Create a gist now

Instantly share code, notes, and snippets.

What would you like to do?
Visualization of molecular dynamics using VisPy
from __future__ import print_function, division
import simflat
import initatoms
import time
import constants
import argparse
from multiprocessing import Process, Queue
from Queue import Empty
import collections
import numpy as np
import imageio
except ImportError:
print("To enable saving screenshots, install `imageio` package")
from vispy import scene, app
from vispy.visuals.transforms import STTransform
# Translation of CoMD to Python
def advanceVelocity(atoms, dt):
for i in range(atoms.nAtoms):
atoms.p[i,0] += dt*atoms.f[i,0]
atoms.p[i,1] += dt*atoms.f[i,1]
atoms.p[i,2] += dt*atoms.f[i,2]
def advancePosition(sim, atoms, dt):
for i in range(atoms.nAtoms):
iSpecies = atoms.species[i]
invMass = 1.0/sim.species[iSpecies].mass
atoms.r[i,0] += dt*atoms.p[i,0]*invMass
atoms.r[i,1] += dt*atoms.p[i,1]*invMass
atoms.r[i,2] += dt*atoms.p[i,2]*invMass
def timestep(sim, nSteps, dt):
for ii in range(nSteps):
advanceVelocity(sim.atoms, 0.5*dt)
advancePosition(sim, sim.atoms, dt)
# redistributeAtoms
sim.ePot = sim.pot.computeForce(sim.atoms)
advanceVelocity(sim.atoms, 0.5*dt)
#print('ke,pe = ',initatoms.kineticEnergy(sim)/sim.atoms.nAtoms,sim.ePot/sim.atoms.nAtoms)
sim.eKinetic = initatoms.kineticEnergy(sim)
def initValidate(sim):
ke = initatoms.kineticEnergy(sim)
pe = sim.ePot
print("Initial PE (cohesive energy) : ",pe/sim.atoms.nAtoms)
print("Initial energy : ",(ke+pe)/sim.atoms.nAtoms," atom count : ",sim.atoms.nAtoms)
firstCall = True
iStepPrev = -1
def printInfo(sim, iStep, elapsedTime):
global firstCall, iStepPrev
if firstCall:
firstCall = False
#print("# Loop Time(fs) Total Energy Potential Energy Kinetic Energy Temperature Performance (us/atom) # Atoms")
print("#{:>6s} {:>10s} {:>18s} {:>18s} {:>18s} {:>12s} {:^12s} {:^12s}".\
format("Loop", "Time(fs)", "Total Energy", "Potential Energy", "Kinetic Energy", "Temperature", "(us/atom)", "# Atoms"))
nEval = iStep - iStepPrev
iStepPrev = iStep
simtime = iStep * sim.dt
n = sim.atoms.nAtoms
eTotal = (sim.ePot + sim.eKinetic)/n
eK = sim.eKinetic / n
eU = sim.ePot / n
Temp = (sim.eKinetic/n)/(constants.kB_eV * 1.5)
timePerAtom = 1.0e6 * elapsedTime/(n*nEval)
print(" {:6d} {:10.2f} {:18.12f} {:18.12f} {:18.12f} {:12.4f} {:10.4f} {:12d}".format(iStep, simtime, eTotal, eU, eK, Temp, timePerAtom, n))
#print(iStep, simtime, eTotal, eU, eK, Temp, timePerAtom, n)
def printPerformanceResults(sim, elapsedTime):
n = sim.atoms.nAtoms
nEval = sim.nSteps - sim.nSkip * sim.printRate
timePerAtom = 1.0e6 * elapsedTime/(n*nEval)
print("Average all atom update rate: %10.2f us/atom" % timePerAtom)
def parseCommandLine():
parser = argparse.ArgumentParser()
parser.add_argument("-x","--nx", type=int, default=4, help="number of unit cells in x")
parser.add_argument("-y","--ny", type=int, default=4, help="number of unit cells in y")
parser.add_argument("-z","--nz", type=int, default=4, help="number of unit cells in z")
parser.add_argument("-N","--nSteps", type=int, default=100, help="total number of time steps")
parser.add_argument("-n","--printRate", type=int, default=10, help="number of steps between output")
parser.add_argument("--skip", type=int, default=1, help="number of blocks to skip in averaged output")
parser.add_argument("-D","--dt", type=float, default=1, help="time step (in fs)")
