A rig
Atomic modules bond the moment they touch edge to edge, and modules bonded together are a rig. Inside a rig no cable is needed: a CLK drives the SEQ to its right, and a QNT puts the CVs to its right on its scale. A strip, the bracket, runs along the top of the whole rig, with the word ATOMIC in its middle.
The rig ends where the modules stop touching: at a space, or at a module from another plugin. Modules apart are separate rigs and know nothing of each other. A bypassed Atomic module does nothing, but it does not split the rig: the modules either side act on each other as though it were not there, and the bracket breaks over it.
A RIG saves the rig, opens saved ones and stores scenes. Nothing bonds to its left, so it always stands at the left end. A GAP splits a rig in two: the bracket and a RIG at the left end run on over both sides, but no module on one side acts on the other.
The bracket
The bracket acts on the whole rig at once. Drag it to move the rig. With the pointer on it, Delete removes the rig, ⌘*-D or Alt-D duplicates it, and the same with Shift held duplicates it with its cables. In a rig with a SEQ or a CLK, the word ATOMIC turns to RESET under the pointer: click it to restart every SEQ and CLK in the rig at once.
Blocks
Modules of one kind standing side by side, with nothing between them, are a block. Four CVs in a row are a block of four CVs; a QNT, then four CVs, is a block of one QNT and a block of four CVs. A block ends at the first module of another kind.
ATNs make two kinds of block, which end each other: ATNs that set a range and ATNs that take a signal (see Taking what stands to the left).
A block is what a SEQ steps through, one step per module, up to 255; a TRG gives a step per trigger. A block of CRVs is also one curve drawn across them all.
Which way each module acts
Each module acts on its neighbours in one direction. Some set something for what stands to their right, some only hold a value for others to read, and some take what stands to their left.
Setting what stands to the right
A QNT sets the scale of the CVs to its right: they show note names and land on its lit keys. An ATN sets the range and offset of the CVs or CRVs to its right.
A QNT's scale holds for every block of CVs to its right until the next QNT, and an ATN's range until the next ATN. A QNT never sets CRVs. An ATN's range carries on only for the kind of block it meets first: in ATN, four CVs, SEQ, four CRVs, SEQ, the ATN sets the range of the CVs, and the CRVs keep their full range. For those CRVs, put a second ATN just before them.
This works because each block takes its scale and range from the QNT or ATN standing just before it, between it and the block before. Where none stands there, it copies the nearest block of its own kind to its left. One case breaks the chain: the CVs after a new QNT keep the earlier ATN's range only when the CVs before were on a QNT of the same variant (keys, roll or divider). After CVs with no QNT, or on another variant, they span the full range again, until an ATN beside the new QNT sets one.
For example, in QNT, four CVs, SEQ, four CVs, SEQ, both blocks of CVs land on the QNT's keys, and the second SEQ plays the same scale as the first. Put an ATN before the second block of CVs and that block keeps the scale but takes the ATN's range. Faders that should stay off the scale go to the left of the QNT.
A CLK drives every SEQ to its right, wherever it stands, until a second CLK further right takes over for the SEQs past it. A CLK with nothing in its RESET restarts whenever the CLK to its left does.
Holding a value
A CV holds a voltage, a CRV a curve and a TRG a row of triggers. They do nothing to their neighbours: a SEQ, a POLY or a MIX to their right reads them.
Taking what stands to the left
A SEQ steps through the modules to its left, one per step. A POLY merges the outputs of modules to its left into one poly cable, and a MIX sums them through a fader each.
An ATN can work the other way too. With the arrow into its IN jack lit, it takes the nearest signal to its left, a SEQ, a CV, a CRV or a MIX, as though cabled into IN, and sets nothing to its right. The ATN guide shows its two arrows and how to switch them.
How far a SEQ, a MIX or a POLY looks
A SEQ looks left for the nearest block of CVs, CRVs, QNTs, TRGs or ATNs, passing over any CLK, SEQ or MIX on the way, and steps through the whole of that block. So CLK, four CVs, SEQ is a sequence of four steps, and so is four CVs, CLK, SEQ. Two SEQs side by side both step through the block to their left, each with its own playhead and rate.
A POLY ends a SEQ's search. A SEQ that meets a POLY before any block arpeggiates the POLY's chord, one channel a step, unless a cable is in its POLY IN. With nothing to its left to step through, it arpeggiates the cable in POLY IN.
A POLY and a MIX look further. Each takes every module of one kind to its left, at any distance, in one block or several, passing over other kinds: a MIX to the right of four SEQs takes all four, even with CVs between them. By default the kind is the nearest one it can take, and the label at its top names it; drag the label to choose another kind, or one block of a kind. Other MIXes and POLYs count as a kind only once every other module to the left has been taken. A POLY takes up to sixteen modules and a MIX fifteen, the ones nearest it; the leftmost of them comes first, on channel 1 or the top fader.
A module already taken by a POLY or a MIX further left is not taken again, so two of them share out one rig: in SEQ, SEQ, CV, CV, MIX, POLY the MIX sums the CVs and the POLY passes over the MIX and merges the SEQs. The POLY and MIX guides list which kinds each takes.
That makes a mix of mixes: in CV, CV, MIX, CV, CV, MIX, MIX, the first MIX sums the two CVs to its left, the second the two CVs it stands after, since the first two are taken, and the third, finding no CV left, sums the two sums.
Nothing looks past the end of the rig or across a GAP.
Cables
A cable into a module's own input changes only that module; the rest of the rig works as before. A QNT with a cable in IN quantizes that cable and still sets the scale of the CVs to its right; a CV with a cable in IN gives the cable's voltage, and a SEQ still steps through it.
Two modules are exceptions. A cable in an ATN's IN makes it scale that cable alone, and it then sets nothing to its right. A cable in a POLY's IN turns the POLY round: it splits that cable onto the CVs and TRGs to its right, up to the next POLY, one channel to each CV and one per trigger to each TRG.
* ⌘ is Ctrl on Windows and Linux.