def test_safemode(self):
fname = data_filename("cv_storage_safemode_test.nc")
if os.path.isfile(fname):
os.remove(fname)
cv = paths.CoordinateFunctionCV('cv', lambda x: x)
traj = paths.Trajectory(list(self.traj))
template = traj[0]
storage_w = paths.Storage(fname, "w")
storage_w.snapshots.save(template)
storage_w.cvs.save(cv)
storage_w.close()
storage_r = paths.Storage(fname, 'r')
# default safemode = False
assert (storage_r.simplifier.safemode is False)
cv_r = storage_r.cvs[0]
assert (cv_r == cv)
assert (cv.cv_callable is not None)
storage_r.close()
storage_r = paths.Storage(fname, 'r')
storage_r.simplifier.safemode = True
cv_r = storage_r.cvs[0]
assert (cv_r == cv)
assert (cv_r.cv_callable is None)
storage_r.close()
def sequential_main(self):
tps_storage = paths.Storage(self.tps_file, mode='r')
# get initial conditions, and stick them in files for each task
initial_snapshots = self.select_snapshots(tps_storage)
engine = self.most_probable_engine(initial_snapshots)
randomizer = create_randomizer(engine)
if self.output:
out_storage = paths.Storage(self.output, mode='w')
out_storage.save(engine)
out_storage.tags['randomizer'] = randomizer
out_storage.save(paths.Trajectory(initial_snapshots))
task_files = self.write_task_files(initial_snapshots, engine,
randomizer)
# tps_storage.close()
# this is the part that will be executed remotely
result_list = [
file_snapshots_committor(task_file, self.n_per_snapshot)
for task_file in task_files
]
runs = self.create_individual_runs(tps_storage, result_list)
tps_storage.close()
if self.output:
out_storage.tags['individual_runs'] = runs
out_storage.close()
return initial_snapshots, runs
def setup(self):
if os.path.isfile(data_filename(self.fname)):
os.remove(data_filename(self.fname))
setup_storage = paths.Storage(data_filename("tps_setup.nc"), "r")
network = setup_storage.networks[0]
tps_ensemble = network.sampling_ensembles[0]
initial_sample = paths.Sample(
replica=0,
trajectory=common.initial_tps_sample.trajectory,
ensemble=tps_ensemble
)
template = initial_sample.trajectory[0]
setup_storage.close()
shoot = oink.ShootingStub(tps_ensemble)
self.storage = paths.Storage(data_filename(self.fname), "w",
template)
self.pseudosim = oink.ShootingPseudoSimulator(
storage=self.storage,
initial_conditions=paths.SampleSet([initial_sample]),
mover=shoot,
network=network
)
nojoin = oink.ShootingStub(tps_ensemble, pre_joined=False)
self.nojoin_pseudosim = oink.ShootingPseudoSimulator(
storage=self.storage,
initial_conditions=paths.SampleSet([initial_sample]),
mover=nojoin,
network=network
)
def test_cannot_guess(self):
filename = self._filename('no-guess')
storage = paths.Storage(filename, 'w')
storage.save(self.traj)
storage.save(self.other_traj)
storage.close()
storage = paths.Storage(filename, 'r')
with pytest.raises(RuntimeError):
self.PARAMETER.get(storage, None)
def test_storage_attribute_function(self):
import os
# test all combinations of (1) with and without UUIDs,
# (2) using partial yes, no all of these must work
for allow_incomplete in (True, False):
# print('ALLOW INCOMPLETE', allow_incomplete)
fname = data_filename("attr_storage_test.nc")
if os.path.isfile(fname):
os.remove(fname)
traj = paths.Trajectory(list(self.traj_simple))
template = traj[0]
storage_w = paths.Storage(fname, "w")
storage_w.snapshots.save(template)
storage_w.trajectories.save(traj)
# compute distance in x[0]
attr1 = FunctionPseudoAttribute(
'f1', paths.Trajectory,
lambda x: x[0].coordinates[0] - x[-1].coordinates[
0]).with_diskcache(allow_incomplete=allow_incomplete)
storage_w.save(attr1)
# let's mess up the order in which we save and
# include reversed ones as well
storage_w.trajectories.save(traj[3:])
storage_w.snapshots.save(traj[1].reversed)
storage_w.trajectories.save(traj.reversed)
# this should be ignored for all is saved already
storage_w.trajectories.save(traj)
storage_w.close()
storage_r = paths.Storage(fname, 'r')
rattr1 = storage_r.attributes['f1']
assert (rattr1._store_dict)
attr_cache = rattr1._store_dict.value_store
