Notice of Obsoletion

This guide is now superseded by a version on steam, which you can find here. Everything in this post still applies, but the steam version should have more concise, up-to-date information.

Due to some nonsense, all of the original image embeds in this guide have died; I've replaced them with hopefully permanent image links, but unfortunately they no longer embed. I apologize for the inconvenience.

Introduction

This is a guide designed to cover everything from the bare basics to the advanced and technical side of ions and prisms. I'll mainly be covering how prisms work and how to configure them properly, not as much how to use ions themselves in a competitive setting. There are plenty of other resources for that already out there (which I'll link below). Chances are if you're a new player (especially if you've been referred to this post), there's a bunch of stuff you can learn from this, so please bear with the lengthy explanations, given that prisms are surprisingly in-depth. Even if you already know how prisms work, you should probably still give this a skim since I'll be including a lot of niche or lesser-known information you might find interesting.

If you have any questions, want help with your own ions/prisms, don't understand something, or want to suggest additions/revisions to this guide, you can reply to this discussion, or preferably you can join the official Cosmoteer Discord, provided you're at least 13 years old (in compliance with Discord's TOS). There are plenty of friendly people on the Discord willing to help with all things shipbuilding or piloting. If you need me specifically, you can ping Captain Redstone#3480 in an appropriate channel for a (hopefully) quick response.

If you haven't already read 0neye's guide to shipbuilding, you should check it out first. I'll be getting into way more detail than he does with prism mechanics specifically, but if you're looking for tips, tricks, lingo, or resources on literally any other topic (such as the proper application of ions in shipbuilding), his guide is the place to go (and it's a good starting ground for better understanding stuff in this guide too).

Note: a lot of the image examples I'll be using are setups I made specifically to show off how ions and prisms work in various scenarios. As such I'll be using extremely inefficient crew and reactor setups so I don't need to spend half an hour optimizing logistics on each example. Don't use this kind of power supply; if you're looking for information on how to properly power ions or other parts, you can reference 0neye's guide (linked above).

Vocabulary/Lingo
The Basics
Free vs Locked
Combination Efficiency (This is the most important part)
Ion Cores and Hitboxes
Damage Control and Allegiance
Overmerging, Overkill, and Falloff
Common Mistakes Compendium
Miscellaneous/Niche Information

Vocabulary/Lingo

[DPS]: An abbreviation for Damage Per Second.
[DPT]: An abbreviation for Damage Per Tick, not to be confused with DPS.
[Emitter]: Short for "Ion Beam Emitter", the part that actually generates and fires ion beams.
[Prism]: Short for "Ion Beam Prism", the focus of this guide. Honestly not sure why I'm even writing this.
[Beam]: Refers to the actual projectile that emitters and prisms fire.
[Ions]: Ions are a sort of generic "wildcard" term. Depending on context it can describe ion emitters specifically, ion beams, or the weapon system as a whole.
[Prism Core]: A collection of prisms arranged to redirect and combine ion beams to focus a large number of input ions into a single or small number of output beams.
[Fixed Weapon/Spinal Weapon]: A weapon with a 0 degree firing arc; one that can't turn. Currently the only spinal weapons are ion emitters (not prisms) and railguns, distinguished ingame by a solid targeting line instead of a normal firing arc.
[Turreted Weapon]: A weapon with a moving turret component that turns to aims at opponents. Note that missile launchers have a 360d firing arc, but don't have an actual turret component.
[Hitscan]: A type of projectile that fires and deals damage to its target at the exact same time, rather than having to fly through the air to hit its target.
[Tick]: Each time the game's physics engine updates. Cosmoteer runs at 30 TPS (Ticks Per Second), meaning the game's physics simulation will update once every 1/30th of a second on 1x speed. This is not to be confused with FPS (Frames Per Second), which is the speed at which the game refreshes what you see onscreen.
[x% Strength]: Refers to how much stronger a given ion beam is than the basic one fired from an ion emitter.

For the sake of time and conciseness I'll be using basic mathematical notation and abbreviations instead of typing really long sentences out. As long as you've taken algebra you should be fine, but if you have trouble understanding a specific paragraph or something, let me know and I'll try to adjust it.

