def generate_data(self, **model_kwargs):
"""
Generates data using the True model, exports traces to `traces/obs`
:param model_kwargs: keyword arguments to pass to `generate_mesh`
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.cwd)
setpar(key="SIMULATION_TYPE", val="1", file="DATA/Par_file")
setpar(key="SAVE_FORWARD", val=".true.", file="DATA/Par_file")
call_solver(PAR.MPIEXEC, "bin/xmeshfem2D", output="mesher.log")
call_solver(PAR.MPIEXEC, "bin/xspecfem2D", output="solver.log")
if PAR.FORMAT.upper() == "SU":
# Work around SPECFEM2D's version dependent file names
for tag in ["d", "v", "a", "p"]:
unix.rename(old=f"single_{tag}.su",
new="single.su",
names=glob(os.path.join("OUTPUT_FILES", "*.su")))
unix.mv(src=glob(os.path.join("OUTPUT_FILES", self.data_wildcard)),
dst=os.path.join("traces", "obs"))
if PAR.SAVETRACES:
self.export_traces(os.path.join(PATH.OUTPUT, "traces", "obs"))
def write_receivers(self):
"""
Write a list of receivers into a text file
!!! This calls on plugins.solver.specfem3d.write_receivers()
but incorrect number of parameters is forwarded !!!
"""
unix.cd(self.cwd)
setpar(key="use_existing_STATIONS", val=".true", file="DATA/Par_file")
_, h = preprocess.load("traces/obs")
solvertools.write_receivers(h.nr, h.rx, h.rz)
def generate_data(self, **model_kwargs):
"""
Generates data using the True model, exports traces to `traces/obs`
:param model_kwargs: keyword arguments to pass to `generate_mesh`
"""
# Create the mesh
self.generate_mesh(**model_kwargs)
# Run the Forward simulation
unix.cd(self.cwd)
setpar(key="SIMULATION_TYPE", val="1", file="DATA/Par_file")
setpar(key="SAVE_FORWARD", val=".true.", file="DATA/Par_file")
if PAR.ATTENUATION:
setpar(key="ATTENUATION", val=".true.", file="DATA/Par_file")
else:
setpar(key="ATTENUATION", val=".false.", file="DATA/Par_file")
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xspecfem3D")
unix.mv(src=glob(os.path.join("OUTPUT_FILES", self.data_wildcard)),
dst=os.path.join("traces", "obs"))
# Export traces to disk for permanent storage
if PAR.SAVETRACES:
self.export_traces(os.path.join(PATH.OUTPUT, "traces", "obs"))
def generate_data(self):
"""
Overload seisflows.solver.base.generate_data. To be run in parallel
Not used if PAR.CASE == "Data"
Generates data in the synthetic-synthetic comparison case.
Automatically calls generate mesh for the true model, rather than
passing them in as kwargs.
Also turns on attenuation for the forward model
!!! attenuation could be moved into parameters.yaml? !!!
