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models.py
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models.py
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import numpy as np
import warnings
from sympy import finite_diff_weights as fd_w
from devito import (Grid, Function, SubDomain, SubDimension, Eq, Inc,
Operator, mmin, mmax, initialize_function, switchconfig,
Abs, sqrt, sin)
from devito.data.allocators import ExternalAllocator
from devito.tools import as_tuple, memoized_func
__all__ = ['Model']
def getmin(f):
try:
return mmin(f)
except ValueError:
return np.min(f)
def getmax(f):
try:
return mmax(f)
except ValueError:
return np.max(f)
_thomsen = [('epsilon', 1), ('delta', 1), ('theta', 0), ('phi', 0)]
class PhysicalDomain(SubDomain):
name = 'nofsdomain'
def __init__(self, so, fs=False):
super(PhysicalDomain, self).__init__()
self.so = so
self.fs = fs
def define(self, dimensions):
map_d = {d: d for d in dimensions}
if self.fs:
map_d[dimensions[-1]] = ('middle', self.so, 0)
return map_d
class FSDomain(SubDomain):
name = 'fsdomain'
def __init__(self, so):
super(FSDomain, self).__init__()
self.size = so
def define(self, dimensions):
"""
Definition of the top part of the domain for wrapped indices FS
"""
z = dimensions[-1]
map_d = {d: d for d in dimensions}
map_d.update({z: ('left', self.size)})
return map_d
@memoized_func
def damp_op(ndim, padsizes, abc_type, fs):
"""
Create damping field initialization operator.
Parameters
----------
padsize : List of tuple
Number of points in the damping layer for each dimension and side.
spacing :
Grid spacing coefficient.
mask : bool, optional
whether the dampening is a mask or layer.
mask => 1 inside the domain and decreases in the layer
not mask => 0 inside the domain and increase in the layer
"""
damp = Function(name="damp", grid=Grid(tuple([11]*ndim)), space_order=0)
eqs = [Eq(damp, 1.0 if abc_type == "mask" else 0.0)]
for (nbl, nbr), d in zip(padsizes, damp.dimensions):
# 3 Point buffer to avoid weird interaction with abc
nbr = nbr - 3
if not fs or d is not damp.dimensions[-1]:
nbl = nbl - 3
dampcoeff = 1.5 * np.log(1.0 / 0.001) / (nbl)
# left
dim_l = SubDimension.left(name='abc_%s_l' % d.name, parent=d,
thickness=nbl)
pos = Abs((nbl - (dim_l - d.symbolic_min) + 1) / float(nbl))
val = dampcoeff * (pos - sin(2*np.pi*pos)/(2*np.pi))
val = -val if abc_type == "mask" else val
eqs += [Inc(damp.subs({d: dim_l}), val/d.spacing)]
# right
dampcoeff = 1.5 * np.log(1.0 / 0.001) / (nbr)
dim_r = SubDimension.right(name='abc_%s_r' % d.name, parent=d,
thickness=nbr)
pos = Abs((nbr - (d.symbolic_max - dim_r) + 1) / float(nbr))
val = dampcoeff * (pos - sin(2*np.pi*pos)/(2*np.pi))
val = -val if abc_type == "mask" else val
eqs += [Inc(damp.subs({d: dim_r}), val/d.spacing)]
return Operator(eqs, name='initdamp')
@switchconfig(log_level='ERROR')
def initialize_damp(damp, padsizes, abc_type="damp", fs=False):
"""
Initialise damping field with an absorbing boundary layer.
Includes basic constant Q setup (not interfaced yet) and assumes that
the peak frequency is 1/(10 * spacing).
Parameters
----------
damp : Function
The damping field for absorbing boundary condition.
nbl : int
Number of points in the damping layer.
spacing :
Grid spacing coefficient.
mask : bool, optional
whether the dampening is a mask or layer.
mask => 1 inside the domain and decreases in the layer
not mask => 0 inside the domain and increase in the layer
"""
op = damp_op(damp.grid.dim, padsizes, abc_type, fs)
op(damp=damp)
class Model(object):
"""
The physical model used in seismic inversion
shape_pml = np.array(shape) + 2 * self.nbl processes.
