def test_adding_invalid_file_to_event_raises():
"""
Adding some invalid things should of course raise.
"""
gen = InputFileGenerator()
with pytest.raises(ValueError):
gen.add_events("some_nonesense")
def test_adding_invalid_file_to_event_raises():
"""
Adding some invalid things should of course raise.
"""
gen = InputFileGenerator()
with pytest.raises(ValueError):
gen.add_events("some_nonesense")
def test_reading_events_from_dictionary(self):
"""
Tests that events can also be passed as dictionaries.
"""
events = [{
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18
}, {
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19}]
gen = InputFileGenerator()
gen.add_events(events)
self.assertEqual(sorted(gen._events), sorted(events))
def test_reading_QuakeML_files(self):
"""
Tests the reading of QuakeML Files.
"""
event_file_1 = os.path.join(self.data_dir, "event1.xml")
event_file_2 = os.path.join(self.data_dir, "event2.xml")
gen = InputFileGenerator()
gen.add_events([event_file_1, event_file_2])
# Sort to be able to compare.
events = sorted(gen._events)
self.assertEqual([{
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18
}, {
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19}],
events)
def test_reading_events_from_dictionary():
"""
Tests that events can also be passed as dictionaries.
"""
events = [{
"description": "Event at a sunny place.",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18
}, {
"description": "Event at a rainy place.",
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19}]
gen = InputFileGenerator()
gen.add_events(events)
assert sorted(gen._events) == sorted(events)
def test_adding_events_as_URL():
"""
QuakeMLs should be downloaded if necessary.
Mock the actual downloading.
"""
event = {"description": "FICTIONAL EVENT IN BAVARIA",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"}
quake_ml_file = os.path.join(DATA, "event1.xml")
with open(quake_ml_file, "rb") as fh:
data = fh.read()
gen = InputFileGenerator()
# Mock the URL
with mock.patch("urllib2.urlopen") as patch:
class Dummy(object):
def read(self):
return data
patch.return_value = Dummy()
gen.add_events("http://some_url.com")
patch.assert_called_once_with("http://some_url.com")
assert [event] == gen._events
def test_adding_multiple_events_JSON():
"""
Tests adding multiple events as JSON.
"""
events = [{
"latitude": 45.0,
"description": "Some description",
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": str(obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000)),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18
}, {
"latitude": 13.93,
"description": "Some other description",
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": str(obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000)),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19}]
gen = InputFileGenerator()
gen.add_events(json.dumps(events))
events[0]["origin_time"] = obspy.UTCDateTime(events[0]["origin_time"])
events[1]["origin_time"] = obspy.UTCDateTime(events[1]["origin_time"])
assert sorted(gen._events) == sorted(events)
def test_adding_multiple_events_JSON():
"""
Tests adding multiple events as JSON.
"""
events = [{
"latitude": 45.0,
"description": "Some description",
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": str(obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000)),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18
}, {
"latitude": 13.93,
"description": "Some other description",
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": str(obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000)),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19}]
gen = InputFileGenerator()
gen.add_events(json.dumps(events))
events[0]["origin_time"] = obspy.UTCDateTime(events[0]["origin_time"])
events[1]["origin_time"] = obspy.UTCDateTime(events[1]["origin_time"])
assert sorted(gen._events) == sorted(events)
def test_adding_events_as_URL():
"""
QuakeMLs should be downloaded if necessary.
Mock the actual downloading.
"""
event = {"description": "FICTIONAL EVENT IN BAVARIA",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"}
quake_ml_file = os.path.join(DATA, "event1.xml")
with open(quake_ml_file, "rb") as fh:
data = fh.read()
gen = InputFileGenerator()
# Mock the URL
with mock.patch("urllib2.urlopen") as patch:
class Dummy(object):
def read(self):
return data
patch.return_value = Dummy()
gen.add_events("http://some_url.com")
patch.assert_called_once_with("http://some_url.com")
assert [event] == gen._events
def main():
gen = InputFileGenerator()
# SES3D 4.0 can only simulate one event at a time.
gen.add_events("../tests/data/event1.xml")
gen.add_stations([
"../tests/data/dataless.seed.BW_FURT",
"../tests/data/dataless.seed.BW_RJOB"
])
# Just perform a standard forward simulation.
gen.config.simulation_type = "normal simulation"
gen.config.output_folder = "../OUTPUT"
# Time configuration.
gen.config.number_of_time_steps = 700
gen.config.time_increment_in_s = 0.75
# SES3D specific configuration
gen.config.output_directory = "../DATA/OUTPUT/1.8s"
# SES3D specific discretization
gen.config.nx_global = 66
gen.config.ny_global = 108
gen.config.nz_global = 28
gen.config.px = 3
gen.config.py = 4
gen.config.pz = 4
# Specify some source time function.
gen.config.source_time_function = np.sin(np.linspace(0, 10, 700))
# Configure the mesh.
gen.config.mesh_min_latitude = -50.0
gen.config.mesh_max_latitude = 50.0
gen.config.mesh_min_longitude = -50.0
gen.config.mesh_max_longitude = 50.0
gen.config.mesh_min_depth_in_km = 0.0
gen.config.mesh_max_depth_in_km = 200.0
# Define the rotation. Take care this is defined as the rotation of the
# mesh. The data will be rotated in the opposite direction! The following
# example will rotate the mesh 5 degrees southwards around the x-axis. For
# a definition of the coordinate system refer to the rotations.py file. The
# rotation is entirely optional.
gen.config.rotation_angle_in_degree = 5.0
gen.config.rotation_axis = [1.0, 0.0, 0.0]
# Define Q
gen.config.is_dissipative = True
gen.config.Q_model_relaxation_times = [1.7308, 14.3961, 22.9973]
gen.config.Q_model_weights_of_relaxation_mechanisms = \
[2.5100, 2.4354, 0.0879]
# Finally write the file to a folder. If not output directory is given, a
# dictionary containing all the files will be returned.
gen.write(format="ses3d_4_0", output_dir="output")
print "Written files to 'output' folder."
def main():
gen = InputFileGenerator()
# SES3D 4.0 can only simulate one event at a time.
gen.add_events("../tests/data/event1.xml")
gen.add_stations(["../tests/data/dataless.seed.BW_FURT",
"../tests/data/dataless.seed.BW_RJOB"])
# Just perform a standard forward simulation.
gen.config.simulation_type = "normal simulation"
gen.config.output_folder = "../OUTPUT"
# Time configuration.
gen.config.number_of_time_steps = 700
gen.config.time_increment_in_s = 0.75
# SES3D specific configuration
gen.config.output_directory = "../DATA/OUTPUT/1.8s"
# SES3D specific discretization
gen.config.nx_global = 66
gen.config.ny_global = 108
gen.config.nz_global = 28
gen.config.px = 3
gen.config.py = 4
gen.config.pz = 4
# Specify some source time function.
gen.config.source_time_function = np.sin(np.linspace(0, 10, 700))
# Configure the mesh.
gen.config.mesh_min_latitude = -50.0
gen.config.mesh_max_latitude = 50.0
gen.config.mesh_min_longitude = -50.0
gen.config.mesh_max_longitude = 50.0
gen.config.mesh_min_depth_in_km = 0.0
gen.config.mesh_max_depth_in_km = 200.0
# Define the rotation. Take care this is defined as the rotation of the
# mesh. The data will be rotated in the opposite direction! The following
# example will rotate the mesh 5 degrees southwards around the x-axis. For
# a definition of the coordinate system refer to the rotations.py file. The
# rotation is entirely optional.
gen.config.rotation_angle_in_degree = 5.0
gen.config.rotation_axis = [1.0, 0.0, 0.0]
# Define Q
gen.config.is_dissipative = True
gen.config.Q_model_relaxation_times = [1.7308, 14.3961, 22.9973]
gen.config.Q_model_weights_of_relaxation_mechanisms = \
[2.5100, 2.4354, 0.0879]
# Finally write the file to a folder. If not output directory is given, a
# dictionary containing all the files will be returned.
gen.write(format="ses3d_4_0", output_dir="output")
print "Written files to 'output' folder."
def test_event_filter():
"""
Tests the filtering of the events.
This is funky. If any filter is given, it will remove all events that do
not have an event_id.
"""
events = \
[{"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"description": "FICTIONAL EVENT IN BAVARIA",
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"},
{"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19,
"description": "GUATEMALA",
"_event_id": "smi:local/Event/2013-01-07T13:58:41.209477"}]
event_file_1 = os.path.join(DATA, "event1.xml")
event_file_2 = os.path.join(DATA, "event2.xml")
gen = InputFileGenerator()
gen.add_events([event_file_1, event_file_2])
assert sorted(gen._events) == sorted(events)
# No applied filter should just result in the same stations being available
# everywhere.
assert sorted(gen._filtered_events) == sorted(gen._events)
# Events filters are a simple list of URLS.
gen.event_filter = ["smi:local/Event/2013-01-07T13:58:41.209477"]
# Only the last event should now be available.
assert sorted(gen._filtered_events) == sorted(events[1:])
# Removing the filter should make the missing events reappear.
gen.event_filter = None
assert sorted(gen._filtered_events) == sorted(gen._events)
gen.station_filter = []
assert sorted(gen._filtered_events) == sorted(gen._events)
def test_wrong_stf_header_format():
"""
Simple test asserting that the correct exceptions get raised when
attempting to write invalid STF headers.
