def generate_mesh(self,
model_path=None,
model_name=None,
model_type='gll'):
""" Performs meshing and database generation
"""
assert (model_name)
assert (model_type)
self.initialize_solver_directories()
unix.cd(self.cwd)
if model_type == 'gll':
assert (exists(model_path))
self.check_mesh_properties(model_path)
unix.cp(glob(model_path + '/' + '*'), self.model_databases)
call_solver(system.mpiexec(), 'bin/xmeshfem3D')
if self.taskid == 0:
self.export_model(PATH.OUTPUT + '/' + model_name)
else:
raise NotImplementedError
def smooth(self, input_path='', output_path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
files = []
files += glob(PATH.MODEL_INIT + '/proc??????_x.bin')
files += glob(PATH.MODEL_INIT + '/proc??????_z.bin')
files += glob(PATH.MODEL_INIT + '/proc??????_NSPEC_ibool.bin')
files += glob(PATH.MODEL_INIT + '/proc??????_jacobian.bin')
for file in files:
unix.cp(file, input_path)
for name in parameters or self.parameters:
print(' smoothing', name)
call_solver(system.mpiexec(),
PATH.SPECFEM_BIN + '/' + 'xsmooth_sem ' + str(span) +
' ' + str(span) + ' ' + name + '_kernel' + ' ' +
input_path + '/ ' + output_path + '/ F',
output=output_path + '/smooth_' + name + '.log')
print('')
# rename output files
files = glob(output_path + '/*')
unix.rename('_smooth', '', files)
def combine(self, input_path='', output_path='', parameters=[]):
""" Sums individual source contributions. Wrapper over xcombine_sem
utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
unix.cd(self.cwd)
names = self.check_source_names()
subset = [names[isrc] for isrc in self._source_subset]
with open('kernel_paths', 'w') as f:
f.writelines([join(input_path, dir) + '\n' for dir in subset])
# SAGA component - include contributions from reference gradient
remainder = list(set(self._source_names) - set(subset))
with open('kernel_paths', 'a') as f:
f.writelines(
[join(PATH.GRAD_AGG, dir) + '\n' for dir in remainder])
for name in parameters or self.parameters:
call_solver(
system.mpiexec(), PATH.SPECFEM_BIN + '/' + 'xcombine_sem ' +
name + '_kernel' + ' ' + 'kernel_paths' + ' ' + output_path)
def combine_vol_data(self, output_path='', quantity=''):
"""
This does not work
Call Specfems executable combine_vol_data_vtk on kernels or model files
"""
if not exists(output_path):
unix.mkdir(output_path)
# This should probably be moved to its own function
# def import_kernels()
unix.cd(self.cwd)
src = glob(join(PATH.GRAD, self.source_name, "*{}*".format(quantity)))
dst = join(self.cwd, "kernels")
unix.mkdir(dst)
unix.ln(src=src, dst=dst)
solver_call = " ".join([
PATH.SPECFEM_BIN + '/' + 'xcombine_vol_data_vtk',
0, # NPROC_START
PAR.NPROC, # NPROC_END
quantity, # QUANTITY
dst, # DIR_IN
dst, # DIR_OUT, we will rename the files first
0 # GPU ACCEL
])
call_solver(system_mpiexec(), solver_call)
unix.rm(dst)
print ''
def smooth(self, input_path='', output_path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
for name in parameters or self.parameters:
print ' smoothing', name
call_solver(system.mpiexec(),
PATH.SPECFEM_BIN + '/' + 'xsmooth_sem ' + str(span) +
' ' + str(span) + ' ' + name + '_kernel' + ' ' +
input_path + '/ ' + output_path + '/ ',
output='/dev/null')
print ''
# rename output files
files = glob(output_path + '/*')
unix.rename('_smooth', '', files)
def generate_mesh(self, model_path=None, model_name=None, model_type='gll'):
""" Performs meshing and database generation
"""
assert(model_name)
assert(model_type)