Any other used term that you're not familiar with can probably be found by checking 0neye's guide's lingo section (linked above), or by using Google.

The Basics

Prisms are a part designed to be used in combination with ion emitters. Prisms can capture and redirect any ion beams hitting them, even across multiple independent ships. They can also receive multiple input ion beams and will combine them to form a single, more powerful output beam. Given enough input ions, this allows you to create an ion beam with far more DPS, allowing vastly more focus fire than ion emitters alone can accomplish (poor focus fire being one of emitters' larger weaknesses). Prisms can also be aimed freely in any direction, allowing ions to easily be used in diagonal builds, or in more complicated ways I'll get into later.

Now, despite being a simple concept, prisms are a very complicated part with a lot of properties and plenty of different applications. Unfortunately this means they're very easy to misuse, and without looking in-depth on part statistics (which a lot of people don't even know about), many players don't even know that they're using prisms incorrectly to begin with. If you just point prisms at other prisms, and/or use something similar to the setups shown below, I'm afraid you're doing it wrong. I'll get to a list of mistakes to watch out for later in the guide, but to understand why they're mistakes you'll probably need to read through other parts of the guide first. If you only want the absolute basics, skip to the "Combination Efficiency" section; it explains how to fix the biggest and most common mistake that you can make.
Here's a couple common (but bad) setups:
https://ibb.co/CMX42WS https://ibb.co/YPYSvpT

Free vs Locked

Prisms have two (and a half) different modes; freely-rotating, and locked (or fixed) position. Freely-rotating is the default; when you place a prism, it'll act like any other turret and will try to target enemy parts automatically. The second mode allows you to lock a prism in a certain position, preventing it from trying to turn and attack opponents. To lock a prism, you need to select it by clicking on it outside of build mode (depending on your settings you might need to hold Ctrl), and click the "Aim Prism" button at the lower left of the screen (as seen below), or alternatively use the keybind Ctrl P (by default). Once you're aiming the prism, simply click in a direction and the prism will rotate to that direction and lock in position. By default the aim function will automatically snap to cardinal/diagonal angles or to other prisms for convenience, but you can override that if you want by holding Ctrl (or whatever key you have bound to "Select Parts"). To unlock a prism, simply select it and hit the "Cancel Weapon Target(s)" button, or the H keybind (by default). Unfortunately there's currently no way to configure prisms in any way within build mode, but you can copy-paste sections of prisms to copy their aim settings, even if you rotate the pasted section.
https://ibb.co/M6LCPsR

Now, you're probably wondering why I said there's two and a half different modes. That's because when you aim a prism, it can actually lock in two different ways; if you click in a direction, the prism will aim at that direction, but if you aim at a second prism (known as linking to a prism), it will try to rotate towards that prism, distinguished by a different targeting icon. The two functions sounds identical, but the key difference is that fixed directions can't move, but other prisms can; if you tell a prism to aim directly forwards towards another prism, it will keep facing forwards regardless of what happens to the prism in front of it. On the other hand, if you tell it to link to the second prism instead, it will continue to aim at that second prism even if it changes position. This is useful for linking prisms between ships, but it also presents a potential pitfall I'll address in the "Common Mistakes" section.
https://ibb.co/Z6wnyrC

Combination Efficiency

This is the part of prisms that almost all new players get wrong. Prisms don't just take any inputs they get and add them up; far from it. Combining beams isn't completely efficient; after a prism receives one input ion, each additional input will lose 25% more damage than the last. This means that if you fire 3 beams into the same prism, the first will do 100% of its original damage; the second will do 75% of its original damage; the third will do 75% of that 75%, or about 56% of its original damage. Adding a fourth beam would do about 42%, a fifth about 32%, a sixth about 24%, etc. In a nutshell, the more inputs you add to a prism, the more damage is lost in converting it to an output beam. What makes this an especially large issue is that the largest beams always take the largest damage losses. For instance, if you aim a 1x strength ion and a 10x strength ion at a prism, the 10x strength will always take the 25% strength decrease. Aiming five 1x ions and a 10x strength ion at a prism will reduce the 10x beam by about 76%, significantly affecting overall damage output.