"""
station = {
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10}
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0}
gen = InputFileGenerator()
gen.add_stations(station)
gen.add_events(event)
# Configure it.
gen.config.number_of_time_steps = 4000
gen.config.time_increment_in_s = 0.13
gen.config.output_folder = "../DATA/OUTPUT/1.8s/"
gen.config.mesh_min_latitude = 34.1
gen.config.mesh_max_latitude = 42.9
gen.config.mesh_min_longitude = 23.1
gen.config.mesh_max_longitude = 42.9
gen.config.mesh_min_depth_in_km = 0.0
gen.config.mesh_max_depth_in_km = 471.0
gen.config.nx_global = 66
gen.config.ny_global = 108
gen.config.nz_global = 28
gen.config.px = 3
gen.config.py = 4
gen.config.pz = 4
gen.config.source_time_function = np.linspace(1.0, 0.0, 4000)
gen.config.is_dissipative = False
gen.config.stf_header = "simple string"
# Write the input files to a dictionary.
with pytest.raises(ValueError):
gen.write(format="ses3d_4_1")
gen.config.stf_header = ["1", "2", "3", "4", "5", "6"]
# Write the input files to a dictionary.
with pytest.raises(ValueError):
gen.write(format="ses3d_4_1")
def test_event_filter():
"""
Tests the filtering of the events.
This is funky. If any filter is given, it will remove all events that do
not have an event_id.
"""
events = \
[{"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"description": "FICTIONAL EVENT IN BAVARIA",
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"},
{"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19,
"description": "GUATEMALA",
"_event_id": "smi:local/Event/2013-01-07T13:58:41.209477"}]
event_file_1 = os.path.join(DATA, "event1.xml")
event_file_2 = os.path.join(DATA, "event2.xml")
gen = InputFileGenerator()
gen.add_events([event_file_1, event_file_2])
assert sorted(gen._events) == sorted(events)
# No applied filter should just result in the same stations being available
# everywhere.
assert sorted(gen._filtered_events) == sorted(gen._events)
# Events filters are a simple list of URLS.
gen.event_filter = ["smi:local/Event/2013-01-07T13:58:41.209477"]
# Only the last event should now be available.
assert sorted(gen._filtered_events) == sorted(events[1:])
# Removing the filter should make the missing events reappear.
gen.event_filter = None
assert sorted(gen._filtered_events) == sorted(gen._events)
gen.station_filter = []
assert sorted(gen._filtered_events) == sorted(gen._events)
def test_real_world_example(self):
"""
Test that compares the created input files to those from a real world
example.
The only artificial thing is the source-time function but that is
trivial to verify.
This is a fairly comprehensive tests but should be used in comparision
with other unit tests.
"""
gen = InputFileGenerator()
axisem_example_path = os.path.join(self.data_dir, "axisem_example")
gen.add_stations([os.path.join(self.data_dir,"dataless.seed.BW_FURT"), os.path.join(self.data_dir,"dataless.seed.BW_RJOB")])
gen.add_events(os.path.join(self.data_dir,"event1.xml"))
# Configure it.
gen.config.dominant_period= 10.0
gen.config.seismogram_length=1000.0
gen.config.number_of_processors=12
gen.config.background_model = 'prem'
# Write the input files to a dictionary.
gen.write(format='axisem', output_dir = path)
# The rest is only for asserting the produced files.
for filename in glob.glob(os.path.join(path, "*_example")):
with open(filename, "rt") as open_file:
real_file = open_file.read()
filename = os.path.basename(filename[:-8])
if filename not in input_files:
msg = "File '%s' has not been generated" % filename
raise AssertionError(msg)
lines = real_file.splitlines()
new_lines = input_files[filename].splitlines()
if len(lines) != len(new_lines):
msg = ("File '%s' does not have the same number of lines "
"for the real (%i lines) and generated (%i lines) "
"input file") % (filename, len(lines), len(new_lines))
raise AssertionError(msg)
for line, new_line in zip(lines, new_lines):
if line != new_line:
msg = "Line differs in file '%s'.\n" % filename
msg += "Expected: \"%s\"\n" % line
msg += "Got: \"%s\"\n" % new_line
raise AssertionError(msg)
def test_test_all_files_have_an_empty_last_line():
"""
Tests that all files have an empty last line.
"""
station = {
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10
}
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0
}
gen = InputFileGenerator()
gen.add_stations(station)
gen.add_events(event)
# Configure it.
gen.config.number_of_time_steps = 4000
gen.config.time_increment_in_s = 0.13
gen.config.output_folder = "../DATA/OUTPUT/1.8s/"
gen.config.mesh_min_latitude = 34.1
gen.config.mesh_max_latitude = 42.9
gen.config.mesh_min_longitude = 23.1
gen.config.mesh_max_longitude = 42.9
gen.config.mesh_min_depth_in_km = 0.0
gen.config.mesh_max_depth_in_km = 471.0
gen.config.nx_global = 66
gen.config.ny_global = 108
gen.config.nz_global = 28
gen.config.px = 3
gen.config.py = 4
gen.config.pz = 4
gen.config.source_time_function = np.linspace(1.0, 0.0, 4000)
gen.config.is_dissipative = False
# Write the input files to a dictionary.
input_files = gen.write(format="ses3d_4_0")
for input_file in input_files.itervalues():
assert input_file.endswith("\n\n") is True
def test_test_all_files_have_an_empty_last_line():
"""
Tests that all files have an empty last line.
"""
station = {
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10}
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0}
gen = InputFileGenerator()
gen.add_stations(station)
gen.add_events(event)
# Configure it.
gen.config.number_of_time_steps = 4000
gen.config.time_increment_in_s = 0.13
gen.config.output_folder = "../DATA/OUTPUT/1.8s/"
gen.config.mesh_min_latitude = 34.1
gen.config.mesh_max_latitude = 42.9
gen.config.mesh_min_longitude = 23.1
gen.config.mesh_max_longitude = 42.9
gen.config.mesh_min_depth_in_km = 0.0
gen.config.mesh_max_depth_in_km = 471.0
gen.config.nx_global = 66
gen.config.ny_global = 108
gen.config.nz_global = 28
gen.config.px = 3
gen.config.py = 4
gen.config.pz = 4
gen.config.source_time_function = np.linspace(1.0, 0.0, 4000)
gen.config.is_dissipative = False
# Write the input files to a dictionary.
input_files = gen.write(format="ses3d_4_0")
for input_file in input_files.itervalues():
assert input_file.endswith("\n\n") is True
def test_adding_dict_with_missing_keys():
"""
Tests the adding of a dictionary with missing keys.
"""
event = {
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18}
gen = InputFileGenerator()
with pytest.raises(ValueError):
gen.add_events(event)
def test_adding_dict_with_missing_keys():
"""
Tests the adding of a dictionary with missing keys.
"""
event = {
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18}
gen = InputFileGenerator()
with pytest.raises(ValueError):
gen.add_events(event)
def test_adding_single_event_dictionary():
"""
Adding a single event dictionary.
"""
event = {
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"description": "Some description",
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18}
gen = InputFileGenerator()
gen.add_events(event)
assert gen._events == [event]
def test_adding_single_event_dictionary():
"""
Adding a single event dictionary.
"""
event = {
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"description": "Some description",
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18}
gen = InputFileGenerator()
gen.add_events(event)
assert gen._events == [event]
def test_reading_QuakeML_from_BytesIO():
"""
Tests the reading of QuakeML from BytesIO.
"""
event_file_1 = os.path.join(DATA, "event1.xml")
event_file_2 = os.path.join(DATA, "event2.xml")
with open(event_file_1, "rb") as fh:
event_file_1_mem = io.BytesIO(fh.read())
with open(event_file_2, "rb") as fh:
event_file_2_mem = io.BytesIO(fh.read())
gen = InputFileGenerator()
gen.add_events([event_file_1_mem, event_file_2_mem])
# Sort to be able to compare.
assert sorted(gen._events) == \
[{"description": "FICTIONAL EVENT IN BAVARIA",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"},
{"description": "GUATEMALA",
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19,
"_event_id": "smi:local/Event/2013-01-07T13:58:41.209477"}]
def test_event_filter_removed_everything_without_an_id():
"""
An applied event filter will remove all events without an id.
"""
events = [{
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"description": "Some description"
}, {
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19,
"description": None}]
gen = InputFileGenerator()
gen.add_events(events)
assert sorted(gen._filtered_events) == sorted(events)
# Applying a filter will remove everything.
gen.event_filter = ["smi://some/url"]
assert sorted(gen._filtered_events) == []
# Removing the filter should make the missing events reappear.
gen.event_filter = None
assert sorted(gen._filtered_events) == sorted(gen._events)
gen.station_filter = []
assert sorted(gen._filtered_events) == sorted(gen._events)
def test_event_dictionary_automatic_type_conversion():
"""
The types for the event dictionary should also undergo automatic type
conversion.
"""
event = {
"description": 1,
"latitude": "1",
"longitude": "2",
"depth_in_km": "3",
"origin_time": "2012-01-01T00:00:00.000000Z",
"m_rr": "-2.11e+18",
"m_tt": "-4.22e+19",
"m_pp": "4.43e+19",
"m_rt": "-9.35e+18",
"m_rp": "-8.38e+18",
"m_tp": "-6.44e+18"}
gen = InputFileGenerator()
gen.add_events(event)
assert type(gen._events[0]["latitude"]) == float
assert type(gen._events[0]["longitude"]) == float
assert type(gen._events[0]["depth_in_km"]) == float
assert type(gen._events[0]["origin_time"]) == obspy.UTCDateTime
assert type(gen._events[0]["m_rr"]) == float
assert type(gen._events[0]["m_tt"]) == float
assert type(gen._events[0]["m_pp"]) == float
assert type(gen._events[0]["m_rt"]) == float
assert type(gen._events[0]["m_rp"]) == float
assert type(gen._events[0]["m_tp"]) == float
assert gen._events == [{
"description": "1",
"latitude": 1.0,
"longitude": 2.0,
"depth_in_km": 3.0,
"origin_time": obspy.UTCDateTime(2012, 1, 1),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18}]
def test_event_dictionary_automatic_type_conversion():
"""
The types for the event dictionary should also undergo automatic type
conversion.
