def get_source_object(self, event_name: str):
"""
Create the source object that the simulation wants
:param event_name: Name of event
:type event_name: str
"""
iteration = self.comm.project.current_iteration
src_info = self.comm.lasif.get_source(event_name)
stf_file = self.comm.lasif.find_stf(iteration)
side_set = "r1"
if isinstance(src_info, list):
src_info = src_info[0]
if self.comm.project.meshes == "multi-mesh":
src = source.seismology.SideSetMomentTensorPoint3D(
latitude=src_info["latitude"],
longitude=src_info["longitude"],
depth_in_m=src_info["depth_in_m"],
mrr=src_info["mrr"],
mtt=src_info["mtt"],
mpp=src_info["mpp"],
mtp=src_info["mtp"],
mrp=src_info["mrp"],
mrt=src_info["mrt"],
source_time_function=stf.Custom(filename=stf_file,
dataset_name="/source"),
side_set_name=side_set,
)
# print(f"Source info: {src_info}")
else:
if self.comm.project.ocean_loading["use"]:
side_set = "r1_ol"
src = source.seismology.SideSetMomentTensorPoint3D(
latitude=src_info["latitude"],
longitude=src_info["longitude"],
depth_in_m=src_info["depth_in_m"],
mrr=src_info["mrr"],
mtt=src_info["mtt"],
mpp=src_info["mpp"],
mtp=src_info["mtp"],
mrp=src_info["mrp"],
mrt=src_info["mrt"],
side_set_name=side_set,
source_time_function=stf.Custom(filename=stf_file,
dataset_name="/source"),
)
return src
def get_source_object(self, event_name: str):
"""
Create the source object that the simulation wants
:param event_name: Name of event
:type event_name: str
"""
from salvus.flow.simple_config import source
from salvus.flow.simple_config import stf
iteration = self.comm.project.current_iteration
src_info = self.comm.lasif.get_source(event_name)
stf_file = self.comm.lasif.find_stf(iteration)
if isinstance(src_info, list):
src_info = src_info[0]
src = source.seismology.MomentTensorPoint3D(
latitude=src_info["latitude"],
longitude=src_info["longitude"],
depth_in_m=src_info["depth_in_m"],
mrr=src_info["mrr"],
mtt=src_info["mtt"],
mpp=src_info["mpp"],
mtp=src_info["mtp"],
mrp=src_info["mrp"],
mrt=src_info["mrt"],
source_time_function=stf.Custom(
filename=stf_file, dataset_name="/source"
),
)
return src
def get_adjoint_source(comm: object, event: str,
iteration: str) -> List[object]:
"""
Get a list of adjoint source objects
:param comm: The lasif communicator object
:type comm: object
:param event: Name of event
:type event: str
:param iteration: Name of iteration
:type iteration: str
:return: Adjoint source objects
:type return: List[object]
"""
from salvus.flow.simple_config import source, stf
import h5py
receivers = place_receivers(comm=comm, event=event)
iteration_name = comm.iterations.get_long_iteration_name(iteration)
adjoint_filename = str(comm.project.paths["adjoint_sources"] /
iteration_name / event / "stf.h5")
p = h5py.File(adjoint_filename, "r")
adjoint_recs = list(p.keys())
adjoint_sources = []
for rec in receivers:
if rec["network-code"] + "_" + rec["station-code"] in adjoint_recs:
adjoint_sources.append(rec)
p.close()
adj_src = [
source.seismology.VectorPoint3DZNE(
latitude=rec["latitude"],
longitude=rec["longitude"],
fz=1.0,
fn=1.0,
fe=1.0,
source_time_function=stf.Custom(
filename=adjoint_filename,
dataset_name=f"/{rec['network-code']}_{rec['station-code']}",
),
) for rec in adjoint_sources
]
return adj_src
def get_adjoint_source_object(self, event_name: str) -> object:
"""
Generate the adjoint source object for the respective event
:param event_name: Name of event
:type event_name: str
:return: Adjoint source object for salvus
:rtype: object
"""
import h5py
from salvus.flow.simple_config import source
from salvus.flow.simple_config import stf
iteration = self.comm.project.current_iteration
receivers = self.comm.lasif.get_receivers(event_name)
adjoint_filename = self.comm.lasif.get_adjoint_source_file(
