mirror of
https://github.com/wassname/simpeg.git
synced 2026-06-28 23:58:09 +08:00
Fix depenencies in notebooks and got tests to work.
This commit is contained in:
GudniRos
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@@ -11,6 +11,175 @@
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"## Forward model a data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"import SimPEG as simpeg\n",
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"import simpegMT as simpegmt\n",
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"import cPickle as pickle"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"## Setup the forward modeling\n",
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"# Read the model\n",
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"modelname = \"simpegTDmodel.con\"\n",
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"sigma = np.loadtxt(modelname)\n",
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"# Make the mesh.\n",
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"mTensor = simpeg.Utils.meshTensor\n",
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"cSize = [50,20]\n",
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"# Cells constant size mesh\n",
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"hx = mTensor([(cSize[0],50)])\n",
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"hy = mTensor([(cSize[0],50)])\n",
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"hz = mTensor([(cSize[1],48)])\n",
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"x0 = np.array([-1250,-1250,- 30*20])\n",
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"mesh3dCons = simpeg.Mesh.TensorMesh([hx,hy,hz],x0)\n",
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"# With padding\n",
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"hPad = mTensor([(cSize[0],5,1.5)])\n",
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"aPad = mTensor([(cSize[1],13,1.3)])\n",
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"bPad = mTensor([(cSize[1],5,-1.5)])\n",
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"hxPad = np.hstack((hPad[::-1],mTensor([(cSize[0],40)]),hPad))\n",
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"hyPad = np.hstack((hPad[::-1],mTensor([(cSize[0],40)]),hPad))\n",
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"hzPad = np.hstack((bPad,mTensor([(cSize[1],30)]),aPad))\n",
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"x0Pad = np.array([-(np.sum(hPad)+1000),-(np.sum(hPad)+1000),-(np.sum(bPad)+600)])\n",
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"mesh3d = simpeg.Mesh.TensorMesh([hxPad,hyPad,hzPad],x0Pad)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"# Load the model to the uniform cell mesh\n",
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"modelUniCell = simpeg.Utils.meshutils.readUBCTensorModel(modelname,mesh3dCons)\n",
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"# Save as a vtk file\n",
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"simpeg.Utils.meshutils.writeVTRFile('modelTDuniMesh.vtr',mesh3dCons,{'S/m':modelUniCell})"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {
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"collapsed": false,
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"scrolled": true
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},
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"outputs": [],
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"source": [
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"# Load the model to the mesh with padding cells\n",
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"modelTD = simpeg.Utils.meshutils.readUBCTensorModel(modelname,mesh3d)\n",
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"# Save as a vtk file\n",
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"simpeg.Utils.meshutils.writeVTRFile('modelTDpaddedMesh.vtr',mesh3d,{'S/m':modelTD})"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"# Define the data locations\n",
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"xG,yG = np.meshgrid(np.linspace(-700,700,8),np.linspace(-700,700,8))\n",
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"zG = np.zeros_like(xG)\n",
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"locs = np.hstack((simpeg.mkvc(xG.ravel(),2),simpeg.mkvc(yG.ravel(),2),simpeg.mkvc(zG.ravel(),2)))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {
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"collapsed": false
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},
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"outputs": [
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{
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"ename": "SolverException",
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"evalue": "Mumps Exception [-13] - An error occurred in a Fortran ALLOCATE statement. The size that the package requested is available in INFO(2). If INFO(2) is negative, then the size that the package requested is obtained by multiplying the absolute value of INFO(2) by 1 million.",
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"output_type": "error",
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"traceback": [
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"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[1;31mSolverException\u001b[0m Traceback (most recent call last)",
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"\u001b[1;32m<ipython-input-7-10aaec78a1f3>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m 20\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 21\u001b[0m \u001b[1;31m# Forward model the data\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 22\u001b[1;33m \u001b[0mfields\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mproblem\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfields\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mmodelTD\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 23\u001b[0m \u001b[0mmtData\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0msurvey\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mprojectFields\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfields\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
