Merge pull request #14 from simpeg-research/simulation

Simulation

Author: lheagy

.bumpversion.cfg

@@ -1,4 +1,4 @@
 [bumpversion]
-current_version = 0.0.7
+current_version = 0.1.0
 files = casingSimulations/info.py setup.py docs/conf.py
 

.travis.yml

@@ -1,33 +1,21 @@
 language: python
 python:
 - 3.6
-- "3.7-dev"
-matrix:
-  allow_failures:
-    - python: "3.7-dev"
 
 env:
   - TEST_DIR=tests
 
 sudo: false
 
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
-      wget http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget http://repo.continuum.io/miniconda/Miniconda3-3.8.3-Linux-x86_64.sh -O miniconda.sh;
-    fi
+  - wget http://repo.continuum.io/miniconda/Miniconda3-3.8.3-Linux-x86_64.sh -O miniconda.sh;
   - chmod +x miniconda.sh
   - ./miniconda.sh -b -p $HOME/miniconda
   - export PATH=/home/travis/anaconda/bin:/home/travis/miniconda/bin:$PATH
   - conda update --yes conda
 
 install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
-      conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython jupyter mkl;
-    else
-      conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython jupyter mkl;
-    fi
+  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython jupyter mkl;
   - python setup.py install
   - pip install -r requirements_dev.txt
 

casingSimulations/info.py

@@ -1,4 +1,4 @@
-__version__   = '0.0.7'
+__version__   = '0.1.0'
 __author__    = 'Lindsey Heagy'
 __license__   = 'MIT'
-__copyright__ = 'Copyright 2018 Lindsey Heagy'
+__copyright__ = 'Copyright 2018-2019 Lindsey Heagy'

casingSimulations/mesh.py

@@ -6,7 +6,7 @@
 import inspect
 
 import properties
-from SimPEG import Utils
+from SimPEG.utils import setKwargs
 
 import discretize
 from discretize import utils
@@ -48,7 +48,7 @@ class BaseMeshGenerator(BaseCasing):
     )
 
     def __init__(self, **kwargs):
-        Utils.setKwargs(self, **kwargs)
+        setKwargs(self, **kwargs)
 
     @property
     def mesh(self):
@@ -411,7 +411,7 @@ def hz(self):
         """
         if getattr(self, '_hz', None) is None:
 
-            self._hz = Utils.meshTensor([
+            self._hz = utils.meshTensor([
                 (self.csz, self.npadz, -self.pfz),
                 (self.csz, self.ncz),
                 (self.csz, self.npadz, self.pfz)
@@ -531,7 +531,10 @@ def __init__(self, **kwargs):
     @property
     def ncx1(self):
         """number of cells with size csx1"""
-        return np.ceil(self.modelParameters.casing_b/self.csx1+2)
+        if getattr(self, '_ncx1', None) is None:
+            self._ncx1 = np.ceil(self.modelParameters.casing_b/self.csx1+2)
+        return self._ncx1
+
 
     @property
     def npadx1(self):
@@ -546,22 +549,22 @@ def hx(self):
         if getattr(self, '_hx', None) is None:
 
             # finest uniform region
-            hx1a = Utils.meshTensor([(self.csx1, self.ncx1)])
+            hx1a = utils.meshTensor([(self.csx1, self.ncx1)])
 
             # pad to second uniform region
-            hx1b = Utils.meshTensor([(self.csx1, self.npadx1, self.pfx1)])
+            hx1b = utils.meshTensor([(self.csx1, self.npadx1, self.pfx1)])
 
             # scale padding so it matches cell size properly
-            dx1 = sum(hx1a)+sum(hx1b)
-            dx1 = np.floor(dx1/self.csx2)
-            hx1b *= (dx1*self.csx2 - sum(hx1a))/sum(hx1b)
+            dx1 = np.sum(hx1a)+np.sum(hx1b)
+            dx1 = 3 #np.floor(dx1/self.csx2)
+            hx1b *= (dx1*self.csx2 - np.sum(hx1a))/np.sum(hx1b)
 
             # second uniform chunk of mesh
             ncx2 = np.ceil((self.domain_x - dx1)/self.csx2)
-            hx2a = Utils.meshTensor([(self.csx2, ncx2)])
+            hx2a = utils.meshTensor([(self.csx2, ncx2)])
 
             # pad to infinity
-            hx2b = Utils.meshTensor([(self.csx2, self.npadx, self.pfx2)])
+            hx2b = utils.meshTensor([(self.csx2, self.npadx, self.pfx2)])
 
             self._hx = np.hstack([hx1a, hx1b, hx2a, hx2b])
 

casingSimulations/model.py

@@ -2,7 +2,8 @@
 import properties
 import json
 import os
-from SimPEG import Maps, Utils
+from SimPEG import maps
+from SimPEG.utils import setKwargs
 from scipy.constants import mu_0
 
 import discretize
@@ -132,7 +133,7 @@ class Wholespace(SurveyParametersMixin, BaseCasing):
     )
 
     def __init__(self, filename=None, **kwargs):
-        Utils.setKwargs(self, **kwargs)
+        setKwargs(self, **kwargs)
 
     def __str__(self):
         return self.info
@@ -858,10 +859,10 @@ def wires(self):
         """
         wires to hook up maps to sigma, mu
 
