def test_system_set_CIDs_MPI():
"""
Test setting the cluster IDs with MPI
"""
cldict = {'contact': 1.1 * 1.1}
syst = cl.SnapSystem(traj, {'contact': ats}, molno, cldict)
syst.get_clusters_mpi('contact')
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]]
if rank == 0:
ind = 0
nind = 0
print(len(syst.clsnaps['contact']))
tclustSnap = syst.clsnaps['contact'][7]
print(tclustSnap.pos[0])
print(tclustSnap.idsToSizes())
while ind < ttotal:
clustSnap = syst.clsnaps['contact'][nind]
if not np.isnan(clustSnap.pos[0][0]):
print("ind is: ", ind)
print("nind is: ", nind)
csizes = clustSnap.idsToSizes()
print("csizes is: ", csizes)
print("actual is: ", clustSizesActual[ind])
assert (csizes == clustSizesActual[ind]).all()
ind += 1
nind += 1
def test_getSizesFromFile():
"""test reading sizes out of a written file"""
tname = "dummyfull4"
fname = 'molsdf4sizesAC'
for i in range(1, 6):
traj = gsd.hoomd.open(
op.join(data_path, tname + '_run' + str(i) + '.gsd'))
box = traj[0].configuration.box
ats = {'aligned': 6}
cldict = {'aligned': 0.35 * 0.35}
molno = 4
atype = 'AB'
compairs = np.array([[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10, 11]])
syst = cl.SnapSystem(traj,
ats,
molno,
cldict,
compairs=compairs,
atype=atype)
syst.get_clusters_serial('aligned', box)
syst.writeSizes('aligned',op.join(data_path,fname + '_run' \
+ str(i) + '.dat'))
fnames = [
op.join(data_path, fname + '_run1.dat'),
op.join(data_path, fname + '_run2.dat'),
op.join(data_path, fname + '_run3.dat'),
op.join(data_path, fname + '_run4.dat'),
op.join(data_path, fname + '_run5.dat')
]
actualSizes1 = np.array([[1, 1, 1, 1], [1, 1, 1, 1], [2, 2, 1, 1],
[2, 2, 2, 2], [2, 2, 2, 2], [4, 4, 4, 4]])
actualSizes2 = np.array([[1, 1, 1, 1], [1, 1, 1, 1], [2, 2, 1, 1],
[2, 2, 2, 2], [4, 4, 4, 4], [4, 4, 4, 4]])
actualSizes3 = np.array([[1, 1, 1, 1], [1, 1, 1, 1], [2, 2, 2, 2],
[2, 2, 2, 2], [2, 2, 2, 2], [2, 2, 2, 2]])
actualSizes4 = np.array([[1, 1, 1, 1], [2, 2, 1, 1], [2, 2, 2, 2],
[2, 2, 2, 2], [4, 4, 4, 4], [4, 4, 4, 4]])
actualSizes5 = np.array([[1, 1, 1, 1], [1, 1, 1, 1], [2, 2, 1, 1],
[2, 2, 2, 2], [2, 2, 2, 2], [2, 2, 2, 2]])
csizes1 = cl.getSizesFromFile([fnames[0]], 6)
assert (csizes1 == actualSizes1).all()
csizes2 = cl.getSizesFromFile([fnames[1]], 6)
assert (csizes2 == actualSizes2).all()
csizes3 = cl.getSizesFromFile([fnames[2]], 6)
assert (csizes3 == actualSizes3).all()
csizes4 = cl.getSizesFromFile([fnames[3]], 6)
assert (csizes4 == actualSizes4).all()
csizes5 = cl.getSizesFromFile([fnames[4]], 6)
assert (csizes5 == actualSizes5).all()
csizes = cl.getSizesFromFile(fnames, 6)
print(csizes)
assert (csizes == np.concatenate(
(csizes1, csizes2, csizes3, csizes4, csizes5), axis=1)).all()
def test_system_init_MPI():
"""
Test the initialization of the system using MPI
"""
cldict = {'contact': 1.1 * 1.1}
syst = cl.SnapSystem(traj, {'contact': ats}, molno, cldict)
assert syst.mpi
assert syst.ats == {'contact': ats}
assert syst.molno == molno
assert syst.cldict == cldict
def test_readCID():
"""
test reading the CID from a file
"""
fname = 'mols8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
box = traj[0].configuration.box
ats = {'contact': 17}
cutoff = 1.1 * 1.1
molno = 8
cldict = {'contact': cutoff}
syst = cl.SnapSystem(traj, ats, molno, cldict)