"""
event = {
"description": 1,
"latitude": "1",
"longitude": "2",
"depth_in_km": "3",
"origin_time": "2012-01-01T00:00:00.000000Z",
"m_rr": "-2.11e+18",
"m_tt": "-4.22e+19",
"m_pp": "4.43e+19",
"m_rt": "-9.35e+18",
"m_rp": "-8.38e+18",
"m_tp": "-6.44e+18"}
gen = InputFileGenerator()
gen.add_events(event)
assert type(gen._events[0]["latitude"]) == float
assert type(gen._events[0]["longitude"]) == float
assert type(gen._events[0]["depth_in_km"]) == float
assert type(gen._events[0]["origin_time"]) == obspy.UTCDateTime
assert type(gen._events[0]["m_rr"]) == float
assert type(gen._events[0]["m_tt"]) == float
assert type(gen._events[0]["m_pp"]) == float
assert type(gen._events[0]["m_rt"]) == float
assert type(gen._events[0]["m_rp"]) == float
assert type(gen._events[0]["m_tp"]) == float
assert gen._events == [{
"description": "1",
"latitude": 1.0,
"longitude": 2.0,
"depth_in_km": 3.0,
"origin_time": obspy.UTCDateTime(2012, 1, 1),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18}]
def test_reading_QuakeML_from_BytesIO():
"""
Tests the reading of QuakeML from BytesIO.
"""
event_file_1 = os.path.join(DATA, "event1.xml")
event_file_2 = os.path.join(DATA, "event2.xml")
with open(event_file_1, "rb") as fh:
event_file_1_mem = io.BytesIO(fh.read())
with open(event_file_2, "rb") as fh:
event_file_2_mem = io.BytesIO(fh.read())
gen = InputFileGenerator()
gen.add_events([event_file_1_mem, event_file_2_mem])
# Sort to be able to compare.
assert sorted(gen._events) == \
[{"description": "FICTIONAL EVENT IN BAVARIA",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"},
{"description": "GUATEMALA",
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19,
"_event_id": "smi:local/Event/2013-01-07T13:58:41.209477"}]
def test_event_filter_removed_everything_without_an_id():
"""
An applied event filter will remove all events without an id.
"""
events = [{
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"description": "Some description"
}, {
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19,
"description": None}]
gen = InputFileGenerator()
gen.add_events(events)
assert sorted(gen._filtered_events) == sorted(events)
# Applying a filter will remove everything.
gen.event_filter = ["smi://some/url"]
assert sorted(gen._filtered_events) == []
# Removing the filter should make the missing events reappear.
gen.event_filter = None
assert sorted(gen._filtered_events) == sorted(gen._events)
gen.station_filter = []
assert sorted(gen._filtered_events) == sorted(gen._events)
def test_adding_single_event_JSON():
"""
Adding a single event as a JSON file.
"""
event = {
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": str(obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000)),
"description": None,
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18}
gen = InputFileGenerator()
gen.add_events(json.dumps(event))
event["origin_time"] = obspy.UTCDateTime(event["origin_time"])
assert gen._events == [event]
def test_adding_single_event_JSON():
"""
Adding a single event as a JSON file.
"""
event = {
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": str(obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000)),
"description": None,
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18}
gen = InputFileGenerator()
gen.add_events(json.dumps(event))
event["origin_time"] = obspy.UTCDateTime(event["origin_time"])
assert gen._events == [event]
def test_additional_attributes_from_event_dicts_are_removed():
"""
No need to carry around additional attributes.
"""
event = {
"latitude": 45.0,
"longitude": 12.1,
"description": "Random description",
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"extra": "blub"}
gen = InputFileGenerator()
gen.add_events(event)
del event["extra"]
assert gen._events == [event]
def test_additional_attributes_from_event_dicts_are_removed():
"""
No need to carry around additional attributes.
"""
event = {
"latitude": 45.0,
"longitude": 12.1,
"description": "Random description",
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"extra": "blub"}
gen = InputFileGenerator()
gen.add_events(event)
del event["extra"]
assert gen._events == [event]
def test_adding_a_catalog_object():
"""
Tests adding an obspy.core.event.Catalog object.
"""
event_file_1 = os.path.join(DATA, "event1.xml")
event_file_2 = os.path.join(DATA, "event2.xml")
cat = obspy.read_events(event_file_1)
cat += obspy.read_events(event_file_2)
gen = InputFileGenerator()
gen.add_events(cat)
assert sorted(gen._events) == \
[{"description": "FICTIONAL EVENT IN BAVARIA",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"},
{"description": "GUATEMALA",
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19,
"_event_id": "smi:local/Event/2013-01-07T13:58:41.209477"}]
def test_adding_a_catalog_object():
"""
Tests adding an obspy.core.event.Catalog object.
"""
event_file_1 = os.path.join(DATA, "event1.xml")
event_file_2 = os.path.join(DATA, "event2.xml")
cat = obspy.readEvents(event_file_1)
cat += obspy.readEvents(event_file_2)
gen = InputFileGenerator()
gen.add_events(cat)
assert sorted(gen._events) == \
[{"description": "FICTIONAL EVENT IN BAVARIA",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"},
{"description": "GUATEMALA",
"latitude": 13.93,
"longitude": -92.47,
"depth_in_km": 28.7,
"origin_time": obspy.UTCDateTime(2012, 11, 7, 16, 35, 55, 200000),
"m_rr": 1.02e+20,
"m_tt": -7.96e+19,
"m_pp": -2.19e+19,
"m_rt": 6.94e+19,
"m_rp": -4.08e+19,
"m_tp": 4.09e+19,
"_event_id": "smi:local/Event/2013-01-07T13:58:41.209477"}]
def test_adding_a_event_object():
"""
Tests adding an already existing event object.
"""
event_file = os.path.join(DATA, "event1.xml")
event = obspy.readEvents(event_file)[0]
gen = InputFileGenerator()
gen.add_events([event])
assert gen._events == [
{"description": "FICTIONAL EVENT IN BAVARIA",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"}]
def test_adding_a_event_object():
"""
Tests adding an already existing event object.
"""
event_file = os.path.join(DATA, "event1.xml")
event = obspy.read_events(event_file)[0]
gen = InputFileGenerator()
gen.add_events([event])
assert gen._events == [
{"description": "FICTIONAL EVENT IN BAVARIA",
"latitude": 45.0,
"longitude": 12.1,
"depth_in_km": 13.0,
"origin_time": obspy.UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": -2.11e+18,
"m_tt": -4.22e+19,
"m_pp": 4.43e+19,
"m_rt": -9.35e+18,
"m_rp": -8.38e+18,
"m_tp": -6.44e+18,
"_event_id": "smi:local/Event/2013-01-05T20:19:58.727909"}]
import os
from wfs_input_generator import InputFileGenerator
gen = InputFileGenerator()
gen.add_events("wfs_input_generator/tests/data/event1.xml")
gen.add_stations(["wfs_input_generator/tests/data/dataless.seed.BW_FURT", "wfs_input_generator/tests/data/dataless.seed.BW_RJOB"])
gen.config.mesh={'mesh':"eucrust_small_new"}
gen.config.model={'model':"model_eucrust_small_new.dat"}
gen.config.parameter={'version':18, 'dimension':3, 'advection':0, 'advection_velocity':(1.0, 1.0, 1.0),\
'anisotropy':0, 'anelasticity':0, 'poroelasticity':0,
'adjoint':0, 'material_reference_values':(3600, 9.0e10, 1.11e11),\
'randomfield':0, 'sourcetype':50, 'source_file':'source.dat', 'sponge':0,\
'meshgenerator':"Gambit3D-Tetra",'fine_output':0, 'restartfile':0,\
'DGMethod':1, 'CK':0,'fluxmethod':0, 'DGCycle':1, 'basisfunction_degree':0,\
'reconstructed_basisfunction_degree':0,'stencil_security_factor':0,\
'reconstruction_type':0, 'exponent_r':0, 'coefficient_epsilon':0,\
'linear_weight':0, 'limiter_security_factor':0, 'minspace_order':5,\
'maxspace_order':5, 'pAdaptivity_file_name':'pAdaptivity_file_name',\
'material_basis_function_order':1, 'courant_number':0.5, 'min_time_step':10000,\
'rotational_output':0, 'rotation_components':(1, 1, 1),\
'variable_output':(0, 0, 0, 0, 0, 0, 1, 1, 1),\
'material_parameters_output':(1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0),\
'output_character':0 , 'output_format':1, 'timestep_output':50,\
'time_output':25, 'output_index':1, 'sampling':1, 'max_time':2000,\
'max_iteration':1000,'max_wallclocktime':1e20, 'delay':0}
test_dir="/home/msimon/svn/repos/verce/All/JRA/JRA1/python/test_ressources/inputfiles/"
def test_simple():
"""
Test a very simple SPECFEM file.
"""
stations = [
{
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10
}, {
"id": "KO.AFSR",
"latitude": 40.000,
"longitude": 33.2345,
"elevation_in_m": 220
}
]
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0}
gen = InputFileGenerator()
gen.add_stations(stations)
gen.add_events(event)
# Configure it.
gen.config.NPROC = 5
gen.config.NSTEP = 10
gen.config.DT = 15
gen.config.SIMULATION_TYPE = 1
# Write the input files to a dictionary.
input_files = gen.write(format="SPECFEM3D_CARTESIAN")
assert bool(input_files)
assert sorted(input_files.keys()) == \
sorted(["Par_file", "CMTSOLUTION", "STATIONS"])
# Assert the STATIONS file.
assert input_files["STATIONS"].splitlines() == [
"ADVT KO 41.00000 33.12340 10.0 0.0",
"AFSR KO 40.00000 33.23450 220.0 0.0"]
# Assert the CMTSOLUTION file.
assert input_files["CMTSOLUTION"].splitlines() == [
"PDE 2012 4 12 7 15 48.50 39.26000 41.04000 5.00000 4.7 4.7 "
"2012-04-12T07:15:48.500000Z_4.7",
"event name: 0000000",
"time shift: 0.0000",
"half duration: 0.0000",
"latitude: 39.26000",
"longitude: 41.04000",
"depth: 5.00000",
"Mrr: 1e+23",
"Mtt: 1e+23",
"Mpp: 1e+23",
"Mrt: 0",
"Mrp: 0",
"Mtp: 0"]
# XXX: Extend test.
par_file = input_files["Par_file"]
assert "SIMULATION_TYPE" in par_file
assert "NSTEP" in par_file
def generate_input_files(self, event_name, template_name, simulation_type,
source_time_function):
"""
Generate the input files for one event.
