 The primary game mode of SpaceChem depicts the internal workings of a Reactor , mapped out to a 10 × 8 regular grid . Each reactor has up to two input and up to two output quadrants , and supports two waldos , red and blue , manipulated through command icons placed on the grid . The player adds commands from an array to direct each waldo independently through the grid . The commands direct the movement of the waldo , to pick up , rotate , and drop atoms and molecules , and to trigger reactor events such as chemical bond formation . The two waldos can also be synchronized , forcing one to wait for the other to reach a synchronization command . The reactors may support specific nodes , set by the player , that act where atomic bonds can be made or broken , where atoms can undergo fission or fusion , or where logic decisions based on atom type can be made . As such , the player is challenged to create a visual program to accept the given inputs , disassemble and reassemble them as necessary , and deliver them to the target output areas to match the required product . The product molecule does not need to match orientation or specific layout of the molecules as long as the molecule is topologically equivalent with respect to atoms , bonds , and bond types ; however , in larger puzzles , these factors will influence the inputs to downstream reactors . While the two waldos can cross over each other without harm , collision of atoms with one another or with the walls of the reactor is not allowed ; such collisions stop the program and force the player to re @-@ evaluate their solution . Similarly , if a waldo delivers the wrong product , the player will need to check their program . The player successfully completes each puzzle by constructing a program capable of repeatedly generating the required output , meeting a certain quota . 
