def test_reaction_info(self):
p_types = ioutils.get_particle_types(self.fname)
reactions = ioutils.get_reactions(self.fname)
self.assertEqual(len(reactions), 3)
self.assertTrue("mylabel" in reactions)
mylabel = reactions["mylabel"]
self.assertEqual(mylabel["n_educts"], 1)
self.assertEqual(mylabel["n_products"], 1)
self.assertAlmostEqual(mylabel["rate"], 0.00001)
self.assertEqual(mylabel["educt_types"][0], p_types["A"])
self.assertEqual(mylabel["product_types"][0], p_types["B"])
self.assertTrue("A->B" in reactions)
atob = reactions["A->B"]
self.assertEqual(atob["n_educts"], 1)
self.assertEqual(atob["n_products"], 1)
self.assertEqual(atob["rate"], 1.)
self.assertEqual(atob["educt_types"][0], p_types["A"])
self.assertEqual(atob["product_types"][0], p_types["B"])
self.assertTrue("B+C->A" in reactions)
fusion = reactions["B+C->A"]
self.assertEqual(fusion["n_educts"], 2)
self.assertEqual(fusion["n_products"], 1)
self.assertAlmostEqual(fusion["rate"], 0.4)
self.assertAlmostEqual(fusion["educt_distance"], 0.2)
correct_educts = (fusion["educt_types"][0] == p_types["B"]
and fusion["educt_types"][1] == p_types["C"])
correct_educts = correct_educts or (
fusion["educt_types"][1] == p_types["B"]
and fusion["educt_types"][0] == p_types["C"])
self.assertTrue(correct_educts)
self.assertEqual(fusion["product_types"][0], p_types["A"])
def test_reaction_info(self):
p_types = ioutils.get_particle_types(self.fname)
reactions = ioutils.get_reactions(self.fname)
self.assertEqual(len(reactions), 3)
self.assertTrue("mylabel" in reactions)
mylabel = reactions["mylabel"]
self.assertEqual(mylabel["n_educts"], 1)
self.assertEqual(mylabel["n_products"], 1)
self.assertAlmostEqual(mylabel["rate"], 0.00001)
self.assertEqual(mylabel["educt_types"][0], p_types["A"])
self.assertEqual(mylabel["product_types"][0], p_types["B"])
self.assertTrue("A->B" in reactions)
atob = reactions["A->B"]
self.assertEqual(atob["n_educts"], 1)
self.assertEqual(atob["n_products"], 1)
self.assertEqual(atob["rate"], 1.)
self.assertEqual(atob["educt_types"][0], p_types["A"])
self.assertEqual(atob["product_types"][0], p_types["B"])
self.assertTrue("B+C->A" in reactions)
fusion = reactions["B+C->A"]
self.assertEqual(fusion["n_educts"], 2)
self.assertEqual(fusion["n_products"], 1)
self.assertAlmostEqual(fusion["rate"], 0.4)
self.assertAlmostEqual(fusion["educt_distance"], 0.2)
correct_educts = (fusion["educt_types"][0] == p_types["B"] and fusion["educt_types"][1] == p_types["C"])
correct_educts = correct_educts or (fusion["educt_types"][1] == p_types["B"] and fusion["educt_types"][0] == p_types["C"])
self.assertTrue(correct_educts)
self.assertEqual(fusion["product_types"][0], p_types["A"])
def __init__(self, filename, name=""):
"""
attempts to open the given trajectory
:param filename: the file name
:param name: the trajectory name inside the file, as given in the simulation
"""
assert _os.path.exists(
filename), "The file '{}' did not exist!".format(filename)
self._filename = filename
self._name = name
self._diffusion_constants = _io_utils.get_diffusion_constants(filename)
self._particle_types = _io_utils.get_particle_types(filename)
self._reactions = []
self._inverse_types_map = {
v: k
for k, v in self.particle_types.items()
}
self._general = GeneralInformation(filename)
for _, reaction in _io_utils.get_reactions(filename).items():
info = ReactionInfo(reaction["name"], reaction["id"],
reaction["n_educts"], reaction["n_products"],
reaction["rate"], reaction["educt_distance"],
reaction["product_distance"],
reaction["educt_types"],
reaction["product_types"],
self._inverse_types_map)
self._reactions.append(info)
def test_reaction_counts_observable(self):
fname = os.path.join(self.dir,
"test_observables_particle_reaction_counts.h5")
context = Context()
context.box_size = [10., 10., 10.]
