def test_pyCEquality():
"""
Trying to find where / why conOptDist and conOptDistC don't
return the same thing
"""
fname = 'mols8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
ats = 17
molno = 8
cutoff = 1.1 * 1.1
t = 97
clustSnap = cl.ContactClusterSnapshot(t, traj, ats, molno)
for i in range(molno):
for j in range(molno):
mol1 = clustSnap.pos[i, :].astype(np.double)
mol2 = clustSnap.pos[j, :].astype(np.double)
r = cl.conOptDistance(mol1, mol2)
rc = conOptDistanceCython(mol1, mol2)
ar = cl.alignedDistance(mol1, mol2)
arc = alignDistancesCython(mol1, mol2)
npt.assert_almost_equal(r, rc, 5)
npt.assert_almost_equal(ar, arc, 5)
def test_dummyfull():
"""
Makes sure that all three cluster types return what is expected,
employing the hand-crafted 6 snapshot system of dummy molecules that
are similar to the 17-bead HOOMD rigid bodies
"""
fname = 'dummyfull4.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
atsCC = 17
atsOC = 12
atsAC = 6
molno = 4
contactcut = 1.1 * 1.1
opticalcut = 0.35 * 0.35
alignedcut = 0.35 * 0.35
ts = range(6)
nclustsActualCC = [4, 2, 1, 1, 1, 1]
nclustsActualOC = [4, 3, 2, 2, 1, 1]
nclustsActualAC = [4, 4, 3, 2, 2, 1]
clustSizesActualCC = [[1, 1, 1, 1], [2, 2, 2, 2], [4, 4, 4, 4],
[4, 4, 4, 4], [4, 4, 4, 4], [4, 4, 4, 4]]
clustSizesActualOC = [[1, 1, 1, 1], [1, 1, 2, 2], [2, 2, 2, 2],
[2, 2, 2, 2], [4, 4, 4, 4], [4, 4, 4, 4]]
clustSizesActualAC = [[1, 1, 1, 1], [1, 1, 1, 1], [2, 2, 1, 1],
[2, 2, 2, 2], [2, 2, 2, 2], [4, 4, 4, 4]]
for t in ts:
print(t)
clustSnapCC = cl.ContactClusterSnapshot(t, traj, atsCC, molno)
clustSnapCC.setClusterID(contactcut)
clustSizeCC = clustSnapCC.idsToSizes()
assert (clustSizeCC == clustSizesActualCC[t]).all()
assert clustSnapCC.nclusts == nclustsActualCC[t]
atype = 'AB'
compairs = [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10, 11]]
clustSnapOC = cl.OpticalClusterSnapshot(t,
traj,
atsOC,
molno,
atype=atype)
clustSnapOC.setClusterID(opticalcut)
clustSizeOC = clustSnapOC.idsToSizes()
assert (clustSizeOC == clustSizesActualOC[t]).all()
assert clustSnapOC.nclusts == nclustsActualOC[t]
clustSnapAC = cl.AlignedClusterSnapshot(t,
traj,
atsAC,
molno,
compairs=compairs,
atype=atype)
clustSnapAC.setClusterID(alignedcut)
clustSizeAC = clustSnapAC.idsToSizes()
assert (clustSizeAC == clustSizesActualAC[t]).all()
assert clustSnapAC.nclusts == nclustsActualAC[t]
def test_clusterPackAndUnpack():
"""
Test to and from array stuff which is basically my own version of
'pickling' in a numpy array for use with mpi4py.