event=event_name, iteration=iteration)
# A workaround needed for a current salvus bug:
# stf_forward = os.path.join(
# self.comm.project.lasif_root,
# "SALVUS_INPUT_FILES",
# f"ITERATION_{iteration}",
# "custom_stf.h5")
# job_name = self._get_job_name(
# event=event_name,
# sim_type="forward",
# new=False)
# stf_forward_path = f"/scratch/snx3000/tsolvi/salvus_flow/run/{job_name}/input/custom_stf.h5"
# copy it:
# os.system(f"scp daint:{stf_forward_path} {stf_forward}")
# f = h5py.File(stf_forward)
# stf_source = f['stf'][()]
p = h5py.File(adjoint_filename)
# if 'stf' in p.keys():
# del p['stf']
adjoint_recs = list(p.keys())
# p.create_dataset(name='stf', data=stf_source)
# p["stf"].attrs["sampling_rate_in_hertz"] = 1 / self.comm.project.time_step
# p["source"].attrs["spatial-type"] = np.string_("moment_tensor")
# p["stf"].attrs["start_time_in_seconds"] = -self.comm.project.time_step
# f.close()
# rec = receivers[0]
# Need to make sure I only take receivers with an adjoint source
adjoint_sources = []
for rec in receivers:
if rec["network-code"] + "_" + rec["station-code"] in adjoint_recs:
adjoint_sources.append(rec)
p.close()
adj_src = [
source.seismology.VectorPoint3DZNE(
latitude=rec["latitude"],
longitude=rec["longitude"],
fz=1.0,
fn=1.0,
fe=1.0,
source_time_function=stf.Custom(
filename=adjoint_filename,
dataset_name="/" + rec["network-code"] + "_" +
rec["station-code"])) for rec in adjoint_sources
]
return adj_src
def get_adjoint_source_object(self, event_name: str) -> object:
"""
Generate the adjoint source object for the respective event
:param event_name: Name of event
:type event_name: str
:return: Adjoint source object for salvus
:rtype: object
"""
import h5py
from salvus.flow.simple_config import source, stf
iteration = self.comm.project.current_iteration
receivers = self.comm.lasif.get_receivers(event_name)
adjoint_filename = self.comm.lasif.get_adjoint_source_file(
event=event_name, iteration=iteration)
# A workaround needed for a current salvus bug:
# stf_forward = os.path.join(
# self.comm.project.lasif_root,
# "SALVUS_INPUT_FILES",
# f"ITERATION_{iteration}",
# "custom_stf.h5")
# job_name = self._get_job_name(
# event=event_name,
# sim_type="forward",
# new=False)
# stf_forward_path = f"/scratch/snx3000/tsolvi/salvus_flow/run/{job_name}/input/custom_stf.h5"
# copy it:
# os.system(f"scp daint:{stf_forward_path} {stf_forward}")
# f = h5py.File(stf_forward)
# stf_source = f['stf'][()]
p = h5py.File(adjoint_filename, "r")
# if 'stf' in p.keys():
# del p['stf']
adjoint_recs = list(p.keys())
# p.create_dataset(name='stf', data=stf_source)
# p["stf"].attrs["sampling_rate_in_hertz"] = 1 / self.comm.project.time_step
# p["source"].attrs["spatial-type"] = np.string_("moment_tensor")
# p["stf"].attrs["start_time_in_seconds"] = -self.comm.project.time_step
# f.close()
# rec = receivers[0]
# Need to make sure I only take receivers with an adjoint source
adjoint_sources = []
for rec in receivers:
if rec["network-code"] + "_" + rec["station-code"] in adjoint_recs:
adjoint_sources.append(rec)
p.close()
if self.comm.project.meshes == "multi-mesh":
adj_src = [
source.seismology.VectorPoint3DZNE(
latitude=rec["latitude"],
longitude=rec["longitude"],
fz=1.0,
fn=1.0,
fe=1.0,
source_time_function=stf.Custom(
filename=adjoint_filename,
dataset_name="/" + rec["network-code"] + "_" +
rec["station-code"],
),
) for rec in adjoint_sources
]
return adj_src
# Get path to meta.json to obtain receiver position, use again for adjoint
meta_json_filename = os.path.join(
self.comm.project.lasif_root,
"SYNTHETICS",
"EARTHQUAKES",
f"ITERATION_{iteration}",
event_name,
"meta.json",
)
# Build meta info dict
import json
with open(meta_json_filename) as json_file:
data = json.load(json_file)