-        :rtype: SimPEG.Maps.Wires
+        :rtype: SimPEG.maps.Wires
         """
         if getattr(self, '_wires', None) is None:
-            self._wires = Maps.Wires(
+            self._wires = maps.Wires(
                 ('sigma', self.mesh.nC), ('mu', self.mesh.nC)
             )
         return self._wires

casingSimulations/physics.py

@@ -1,4 +1,4 @@
-from SimPEG import Utils
+from SimPEG.utils import ndgrid, mkvc, sdiag
 import discretize
 
 import numpy as np
@@ -40,9 +40,9 @@ def casing_currents(j, mesh, model_parameters):
         (mesh.gridFz[:, 2] >= casing_z[0])
     )
 
-    jA = Utils.sdiag(mesh.area) * j
+    jA = sdiag(mesh.area) * j
 
-    jACasing = Utils.sdiag(
+    jACasing = sdiag(
         np.hstack([casing_faces_x, casing_faces_y, casing_faces_z])
     ) * jA
 
@@ -187,7 +187,7 @@ def plot_currents_over_freq(
     for i, f in enumerate(modelParameters.freqs):
         for srcind in srcinds:
             # src = survey.getSrcByFreq(survey.freqs[freqind])[srcind]
-            # j = Utils.mkvc(fields[mur][src, 'j'].copy())
+            # j = mkvc(fields[mur][src, 'j'].copy())
 
             Iind = i + srcind*len(modelParameters.freqs)
 
@@ -360,7 +360,7 @@ def plot_j_over_mu_z(
     x_plt = np.r_[r]
     z_plt = np.linspace(xlim[0], xlim[1], int(xlim[1]-xlim[0]))
 
-    XYZ = Utils.ndgrid(x_plt, np.r_[0], z_plt)
+    XYZ = ndgrid(x_plt, np.r_[0], z_plt)
 
     Pfx = mesh.getInterpolationMat(XYZ, 'Fx')
     Pfz = mesh.getInterpolationMat(XYZ, 'Fz')
@@ -391,10 +391,10 @@ def plot_j_over_mu_z(
     for i, mur in enumerate(modelParameters.muModels):
         for srcind in srcinds:
             src = survey.getSrcByFreq(survey.freqs[freqind])[srcind]
-            j = Utils.mkvc(fields[mur][src, 'j'].copy())
+            j = mkvc(fields[mur][src, 'j'].copy())
 
             if subtract is not None:
-                j = j - Utils.mkvc(
+                j = j - mkvc(
                     fields[subtract][src, 'j'].copy()
                 )
 
@@ -469,7 +469,7 @@ def plot_j_over_freq_z(
     x_plt = np.r_[r]
     z_plt = np.linspace(xlim[0], xlim[1], int(xlim[1]-xlim[0]))
 
-    XYZ = Utils.ndgrid(x_plt, np.r_[0], z_plt)
+    XYZ = ndgrid(x_plt, np.r_[0], z_plt)
 
     Pfx = mesh.getInterpolationMat(XYZ, 'Fx')
     Pfz = mesh.getInterpolationMat(XYZ, 'Fz')
@@ -498,10 +498,10 @@ def plot_j_over_freq_z(
     for i, freq in enumerate(modelParameters.freqs):
         for srcind in srcinds:
             src = survey.getSrcByFreq(freq)[srcind]
-            j = Utils.mkvc(fields[mur][src, 'j'].copy())
+            j = mkvc(fields[mur][src, 'j'].copy())
 
             if subtract is not None:
-                j = j - Utils.mkvc(
+                j = j - mkvc(
                     fields[subtract][src, 'j'].copy()
                 )
 
@@ -576,7 +576,7 @@ def plot_j_over_mu_x(
     x_plt = np.linspace(xlim[0], xlim[1], xlim[1])
     z_plt = np.r_[z]
 
-    XYZ = Utils.ndgrid(x_plt, np.r_[0], z_plt)
+    XYZ = ndgrid(x_plt, np.r_[0], z_plt)
 
