Creating replicas of structures

To create replicas of structures using SAMSON’s Python API, call their clone() function. You can then programatically edit these structures.

The example below shows how to start from a single nanotube to create a model of a nanotube “fabric” through a series of undoable steps.

Precisely, the scripts starts from a nanotube and performs the following steps:

replicate the nanotube in two directions to create a grid of nanotubes;
apply sine function to these nanotubes in the third direction to weave them with each other.

Visit the corresponding tutorial for the full explanation.

# get an indexer of all structural models in the active document
indexerOfStructuralModels = SAMSON.getNodes('n.t sm')
# get the first structural model from the indexer
nanotube = indexerOfStructuralModels[0]

# get an indexer of all atoms in the nanotube
indexerOfAtoms = nanotube.getNodes('n.t a')
a = indexerOfAtoms[0]
minX = maxX = a.getX()
minY = maxY = a.getY()
# go through all atoms in the indexer
for a in indexerOfAtoms:
    x = a.getX()
    y = a.getY()
    minX = min(minX, x)
    maxX = max(maxX, x)
    minY = min(minY, y)
    maxY = max(maxY, y)

length   = (maxX - minX)           # the nanotube's length
diameter = (maxY - minY)           # the nanotube's diameter
numReplicasX = 10                  # the number of replicas in one direction
distance = length / numReplicasX   # set еру distance between nanotubes based on the number of replicas

A = 0.75 * diameter                # set an amplitude for sine function

# get the active document
document = SAMSON.getActiveDocument()

# start holding to allow for undo/redo
SAMSON.beginHolding("Replicate nanotubes")

for r in range(numReplicasX-1):
    # create a replica
    replica = nanotube.clone()  # clone the original nanotube
    SAMSON.hold(replica)        # hold the replica node for undo/redo
    replica.create()            # create the replica
    document.addChild(replica)  # add the replica to the document

    # shift the replica in Y-direction
    dy = (r + 1) * distance
    # get an indexer of all atoms in the replicated nanotube
    indexerOfAtoms = replica.getNodes('n.t a')
    # loop over all atoms in the replicated nanotube
    for a in indexerOfAtoms:
        # shift atoms in the Y-direction
        a.setY(a.getY() + dy)

# end holding for undo/redo
SAMSON.endHolding()

# import the necessary functions and constants
from math import sin, pi

# get an indexer of all structural models in the active document
indexerOfStructuralModels = SAMSON.getNodes('n.t sm')

sign = 1  # used to change the phase of the sine function

# start holding to allow for undo/redo
SAMSON.beginHolding("Replicate nanotubes")

# loop through all structural models (all nanotubes)
for original in indexerOfStructuralModels:
    # create a replica
    replica = original.clone()   # clone the original nanotube
    SAMSON.hold(replica)         # hold the replica node for undo/redo
    replica.create()             # create the replica
    document.addChild(replica)   # add it to the document

    # for shifting nanotubes from the border
    shift = distance / 2.0

    # get an indexer of all atoms in the replicated nanotube
    indexerOfAtomsInReplica = replica.getNodes('n.t a')

    # rotate the replica by 90 degrees by changing x and y coordinates of its atoms
    # and shift the replica from the borders to have '#' pattern
    for a in indexerOfAtomsInReplica:
        x = a.getX()
        y = a.getY()
        a.setY(x - shift)
        a.setX(y + shift)

    # apply sine function in Z-direction to original and replicated nanotubes

    # get an indexer of all atoms in the original nanotube
    indexerOfAtomsInOriginal = original.getNodes('n.t a')
    # loop over all atoms in the original nanotube
    for a in indexerOfAtomsInOriginal:
        w = a.getX() / distance  # [dimensionless quantity]
        # apply sine function to the Z-coordinate of an atom
        a.setZ(a.getZ() + A * sign * sin(pi * w.value))

