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# demonstration of a particle cloud (non-interacting)
# similar to particle01.py except that each new state is retained in
# memory and used to assemble a movie with the number of states
# provided below
from random import random
from pymol import cmd
from time import sleep
particle_count = 1000
box_size = 500.0
n_states = 200
# constants
half_box = box_size / 2
# create N particle system [x,y,z,r,vx,vy,vz]
particle = []
for resi in range(0,particle_count):
particle.append([resi] +
map(lambda x:(random()-0.5)*box_size/2,[0]*3) + # x,y,z
[random()+0.5] + # r
map(lambda x:(random()-0.5),[0]*3) # vx,vy,vz
)
# create cloud object
for part in particle:
cmd.pseudoatom("cloud",
resi = part[0],
pos = part[1:4],
vdw = part[4])
# draw spheres efficiently
cmd.show_as("spheres")
cmd.unset("cull_spheres")
# defer geometry generation until needed
cmd.set("defer_builds",1)
# position the camera
cmd.zoom()
cmd.zoom("center",box_size)
# let there be color
cmd.spectrum()
# this is the main loop
def simulation():
state = 1
import traceback
try:
while state < n_states:
state = state + 1
for part in particle:
# simplistic Euler intergration
# p = p + v
part[1] = (half_box + part[1] + part[5]) % box_size - half_box
part[2] = (half_box + part[2] + part[6]) % box_size - half_box
part[3] = (half_box + part[3] + part[7]) % box_size - half_box
# v = v + pseudo-gravitational acceleration
factor = max(0.1*box_size, 0.1*(part[1]**2+part[2]**2+part[3]**2)**1.5)
part[5] = part[5] - part[1] / factor
part[6] = part[6] - part[2] / factor
part[7] = part[7] - part[3] / factor
# copy initial coordinates to a new state
cmd.create("cloud","cloud",1,state)
# update the new state coordinates
cmd.alter_state(state,"cloud","(x,y,z) = particle[int(resi)][1:4]",space=globals())
cmd.forward()
cmd.refresh()
# don't hog the CPU entirely
sleep(0.01)
cmd.mplay()
except:
traceback.print_exc()
# launch the main loop in a separate thread
import threading
thread = threading.Thread(target=simulation)
thread.setDaemon(1)
thread.start()
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