This simplifies into two easy rules for avoiding major DPS loss. If you're only going to get one takeaway from this entire guide, make it this:

Don't combine more than two beams at once
Don't combine beams of unequal strength

Following these two rules creates what's known as a "two-to-one" (written as 2:1) "combination", a term you'll hear a lot when discussing efficient ions. Using 2:1 combinations will naturally form a neat little tree-like structure that's both easy to make and is effective:
https://ibb.co/gDRK4fZ

To give you an idea of how much of a difference this can make, here are some comparisons between a properly-made core and two common types of improper cores. Notice how this becomes a bigger and bigger issue as ion cores get larger:
https://ibb.co/5BZ5NY5 https://ibb.co/tCG6CDn https://ibb.co/g64mnh8 https://ibb.co/XJfxM3W

Here's a couple interesting side effects of how prism combination works:

Since you always want two inputs to each output, the ideal number of emitters you want to use with a single output is always a power of 2.
Because the largest beam takes the biggest hit, with repeated uneven inputs (such as the examples seen above) you'll very quickly hit a damage cap due to progressively larger chunks being taken out of the strongest beam. It ends up working out so that no matter how many beams you add each time, the maximum damage you'll ever reach is 4x the default beam strength. You could combine a million different ions this way and it would never reach the strength of 8 ions combined properly.

Ion Cores and Hitboxes

Ion cores (sometimes called prism cores) refer to an area of a ship where ions are combined and eventually fired out of the ship. Ion cores should always be buried deep within a ship for better protection since ions prisms are pretty delicate (which I'll talk about in the "Damage Control and Allegiance" section). Unlike non-spinal weapons, you can recede ions really far into your ship because beams can be fired through thin, long shielded armor barrels, which opponents are lucky to get a single shot started down. Now, using up large sections of a ship's internals to build an ion core makes surrounding crew logistics difficult, and can mean your ship needs to be physically larger (usually a downside). Because of this (and players' competitive nature), it's commonplace to see people trying to compact ion cores as much as possible. Making a compact ion core is more difficult than you'd think, though; the smaller you try to make an ion core, the more prisms get in the way of each other. You can spend about as much time optimizing a prism core as you want; you can spend 30 seconds and get a decent core, or you can spend 3 hours and get one so stupidly compact it's impossible to see how it works without a diagram. Note the actual advantage you get from compacting an ion core will become smaller and smaller as it takes more and more time to figure out, so don't worry too much about making it absolutely perfect.

Here's a bunch of information on how to make ion cores, and how to compact them:

Ion beams are only half a meter wide, and prisms' hitbox is only a circular area instead of a full rectangle, which means you can fire beams between other prisms pretty easily. This is great both for compact outputs and for getting power from once place to another in a tight situation.
https://ibb.co/6nH5B1x
If you have all of your emitters and your first set of prisms in a row, simply offsetting any other prisms by one tile to the side will prevent them from accidentally interfering with both top and emitters in any way. If it weren't for this, you'd need more than twice the number of prisms to prevent emitters from interfering with other prisms.
https://ibb.co/j9CcK5n
Because ions are only half a meter wide, it's sometimes helpful to fill an armor barrel with armor triangles. Doing so leaves a one-meter gap that your ions can still fire through, and having the extra armor there increases the overall durability of the barrel slightly, while the smaller gaps make it harder for stray enemy shots to get down the barrel.
Instead of having a large wall of ions, fire two sets of emitters directly at each other such that prisms put in front of emitters will get hit by two beams, not just one. This more than cuts the required number of prisms in half, saving a bunch of money and space.
https://ibb.co/L6mGTHZ
Even if your number of ion emitters isn't a power of two, you can still make a 100% efficient ion core by outputting multiple beams of different strengths. For instance, if you have 24 emitters, you can combine 8 of those ions into an output three different times, and just have three outputs.
If you need an ion to aim at a very specific angle, you can tell it to aim very far away to allow more precision. Sometimes it can be helpful to temporarily add structure where you're aiming to give yourself a reference of where you're moving targets from and to. Prisms don't care whether they're targeting a location or another prism, they'll still automatically fire at prisms they're pointed towards, even if there's a prism far in front of or behind their actual target location.
By firing ions at an extremely precise and shallow angle, you can hit a prism even if there are other prisms directly in front of and behind it.
https://ibb.co/YXdkfGn
Don't use prisms for the sole purpose of redirecting beams unless absolutely necessary. They cost a lot, and often times with larger cores adding a prism to "help untangle" ions leaves you with even less space further down.
If you're running out of space and can't figure out a good approach, it can sometimes help to move the initial set of prisms from the bottom to the top or vice versa. This allows beams to be fired diagonally through the gap created, away from really compact parts of a core you might not be able to get through otherwise.