    # loop over all atoms in the replicated nanotube
    for a in indexerOfAtomsInReplica:
        # [dimensionless quantity], take into account the shift we did previously
        w = (a.getY() - shift) / distance
        # apply sine function to the Z-coordinate of an atom
        a.setZ(a.getZ() + A * sign * sin(pi * w.value))

    # change the phase to the opposite one
    sign = -1 * sign

# end holding for undo/redo
SAMSON.endHolding()

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# get an indexer of all structural models in the active document

indexerOfStructuralModels = SAMSON.getNodes('n.t sm')

# get the first structural model from the indexer

nanotube = indexerOfStructuralModels[0]

# get an indexer of all atoms in the nanotube

indexerOfAtoms = nanotube.getNodes('n.t a')

a = indexerOfAtoms[0]

minX = maxX = a.getX()

minY = maxY = a.getY()

# go through all atoms in the indexer

for a in indexerOfAtoms:

x = a.getX()

y = a.getY()

minX = min(minX, x)

maxX = max(maxX, x)

minY = min(minY, y)

maxY = max(maxY, y)

length = (maxX - minX) # the nanotube's length

diameter = (maxY - minY) # the nanotube's diameter

numReplicasX = 10 # the number of replicas in one direction

distance = length / numReplicasX # set еру distance between nanotubes based on the number of replicas

A = 0.75 * diameter # set an amplitude for sine function

# get the active document

document = SAMSON.getActiveDocument()

# start holding to allow for undo/redo

SAMSON.beginHolding("Replicate nanotubes")

for r in range(numReplicasX-1):

# create a replica

replica = nanotube.clone() # clone the original nanotube

SAMSON.hold(replica) # hold the replica node for undo/redo

replica.create() # create the replica

document.addChild(replica) # add the replica to the document

# shift the replica in Y-direction

dy = (r + 1) * distance

# get an indexer of all atoms in the replicated nanotube

indexerOfAtoms = replica.getNodes('n.t a')

# loop over all atoms in the replicated nanotube

for a in indexerOfAtoms:

# shift atoms in the Y-direction

a.setY(a.getY() + dy)

# end holding for undo/redo

SAMSON.endHolding()

# import the necessary functions and constants

from math import sin, pi

# get an indexer of all structural models in the active document

indexerOfStructuralModels = SAMSON.getNodes('n.t sm')

sign = 1 # used to change the phase of the sine function

# start holding to allow for undo/redo

SAMSON.beginHolding("Replicate nanotubes")

# loop through all structural models (all nanotubes)

for original in indexerOfStructuralModels:

# create a replica

replica = original.clone() # clone the original nanotube

SAMSON.hold(replica) # hold the replica node for undo/redo

replica.create() # create the replica

document.addChild(replica) # add it to the document

# for shifting nanotubes from the border

shift = distance / 2.0

# get an indexer of all atoms in the replicated nanotube

indexerOfAtomsInReplica = replica.getNodes('n.t a')

# rotate the replica by 90 degrees by changing x and y coordinates of its atoms

# and shift the replica from the borders to have '#' pattern

for a in indexerOfAtomsInReplica:

x = a.getX()

y = a.getY()

a.setY(x - shift)

a.setX(y + shift)

# apply sine function in Z-direction to original and replicated nanotubes

# get an indexer of all atoms in the original nanotube

indexerOfAtomsInOriginal = original.getNodes('n.t a')

# loop over all atoms in the original nanotube

for a in indexerOfAtomsInOriginal:

w = a.getX() / distance # [dimensionless quantity]

# apply sine function to the Z-coordinate of an atom

a.setZ(a.getZ() + A * sign * sin(pi * w.value))

# loop over all atoms in the replicated nanotube

for a in indexerOfAtomsInReplica:

# [dimensionless quantity], take into account the shift we did previously

w = (a.getY() - shift) / distance

# apply sine function to the Z-coordinate of an atom

a.setZ(a.getZ() + A * sign * sin(pi * w.value))

# change the phase to the opposite one

sign = -1 * sign

# end holding for undo/redo

SAMSON.endHolding()

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