Parameters
----------
origin : tuple of floats
Origin of the model in m as a tuple in (x,y,z) order.
spacing : tuple of floats
Grid size in m as a Tuple in (x,y,z) order.
shape : tuple of int
Number of grid points size in (x,y,z) order.
space_order : int
Order of the spatial stencil discretisation.
m : array_like or float
Squared slownes in s^2/km^2
nbl : int, optional
The number of absorbin layers for boundary damping.
dtype : np.float32 or np.float64
Defaults to 32.
epsilon : array_like or float, optional
Thomsen epsilon parameter (0<epsilon<1).
delta : array_like or float
Thomsen delta parameter (0<delta<1), delta<epsilon.
theta : array_like or float
Tilt angle in radian.
phi : array_like or float
Asymuth angle in radian.
dt: Float
User provided computational time-step
"""
def __init__(self, origin, spacing, shape, space_order=8, nbl=40, dtype=np.float32,
m=None, epsilon=None, delta=None, theta=None, phi=None, rho=None,
b=None, qp=None, lam=None, mu=None, dm=None, fs=False, **kwargs):
# Setup devito grid
self.shape = tuple(shape)
self.nbl = int(nbl)
self.origin = tuple([dtype(o) for o in origin])
abc_type = "mask" if (qp is not None or mu is not None) else "damp"
self.fs = fs
# Origin of the computational domain with boundary to inject/interpolate
# at the correct index
origin_pml = [dtype(o - s*nbl) for o, s in zip(origin, spacing)]
shape_pml = np.array(shape) + 2 * self.nbl
if fs:
fsdomain = FSDomain(space_order + 1)
physdomain = PhysicalDomain(space_order + 1, fs=fs)
subdomains = (physdomain, fsdomain)
origin_pml[-1] = origin[-1]
shape_pml[-1] -= self.nbl
else:
subdomains = ()
# Physical extent is calculated per cell, so shape - 1
extent = tuple(np.array(spacing) * (shape_pml - 1))
self.grid = Grid(extent=extent, shape=shape_pml, origin=tuple(origin_pml),
dtype=dtype, subdomains=subdomains)
# Absorbing boundary layer
if self.nbl != 0:
# Create dampening field as symbol `damp`
self.damp = Function(name="damp", grid=self.grid, space_order=0)
initialize_damp(self.damp, self.padsizes, abc_type=abc_type, fs=fs)
self._physical_parameters = ['damp']
else:
self.damp = 1
self._physical_parameters = []
# Seismic fields and properties
self.scale = 1
self._space_order = space_order
# Create square slowness of the wave as symbol `m`
if m is not None:
self._m = self._gen_phys_param(m, 'm', space_order)
# density
self._init_density(rho, b, space_order)
self._dm = self._gen_phys_param(dm, 'dm', space_order)
# Model type
self._is_viscoacoustic = qp is not None
self._is_elastic = mu is not None
self._is_tti = any(p is not None for p in [epsilon, delta, theta, phi])
# Additional parameter fields for Viscoacoustic operators
if self._is_viscoacoustic:
self.qp = self._gen_phys_param(qp, 'qp', space_order)
# Additional parameter fields for TTI operators
if self._is_tti:
epsilon = 1 if epsilon is None else 1 + 2 * epsilon
delta = 1 if delta is None else 1 + 2 * delta
self.epsilon = self._gen_phys_param(epsilon, 'epsilon', space_order)
self.scale = np.sqrt(np.max(epsilon))
self.delta = self._gen_phys_param(delta, 'delta', space_order)
self.theta = self._gen_phys_param(theta, 'theta', space_order)
if self.grid.dim == 3:
self.phi = self._gen_phys_param(phi, 'phi', space_order)
# Additional parameter fields for elastic
if self._is_elastic:
self.lam = self._gen_phys_param(lam, 'lam', space_order, is_param=True)
self.mu = self._gen_phys_param(mu, 'mu', space_order, is_param=True)
# User provided dt
self._dt = kwargs.get('dt')
def _init_density(self, rho, b, so):
"""
Initialize density parameter. Depending on variance in density
either density or inverse density is setup.
