def main():
trajFile, outFile, nSteps = getArgs(argv)
nAve = 1
circ = None
frames = []
with open(trajFile,'r') as inp:
for n in range(nSteps):
# How should block averaging of interfaces be done?
# t, atoms = combineFrames(inp,nAve)
# t, atoms = readFrame(inp)
t, box, atoms = readTrj(inp)
# remove vaporized chains by uncommenting last two mask conditions
# mask = (atoms[:,0] == 1) # & (atoms[:,3] < 20) & (abs(atoms[:,2]) < 60)
# atoms = atoms[mask][:,1:]
mask = (atoms[:,1] == 1)
atoms = atoms[mask][:,2:]
atoms = atoms * (box[:,1] - box[:,0]) + box[:,0]
# Find the center of mass in the xy direction and center droplet
atoms, center = centerAtoms(atoms)
# # make box
# box = np.array([atoms.min(0)-0.01,atoms.max(0)+0.01]).T
# box[1,:] += [-7,7]
atoms[:,2] -= box[2,0]
box[2,:] -= box[2,0]
box[2,1] += 0.10
# find interfacial atoms
print t
interface = findCylinderInterface(atoms, box)
# pyplot.show()
# Calculate the contact angle
if not ((n+1) % nAve):
try:
angle, z0, R = contactAngle(interface[(interface[:,1] < 30) &
(abs(interface[:,0]) < 100)], box)
except RuntimeError:
print 'No interface'
circ = None
except IndexError:
print 'Empty interface'
else:
# pyplot.plot(interface[:,0],interface[:,1],'o')
circ = pyplot.Circle((0,z0), radius=R, fill=False)
frames.append([t*0.002,angle,center])
# plotInterface(atoms,box,interface,circ,(t,angle))
# pyplot.savefig('test.png')
# pyplot.show()
plotAngle(frames)
pyplot.savefig('full.png')
# pyplot.show()
writeData(outFile,frames)
print 'Finished analyzing trajectory'
def main():
# Command line args processing
trajFile, outFile, nFrames, nInsert, nSlices = getArgs(argv)
outFile = '%s_%d' % (outFile, nInsert)
# params = (a,b,r_cut,nAtomsPerPart,nPart)
params = (25*0.5, 50*0.5, RC, 4684, 54)
with open('density_'+outFile, 'w') as otp:
otp.write('# Density profiles\n')
with open('height_'+outFile, 'w') as otp:
otp.write('# height profiles at two cut-offs\n')
with open(trajFile,'r') as inp:
for n in range(nFrames):
# read data and separate by atomtypes
time, box, frame = readTrj(inp)
frame = frame[frame[:,0].argsort()]
particles = frame[frame[:,1] >= 3][:,2:]
polymers = frame[frame[:,1] == 1][:,4]
pmin = polymers.min()
cutOff = 0.85
density, height85, porosity = findHeight(particles, box, nInsert, nSlices, params, polymers, cutOff)
cutOff = 0.99
height99 = integrateHeight(np.copy(density), cutOff)
# rescale height
dmax = density[-1,0]
density[:,0] /= dmax
height85 /= dmax
height99 /= dmax
# concatenate porosity and density???
# output density and height values
with open('density_'+outFile, 'a') as otp:
header = '# time: %d\n# z density porosity' % time
np.savetxt(otp, density, fmt='%.5f', header=header, footer='\n', comments='')
with open('height_'+outFile, 'a') as otp:
np.savetxt(otp, [[time, height85, height99, density[0,0]]], fmt='%d %.5f %.5f %.5f',comments='')
print 'Finished analyzing trajectory'