top_file="W11_large.psf"
traj_file="DH5_423_0.dcd"
label="o2"
tfname=label+"_traj"
sfname=label+"_sf"
if not os.path.isfile(sfname+".npz"): #check to see if SF needs to be calculated
if not os.path.isfile(tfname+".npz"): #check to see if trajectory needs to be processed
print "processing trajectory file "+traj_file
lt.process(top_file,traj_file,tfname) #Process trajectory into numpy array. Commented to run on windows
print 'done'
traj=np.load(tfname+".npz") #load processed trajectory
rad=dens.load_radii("radii.txt") #load radii definitions from file
dens.compute_sf(traj['coords'],traj['dims'],traj['typ'],sfname,rad) #compute time-averaged 3d structure factor and save to sfname.npz
dpl=np.load(sfname+".npz") #load 3d SF
grid=dpl['kgridplt']
p2d.mainlabel="W623" #title for plots
dir=p2d.mainlabel+"_plots"+fd #set up directories for saving plots
sfdir=dir+"structure_factor"+fd
sfsubdir=sfdir+"additional_plots"+fd
EWdir=dir+"Ewald_Corrected"+fd
p2d.path=EWdir
p2d.Plot_Ewald_Sphere_Correction(grid,1.54) #compute Ewald-corrected SF cross sections in xy,xz,yz planes
typ = np.zeros(Nlat, dtype=object)
typ[:] = args.lattice_label
print("saving...")
np.savez_compressed(sfname,
dims=dims,
coords=coords,
name=name,
typ=typ)
rad = dens.load_radii("%s/radii.txt" %
location) # load radii definitions from file
print("computing SF...")
dens.compute_sf(
coords, dims, typ, sfname, rad, ucell, args.spatial_resolution
) # compute time-averaged 3d structure factor and save to sfname.npz
elif args.random_counts > 0: # create a random trajectory
spcheck = 0 # check if simulating a single particle.
Rboxsize = 100.0
BUFFsize = 10000000
sfname = 'RND'
print("generating random trajectory...")
Rsteps = args.random_timesteps
Ratoms = args.random_counts
dims = np.ones((Rsteps, 3)) * Rboxsize