assert (attr_cache.allow_incomplete == allow_incomplete)
for idx, traj in enumerate(storage_r.trajectories):
if not allow_incomplete or attr_cache[traj] is not None:
assert_close_unit(attr_cache[traj], attr1(traj))
storage_r.close()
if os.path.isfile(fname):
os.remove(fname)
def test_storage(self):
self.storage.tag['simulation'] = self.simulation
self.storage.close()
read_store = paths.Storage(self.filename, 'r')
sim = read_store.tag['simulation']
new_filename = data_filename("test2.nc")
sim.storage = paths.Storage(new_filename, 'w')
sim.output_stream = open(os.devnull, 'w')
sim.run(n_per_snapshot=2)
if os.path.isfile(new_filename):
os.remove(new_filename)
def file_snapshots_committor(task_file_name, n_per_snapshot):
"""Run the committor for all snapshots in an input file.
Returns
-------
list
tuples of ``(uuid, state_name)``, where ``uuid`` is the UUID of the
original snapshot and ``state_name`` is the name of the final volume
the shot landed in
"""
tmp_filename = "tmp_out_" + task_file_name
task_file = paths.Storage(task_file_name, mode='r')
states = task_file.tags['states']
initial_snapshots = task_file.tags['initial_snapshots']
storage = paths.Storage(tmp_filename, mode='w')
sim = paths.CommittorSimulation(storage=storage,
engine=task_file.tags['engine'],
states=states,
randomizer=task_file.tags['randomizer'],
initial_snapshots=initial_snapshots)
sim.output_stream.write("Running file: " + task_file_name + "\n")
sim.run(n_per_snapshot)
# now we convert the results to a format that can be returned over dask
analyzer = paths.ShootingPointAnalysis(steps=None, states=states)
key_to_init_uuid = {
analyzer.hash_function(snap): snap.__uuid__
for snap in initial_snapshots
}
def final_state_name(step):
state_list = analyzer.analyze_single_step(step)
if len(state_list) > 1:
raise RuntimeError("State definitions are overlapping!")
return state_list[0].name
def initial_snapshot_uuid(step):
key = analyzer.step_key(step)
return key_to_init_uuid[analyzer.hash_function(key)]
# return pairs (initial_snapshot_uuid, final_state_name)
# this is and (int, str) tuple for each step; should be trivial to
# communicate back
return_value = [(initial_snapshot_uuid(step), final_state_name(step))
for step in storage.steps]
# cleanup
task_file.close()
storage.close()
os.remove(tmp_filename)
return return_value
def test_store_nonperiodic(self):
testsystem = openmmtools.testsystems.AlanineDipeptideVacuum()
snap = paths.engines.openmm.snapshot_from_testsystem(testsystem,
periodic=False)
storage = paths.Storage("test.nc", 'w')
storage.save(snap)
storage.close()
load = paths.Storage("test.nc", 'r')
reloaded = load.snapshots[0]
npt.assert_array_equal(snap.coordinates, reloaded.coordinates)
npt.assert_array_equal(snap.box_vectors, reloaded.box_vectors)
assert snap.box_vectors is None
assert reloaded.box_vectors is None
def test_storage(self):
analyzer = paths.ChannelAnalysis(steps=None, channels=self.channels)
analyzer._results = self.toy_results
analyzer.treat_multiples = 'newest'
storage = paths.Storage(data_filename('test.nc'), 'w')
storage.tag['analyzer'] = analyzer
storage.sync()
storage.close()
new_store = paths.Storage(data_filename('test.nc'), 'r')
reloaded = storage.tag['analyzer']
assert_equal(reloaded._results, self.toy_results)
if os.path.isfile(data_filename('test.nc')):
os.remove(data_filename('test.nc'))
def test_md_main(md_fixture, inp):
tempdir = tempfile.mkdtemp()
try:
store_name = os.path.join(tempdir, "md.nc")
storage = paths.Storage(store_name, mode='w')
engine, ens, snapshot = md_fixture
if inp == 'nsteps':
nsteps, ensembles = 5, None
elif inp == 'ensemble':
nsteps, ensembles = None, [ens]
else: # -no-cov-
raise RuntimeError("pytest went crazy")
traj, foo = md_main(output_storage=storage,
engine=engine,
ensembles=ensembles,
nsteps=nsteps,
initial_frame=snapshot)
assert isinstance(traj, paths.Trajectory)
assert foo is None
assert len(traj) == 5
assert len(storage.trajectories) == 1
storage.close()
finally:
os.remove(store_name)
os.rmdir(tempdir)
def setup(self):
