def test_newrdf(): from chemlab.molsim.rdf import distance_histogram system = datafile("tests/data/rdf/cry.gro").read('system') #system = datafile("/home/gabriele/projects/LiCl/molfrac-0.39-48668/opt.gro").read('system') size = system.box_vectors[0,0]/2 timer.start() rdf_old = rdf(system.r_array[system.type_array == 'Cl'], system.r_array[system.type_array == 'Li'], binsize=0.2, cutoff=size, periodic=system.box_vectors, normalize=False) timer.stop() timer.start() rdf_new = distance_histogram(system.r_array[system.type_array == 'Cl'], system.r_array[system.type_array == 'Li'], binsize=0.2, cutoff=size, periodic=system.box_vectors) timer.stop() 1/0 plot(rdf_new, 'r') plot(rdf_old[1], 'b') show()
def test_rdf(): #system = datafile("tests/data/rdf/cry.gro").read('system') # Fix for this particular system water.gro #system.r_array += system.box_vectors[0,0]/2 gro_rdf = np.loadtxt("tests/data/rdf/rdf.xvg", skiprows=13,unpack=True) #nbins = len(gro_rdf[0]) size = system.box_vectors[0,0]/2 rdf=rdf(system.r_array[system.type_array == 'Cl'], system.r_array[system.type_array == 'Li'], binsize=0.002, cutoff=size, periodic = system.box_vectors) plot(gro_rdf[0], gro_rdf[1], color='blue') plot(rdf[0], rdf[1], 'red') show()
def test_rdf_oxy(): system = datafile("examples/gromacs_tutorial/confout.gro").read('system') # Fix for this particular system water.gro #system.r_array += system.box_vectors[0,0]/2 gro_rdf = np.loadtxt("examples/gromacs_tutorial/rdf.xvg", skiprows=13,unpack=True) #nbins = len(gro_rdf[0]) size = system.box_vectors[0,0]/2 rd=rdf(system.r_array[system.type_array == 'O'], system.r_array[system.type_array == 'O'], binsize=0.002, cutoff=size, periodic = system.box_vectors) plot(gro_rdf[0], gro_rdf[1], color='blue') plot(rd[0], rd[1], 'red') show()
def plot_rdf(type_a, type_b): s = current_system() rd = rdf(s.r_array[s.type_array == type_a], s.r_array[s.type_array == type_b], periodic=s.box_vectors) plot(rd[0], rd[1])
def get_rdf(arguments): return rdf(arguments[0], arguments[1], periodic=arguments[2])