def __init__(self,
tfml_file,
system_name='magma',
p_name='Pressure',
f_name='Porosity',
c_name='c',
n_name='n',
m_name='m',
d_name='d',
N_name='N',
h_squared_name='h_squared',
x0_name='x0'):
"""read the tfml_file and use libspud to populate the internal parameters
c: wavespeed
n: permeability exponent
m: bulk viscosity exponent
d: wave dimension
N: number of collocation points
x0: coordinate wave peak
h_squared: the size of the system in compaction lengths
squared (h/delta)**2
"""
# initialize libspud and extract parameters
libspud.clear_options()
libspud.load_options(tfml_file)
# get model dimension
self.dim = libspud.get_option("/geometry/dimension")
self.system_name = system_name
# get solitary wave parameters
path = "/system::" + system_name + "/coefficient::"
scalar_value = "/type::Constant/rank::Scalar/value::WholeMesh/constant"
vector_value = "/type::Constant/rank::Vector/value::WholeMesh/constant::dim"
c = libspud.get_option(path + c_name + scalar_value)
n = int(libspud.get_option(path + n_name + scalar_value))
m = int(libspud.get_option(path + m_name + scalar_value))
d = float(libspud.get_option(path + d_name + scalar_value))
N = int(libspud.get_option(path + N_name + scalar_value))
self.h = np.sqrt(
libspud.get_option(path + h_squared_name + scalar_value))
self.x0 = np.array(libspud.get_option(path + x0_name + vector_value))
self.swave = SolitaryWave(c, n, m, d, N)
self.rmax = self.swave.r[-1]
self.tfml_file = tfml_file
# check that d <= dim
assert (d <= self.dim)
# sort out appropriate index for calculating distance r
if d == 1:
self.index = [self.dim - 1]
else:
self.index = range(0, int(d))
# check that the origin point is the correct dimension
assert (len(self.x0) == self.dim)
#read in information for constructing Function space and dolfin objects
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option(
"/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option(
"/geometry/mesh[0]/source[0]/diagonal")
mesh = df.UnitSquareMesh(number_cells[0], number_cells[1],
diagonal)
elif meshtype == 'Rectangle':
x0 = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/lower_left")
x1 = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/upper_right")
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/number_cells")
diagonal = libspud.get_option(
"/geometry/mesh[0]/source[0]/diagonal")
mesh = df.RectangleMesh(x0[0], x0[1], x1[0], x1[1],
number_cells[0], number_cells[1], diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option(
"/geometry/mesh[0]/source[0]/number_cells")
mesh = df.UnitCubeMesh(number_cells[0], number_cells[1],
number_cells[2])
elif meshtype == 'Box':
x0 = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/lower_back_left")
x1 = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/upper_front_right")
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/number_cells")
mesh = df.BoxMesh(x0[0], x0[1], x0[2], x1[0], x1[1], x1[2],
number_cells[0], number_cells[1],
number_cells[2])
elif meshtype == 'UnitInterval':
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::UnitInterval/number_cells")
mesh = df.UnitIntervalMesh(number_cells)
elif meshtype == 'Interval':
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/number_cells")
left = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/left")
right = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/right")
mesh = df.IntervalMesh(number_cells, left, right)
elif meshtype == 'File':
mesh_filename = libspud.get_option(
"/geometry/mesh::Mesh/source::File/file")
print "tfml_file = ", self.tfml_file, "mesh_filename=", mesh_filename
mesh = df.Mesh(mesh_filename)
else:
df.error("Error: unknown mesh type " + meshtype)
#set the functionspace for n-d solitary waves
path = "/system::" + system_name + "/field::"
p_family = libspud.get_option(path + p_name +
"/type/rank/element/family")