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"\u001b[1;32m/media/gudni/ExtraDrive1/Codes/python/simpegmt/simpegMT/ProblemMT3D/Problems.pyc\u001b[0m in \u001b[0;36mfields\u001b[1;34m(self, m)\u001b[0m\n\u001b[0;32m 100\u001b[0m \u001b[0mA\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgetA\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfreq\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 101\u001b[0m \u001b[0mrhs\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgetRHS\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfreq\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 102\u001b[1;33m \u001b[0mAinv\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSolver\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mA\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msolverOpts\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 103\u001b[0m \u001b[0me_s\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mAinv\u001b[0m \u001b[1;33m*\u001b[0m \u001b[0mrhs\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 104\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
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"\u001b[1;32m/media/gudni/ExtraDrive1/Codes/python/pymatsolver/pymatsolver/Mumps/__init__.pyc\u001b[0m in \u001b[0;36m__init__\u001b[1;34m(self, A, symmetric, fromPointer)\u001b[0m\n\u001b[0;32m 96\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 97\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mfromPointer\u001b[0m \u001b[1;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 98\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfactor\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 99\u001b[0m \u001b[1;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfromPointer\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0m_Pointer\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 100\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mpointer\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mfromPointer\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
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"\u001b[1;32m/media/gudni/ExtraDrive1/Codes/python/pymatsolver/pymatsolver/Mumps/__init__.pyc\u001b[0m in \u001b[0;36mfactor\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m 132\u001b[0m self.A.indptr+1)\n\u001b[0;32m 133\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mierr\u001b[0m \u001b[1;33m<\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 134\u001b[1;33m \u001b[1;32mraise\u001b[0m \u001b[0mSolverException\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"Mumps Exception [%d] - %s\"\u001b[0m \u001b[1;33m%\u001b[0m \u001b[1;33m(\u001b[0m\u001b[0mierr\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0m_mumpsErrors\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mierr\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 135\u001b[0m \u001b[1;32melif\u001b[0m \u001b[0mierr\u001b[0m \u001b[1;33m>\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 136\u001b[0m \u001b[1;32mprint\u001b[0m \u001b[1;34m\"Mumps Warning [%d] - %s\"\u001b[0m \u001b[1;33m%\u001b[0m \u001b[1;33m(\u001b[0m\u001b[0mierr\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0m_mumpsErrors\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mierr\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
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"\u001b[1;31mSolverException\u001b[0m: Mumps Exception [-13] - An error occurred in a Fortran ALLOCATE statement. The size that the package requested is available in INFO(2). If INFO(2) is negative, then the size that the package requested is obtained by multiplying the absolute value of INFO(2) by 1 million."
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]
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}
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],
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"source": [
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"# Make the receiver list\n",
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"rxList = []\n",
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"for rxType in ['zxxr','zxxi','zxyr','zxyi','zyxr','zyxi','zyyr','zyyi']:\n",
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" rxList.append(simpegmt.SurveyMT.RxMT(locs,rxType)) \n",
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"# Source list\n",
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"srcList =[]\n",
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"freqs = np.logspace(3,0,13)\n",
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"for freq in freqs:\n",
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" srcList.append(simpegmt.SurveyMT.srcMT_polxy_1Dprimary(rxList,freq))\n",
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"# Survey MT\n",
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"survey = simpegmt.SurveyMT.SurveyMT(srcList)\n",
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"\n",
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"# Setup the problem object\n",
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"sigma1d = mesh3d.r(modelTD,'CC','CC','M')[0,0,:] # Use the edge column as a background model\n",
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"problem = simpegmt.ProblemMT3D.eForm_ps(mesh3d,sigmaPrimary = sigma1d)\n",
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"problem.verbose = False\n",
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"from pymatsolver import MumpsSolver\n",
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"problem.Solver = MumpsSolver\n",
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"problem.pair(survey)\n",
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"\n",
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"# Forward model the data\n",
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"fields = problem.fields(modelTD)\n",
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"mtData = survey.projectFields(fields)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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" 50*50*48"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"np.sum(modTD<1e-7)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
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"outputs": [],
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"source": [
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"45000/50**2"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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@@ -18,9 +187,7 @@
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Define the model\n"
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]
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"source": []
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}
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],
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"metadata": {
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@@ -23,40 +23,19 @@ class eForm_ps(BaseMTProblem):
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_fieldType = 'e'
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_eqLocs = 'FE'
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fieldsPair = FieldsMT_3D
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# Need to add the src ....