# As a test system, let's use 1D motion on a flat potential. If the
# velocity is positive, you right the state on the right. If it is
# negative, you hit the state on the left.
pes = toys.LinearSlope(m=[0.0], c=[0.0]) # flat line
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
integrator = toys.LeapfrogVerletIntegrator(0.1)
options = {
'integ': integrator,
'n_frames_max': 100000,
'n_steps_per_frame': 5
}
self.engine = toys.Engine(options=options, topology=topology)
self.snap0 = toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=self.engine)
cv = paths.FunctionCV("Id", lambda snap : snap.coordinates[0][0])
self.left = paths.CVDefinedVolume(cv, float("-inf"), -1.0)
self.right = paths.CVDefinedVolume(cv, 1.0, float("inf"))
self.state_labels = {"Left" : self.left,
"Right" : self.right,
"None" : ~(self.left | self.right)}
randomizer = paths.NoModification()
self.filename = data_filename("committor_test.nc")
self.storage = paths.Storage(self.filename, mode="w")
self.storage.save(self.snap0)
self.simulation = CommittorSimulation(storage=self.storage,
engine=self.engine,
states=[self.left, self.right],
randomizer=randomizer,
initial_snapshots=self.snap0)
self.simulation.output_stream = open(os.devnull, 'w')
def test_storage(self):
import os
fname = data_filename("interface_set_storage_test.nc")
if os.path.isfile(fname):
os.remove(fname)
template_traj = make_1d_traj([0.0])
template = template_traj[0]
storage_w = paths.Storage(fname, "w")
storage_w.save(template_traj)
storage_w.save(self.increasing_set)
storage_w.sync_all()
storage_r = paths.AnalysisStorage(fname)
reloaded = storage_r.interfacesets[0]
assert_items_equal(reloaded.lambdas, self.increasing_set.lambdas)
assert_equal(reloaded.period_min, self.increasing_set.period_min)
assert_equal(reloaded.period_max, self.increasing_set.period_max)
for (truth, beauty) in zip(self.increasing_set, reloaded):
assert_equal(truth, beauty)
for (v, l) in zip(reloaded.volumes, reloaded.lambdas):
assert_equal(reloaded.get_lambda(v), l)
if os.path.isfile(fname):
os.remove(fname)
def create_file(self, getter):
filename = self._filename(getter)
storage = paths.Storage(filename, 'w')
storage.save(self.traj)
storage.save(self.other_traj)
get_type, getter_style = self._parse_getter(getter)
main, other = {
'traj': (self.traj, self.other_traj),
'sset': (self.sample_set, self.other_sample_set)
}[get_type]
if get_type == 'sset':
storage.save(self.sample_set)
storage.save(self.other_sample_set)
tag, other_tag = {
'name': ('traj', None),
'number': (None, None),
'tag-final': ('final_conditions', 'initial_conditions'),
'tag-initial': ('initial_conditions', None)
}[getter_style]
if tag:
storage.tags[tag] = main
if other_tag:
storage.tags[other_tag] = other
storage.close()
return filename
def test_contents_table_error():
runner = CliRunner()
with runner.isolated_filesystem():
storage = paths.Storage("temp.nc", mode='w')
storage.close()
results = runner.invoke(contents, ['temp.nc', '--table', 'foo'])
assert results.exit_code != 0
def _getter_test(self, getter):
test_file = self.create_file(getter)
storage = paths.Storage(self._filename(getter), mode='r')
get_arg = self.get_arg[getter]
obj = self.PARAMETER.get(storage, get_arg)
assert obj.__uuid__ == self.obj.__uuid__
assert obj == self.obj
def test_contents(tps_fixture):
# we just do a full integration test of this one
scheme, network, engine, init_conds = tps_fixture
runner = CliRunner()
with runner.isolated_filesystem():
storage = paths.Storage("setup.nc", 'w')