p_degree = libspud.get_option(path + p_name +
"/type/rank/element/degree")
f_family = libspud.get_option(path + f_name +
"/type/rank/element/family")
f_degree = libspud.get_option(path + f_name +
"/type/rank/element/degree")
pe = df.FiniteElement(p_family, mesh.ufl_cell(), p_degree)
ve = df.FiniteElement(f_family, mesh.ufl_cell(), f_degree)
e = pe * ve
self.functionspace = df.FunctionSpace(mesh, e)
#work out the order of the fields
for i in xrange(
libspud.option_count("/system::" + system_name + "/field")):
name = libspud.get_option("/system::" + system_name + "/field[" +
` i ` + "]/name")
if name == f_name:
self.f_index = i
if name == p_name:
self.p_index = i
class TFSolitaryWave:
""" class for calculating and evaluating solitary wave profiles with data from TerraFERMA .tfml input files
"""
def __init__(self,
tfml_file,
system_name='magma',
p_name='Pressure',
f_name='Porosity',
c_name='c',
n_name='n',
m_name='m',
d_name='d',
N_name='N',
h_squared_name='h_squared',
x0_name='x0'):
"""read the tfml_file and use libspud to populate the internal parameters
c: wavespeed
n: permeability exponent
m: bulk viscosity exponent
d: wave dimension
N: number of collocation points
x0: coordinate wave peak
h_squared: the size of the system in compaction lengths
squared (h/delta)**2
"""
# initialize libspud and extract parameters
libspud.clear_options()
libspud.load_options(tfml_file)
# get model dimension
self.dim = libspud.get_option("/geometry/dimension")
self.system_name = system_name
# get solitary wave parameters
path = "/system::" + system_name + "/coefficient::"
scalar_value = "/type::Constant/rank::Scalar/value::WholeMesh/constant"
vector_value = "/type::Constant/rank::Vector/value::WholeMesh/constant::dim"
c = libspud.get_option(path + c_name + scalar_value)
n = int(libspud.get_option(path + n_name + scalar_value))
m = int(libspud.get_option(path + m_name + scalar_value))
d = float(libspud.get_option(path + d_name + scalar_value))
N = int(libspud.get_option(path + N_name + scalar_value))
self.h = np.sqrt(
libspud.get_option(path + h_squared_name + scalar_value))
self.x0 = np.array(libspud.get_option(path + x0_name + vector_value))
self.swave = SolitaryWave(c, n, m, d, N)
self.rmax = self.swave.r[-1]
self.tfml_file = tfml_file
# check that d <= dim
assert (d <= self.dim)
# sort out appropriate index for calculating distance r
if d == 1:
self.index = [self.dim - 1]
else:
self.index = range(0, int(d))
# check that the origin point is the correct dimension
assert (len(self.x0) == self.dim)
#read in information for constructing Function space and dolfin objects
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option(
"/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option(
"/geometry/mesh[0]/source[0]/diagonal")
mesh = df.UnitSquareMesh(number_cells[0], number_cells[1],
diagonal)
elif meshtype == 'Rectangle':
x0 = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/lower_left")
x1 = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/upper_right")
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/number_cells")
diagonal = libspud.get_option(
"/geometry/mesh[0]/source[0]/diagonal")
mesh = df.RectangleMesh(x0[0], x0[1], x1[0], x1[1],
number_cells[0], number_cells[1], diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option(
"/geometry/mesh[0]/source[0]/number_cells")
mesh = df.UnitCubeMesh(number_cells[0], number_cells[1],
number_cells[2])
elif meshtype == 'Box':
x0 = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/lower_back_left")
x1 = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/upper_front_right")
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/number_cells")
mesh = df.BoxMesh(x0[0], x0[1], x0[2], x1[0], x1[1], x1[2],
number_cells[0], number_cells[1],
number_cells[2])
elif meshtype == 'UnitInterval':
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::UnitInterval/number_cells")