:param event_name: The name of the event for which to generate the
input files.
:param template_name: The name of the input file template
:param simulation_type: The type of simulation to perform. Possible
values are: 'normal simulation', 'adjoint forward', 'adjoint
reverse'
:param source_time_function: A function source_time_function(npts,
delta), taking the requested number of samples and the time spacing
and returning an appropriate source time function as numpy array.
"""
from lasif import utils
from wfs_input_generator import InputFileGenerator
# Get the events
all_events = self.get_event_dict()
if event_name not in all_events:
msg = "Event '%s' not found in project." % event_name
raise ValueError(msg)
event = self.get_event(event_name)
# Get the input file templates.
template_filename = os.path.join(self.paths["templates"],
template_name + ".xml")
if not os.path.exists(template_filename):
msg = "Template '%s' does not exists." % template_name
raise ValueError(msg)
input_file = utils.read_ses3d_4_0_template(template_filename)
# Get all stations and create a dictionary for the input file
# generator.
stations = self.get_stations_for_event(event_name)
stations = [{
"id": key,
"latitude": value["latitude"],
"longitude": value["longitude"],
"elevation_in_m": value["elevation"],
"local_depth_in_m": value["local_depth"]
} for key, value in stations.iteritems()]
# Add the event and the stations to the input file generator.
gen = InputFileGenerator()
gen.add_events(event)
gen.add_stations(stations)
npts = input_file["simulation_parameters"]["number_of_time_steps"]
delta = input_file["simulation_parameters"]["time_increment"]
# Time configuration.
gen.config.number_of_time_steps = npts
gen.config.time_increment_in_s = delta
# SES3D specific configuration
gen.config.output_folder = input_file["output_directory"]
gen.config.simulation_type = simulation_type
gen.config.adjoint_forward_wavefield_output_folder = \
input_file["adjoint_output_parameters"][
"forward_field_output_directory"]
gen.config.adjoint_forward_sampling_rate = \
input_file["adjoint_output_parameters"][
"sampling_rate_of_forward_field"]
gen.config.is_dissipative = \
input_file["simulation_parameters"]["is_dissipative"]
# Discretization
disc = input_file["computational_setup"]
gen.config.nx_global = disc["nx_global"]
gen.config.ny_global = disc["ny_global"]
gen.config.nz_global = disc["nz_global"]
gen.config.px = disc["px_processors_in_theta_direction"]
gen.config.py = disc["py_processors_in_phi_direction"]
gen.config.pz = disc["pz_processors_in_r_direction"]
gen.config.lagrange_polynomial_degree = \
disc["lagrange_polynomial_degree"]
# Configure the mesh.
gen.config.mesh_min_latitude = \
self.domain["bounds"]["minimum_latitude"]
gen.config.mesh_max_latitude = \
self.domain["bounds"]["maximum_latitude"]
gen.config.mesh_min_longitude = \
self.domain["bounds"]["minimum_longitude"]
gen.config.mesh_max_longitude = \
self.domain["bounds"]["maximum_longitude"]
gen.config.mesh_min_depth_in_km = \
self.domain["bounds"]["minimum_depth_in_km"]
gen.config.mesh_max_depth_in_km = \
self.domain["bounds"]["maximum_depth_in_km"]
gen.config.rotation_angle_in_degree = self.domain["rotation_angle"]
gen.config.rotation_axis = self.domain["rotation_axis"]
gen.config.source_time_function = source_time_function(
int(npts), float(delta))
output_dir = self.get_output_folder("input_files___%s" % template_name)
gen.write(format="ses3d_4_0", output_dir=output_dir)
print "Written files to '%s'." % output_dir
def compute(self):
gen = InputFileGenerator()
userconf = json.load(open(self.parameters["solver_conf_file"]))
fields = userconf["fields"]
for x in fields:
gen.add_configuration({x["name"]: self.strToBool(x["value"])})
with open(self.parameters["quakeml"], "r") as events:
quakeml = events.read()
#unicode_qml=quakeml.decode('utf-8')
#data = unicode_qml.encode('ascii','ignore')
##
cat = readQuakeML(quakeml)
events = []
#cat = obspy.readEvents(data)
#Remove all events with no moment tensor.
for event in cat:
for fm in event.focal_mechanisms:
if fm.moment_tensor and fm.moment_tensor.tensor:
events.append(event)
break
cat.events = events
gen.add_events(cat)
evn = 0
outputdir = ""
for x in userconf["events"]:
gen.event_filter = [x]
if self.parameters["station_format"] == "stationXML":
gen.add_stations(self.parameters["stations_file"])
if self.parameters["station_format"] == "points":
stlist = []
with open(self.parameters["stations_file"]) as f:
k = False
for line in f:
if (k == False):
k = True
else:
station = {}
l = line.strip().split(" ")
station.update({"id": l[1] + "." + l[0]})
station.update({"latitude": float(l[3])})
station.update({"longitude": float(l[2])})
station.update({"elevation_in_m": float(l[4])})
station.update({"local_depth_in_m": float(l[5])})
stlist.append(station)
gen.add_stations(stlist)
gen.station_filter = userconf["stations"]
outputdir = self.outputdest + userconf["runId"] + "/" + userconf[
"runId"] + "_" + str(evn) + "/DATA"
output_files = gen.write(format=userconf["solver"],
output_dir=outputdir)
locations = []
for x in output_files.keys():
locations.append("file://" + socket.gethostname() + outputdir +
"/" + x)
self.addOutput(gen._filtered_events,
location=locations,
metadata=self.extractEventMetadata(
outputdir, gen._filtered_events),
control={"con:immediateAccess": "true"})
evn += 1
self.addOutput(outputdir,
location=locations,
metadata={"to_xdecompose": str(outputdir)},
control={"con:immediateAccess": "true"})
from wfs_input_generator import InputFileGenerator
from obspy.core import UTCDateTime
gen = InputFileGenerator()
seissol_example_path = 'wfs_input_generator/tests/data/seissol_example/'
data_dir = 'wfs_input_generator/tests/data/'
import glob
gen.add_stations(glob.glob(data_dir+'*dataless*'))
event = {"latitude": 48.9,"longitude": -2.3,"depth_in_km": 200.0,"origin_time":\
UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),"m_rr": -2.11e+18,"m_tt": \
-4.22e+19,"m_pp": 4.43e+19,"m_rt": -9.35e+18,"m_rp": -8.38e+18,"m_tp": -6.44e+18}
gen.add_events(event)
gen.config.mesh = 'most_simple_tet'
gen.config.model = 'PREM'
gen.config.working_directory = seissol_example_path
gen.config.max_time = 1000.0
gen.config.number_of_processors = 16
gen.write(format = 'seissol_1_0', output_dir = seissol_example_path)
This also (at least right now) serves as the documentation of the specific
writer.
:copyright:
Lion Krischer ([email protected]), 2013
:license:
GNU General Public License, Version 3
(http://www.gnu.org/copyleft/gpl.html)
"""
import numpy as np
from wfs_input_generator import InputFileGenerator
gen = InputFileGenerator()
# SES3D 4.0 can only simulate one event at a time.
gen.add_events("../tests/data/event1.xml")
gen.add_stations(["../tests/data/dataless.seed.BW_FURT",
"../tests/data/dataless.seed.BW_RJOB"])
# Just perform a standard forward simulation.
gen.config.simulation_type = "normal simulation"
gen.config.output_folder = "../OUTPUT"
# Time configuration.
gen.config.number_of_time_steps = 700
gen.config.time_increment_in_s = 0.75
# SES3D specific configuration
gen.config.output_directory = "../DATA/OUTPUT/1.8s"
# SES3D specific discretization
def test_against_example_file():
"""
Tests against a known example file.