for obj in tps_fixture:
storage.save(obj)
storage.tags['initial_conditions'] = init_conds
results = runner.invoke(contents, ['setup.nc'])
cwd = os.getcwd()
expected = [
f"Storage @ '{cwd}/setup.nc'", "CVs: 1 item", "* x",
"Volumes: 8 items", "* A", "* B", "* plus 6 unnamed items",
"Engines: 2 items", "* flat", "* plus 1 unnamed item",
"Networks: 1 item", "* 1 unnamed item", "Move Schemes: 1 item",
"* 1 unnamed item", "Simulations: 0 items", "Tags: 1 item",
"* initial_conditions", "", "Data Objects:",
"Steps: 0 unnamed items", "Move Changes: 0 unnamed items",
"SampleSets: 1 unnamed item", "Trajectories: 1 unnamed item",
f"Snapshots: {2*len(init_conds[0])} unnamed items", ""
]
assert_click_success(results)
assert results.output.split('\n') == expected
for truth, beauty in zip(expected, results.output.split('\n')):
assert truth == beauty
def test_contents_table(tps_fixture, table):
scheme, network, engine, init_conds = tps_fixture
runner = CliRunner()
with runner.isolated_filesystem():
storage = paths.Storage("setup.nc", 'w')
for obj in tps_fixture:
storage.save(obj)
storage.tags['initial_conditions'] = init_conds
results = runner.invoke(contents, ['setup.nc', '--table', table])
cwd = os.getcwd()
expected = {
'volumes': [
f"Storage @ '{cwd}/setup.nc'", "volumes: 8 items", "* A",
"* B", "* plus 6 unnamed items", ""
],
'trajectories': [
f"Storage @ '{cwd}/setup.nc'", "trajectories: 1 unnamed item",
""
],
'tags': [
f"Storage @ '{cwd}/setup.nc'", "tags: 1 item",
"* initial_conditions", ""
],
}[table]
assert results.output.split("\n") == expected
assert_click_success(results)
def setup(self):
# As a test system, let's use 1D motion on a flat potential. If the
# velocity is positive, you right the state on the right. If it is
# negative, you hit the state on the left.
pes = toys.LinearSlope(m=[0.0], c=[0.0]) # flat line
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
integrator = toys.LeapfrogVerletIntegrator(0.1)
options = {
'integ': integrator,
'n_frames_max': 100000,
'n_steps_per_frame': 5
}
self.engine = toys.Engine(options=options, topology=topology)
self.snap0 = toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=self.engine)
cv = paths.FunctionCV("Id", lambda snap: snap.coordinates[0][0])
starting_volume = paths.CVDefinedVolume(cv, -0.01, 0.01)
forward_ensemble = paths.LengthEnsemble(5)
backward_ensemble = paths.LengthEnsemble(3)
randomizer = paths.NoModification()
self.filename = data_filename("shoot_from_snaps.nc")
self.storage = paths.Storage(self.filename, 'w')
self.simulation = ShootFromSnapshotsSimulation(
storage=self.storage,
engine=self.engine,
starting_volume=starting_volume,
forward_ensemble=forward_ensemble,
backward_ensemble=backward_ensemble,
randomizer=randomizer,
initial_snapshots=self.snap0)
self.simulation.output_stream = open(os.devnull, "w")
def test_storage(self):
plmd = PLUMEDInterface(self.topology)
dist = PLUMEDCV("dist", plmd, "DISTANCE ATOMS=7,9")
store = paths.Storage("test.nc", "w")
store.save(self.trajectory[:2])
store.save(dist)
store.sync()
store.close()
store2 = paths.Storage('test.nc', 'r')
dist2 = store2.cvs[dist.name]
store2.close()
np.testing.assert_almost_equal(dist(self.trajectory),
dist2(self.trajectory),
decimal=6)
def setup(self):
test_dir = "one_way_tps_examples"
self.data_filename = lambda f : \
data_filename(os.path.join(test_dir, f))
old_store = paths.Storage(data_filename("tps_setup.nc"), "r")
self.network = old_store.networks[0]
tps_ensemble = self.network.sampling_ensembles[0]