meta_recs = data["forward_run_input"]["output"]["point_data"][
"receiver"]
meta_info_dict = {}
for rec in meta_recs:
if rec["network_code"] + "_" + rec["station_code"] in adjoint_recs:
rec_name = rec["network_code"] + "_" + rec["station_code"]
meta_info_dict[rec_name] = {}
# this is the rotation from XYZ to ZNE,
# we still need to transpose to get ZND -> XYZ
meta_info_dict[rec_name]["rotation_on_input"] = {
"matrix":
np.array(rec["rotation_on_output"]["matrix"]).T.tolist()
}
meta_info_dict[rec_name]["location"] = rec["location"]
adj_src = [
source.cartesian.VectorPoint3D(
x=meta_info_dict[rec["network-code"] + "_" +
rec["station-code"]]["location"][0],
y=meta_info_dict[rec["network-code"] + "_" +
rec["station-code"]]["location"][1],
z=meta_info_dict[rec["network-code"] + "_" +
rec["station-code"]]["location"][2],
fx=1.0,
fy=1.0,
fz=1.0,
source_time_function=stf.Custom(
filename=adjoint_filename,
dataset_name="/" + rec["network-code"] + "_" +
rec["station-code"],
),
rotation_on_input=meta_info_dict[rec["network-code"] + "_" +
rec["station-code"]]
["rotation_on_input"],
) for rec in adjoint_sources
]
return adj_src
def create_salvus_forward_simulation(
comm: object,
event: str,
iteration: str,
mesh=None,
side_set: str = None,
):
"""
Create a Salvus simulation object based on simulation and salvus
specific parameters specified in config file.
:param comm: The lasif communicator object
:type comm: object
:param event: Name of event
:type event: str
:param iteration: Name of iteration
:type iteration: str
:param mesh: Path to mesh or Salvus mesh object, if None it will use
the domain file from config file, defaults to None
:type mesh: Union[str, salvus.mesh.unstructured_mesh.UnstructuredMesh],
optional
:param side_set: Name of side set on mesh to place receivers,
defaults to None.
:type side_set: str, optional
"""
import salvus.flow.simple_config as sc
from salvus.flow.simple_config import stf
source_info = prepare_source(comm=comm, event=event, iteration=iteration)
iteration = comm.iterations.get_long_iteration_name(iteration)
receivers = place_receivers(comm=comm, event=event)
stf_path = os.path.join(comm.project.paths["salvus_files"], iteration,
"stf.h5")
if mesh is None:
mesh = comm.project.lasif_config["domain_settings"]["domain_file"]
if side_set is None:
recs = [
sc.receiver.seismology.Point3D(
latitude=rec["latitude"],
longitude=rec["longitude"],
network_code=rec["network-code"],
station_code=rec["station-code"],
fields=["displacement"],
) for rec in receivers
]
else:
recs = [
sc.receiver.seismology.SideSetPoint3D(
latitude=rec["latitude"],
longitude=rec["longitude"],
network_code=rec["network-code"],
station_code=rec["station-code"],
side_set_name=side_set,
fields=["displacement"],
) for rec in receivers
]
sources = [
sc.source.seismology.MomentTensorPoint3D(
latitude=src["latitude"],
longitude=src["longitude"],
depth_in_m=src["depth_in_m"],
mrr=src["mrr"],
mtt=src["mtt"],
mpp=src["mpp"],
mtp=src["mtp"],
mrp=src["mrp"],
mrt=src["mrt"],
source_time_function=stf.Custom(filename=stf_path,
dataset_name="/source"),
) for src in source_info
]
w = sc.simulation.Waveform(
mesh=mesh,
sources=sources,
receivers=recs,
)
sim_set = comm.project.simulation_settings
sal_set = comm.project.salvus_settings
w.physics.wave_equation.end_time_in_seconds = sim_set["end_time_in_s"]
w.physics.wave_equation.time_step_in_seconds = sim_set["time_step_in_s"]
w.physics.wave_equation.start_time_in_seconds = sim_set["start_time_in_s"]
w.physics.wave_equation.attenuation = sal_set["attenuation"]
import lasif.domain
domain = lasif.domain.HDF5Domain(mesh,
sim_set["absorbing_boundaries_in_km"])
if not domain.is_global_domain():
absorbing = sc.boundary.Absorbing(
width_in_meters=comm.project.