self.initialize_solver_directories()
unix.cd(self.cwd)
if model_type in ['gll']:
par = getpar('MODEL').strip()
if par != 'gll':
if self.taskid == 0:
print 'WARNING: Unexpected Par_file setting:'
print 'MODEL =', par
assert(exists(model_path))
self.check_mesh_properties(model_path)
src = glob(model_path +'/'+ '*')
dst = self.model_databases
unix.cp(src, dst)
call_solver(system.mpiexec(), 'bin/xmeshfem3D')
call_solver(system.mpiexec(), 'bin/xgenerate_databases')
if self.taskid == 0:
self.export_model(PATH.OUTPUT +'/'+ model_name)
else:
raise NotImplementedError
def generate_mesh(self,
model_path=None,
model_name=None,
model_type='gll'):
""" Performs meshing and database generation
"""
print 'specfem3d_nz.generate mesh'
assert (model_name)
assert (model_type)
unix.cd(self.cwd)
if model_type in ['gll']:
par = getpar('MODEL').strip()
if par != 'gll':
if self.taskid == 0:
print 'WARNING: Unexpected Par_file setting:'
print 'MODEL =', par
assert (exists(model_path))
self.check_mesh_properties(model_path)
src = glob(model_path + '/' + '*')
dst = self.model_databases
unix.cp(src, dst)
call_solver(system.mpiexec(), 'bin/xgenerate_databases')
if self.taskid == 0:
self.export_model(PATH.OUTPUT + '/' + model_name)
else:
raise NotImplementedError
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 smooth(self, input_path='', output_path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
for name in parameters or self.parameters:
print ' smoothing', name
call_solver(
system.mpiexec(),
PATH.SPECFEM_BIN +'/'+ 'xsmooth_sem '
+ str(span) + ' '
+ str(span) + ' '
+ name + '_kernel' + ' '
+ input_path + '/ '
+ output_path + '/ ',
output='/dev/null')
print ''
# rename output files
files = glob(output_path+'/*')
unix.rename('_smooth', '', files)
def combine(self, input_path='', output_path='', parameters=[]):
""" Sums individual source contributions. Wrapper over xcombine_sem
utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
unix.cd(self.cwd)
names = self.check_source_names()
subset = [names[isrc] for isrc in self._source_subset]
with open('kernel_paths', 'w') as f:
f.writelines([join(input_path, dir)+'\n' for dir in subset])
# SAGA component - include contributions from reference gradient
remainder = list(set(self._source_names) - set(subset))
with open('kernel_paths', 'a') as f:
f.writelines([join(PATH.GRAD_AGG, dir)+'\n' for dir in remainder])
for name in parameters or self.parameters:
call_solver(
system.mpiexec(),
PATH.SPECFEM_BIN +'/'+ 'xcombine_sem '
+ name + '_kernel' + ' '
+ 'kernel_paths' + ' '
+ output_path)
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 adjoint(self):
""" Calls SPECFEM3D_GLOBE adjoint solver
"""
solvertools.setpar('SIMULATION_TYPE', '3')
solvertools.setpar('SAVE_FORWARD', '.false.')
unix.rm('SEM')
unix.ln('traces/adj', 'SEM')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
def adjoint(self):
""" Calls SPECFEM3D_GLOBE adjoint solver
"""
solvertools.setpar('SIMULATION_TYPE', '3')
solvertools.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_GLOBE forward solver
"""
solvertools.setpar('SIMULATION_TYPE', '1')
solvertools.setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
if PAR.FORMAT in ['ASCII', 'ascii']:
src = glob('OUTPUT_FILES/*.sem.ascii')
dst = path
unix.mv(src, dst)
def forward(self, path='traces/syn'):
""" Calls SPECFEM3D_GLOBE forward solver
"""
solvertools.setpar('SIMULATION_TYPE', '1')
solvertools.setpar('SAVE_FORWARD', '.true.')
