stack

The stack command is used to stack the current structure. The type of stacking depends on the current structure. Currently available structures:

  • graphene/boronnitride (creates a stack of sheets)

  • cnt (creates a periodic stack of parallel cnts)

Depending on which structure is stacked, different arguments and commands for further customization are available:

graphene/boronnitride stacking

interlayer_spacing

the interlayer_spacing arg sets the distance between adjacent sheets Angstrom. the arg requires one floating point value. example: interlayer_spacing=5.0. The default for graphene is interlayer_spacing=3.35, the default for boronnitride interlayer_spacing=3.5. graphene will have ABA stacking and boronnitride will have AA’ stacking.

number_of_layers

the number_of_layers arg sets the number of sheets that the stack will contain. the arg requires one integer value. example: number_of_layers=5.

Example build:

CONAN-build: build type=graphene
CONAN-build: stack interlayer_spacing=5.0 number_of_layers=5

will yield the following structure:

Graphene_stacked

cnt stacking

Cnt stacking will create a periodic boox of parallel cnts

multiplicity

the multiplicity arg sets the number of unit cells in x and y directions. the arg requires two integer values. example: multiplicity=2 3.

tube_distance=

the tube_distance arg sets the distance between parallel tubes in Angstrom. the arg requires one floating point value. example: tube_distance=1.0.

example build:

CONAN-build: build type=cnt armchair tube_size=8 tube_length=10.0
CONAN-build: stack multiplcity=2 2 tube_distance=1.0

will yield the following structure:

cnt_stacked

add

the add command is used to place functional groups at a specific position. Functional groups are taken from the .xyz files in /current_version/structures/ and selected with the group argument. group=OH will search for a file called “OH.xyz” in the structures folder and add its contents to the sheet. The position can be specified using the position, which takes in the index of the atom the group should be placed on. When using VMD the indices can be shown using the vmd show_index command in conan. The command tries to take into account the local topology of the structure, so placements on curved surfaces (like the inside of a Pore) are possible.

undo

The last command can be reset using the undo command.