"""
unix.cd(self.cwd)
setpar(key="SIMULATION_TYPE", val="1", file="DATA/Par_file")
setpar(key="SAVE_FORWARD", val=".true.", file="DATA/Par_file")
if PAR.ATTENUATION:
setpar(key="ATTENUATION ", val=".true.", file="DATA/Par_file")
else:
setpar(key="ATTENUATION ", val=".false.", file="DATA/Par_file")
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xspecfem3D")
# move ASCII .sem? files into appropriate directory
unix.mv(src=glob(os.path.join("OUTPUT_FILES", self.data_wildcard)),
dst=os.path.join("traces", "obs"))
# Export traces to permanent storage on disk
if PAR.SAVETRACES:
self.export_traces(os.path.join(PATH.OUTPUT, "traces", "obs"))
def write_sources(par, h, path="."):
"""
Writes FORCESOLUTION source information to text file
:type par: dict
:param par: seisflows.PAR
:type h:
:param h:
:type path: str
:param path: path to write sources to
"""
file = os.path.join(findpath("seisflows.plugins"), "specfem3d",
"FORCESOLUTION")
with open(file, "r") as f:
lines = f.readlines()
file = "DATA/FORCESOURCE"
with open(file, "w") as f:
f.writelines(lines)
# adjust coordinates
setpar("xs", h.sx[0], file)
setpar("zs", h.sz[0], file)
setpar("ts", h.ts, file)
# adjust wavelet
setpar("f0", par["F0"], file)
def adjoint(self):
"""
Calls SPECFEM2D adjoint solver, creates the `SEM` folder with adjoint
traces which is required by the adjoint solver
"""
setpar(key="SIMULATION_TYPE", val="3", file="DATA/Par_file")
setpar(key="SAVE_FORWARD", val=".false.", file="DATA/Par_file")
unix.rm("SEM")
unix.ln("traces/adj", "SEM")
# Deal with different SPECFEM2D name conventions for regular traces and
# "adjoint" traces
if PAR.FORMAT.upper == "SU":
unix.rename(old=".su",
new=".su.adj",
names=glob(os.path.join("traces", "adj", "*.su")))
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xmeshfem2D")
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xspecfem2D")
def forward(self, path='traces/syn'):
"""
Calls SPECFEM2D forward solver, exports solver outputs to traces dir
:type path: str
:param path: path to export traces to after completion of simulation
"""
setpar(key="SIMULATION_TYPE", val="1", file="DATA/Par_file")
setpar(key="SAVE_FORWARD", val=".true.", file="DATA/Par_file")
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xmeshfem2D")
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xspecfem2D")
if PAR.FORMAT.upper() == "SU":
# Work around SPECFEM2D's version dependent file names
for tag in ["d", "v", "a", "p"]:
unix.rename(old=f"single_{tag}.su",
new="single.su",
names=glob(os.path.join("OUTPUT_FILES", "*.su")))
unix.mv(src=glob(os.path.join("OUTPUT_FILES", self.data_wildcard)),
dst=path)
def check_solver_parameter_files(self):
"""
Checks solver parameters. Only slightly different to Specfem3D as it
is run by the main task, not be an array process, so no need to check
task_id
"""
nt = getpar(key="NSTEP", cast=int)
dt = getpar(key="DT", cast=float)
if nt != PAR.NT:
warnings.warn("Specfem3D NSTEP != PAR.NT\n"
"overwriting Specfem3D with Seisflows parameter")
setpar(key="NSTEP", val=PAR.NT)
if dt != PAR.DT:
warnings.warn("Specfem3D DT != PAR.DT\n"
"overwriting Specfem3D with Seisflows parameter")
setpar(key="DT", val=PAR.DT)
if self.mesh_properties.nproc != PAR.NPROC:
warnings.warn("Specfem3D mesh nproc != PAR.NPROC")
if "MULTIPLES" in PAR:
raise NotImplementedError
def write_sources(PAR, h, path='.'):
""" Writes source information to text file
"""
filename = findpath('seisflows.plugins') + '/' + 'specfem3d/SOURCE'
with open(filename, 'r') as f:
lines = f.readlines()
filename = 'DATA/SOURCE'
with open(filename, 'w') as f:
f.writelines(lines)
# adjust coordinates
setpar('xs', h.sx[0], filename)
setpar('zs', h.sz[0], filename)
setpar('ts', h.ts, filename)
# adjust wavelet
setpar('f0', PAR['F0'], filename)
def adjoint(self):
"""
Calls SPECFEM3D adjoint solver, creates the `SEM` folder with adjoint