simulation_settings["absorbing_boundaries_in_km"] * 1000.0,
side_sets=["r0", "t0", "t1", "p0", "p1"],
taper_amplitude=1.0 /
comm.project.simulation_settings["minimum_period_in_s"],
)
w.physics.wave_equation.boundaries = [absorbing]
w.output.memory_per_rank_in_MB = 4000.0
w.output.volume_data.format = "hdf5"
w.output.volume_data.filename = "output.h5"
w.output.volume_data.fields = ["adjoint-checkpoint"]
w.output.volume_data.sampling_interval_in_time_steps = (
"auto-for-checkpointing")
w.validate()
return w
def get_adjoint_source_object(event_name, adjoint_filename,
receiver_json_path, proc_filename,
misfits, forward_meta_json_filename) -> object:
"""
Generate the adjoint source object for the respective event
:param event_name: Name of event
:type event_name: str
:return: Adjoint source object for salvus
:rtype: object
"""
receivers = build_or_get_receiver_info(receiver_json_path, proc_filename)
adjoint_recs = list(misfits[event_name].keys())
# Need to make sure I only take receivers with an adjoint source
adjoint_sources = []
for rec in receivers:
if (
rec["network-code"] + "_" + rec["station-code"] in adjoint_recs
or rec["network-code"] + "." + rec[
"station-code"] in adjoint_recs
):
adjoint_sources.append(rec)
# Build meta_info_dict
with open(forward_meta_json_filename) as json_file:
data = json.load(json_file)
meta_recs = data["forward_run_input"]["output"]["point_data"]["receiver"]
meta_info_dict = {}
for rec in meta_recs:
if (
rec["network_code"] + "_" + rec["station_code"] in adjoint_recs
or rec["network_code"] + "." + rec[
"station_code"] in adjoint_recs
):
rec_name = rec["network_code"] + "_" + rec["station_code"]
meta_info_dict[rec_name] = {}
# this is the rotation from XYZ to ZNE,
# we still need to transpose to get ZNE -> XYZ
meta_info_dict[rec_name]["rotation_on_input"] = {
"matrix": np.array(
rec["rotation_on_output"]["matrix"]).T.tolist()
}
meta_info_dict[rec_name]["location"] = rec["location"]
adj_src = [
source.cartesian.VectorPoint3D(
x=meta_info_dict[rec["network-code"] + "_" + rec["station-code"]][
"location"
][0],
y=meta_info_dict[rec["network-code"] + "_" + rec["station-code"]][
"location"
][1],
z=meta_info_dict[rec["network-code"] + "_" + rec["station-code"]][
"location"
][2],
fx=1.0,
fy=1.0,
fz=1.0,
source_time_function=stf.Custom(
filename=adjoint_filename,
dataset_name="/" + rec["network-code"] + "_" + rec[
"station-code"],
),
rotation_on_input=meta_info_dict[
rec["network-code"] + "_" + rec["station-code"]
]["rotation_on_input"],
)
for rec in adjoint_sources
]
return adj_src
def get_adjoint_source_object(self, event_name: str) -> object:
"""
Generate the adjoint source object for the respective event
:param event_name: Name of event
:type event_name: str
:return: Adjoint source object for salvus
:rtype: object
"""
import h5py
iteration = self.comm.project.current_iteration
receivers = self.comm.lasif.get_receivers(event_name)
if not self.comm.project.hpc_processing:
adjoint_filename = self.comm.lasif.get_adjoint_source_file(