syst.get_clusters_serial('contact', box)
syst.writeCIDs('contact', op.join(data_path, 'mols8cIDs.dat'))
systwrit = cl.SnapSystem(traj, ats, molno, cldict)
for i in range(len(systwrit.clsnaps['contact'])):
snapf = systwrit.clsnaps['contact'][i]
snapf.setClusterIDFromFile(op.join(data_path, 'mols8cIDs.dat'))
snap = syst.clsnaps['contact'][i]
assert (snapf.clusterIDs == snap.clusterIDs).all()
def test_writeSizes():
"""
test writing out the clusterIDs
"""
fname = 'mols8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
box = traj[0].configuration.box
ats = {'contact': 17}
cutoff = 1.1 * 1.1
molno = 8
cldict = {'contact': cutoff}
syst = cl.SnapSystem(traj, ats, molno, cldict)
syst.get_clusters_serial('contact', box)
syst.writeSizes('contact', op.join(data_path, 'mols8sizes.dat'))
def test_full_system_set_CIDs_MPI():
"""
Test setting the cluster IDs with MPI for all cluster types
"""
cldict = {
'contact': 1.1 * 1.1,
'optical': 0.35 * 0.35,
'aligned': 0.35 * 0.35
}
traj = gsd.hoomd.open(
'/home/rachael/Analysis_and_run_code/analysis/cluster_analysis/clustering/data/dummyfull4.gsd'
)
ats = {'contact': 17, 'optical': 12, 'aligned': 6}
molno = 4
compairs = np.array([[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10, 11]])
atype = 'AB'
syst = cl.SnapSystem(traj,
ats,
molno,
cldict,
compairs=compairs,
atype=atype)
syst.get_clusters_mpi('contact')
syst.get_clusters_mpi('optical')
syst.get_clusters_mpi('aligned')
ttotal = 6
cSizesActual = dict()
cSizesActual['contact'] = [[1, 1, 1, 1], [2, 2, 2, 2], [4, 4, 4, 4],
[4, 4, 4, 4], [4, 4, 4, 4], [4, 4, 4, 4]]
cSizesActual['optical'] = [[1, 1, 1, 1], [1, 1, 2, 2], [2, 2, 2, 2],
[2, 2, 2, 2], [4, 4, 4, 4], [4, 4, 4, 4]]
cSizesActual['aligned'] = [[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 key in cSizesActual.keys():
if rank == 0:
ind = 0
nind = 0
while ind < ttotal:
clustSnap = syst.clsnaps[key][nind]
if not np.isnan(clustSnap.pos[0][0]):
csizes = clustSnap.idsToSizes()
assert (csizes == cSizesActual[key][ind]).all()
ind += 1
nind += 1
def test_linearFit():
"""test Smol linear fitting on dummy runs"""
tname = "dummyfull4"
fname = 'molsdf4sizesAC'
for i in range(1, 6):
traj = gsd.hoomd.open(
op.join(data_path, tname + '_run' + str(i) + '.gsd'))
box = traj[0].configuration.box
ats = {'aligned': 6}
cldict = {'aligned': 0.35 * 0.35}
molno = 4
atype = 'AB'
compairs = np.array([[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10, 11]])
syst = cl.SnapSystem(traj,
ats,
molno,
cldict,
compairs=compairs,
atype=atype)
syst.get_clusters_serial('aligned', box)
syst.writeSizes('aligned',op.join(data_path,fname + '_run' \
+ str(i) + '.dat'))
fnames = [
op.join(data_path, fname + '_run1.dat'),
op.join(data_path, fname + '_run2.dat'),
op.join(data_path, fname + '_run3.dat'),
op.join(data_path, fname + '_run4.dat'),
op.join(data_path, fname + '_run5.dat')
]
(tc, sigtc,
mu2s) = cl.linearWithErrors(fnames,
6,
dt=0.5,
fullreturn=True,
plotstats=[
op.join(data_path, fname + 'dummyfull4'),
't (0.5)', '$\mu_2$',
['o', 'x', '^', 'v', 's']
])
(tct, R2t) = cl.linearFit(0.5 * np.arange(6), mu2s[:, 2])
npt.assert_almost_equal(2 / tct, 0.5091, 4)
npt.assert_almost_equal(R2t, 0.6727, 4)
actualMu2s = np.array([[1, 1, 1, 1, 1, 1], [1, 1, 1, 3 / 2, 1, 11 / 10],
[3 / 2, 3 / 2, 2, 2, 3 / 2, 17 / 10],
