def testRotationNone(self):
""" Check that by default no rotation is applied and that random rotation has an effect."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 1,
'number_of_steps': 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
# Check rotation angle.
with h5py.File(
os.path.join(test_interactor.output_path,
'pmi_out_0000001.h5'), 'r') as h5:
angle = h5['data/angle'].value
self.assertEqual(angle[0, 0], 0.)
self.assertEqual(angle[0, 1], 0.)
self.assertEqual(angle[0, 2], 0.)
self.assertEqual(angle[0, 3], 0.)
# Get atom positions.
atom_positions = h5['data/snp_0000001/r'].value
# Now do same calculation again.
test_interactor.backengine()
# Get atom positions from new calculation.
with h5py.File(
os.path.join(test_interactor.output_path,
'pmi_out_0000001.h5'), 'r') as h5:
new_atom_positions = h5['data/snp_0000001/r'].value
# They should coincide since no rotation has been applied.
self.assertAlmostEqual(
1e10 * numpy.linalg.norm(atom_positions - new_atom_positions), 0.0,
7)
def testRotationRandom(self):
""" Check that by default no rotation is applied and that random rotation has an effect."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 1,
'number_of_steps': 100,
'random_rotation': True,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
# Check rotation angle.
with h5py.File(
os.path.join(test_interactor.output_path,
'pmi_out_0000001.h5'), 'r') as h5:
angle = h5['data/angle'].value[0]
# Check we have a non-zero rotation.
self.assertNotEqual(numpy.linalg.norm(angle), 0.)
def testIssue53(self):
""" Check that xmdyn_demo writes the Nph variable according to bugfix 53."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 10,
'number_of_steps': 100,
}
pmi = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('2nip.pdb'))
# Call backengine
status = pmi.backengine()
h5 = h5py.File('pmi/pmi_out_0000001.h5')
Nph = h5['/data/snp_0000001/Nph']
self.assertEqual(Nph.shape, (1, ))
def testBackengine(self):
""" Check that the backengine method works correctly. """
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {'number_of_trajectories' : 1,
'number_of_steps' : 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path = TestUtilities.generateTestFilePath('sample.h5') )
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
self.assertTrue( 'pmi_out_0000001.h5' in os.listdir( test_interactor.output_path ) )
def testBackengine(self):
""" Check that the backengine method works correctly. """
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 1,
'number_of_steps': 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
self.assertTrue(
'pmi_out_0000001.h5' in os.listdir(test_interactor.output_path))
def reference2NIP(self):
""" Testing that diffraction intensities with 9fs 5keV pulses through SPB-SFX KB beamline are of the order of Yoon 2016. """
source_file = "/data/netapp/grotec/datadump/5keV_9fs_2015_slice12_fromYoon2016.h5"
#source_file = TestUtilities.generateTestFilePath("FELsource_out.h5")
# Propagate
propagator = XFELPhotonPropagator(parameters=None,
input_path=source_file,
output_path="prop_out.h5")
propagator.backengine()
propagator.saveH5()
pmi = XMDYNDemoPhotonMatterInteractor(
parameters=None,
input_path=propagator.output_path,
output_path="pmi",
sample_path=TestUtilities.generateTestFilePath("sample.h5"))
pmi.backengine()
# Diffraction with parameters.
diffraction_parameters = {
'uniform_rotation': True,
'calculate_Compton': False,
'slice_interval': 100,
'number_of_slices': 100,
'pmi_start_ID': 1,
'pmi_stop_ID': 1,
'number_of_diffraction_patterns': 1,
'beam_parameter_file':
TestUtilities.generateTestFilePath('s2e.beam'),
'beam_geometry_file':
TestUtilities.generateTestFilePath('s2e.geom'),
'number_of_MPI_processes': 8,
}
diffractor = SingFELPhotonDiffractor(parameters=diffraction_parameters,
input_path=pmi.output_path,
output_path="diffr_out.h5")
diffractor.backengine()
def testLoadPDBFile(self):
""" Check that the sample can be taken from a pdb directly. """
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {'number_of_trajectories' : 10,
'number_of_steps' : 100,
}
pmi = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('2nip.pdb') )
# Call backengine
status = pmi.backengine()
self.assertEqual(status, 0 )
def testOPMD(self):
""" Check that the input directory scanner filters out the opmd files."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Setup parameters.