mesh = df.UnitIntervalMesh(number_cells)
elif meshtype == 'Interval':
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/number_cells")
left = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/left")
right = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/right")
mesh = df.IntervalMesh(number_cells, left, right)
elif meshtype == 'File':
mesh_filename = libspud.get_option(
"/geometry/mesh::Mesh/source::File/file")
print "tfml_file = ", self.tfml_file, "mesh_filename=", mesh_filename
mesh = df.Mesh(mesh_filename)
else:
df.error("Error: unknown mesh type " + meshtype)
#set the functionspace for n-d solitary waves
path = "/system::" + system_name + "/field::"
p_family = libspud.get_option(path + p_name +
"/type/rank/element/family")
p_degree = libspud.get_option(path + p_name +
"/type/rank/element/degree")
f_family = libspud.get_option(path + f_name +
"/type/rank/element/family")
f_degree = libspud.get_option(path + f_name +
"/type/rank/element/degree")
pe = df.FiniteElement(p_family, mesh.ufl_cell(), p_degree)
ve = df.FiniteElement(f_family, mesh.ufl_cell(), f_degree)
e = pe * ve
self.functionspace = df.FunctionSpace(mesh, e)
#work out the order of the fields
for i in xrange(
libspud.option_count("/system::" + system_name + "/field")):
name = libspud.get_option("/system::" + system_name + "/field[" +
` i ` + "]/name")
if name == f_name:
self.f_index = i
if name == p_name:
self.p_index = i
def getr(self, x):
""" return radial position with respect to wave origin x0
for solitarywave of dimension d in overall dimension dim
assuming x is a numpy array of points of dimension d"""
# check that x is the right shaped numpy array
if len(x.shape) == 1: # 1-D array
if self.dim == 1:
npnts = x.shape[0]
else:
assert (x.shape == self.x0.shape)
npnts = 1
else: #n-D array
assert (x.shape[-1] == self.x0.shape[0])
npnts = x.shape[0]
if npnts == 1:
dx = x[self.index] - self.x0[self.index]
r = self.h * np.sqrt(np.sum(dx * dx))
else:
dx = x[:, self.index] - self.x0[self.index]
r = self.h * np.sqrt(np.sum(dx * dx, 1))
return r
def eval(self, x):
""" calculate position r given numpy array of x-coordinates
and return appropriate solitary wave amplitude
"""
# calculate radial coordinate r of x
r = self.getr(x)
# check if r is a scalar
if np.isscalar(r):
if r > self.rmax:
f = 1.
else:
f = self.swave.interp(np.array([r]))
else:
f = np.ones(r.shape)
omega = r <= self.rmax # r within collocation domain
f[omega] = self.swave.finterp(r[omega])
return f
def geterrors(self, checkpoint_file):
"""
reads checkpoint file and accompanying .xml solution file and
extracts the time, and calculates shape and phase errors for the solitary waves
"""
# this seems to be a dangerous thing but I'm going to clear
# the option then load the new ones from the checkpoint file
libspud.clear_options()
libspud.load_options(checkpoint_file)
time = libspud.get_option("/timestepping/current_time")
dt = libspud.get_option(
"/timestepping/timestep/coefficient/type/rank/value/constant")
print "t=", time, " dt=", dt
#load xml file
xml_file = checkpoint_file.replace("checkpoint", self.system_name)
xml_file = xml_file.replace("tfml", "xml")
# load function and extract porosity
u = df.Function(self.functionspace, xml_file)
fields = u.split(deepcopy=True)
f = fields[self.f_index]
#initialize Error Object
err = WaveError(f, self.swave, self.x0, self.h)
#minimize error using fsolve
#out = err.min_grad(delta_0)
delta_0 = np.zeros(self.dim)
out = err.min_grad_z(delta_0[-1])
delta = out[0]
err_min = out[1]
elapsed_time = out[2]
L2_f = err.L2_f
rel_error = err_min / L2_f
c_rel_error = np.sign(delta) * np.sqrt(np.dot(
delta, delta)) / (self.swave.c * time)
#print "delta=",delta, " err =",err_min, " elapsed_time=",elapsed_time
#print "L2_f=",L2_f, "rel_err =",rel_error, " c_rel_error=",c_rel_error