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# Set new properties
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# Background model
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# Shouldn't need the commented block.
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# @property
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# def backModel(self):
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# """
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# Sets the model, and removes dependent mass matrices.
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# """
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# return getattr(self, '_backModel', None)
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# @backModel.setter
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# def backModel(self, value):
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# if value is self.backModel:
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# return # it is the same!
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# self._backModel = Models.Model(value, self.mapping)
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# for prop in self.deleteTheseOnModelUpdate:
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# if hasattr(self, prop):
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# delattr(self, prop)
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# @property
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# def MeDeltaSigma(self):
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# #TODO: hardcoded to sigma as the model
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# if getattr(self, '_MeDeltaSigma', None) is None:
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# sigma = self.curModel
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# sigmaBG = self.backModel
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# self._MeDeltaSigma = self.mesh.getEdgeInnerProduct(sigma - sigmaBG)
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# return self._MeDeltaSigma
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_sigmaPrimary = None
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def __init__(self, mesh, **kwargs):
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BaseMTProblem.__init__(self, mesh, **kwargs)
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@property
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def sigmaPrimary(self):
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return self._sigmaPrimary
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@sigmaPrimary.setter
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def sigmaPrimary(self, val):
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# Note: TODO add logic for val, make sure it is the correct size.
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self._sigmaPrimary = val
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def getA(self, freq):
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"""
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Function to get the A matrix.
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@@ -36,7 +36,7 @@ def setupSurvey(sigmaHalf,tD=True):
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srcList.append(simpegmt.SurveyMT.srcMT_polxy_1DhomotD(rxList,freq))
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else:
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for freq in freqs:
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srcList.append(simpegmt.SurveyMT.srcMT_polxy_1Dprimary(rxList,freq,sigma))
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srcList.append(simpegmt.SurveyMT.srcMT_polxy_1Dprimary(rxList,freq))
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survey = simpegmt.SurveyMT.SurveyMT(srcList)
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return survey, sigma, m1d
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@@ -63,7 +63,7 @@ def appRes_TotalFieldNorm(sigmaHalf):
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# Make the survey
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survey, sigma, mesh = setupSurvey(sigmaHalf)
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problem = simpegmt.ProblemMT1D.eForm_TotalField(mesh,sigma)
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problem = simpegmt.ProblemMT1D.eForm_TotalField(mesh)
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problem.pair(survey)
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# Get the fields
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@@ -99,7 +99,7 @@ def appRes_psFieldNorm(sigmaHalf):
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# Make the survey
