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)