#print "L2_error=",err_min," delta=",delta," rel_error=",rel_error," c_rel_error=",c_rel_error
return [time, dt, err_min, delta, rel_error, c_rel_error, elapsed_time]
def __init__(self, tfml_file,system_name='magma',p_name='Pressure',f_name='Porosity',c_name='c',n_name='n',m_name='m',d_name='d',N_name='N',h_squared_name='h_squared',x0_name='x0'):
"""read the tfml_file and use libspud to populate the internal parameters
c: wavespeed
n: permeability exponent
m: bulk viscosity exponent
d: wave dimension
N: number of collocation points
x0: coordinate wave peak
h_squared: the size of the system in compaction lengths
squared (h/delta)**2
"""
# initialize libspud and extract parameters
libspud.clear_options()
libspud.load_options(tfml_file)
# get model dimension
self.dim = libspud.get_option("/geometry/dimension")
self.system_name = system_name
# get solitary wave parameters
path="/system::"+system_name+"/coefficient::"
scalar_value="/type::Constant/rank::Scalar/value::WholeMesh/constant"
vector_value="/type::Constant/rank::Vector/value::WholeMesh/constant::dim"
c = libspud.get_option(path+c_name+scalar_value)
n = int(libspud.get_option(path+n_name+scalar_value))
m = int(libspud.get_option(path+m_name+scalar_value))
d = float(libspud.get_option(path+d_name+scalar_value))
N = int(libspud.get_option(path+N_name+scalar_value))
self.h = np.sqrt(libspud.get_option(path+h_squared_name+scalar_value))
self.x0 = np.array(libspud.get_option(path+x0_name+vector_value))
self.swave = SolitaryWave(c,n,m,d,N)
self.rmax = self.swave.r[-1]
self.tfml_file = tfml_file
# check that d <= dim
assert (d <= self.dim)
# sort out appropriate index for calculating distance r
if d == 1:
self.index = [self.dim - 1]
else:
self.index = range(0,int(d))
# check that the origin point is the correct dimension
assert (len(self.x0) == self.dim)
#read in information for constructing Function space and dolfin objects
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = df.UnitSquareMesh(number_cells[0],number_cells[1],diagonal)
elif meshtype == 'Rectangle':
x0 = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/lower_left")
x1 = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/upper_right")
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = df.RectangleMesh(x0[0],x0[1],x1[0],x1[1],number_cells[0],number_cells[1],diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
mesh = df.UnitCubeMesh(number_cells[0],number_cells[1],number_cells[2])
elif meshtype == 'Box':
x0 = libspud.get_option("/geometry/mesh::Mesh/source::Box/lower_back_left")
x1 = libspud.get_option("/geometry/mesh::Mesh/source::Box/upper_front_right")
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Box/number_cells")
mesh = df.BoxMesh(x0[0],x0[1],x0[2],x1[0],x1[1],x1[2],number_cells[0],number_cells[1],number_cells[2])
elif meshtype == 'UnitInterval':
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::UnitInterval/number_cells")
mesh = df.UnitIntervalMesh(number_cells)
elif meshtype == 'Interval':
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Interval/number_cells")
left = libspud.get_option("/geometry/mesh::Mesh/source::Interval/left")
right = libspud.get_option("/geometry/mesh::Mesh/source::Interval/right")
mesh = df.IntervalMesh(number_cells,left,right)
elif meshtype == 'File':
mesh_filename = libspud.get_option("/geometry/mesh::Mesh/source::File/file")
print "tfml_file = ",self.tfml_file, "mesh_filename=",mesh_filename
mesh = df.Mesh(mesh_filename)
else:
df.error("Error: unknown mesh type "+meshtype)
#set the functionspace for n-d solitary waves
path="/system::"+system_name+"/field::"
p_family = libspud.get_option(path+p_name+"/type/rank/element/family")
p_degree = libspud.get_option(path+p_name+"/type/rank/element/degree")
f_family = libspud.get_option(path+f_name+"/type/rank/element/family")