context.particle_types.add("A", .0)
context.particle_types.add("B", .0)
context.particle_types.add("C", .0)
context.reactions.add_conversion("mylabel", "A", "B", .00001)
context.reactions.add_conversion("A->B", "A", "B", 1e16)
context.reactions.add_fusion("B+C->A", "B", "C", "A", 1e16, 1.0, .5,
.5)
sim = Simulation("CPU", context)
sim.add_particle("A", common.Vec(0, 0, 0))
sim.add_particle("B", common.Vec(1.0, 1.0, 1.0))
sim.add_particle("C", common.Vec(1.1, 1.0, 1.0))
n_timesteps = 1
handle = sim.register_observable_reaction_counts(1)
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"reactions", int(3))
loop = sim.create_loop(1)
loop.use_reaction_scheduler("Gillespie")
loop.write_config_to_file(f)
loop.run(1)
import readdy.util.io_utils as io_utils
reactions = io_utils.get_reactions(fname)
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/reactions"]
time_series = f2["readdy/observables/reactions/time"]
np.testing.assert_equal(time_series,
np.array(range(0, n_timesteps + 1)))
def get_item(name, collection):
return next(x for x in collection if x["name"] == name)
mylabel_id = get_item("mylabel", reactions.values())["id"]
atob_id = get_item("A->B", reactions.values())["id"]
fusion_id = get_item("B+C->A", reactions.values())["id"]
# counts of first time step, time is first index
np.testing.assert_equal(data["counts/" + str(mylabel_id)][0],
np.array([0]))
np.testing.assert_equal(data["counts/" + str(atob_id)][0],
np.array([0]))
np.testing.assert_equal(data["counts/" + str(fusion_id)][0],
np.array([0]))
# counts of second time step
np.testing.assert_equal(data["counts/" + str(mylabel_id)][1],
np.array([0]))
np.testing.assert_equal(data["counts/" + str(atob_id)][1],
np.array([1]))
np.testing.assert_equal(data["counts/" + str(fusion_id)][1],
np.array([1]))
def test_reaction_counts_observable(self):
fname = os.path.join(self.dir, "test_observables_particle_reaction_counts.h5")
sim = Simulation("CPU")
sim.context.box_size = [10., 10., 10.]
sim.context.particle_types.add("A", .0)
sim.context.particle_types.add("B", .0)
sim.context.particle_types.add("C", .0)
sim.context.reactions.add_conversion("mylabel", "A", "B", .00001)
sim.context.reactions.add_conversion("A->B", "A", "B", 1e16)
sim.context.reactions.add_fusion("B+C->A", "B", "C", "A", 1e16, 1.0, .5, .5)
sim.add_particle("A", common.Vec(0, 0, 0))
sim.add_particle("B", common.Vec(1.0, 1.0, 1.0))
sim.add_particle("C", common.Vec(1.1, 1.0, 1.0))
n_timesteps = 1
handle = sim.register_observable_reaction_counts(1)
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"reactions", int(3))
loop = sim.create_loop(1)
loop.use_reaction_scheduler("Gillespie")
loop.write_config_to_file(f)
loop.run(1)
import readdy.util.io_utils as io_utils
reactions = io_utils.get_reactions(fname)
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/reactions"]
time_series = f2["readdy/observables/reactions/time"]
np.testing.assert_equal(time_series, np.array(range(0, n_timesteps+1)))
def get_item(name, collection):
return next(x for x in collection if x["name"] == name)
mylabel_id = get_item("mylabel", reactions.values())["id"]
atob_id = get_item("A->B", reactions.values())["id"]
fusion_id = get_item("B+C->A", reactions.values())["id"]
# counts of first time step, time is first index
np.testing.assert_equal(data["counts/"+str(mylabel_id)][0], np.array([0]))
np.testing.assert_equal(data["counts/"+str(atob_id)][0], np.array([0]))
np.testing.assert_equal(data["counts/"+str(fusion_id)][0], np.array([0]))
# counts of second time step
np.testing.assert_equal(data["counts/"+str(mylabel_id)][1], np.array([0]))
np.testing.assert_equal(data["counts/"+str(atob_id)][1], np.array([1]))
np.testing.assert_equal(data["counts/"+str(fusion_id)][1], np.array([1]))
def __init__(self, filename, name=""):
"""
attempts to open the given trajectory
:param filename: the file name
:param name: the trajectory name inside the file, as given in the simulation
"""
assert _os.path.exists(filename), "The file '{}' did not exist!".format(filename)
self._filename = filename
self._name = name
self._diffusion_constants = _io_utils.get_diffusion_constants(filename)
self._particle_types = _io_utils.get_particle_types(filename)
self._reactions = []
self._inverse_types_map = {v: k for k, v in self.particle_types.items()}
self._general = GeneralInformation(filename)
for _, reaction in _io_utils.get_reactions(filename).items():
info = ReactionInfo(reaction["name"], reaction["id"], reaction["n_educts"],
reaction["n_products"], reaction["rate"], reaction["educt_distance"],
reaction["product_distance"], reaction["educt_types"], reaction["product_types"],
self._inverse_types_map)
self._reactions.append(info)
def test_reactions_observable(self):
fname = os.path.join(self.dir, "test_observables_particle_reactions.h5")
sim = Simulation("CPU")
sim.context.box_size = [10.,10.,10.]