parser.add_argument("-l","--lat", type=float, default=-1, help="lattice parameter (Angstroms)")
parser.add_argument("-T","--temp", type=float, default=600, help="initial temperature (K)")
args = parser.parse_args()
return args
def run_comd(pos_queue):
cmd = parseCommandLine()
# init subsystems
sim = simflat.initSimulation(cmd)
print('nAtoms = ',sim.atoms.nAtoms)
#for i in range(min(sim.atoms.nAtoms, 10)):
#for i in range(sim.atoms.nAtoms):
# print i,sim.atoms.r[i,:]
sim.ePot = sim.pot.computeForce(sim.atoms)
sim.eKinetic = initatoms.kineticEnergy(sim)
timestepTime = 0.0
timestepTimeOneIteration = 0.0
iStep = 0
for jStep in range(0, sim.nSteps, sim.printRate):
printInfo(sim, iStep, timestepTimeOneIteration)
start = time.clock()
timestep(sim, sim.printRate, sim.dt)
end = time.clock()
timestepTimeOneIteration = end - start
if jStep >= sim.nSkip * sim.printRate:
timestepTime += timestepTimeOneIteration
iStep += sim.printRate
printInfo(sim, iStep, timestepTimeOneIteration)
printPerformanceResults(sim, timestepTime)
# validate result
# Start of visualization code
class AtomCanvas(scene.SceneCanvas):
def __init__(self):
scene.SceneCanvas.__init__(self, keys='interactive', bgcolor='black',
size=(800, 600), show=True)
self.view = self.central_widget.add_view()
# Try different cameras = 'fly' = 'turntable' = 'panzoom' = 'arcball' = scene.cameras.TurntableCamera(fov=0.0, elevation=10.0, azimuth=40.0, scale_factor=30.0)
self.axis = scene.visuals.XYZAxis(parent=self.view.scene)
# Number of previous positions to keep in the visualization
# Set to 1 to see only the current position
self.ntrails = 50
self.pos = collections.deque(maxlen=self.ntrails)
self.particles = collections.deque(maxlen=self.ntrails)
def add_positions(self, pos):
if len(self.particles) < self.ntrails:
alpha = 0.9 # transparency of the current position
for i in range(len(self.particles)):
self.particles[i].set_data(self.pos[i], edge_color=None, face_color=(1,1,1,alpha), size=10)
# Adjust the decay of transparency for the trails
alpha*= 0.95
def screenshot():
global app_obj
writer = imageio.get_writer('screenshot.png')
im = app_obj.render()
# Save animation clips.
# Using global variables not the best, but okay for a simple script.
save_animation = False
animation_timer = None
animation_writer = None
def toggle_saving_animation():
global save_animation, animation_timer, animation_writer
if save_animation:
save_animation = False
animation_writer = None
animation_writer = imageio.get_writer('animation.gif', duration=0.1)
save_animation = True
def save_animation_frame(event):
global app_obj, animation_writer
if animation_writer:
im = app_obj.render()
def check_queue(event):
global app_obj, pos_queue
pos = pos_queue.get(False)
except Empty:
if __name__ == '__main__':
global app_obj, pos_queue
# Use separate processes for the display loop and the simulation.
# Communicate positions from the simulation to the display via a queue
pos_queue = Queue()
canvas = AtomCanvas()
app_obj = canvas
def on_key_press(ev):
if == 'S':
if == 'A':
# Set a timer to check the queue for new positions
timer = app.Timer(connect=check_queue)
# For saving animation clips
animation_timer = app.Timer(0.1,connect=save_animation_frame)
# Start simulation
p = Process(target=run_comd, args=(pos_queue,))
# Start GUI event loop
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment