def test_single_name(self):
u = make_Universe(trajectory=True)
w = XYZWriter(self.outfile, atoms='ABC')
w.write(u.trajectory.ts)
w.close()
u2 = mda.Universe(self.outfile)
assert_(all(u2.atoms.names == 'ABC'))
def test_list_names(self):
u = make_Universe(trajectory=True)
names = ['A', 'B', 'C', 'D', 'E'] * 25
w = XYZWriter(self.outfile, atoms=names)
w.write(u.trajectory.ts)
w.close()
u2 = mda.Universe(self.outfile)
assert_(all(u2.atoms.names == names))
def test_single_name(self):
u = make_Universe(trajectory=True)
w = XYZWriter(self.outfile, atoms='ABC')
w.write(u.trajectory.ts)
w.close()
u2 = mda.Universe(self.outfile)
assert_(all(u2.atoms.names == 'ABC'))
def test_no_names(self, outfile):
u = make_Universe(trajectory=True)
w = XYZWriter(outfile)
w.write(u.trajectory.ts)
w.close()
u2 = mda.Universe(outfile)
assert all(u2.atoms.names == 'X')
def test_list_names(self):
u = make_Universe(trajectory=True)
names = ['A', 'B', 'C', 'D', 'E'] * 25
w = XYZWriter(self.outfile, atoms=names)
w.write(u.trajectory.ts)
w.close()
u2 = mda.Universe(self.outfile)
assert_(all(u2.atoms.names == names))
import math
import os
import numpy as np
from MDAnalysis import Universe
from MDAnalysis.coordinates.XYZ import XYZWriter
from MDAnalysis.core.groups import Atom, AtomGroup
import matplotlib.pyplot as plt
os.chdir('/home/jinho93/oxides/cluster/zno')
with open('POSCAR.xyz') as f,\
XYZWriter('output2.xyz') as znw, \
XYZWriter('output.xyz') as w:
u = Universe(f)
i: Atom
rnd = np.random.rand(len(u.atoms))
m = max(np.array(u.coord)[:, 2])
n = 0
ind = []
oxy = []
zinc = []
for j, i in enumerate(u.atoms):
if i.atomic_name == 'Zn':
if rnd[j] > 0.3 * math.exp((i.position[2] - m) * 0.5):
zinc.append(j)
else:
n += 1
else:
oxy.append(j)
ind.extend(oxy)
ind.extend(zinc)