sim.context.particle_types.add("A", .0)
sim.context.particle_types.add("B", .0)
sim.context.particle_types.add("C", .0)
sim.context.reactions.add_conversion("mylabel", "A", "B", .00001)
sim.context.reactions.add_conversion("A->B", "A", "B", 1.)
sim.context.reactions.add_fusion("B+C->A", "B", "C", "A", 1.0, 1.0, .5, .5)
sim.add_particle("A", common.Vec(0, 0, 0))
sim.add_particle("B", common.Vec(1.0, 1.0, 1.0))
sim.add_particle("C", common.Vec(1.1, 1.0, 1.0))
n_timesteps = 1
handle = sim.register_observable_reactions(1)
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"reactions", int(3))
loop = sim.create_loop(1)
loop.write_config_to_file(f)
loop.run(n_timesteps)
type_str_to_id = {k: x["type_id"] for k, x in ioutils.get_particle_types(fname).items()}
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/reactions"]
time_series = f2["readdy/observables/reactions/time"]
np.testing.assert_equal(time_series, np.array(range(0, n_timesteps+1)))
def get_item(name, collection):
return next(x for x in collection if x["name"] == name)
import readdy.util.io_utils as io_utils
reactions = io_utils.get_reactions(fname)
mylabel_reaction = get_item("mylabel", reactions.values())
np.testing.assert_allclose(mylabel_reaction["rate"], .00001)
np.testing.assert_equal(mylabel_reaction["n_educts"], 1)
np.testing.assert_equal(mylabel_reaction["n_products"], 1)
np.testing.assert_equal(mylabel_reaction["educt_types"], [type_str_to_id["A"], 0])
np.testing.assert_equal(mylabel_reaction["product_types"], [type_str_to_id["B"], 0])
atob_reaction = get_item("A->B", reactions.values())
np.testing.assert_equal(atob_reaction["rate"], 1.)
np.testing.assert_equal(atob_reaction["n_educts"], 1)
np.testing.assert_equal(atob_reaction["n_products"], 1)
np.testing.assert_equal(mylabel_reaction["educt_types"], [type_str_to_id["A"], 0])
np.testing.assert_equal(mylabel_reaction["product_types"], [type_str_to_id["B"], 0])
fusion_reaction = get_item("B+C->A", reactions.values())
np.testing.assert_equal(fusion_reaction["rate"], 1.)
np.testing.assert_equal(fusion_reaction["educt_distance"], 1.)
np.testing.assert_equal(fusion_reaction["n_educts"], 2)
np.testing.assert_equal(fusion_reaction["n_products"], 1)
np.testing.assert_equal(fusion_reaction["educt_types"], [type_str_to_id["B"], type_str_to_id["C"]])
np.testing.assert_equal(fusion_reaction["product_types"], [type_str_to_id["A"], 0])
records = data["records"][:]
np.testing.assert_equal(len(records), 2)
# records of 1st time step
for record in records[1]:
np.testing.assert_equal(record["reaction_type"] == 0 or record["reaction_type"] == 1, True)
if record["reaction_type"] == 0:
np.testing.assert_equal(record["position"], np.array([.0, .0, .0]))
np.testing.assert_equal(record["reaction_id"], atob_reaction["id"])
elif record["reaction_type"] == 1:
# fusion
np.testing.assert_allclose(record["position"], np.array([1.05, 1.0, 1.0]))
np.testing.assert_equal(record["reaction_id"], fusion_reaction["id"])
def test_reaction_info_all(self):
reactions_all = ioutils.get_reactions(self.fname)
np.testing.assert_equal(len(reactions_all), 3)