[2, 2, 2, 2, 2, 2], [2, 4, 2, 4, 2, 14 / 5],
[4, 4, 2, 4, 2, 16 / 5]])
npt.assert_array_almost_equal(actualMu2s, mu2s)
def test_mu2vtime():
"""
test the (serial) version of getting the mass-averaged cluster size v time
"""
fname = 'mols8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
ats = {'contact': 17}
cutoff = 1.1 * 1.1
molno = 8
cldict = {'contact': cutoff}
box = traj[0].configuration.box
syst = cl.SnapSystem(traj, ats, molno, cldict)
syst.get_clusters_serial('contact', box)
mu2vtime = syst.getMassAvVsTime('contact')
assert np.shape(mu2vtime)[1] == len(traj)
assert not (np.isnan(mu2vtime)).all()
def test_trajectory():
"""
Try running on an xtc trajectory (from a pull simulation)
"""
trj = op.join(data_path, 'md_whole.xtc')
tpr = op.join(data_path, 'md_dummy.tpr')
molno = 100
ats = 33
tstart = 0
ttotal = 4000
comIDs = COMS
cainds = CAINDS
oainds = OAINDS
cldict = {'contact': 0.5 * 0.5, 'optical': 0.7 * 0.7}
start = time.time()
syst = cl.SnapSystem(trj,
ats,
molno,
cldict,
compairs=comIDs,
ttotal=ttotal,
tstart=tstart,
tpr=tpr)
end = time.time()
print("Time to setup: " + str(end - start) + "\n")
start = time.time()
syst.get_clusters_serial('contact',
np.array([[24.25935], [24.25935], [24.25935]]))
end = time.time()
print("Time to get contact: " + str(end - start) + "\n")
start = time.time()
syst.get_clusters_serial('optical',
np.array([[24.25935], [24.25935], [24.25935]]))
end = time.time()
print("Time to get optical: " + str(end - start) + "\n")
syst.writeCIDs('contact', 'contact-CIDs.dat')
syst.writeCIDs('optical', 'optical-CIDs.dat')
syst.writeSizes('contact', 'contact-sizes.dat')
syst.writeSizes('optical', 'optical-sizes.dat')
start = time.time()
syst.writeNNAngSpread('contact', 'nn-angspread-contact.dat', cainds)
syst.writeNNAngSpread('optical', 'nn-angspread-optical.dat', oainds)
end = time.time()
print("Time to get/write NN angle data: " + str(end - start) + "\n")
def run_ang_spread():
"""
Try running on an xtc trajectory (from a pull simulation)
"""
trj = op.join(data_path, 'md_whole.xtc')
tpr = op.join(data_path, 'md_dummy.tpr')
molno = 100
ats = 33
tstart = 0
ttotal = 4000
cainds = range(12, 23)
oainds = range(0, 3)
cfname = op.join(data_path, 'angle-spread-contact.dat')
ofname = op.join(data_path, 'angle-spread-optical.dat')
comIDs = np.array([[12, 13, 14], [16, 17, 18], [20, 21, 22]])
cldict = {'contact': 0.5 * 0.5, 'optical': 0.7 * 0.7}
cfname = op.join(data_path, 'contact-CIDs.dat')
ofname = op.join(data_path, 'optical-CIDs.dat')
start = time.time()
syst = cl.SnapSystem(trj,
ats,
molno,
cldict,
compairs=comIDs,
ttotal=ttotal,
tstart=tstart,
tpr=tpr)
end = time.time()
print("Time to setup: " + str(end - start) + "\n")
start = time.time()
syst.get_clusters_from_file('contact', cfname)
end = time.time()
print("Time to get contact: " + str(end - start) + "\n")
start = time.time()
syst.get_clusters_from_file('optical', ofname)
end = time.time()
print("Time to get optical: " + str(end - start) + "\n")
start = time.time()
syst.writeAngSpread('contact', cfname, cainds)
syst.writeAngSpread('optical', ofname, oainds)
end = time.time()
print("Time to get angle spread: " + str(end - start))
def test_intermixsetup():
fname = 'dummyfull2type_run1.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
