs I want. If you click on the gray rectangle at the far right of the screen next to a used output space, you can drag and drop output notes. Noting that I needed to leave half the molecule untouched, and have an extra nitrogen to glue back on later but can't do it here, I realize that I'll have to throw them both through a mixed output -- and your notes have extra grids to represent that. Also note the lower right tells you it's connected to the Recycler, which is where the extra carbon will go.
http://steamcommunity.com/sharedfiles/filedetails/?id=116964758
What that means is that I want to alternate those two outputs in that pipe. Every time I break up a cyanogen, I want to push through the CN half, followed by the lone N atom, in those positions. So far, I chose the order and positions arbitrarily -- right now I'm only worried about "pieces go this way".
Same story for the hydrogen reactor. Since I'm already using mixed output, I figure I might as well go all the way and show just how powerful it can be. I plan to stagger the hydrogen atoms apart in the positioning I want them in the Assembler to stick it all together with minimal fuss.
http://steamcommunity.com/sharedfiles/filedetails/?id=116964795
Oh, and here's what the editor for the notes looks like.
http://steamcommunity.com/sharedfiles/filedetails/?id=116964900
And when you go into the third reactor at the end, your output notes from the others show up as expected inputs wherever they're piped to!
http://steamcommunity.com/sharedfiles/filedetails/?id=116964953
Note that we haven't actually placed any waldo code yet. This is purely a conceptual and organizational step to wrap your head around the problem, and make it easier to keep track of what you're doing. This is just a broad scale of what I want to happen.
The next step is making it happen! I build the waldo track to produce the thing I wrote down.
http://steamcommunity.com/sharedfiles/filedetails/?id=116965029
http://steamcommunity.com/sharedfiles/filedetails/?id=116965070
Upon completing each circuit, I test it to make sure it's doing the step I want it to and depositing the right things in the right places.
And then I go into the third reactor and think...you know...I probably could put everything together from here, but it would probably be a mess and I'm lazy. So I start thinking, what would be the most convenient way these could pop in? And when I think of it, I go back and edit the notes to reflect what would be really, really convenient to have.
http://steamcommunity.com/sharedfiles/filedetails/?id=116965187
And then I go back into the first two reactors and make that happen instead.
http://steamcommunity.com/sharedfiles/filedetails/?id=116965272
http://steamcommunity.com/sharedfiles/filedetails/?id=116965359
Again, testing them to make sure it follows.
Note the vastly simpler flow control in the cyanogen reactor once I realize I want the two pieces dropped in the same place. The red guy just deals with the junk carbon now, and the blue grabs the two pieces we want and handles them identically. Don't worry about the flip-flop -- it's a toy you get much later in the game, but all you really need to know for now is that I used it to make my notes happen.
Also note that I had the cyanogen reactor change the order of its outputs to drop the single nitrogen first, and you're about to see why. Here's what I do in the last reactor.
http://steamcommunity.com/sharedfiles/filedetails/?id=116965470
Because of how I placed all these mixed outputs, all I have to do is have red collect the nitrogen I want at the T of the final molecule and have it sit still while blue spawns all the other stuff around it and bonds everything in one step.
Here's what it looks like from outside.
http://steamcommunity.com/sharedfiles/filedetails/?id=116965577
As you advance through the game, you'll have a bunch of reactors with a ton of output notes, and they clutter up the screen. You can right-click and hide them from the external view -- they'll still show up inside the reactors. You'll probably want to hide...most of them throughout the game.
I gave it a go, watched it build and drop off one molecule, then hit full speed and saw a victory screen. Thankfully with nothing breaking along the way this time, but inevitably it will happen most of the time. By the end of the game you will grow to despise the broken reactor sound.
That's the general approach I take to solving these puzzles. Get a handle on the general flow of pieces, chart out where I want the pieces to specifically end up, adjust as necessary to make the later parts easier, and then make each piece happen.
Hope that helps! If anything about that was unclear, just say something and I'll try to go into better detail. :)
Ah, that. Well, you can't have 3 inputs per reactor; 2 inputs and 2 outputs max.
However, you can use the output of one reactor as the input of another. So you can create a partial product out of 2 inputs in one reactor, and then use its output and the third input in another reactor to build the final product.
Since you mention 3 inputs, can I take it you've reached mission 2.6, "Sleepless on Sernimir IV"? That's where this first becomes an issue. You start with H, O and C and have to make CH2O. Since you have 3 inputs, you need to use 2 reactors. Now, there are 3 ways to connect the reactors:
Scheme I : O,H first, then C
Scheme II : H,C first, then O
Scheme III : O,C first, then H
In production missions, you have to break down the full reaction scheme into sub-reactions, with each reactor taking care of one of the sub-reactions. Usually, there will be multiple ways of creating the end-product, labeled here as I, II and III? Which one should you use? Well that's just it: they'll all work :D.
Of course, some schemes will be more efficient or easier to use than others. In this case, Scheme I is rather nasty, so that's probably not the way to go. II and III are both easy to implement, but III will be slightly faster because the bottleneck will be attaching the second H, so doing that as the last step saves a little bit of time.
EDIT:
Oh, one final note. When you output stuff, it'll appear in the next reactor in the order and form that you've outputted it. In the screenshots, I've attached notes to the output of reactor 1, so you can see what it should output. However, a note is only a hint; it does not determine what the output actually is.
EDIT 2:
I just realized a version of scheme I that isn't as messy:
I know this sounds insane, but knowing how to do these kinds of input/output/bonder placement manipulations will become so incredibly useful at the later stages of the game.
One thing you have to be careful with (or exploit) with production levels is that molecules are not repositioned at all. If you output an atom in the upper-left of an output, when it comes into another reactor, it will be in the upper-left of the input. As such, you usually want to be consistent with where you drop molecules. In research levels it doesn't matter, but in production levels it can kill you since you can miss grabbing inputs.