f_degree = libspud.get_option(path+f_name+"/type/rank/element/degree")
pe = df.FiniteElement(p_family, mesh.ufl_cell(), p_degree)
ve = df.FiniteElement(f_family, mesh.ufl_cell(), f_degree)
e = pe*ve
self.functionspace = df.FunctionSpace(mesh, e)
#work out the order of the fields
for i in xrange(libspud.option_count("/system::"+system_name+"/field")):
name = libspud.get_option("/system::"+system_name+"/field["+`i`+"]/name")
if name == f_name:
self.f_index = i
if name == p_name:
self.p_index = i
pl.hold(False)
# let's calculate w(c) for various waves
N = 300
m = 1
n = 2
nc = 20
c = linspace(1.1*n,10,nc)
Aar = zeros((3,nc))
war = zeros((3,nc))
for d in range(1,4):
print 'd = ',d
print 'c A w'
for i in xrange(len(c)):
sw = SolitaryWave(c[i],n,m,d,N)
A,w = velmax(sw)
Aar[d-1,i] = A
war[d-1,i] = w
print c[i],A,w
pl.figure()
plotvelmax(c,war,n,m)
pl.figure()
plotampmax(c,Aar,n,m)
pl.show()
## quick test script
#d= 2
#m = 1
class TFSolitaryWave:
""" class for calculating and evaluating solitary wave profiles with data from TerraFERMA .tfml input files
"""
def __init__(self, tfml_file,system_name='magma',p_name='Pressure',f_name='Porosity',c_name='c',n_name='n',m_name='m',d_name='d',N_name='N',h_squared_name='h_squared',x0_name='x0'):
"""read the tfml_file and use libspud to populate the internal parameters
c: wavespeed
n: permeability exponent
m: bulk viscosity exponent
d: wave dimension
N: number of collocation points
x0: coordinate wave peak
h_squared: the size of the system in compaction lengths
squared (h/delta)**2
"""
# initialize libspud and extract parameters
libspud.clear_options()
libspud.load_options(tfml_file)
# get model dimension
self.dim = libspud.get_option("/geometry/dimension")
self.system_name = system_name
# get solitary wave parameters
path="/system::"+system_name+"/coefficient::"
scalar_value="/type::Constant/rank::Scalar/value::WholeMesh/constant"
vector_value="/type::Constant/rank::Vector/value::WholeMesh/constant::dim"
c = libspud.get_option(path+c_name+scalar_value)
n = int(libspud.get_option(path+n_name+scalar_value))
m = int(libspud.get_option(path+m_name+scalar_value))
d = float(libspud.get_option(path+d_name+scalar_value))
N = int(libspud.get_option(path+N_name+scalar_value))
self.h = np.sqrt(libspud.get_option(path+h_squared_name+scalar_value))
self.x0 = np.array(libspud.get_option(path+x0_name+vector_value))
self.swave = SolitaryWave(c,n,m,d,N)
self.rmax = self.swave.r[-1]
self.tfml_file = tfml_file
# check that d <= dim
assert (d <= self.dim)
# sort out appropriate index for calculating distance r
if d == 1:
self.index = [self.dim - 1]
else:
self.index = range(0,int(d))
# check that the origin point is the correct dimension
assert (len(self.x0) == self.dim)
#read in information for constructing Function space and dolfin objects
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = df.UnitSquareMesh(number_cells[0],number_cells[1],diagonal)
elif meshtype == 'Rectangle':
x0 = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/lower_left")
x1 = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/upper_right")
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = df.RectangleMesh(x0[0],x0[1],x1[0],x1[1],number_cells[0],number_cells[1],diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
mesh = df.UnitCubeMesh(number_cells[0],number_cells[1],number_cells[2])
elif meshtype == 'Box':
x0 = libspud.get_option("/geometry/mesh::Mesh/source::Box/lower_back_left")
x1 = libspud.get_option("/geometry/mesh::Mesh/source::Box/upper_front_right")
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Box/number_cells")
mesh = df.BoxMesh(x0[0],x0[1],x0[2],x1[0],x1[1],x1[2],number_cells[0],number_cells[1],number_cells[2])
elif meshtype == 'UnitInterval':
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::UnitInterval/number_cells")
mesh = df.UnitIntervalMesh(number_cells)
elif meshtype == 'Interval':