self.shoot = oink.ShootingStub(tps_ensemble, pre_joined=False)
self.converter = StupidOneWayTPSConverter(
storage=paths.Storage(self.data_filename("output.nc"), "w"),
initial_file="file0.data",
mover=self.shoot,
network=self.network,
options=oink.TPSConverterOptions(includes_shooting_point=False,
trim=False))
old_store.close()
def test_storage(self):
plmd = PLUMEDInterface(self.topology)
plmd.set("", "UNITS LENGTH=nm")
plmd.set(
"", "MOLINFO STRUCTURE=" +
data_filename("plumed_wrapper/AD_initial_frame.pdb"))
store = paths.Storage("test.nc", "w")
store.save(self.trajectory[:2])
store.tags['a'] = plmd
store.sync()
store.close()
store2 = paths.Storage('test.nc', 'r')
plmd2 = store2.tags['a']
store2.close()
np.testing.assert_array_equal(plmd.get(), plmd2.get())
def test_store_and_reload(self):
if os.path.isfile(data_filename("output.nc")):
os.remove(data_filename("output.nc"))
storage = paths.Storage(data_filename("output.nc"), 'w')
annotated = AnnotatedTrajectory(self.traj, self.annotations)
storage.tag['traj1'] = annotated
storage.close()
analysis = paths.Storage(data_filename("output.nc"), 'r')
reloaded = analysis.tag['traj1']
assert len(reloaded.trajectory) == 13
assert len(reloaded.annotations) == 4
self._check_standard_annotated_trajectory(reloaded)
if os.path.isfile(data_filename("output.nc")):
os.remove(data_filename("output.nc"))
def make_input_file(tps_network_and_traj):
input_file = paths.Storage("setup.nc", mode='w')
for obj in tps_network_and_traj:
input_file.save(obj)
input_file.tags['template'] = input_file.snapshots[0]
input_file.close()
return "setup.nc"
def setup(self):
# PES is one-dimensional linear slope (y(x) = x)
pes = toys.LinearSlope(m=[-1.0], c=[0.0])
# one particle with mass 1.0
topology = toys.Topology(n_spatial=1, masses=[1.0], pes=pes)
integrator = toys.LeapfrogVerletIntegrator(0.02)
options = {
'integ': integrator,
'n_frames_max': 1000,
'n_steps_per_frame': 5
}
self.engine = toys.Engine(options=options, topology=topology)
# test uses three snapshots with different velocities
# 0: direction ok, velocity too low => falls back to dividing surface
# 1: wrong direction => backward shot towards B
# 2: direction ok, velocity high enough => successfull new trajectory
self.initial_snapshots = [
toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]),
engine=self.engine),
toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[-1.0]]),
engine=self.engine),
toys.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[2.0]]),
engine=self.engine)
]
# reaction coordinate is just x coordinate
rc = paths.FunctionCV("Id", lambda snap: snap.coordinates[0][0])
# state A: [-inf, -1]
self.state_A = paths.CVDefinedVolume(rc, float("-inf"), -1.0)
# area between A and dividing surface: [-1, 0]
self.towards_A = paths.CVDefinedVolume(rc, -1.0, 0.0)
# state B: [1, inf]
self.state_B = paths.CVDefinedVolume(rc, 1.0, float("inf"))
# define state labels
self.state_labels = {
"A": self.state_A,
"B": self.state_B,
"ToA": self.towards_A,
"None": ~(self.state_A | self.state_B | self.towards_A)
}
# velocities are not randomized
randomizer = paths.NoModification()
self.filename = data_filename("rf_test.nc")
self.storage = paths.Storage(self.filename, mode="w")
self.storage.save(self.initial_snapshots)
self.simulation = ReactiveFluxSimulation(
storage=self.storage,
engine=self.engine,
states=[self.state_A, self.state_B],
randomizer=randomizer,
initial_snapshots=self.initial_snapshots,
rc=rc)
self.simulation.output_stream = open(os.devnull, 'w')
