def check_solver_parameter_files(self):
""" Checks solver parameters
"""
nt = getpar('nt', cast=int)
dt = getpar('deltat', cast=float)
f0 = getpar('f0', file='DATA/SOURCE', cast=float)
if nt != PAR.NT:
if self.taskid == 0: print("WARNING: nt != PAR.NT")
setpar('nt', PAR.NT)
if dt != PAR.DT:
if self.taskid == 0: print("WARNING: dt != PAR.DT")
setpar('deltat', PAR.DT)
if f0 != PAR.F0:
if self.taskid == 0: print("WARNING: f0 != PAR.F0")
setpar('f0', PAR.F0, filename='DATA/SOURCE')
if self.mesh_properties.nproc != PAR.NPROC:
if self.taskid == 0:
print('Warning: mesh_properties.nproc != PAR.NPROC')
if 'MULTIPLES' in PAR:
if PAR.MULTIPLES:
setpar('absorbtop', '.false.')
else:
setpar('absorbtop', '.true.')
def generate_data(self, **model_kwargs):
""" Generates data (perform meshing and database generation first)
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.cwd)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.false.')
call_solver(system.mpiexec(), 'bin/xmeshfem2D', output='mesher.log')
call_solver(system.mpiexec(), 'bin/xspecfem2D', output='solver.log')
if PAR.FORMAT in ['SU', 'su']:
src = glob('OUTPUT_FILES/*.su')
# work around SPECFEM2D's different file names (depending on the
# version used :
# ?? junliu
# _d?
unix.rename('single_d.su', 'single.su', src)
src = glob('OUTPUT_FILES/*.su')
dst = 'traces/obs'
unix.mv(src, dst)
if PAR.SAVETRACES:
self.export_traces(PATH.OUTPUT + '/' + 'traces/obs')
def generate_mesh(self,
model_path=None,
model_name=None,
model_type='gll'):
""" Performs meshing and database generation
"""
# Assert that the model name and path are not empty
assert (model_name)
assert (model_type)
self.initialize_solver_directories()
unix.cd(self.cwd)
assert (exists(model_path)) # Check that the path exist
# Fill _mesh_properties which contain the number of integration points,
# the number of procs used and the coordinates of the points
self.check_mesh_properties(model_path)
# Copy the model files (ex: proc000023_vp.bin ...) into DATA
# modify by junliu
# it seems that should change the model_type
setpar('MODEL', model_type)
print model_type
src = glob(join(model_path, '*'))
dst = join(self.cwd, 'DATA')
unix.cp(src, dst)
# Export the model into output folder
if self.taskid == 0:
self.export_model(PATH.OUTPUT + '/' + model_name)
def check_solver_parameter_files(self):
""" Checks solver parameters
"""
nt = getpar('nt', cast=int)
dt = getpar('deltat', cast=float)
f0 = getpar('f0', file='DATA/SOURCE', cast=float)
if nt != PAR.NT:
if self.taskid == 0: print "WARNING: nt != PAR.NT"
setpar('nt', PAR.NT)
if dt != PAR.DT:
if self.taskid == 0: print "WARNING: dt != PAR.DT"
setpar('deltat', PAR.DT)
if f0 != PAR.F0:
if self.taskid == 0: print "WARNING: f0 != PAR.F0"
setpar('f0', PAR.F0, filename='DATA/SOURCE')
if self.mesh_properties.nproc != PAR.NPROC:
if self.taskid == 0:
print 'Warning: mesh_properties.nproc != PAR.NPROC'
if 'MULTIPLES' in PAR:
if PAR.MULTIPLES:
setpar('absorbtop', '.false.')
else:
setpar('absorbtop', '.true.')
def write_receivers(self):
unix.cd(self.cwd)
key = 'use_existing_STATIONS'
val = '.true.'
setpar(key, val)
_, h = preprocess.load('traces/obs')
solvertools.write_receivers(h.nr, h.rx, h.rz)
def write_receivers(self):
unix.cd(self.cwd)
key = 'use_existing_STATIONS'
val = '.true.'
setpar(key, val)
_, h = preprocess.load('traces/obs')
solvertools.write_receivers(h.nr, h.rx, h.rz)
def adjoint(self):
""" Calls SPECFEM3D adjoint solver
"""
setpar('SIMULATION_TYPE', '3')
setpar('SAVE_FORWARD', '.false.')
unix.rm('SEM')
unix.ln('traces/adj', 'SEM')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
def adjoint(self):
""" Calls SPECFEM3D adjoint solver
"""
setpar('SIMULATION_TYPE', '3')
setpar('SAVE_FORWARD', '.false.')
