CODEWITHSUNDEEP
python
scrayon
scrayon

Reputation: 497

Randomizing (x,y,z) coordinates within a box

I am fairly new to python and in my current assignment it looked at particles in 3D.

The first part of the question asked to create a program that put identical, non overlapping particles in a cubic lattice. So my code below just iterates through every combination possible, puts it in an XYZ file.

The xyz file is in this format:

1000.000000
comment goes here
H 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.000000
H 0.000000 0.000000 2.000000
H 0.000000 0.000000 3.000000
H 0.000000 0.000000 4.000000
H 0.000000 0.000000 5.000000
H 0.000000 0.000000 6.000000
H 0.000000 0.000000 7.000000
H 0.000000 0.000000 8.000000

The next part which I am stuck on wants me to do the same thing but put them in a random fashion and limit the number of particles that I have. This is the code I had for the first part. 

import itertools #will help iterating particles 

#we must set the values of diameter and Length
L=10
d=.5

#this is the intial coordinates of the first particle
x,y,z = 0,0,0
counter=0

#The particles will be spread across, the below ensures that there is no overlap of particles
with open("question1.xyz","w") as file:
    file.write("\ncomment goes here\n") #add comments into the 2nd line of the xyz file
    for x,y,z in itertools.product(range(L),repeat = 3):
        file.write('H %f %f %f\n' % (x, y, z))
        counter=counter+1

#this will put the number of particles as the first line
with open("question1.xyz") as infile:
    with open("q1Output.xyz","w") as outfile:
        for i,line in enumerate(infile):
            if i==0:
                outfile.write('%f\n'%counter)
            else:
                outfile.write(line)

The part I am confused on is how I should randomize my particles/coordinates and ensure there is no overlap.

Any ideas? Thanks in advance!

**Edit: This is what I have so far, apart of the questions askts to vary L and try to minimize the amount of time it takes to run the program - not sure whats 

import random
import time

start_time=time.time() 

text_file=open("textfile.xyz","w")
text_file.write("512\n")
text_file.write("Comment goes here\n")

L=12.5
d=1

#place particles
for partciles in range(0,512)
    proxcheck=1
    while proxcheck !=2 #when the particles has been placed, proxcheck will be set=2, and the program will move onto next
    x,y,z=random.random()*L,random.random()*L,random.random()*L #random numbers for positions
    skipfirsttwolines,proxcheck=0,1;

For line in text_file
    skipfirsttwolines=skipfirsttwolines+1;
    if skipfirsttwolines>2: #in xyz file we dont look at first two lines
        proxcheck=0 #if no overlap particle will be placed
        oldvals=line.split(none)
        oldx=float(oldvals[1])
        oldy=float(oldvals[2])
        oldz=float(oldvals[3])

Not sure where to go from here or if I should even take this approach in ensuring no overlap

@david:

This is what I was thinking, any suggestions?

x,y,z=[],[],[]
for j in range(0,512):
    x.append(0)
    y.append(0)
    z.append(0)
xyz_line = '\n{0} {1} {2} {3}'.format('O',x[0],y[0],z[0])
f.write(xyz_line)

Upvotes: 3

Views: 3573

Answers (1)

David Robinson
David Robinson

Reputation: 78590

You can create a random point with the code

import random

p = (random.randint(0, L), random.randint(0, L), random.randint(0, L))

But if you need to prevent having two in the same place, you can do (after setting num_points to the number of points you want):

points = set()
while len(points) < num_points:
    p = (random.randint(0, L), random.randint(0, L), random.randint(0, L))
    if p not in points:
        points.add(p)

To write the resulting points to a file:

for p in points:
    f.write("%s %s %s\n" % p)

Upvotes: 3

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