def test_gridcenter(u1):
gridcenter = np.array([10, 10, 10])
xdim = 190
ydim = 200
zdim = 210
ag = u1.select_atoms('name OD1', updating=True)
serial = serial_density.DensityAnalysis(ag,
gridcenter=gridcenter,
xdim=xdim,
ydim=ydim,
zdim=zdim).run()
parallel = DensityAnalysis(u1.atoms,
atomselection='name OD1',
updating=True,
gridcenter=gridcenter,
xdim=xdim,
ydim=ydim,
zdim=zdim)
core_number = 4
parallel.run(n_blocks=core_number, n_jobs=core_number)
assert_almost_equal(serial.density.grid, parallel.density.grid)
assert_almost_equal(parallel._gridcenter, gridcenter)
assert len(parallel.density.edges[0]) == xdim + 1
assert len(parallel.density.edges[1]) == ydim + 1
assert len(parallel.density.edges[2]) == zdim + 1
def test_userdefn_boxshape(self, universe):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=1.0,
xdim=8.0,
ydim=12.0,
zdim=17.0,
gridcenter=self.gridcenters['static_defined']).run()
assert D.density.grid.shape == (8, 12, 17)
def test_ValueError_userdefn_xdim_type(self, universe):
# Test xdim != int or float
with pytest.raises(ValueError,
match="xdim, ydim, and zdim must be numbers"):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta,
xdim="MDAnalysis",
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters['static_defined']).run(step=5)
def test_ValueError_userdefn_gridcenter_type(self, universe):
# Test gridcenter includes non-numeric strings
with pytest.raises(ValueError,
match="Non-number values assigned to gridcenter"):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta,
xdim=10.0,
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters['error2']).run(step=5)
def test_ValueError_userdefn_gridcenter_shape(self, universe):
# Test len(gridcenter) != 3
with pytest.raises(ValueError,
match="gridcenter must be a 3D coordinate"):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta,
xdim=10.0,
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters['error1']).run(step=5)
def test_warn_userdefn_smallgrid(self, universe):
regex = ("Atom selection does not fit grid --- "
"you may want to define a larger box")
with pytest.warns(UserWarning, match=regex):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta,
xdim=1.0,
ydim=2.0,
zdim=2.0,
padding=0.0,
gridcenter=self.gridcenters['static_defined']).run(step=5)
def test_warn_userdefn_padding(self, universe):
regex = ("Box padding \(currently set at 1\.0\) is not used "
"in user defined grids\.")
with pytest.warns(UserWarning, match=regex):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta,
xdim=100.0,
ydim=100.0,
zdim=100.0,
padding=1.0,
gridcenter=self.gridcenters['static_defined']).run(step=5)
def test_density_values(u1, n_blocks, stop, step):
parallel = DensityAnalysis(u1.atoms,
atomselection='name OD1',
updating=True)
parallel.run(n_blocks=n_blocks,
n_jobs=n_blocks,
start=0,
stop=stop,
step=step)
ag = u1.select_atoms('name OD1', updating=True)
serial = serial_density.DensityAnalysis(ag).run(start=0,
stop=stop,
step=step)
assert np.sum(serial.density.grid) == np.sum(parallel.density.grid)
assert_almost_equal(serial.density.grid, parallel.density.grid, decimal=16)
def check_DensityAnalysis(self,
ag,
ref_meandensity,
tmpdir,
runargs=None,
**kwargs):
runargs = runargs if runargs else {}
with tmpdir.as_cwd():
D = density.DensityAnalysis(ag, delta=self.delta,
**kwargs).run(**runargs)
assert_almost_equal(D.density.grid.mean(),
ref_meandensity,
err_msg="mean density does not match")
D.density.export(self.outfile)
D2 = density.Density(self.outfile)
assert_almost_equal(
D.density.grid,
D2.grid,
decimal=self.precision,
err_msg="DX export failed: different grid sizes")