Damage Control and Allegiance

One of the big downsides of using prisms is that they're one of the most fragile weapons in the game, barely edged out by railguns. Prisms have the same health as an armor 1X2 and have a ridiculous 100 meters of penetration resistance (as of 0.15.16. This may be subject to change in the future). But similarly to railguns, once a single prism in a core is destroyed, the rest of the core will usually go with it. Most people don't know this, but a large number of explosions in Cosmoteer happen relative to filled ammunition; for instance, an empty ammo storage has no collateral damage, while a full ammo storage will cause a small explosion and a lot of fires. Prisms are no exception; they'll do up to 10,000 damage in a 3-tile radius to the surrounding 360d area, multiplied by the beam's extra (or reduced) strength. (Due to the way Cosmoteer calculates explosions, actual damage can be much lower.) This means that prisms with a standard single input will barely scratch surrounding parts, while output prisms on giant cores will basically vaporize anything in a 4-5 tile radius. Since prism cores are often extremely compact, they will almost always cause a massive chain-reaction (unless designed to prevent this), destroying the entire core and sometimes surrounding emitters/structure.
https://ibb.co/4T0YV1k

Another reason that ions can be very fragile is due to the way ship allegiance works. In Cosmoteer your ships are set to "Player 1", and opposing ships are set to "Player 2". Any useless scraps of a ship left behind in battle are given the "Junk" allegiance, which prevents them from being automatically targeted by weapons, among other things. Junk is created when a ship, or piece of a ship, loses its last weapon or crewmember. Most of the time if a prism section is disconnected, it won't have any crew and will thus be set to junk. The problem with this is that ion emitters will still be set to target those prisms (since binding to a prism and targeting a part are effectively the same thing) and fire on them. Since those prisms are now set to junk, the emitters will actually damage them, quickly causing them to explode. This means that even if prisms themselves aren't hit, damage to a prism core (especially if it isn't secured very well) can cause it to self-destruct. Structure is by far the cheapest part in the game; if your core isn't being held together by much, spare a few hundred credits and add some more supports, it can make much more of a difference than you'd think.
https://ibb.co/3F46yh9

Overmerging, Overkill, and Falloff

Due to the game's mechanics, there are three different ways that ions can lose DPS aside from simply being combined:

Overmerging

Since merging two beams reduces one beam by 25%, every merge you make will lower those beams' combined damage output by 12.5%. If you have a very large number of input ions, merging them all into a single beam can end up reducing total damage output significantly. By the time you combine 32 input beams into a single output, you've lost 48.71% of those original beams' damage. The best way to get around this is to use multiple output beams in a prism core. Having multiple outputs reduces the number of times damage is lost by combining beams; reduces cost slightly by eliminating a few prisms; and helps alleviate issues with part overkill (which I'll explain in a minute).
https://ibb.co/tcRRrZ2

So, if combining beams reduces cost-efficiency by that much, is merging prisms even worth it? Usually, yes. Although having more outputs makes prisms do a lot more damage, it also makes them a lot harder to properly defend, since you usually need a wider, more exposed barrel to fit them all. Even focusing them all through a single meter-wide point and having them spread out later can cause issues with overkill at closer ranges. Since ion ships can vary so much, there isn't really an optimal number of outputs that works for every scenario; if you're at a complete loss, I'd suggest two or three. Really, though, it shouldn't be too hard to experiment with balancing out offense and defense. If you have too many outputs (or forgo merging entirely and use lots of surface prisms) it can raise your raw DPS immensely, but it also tends to make your defense much worse. On the other hand, focusing everything you have into a single beam, though easy to defend, starts to become extremely cost-inefficient and can be very heavy depending on armor configurations. It might take some time to get used to this balance, but just be patient, and remember that you can always ask a community member for building advice if you need it.