unix.rm('SEM')
unix.ln('traces/adj', 'SEM')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
def forward(self, path='traces/syn'):
""" Calls SPECFEM3D forward solver
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xgenerate_databases')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
if PAR.FORMAT in ['SU', 'su']:
src = glob('OUTPUT_FILES/*_d?_SU')
dst = path
unix.mv(src, dst)
def forward(self, path='traces/syn'):
""" Calls SPECFEM2D forward solver
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xmeshfem2D')
call_solver(system.mpiexec(), 'bin/xspecfem2D')
if PAR.FORMAT in ['SU', 'su']:
filenames = glob('OUTPUT_FILES/*.su')
unix.mv(filenames, path)
def forward(self, path='traces/syn'):
""" Calls SPECFEM2D forward solver
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xmeshfem2D')
call_solver(system.mpiexec(), 'bin/xspecfem2D')
if PAR.FORMAT in ['SU', 'su']:
filenames = glob('OUTPUT_FILES/*.su')
unix.mv(filenames, path)
def forward(self, path='traces/syn'):
""" Calls SPECFEM3D forward solver
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xgenerate_databases')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
if PAR.FORMAT in ['SU', 'su']:
src = glob('OUTPUT_FILES/*_d?_SU')
dst = path
unix.mv(src, dst)
def adjoint(self):
""" Calls SPECFEM2D adjoint solver
"""
setpar('SIMULATION_TYPE', '3')
setpar('SAVE_FORWARD', '.false.')
unix.rm('SEM')
unix.ln('traces/adj', 'SEM')
# hack to deal with different SPECFEM2D name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob('traces/adj/*.su')
unix.rename('.su', '.su.adj', files)
call_solver(system.mpiexec(), 'bin/xspecfem2D')
def check_solver_parameter_files(self):
""" Checks solver parameters
"""
found = False
for ntStr in ['NSTEP', 'nt']: # Different specfem conventions
try:
nt = getpar(ntStr, cast=int, noOutput=True)
found = True
except Exception:
pass
if not found:
raise Exception('Not found in Specfem Par_file: NSTEP or nt')
found = False
for dtStr in ['DT', 'deltat']: # Different specfem conventions
try:
dt = getpar(dtStr, cast=float, noOutput=True)
found = True
except Exception:
pass
if not found:
raise Exception('Not found in Specfem Par_file: DT or deltat')
f0 = getpar('f0', file='DATA/SOURCE', cast=float)
if nt != PAR.NT:
if self.taskid == 0:
print "WARNING: nt != PAR.NT", nt, PAR.NT
setpar('nt', PAR.NT)
if dt != PAR.DT:
if self.taskid == 0:
print "WARNING: dt != PAR.DT", dt, PAR.DT
setpar('deltat', PAR.DT)
if f0 != PAR.F0:
if self.taskid == 0:
print "WARNING: f0 != PAR.F0"
setpar('f0', PAR.F0, filename='DATA/SOURCE')
if self.mesh_properties.nproc != PAR.NPROC:
if self.taskid == 0:
print 'Warning: mesh_properties.nproc != PAR.NPROC'
if 'MULTIPLES' in PAR:
if PAR.MULTIPLES:
setpar('absorbtop', '.false.')
else:
setpar('absorbtop', '.true.')
def adjoint(self):
""" Calls SPECFEM2D adjoint solver
"""
setpar('SIMULATION_TYPE', '3')
setpar('SAVE_FORWARD', '.false.')
unix.rm('SEM')
unix.ln('traces/adj', 'SEM')
# hack to deal with different SPECFEM2D name conventions for
# regular traces and 'adjoint' traces
if PAR.FORMAT in ['SU', 'su']:
files = glob('traces/adj/*.su')
unix.rename('.su', '.su.adj', files)
call_solver(system.mpiexec(), 'bin/xmeshfem2D')
call_solver(system.mpiexec(), 'bin/xspecfem2D')
def forward(self, path='traces/syn'):
""" Calls SPECFEM2D forward solver
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xmeshfem2D')
call_solver(system.mpiexec(), 'bin/xspecfem2D')
if PAR.FORMAT in ['SU', 'su']:
filenames = glob('OUTPUT_FILES/*.su')
# work around SPECFEM2D's different file names (depending on the
# version used :
unix.rename('single_p.su', 'single.su', filenames)
filenames = glob('OUTPUT_FILES/*.su')
unix.mv(filenames, path)
def generate_data(self, **model_kwargs):
""" Generates data
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.cwd)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
if PAR.FORMAT in ['ASCII', 'ascii']:
src = glob('OUTPUT_FILES/*.sem.ascii')
dst = 'traces/obs'
unix.mv(src, dst)
if PAR.SAVETRACES:
self.export_traces(PATH.OUTPUT+'/'+'traces/obs')
def generate_data(self, **model_kwargs):
""" Generates data
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.cwd)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
if PAR.FORMAT in ['ASCII', 'ascii']:
src = glob('OUTPUT_FILES/*.sem.ascii')
dst = 'traces/obs'
unix.mv(src, dst)
if PAR.SAVETRACES:
self.export_traces(PATH.OUTPUT + '/' + 'traces/obs')
def generate_data(self, **model_kwargs):
""" Generates data
"""
self.generate_mesh(**model_kwargs)
unix.cd(self.cwd)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.false.')
