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Merge branch 'master' of https://github.com/simpeg/simpeg into dev

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This commit is contained in:
Rowan Cockett
2016-01-28 22:29:59 -08:00
parent caba2b6752 d7be0ada31
commit 20d5582c0f
11 changed files with 129 additions and 31 deletions
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README.rst
+1 -1
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@@ -17,7 +17,7 @@ SimPEG
:target: https://github.com/simpeg/simpeg/blob/master/LICENSE
:alt: BSD 3 clause license.
.. image:: https://img.shields.io/travis/simpeg/simpeg.svg
.. image:: https://api.travis-ci.org/simpeg/simpeg.svg?branch=master
:target: https://travis-ci.org/simpeg/simpeg
:alt: Travis CI build status
SimPEG/EM/TDEM/BaseTDEM.py
+2 -2
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@@ -31,7 +31,7 @@ class FieldsTDEM(Problem.TimeFields):
class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
"""docstring for ProblemTDEM1D"""
"""docstring for BaseTDEMProblem"""
def __init__(self, mesh, mapping=None, **kwargs):
BaseTimeProblem.__init__(self, mesh, mapping=mapping, **kwargs)
@@ -43,7 +43,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
# Create a fields storage object
F = self._FieldsForward_pair(self.mesh, self.survey)
for src in self.survey.srcList:
# Set the initial conditions
# Set the initial conditions
F[src,:,0] = src.getInitialFields(self.mesh)
F = self.forward(m, self.getRHS, F=F)
if self.verbose: print '%s\nDone calculating fields(m)\n%s'%('*'*50,'*'*50)
SimPEG/EM/TDEM/SurveyTDEM.py
+24 -6
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@@ -99,14 +99,33 @@ class SrcTDEM_VMD_MVP(SrcTDEM):
class SrcTDEM_CircularLoop_MVP(SrcTDEM):
def __init__(self,rxList,loc,radius):
def __init__(self,rxList,loc,radius,waveformType):
self.loc = loc
self.radius = radius
SrcTDEM.__init__(self,rxList)
self.waveformType = waveformType
SrcTDEM.__init__(self,rxList)
def getInitialFields(self, mesh):
"""Circular Loop, magnetic vector potential"""
if self.waveformType == "STEPOFF":
print ">> Step waveform: Non-zero initial condition"
if mesh._meshType is 'CYL':
if mesh.isSymmetric:
MVP = MagneticLoopVectorPotential(self.loc, mesh, 'Ey', self.radius)
else:
raise NotImplementedError('Non-symmetric cyl mesh not implemented yet!')
elif mesh._meshType is 'TENSOR':
MVP = MagneticLoopVectorPotential(self.loc, mesh, ['Ex','Ey','Ez'], self.radius)
else:
raise Exception('Unknown mesh for CircularLoop')
return {"b": mesh.edgeCurl*MVP}
elif self.waveformType == "GENERAL":
print ">> General waveform: Zero initial condition"
return {"b": np.zeros(mesh.nF)}
else:
raise NotImplementedError("Only use STEPOFF or GENERAL")
def getMeS(self, mesh, MfMui):
if mesh._meshType is 'CYL':
if mesh.isSymmetric:
MVP = MagneticLoopVectorPotential(self.loc, mesh, 'Ey', self.radius)
@@ -115,9 +134,8 @@ class SrcTDEM_CircularLoop_MVP(SrcTDEM):
elif mesh._meshType is 'TENSOR':
MVP = MagneticLoopVectorPotential(self.loc, mesh, ['Ex','Ey','Ez'], self.radius)
else:
raise Exception('Unknown mesh for CircularLoop')
return {"b": mesh.edgeCurl*MVP}
raise Exception('Unknown mesh for CircularLoop')
return mesh.edgeCurl.T*MfMui*mesh.edgeCurl*MVP
class SurveyTDEM(Survey.BaseSurvey):
SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
+43
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@@ -0,0 +1,43 @@
from SimPEG import *
import SimPEG.EM as EM
def run(XYZ=None, loc=np.r_[0.,0.,0.], sig=1.0, freq=1.0, orientation='Z', plotIt=True):
"""
EM: Magnetic Dipole in a Whole-Space
====================================
Here we plot the magnetic flux density from a harmonic dipole in a wholespace.
"""
if XYZ is None:
x = np.arange(-100.5,100.5,step = 1.) #(avoid putting measurement points where source is located)
y = np.r_[0]
z = x
XYZ = Utils.ndgrid(x,y,z)
Bx, By, Bz = EM.Analytics.FDEM.MagneticDipoleWholeSpace(XYZ, loc, sig, freq, orientation=orientation)
absB = np.sqrt(Bx*Bx.conj()+By*By.conj()+Bz*Bz.conj()).real
if plotIt:
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
fig, ax = plt.subplots(1,1,figsize=(6,5))
bxplt = Bx.reshape(x.size,z.size)
bzplt = Bz.reshape(x.size,z.size)
pc = ax.pcolor(x,z,absB.reshape(x.size,z.size),norm=LogNorm())
ax.streamplot(x,z,bxplt.real,bzplt.real,color='k',density=1)
ax.set_xlim([x.min(),x.max()])
ax.set_ylim([z.min(),z.max()])
ax.set_xlabel('x')
ax.set_ylabel('z')
cb = plt.colorbar(pc,ax = ax)
cb.set_label('|B| (T)')
plt.show()
return fig, ax
if __name__ == '__main__':
run()
SimPEG/Examples/EM_FDEM_1D_Inversion.py → SimPEG/Examples/EM_TDEM_1D_Inversion.py
+2 -2
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@@ -5,10 +5,10 @@ from scipy.constants import mu_0
def run(plotIt=True):
"""
EM: FDEM: 1D: Inversion
EM: TDEM: 1D: Inversion
=======================
Here we will create and run a FDEM 1D inversion.