"""
stations = [
{
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10
}, {
"id": "KO.AFSR",
"latitude": 40.000,
"longitude": 33.2345,
"elevation_in_m": 220
}
]
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0}
gen = InputFileGenerator()
gen.add_stations(stations)
gen.add_events(event)
# Configure it. Emulate an example in the SPECFEM directory.
gen.config.NPROC_XI = 2
gen.config.NPROC_ETA = 2
gen.config.RECORD_LENGTH_IN_MINUTES = 10.0
gen.config.SIMULATION_TYPE = 1
gen.config.NCHUNKS = 6
gen.config.NEX_XI = 64
gen.config.NEX_ETA = 64
gen.config.MODEL = "1D_isotropic_prem"
# Non-standard values in the example file.
gen.config.ANGULAR_WIDTH_XI_IN_DEGREES = 20.0
gen.config.ANGULAR_WIDTH_ETA_IN_DEGREES = 20.0
gen.config.CENTER_LATITUDE_IN_DEGREES = 40.0
gen.config.CENTER_LONGITUDE_IN_DEGREES = 25.0
gen.config.WRITE_SEISMOGRAMS_BY_MASTER = False
gen.config.NTSTEP_BETWEEN_OUTPUT_INFO = 500
gen.config.NTSTEP_BETWEEN_FRAMES = 50
gen.config.MOVIE_COARSE = True
# Write the input files to a dictionary.
input_files = gen.write(format="SPECFEM3D_GLOBE")
assert bool(input_files)
assert sorted(input_files.keys()) == \
sorted(["Par_file", "CMTSOLUTION", "STATIONS"])
# Assert the STATIONS file.
assert input_files["STATIONS"].splitlines() == [
"ADVT KO 41.00000 33.12340 10.0 0.0",
"AFSR KO 40.00000 33.23450 220.0 0.0"]
# Assert the CMTSOLUTION file.
assert input_files["CMTSOLUTION"].splitlines() == [
"PDE 2012 4 12 7 15 48.50 39.26000 41.04000 5.00000 4.7 4.7 "
"2012-04-12T07:15:48.500000Z_4.7",
"event name: 0000000",
"time shift: 0.0000",
"half duration: 0.0000",
"latitude: 39.26000",
"longitude: 41.04000",
"depth: 5.00000",
"Mrr: 1e+23",
"Mtt: 1e+23",
"Mpp: 1e+23",
"Mrt: 0",
"Mrp: 0",
"Mtp: 0"]
par_file = input_files["Par_file"]
assert "SIMULATION_TYPE" in par_file
assert "NSTEP" in par_file
# Example Par_file from the repository.
original_par_file = os.path.join(DATA, "specfem_globe",
"Par_file")
with open(original_par_file, "rt") as fh:
original_par_file = fh.read().strip()
assert original_par_file == par_file
def generate_input_files(self, event_name, template_name, simulation_type,
source_time_function):
"""
Generate the input files for one event.
:param event_name: The name of the event for which to generate the
input files.
:param template_name: The name of the input file template
:param simulation_type: The type of simulation to perform. Possible
values are: 'normal simulation', 'adjoint forward', 'adjoint
reverse'
:param source_time_function: A function source_time_function(npts,
delta), taking the requested number of samples and the time spacing
and returning an appropriate source time function as numpy array.
"""
from lasif import utils
from wfs_input_generator import InputFileGenerator
# Get the events
all_events = self.get_event_dict()
if event_name not in all_events:
msg = "Event '%s' not found in project." % event_name
raise ValueError(msg)
event = self.get_event(event_name)
# Get the input file templates.
template_filename = os.path.join(self.paths["templates"],
template_name + ".xml")
if not os.path.exists(template_filename):
msg = "Template '%s' does not exists." % template_name
raise ValueError(msg)
input_file = utils.read_ses3d_4_0_template(template_filename)
# Get all stations and create a dictionary for the input file
# generator.
stations = self.get_stations_for_event(event_name)
stations = [{"id": key, "latitude": value["latitude"],
"longitude": value["longitude"],
"elevation_in_m": value["elevation"],
"local_depth_in_m": value["local_depth"]} for key, value in
stations.iteritems()]
# Add the event and the stations to the input file generator.
gen = InputFileGenerator()
gen.add_events(event)
gen.add_stations(stations)
npts = input_file["simulation_parameters"]["number_of_time_steps"]
delta = input_file["simulation_parameters"]["time_increment"]
# Time configuration.
gen.config.number_of_time_steps = npts
gen.config.time_increment_in_s = delta
# SES3D specific configuration
gen.config.output_folder = input_file["output_directory"]
gen.config.simulation_type = simulation_type
gen.config.adjoint_forward_wavefield_output_folder = \
input_file["adjoint_output_parameters"][
"forward_field_output_directory"]
gen.config.adjoint_forward_sampling_rate = \
input_file["adjoint_output_parameters"][
"sampling_rate_of_forward_field"]
gen.config.is_dissipative = \
input_file["simulation_parameters"]["is_dissipative"]
# Discretization
disc = input_file["computational_setup"]
gen.config.nx_global = disc["nx_global"]
gen.config.ny_global = disc["ny_global"]
gen.config.nz_global = disc["nz_global"]
gen.config.px = disc["px_processors_in_theta_direction"]
gen.config.py = disc["py_processors_in_phi_direction"]
gen.config.pz = disc["pz_processors_in_r_direction"]
gen.config.lagrange_polynomial_degree = \
disc["lagrange_polynomial_degree"]
# Configure the mesh.
gen.config.mesh_min_latitude = \
self.domain["bounds"]["minimum_latitude"]
gen.config.mesh_max_latitude = \
self.domain["bounds"]["maximum_latitude"]
gen.config.mesh_min_longitude = \
self.domain["bounds"]["minimum_longitude"]
gen.config.mesh_max_longitude = \
self.domain["bounds"]["maximum_longitude"]
gen.config.mesh_min_depth_in_km = \
self.domain["bounds"]["minimum_depth_in_km"]
gen.config.mesh_max_depth_in_km = \
self.domain["bounds"]["maximum_depth_in_km"]
gen.config.rotation_angle_in_degree = self.domain["rotation_angle"]
gen.config.rotation_axis = self.domain["rotation_axis"]
gen.config.source_time_function = source_time_function(int(npts),
float(delta))
output_dir = self.get_output_folder("input_files___%s" % template_name)
gen.write(format="ses3d_4_0", output_dir=output_dir)
print "Written files to '%s'." % output_dir
:copyright:
Lion Krischer ([email protected]), 2013
:license:
GNU Lesser General Public License, Version 3
(http://www.gnu.org/copyleft/lesser.html)
"""
from wfs_input_generator import InputFileGenerator
import os
gen = InputFileGenerator()
# Paths to the used event and station data.
data_path = os.path.join(os.pardir, "tests", "data")
gen.add_events(os.path.join(data_path, "event1.xml"))
gen.add_stations([os.path.join(data_path, "dataless.seed.BW_FURT"),
os.path.join(data_path, "dataless.seed.BW_RJOB")])
# Time configuration
gen.config.time_config.time_steps = 700
gen.config.time_config.time_delta = 0.75
# Configure the mesh. Make it have ten elements in each direction.
gen.config.mesh.n_north_south = 10
gen.config.mesh.n_west_east = 10
gen.config.mesh.n_down_up = 10
gen.config.mesh.min_latitude = -10.0
gen.config.mesh.max_latitude = 10.0
gen.config.mesh.min_longitude = 0.0
gen.config.mesh.max_latitude = 20.0
def generate_input_files(self, iteration_name, event_name,
simulation_type):
"""
Generate the input files for one event.
:param iteration_name: The name of the iteration.
:param event_name: The name of the event for which to generate the
input files.
:param simulate_type: The type of simulation to perform. Possible
values are: 'normal simulate', 'adjoint forward', 'adjoint
reverse'
"""
from wfs_input_generator import InputFileGenerator
# =====================================================================
# read iteration xml file, get event and list of stations
# =====================================================================
iteration = self.comm.iterations.get(iteration_name)
# Check that the event is part of the iterations.
if event_name not in iteration.events:
msg = ("Event '%s' not part of iteration '%s'.\nEvents available "
"in iteration:\n\t%s" %
(event_name, iteration_name, "\n\t".join(
sorted(iteration.events.keys()))))
raise ValueError(msg)
event = self.comm.events.get(event_name)
stations_for_event = iteration.events[event_name]["stations"].keys()
# Get all stations and create a dictionary for the input file
# generator.
stations = self.comm.query.get_all_stations_for_event(event_name)
stations = [{"id": key, "latitude": value["latitude"],
"longitude": value["longitude"],
"elevation_in_m": value["elevation_in_m"],
"local_depth_in_m": value["local_depth_in_m"]}
for key, value in stations.iteritems()
if key in stations_for_event]
# =====================================================================
# set solver options
# =====================================================================
solver = iteration.solver_settings
# Currently only SES3D 4.1 is supported
solver_format = solver["solver"].lower()
if solver_format not in ["ses3d 4.1", "ses3d 2.0",
"specfem3d cartesian", "specfem3d globe cem"]:
msg = ("Currently only SES3D 4.1, SES3D 2.0, SPECFEM3D "
"CARTESIAN, and SPECFEM3D GLOBE CEM are supported.")
raise ValueError(msg)
solver_format = solver_format.replace(' ', '_')
solver_format = solver_format.replace('.', '_')
solver = solver["solver_settings"]
# =====================================================================
# create the input file generator, add event and stations,
# populate the configuration items
# =====================================================================
# Add the event and the stations to the input file generator.
gen = InputFileGenerator()
gen.add_events(event["filename"])
gen.add_stations(stations)
if solver_format in ["ses3d_4_1", "ses3d_2_0"]:
# event tag
gen.config.event_tag = event_name
# Time configuration.
npts = solver["simulation_parameters"]["number_of_time_steps"]
delta = solver["simulation_parameters"]["time_increment"]
gen.config.number_of_time_steps = npts
gen.config.time_increment_in_s = delta
# SES3D specific configuration
gen.config.output_folder = solver["output_directory"].replace(
"{{EVENT_NAME}}", event_name.replace(" ", "_"))
gen.config.simulate_type = simulation_type
gen.config.adjoint_forward_wavefield_output_folder = \
solver["adjoint_output_parameters"][
"forward_field_output_directory"].replace(
"{{EVENT_NAME}}", event_name.replace(" ", "_"))
gen.config.adjoint_forward_sampling_rate = \
solver["adjoint_output_parameters"][
"sampling_rate_of_forward_field"]
# Visco-elastic dissipation
diss = solver["simulation_parameters"]["is_dissipative"]
