[Fittesbane]

I wrote this program to export the coordinates of randomly generated "atoms" to a .xyz file for viewing in Jmol, but the portion of code that I wrote to prevent new atoms from being generated too close to others hasn't worked despite my having tried everything that I can think of(without fail, there is always at least on pair of atoms that are MUCH closer together than 1Å). I'm fairly new to programming and am confident that I made an idiot's mistake somewhere, but hopefully somebody can help me see it. I appreciate your help.

import random

##Initialize atoms

atomlist = []

atomnumb = input("number of atoms")

a = open('atoms.xyz','w')

a.write(str(atomnumb)+'\n')

a.write('\n')

[b]x=3.0*random.random()

y=3.0*random.random()

atomlist.append([x,y])

for n in range(atomnumb):

        ##Keep atoms from initializing too close together.(<1)

    for m in range(len(atomlist)):

        while (abs(x-atomlist[m][0])**2)+(abs(y-atomlist[m][1])**2)<1.0:##Pythagorean theorem

            x=3.0*random.random()

            y=3.0*random.random()

    atomlist.append([x,y])[/b]

    a.write('5           '+str(x)+'            '+str(y)+'             0\n')

a.close()

[Mekire]

You are only checking how close your new point is to one other point at a time. If it finds it is too close it generates a new random set of coordinates that have no relation to the previously tested cells.

I wrote a simple version that does what you ask, but by the nature of this it is pretty inefficient. Also as every new cell is completely random as long as it isn't near any preexisting ones, it is possible for the program to be unable to find a solution in which case it never breaks out of the loop. Maybe you can add some constraints to limit how many attempts it will make.

Code:

Spoiler

import random
import math
import sys

#Version compatibility with python 3
if sys.version_info[0] == 3: raw_input = input

##Initialize atoms
while 1:
    try:
        atomnumb = int(raw_input("Number of atoms: "))
        if atomnumb < 0:
            raise ValueError
        break
    except ValueError:
        print("A number greater than 0 please.")

atomlist = []
for n in range(atomnumb):
    while 1:
        x=3.0*random.random()
        y=3.0*random.random()
        if not any([math.hypot((x-i),(y-j))<1.0 for i,j in atomlist]):
            atomlist.append((x,y))
            break

####Just print stuff down here.
print("Atoms:")
for atom in atomlist:
    print(atom)
print("")

for a in atomlist:
    for d in atomlist:
        if a != d:
            s_a = "({:.2f},{:.2f})".format(*a)
            s_d = "({:.2f},{:.2f})".format(*d)
            c = math.hypot((a[0]-d[0]),(a[1]-d[1]))
            print("Atom at {} and atom at {} are {:.2f} apart.".format(s_a,s_d,c))

Sample output:

Spoiler

Number of atoms: 4
Atoms:
(2.212313836218266, 0.7108530434505632)
(1.769904272831844, 1.7430962183177003)
(0.8679010014836237, 0.5531522224276969)
(0.2937733480176512, 1.97688265623)

Atom at (2.21,0.71) and atom at (1.77,1.74) are 1.12 apart.
Atom at (2.21,0.71) and atom at (0.87,0.55) are 1.35 apart.
Atom at (2.21,0.71) and atom at (0.29,1.98) are 2.30 apart.
Atom at (1.77,1.74) and atom at (2.21,0.71) are 1.12 apart.
Atom at (1.77,1.74) and atom at (0.87,0.55) are 1.49 apart.
Atom at (1.77,1.74) and atom at (0.29,1.98) are 1.49 apart.
Atom at (0.87,0.55) and atom at (2.21,0.71) are 1.35 apart.
Atom at (0.87,0.55) and atom at (1.77,1.74) are 1.49 apart.
Atom at (0.87,0.55) and atom at (0.29,1.98) are 1.54 apart.
Atom at (0.29,1.98) and atom at (2.21,0.71) are 2.30 apart.
Atom at (0.29,1.98) and atom at (1.77,1.74) are 1.49 apart.
Atom at (0.29,1.98) and atom at (0.87,0.55) are 1.54 apart.

I think that does what you are looking for. Probably a better solution though.
-Mek

This post has been edited by Mekire: 08 March 2013 - 11:27 PM