Part Overkill

Part overkill is an effect in which doing too much damage to a part wastes potential DPS. This technically applies to all weapons, but it's by far the most noticeable with large ions because of their massive damage per hit and tight focus fire. During a single tick, Cosmoteer's physics engine will figure out which projectiles are about to hit which part(s); then it applies all of that damage; and only then it checks if the part should be destroyed or not. Since the physics engine only checks if the part should be destroyed after all of the damage has been applied, doing more damage to a part than it has hitpoints will waste a bit of damage. What makes this even worse for ions is that they don't actually register a hit every tick, but every third tick. This means that each "packet" of damage will do three times as much damage at once, compared to most other weapons. To give this effect some actual numbers, 32 emitters combined into one beam will do roughly 35,000 raw DPS at mid range, resulting in each hit doing roughly 3,500 damage. A normal piece of armor has 4,000 health; pointing this ion at a piece of armor will do 3,500 damage, lowering the armor's health to 500, then 3,500 a second time, bringing the armor's health to 0 (-3,000), destroying it. Even though the ion should theoretically be able to do 7,000 damage in two hits, those hits only applied 4,000 effective damage to the armor, wasting 3,000 potential damage, or about 43% of the ion's potential DPS. This becomes an even bigger deal when targeting weaker parts like corridors that only have 1000 health; with this same setup, the ion will apply 3,500 damage to each corridor, instantly destroying it but also wasting 2,500 damage (roughly 71% of its max DPS) in the process. At a certain point, adding more power to ions becomes completely meaningless since it can one-shot almost any part in the game. Smaller beams aren't immune to this effect either; So, how do you try to fix this?
https://ibb.co/vcFtVBw

The main solution to part overkill is using multiple output beams to help distribute damage over a wider area rather than doing all of its damage in the same spot. This gives the added bonus of actually doing more raw DPS anyway, due to combining beams fewer times. Note that having multiple ions hit the exact same part does not minimize part overkill (since each tick calculates all projectiles' damage before removing parts), so focusing lots of beams onto a single tile doesn't help. Having multiple output beams in parallel of each other is best for DPS, but at the same time having too many outputs in parallel requires a wide barrel, which is very hard to defend. A happy medium is to aim your outputs all at a single point very close or inside the front of your ship; this allows you to make the barrel very tight in some places, increasing defense, but also allows the beams to spread back out afterwards. It's a good solution, but unfortunately it still isn't perfect, since being too close to an opponent doesn't let the beams spread out, which can often cause them to hit the same few parts, wasting damage. On the other hand, being too far from an opponent often hurts focus fire significantly.

The last thing to note about part overkill is that it affects all ions to some degree, it just only becomes an issue with extremely powerful beams. If you think about it, even if you're doing very little damage per tick, some amount of damage will always be lost when destroying a part, even if it's insignificant. Even though the maximum damage lost is always the same relative to an ion's base DPS, the damage lost can still change significantly relative to the max health of parts you're hitting. As you get closer to doing as much damage as a part has health, you'll deal the finishing blow more often, both opening up the possibility of dealing excessive damage more often and raising the amount of excessive damage you can deal at once. You can think of it almost like a ladder; raising your foot makes no difference until reaching the next rung, and if you don't reach that rung the effort is wasted. The main difference is that ions' "ladder" has rungs placed at unit fractions of the ladder's length (1/1, 1/2, 1/3, 1/4, etc), causing the gaps between rungs to become progressively larger as you climb it. Since different parts have different amounts of health (changing where overkill starts and stops), and because of falloff (which I'll get to in a second), there aren't really any "magic numbers" where raising an ion's DPS increases its average damage-efficiency. On average, raising ions' base DPS becomes more and more damage-inefficient all the way up to the point where adding more base DPS stops increasing applied DPS entirely. The best solution, as previously mentioned, is to use multiple smaller output beams to both increase combination efficiency and lower potential overkill for both beams combined. Just keep in mind that there's a balance to be struck; using fewer stronger beams lowers overall damage output, but using more weaker beams lowers focus fire, and in turn drill speed.
https://ibb.co/dJbLGvm