gen.config.is_dissipative = diss
# Only SES3D 4.1 has the relaxation parameters.
if solver_format == "ses3d_4_1":
gen.config.Q_model_relaxation_times = \
solver["relaxation_parameter_list"]["tau"]
gen.config.Q_model_weights_of_relaxation_mechanisms = \
solver["relaxation_parameter_list"]["w"]
# Discretization
disc = solver["computational_setup"]
gen.config.nx_global = disc["nx_global"]
gen.config.ny_global = disc["ny_global"]
gen.config.nz_global = disc["nz_global"]
gen.config.px = disc["px_processors_in_theta_direction"]
gen.config.py = disc["py_processors_in_phi_direction"]
gen.config.pz = disc["pz_processors_in_r_direction"]
gen.config.lagrange_polynomial_degree = \
disc["lagrange_polynomial_degree"]
# Configure the mesh.
domain = self.comm.project.domain
gen.config.mesh_min_latitude = \
domain["bounds"]["minimum_latitude"]
gen.config.mesh_max_latitude = \
domain["bounds"]["maximum_latitude"]
gen.config.mesh_min_longitude = \
domain["bounds"]["minimum_longitude"]
gen.config.mesh_max_longitude = \
domain["bounds"]["maximum_longitude"]
gen.config.mesh_min_depth_in_km = \
domain["bounds"]["minimum_depth_in_km"]
gen.config.mesh_max_depth_in_km = \
domain["bounds"]["maximum_depth_in_km"]
# Set the rotation parameters.
gen.config.rotation_angle_in_degree = domain["rotation_angle"]
gen.config.rotation_axis = domain["rotation_axis"]
# Make source time function
gen.config.source_time_function = \
iteration.get_source_time_function()["data"]
elif solver_format == "specfem3d_cartesian":
gen.config.NSTEP = \
solver["simulation_parameters"]["number_of_time_steps"]
gen.config.DT = \
solver["simulation_parameters"]["time_increment"]
gen.config.NPROC = \
solver["computational_setup"]["number_of_processors"]
if simulation_type == "normal simulation":
msg = ("'normal_simulate' not supported for SPECFEM3D "
"Cartesian. Please choose either 'adjoint_forward' or "
"'adjoint_reverse'.")
raise NotImplementedError(msg)
elif simulation_type == "adjoint forward":
gen.config.SIMULATION_TYPE = 1
elif simulation_type == "adjoint reverse":
gen.config.SIMULATION_TYPE = 2
else:
raise NotImplementedError
solver_format = solver_format.upper()
elif solver_format == "specfem3d_globe_cem":
cs = solver["computational_setup"]
gen.config.NPROC_XI = cs["number_of_processors_xi"]
gen.config.NPROC_ETA = cs["number_of_processors_eta"]
gen.config.NCHUNKS = cs["number_of_chunks"]
gen.config.NEX_XI = cs["elements_per_chunk_xi"]
gen.config.NEX_ETA = cs["elements_per_chunk_eta"]
gen.config.OCEANS = cs["simulate_oceans"]
gen.config.ELLIPTICITY = cs["simulate_ellipticity"]
gen.config.TOPOGRAPHY = cs["simulate_topography"]
gen.config.GRAVITY = cs["simulate_gravity"]
gen.config.ROTATION = cs["simulate_rotation"]
gen.config.ATTENUATION = cs["simulate_attenuation"]
gen.config.ABSORBING_CONDITIONS = True
if cs["fast_undo_attenuation"]:
gen.config.PARTIAL_PHYS_DISPERSION_ONLY = True
gen.config.UNDO_ATTENUATION = False
else:
gen.config.PARTIAL_PHYS_DISPERSION_ONLY = False
gen.config.UNDO_ATTENUATION = True
gen.config.GPU_MODE = cs["use_gpu"]
gen.config.SOURCE_TIME_FUNCTION = \
iteration.get_source_time_function()["data"]
if simulation_type == "normal simulation":
gen.config.SIMULATION_TYPE = 1
gen.config.SAVE_FORWARD = False
elif simulation_type == "adjoint forward":
gen.config.SIMULATION_TYPE = 1
gen.config.SAVE_FORWARD = True
elif simulation_type == "adjoint reverse":
gen.config.SIMULATION_TYPE = 2
gen.config.SAVE_FORWARD = True
else:
raise NotImplementedError
# Use the current domain setting to derive the bounds in the way
# SPECFEM specifies them.
domain = self.comm.project.domain
lat_range = domain["bounds"]["maximum_latitude"] - \
domain["bounds"]["minimum_latitude"]
lng_range = domain["bounds"]["maximum_longitude"] - \
domain["bounds"]["minimum_longitude"]
c_lat = \
domain["bounds"]["minimum_latitude"] + lat_range / 2.0
c_lng = \
domain["bounds"]["minimum_longitude"] + lng_range / 2.0
# Rotate the point.
c_lat_1, c_lng_1 = rotations.rotate_lat_lon(
c_lat, c_lng, domain["rotation_axis"],
domain["rotation_angle"])
# SES3D rotation.
A = rotations._get_rotation_matrix(
domain["rotation_axis"], domain["rotation_angle"])
latitude_rotation = -(c_lat_1 - c_lat)
longitude_rotation = c_lng_1 - c_lng
# Rotate the latitude. The rotation axis is latitude 0 and
# the center longitude + 90 degree
B = rotations._get_rotation_matrix(
rotations.lat_lon_radius_to_xyz(0.0, c_lng + 90, 1.0),
latitude_rotation)
# Rotate around the North pole.
C = rotations._get_rotation_matrix(
[0.0, 0.0, 1.0], longitude_rotation)
D = A * np.linalg.inv(C * B)
axis, angle = rotations._get_axis_and_angle_from_rotation_matrix(D)
rotated_axis = rotations.xyz_to_lat_lon_radius(*axis)
# Consistency check
if abs(rotated_axis[0] - c_lat_1) >= 0.01 or \
abs(rotated_axis[1] - c_lng_1) >= 0.01:
axis *= -1.0
angle *= -1.0
rotated_axis = rotations.xyz_to_lat_lon_radius(*axis)
if abs(rotated_axis[0] - c_lat_1) >= 0.01 or \
abs(rotated_axis[1] - c_lng_1) >= 0.01:
msg = "Failed to describe the domain in terms that SPECFEM " \
"understands"
raise LASIFError(msg)
gen.config.ANGULAR_WIDTH_XI_IN_DEGREES = lng_range
gen.config.ANGULAR_WIDTH_ETA_IN_DEGREES = lat_range
gen.config.CENTER_LATITUDE_IN_DEGREES = c_lat_1
gen.config.CENTER_LONGITUDE_IN_DEGREES = c_lng_1
gen.config.GAMMA_ROTATION_AZIMUTH = angle
gen.config.MODEL = cs["model"]
pp = iteration.get_process_params()
gen.config.RECORD_LENGTH_IN_MINUTES = \
(pp["npts"] * pp["dt"]) / 60.0
solver_format = solver_format.upper()
else:
msg = "Unknown solver '%s'." % solver_format
raise NotImplementedError(msg)
# =================================================================
# output
# =================================================================
output_dir = self.comm.project.get_output_folder(
"input_files___ITERATION_%s__%s__EVENT_%s" % (
iteration_name, simulation_type.replace(" ", "_"),
event_name))
gen.write(format=solver_format, output_dir=output_dir)
print "Written files to '%s'." % output_dir
def test_real_world_example():
"""
Test that compares the created input files to those from a real world
example.
The only artificial thing is the source-time function but that is
trivial to verify.
This is a fairly comprehensive tests but should be used in comparision
with other unit tests.
"""
stations = [{
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10
}, {
"id": "KO.AFSR",
"latitude": 40.000,
"longitude": 33.2345,
"elevation_in_m": 220
}]
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0
}
gen = InputFileGenerator()
gen.add_stations(stations)
gen.add_events(event)
# Configure it.
gen.config.number_of_time_steps = 4000
gen.config.time_increment_in_s = 0.13
gen.config.output_folder = "../DATA/OUTPUT/1.8s/"
gen.config.mesh_min_latitude = 34.1
gen.config.mesh_max_latitude = 42.9
gen.config.mesh_min_longitude = 23.1
gen.config.mesh_max_longitude = 42.9
gen.config.mesh_min_depth_in_km = 0.0
gen.config.mesh_max_depth_in_km = 471.0
gen.config.nx_global = 66
gen.config.ny_global = 108
gen.config.nz_global = 28
gen.config.px = 3
gen.config.py = 4
gen.config.pz = 4
gen.config.source_time_function = np.linspace(1.0, 0.0, 4000)
gen.config.is_dissipative = False
gen.config.adjoint_forward_wavefield_output_folder = \
"/tmp/some_folder/"
gen.config.displacement_snapshot_sampling = 15000
gen.config.Q_model_relaxation_times = [1.7308, 14.3961, 22.9973]
gen.config.Q_model_weights_of_relaxation_mechanisms = \
[2.5100, 2.4354, 0.0879]
# Write the input files to a dictionary.
input_files = gen.write(format="ses3d_4_0")
# The rest is only for asserting the produces files.
path = os.path.join(DATA, "ses3d_4_0_real_world_example")
for filename in glob.glob(os.path.join(path, "*")):
with open(filename, "rt") as open_file:
real_file = open_file.read()
filename = os.path.basename(filename)
if filename not in input_files:
msg = "File '%s' has not been generated" % filename
raise AssertionError(msg)
lines = real_file.splitlines()
new_lines = input_files[filename].splitlines()
if len(lines) != len(new_lines):
msg = ("File '%s' does not have the same number of lines "
"for the real (%i lines) and generated (%i lines) "
"input file") % (filename, len(lines), len(new_lines))
raise AssertionError(msg)
for line, new_line in zip(lines, new_lines):
if line != new_line:
msg = "Line differs in file '%s'.\n" % filename
msg += "Expected: \"%s\"\n" % line
msg += "Got: \"%s\"\n" % new_line
raise AssertionError(msg)
def compute(self):
gen = InputFileGenerator()
userconf = json.load(open(self.parameters["solver_conf_file"]))
fields = userconf["fields"]
for x in fields:
gen.add_configuration({x["name"]:self.strToBool(x["value"])})
with open (self.parameters["quakeml"], "r") as events:
quakeml=events.read()
#unicode_qml=quakeml.decode('utf-8')
#data = unicode_qml.encode('ascii','ignore')
##
cat=readQuakeML(quakeml)
events = []
#cat = obspy.readEvents(data)
#Remove all events with no moment tensor.