def test_mention_only(self):
storage_w = paths.Storage(self.filename, "w")
template = self.template_snapshot
storage_w.snapshots.add_type(template)
test_snap = self.traj[2]
# only touch a new snapshot
storage_w.snapshots.only_mention = True
storage_w.snapshots.save(test_snap)
# check that the snapshot is there
assert (len(storage_w.snapshots) == 4)
# in the memory uuid index
assert (test_snap.__uuid__ in storage_w.snapshots.index)
# and stored
assert (test_snap.__uuid__ == storage_w.snapshots.vars['uuid'][1])
# but no real snapshot has been stored
# print len(storage_w.objects['snapshot0'])
assert (len(storage_w.objects['snapshot0']) == 2)
# switch on normal saving
storage_w.snapshots.only_mention = False
test_snap = self.traj[4]
storage_w.snapshots.mention(test_snap)
# check that the snapshot is there
assert (len(storage_w.snapshots) == 6)
# in the memory uuid index
assert (test_snap.__uuid__ in storage_w.snapshots.index)
# and stored
assert (test_snap.__uuid__ == storage_w.snapshots.vars['uuid'][2])
# but no real snapshot has been stored
assert (len(storage_w.objects['snapshot0']) == 2)
# try to now add it
storage_w.snapshots.save(test_snap)
# check that the snapshot is not stored again (only 3 snapshots)
assert (len(storage_w.snapshots) == 6)
assert (len(storage_w.objects['snapshot0']) == 4)
# print storage_w.objects['snapshot0'][1].coordinates
# print template.coordinates
# print storage_w.objects['snapshot0'][0].coordinates
# print test_snap.coordinates
# print storage_w.objects['snapshot0'].vars['statics'][0].coordinates
# print storage_w.objects['snapshot0'].vars['statics'][1].coordinates
# print storage_w.objects['snapshot0'].index
compare_snapshot(storage_w.objects['snapshot0'][4], test_snap)
storage_w.close()
def create_file(self, getter):
filename = self._filename(getter)
storage = paths.Storage(filename, 'w')
storage.save(self.other_snap)
if getter != 'none-num':
storage.save(self.init_snap)
storage.tags['initial_snapshot'] = self.init_snap
storage.close()
return filename
def setup(self):
self.tmpdir = tempfile.mkdtemp()
self.storage_filename = os.path.join(self.tmpdir, "test.nc")
self.storage = paths.Storage(self.storage_filename, mode='w')
snap = make_1d_traj([1])[0]
self.storage.save(snap)
self.cv_x = paths.CoordinateFunctionCV("x", lambda s: s.xyz[0][0])
self.cv_y = paths.CoordinateFunctionCV("y", lambda s: s.xyz[0][1])
self.storage.save([self.cv_x, self.cv_y])
def _workaround(self, name):
# this is messed up... for some reason, storage doesn't create a new
# file in append mode. That may be a bug
import openpathsampling as paths
needs_workaround = (self.mode == 'a' and not os.path.exists(name)
and not self._is_simstore(name))
if needs_workaround:
st = paths.Storage(name, mode='w')
st.close()
def test_pathsampling_main(tps_fixture):
scheme, _, _, init_conds = tps_fixture
with CliRunner().isolated_filesystem():
storage = paths.Storage("tps.nc", mode='w')
final, sim = pathsampling_main(storage, scheme, init_conds, 10)
assert isinstance(final, paths.SampleSet)
assert isinstance(sim, paths.PathSampling)
assert len(storage.steps) == 11
assert len(storage.schemes) == 1
def test_save_initial_scheme(self, tmpdir):
# check that we actually save scheme when we save this
filename = tmpdir.join("temp.nc")
storage = paths.Storage(str(filename), mode='w')
assert len(storage.schemes) == 0
sim = paths.PathSampling(storage=storage,
move_scheme=self.scheme,
sample_set=self.init_cond)
assert len(storage.schemes) == 1