compairs = np.array([[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10, 11]])
molno = 4
contactcut = 1.1 * 1.1
opticalcut = 0.35 * 0.35
ats = {'contact': 17, 'optical': 12}
cutoff = {'contact': contactcut, 'optical': opticalcut}
Syst = cl.SnapSystem(traj,
ats,
molno,
cutoff,
compairs=compairs,
atype='AB',
ttotal=6,
tstart=0,
het=True,
typelist=[u'EA', u'EB'])
boxL = traj[0].configuration.box[0]
Syst.get_clusters_serial('contact', boxL)
Syst.get_clusters_serial('optical', boxL)
intermixlistC = Syst.writeIntermix('contact',
'dummyfull2type_run1_cImix.dat',
returnmat=True)
intermixlistO = Syst.writeIntermix('optical',
'dummyfull2type_run1_oImix.dat',
returnmat=True)
iC0 = np.array([[1, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0]])
iC1 = np.array([[2, 0, 1, 1], [2, 0, 1, 1]])
iC2 = np.array([[4, 1, 2, 3]])
iC3 = np.array([[4, 0, 4, 4]])
iC4 = np.array([[4, 1, 4, 5]])
iC5 = np.array([[4, 2, 4, 6]])
iCs = [iC0, iC1, iC2, iC3, iC4, iC5]
iO0 = iC0
iO1 = np.array([[1, 0, 0, 0], [1, 0, 0, 0], [2, 0, 1, 1]])
iO2 = np.array([[2, 0, 1, 1], [2, 0, 1, 1]])
iO3 = np.array([[2, 0, 1, 1], [2, 0, 1, 1]])
iO4 = np.array([[4, 1, 2, 3]])
iO5 = np.array([[4, 2, 2, 4]])
iOs = [iO0, iO1, iO2, iO3, iO4, iO5]
return (intermixlistC, intermixlistO, iCs, iOs)
def analyze_clusters():
data_path = '/home/rachael/coarsegraining/CG/active_learning/martini-assembly/dfmi/4_production'
#where to look for data
trj = op.join(data_path, 'md_whole.xtc')
tpr = op.join(data_path, 'md_dummy.tpr')
molno = 100 #number of molecules
ats = 33 #number of atoms per molecule
tstart = 0
ttotal = 4000
comIDs = np.array([[9, 10, 11], [13, 14, 15],
[18, 19, 20]]) #index of beads comprising aromatics
cldict = {
'contact': 0.5 * 0.5,
'optical': 0.7 * 0.7
} #cutoffs for different cluster types
start = time.time()
outGro = op.join(data_path, 'conf')
syst = cl.SnapSystem(trj,
ats,
molno,
cldict,
compairs=comIDs,
ttotal=ttotal,
tstart=tstart,
tpr=tpr,
outGro=outGro)
end = time.time()
print("Time to setup: " + str(end - start) + "\n")
start = time.time()
syst.get_clusters_serial('contact',
np.array([[24.25935], [24.25935], [24.25935]]))
end = time.time()
print("Time to get contact: " + str(end - start) + "\n")
start = time.time()
syst.get_clusters_serial('optical',
np.array([[19.97738], [19.97738], [19.97738]]))
end = time.time()
print("Time to get optical: " + str(end - start) + "\n")
syst.writeCIDs('contact', 'pull-test-contact-CIDs-dfmi.dat')
syst.writeCIDs('optical', 'pull-test-optical-CIDs-dfmi.dat')
syst.writeSizes('contact', 'pull-test-contact-sizes-dfmi.dat')
syst.writeSizes('optical', 'pull-test-optical-sizes-dfmi.dat')
def test_get_clusters_serial_full():
"""
test the serial implementation of setting all the cluster correctly
for all cluster types
"""
fname = 'dummyfull4.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
box = traj[0].configuration.box
ats = {'contact': 17, 'optical': 12, 'aligned': 6}
molno = 4
cldict = {
'contact': 1.1 * 1.1,
'optical': 0.35 * 0.35,
'aligned': 0.35 * 0.35
}
compairs = np.array([[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10, 11]])
atype = 'AB'
syst = cl.SnapSystem(traj,
ats,
molno,
cldict,
compairs=compairs,
atype=atype)
syst.get_clusters_serial('contact', box)
syst.get_clusters_serial('optical', box)