Damage Falloff

If you've checked the stats of ion emitters, you'll notice that ions' damage decreases linearly from 2,500 DPS to 1,750 DPS (a 30% decrease) when going from point blank to its maximum range of 300 meters. This rule applies to all ion beams, regardless of source or strength. The important part is that if a beam loses X% of its damage, that loss carries over to any other prisms it hits; only the range is reset. As an example, if you have a default ion firing at max range (2,500-30% = 1,750) and it hits a second prism, that second prism's base damage will now be 1,750, going down to 1,750-30% = 1,225 damage at maximum range. Of the three forms of DPS loss, this is by far the smallest issue, since even some of the larger and looser competitively designed ion cores simply don't take up enough space to make more than about 2% of difference. The only real thing you want to avoid is pointing ions really far across an ion core to merge with a shorter beam, because it slightly lowers the long beam's DPS. This also means the shorter beam with slightly more damage takes the 25% combination hit. Even in this case, though, it's barely noticeable. Really the only time it'll ever make a major impact is with incredibly large ion cores that are several times larger than the build grid itself.
https://ibb.co/LkCJwg9

Common Mistakes Compendium

Not properly combining beams: By far the biggest mistake people make is combining beams badly. Most issues can be boiled down to using more than two inputs for a prism and/or firing beams of unequal strength at a prism. Some common examples of this are firing a bunch of emitters at a single line of prisms, or firing a large number of ions at a single prism.
Facing emitters away from each other/all in one direction: As previously mentioned, facing emitters towards each other cuts prism costs (and space) in more than half. If you face emitters away from each other, or all in one direction, you lose this bonus and lose a bunch of money for no good reason.
Forgetting to lock prisms: Often times people will place a prism facing in X direction, and forget to actually tell it to fire in that same direction. This means that the prism isn't locked, and it will often try to rotate away from its intended destination to aim at enemy ships. If your ions are intermittently cutting out when turning, this is probably the reason.
Not protecting your prisms well: Prisms have a fair amount of health, but with all but the smallest of ships they can still be destroyed in a fraction of a second. Make sure prisms are significantly shielded, and, when applicable, hidden behind plenty of armor.
Not considering damage control: Especially with stronger ions, prisms explode and can chain-react with each other. If possible, keep prisms or sections of prisms apart from each other so that they don't all explode at once.
Not properly securing ion cores: Having part of your ion core being disconnected from the rest of the ship causes it to self-destruct, and even if it didn't, all of your finely-tuned angles would almost certainly get messed up. Make sure your ion core is secured to the rest of the ship in several different places.
Using only one output on large cores: For multiple aforementioned reasons, having only one output ion actually hurts potential DPS significantly. Using a bunch of smaller outputs becomes more and more efficient the larger the core is.
Not giving emitters 100% uptime: Every time an emitter flickers off for a second, the prism it's aiming at will have only one input, giving the next prism an uneven input, and the next, continuing on until it affects your output beam pretty significantly. Having just one ion temporarily offline can make a significant DPS impact, so properly supplying ions is nearly as important as setting up prisms properly in the first place.
Receding prisms too far: While moving prisms further back to protect them is great, you need to be careful because it hurts both their range and DPS (the former of which can be alleviated using a secondary output prism, though it's not a great solution). This applies both to protection in front of prisms, and to the way ion cores themselves are laid out.
Using extraneous prisms: Prisms are rather expensive, so adding prisms you don't necessarily need hurts cost-efficiency. In some cases, adding prisms can actually be bad, since powered prisms explode. Having an extra prism can be the difference between prisms chain-reacting or not.
Unnecessary redirection: Prisms take 0.2 seconds to turn input(s) into an output, which means the more prisms an ion needs to get through, the longer it takes to reach an output prism and fire. Ions will only attempt to fire once they have a target in range, so the longer it takes for a prism core to 'warm up', the more potential damage is wasted. This can make a surprisingly large difference against extremely agile opponents, since they'll often duck in and out of your range quickly, making your ion core have to spend time warming up over and over again.
Linking to a prism instead of to a location: Sometimes it can be useful to aim an output prism at a second output prism near the surface of a ship, such as for range extension, or to let the second prism rotate and have the first one act as a fixed backup. In this scenario, you want the first output prism to be aiming forwards, not linked to the secondary output prism. If you link it to the second prism and the second prism is destroyed, it will no longer be linked to anything, and it will try to rotate toward enemies instead of firing straight down the barrel.
Accidentally unbinding prisms: Telling your ship to attack a specific part will automatically turn all freely-rotating prisms to that target, but not locked prisms. However, selecting a prism and then targeting a part will overwrite any aiming settings it had, since linking prisms and targeting parts are effectively the same thing (as previously discussed). If you forget to deselect a prism or have hotkeys applied slightly wrong, it's very easy to accidentally unbind it (and any other ions feeding it) from the rest of the core.
Having unlocked output prisms too close to each other: If you have a large number of freely-rotating output prisms, make sure that when they rotate they don't run into each other, which sacrifices accuracy, focus, and DPS. Sometimes, on really large ion cores, people will cluster a bunch of prisms together, and unless they fire perfectly straight it often creates lots of extra combinations you don't want.
Trying to build up energy using two prisms facing each other: While it sounds and looks cool, this is an extremely ineffective tactic for a ton of reasons. For example, it only does extra damage for two hits, and the build of power naturally causing a bad merge, quickly limiting how much extra damage you can actually get anyway.