call_solver(system.mpiexec(), 'bin/xspecfem3D')
if PAR.FORMAT in ['ASCII', 'ascii']:
src = glob('OUTPUT_FILES/*.sem.ascii')
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 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_att(self):
""" Calls SPECFEM2D adjoint solver
"""
unix.rm('SEM')
unix.ln('traces/adj_att', '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_att/*.su')
unix.rename('.su', '.su.adj', files)
call_solver(system.mpiexec(), 'bin/xspecfem2D')
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 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 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 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 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 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 combine(self, input_path='', output_path='', parameters=[]):
""" Sums individual source contributions. Wrapper over xcombine_sem
utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
unix.cd(self.cwd)
with open('kernel_paths', 'w') as file:
file.writelines(
[join(input_path, name + '\n') for name in self.source_names])
for name in parameters or self.parameters:
call_solver(
system.mpiexec(), PATH.SPECFEM_BIN + '/' + 'xcombine_sem ' +
name + '_kernel' + ' ' + 'kernel_paths' + ' ' + output_path)
def smooth(self, input_path='', output_path='', parameters=[], span=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
src = '/scratch/gpfs/etienneb/2D_inversion_80_elem/model_init80/proc000000_x.bin'
dst = '/scratch/gpfs/etienneb/2D_inversion_80_elem/scratch/evalgrad/kernels/sum_nosmooth'
unix.cp(src, dst)
src = '/scratch/gpfs/etienneb/2D_inversion_80_elem/model_init80/proc000000_z.bin'
unix.cp(src, dst)
src = '/scratch/gpfs/etienneb/2D_inversion_80_elem/model_init80/proc000000_NSPEC_ibool.bin'
unix.cp(src, dst)
src = '/scratch/gpfs/etienneb/2D_inversion_80_elem/model_init80/proc000000_jacobian.bin'
unix.cp(src, dst)
print input_path
for name in parameters or self.parameters:
print ' smoothing', name
call_solver(
system.mpiexec(),
PATH.SPECFEM_BIN +'/'+ 'xsmooth_sem '
+ str(span) + ' '
+ str(span) + ' '
+ name + '_kernel' + ' '
+ input_path + '/ '
+ output_path + '/ T',
output='/scratch/gpfs/etienneb/2D_inversion_80_elem/smooth_output.log')
print ''
# rename output files
files = glob(output_path+'/*')
unix.rename('_smooth', '', files)
def combine(self, input_path='', output_path='', parameters=[]):
""" Sums individual source contributions. Wrapper over xcombine_sem
utility.
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
unix.cd(self.cwd)
with open('kernel_paths', 'w') as file:
file.writelines([join(input_path, name+'\n')
for name in self.source_names])
for name in parameters or self.parameters:
call_solver(
system.mpiexec(),
PATH.SPECFEM_BIN +'/'+ 'xcombine_sem '
+ name + '_kernel' + ' '
+ 'kernel_paths' + ' '
+ output_path)
def generate_mesh(self, model_path=None, model_name=None, model_type='gll'):
""" Performs meshing and database generation
"""
assert(model_name)
assert(model_type)
self.initialize_solver_directories()
unix.cd(self.cwd)
if model_type == 'gll':
assert (exists(model_path))
self.check_mesh_properties(model_path)
unix.cp(glob(model_path +'/'+ '*'), self.model_databases)
call_solver(system.mpiexec(), 'bin/xmeshfem3D')
if self.taskid == 0:
self.export_model(PATH.OUTPUT +'/'+ model_name)
else:
raise NotImplementedError
def smooth(self,
input_path='',
output_path='',
parameters=[],
span_h=0.,
span_v=0.):
""" Smooths kernels by convolving them with a Gaussian. Wrapper over
xsmooth_sem utility.
smooth() in base.py has the incorrect command line call, specfem
requires that NPROC be specified
"""
if not exists(input_path):
raise Exception
if not exists(output_path):
unix.mkdir(output_path)
# apply smoothing operator
unix.cd(self.cwd)
print 'smoothing parameters ', self.parameters
for name in parameters or self.parameters:
print 'smoothing', name
solver_call = " ".join([
PATH.SPECFEM_BIN + '/' + 'xsmooth_sem', # ./bin/xsmooth_sem
str(span_h), # SIGMA_H
str(span_v), # SIGMA_V
name + '_kernel', # KERNEL_NAME
input_path + '/', # INPUT_DIR
output_path + '/', # OUTPUT_DIR
'.false' # USE_GPU
])
call_solver(system.mpiexec(), solver_call)
print ''
# rename output files
files = glob(output_path + '/*')
unix.rename('_smooth', '', files)