syst.get_clusters_serial('aligned', box)
cSizesActual = dict()
cSizesActual['contact'] = [[1, 1, 1, 1], [2, 2, 2, 2], [4, 4, 4, 4],
[4, 4, 4, 4], [4, 4, 4, 4], [4, 4, 4, 4]]
cSizesActual['optical'] = [[1, 1, 1, 1], [1, 1, 2, 2], [2, 2, 2, 2],
[2, 2, 2, 2], [4, 4, 4, 4], [4, 4, 4, 4]]
cSizesActual['aligned'] = [[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 key in ats.keys():
cid = 0
clsnaps = syst.clsnaps[key]
for clsnap in clsnaps:
csizes = clsnap.idsToSizes()
assert (cSizesActual[key][cid] == csizes).all()
cid += 1
def test_writeout():
"""
Test the MPI writing out of cluster stuff
"""
cldict = {'contact': 1.1 * 1.1}
syst = cl.SnapSystem(traj, {'contact': ats}, molno, cldict)
syst.get_clusters_mpi('contact')
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]]
if rank == 0:
syst.writeCIDs('contact', 'dummyCIDs.dat')
syst.writeSizes('contact', 'dummysizes.dat')
try:
fCIDs = open('dummyCIDs.dat')
except IOError:
print("ERROR! cluster index file was not written.")
return False
try:
fsizes = open('dummysizes.dat')
except IOError:
print("ERROR! cluster sizes file was not written.")
return False
lind = 0
for line in fsizes:
try:
assert (clustSizesActual[lind] == [
int(n) for n in line.split()
])
lind += 1
except AssertionError:
print("{0} is not equal to {1}.".format(
clustSizesActual[lind], [int(n) for n in line.split()]))
return False
fCIDs.close()
fsizes.close()
return True
def test_write_out_frame():
fname = 'mols8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
box = traj[0].configuration.box
ats = {'contact': 17}
cutoff = 1.1 * 1.1
molno = 8
cldict = {'contact': cutoff}
syst = cl.SnapSystem(traj, ats, molno, cldict)
syst.get_clusters_serial('contact', box)
syst.writeCIDs('contact', op.join(data_path, 'mols8cIDs.dat'))
cIDfile = op.join(data_path, 'mols8cIDs.dat')
cIDfile = open(cIDfile)
lines = cIDfile.readlines()
cIDfile.close()
line = lines[35]
cIDsf = [float(c) for c in line.split()]
cIDs = [int(c) for c in cIDsf]
cl.writeFrameForVMD(cIDs, molno, ats['contact'],
op.join(data_path, 'testframe35.dat'))
def test_get_clusters_serial():
"""
test the serial implementation of setting all the clusters correctly
"""
fname = 'dummy8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
ats = {'contact': 2}
cutoff = 1.1 * 1.1
molno = 8
cldict = {'contact': cutoff}
syst = cl.SnapSystem(traj, ats, molno, cldict)
box = traj[0].configuration.box
syst.get_clusters_serial('contact', box)
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]]
cid = 0
clsnaps = syst.clsnaps['contact']
for clsnap in clsnaps:
csizes = clsnap.idsToSizes()
assert (clustSizesActual[cid] == csizes).all()
cid += 1
def test_trajectory():
"""
Try running on an xtc trajectory (from a pull simulation)
"""
trj = op.join(data_path, 'pull_whole.xtc')
tpr = op.join(data_path, 'pull.tpr')
molno = 2
ats = 29
tstart = 0
ttotal = 498
comIDs = np.array([[9, 10, 11], [13, 14, 15], [18, 19, 20]])
cldict = {'contact': 0.5 * 0.5, 'optical': 0.7 * 0.7}
start = time.time()
syst = cl.SnapSystem(trj,
ats,
molno,
cldict,
compairs=comIDs,
ttotal=ttotal,
tstart=tstart,
tpr=tpr)
end = time.time()
print("Time to setup: " + str(end - start) + "\n")
start = time.time()
syst.get_clusters_serial('contact',
np.array([[24.25935], [24.25935], [24.25935]]))
end = time.time()