Miscellaneous/Niche Information

Just as holding Ctrl (or aforementioned keybind) prevents an aimed prism's target rotation from snapping to cardinal/diagonal directions, it also allows you to target a location on top of a prism instead of targeting the prism itself. This can be helpful when trying to compact ion cores, as well as in a couple of niche cases, such as allowing secondary prisms to stay locked in a given direction after their intended output prism has been destroyed.
Currently you cannot give prisms a default angle without locking them. This means that diagonal freely-rotating prisms won't face completely forwards until they are given a target, at which point they'll need a bit of time to turn.
The mechanic of prisms powering each other isn't affected by ship allegiance; firing an ion beam at an enemy prism will actually cause that prism to redirect damage back at you (though it will still take damage).
Prisms are the only weapon in the game that cannot fire at things on their own. All other weapons in the game will get within range of an opponent and start to attack automatically. However, prisms need to work a little differently, since the part that controls when to fire and the part that actually fires can be different. If a freely-rotating prism tries to fire, any prisms facing it will notice and try to fire as well; any prisms facing those prisms will try to fire; and this continues on until it reaches emitters. This means two things: Firstly, emitters will only start to fire once the output prism is fully in range; and secondly, there's a very small delay between getting in range of a target and the emitters starting to fire, since it takes a tick for prisms to notice that they need to fire.
If you know your ion core is about to take a giant hit, set all of your ions to hold fire. Since prisms only explode when powered, turning off all of your ions in enough time allows your core to take a few hits without catastrophic chain-reaction damage. This makes having plenty of supports for ion cores even more useful. Note: setting emitters or linked prisms to "fire at target" won't stop them from firing, since they already have a target, namely the prism they're bound to. Additionally, if prisms receive power, they'll redirect it regardless of firing setting, so if your emitters are set to autofire, changing prisms to hold fire won't actually stop them from firing. This doesn't apply to prisms aiming at a direction, or to output prisms, since neither technically have a target at idle.
https://ibb.co/h9VKkv1
If you have a prism bound to a location rather than to a prism or enemy part, setting it to "fire at target" will act like "hold fire," since it technically doesn't have an actual target. Even if there's a prism directly in front of it, because it's not bound to that prism directly, it can't see if the prism wants to fire or not; therefore, it will never try to fire itself. This isn't usually a big deal, but it does mean that setting all prisms (instead of just output prisms) in some ion cores to "fire at target" may partially or fully stop the core from firing.
Emitters themselves actually have a worse power/DPS ratio than most other weapons, and also have a worse cost/DPS than most other weapons, especially when using prisms. Ions' biggest advantage is being able to focus a tremendous amount of damage in a very small space. A lot of Cosmoteer's ship design revolves around balancing surface area for weapons, defenses, and thrusters. Since you can set up ion cores inside of your ship, ions have by far the highest potential DPS/surface area out of any weapon, giving you way more room for defenses than you'd have otherwise. Other things that make ions powerful are their great focus fire (they dig a far straighter hole in opponents than most other weapons) and their hitscan property.