Here we will create and run a TDEM 1D inversion.
"""
SimPEG/Examples/__init__.py
+8 -6
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@@ -1,7 +1,8 @@
# Run this file to add imports.
##### AUTOIMPORTS #####
import EM_FDEM_1D_Inversion
import EM_FDEM_Analytic_MagDipoleWholespace
import EM_TDEM_1D_Inversion
import FLOW_Richards_1D_Celia1990
import Forward_BasicDirectCurrent
import Inversion_Linear
@@ -13,7 +14,7 @@ import Mesh_QuadTree_FaceDiv
import Mesh_QuadTree_HangingNodes
import Mesh_Tensor_Creation
__examples__ = ["EM_FDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Forward_BasicDirectCurrent", "Inversion_Linear", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation"]
__examples__ = ["EM_FDEM_Analytic_MagDipoleWholespace", "EM_TDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Forward_BasicDirectCurrent", "Inversion_Linear", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation"]
##### AUTOIMPORTS #####
@@ -28,16 +29,17 @@ if __name__ == '__main__':
from SimPEG import Examples
# Create the examples dir in the docs folder.
docExamplesDir = os.path.sep.join(os.path.realpath(__file__).split(os.path.sep)[:-3] + ['docs', 'examples'])
fName = os.path.realpath(__file__)
docExamplesDir = os.path.sep.join(fName.split(os.path.sep)[:-3] + ['docs', 'examples'])
shutil.rmtree(docExamplesDir)
os.makedirs(docExamplesDir)
# Get all the python examples in this folder
thispath = os.path.sep.join(__file__.split(os.path.sep)[:-1])
thispath = os.path.sep.join(fName.split(os.path.sep)[:-1])
exfiles = [f[:-3] for f in os.listdir(thispath) if os.path.isfile(os.path.join(thispath, f)) and f.endswith('.py') and not f.startswith('_')]
# Add the imports to the top in the AUTOIMPORTS section
f = file(__file__, 'r')
f = file(fName, 'r')
inimports = False
out = ''
for line in f:
@@ -52,7 +54,7 @@ if __name__ == '__main__':
out += '\n##### AUTOIMPORTS #####\n'
f.close()
f = file(__file__, 'w')
f = file(fName, 'w')
f.write(out)
f.close()
SimPEG/Problem.py
+8
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@@ -158,6 +158,9 @@ class BaseProblem(object):
class BaseTimeProblem(BaseProblem):
"""Sets up that basic needs of a time domain problem."""
waveformType = "STEPOFF"
current = None
@property
def timeSteps(self):
@@ -184,6 +187,11 @@ class BaseTimeProblem(BaseProblem):
self._timeSteps = Utils.meshTensor(value)
del self.timeMesh
def currentwaveform(self, wave):
self._timeSteps = np.diff(wave[:,0])
self.current = wave[:,1]
self.waveformType = "GENERAL"
@property
def nT(self):
"Number of time steps."
SimPEG/Regularization.py
+1 -1
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@@ -24,7 +24,7 @@ class BaseRegularization(object):
Utils.setKwargs(self, **kwargs)
self.mesh = mesh
assert isinstance(mesh, Mesh.BaseMesh), "mesh must be a SimPEG.Mesh object."
self.mapping = mapping or Maps.IdentityMap(mesh)
self.mapping = mapping or self.mapPair(mesh)
self.mapping._assertMatchesPair(self.mapPair)
self.indActive = indActive
docs/examples/EM_FDEM_Analytic_MagDipoleWholespace.rst
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@@ -0,0 +1,26 @@
.. _examples_EM_FDEM_Analytic_MagDipoleWholespace:
.. --------------------------------- ..
.. ..
.. THIS FILE IS AUTO GENEREATED ..
.. ..
.. SimPEG/Examples/__init__.py ..
.. ..
.. --------------------------------- ..
EM: Magnetic Dipole in a Whole-Space
====================================
Here we plot the magnetic flux density from a harmonic dipole in a wholespace.
.. plot::
from SimPEG import Examples
Examples.EM_FDEM_Analytic_MagDipoleWholespace.run()
.. literalinclude:: ../../SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
:language: python
:linenos:
docs/examples/EM_FDEM_1D_Inversion.rst → docs/examples/EM_TDEM_1D_Inversion.rst
+5 -5
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@@ -1,4 +1,4 @@
.. _examples_EM_FDEM_1D_Inversion:
.. _examples_EM_TDEM_1D_Inversion:
.. --------------------------------- ..
.. ..
@@ -9,18 +9,18 @@
.. --------------------------------- ..
EM: FDEM: 1D: Inversion
EM: TDEM: 1D: Inversion
=======================
Here we will create and run a FDEM 1D inversion.
Here we will create and run a TDEM 1D inversion.
.. plot::
from SimPEG import Examples
Examples.EM_FDEM_1D_Inversion.run()
Examples.EM_TDEM_1D_Inversion.run()
.. literalinclude:: ../../SimPEG/Examples/EM_FDEM_1D_Inversion.py
.. literalinclude:: ../../SimPEG/Examples/EM_TDEM_1D_Inversion.py
:language: python
:linenos:
docs/index.rst
+9 -8
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@@ -44,6 +44,15 @@ About SimPEG
api_bigPicture
api_installing
Examples
********
.. toctree::
:maxdepth: 2
api_Examples
Packages
********
@@ -53,14 +62,6 @@ Packages
em/index
flow/index
Examples
********
.. toctree::
:maxdepth: 2
api_Examples
Finite Volume
*************