call_solver(system.mpiexec(), 'bin/xmeshfem2D', output='mesher.log')
call_solver(system.mpiexec(), 'bin/xspecfem2D')
if PAR.FORMAT in ['SU', 'su']:
src = glob('OUTPUT_FILES/*.su')
dst = 'traces/obs'
unix.mv(src, dst)
if PAR.SAVETRACES:
self.export_traces(PATH.OUTPUT + '/' + 'traces/obs')
def check_solver_parameter_files(self):
""" Checks solver parameters
"""
nt = getpar('NSTEP', cast=int)
dt = getpar('DT', cast=float)
if nt != PAR.NT:
if self.taskid == 0: print "WARNING: nt != PAR.NT"
setpar('NSTEP', PAR.NT)
if dt != PAR.DT:
if self.taskid == 0: print "WARNING: dt != PAR.DT"
setpar('DT', PAR.DT)
if self.mesh_properties.nproc != PAR.NPROC:
if self.taskid == 0:
print 'Warning: mesh_properties.nproc != PAR.NPROC'
if 'MULTIPLES' in PAR:
raise NotImplementedError
def check_solver_parameter_files(self):
""" Checks solver parameters
"""
nt = getpar('NSTEP', cast=int)
dt = getpar('DT', cast=float)
if nt != PAR.NT:
if self.taskid == 0: print "WARNING: nt != PAR.NT"
setpar('NSTEP', PAR.NT)
if dt != PAR.DT:
if self.taskid == 0: print "WARNING: dt != PAR.DT"
setpar('DT', PAR.DT)
if self.mesh_properties.nproc != PAR.NPROC:
if self.taskid == 0:
print 'Warning: mesh_properties.nproc != PAR.NPROC'
if 'MULTIPLES' in PAR:
raise NotImplementedError
def generate_data(self, **model_kwargs):
"""
Generates data in the synthetic-synthetic comparison case.
Not for use in the real-data problem. Differs from specfem3d.nz in that
it automatically calls generate mesh for the true model, rather than
passing them in as kwargs.
"""
# Prepare for the forward simulation
self.generate_mesh(**model_kwargs)
print 'specfem3d_nz.generate data'
unix.cd(self.cwd)
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
setpar('ATTENUATION ', '.true.')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
# seismic unix format
if PAR.FORMAT in ['SU', 'su']:
src = glob('OUTPUT_FILES/*_d?_SU')
dst = 'traces/obs'
unix.mv(src, dst)
# ascii sem output format
elif PAR.FORMAT == "ascii":
src = glob('OUTPUT_FILES/*sem?')
dst = 'traces/obs'
unix.mv(src, dst)
if PAR.SAVETRACES:
self.export_traces(PATH.OUTPUT + '/' + 'traces/obs')
def write_sources(PAR, h, path='.'):
""" Writes source information to text file
"""
file = findpath('sesiflows.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 forward(self, path='traces/syn'):
""" Calls SPECFEM3D forward solver and then moves files into path
"""
setpar('SIMULATION_TYPE', '1')
setpar('SAVE_FORWARD', '.true.')
setpar('ATTENUATION ', '.true.')
call_solver(system.mpiexec(), 'bin/xgenerate_databases')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
# seismic unix output format
if PAR.FORMAT in ['SU', 'su']:
src = glob('OUTPUT_FILES/*_d?_SU')
dst = path
unix.mv(src, dst)
# ascii sem output format
elif PAR.FORMAT == "ascii":
src = glob('OUTPUT_FILES/*sem?')
dst = path
unix.mv(src, dst)
def write_sources(coords, path='.', ws=1., suffix=''):
""" Writes source information to text file
"""
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)
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)