pmi_parameters = {'number_of_trajectories' : 10,
'number_of_steps' : 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=TestUtilities.generateTestFilePath('prop_out'),
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5') )
# Call backengine
status = test_interactor.backengine()
self.assertEqual(status, 0 )
def testBackengineDefaultPaths(self):
""" Check that the backengine method works correctly. """
# Prepare input.
shutil.copytree( TestUtilities.generateTestFilePath('prop_out'), os.path.abspath( 'prop' ) )
self.__dirs_to_remove.append( 'prop' )
self.__dirs_to_remove.append( 'pmi' )
test_interactor = XMDYNDemoPhotonMatterInteractor(sample_path=TestUtilities.generateTestFilePath('sample.h5') )
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
self.assertTrue( os.path.isdir( os.path.abspath( 'prop' ) ) )
self.assertIn( 'pmi_out_0000001.h5' , os.listdir( test_interactor.output_path ) )
self.assertIn( 'pmi_out_0000002.h5' , os.listdir( test_interactor.output_path ) )
def testLoadPDBFile(self):
""" Check that the sample can be taken from a pdb directly. """
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {
'number_of_trajectories': 10,
'number_of_steps': 100,
}
pmi = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('2nip.pdb'))
# Call backengine
status = pmi.backengine()
self.assertEqual(status, 0)
def testOPMD(self):
""" Check that the input directory scanner filters out the opmd files."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Setup parameters.
pmi_parameters = {
'number_of_trajectories': 10,
'number_of_steps': 100,
}
test_interactor = XMDYNDemoPhotonMatterInteractor(
parameters=pmi_parameters,
input_path=TestUtilities.generateTestFilePath('prop_out'),
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
self.assertEqual(status, 0)
def testIssue53(self):
""" Check that xmdyn_demo writes the Nph variable according to bugfix 53."""
# Clean up.
self.__dirs_to_remove.append('pmi')
# Get test instance.
pmi_parameters = {'number_of_trajectories' : 10,
'number_of_steps' : 100,
}
pmi = XMDYNDemoPhotonMatterInteractor(parameters=pmi_parameters,
input_path=self.input_h5,
output_path='pmi',
sample_path=TestUtilities.generateTestFilePath('2nip.pdb') )
# Call backengine
status = pmi.backengine()
h5 = h5py.File('pmi/pmi_out_0000001.h5')
Nph = h5['/data/snp_0000001/Nph']
self.assertEqual(Nph.shape, (1,))
def testBackengineDefaultPaths(self):
""" Check that the backengine method works correctly. """
# Prepare input.
shutil.copytree(TestUtilities.generateTestFilePath('prop_out'),
os.path.abspath('prop'))
self.__dirs_to_remove.append('prop')
self.__dirs_to_remove.append('pmi')
test_interactor = XMDYNDemoPhotonMatterInteractor(
sample_path=TestUtilities.generateTestFilePath('sample.h5'))
# Call backengine
status = test_interactor.backengine()
# Check that the backengine returned zero.
self.assertEqual(status, 0)
# Check we have generated the expected output.
self.assertTrue(os.path.isdir(os.path.abspath('prop')))
self.assertIn('pmi_out_0000001.h5',
os.listdir(test_interactor.output_path))
self.assertIn('pmi_out_0000002.h5',
os.listdir(test_interactor.output_path))
import sys
from SimEx.Calculators.XMDYNDemoPhotonMatterInteractor import XMDYNDemoPhotonMatterInteractor
# Define the input path (location of propagated pulse data).
prop_path = "prop_out/prop_s2e_example.h5"
# Define the sample as pdb code + ".pdb" extension.
sample="2NIP.pdb"
# Setup propagation parameters.
parameters=None
# Construct the propagator
pmi_calculator = XMDYNDemoPhotonMatterInteractor( parameters=parameters, input_path=prop_path,
sample_path=sample)
# Read the data.
pmi_calculator._readH5()
# Call the backengine.
status = pmi_calculator.backengine()
if status != 0:
print("PMI calculation failed, check output.")
sys.exit()
print("PMI calculation succeeded.")
