def testSpatialData(self):
""" Test that the query for the spatial data works. """
ps = ProcessStatistics(processes=[0],
time_interval=0.3,
spatially_resolved=True)
ref_data = "REFERENCE"
ps._ProcessStatistics__spatial_data = ref_data
# Check by reference.
self.assertTrue(ps.spatialData() == ref_data)
def testConstruction(self):
""" Test that we can construct a valid ProcessStatistics object. """
ps0 = ProcessStatistics(processes=[1, 2, 5],
time_interval=2.3,
spatially_resolved=True)
# Check values on the class.
self.assertEqual(ps0._ProcessStatistics__processes, [1, 2, 5])
self.assertEqual(ps0._ProcessStatistics__current_count, 0)
self.assertAlmostEqual(ps0._ProcessStatistics__time_interval, 2.3, 10)
self.assertTrue(ps0._ProcessStatistics__spatially_resolved)
self.assertTrue(ps0._ProcessStatistics__spatial_data is None)
# Construct with default time interval and spatial resolution.
ps0 = ProcessStatistics(processes=[1, 2, 5])
self.assertAlmostEqual(ps0._ProcessStatistics__time_interval, 1.0, 10)
self.assertFalse(ps0._ProcessStatistics__spatially_resolved)
self.assertTrue(ps0._ProcessStatistics__spatial_data is None)
def testPrintResults(self):
""" Test that we can print the results """
# Setup.
ps = ProcessStatistics(processes=[0], time_interval=0.3)
# Add data on the class.
ps._ProcessStatistics__data = [0, 12, 245, 1435]
stream = StringIO.StringIO()
ps.printResults(stream)
# Reference checked by hand.
ref_value = \
""" time (t) count (n) (dn/dt) (n/t)
0.30000 12 40.00000 40.00000
0.60000 257 816.66667 428.33333
0.90000 1692 4783.33333 1880.00000
"""
if MPICommons.isMaster():
self.assertEqual(stream.getvalue(), ref_value)
else:
self.assertEqual(stream.getvalue(), "")
def testSetup(self):
""" Test that the setup function stores the time properly. """
ps = ProcessStatistics(processes=[0], time_interval=2.3)
# Check initial value.
self.assertAlmostEqual(ps._ProcessStatistics__last_time, 0.0, 10)
# Call setup.
ps.setup("dummy_step", "dummy_time", "dummy_config")
self.assertEqual(ps._ProcessStatistics__last_time, "dummy_time")
class DummyConfig:
def sites(self):
return [1, 2, 3, 4, 5]
ps = ProcessStatistics(processes=[0],
time_interval=2.3,
spatially_resolved=True)
ps.setup("dummy_step", "dummy_time", DummyConfig())
self.assertEqual(ps._ProcessStatistics__last_time, "dummy_time")
self.assertEqual(len(ps._ProcessStatistics__spatial_data), 5)
self.assertAlmostEqual(
numpy.linalg.norm(ps._ProcessStatistics__spatial_data), 0.0, 10)
def testConstructionFail(self):
""" Test that construction fails with wrong input. """
# Fail because of missing processes input.
self.assertRaises(Error, lambda: ProcessStatistics(time_interval=2.3))
# Wrong type.
self.assertRaises(
Error,
lambda: ProcessStatistics(processes=["1", "2"], time_interval=2.3))
self.assertRaises(
Error, lambda: ProcessStatistics(processes=0, time_interval=2.3))
self.assertRaises(
Error, lambda: ProcessStatistics(processes=[1], time_interval=1))
self.assertRaises(
Error, lambda: ProcessStatistics(
processes=[1], time_interval=1.0, spatially_resolved="YES"))
# Wrong value.
self.assertRaises(
Error,
lambda: ProcessStatistics(processes=[-1], time_interval=2.3))
self.assertRaises(
Error,
lambda: ProcessStatistics(processes=[1], time_interval=-1.0))
#NiO process
import time
from KMCLib import *
from KMCLib.Analysis.TimeStepDistribution import TimeStepDistribution
from KMCLib.Analysis.ProcessStatistics import ProcessStatistics
from matplotlib import pyplot as plt
t_calstart = time.clock()
configuration = KMCConfigurationFromScript("config.py")
interactions = KMCInteractionsFromScript("interactions.py")
model = KMCLatticeModel(configuration=configuration, interactions=interactions)
control_parameters = KMCControlParameters(number_of_steps=10000000,
dump_interval=10000,
analysis_interval=1)
#set up the analysis
tsd = TimeStepDistribution(binsize=0.001)
pst = ProcessStatistics()
# Run the simulation - save trajectory to 'NiO POM.py'
model.run(control_parameters,
trajectory_filename="NiO POM.py",
analysis=[tsd, pst])
t_calend = time.clock()
print("sim complete time cost is :", t_calend - t_calstart)
#length of lattice
size = 100
def testRegisterStepAndFinalize(self):
""" Test the step registration. """
ps = ProcessStatistics(processes=[0],
time_interval=0.3,
spatially_resolved=True)
class DummyConfig:
def latestEventProcess(self):
return 0
def latestEventSite(self):
return 1
def sites(self):
return [1, 2, 3]
# Set the initial time.
config = DummyConfig()
ps.setup("dummy_step", 0.0, config)
# Set the current count.
ps._ProcessStatistics__current_count = 156
# Check initial value.
self.assertEqual(ps._ProcessStatistics__data, [])
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[0], 0.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[1], 0.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[2], 0.0, 10)
# Register the step.
time = 1.0
ps.registerStep("dummy_step", time, config)
# Check the result.
self.assertEqual(ps._ProcessStatistics__data, [156])
self.assertEqual(ps._ProcessStatistics__current_count, 1)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[0], 0.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[1], 1.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[2], 0.0, 10)
# Add again.
time += 0.2
ps.registerStep("dummy_step", time, config)
self.assertEqual(ps._ProcessStatistics__data, [156])
self.assertEqual(ps._ProcessStatistics__current_count, 2)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[0], 0.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[1], 2.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[2], 0.0, 10)
# Add again.
time += 0.5
ps.registerStep("dummy_step", time, config)
self.assertEqual(ps._ProcessStatistics__data, [156, 2])
self.assertEqual(ps._ProcessStatistics__current_count, 1)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[0], 0.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[1], 3.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[2], 0.0, 10)
# Now with another dummy config.
class DummyConfig1:
def latestEventProcess(self):
return 1
def latestEventSite(self):
return 1
config = DummyConfig1()
time += 0.5
ps.registerStep("dummy_step", time, config)
self.assertEqual(ps._ProcessStatistics__data, [156, 2, 1])
self.assertEqual(ps._ProcessStatistics__current_count, 0)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[0], 0.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[1], 3.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[2], 0.0, 10)
# Finalize.
ps.finalize()
# Check that the spatially resolved data gets divided by the total time.
total_t = 0.5 + 0.5 + 0.2 + 1.0
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[0], 0.0, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[1],
3.0 / total_t, 10)
self.assertAlmostEqual(ps._ProcessStatistics__spatial_data[2], 0.0, 10)