"""
if rho is not None:
rm, rM = np.amin(rho), np.amax(rho)
if rm/rM > .1:
self.irho = self._gen_phys_param(np.reciprocal(rho), 'irho', so)
self.rho = 1 / self.irho
else:
self.rho = self._gen_phys_param(rho, 'rho', so)
self.irho = 1 / self.rho
elif b is not None:
self.irho = self._gen_phys_param(b, 'irho', so)
else:
self.irho = 1
@property
def padsizes(self):
padsizes = [(self.nbl, self.nbl) for _ in range(self.dim-1)]
padsizes.append((0 if self.fs else self.nbl, self.nbl))
return tuple(p for p in padsizes)
def physical_params(self, **kwargs):
"""
Return all set physical parameters and update to input values if provided
"""
params = {i: kwargs.get(i, getattr(self, i)) for i in self.physical_parameters
if isinstance(getattr(self, i), Function)}
if not kwargs.get('born', False):
params.pop('dm', None)
return params
@property
def zero_thomsen(self):
out = {}
for (t, v) in _thomsen:
try:
out.update({getattr(self, t): v})
except AttributeError:
pass
return out
@switchconfig(log_level='ERROR')
def _gen_phys_param(self, field, name, space_order, is_param=False,
default_value=0):
"""
Create symbolic object an initiliaze its data
"""
if field is None:
return default_value
if isinstance(field, np.ndarray) and (name == 'm' or
np.min(field) != np.max(field)):
if field.shape == self.shape:
function = Function(name=name, grid=self.grid, space_order=space_order,
parameter=is_param)
initialize_function(function, field, self.padsizes)
else:
# We take advantage of the external allocator
function = Function(name=name, grid=self.grid, space_order=space_order,
allocator=ExternalAllocator(field),
initializer=lambda x: None, parameter=is_param)
else:
return np.amin(field)
self._physical_parameters.append(name)
return function
@property
def physical_parameters(self):
"""
List of physical parameteres
"""
return as_tuple(self._physical_parameters)
@property
def dim(self):
"""
Spatial dimension of the problem and model domain.
"""
return self.grid.dim
@property
def spacing(self):
"""
Grid spacing for all fields in the physical model.
"""
return self.grid.spacing
@property
def space_dimensions(self):
"""
Spatial dimensions of the grid
"""
return self.grid.dimensions
@property
def dtype(self):
"""
Data type for all assocaited data objects.
"""
return self.grid.dtype
@property
def domain_size(self):
"""
Physical size of the domain as determined by shape and spacing
"""
return tuple((d-1) * s for d, s in zip(self.shape, self.spacing))
@property
def space_order(self):
"""
Spatial discretization order
"""
return self._space_order
@property
def dt(self):
"""
User provided dt
"""
return self._dt
@dt.setter
def dt(self, dt):
"""
Set user provided dt to overwrite the default CFL value.
"""
self._dt = dt
@property
def is_tti(self):
"""
Whether the model is TTI or isotopic
"""
return self._is_tti
@property
def is_viscoacoustic(self):
"""
Whether the model is TTI or isotopic
"""
return self._is_viscoacoustic
@property
def is_elastic(self):
"""
Whether the model is TTI or isotopic
"""
return self._is_elastic
@property
def _max_vp(self):
"""
Maximum velocity
"""
if self.is_elastic:
return np.sqrt(getmin(self.irho) * (getmax(self.lam) + 2 * getmax(self.mu)))
else:
return np.sqrt(1./getmin(self.m))
@property
def _cfl_coeff(self):
"""
Courant number from the physics and spatial discretization order.
The CFL coefficients are described in:
- https://doi.org/10.1137/0916052 for the elastic case
- https://library.seg.org/doi/pdf/10.1190/1.1444605 for the acoustic case
"""
# Elasic coefficient (see e.g )
if self.is_elastic:
so = max(self._space_order // 2, 2)
coeffs = fd_w(1, range(-so, so), .5)
c_fd = sum(np.abs(coeffs[-1][-1])) / 2
return .9 * np.sqrt(self.dim) / self.dim / c_fd
a1 = 4 # 2nd order in time
so = max(self._space_order // 2, 4)
coeffs = fd_w(2, range(-so, so), 0)[-1][-1]
return .9 * np.sqrt(a1/float(self.grid.dim * sum(np.abs(coeffs))))
@property
def _thomsen_scale(self):
# Update scale for tti
if self.is_tti:
return np.sqrt(1 + 2 * getmax(self.epsilon))
return 1
@property
def critical_dt(self):
"""
Critical computational time step value from the CFL condition.