for event in cat:
for fm in event.focal_mechanisms:
if fm.moment_tensor and fm.moment_tensor.tensor:
events.append(event)
break
cat.events = events
gen.add_events(cat)
evn=0
outputdir=""
for x in userconf["events"]:
gen.event_filter=[x]
if self.parameters["station_format"]=="stationXML":
gen.add_stations(self.parameters["stations_file"])
if self.parameters["station_format"]=="points":
stlist = []
with open(self.parameters["stations_file"]) as f:
k=False
for line in f:
if (k==False):
k=True
else:
station={}
l=line.strip().split(" ")
station.update({"id":l[1]+"."+l[0]})
station.update({"latitude":float(l[3])})
station.update({"longitude":float(l[2])})
station.update({"elevation_in_m":float(l[4])})
station.update({"local_depth_in_m":float(l[5])})
stlist.append(station)
gen.add_stations(stlist)
gen.station_filter = userconf["stations"]
outputdir=self.outputdest+userconf["runId"]+"/"+userconf["runId"]+"_"+str(evn)+"/DATA"
output_files = gen.write(format=userconf["solver"], output_dir=outputdir)
locations = []
for x in output_files.keys():
locations.append("file://"+socket.gethostname()+outputdir+"/"+x)
self.addOutput(gen._filtered_events,location=locations,metadata=self.extractEventMetadata(outputdir,gen._filtered_events),control={"con:immediateAccess":"true"})
evn+=1
self.addOutput(outputdir,location=locations,metadata={"to_xdecompose":str(outputdir)},control={"con:immediateAccess":"true"})
def test_simple():
"""
Test a very simple SPECFEM file.
"""
stations = [
{
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10
}, {
"id": "KO.AFSR",
"latitude": 40.000,
"longitude": 33.2345,
"elevation_in_m": 220
}
]
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0}
gen = InputFileGenerator()
gen.add_stations(stations)
gen.add_events(event)
# Configure it.
gen.config.NPROC_XI = 5
gen.config.NPROC_ETA = 5
gen.config.RECORD_LENGTH_IN_MINUTES = 15
gen.config.SIMULATION_TYPE = 1
gen.config.NCHUNKS = 1
gen.config.NEX_XI = 240
gen.config.NEX_ETA = 240
gen.config.NPROC_XI = 5
gen.config.NPROC_ETA = 5
gen.config.MODEL = "CEM_REQUEST"
# Write the input files to a dictionary.
input_files = gen.write(format="SPECFEM3D_GLOBE_CEM")
assert bool(input_files)
assert sorted(input_files.keys()) == \
sorted(["Par_file", "CMTSOLUTION", "STATIONS"])
# Assert the STATIONS file.
assert input_files["STATIONS"].splitlines() == [
"ADVT KO 41.00000 33.12340 10.0 0.0",
"AFSR KO 40.00000 33.23450 220.0 0.0"]
# Assert the CMTSOLUTION file.
assert input_files["CMTSOLUTION"].splitlines() == [
"PDE 2012 4 12 7 15 48.50 39.26000 41.04000 5.00000 4.7 4.7 "
"2012-04-12T07:15:48.500000Z_4.7",
"event name: 0000000",
"time shift: 0.0000",
"half duration: 0.0000",
"latitude: 39.26000",
"longitude: 41.04000",
"depth: 5.00000",
"Mrr: 1e+23",
"Mtt: 1e+23",
"Mpp: 1e+23",
"Mrt: 0",
"Mrp: 0",
"Mtp: 0"]
# Compare the Par_file to a working one.
par_file = input_files["Par_file"]
with open(os.path.join(DATA, "specfem_globe_cem", "Par_file")) as fh:
expected_par_file = fh.read()
actual_par_file_lines = par_file.splitlines()
expected_par_file_lines = expected_par_file.splitlines()
for actual, expected in zip(actual_par_file_lines,
expected_par_file_lines):
assert actual == expected
def test_external_source_time_function():
"""
Test a very simple SPECFEM file.
"""
stations = [
{
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10
}, {
"id": "KO.AFSR",
"latitude": 40.000,
"longitude": 33.2345,
"elevation_in_m": 220
}
]
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0}
gen = InputFileGenerator()
gen.add_stations(stations)
gen.add_events(event)
# Configure it.
gen.config.NPROC_XI = 5
gen.config.NPROC_ETA = 5
gen.config.RECORD_LENGTH_IN_MINUTES = 15
gen.config.SIMULATION_TYPE = 1
gen.config.NCHUNKS = 1
gen.config.NEX_XI = 240
gen.config.NEX_ETA = 240
gen.config.NPROC_XI = 5
gen.config.NPROC_ETA = 5
gen.config.MODEL = "CEM_REQUEST"
# Write the input files to a dictionary.
input_files = gen.write(format="SPECFEM3D_GLOBE_CEM")
# If no source time is specified the external source time function flag
# must be false.
assert sorted(input_files.keys()) == \
["CMTSOLUTION", "Par_file", "STATIONS"]
assert "EXTERNAL_SOURCE_TIME_FUNCTION = .false." in \
input_files["Par_file"]
# Now if one is specified it should also be written.
gen.config.SOURCE_TIME_FUNCTION = np.arange(10)
input_files = gen.write(format="SPECFEM3D_GLOBE_CEM")
assert sorted(input_files.keys()) == \
["CMTSOLUTION", "Par_file", "STATIONS", "STF"]
assert "EXTERNAL_SOURCE_TIME_FUNCTION = .true." in \
input_files["Par_file"]
data = []
for line in input_files["STF"].splitlines():
if line.startswith("#"):
continue
data.append(float(line.strip()))
assert data == map(float, range(10))
def test_real_world_examlpe(self):
"""
Test that compares the created input files to those from a real world
example.
The only artificial thing is the source-time function but that is
trivial to verify.
This is a fairly comprehensive tests but should be used in comparision
with other unit tests.
"""
stations = [
{
"id": "KO.ADVT",
"latitude": 41.0,
"longitude": 33.1234,
"elevation_in_m": 10
}, {
"id": "KO.AFSR",
"latitude": 40.000,
"longitude": 33.2345,
"elevation_in_m": 220
}
]
event = {
"latitude": 39.260,
"longitude": 41.040,
"depth_in_km": 5.0,
"origin_time": UTCDateTime(2012, 4, 12, 7, 15, 48, 500000),
"m_rr": 1.0e16,
"m_tt": 1.0e16,
"m_pp": 1.0e16,
"m_rt": 0.0,
"m_rp": 0.0,
"m_tp": 0.0}
gen = InputFileGenerator()
gen.add_stations(stations)
gen.add_events(event)
# Configure it.
gen.config.number_of_time_steps = 4000
gen.config.time_increment_in_s = 0.13
gen.config.output_folder = "../DATA/OUTPUT/1.8s/"
gen.config.mesh_min_latitude = 34.1
gen.config.mesh_max_latitude = 42.9
gen.config.mesh_min_longitude = 23.1
gen.config.mesh_max_longitude = 42.9
gen.config.mesh_min_depth_in_km = 0.0
gen.config.mesh_max_depth_in_km = 471.0
gen.config.nx_global = 66
gen.config.ny_global = 108
gen.config.nz_global = 28
gen.config.px = 3
gen.config.py = 4
gen.config.pz = 4
gen.config.source_time_function = np.linspace(1.0, 0.0, 4000)
gen.config.is_dissipative = False
gen.config.adjoint_forward_wavefield_output_folder = \
"/tmp/some_folder/"
gen.config.displacement_snapshot_sampling = 15000
gen.config.Q_model_relaxation_times = [1.7308, 14.3961, 22.9973]
gen.config.Q_model_weights_of_relaxation_mechanisms = \
[2.5100, 2.4354, 0.0879]
# Write the input files to a dictionary.
input_files = gen.write(format="ses3d_4_0")
# The rest is only for asserting the produces files.
path = os.path.join(self.data_dir, "ses3d_4_0_real_world_example")
for filename in glob.glob(os.path.join(path, "*")):
with open(filename, "rt") as open_file:
real_file = open_file.read().strip()
filename = os.path.basename(filename)
if filename not in input_files:
msg = "File '%s' has not been generated" % filename
raise AssertionError(msg)
lines = real_file.splitlines()
new_lines = input_files[filename].splitlines()
if len(lines) != len(new_lines):
msg = ("File '%s' does not have the same number of lines "
"for the real (%i lines) and generated (%i lines) "
"input file") % (filename, len(lines), len(new_lines))
raise AssertionError(msg)
for line, new_line in zip(lines, new_lines):
if line != new_line:
msg = "Line differs in file '%s'.\n" % filename
msg += "Expected: \"%s\"\n" % line
msg += "Got: \"%s\"\n" % new_line
raise AssertionError(msg)
def generate_input_files(self, iteration_name, event_name,
simulation_type):
"""
Generate the input files for one event.
:param iteration_name: The name of the iteration.
:param event_name: The name of the event for which to generate the
input files.
