Creation of a nanotube fabric: replication, modification of positions
In this tutorial, we will weave a nanotube fabric, numerically, of course. To do so, we need to perform the following steps:
- create one nanotube using the Nanotube Creator Editor;
- replicate this 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.
To create a nanotube, we will use the Nanotube Creator Editor (if you do not have it, you can add it via the provided link).
For the sake of simplicity, we will create a nanotube in the X-direction with the size of 400 Å. To create a nanotube with specific parameters, double-click on the Nanotube Creator Editor’s icon and set parameters as on the image below.
To generate a nanotube with the given parameters, press the Generate button.
Now, let’s open the Python Scripting app. Let’s import the necessary functions and constants we will be using later.
from math import sin, pi
The nanotube created with the Nanotube Creator editor is stored in a structural group of the data graph. For the simplicity, let’s assume that we have only one nanotube created in the active document. Then, to get this nanotube object in python, we need to get the first structural group in the active document:
indexerOfStructuralGroups = SAMSON.getNodes('n.t sg') # get an indexer of all structural groups in the active document nanotubeGroup = indexerOfStructuralGroups # get the first structural group from the indexer
Let us now create a nanotube fabric by replicating the created nanotube in XY-plane and modifying Z-coordinate of atoms in nanotubes to weave these nanotubes with each other.
Before setting up parameters for the fabric, we need to find a bounding box of the created nanotube:
indexerOfAtoms = nanotubeGroup.getNodes('n.t a') # get an indexer of all atoms in the nanotube a = indexerOfAtoms minX = maxX = a.getX() minY = maxY = a.getY() for a in indexerOfAtoms: # go through all atoms in the indexer x = a.getX() y = a.getY() minX = min(minX, x) maxX = max(maxX, x) minY = min(minY, y) manY = max(maxY, y)
Let’s now set up parameters for creation of a nanotube fabric. We will set the number of replicas in one direction (number of replicas in the perpendicular direction will be the same), and based on it we will compute the distance between replicas. You can do it differently by specifying the distance between nanotubes and then computing the number of replicas.
length = (maxX - minX) # nanotube's length diameter = (maxY - minY) # nanotube's diameter numReplicasX = 10 # number of replicas in one direction distance = length / numReplicasX # set distance between nanotubes based on the number of replicas
We will be using the sine function for modifying nanotubes with its half-period set equal to the distance between nanotubes and an amplitude equal to 1.5 of the nanotube’s radius.
A = 0.75 * diameter # set an amplitude for sine function
Now, let’s replicate the nanotube in the Y-direction by copying it and shifting the copies in the Y-direction. The replicas will be added to the structural model with the replicated nanotube.
structuralModel = nanotubeGroup.getParent().getParent() # get a structural model where the nanotube is # the nanotube group's parent is a structural root - a hidden root node in a structural model for r in range(numReplicasX-1): # create a replica replica = nanotubeGroup.clone() # clone the original nanotube replica.create() # create the replica structuralModel.addChild(replica) # add the replica to the structural model # shift the replica in Y-direction dy = (r + 1) * distance indexerOfAtoms = replica.getNodes('n.t a') # get an indexer of all atoms in the replicated nanotube for a in indexerOfAtoms: # loop over all atoms in the replicated nanotube a.setY(a.getY() + dy) # shift atoms in the Y-direction
After doing that, we will get a set of nanotubes looking like this:
Now, we will replicate these nanotubes in the X-direction by copying them and rotating the replicas by 90 degrees. These replicas will also be shifted from the boundaries to have the # pattern. Then, we will apply the sine function in Z-direction to all nanotubes with changing its phase to have a weaved pattern.
indexerOfStructuralGroups = SAMSON.getNodes('n.t sg') # get an indexer of all structural groups in the active document sign = 1 # used to change the phase of the sine function for original in indexerOfStructuralGroups: # loop through all structural groups (all nanotubes) # create a replica replica = original.clone() # clone the original nanotube replica.create() # create the replica structuralModel.addChild(replica) # add it to the structural model shift = distance / 2.0 # for shifting nanotubes from the border indexerOfAtomsInReplica = replica.getNodes('n.t a') # get an indexer of all atoms in the replicated nanotube # 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 indexerOfAtomsInOriginal = original.getNodes('n.t a') # get an indexer of all atoms in the original nanotube for a in indexerOfAtomsInOriginal: # loop over all atoms in the original nanotube w = a.getX() / distance # [dimensionless quantity] a.setZ(a.getZ() + A * sign * sin(pi * w.value)) # apply sine function to the Z-coordinate of an atom for a in indexerOfAtomsInReplica: # loop over all atoms in the replicated nanotube w = (a.getY() - shift) / distance # [dimensionless quantity], take into account the shift we did previously a.setZ(a.getZ() + A * sign * sin(pi * w.value)) # apply sine function to the Z-coordinate of an atom sign = -1 * sign # change the phase to the opposite one
After that, we will get a grid of nanotubes, where nanotubes are woven with each other.
A close-up of the created system. For this pictire, the default bond radius was set equal to the default atom radius in Preferences → Rendering → Structural model.
Of course, the created nanotube fabric should be later minimized.