     Pfx = mesh.getInterpolationMat(XYZ, 'Fx')
     Pfz = mesh.getInterpolationMat(XYZ, 'Fz')
@@ -605,10 +605,10 @@ def plot_j_over_mu_x(
     for i, f in enumerate(modelParameters.freqs):
         for srcind in srcinds:
             src = survey.getSrcByFreq(survey.freqs[freqind])[srcind]
-            j = Utils.mkvc(fields[mur][src, 'j'].copy())
+            j = mkvc(fields[mur][src, 'j'].copy())
 
             if subtract is not None:
-                j = j - Utils.mkvc(
+                j = j - mkvc(
                     fields[subtract][src, 'j'].copy()
                 )
 

casingSimulations/run.py

@@ -8,9 +8,11 @@
 import discretize
 from discretize import utils
 import properties
-from SimPEG.EM import FDEM, TDEM
-from SimPEG import Utils, Maps
-from SimPEG.EM.Static import DC
+from SimPEG import maps
+from SimPEG.electromagnetics import frequency_domain as fdem
+from SimPEG.electromagnetics import time_domain as tdem
+from SimPEG.electromagnetics import resistivity as dc
+from SimPEG.utils import setKwargs
 
 try:
     from pymatsolver import Pardiso as Solver
@@ -81,7 +83,7 @@ class BaseSimulation(BaseCasing):
 
     def __init__(self, **kwargs):
         # set keyword arguments
-        Utils.setKwargs(self, **kwargs)
+        setKwargs(self, **kwargs)
 
         # if the working directory does not exsist, create it
         if not os.path.isdir(self.directory):
@@ -121,6 +123,11 @@ def prob(self):
     def survey(self):
         return self._survey
 
+    @property
+    def mesh(self):
+        return self.meshGenerator.mesh
+
+
     def write_py(self, includeDC=True, include2D=True):
         """
         Write a python script for running the simulation
@@ -222,7 +229,7 @@ class SimulationFDEM(BaseSimulation):
         choices=["e", "b", "h", "j"]
     )
 
-    physics = "FDEM"
+    physics = "fdem"
 
     def __init__(self, **kwargs):
         super(SimulationFDEM, self).__init__(**kwargs)
@@ -231,7 +238,7 @@ def __init__(self, **kwargs):
     def prob(self):
         if getattr(self, '_prob', None) is None:
             self._prob = getattr(
-                FDEM, 'Problem3D_{}'.format(self.formulation)
+                fdem, 'Problem3D_{}'.format(self.formulation)
             )(
                 self.meshGenerator.mesh,
                 sigmaMap=self.physprops.wires.sigma,
@@ -241,12 +248,12 @@ def prob(self):
             )
 
             if getattr(self, 'srcList') is not None:
-                self._survey = FDEM.Survey(self.srcList.srcList)
+                self._survey = fdem.Survey(self.srcList.srcList)
             elif getattr(self, 'src') is not None:
-                self._survey = FDEM.Survey(self.src.srcList)
+                self._survey = fdem.Survey(self.src.srcList)
             else:
                 raise Exception("one of src, srcList must be set")
-            self._prob.pair(self._survey)
+            self._prob.survey = self._survey
         return self._prob
 
     @property
@@ -269,7 +276,7 @@ class SimulationTDEM(BaseSimulation):
         choices=["e", "b", "h", "j"]
     )
 
-    physics = "TDEM"
+    physics = "tdem"
 
     def __init__(self, **kwargs):
         super(SimulationTDEM, self).__init__(**kwargs)
@@ -278,7 +285,7 @@ def __init__(self, **kwargs):
     def prob(self):
         if getattr(self, '_prob', None) is None:
             self._prob = getattr(
-                    TDEM, 'Problem3D_{}'.format(self.formulation)
+                    tdem, 'Problem3D_{}'.format(self.formulation)
                     )(
                     self.meshGenerator.mesh,
                     timeSteps=self.modelParameters.timeSteps,
@@ -288,9 +295,9 @@ def prob(self):
                     verbose=self.verbose
                 )
 
-            self._survey = TDEM.Survey(self.srcList.srcList)
+            self._survey = tdem.Survey(self.srcList.srcList)
 
-            self._prob.pair(self._survey)
+            self._prob.survey = self._survey
         return self._prob
 
     @property
@@ -324,22 +331,22 @@ class SimulationDC(BaseSimulation):
         default="phi"
     )
 
-    physics = "DC"
+    physics = "dc"
 
     def __init__(self, **kwargs):
         super(SimulationDC, self).__init__(**kwargs)
 
-        self._prob = DC.Problem3D_CC(
+        self._prob = dc.Problem3D_CC(
             self.meshGenerator.mesh,
             sigmaMap=self.physprops.wires.sigma,
             bc_type='Dirichlet',
             Solver=Solver
         )
         self._srcList = [
-            DC.Src.Dipole([], self.src_a[i, :], self.src_b[i, :])
+            dc.sources.Dipole([], self.src_a[i, :], self.src_b[i, :])
             for i in range(self.src_a.shape[0])
         ]
         # self._src = DC.Src.Dipole([], self.src_a, self.src_b)
-        self._survey = DC.Survey(self._srcList)
+        self._survey = dc.Survey(self._srcList)
 
-        self._prob.pair(self._survey)
+        self._prob.survey = self._survey