event=event_name, iteration=iteration)
if not self.comm.project.hpc_processing:
p = h5py.File(adjoint_filename, "r")
adjoint_recs = list(p.keys())
p.close()
else:
forward_job = self.get_job(event_name, sim_type="forward")
# remote synthetics
remote_meta_path = forward_job.output_path / "meta.json"
hpc_cluster = get_site(self.comm.project.site_name)
meta_json_filename = "meta.json"
if os.path.exists(meta_json_filename):
os.remove(meta_json_filename)
hpc_cluster.remote_get(remote_meta_path, meta_json_filename)
proc_job = self.get_job(event_name, sim_type="hpc_processing")
remote_misfit_dict_toml = str(proc_job.stdout_path.parent /
"output" / "misfit_dict.toml")
adjoint_filename = "REMOTE:" + str(
proc_job.stdout_path.parent / "output" / "stf.h5")
local_misfit_dict = "misfit_dict.toml"
if os.path.exists(local_misfit_dict):
os.remove(local_misfit_dict)
hpc_cluster.remote_get(remote_misfit_dict_toml, local_misfit_dict)
misfits = toml.load(local_misfit_dict)
adjoint_recs = list(misfits[event_name].keys())
if os.path.exists(local_misfit_dict):
os.remove(local_misfit_dict)
# Need to make sure I only take receivers with an adjoint source
adjoint_sources = []
for rec in receivers:
if (rec["network-code"] + "_" + rec["station-code"] in adjoint_recs
or rec["network-code"] + "." + rec["station-code"]
in adjoint_recs):
adjoint_sources.append(rec)
# print(adjoint_sources)
# Get path to meta.json to obtain receiver position, use again for adjoint
if not self.comm.project.hpc_processing:
meta_json_filename = os.path.join(
self.comm.project.lasif_root,
"SYNTHETICS",
"EARTHQUAKES",
f"ITERATION_{iteration}",
event_name,
"meta.json",
)
# Build meta info dict
with open(meta_json_filename) as json_file:
data = json.load(json_file)
meta_recs = data["forward_run_input"]["output"]["point_data"][
"receiver"]
meta_info_dict = {}
for rec in meta_recs:
if (rec["network_code"] + "_" + rec["station_code"] in adjoint_recs
or rec["network_code"] + "." + rec["station_code"]
in adjoint_recs):
rec_name = rec["network_code"] + "_" + rec["station_code"]
meta_info_dict[rec_name] = {}
# this is the rotation from XYZ to ZNE,
# we still need to transpose to get ZNE -> XYZ
meta_info_dict[rec_name]["rotation_on_input"] = {
"matrix":
np.array(rec["rotation_on_output"]["matrix"]).T.tolist()
}
meta_info_dict[rec_name]["location"] = rec["location"]
adj_src = [
source.cartesian.VectorPoint3D(
x=meta_info_dict[rec["network-code"] + "_" +
rec["station-code"]]["location"][0],
y=meta_info_dict[rec["network-code"] + "_" +
rec["station-code"]]["location"][1],
z=meta_info_dict[rec["network-code"] + "_" +
rec["station-code"]]["location"][2],
fx=1.0,
fy=1.0,
fz=1.0,
source_time_function=stf.Custom(
filename=adjoint_filename,
dataset_name="/" + rec["network-code"] + "_" +
rec["station-code"],
),
rotation_on_input=meta_info_dict[rec["network-code"] + "_" +
rec["station-code"]]
["rotation_on_input"],
) for rec in adjoint_sources
]
if os.path.exists(
meta_json_filename) and self.comm.project.hpc_processing:
os.remove(meta_json_filename)
return adj_src