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])
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])