:param simulate_type: The type of simulation to perform. Possible
values are: 'normal simulate', 'adjoint forward', 'adjoint
reverse'
"""
from wfs_input_generator import InputFileGenerator
# =====================================================================
# read iteration xml file, get event and list of stations
# =====================================================================
iteration = self.comm.iterations.get(iteration_name)
# Check that the event is part of the iterations.
if event_name not in iteration.events:
msg = ("Event '%s' not part of iteration '%s'.\nEvents available "
"in iteration:\n\t%s" %
(event_name, iteration_name, "\n\t".join(
sorted(iteration.events.keys()))))
raise ValueError(msg)
event = self.comm.events.get(event_name)
stations_for_event = list(
iteration.events[event_name]["stations"].keys())
# Get all stations and create a dictionary for the input file
# generator.
stations = self.comm.query.get_all_stations_for_event(event_name)
stations = [{
"id": key,
"latitude": value["latitude"],
"longitude": value["longitude"],
"elevation_in_m": value["elevation_in_m"],
"local_depth_in_m": value["local_depth_in_m"]
} for key, value in stations.items() if key in stations_for_event]
# =====================================================================
# set solver options
# =====================================================================
solver = iteration.solver_settings
# Currently only SES3D 4.1 is supported
solver_format = solver["solver"].lower()
if solver_format not in [
"ses3d 4.1", "ses3d 2.0", "specfem3d cartesian",
"specfem3d globe cem"
]:
msg = ("Currently only SES3D 4.1, SES3D 2.0, SPECFEM3D "
"CARTESIAN, and SPECFEM3D GLOBE CEM are supported.")
raise ValueError(msg)
solver_format = solver_format.replace(' ', '_')
solver_format = solver_format.replace('.', '_')
solver = solver["solver_settings"]
# =====================================================================
# create the input file generator, add event and stations,
# populate the configuration items
# =====================================================================
# Add the event and the stations to the input file generator.
gen = InputFileGenerator()
gen.add_events(event["filename"])
gen.add_stations(stations)
if solver_format in ["ses3d_4_1", "ses3d_2_0"]:
# event tag
gen.config.event_tag = event_name
# Time configuration.
npts = solver["simulation_parameters"]["number_of_time_steps"]
delta = solver["simulation_parameters"]["time_increment"]
gen.config.number_of_time_steps = npts
gen.config.time_increment_in_s = delta
# SES3D specific configuration
gen.config.output_folder = solver["output_directory"].replace(
"{{EVENT_NAME}}", event_name.replace(" ", "_"))
gen.config.simulation_type = simulation_type
gen.config.adjoint_forward_wavefield_output_folder = \
solver["adjoint_output_parameters"][
"forward_field_output_directory"].replace(
"{{EVENT_NAME}}", event_name.replace(" ", "_"))
gen.config.adjoint_forward_sampling_rate = \
solver["adjoint_output_parameters"][
"sampling_rate_of_forward_field"]
# Visco-elastic dissipation
diss = solver["simulation_parameters"]["is_dissipative"]
gen.config.is_dissipative = diss
# Only SES3D 4.1 has the relaxation parameters.
if solver_format == "ses3d_4_1":
gen.config.Q_model_relaxation_times = \
solver["relaxation_parameter_list"]["tau"]
gen.config.Q_model_weights_of_relaxation_mechanisms = \
solver["relaxation_parameter_list"]["w"]
# Discretization
disc = solver["computational_setup"]
gen.config.nx_global = disc["nx_global"]
gen.config.ny_global = disc["ny_global"]
gen.config.nz_global = disc["nz_global"]
gen.config.px = disc["px_processors_in_theta_direction"]
gen.config.py = disc["py_processors_in_phi_direction"]
gen.config.pz = disc["pz_processors_in_r_direction"]
gen.config.lagrange_polynomial_degree = \
disc["lagrange_polynomial_degree"]
# Configure the mesh.
domain = self.comm.project.domain
gen.config.mesh_min_latitude = domain.min_latitude
gen.config.mesh_max_latitude = domain.max_latitude
gen.config.mesh_min_longitude = domain.min_longitude
gen.config.mesh_max_longitude = domain.max_longitude
gen.config.mesh_min_depth_in_km = domain.min_depth_in_km
gen.config.mesh_max_depth_in_km = domain.max_depth_in_km
# Set the rotation parameters.
gen.config.rotation_angle_in_degree = \
domain.rotation_angle_in_degree
gen.config.rotation_axis = domain.rotation_axis
# Make source time function
gen.config.source_time_function = \
iteration.get_source_time_function()["data"]
elif solver_format == "specfem3d_cartesian":
gen.config.NSTEP = \
solver["simulation_parameters"]["number_of_time_steps"]
gen.config.DT = \
solver["simulation_parameters"]["time_increment"]
gen.config.NPROC = \
solver["computational_setup"]["number_of_processors"]
if simulation_type == "normal simulation":
msg = ("'normal_simulate' not supported for SPECFEM3D "
"Cartesian. Please choose either 'adjoint_forward' or "
"'adjoint_reverse'.")
raise NotImplementedError(msg)
elif simulation_type == "adjoint forward":
gen.config.SIMULATION_TYPE = 1
elif simulation_type == "adjoint reverse":
gen.config.SIMULATION_TYPE = 2
else:
raise NotImplementedError
solver_format = solver_format.upper()
elif solver_format == "specfem3d_globe_cem":
cs = solver["computational_setup"]
gen.config.NPROC_XI = cs["number_of_processors_xi"]
gen.config.NPROC_ETA = cs["number_of_processors_eta"]
gen.config.NCHUNKS = cs["number_of_chunks"]
gen.config.NEX_XI = cs["elements_per_chunk_xi"]
gen.config.NEX_ETA = cs["elements_per_chunk_eta"]
gen.config.OCEANS = cs["simulate_oceans"]
gen.config.ELLIPTICITY = cs["simulate_ellipticity"]
gen.config.TOPOGRAPHY = cs["simulate_topography"]
gen.config.GRAVITY = cs["simulate_gravity"]
gen.config.ROTATION = cs["simulate_rotation"]
gen.config.ATTENUATION = cs["simulate_attenuation"]
gen.config.ABSORBING_CONDITIONS = True
if cs["fast_undo_attenuation"]:
gen.config.PARTIAL_PHYS_DISPERSION_ONLY = True
gen.config.UNDO_ATTENUATION = False
else:
gen.config.PARTIAL_PHYS_DISPERSION_ONLY = False
gen.config.UNDO_ATTENUATION = True
gen.config.GPU_MODE = cs["use_gpu"]
gen.config.SOURCE_TIME_FUNCTION = \
iteration.get_source_time_function()["data"]
if simulation_type == "normal simulation":
gen.config.SIMULATION_TYPE = 1
gen.config.SAVE_FORWARD = False
elif simulation_type == "adjoint forward":
gen.config.SIMULATION_TYPE = 1
gen.config.SAVE_FORWARD = True
elif simulation_type == "adjoint reverse":
gen.config.SIMULATION_TYPE = 2
gen.config.SAVE_FORWARD = True
else:
raise NotImplementedError
# Use the current domain setting to derive the bounds in the way
# SPECFEM specifies them.
domain = self.comm.project.domain
lat_range = domain.max_latitude - \
domain.min_latitude
lng_range = domain.max_longitude - \
domain.min_longitude
c_lat = \
domain.min_latitude + lat_range / 2.0
c_lng = \
domain.min_longitude + lng_range / 2.0
# Rotate the point.
c_lat_1, c_lng_1 = rotations.rotate_lat_lon(
c_lat, c_lng, domain.rotation_axis,
domain.rotation_angle_in_degree)
# SES3D rotation.
A = rotations._get_rotation_matrix(domain.rotation_axis,
domain.rotation_angle_in_degree)
latitude_rotation = -(c_lat_1 - c_lat)
longitude_rotation = c_lng_1 - c_lng
# Rotate the latitude. The rotation axis is latitude 0 and
# the center longitude + 90 degree
B = rotations._get_rotation_matrix(
rotations.lat_lon_radius_to_xyz(0.0, c_lng + 90, 1.0),
latitude_rotation)
# Rotate around the North pole.
C = rotations._get_rotation_matrix([0.0, 0.0, 1.0],
longitude_rotation)
D = A * np.linalg.inv(C * B)
axis, angle = rotations._get_axis_and_angle_from_rotation_matrix(D)
rotated_axis = rotations.xyz_to_lat_lon_radius(*axis)
# Consistency check
if abs(rotated_axis[0] - c_lat_1) >= 0.01 or \
abs(rotated_axis[1] - c_lng_1) >= 0.01:
axis *= -1.0
angle *= -1.0
rotated_axis = rotations.xyz_to_lat_lon_radius(*axis)
if abs(rotated_axis[0] - c_lat_1) >= 0.01 or \
abs(rotated_axis[1] - c_lng_1) >= 0.01:
msg = "Failed to describe the domain in terms that SPECFEM " \
"understands. The domain definition in the output " \
"files will NOT BE CORRECT!"
warnings.warn(msg, LASIFWarning)
gen.config.ANGULAR_WIDTH_XI_IN_DEGREES = lng_range
gen.config.ANGULAR_WIDTH_ETA_IN_DEGREES = lat_range
gen.config.CENTER_LATITUDE_IN_DEGREES = c_lat_1
gen.config.CENTER_LONGITUDE_IN_DEGREES = c_lng_1
gen.config.GAMMA_ROTATION_AZIMUTH = angle
gen.config.MODEL = cs["model"]
pp = iteration.get_process_params()
gen.config.RECORD_LENGTH_IN_MINUTES = \
(pp["npts"] * pp["dt"]) / 60.0
solver_format = solver_format.upper()
else:
msg = "Unknown solver '%s'." % solver_format
raise NotImplementedError(msg)
# =================================================================
# output
# =================================================================
output_dir = self.comm.project.get_output_folder(
type="input_files",
tag="ITERATION_%s__%s__EVENT_%s" %
(iteration_name, simulation_type.replace(" ", "_"), event_name))
gen.write(format=solver_format, output_dir=output_dir)
print("Written files to '%s'." % output_dir)