traces which is required by the adjoint solver
"""
setpar(key="SIMULATION_TYPE", val="3", file="DATA/Par_file")
setpar(key="SAVE_FORWARD", val=".false.", file="DATA/Par_file")
setpar(key="ATTENUATION", val=".false.", file="DATA/Par_file")
unix.rm("SEM")
unix.ln("traces/adj", "SEM")
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xspecfem3D")
def forward(self, path="traces/syn"):
"""
Calls SPECFEM3D forward solver, exports solver outputs to traces dir
:type path: str
:param path: path to export traces to after completion of simulation
"""
# Set parameters and run forward simulation
setpar(key="SIMULATION_TYPE", val="1", file="DATA/Par_file")
setpar(key="SAVE_FORWARD", val=".true.", file="DATA/Par_file")
if PAR.ATTENUATION:
setpar(key="ATTENUATION", val=".true.", file="DATA/Par_file")
else:
setpar(key="ATTENUATION", val=".false`.", file="DATA/Par_file")
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xgenerate_databases")
call_solver(mpiexec=PAR.MPIEXEC, executable="bin/xspecfem3D")
# Find and move output traces, by default to synthetic traces dir
unix.mv(src=glob(os.path.join("OUTPUT_FILES", self.data_wildcard)),
dst=path)
def check_solver_parameter_files(self):
"""
Checks SPECFEM2D Par_file for acceptable parameters and matches with
the internally set parameters
"""
# Check the number of steps in the SPECFEM2D Par_file
nt_str, nt, nt_i = getpar(key="NSTEP", file="DATA/Par_file")
if int(nt) != PAR.NT:
if self.taskid == 0:
print(
msg.cli(
f"SPECFEM2D {nt_str}=={nt} is not equal "
f"SeisFlows3 PAR.NT=={PAR.NT}. Please ensure "
f"that these values match in both files.",
header="parameter match error",
border="="))
sys.exit(-1)
dt_str, dt, dt_i = getpar(key="DT", file="DATA/Par_file")
if float(dt) != PAR.DT:
if self.taskid == 0:
print(
msg.cli(
f"SPECFEM2D {dt_str}=={dt} is not equal "
f"SeisFlows3 PAR.DT=={PAR.DT}. Please ensure "
f"that these values match in both files.",
header="parameter match error",
border="="))
sys.exit(-1)
# Check the central frequency in the SPECFEM2D SOURCE file
f0_str, f0, f0_i = getpar(key="f0", file="DATA/SOURCE")
if float(f0) != PAR.F0:
if self.taskid == 0:
print(
msg.cli(
f"SPECFEM2D {f0_str}=={f0} is not equal "
f"SeisFlows3 PAR.F0=={PAR.F0}. Please ensure "
f"that these values match the DATA/SOURCE file.",
header="parameter match error",
border="="))
sys.exit(-1)
# Ensure that NPROC matches the MESH values
nproc = self.mesh_properties.nproc
if nproc != PAR.NPROC:
if self.taskid == 0:
print(
msg.cli(
f"SPECFEM2D mesh NPROC=={nproc} is not equal"
f"SeisFlows3 PAR.NPROC=={PAR.NPROC}. "
f"Please check that your mesh matches this val.",
header="parameter match error",
border="="))
sys.exit(-1)
if "MULTIPLES" in PAR:
if PAR.MULTIPLES:
setpar(key="absorbtop", val=".false.", file="DATA/Par_file")
else:
setpar(key="absorbtop", val=".true.", file="DATA/Par_file")
def write_sources(coords, path='.', ws=1., suffix=''):
"""
Writes source information to text file
TODO this has to be adapted for new versions of specfem because the
source file format has changed
"""
sx, sy, sz = coords
filename = findpath('seisflows.plugins') + '/' + 'solver/specfem2d/SOURCE'
with open(filename, 'r') as f:
lines = f.readlines()
filename = 'DATA/SOURCE' + suffix
with open(filename, 'w') as f:
f.writelines(lines)
# adjust source coordinates
setpar('xs', sx, filename)
setpar('zs', sy, filename)
# setpar('ts', ts[0], filename)
# adjust source amplitude
try:
fs = float(getpar('factor', filename))
fs *= ws
setpar('factor', str(fs), filename)
except:
pass
# adjust source wavelet
if 1:
# Ricker wavelet
setpar('time_function_type', 1, filename)
elif 0:
# first derivative of Gaussian
setpar('time_function_type', 2, filename)
elif 0:
# Gaussian
setpar('time_function_type', 3, filename)
elif 0:
# Dirac
setpar('time_function_type', 4, filename)
elif 0:
# Heaviside
setpar('time_function_type', 5, filename)