print("Time to get contact: " + str(end - start) + "\n")
start = time.time()
syst.get_clusters_serial('optical',
np.array([[24.25935], [24.25935], [24.25935]]))
end = time.time()
print("Time to get optical: " + str(end - start) + "\n")
syst.writeCIDs('contact', 'pull-test-contact-CIDs.dat')
syst.writeCIDs('optical', 'pull-test-optical-CIDs.dat')
syst.writeSizes('contact', 'pull-test-contact-sizes.dat')
syst.writeSizes('optical', 'pull-test-optical-sizes.dat')
def test_getLengthDistribution():
"""
test getting the length distribution from a trajectory
"""
fname = 'dummyfull4.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
box = traj[0].configuration.box
ats = {'contact': 17, 'optical': 12, 'aligned': 6}
molno = 4
cldict = {
'contact': 1.1 * 1.1,
'optical': 0.35 * 0.35,
'aligned': 0.35 * 0.35
}
compairs = np.array([[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10, 11]])
atype = 'AB'
syst = cl.SnapSystem(traj,
ats,
molno,
cldict,
compairs=compairs,
atype=atype)
syst.get_clusters_serial('contact', box)
syst.get_clusters_serial('optical', box)
syst.get_clusters_serial('aligned', box)
box = traj[0].configuration.box[0:3]
ldistribt = syst.getLengthDistribution('contact', cldict['contact'], box,
conOptDistanceCython)
npt.assert_array_almost_equal(ldistribt,
np.array([[0., 0., 0., 0.],
[2.92, 2.92, 1.22, 1.22],
[4.92, 4.92, 4.92, 4.92],
[4.12, 4.12, 4.12, 4.12],
[3.08, 3.08, 3.08, 3.08],
[1.93, 1.93, 1.93, 1.93]]),
decimal=2)
atype = u'LS' #optical/aligned bead type
combeadtype = 'E' #bead type of center of mass bead
colors = {'contact': 'red', 'optical': 'blue'}
fbase = 'mols'+str(molnolabel)+'_' + str(AAdlabel)+'-'\
+str(SCdlabel)+'-'+str(BBdlabel)+'_short_run' #template of .gsd file name
fnames = [fbase + r + '.gsd' for r in runs]
start = time()
traj = gsd.hoomd.open(fname)
box = traj[0].configuration.box[0:3]
Systs = [
cl.SnapSystem(traj,
ats,
molno,
cutoff,
compairs=compairs,
ttotal=ttotal,
tstart=tstart,
atype=atype) for fname in fnames
]
end = time()
print("Time to setup clusters: ", end - start)
#Find all cluster IDs
start = time()
lind = 0
for Syst in Systs:
Syst.get_clusters_serial('contact', box, lcompute=None)
Syst.get_clusters_serial('optical', box, lcompute=None)
lind += 1
end = time()
def test_clusters_and_length_serial():
"""
test reusing the BallTree from cluster computation for the length
distribution computation
"""
fname = 'mols8.gsd'
traj = gsd.hoomd.open(op.join(data_path, fname))
snap = traj[0]
box = snap.configuration.box[0:3]
ats = {'contact': 17, 'optical': 12, 'aligned': 6}
cldict = {
'contact': 1.1 * 1.1,
'optical': 0.35 * 0.35,
'aligned': 0.35 * 0.35
}
molno = 8
syst = cl.SnapSystem(traj, ats, molno, cldict)
syst.get_clusters_serial('contact',
box,
lcompute=op.join(data_path, 'mols8CLdistrib.dat'))
syst.get_clusters_serial('optical',
box,
lcompute=op.join(data_path, 'mols8OLdistrib.dat'))
syst.get_clusters_serial('aligned',
box,
lcompute=op.join(data_path, 'mols8ALdistrib.dat'))
filecidbase = op.join(data_path, 'mols8CIDs_')
fileszbase = op.join(data_path, 'mols8sizes_')
syst.writeCIDs('contact', filecidbase + 'C.dat')
syst.writeSizes('contact', fileszbase + 'C.dat')
syst.writeCIDs('optical', filecidbase + 'O.dat')
syst.writeSizes('optical', fileszbase + 'O.dat')