"""
fname = 'mols8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
ats = 17
cutoff = 1.1 * 1.1
molno = 8
t = 97
clustSnap = cl.ContactClusterSnapshot(t, traj, ats, molno)
clustSnap.setClusterID(cutoff)
carray = clustSnap.toArray()
clustSnap2 = cl.ContactClusterSnapshot(0, carray, ats, molno)
assert clustSnap.timestep == clustSnap2.timestep
assert clustSnap.ats == clustSnap2.ats
assert clustSnap.nclusts == clustSnap2.nclusts
assert (clustSnap.pos == clustSnap2.pos).all()
assert (clustSnap.clusterIDs == clustSnap2.clusterIDs).all()
def test_fixPBC():
"""
test fixing clusters across PBCs
"""
fname = 'dummy2PBC.gsd'
cutoff = 0.6
traj = gsd.hoomd.open(op.join(data_path, fname))
clustSnap = cl.ContactClusterSnapshot(0, traj, 3, 2)
clustSnap.setClusterID(cutoff)
fixedXYZ = clustSnap.fixPBC(0,
cutoff,
writegsd=op.join(data_path,
'dummy2PBCunwrapped.gsd'))
npt.assert_array_almost_equal(
fixedXYZ,
np.array([[0., 0., 4.75, 0., 0., 5.25, 0., 0., 5.75],
[-0.5, 0., 5.25, -0.5, 0., 5.75, -0.5, 0., 6.25]]))
def test_ContactClusterSnapshot_init():
"""
Testing the instantiation of a Cluster Snapshot
"""
fname = 'mols8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
ats = 17
molno = 8
cutoff = 1.1 * 1.1
t = 97
clustSnap = cl.ContactClusterSnapshot(t, traj, ats, molno)
clustSnap.setClusterID(cutoff)
assert clustSnap.timestep == t
sz = np.shape(traj[t].particles.position)
assert len(clustSnap.clusterIDs) == sz[0] / ats
assert clustSnap.nclusts == 2
def test_mu2():
"""
test mass-averaged cluster size instantiation
"""
fname = 'dummy8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
ats = 2
molno = 8
cutoff = 1.1 * 1.1
ts = range(8)
mu2s = np.array([1, 2, 5 / 2, 11 / 4, 17 / 4, 17 / 4, 8, 8])
for t in ts:
clustSnap = cl.ContactClusterSnapshot(t, traj, ats, molno)
clustSnap.setClusterID(cutoff)
clustSize = clustSnap.idsToSizes()
mu2 = cl.massAvSize(clustSize)
npt.assert_almost_equal(mu2, mu2s[t], 10)
def test_dummy8():
"""
Makes sure that contact clusters return what is expected, employing
the hand-crafted 8 snapshot system of 2 atoms in each molecule
"""
fname = 'dummy8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
ats = 2
molno = 8
cutoff = 1.1 * 1.1
ts = range(8)
clustSizesActual = [[1, 1, 1, 1, 1, 1, 1, 1], [1, 2, 2, 1, 3, 3, 1, 3],
[1, 3, 3, 3, 3, 3, 1, 3], [2, 3, 3, 3, 3, 3, 2, 3],
[5, 5, 5, 5, 3, 3, 5, 3], [5, 5, 5, 5, 3, 3, 5, 3],
[8, 8, 8, 8, 8, 8, 8, 8], [8, 8, 8, 8, 8, 8, 8, 8]]
nclustsActual = [8, 5, 4, 3, 2, 2, 1, 1]
for t in ts:
clustSnap = cl.ContactClusterSnapshot(t, traj, ats, molno)
clustSnap.setClusterID(cutoff)
clustSize = clustSnap.idsToSizes()
assert (clustSize == clustSizesActual[t]).all()
assert clustSnap.nclusts == nclustsActual[t]
for r in range(size):
if rem != 0:
if r < rem:
ts = r * (num + 1) + np.arange(num + 1)
tslist[currid:(len(ts) + currid)] = ts
else:
ts = r * (num + 1) - (r - rem) + np.arange(num)
tslist[currid:(len(ts) + currid)] = ts
tslist[(len(ts) + currid):(len(ts) + currid + (r - rem) +
1)] = -1
currid += num + 1
else:
tslist = np.arange(num * size)
print(tslist)
clusters = [cl.ContactClusterSnapshot(t, traj, ats, molno) for t in tslist]
carraylen = clusters[0].getCArrayLen()
clusterarray = np.zeros(carraylen * len(clusters))
cind = 0
for cls in clusters:
carray = cls.toArray()
clusterarray[(cind * carraylen):(cind * carraylen +
carraylen)] = carray
cind += 1
else:
tCSnap = cl.ContactClusterSnapshot(0, traj, ats, molno)
carraylen = tCSnap.getCArrayLen()
clusterarray = None
if rem == 0:
ncsnaps = num
else: