def main():
try:
filename = sys.argv[1]
except IndexError:
print "No Filename given"
sys.exit()
try:
R = float(sys.argv[2])
except IndexError:
print "Using default R value"
R = 25.0
a, b, c, atomRadius, nPerPart = 12.5, 12.5, 25, 1, 4684
areaDensity = 4*np.pi*(((a*b)**1.6 + (a*c)**1.6 + (b*c)**1.6)/3)**(1/1.6)/nPerPart
sideLength = 4*R
# generate a surface with a hole in the center
surface = makeSurface(areaDensity, sideLength, R)
# surface = np.around(surface,6)
box = makeBox(3, surface)
# generate index information for configuration file
info = makeFile(surface)
# combine coordinate and index info
atoms = np.concatenate((info.astype('|S10'), surface.astype('|S10')), axis=1)
# generate input files for lammps and VMD
write_conf(filename+'_out', atoms, title='Surface with cut-out R = %d' % R, box=box)
write_xyz(filename+'_out', atoms[:,2:])
def main():
try:
filename = sys.argv[1]
except IndexError:
print "No Filename given"
sys.exit()
a, b, c, atomRadius, nPerPart = 12.5, 12.5, 25, 1, 4684
areaDensity = 4*np.pi*(((a*b)**1.6 + (a*c)**1.6 + (b*c)**1.6)/3)**(1/1.6)/nPerPart
try:
cylDims = (float(sys.argv[2]),100)
except IndexError:
cylDims = (25,100)
print "Default R value used"
# generate a cylinder with length L and radius R
cylinder = makeCylinder(areaDensity, cylDims)
box = makeBox(3, cylinder)
# generate indices, molecule, and atom types
info = makeFile(cylinder)
# combine coordinate and index information
atoms = np.concatenate((info.astype('|S10'), cylinder.astype('|S10')), axis=1)
# generate input files for VMD and LAMMPS
write_conf(filename+'_out', atoms, title='Capillary R = %d' % cylDims[0], box=box)
write_xyz(filename+'_out', atoms[:,2:])