syst.writeCIDs('aligned', filecidbase + 'A.dat')
syst.writeSizes('aligned', fileszbase + 'A.dat')
lC = open(op.join(data_path, 'mols8CLdistrib.dat'))
lO = open(op.join(data_path, 'mols8OLdistrib.dat'))
lA = open(op.join(data_path, 'mols8ALdistrib.dat'))
linesC = lC.readlines()
linesO = lO.readlines()
linesA = lA.readlines()
lC.close()
lO.close()
lA.close()
flinesC = np.array([float(f) for f in linesC[len(linesC) - 1].split()])
flinesO = np.array([float(f) for f in linesO[len(linesO) - 1].split()])
flinesA = np.array([float(f) for f in linesA[len(linesA) - 1].split()])
npt.assert_array_almost_equal(
flinesC,
np.array([6.25, 6.25, 6.25, 6.25, 6.25, 6.25, 6.25, 6.25]),
decimal=2)
npt.assert_array_almost_equal(
flinesO,
np.array([0., 4.18, 0., 4.18, 4.18, 4.18, 4.18, 4.18]),
decimal=2)
npt.assert_array_almost_equal(
flinesA, np.array([0., 0., 0., 1.03, 0.98, 0., 1.03, 0.98]), decimal=2)
BBdlabel = BBBB #BB bead parameter label
dt = 1.0 #assumed timestep
atype = u'LS' #optical/aligned bead type
colors = {'contact':'red','optical':'blue'}
typelist = [u'EA',u'EB']
fbase = 'mols'+str(molnolabel)+'_' + str(AAdlabel)+'-02-'\
+str(SCdlabel)+'-150-'+str(BBdlabel)+'_small_run' #template of .gsd file name
fnames = [save_path + '/' + fbase + str(r) + '.gsd' for r in range(1,runs+1)]
start = time()
traj = gsd.hoomd.open(fnames[0])
box = traj[0].configuration.box[0:3]
Systs = [cl.SnapSystem(fname,ats,molno,cutoff,
compairs=compairs,ttotal=ttotal,tstart=tstart,
atype=atype,het=True,typelist=typelist) for fname in fnames]
end = time()
print("Time to setup clusters: ",end-start)
#Find all cluster IDs
start = time()
lind = 0
for Syst in Systs:
Syst.get_clusters_serial('contact',box,lcompute=None)
Syst.get_clusters_serial('optical',box,lcompute=None)
lind += 1
end = time()
print("Time to get clusters: ",end-start)
fnames = []
ldfnames = []
for i in range(runs):
fname = op.join(traj_path, fbase + str(i + 1) + '.gsd')
fnames.append(fname)
ldfname = op.join(data_path, fbase + 'ldistrib' + str(i + 1))
ldfnames.append(ldfname)
start = time()
traj = gsd.hoomd.open(fname)
box = traj[0].configuration.box[0:3]
Systs = [
cl.SnapSystem(gsd.hoomd.open(fname),
ats,
molno,
cutoff,
compairs=compairs,
ttotal=ttotal,
tstart=tstart,
atype=atype) for fname in fnames
]
end = time()
if rank == 0:
print("Time to setup clusters: ", end - start)
#Find all cluster IDs
start = time()
lind = 0
for Syst in Systs:
ldfnameC = ldfnames[lind] + '_C.dat'
ldfnameO = ldfnames[lind] + '_O.dat'
cidNameC = op.join(
test long run with mpi (run with mpiexec)
"""
from __future__ import absolute_import, division, print_function
import os.path as op
import numpy as np
import numpy.testing as npt
import clustering as cl
import gsd.hoomd
import sys
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
data_path = op.join(cl.__path__[0], 'data')
ats = 17
molno = 10000
trajname = op.join(data_path, 'mols10000_740-0-0_run1.gsd')
cutoff = 1.1 * 1.1
traj = gsd.hoomd.open(trajname)
cldict = {'contact': 1.1 * 1.1}
syst = cl.SnapSystem(traj, ats, molno, cldict, 12)
syst.get_clusters_mpi('contact', 12)
if rank == 0:
print("writing clusterIDs")
syst.writeCIDs('contact', op.join(data_path, 'mols10KcIDs.dat'))
print("writing cluster sizes")
syst.writeSizes('contact', op.join(data_path, 'mols10KcSizes.dat'))