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Interval/number_cells")
left = libspud.get_option("/geometry/mesh::Mesh/source::Interval/left")
right = libspud.get_option("/geometry/mesh::Mesh/source::Interval/right")
mesh = df.IntervalMesh(number_cells,left,right)
elif meshtype == 'File':
mesh_filename = libspud.get_option("/geometry/mesh::Mesh/source::File/file")
print "tfml_file = ",self.tfml_file, "mesh_filename=",mesh_filename
mesh = df.Mesh(mesh_filename)
else:
df.error("Error: unknown mesh type "+meshtype)
#set the functionspace for n-d solitary waves
path="/system::"+system_name+"/field::"
p_family = libspud.get_option(path+p_name+"/type/rank/element/family")
p_degree = libspud.get_option(path+p_name+"/type/rank/element/degree")
f_family = libspud.get_option(path+f_name+"/type/rank/element/family")
f_degree = libspud.get_option(path+f_name+"/type/rank/element/degree")
pe = df.FiniteElement(p_family, mesh.ufl_cell(), p_degree)
ve = df.FiniteElement(f_family, mesh.ufl_cell(), f_degree)
e = pe*ve
self.functionspace = df.FunctionSpace(mesh, e)
#work out the order of the fields
for i in xrange(libspud.option_count("/system::"+system_name+"/field")):
name = libspud.get_option("/system::"+system_name+"/field["+`i`+"]/name")
if name == f_name:
self.f_index = i
if name == p_name:
self.p_index = i
def getr(self,x):
""" return radial position with respect to wave origin x0
for solitarywave of dimension d in overall dimension dim
assuming x is a numpy array of points of dimension d"""
# check that x is the right shaped numpy array
if len(x.shape) == 1: # 1-D array
if self.dim == 1:
npnts = x.shape[0]
else:
assert(x.shape == self.x0.shape)
npnts = 1
else: #n-D array
assert(x.shape[-1] == self.x0.shape[0])
npnts = x.shape[0]
if npnts == 1:
dx = x[self.index] - self.x0[self.index]
r = self.h*np.sqrt(np.sum(dx*dx))
else:
dx = x[:,self.index] - self.x0[self.index]
r = self.h*np.sqrt(np.sum(dx*dx,1))
return r
def eval(self,x):
""" calculate position r given numpy array of x-coordinates
and return appropriate solitary wave amplitude
"""
# calculate radial coordinate r of x
r = self.getr(x)
# check if r is a scalar
if np.isscalar(r):
if r > self.rmax:
f = 1.
else:
f = self.swave.interp(np.array([r]))
else:
f = np.ones(r.shape)
omega = r <= self.rmax # r within collocation domain
f[omega] = self.swave.finterp(r[omega])
return f
def geterrors(self,checkpoint_file):
"""
reads checkpoint file and accompanying .xml solution file and
extracts the time, and calculates shape and phase errors for the solitary waves
"""
# this seems to be a dangerous thing but I'm going to clear
# the option then load the new ones from the checkpoint file
libspud.clear_options()
libspud.load_options(checkpoint_file)
time = libspud.get_option("/timestepping/current_time")
dt = libspud.get_option("/timestepping/timestep/coefficient/type/rank/value/constant")
print "t=",time," dt=", dt
#load xml file
xml_file = checkpoint_file.replace("checkpoint",self.system_name)
xml_file = xml_file.replace("tfml","xml")
# load function and extract porosity
u = df.Function(self.functionspace,xml_file)
fields = u.split(deepcopy = True)
f = fields[self.f_index]
#initialize Error Object
err = WaveError(f,self.swave,self.x0,self.h)
#minimize error using fsolve
#out = err.min_grad(delta_0)
delta_0=np.zeros(self.dim)
out = err.min_grad_z(delta_0[-1])
delta = out[0]
err_min = out[1]
elapsed_time = out[2]
L2_f= err.L2_f
rel_error = err_min/L2_f
c_rel_error = np.sign(delta)*np.sqrt(np.dot(delta,delta))/(self.swave.c*time)
#print "delta=",delta, " err =",err_min, " elapsed_time=",elapsed_time
#print "L2_f=",L2_f, "rel_err =",rel_error, " c_rel_error=",c_rel_error
#print "L2_error=",err_min," delta=",delta," rel_error=",rel_error," c_rel_error=",c_rel_error
return [time,dt,err_min,delta,rel_error,c_rel_error,elapsed_time]