Despite prisms having a full 360d firing arc, they have by far the slowest turning speed of any weapon in the game, at 20d/s. This means that freely-rotating output prisms often turn more slowly than your actual ship, which is something to watch out for. Even worse, if you spend a long time facing away from a targeted part for maneuvering purposes, it will keep rotating towards that part, eventually facing in the completely wrong direction. Either untarget the prism, or give yourself a bunch of time when turning back towards the opponent, since the prism takes an entire 9 seconds to turn the 180d back toward the opponent.
You can calculate the damage loss on a prism's Xth input beam using the formula 0.75^(X-1).
You can calculate the DPS of a set of ions by using the formula 2,500*(1.75^X) where X is the number of levels of combination. For instance, 8 input ions combine 3 times to make 4, 2, and 1; 2,500*(1.75^3) = roughly 13,398 DPS. Note that ingame results will be a hair lower due to falloff.
When combining two ion beams, the output will never be lower than the strongest input. This prevents the combination of a 100x and a 1x beam actively lowering damage output to 76x.
I mentioned before that copy-pasting prisms keeps their aiming data, but if you're replacing existing prisms' settings with new ones, you don't actually need to remove them first. Simply going to build or blueprint mode and pasting the new section on top of the old section will copy aiming data even if it doesn't change any parts. Note that prisms linked to other prisms will lose that link if only the first prism is copied.
https://ibb.co/sRfd2m0
Autofiring ions can be good or bad. Depending on how your supply system is set up, autofiring will either cause outages (due to running out of power), or prevent outages (as ions tend to flicker when first turning on while crew exit their quarters). Additionally, it can give you a better indication of your range (outside of DC mode where you already see range indicators), though this might also help the opponent stay out of your range.
If a ship with prisms has all of its CRs disabled, prisms will freeze in place. They'll neither turn toward their destination, nor turn back toward their default position.
If a prism is powered off, it freezes as if it has no CR, and otherwise functions like it's set to hold fire.
When loading a ship with "start empty" enabled, prisms spawn in at their default position (the direction that they show up in blueprint mode), not their targeted position. Once the ship's CR comes online, the prisms will automatically turn to their normal angles. This means that the angle at which the prisms are built can affect how long it takes for them to reach their intended position.
You can easily calculate the DPS of an ion beam using developer mode's "Part Debugger" tool under "Sim". By selecting a prism, you can see how much "ion energy" it is redirecting. Ion energy is an internal component that is responsible for transferring power between prisms. Each ion energy is effectively worth 2.5 DPS, so you can simply multiply the amount of ion energy listed by 2.5.
https://ibb.co/8dTfNBr
Shields can partially or fully absorb prism explosions.
Emitters and prisms only actually start to or stop firing every 0.2 seconds, but the beam itself does damage every 0.1 seconds.
Prisms are the only energy-based weapon that aren't affected by power-draining weapons such as electro-bolts or EMPs.
Since firing ions at an enemy prism still powers it, you can cause enemy prisms to explode on destruction even if they weren't originally firing.
As long as you combine beams 2:1, the minimum number of prisms you can use will always be the number of emitters minus the number of outputs. If you have 16 inputs and 1 output, you can use 15 prisms, and with 16 prisms and 4 outputs, you can use 12 prisms. This even works for uneven outputs; combining 16 inputs into three outputs of 4x, 8x, and 4x can be brought down to 13 prisms.

Huge thanks to @Oneye for helping with formatting and verifying everything makes sense, and to my mom for helping me hunt for and fix grammatical issues!