"""
# For a fixed time order this number decreases as the space order increases.
#
# The CFL condtion is then given by
# dt <= coeff * h / (max(velocity))
dt = self._cfl_coeff * np.min(self.spacing) / (self._thomsen_scale*self._max_vp)
dt = self.dtype("%.3e" % dt)
if self.dt:
if self.dt > dt:
warnings.warn("Provided dt=%s is bigger than maximum stable dt %s "
% (self.dt, dt))
else:
return self.dtype("%.3e" % self.dt)
return dt
@property
def dm(self):
"""
Model perturbation for linearized modeling
"""
return self._dm
@dm.setter
def dm(self, dm):
"""
Set a new model perturbation.
Parameters
----------
dm : float or array
New model perturbation
"""
# Update the square slowness according to new value
if isinstance(dm, np.ndarray):
if not isinstance(self._dm, Function):
self._dm = self._gen_phys_param(dm, 'dm', self.space_order)
elif dm.shape == self.shape:
initialize_function(self._dm, dm, self.padsizes)
elif dm.shape == self.dm.shape:
self.dm.data[:] = dm[:]
else:
raise ValueError("Incorrect input size %s for model of size" % dm.shape +
" %s without or %s with padding" % (self.shape,
self.dm.shape))
else:
try:
self._dm.data = dm
except AttributeError:
self._dm = dm
@property
def m(self):
"""
Function holding the squared slowness in s^2/km^2.
"""
return self._m
@m.setter
def m(self, m):
"""
Set a new squared slowness model.
Parameters
----------
m : float or array
New squared slowness in s^2/km^2.
"""
# Update the square slowness according to new value
if isinstance(m, np.ndarray):
if m.shape == self.m.shape:
self.m.data[:] = m[:]
elif m.shape == self.shape:
initialize_function(self._m, m, self.padsizes)
else:
raise ValueError("Incorrect input size %s for model of size" % m.shape +
" %s without or %s with padding" % (self.shape,
self.m.shape))
else:
self._m.data = m
@property
def vp(self):
"""
Symbolic representation of the velocity
vp = sqrt(1 / m)
"""
return sqrt(1 / self.m)
@property
def spacing_map(self):
"""
Map between spacing symbols and their values for each `SpaceDimension`.
"""
sp_map = self.grid.spacing_map
sp_map.update({self.grid.time_dim.spacing: self.critical_dt})
return sp_map
class EmptyModel(object):
"""
An pseudo Model structure that does not contain any physical field
but only the necessary information to create an operator.
This Model should not be used for propagation.
"""
def __init__(self, tti, visco, elastic, spacing, fs, space_order, p_params):
self.is_tti = tti
self.is_viscoacoustic = visco
self.is_elastic = elastic
self.spacing = spacing
self.fs = fs
N = 2 * space_order + 1
if fs:
fsdomain = FSDomain(N)
physdomain = PhysicalDomain(N, fs=fs)
subdomains = (physdomain, fsdomain)
else:
subdomains = ()
self.grid = Grid(tuple([N]*len(spacing)),
extent=[s*(N-1) for s in spacing],
subdomains=subdomains)
self.dimensions = self.grid.dimensions
# Create the function for the physical parameters
self.damp = Function(name='damp', grid=self.grid, space_order=0)
for p in set(p_params) - {'damp'}:
setattr(self, p, Function(name=p, grid=self.grid, space_order=space_order))
if 'irho' not in p_params:
self.irho = 1 if 'rho' not in p_params else 1 / self.rho
@property
def spacing_map(self):
"""
Map between spacing symbols and their values for each `SpaceDimension`.
"""
return self.grid.spacing_map
@property
def critical_dt(self):
"""
User provided dt
"""
return self.grid.time_dim.spacing
@property
def dim(self):
"""
Spatial dimension of the problem and model domain.
"""
return self.grid.dim
@property
def zero_thomsen(self):
out = {}
for (t, v) in _thomsen:
try:
out.update({getattr(self, t): v})
except AttributeError:
pass
return out