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survey, sigma, mesh = setupSurvey(sigmaHalf,False)
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problem = simpegmt.ProblemMT1D.eForm_psField(mesh)
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problem = simpegmt.ProblemMT1D.eForm_psField(mesh, sigmaPrimary = sigma)
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problem.pair(survey)
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# Get the fields
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@@ -117,7 +117,7 @@ def appPhs_psFieldNorm(sigmaHalf):
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# Make the survey
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survey, sigma, mesh = setupSurvey(sigmaHalf,False)
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problem = simpegmt.ProblemMT1D.eForm_psField(mesh)
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problem = simpegmt.ProblemMT1D.eForm_psField(mesh, sigmaPrimary = sigma)
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problem.pair(survey)
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# Get the fields
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@@ -109,7 +109,7 @@ def dataMis_AnalyticPrimarySecondary(sigmaHalf):
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# Make the survey
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# Primary secondary
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surveyPS, sigmaPS, mesh = setupSurvey(sigmaHalf,False)
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problemPS = simpegmt.ProblemMT1D.eForm_psField(mesh,sigma)
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problemPS = simpegmt.ProblemMT1D.eForm_psField(mesh,sigmaPS)
|
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problemPS.pair(surveyPS)
|
||||
# Analytic data
|
||||
dataAna = calculateAnalyticSolution(surveyPS.srcList,mesh,sigma)
|
||||
|
||||
@@ -18,7 +18,7 @@ def getInputs():
|
||||
# M = simpeg.Mesh.TensorMesh([[(100,5,-1.5),(100.,10),(100,5,1.5)],[(100,5,-1.5),(100.,10),(100,5,1.5)],[(100,5,1.6),(100.,10),(100,3,2)]], x0=['C','C',-3529.5360])
|
||||
M = simpeg.Mesh.TensorMesh([[(1000,6,-1.5),(1000.,6),(1000,6,1.5)],[(1000,6,-1.5),(1000.,2),(1000,6,1.5)],[(1000,10,-1.3),(1000.,2),(1000,10,1.3)]], x0=['C','C','C'])# Setup the model
|
||||
# Set the frequencies
|
||||
freqs = np.logspace(3,-3,7)
|
||||
freqs = np.logspace(1,-3,5)
|
||||
elev = 0
|
||||
|
||||
## Setup the the survey object
|
||||
@@ -73,12 +73,12 @@ def runSimpegMTfwd_eForm_ps(inputsProblem):
|
||||
srcList =[]
|
||||
sigma1d = M.r(sigBG,'CC','CC','M')[0,0,:]
|
||||
for freq in freqs:
|
||||
srcList.append(simpegmt.SurveyMT.srcMT_polxy_1Dprimary(rxList,freq,sigma1d))
|
||||
srcList.append(simpegmt.SurveyMT.srcMT_polxy_1Dprimary(rxList,freq))
|
||||
# Survey MT
|
||||
survey = simpegmt.SurveyMT.SurveyMT(srcList)
|
||||
|
||||
## Setup the problem object
|
||||
problem = simpegmt.ProblemMT3D.eForm_ps(M)
|
||||
problem = simpegmt.ProblemMT3D.eForm_ps(M,sigmaPrimary=sigma1d)
|
||||
problem.verbose = False
|
||||
from pymatsolver import MumpsSolver
|
||||
problem.Solver = MumpsSolver
|
||||
@@ -106,19 +106,19 @@ def appResPhsHalfspace_eFrom_ps_Norm(sigmaHalf,appR=True):
|
||||
# Calculate the app phs
|
||||
app_rpxy, app_rpyx = np.array(getAppResPhs(data))
|
||||
if appR:
|
||||
return np.linalg.norm(np.abs(app_rpxy[0,:] - np.ones(survey.nFreq)/sigmaHalf) * sigmaHalf)
|
||||
return np.all(np.abs(app_rpxy[0,:] - np.ones(survey.nFreq)/sigmaHalf) * sigmaHalf < .35)
|
||||
else:
|
||||
return np.linalg.norm(np.abs(app_rpxy[1,:] + np.ones(survey.nFreq)*135) / 135)
|
||||
return np.all(np.abs(app_rpxy[1,:] + np.ones(survey.nFreq)*135) / 135 < .35)
|
||||
|
||||
class TestAnalytics(unittest.TestCase):
|
||||
|
||||
def setUp(self):
|
||||
pass
|
||||
def test_appRes2en1(self):self.assertLess(appResPhsHalfspace_eFrom_ps_Norm(2e-1), TOLr)
|
||||
def test_appRes2en2(self):self.assertLess(appResPhsHalfspace_eFrom_ps_Norm(2e-2), TOLr)
|
||||
def test_appRes2en3(self):self.assertLess(appResPhsHalfspace_eFrom_ps_Norm(2e-3), TOLr)
|
||||
def test_appRes2en1(self):self.assertLess(appResPhsHalfspace_eFrom_ps_Norm(2e-1,False), TOLr)
|
||||
def test_appRes2en2(self):self.assertLess(appResPhsHalfspace_eFrom_ps_Norm(2e-2,False), TOLr)
|
||||
def test_appRes2en3(self):self.assertLess(appResPhsHalfspace_eFrom_ps_Norm(2e-3,False), TOLr)
|
||||
# def test_appRes2en1(self):self.assertTrue(appResPhsHalfspace_eFrom_ps_Norm(2e-1))
|
||||
def test_appRes1en2(self):self.assertTrue(appResPhsHalfspace_eFrom_ps_Norm(1e-2))
|
||||
def test_appRes1en3(self):self.assertTrue(appResPhsHalfspace_eFrom_ps_Norm(1e-3))
|
||||
# def test_appRes2en1(self):self.assertTrue(appResPhsHalfspace_eFrom_ps_Norm(2e-1,False))
|
||||
def test_appPhs1en2(self):self.assertTrue(appResPhsHalfspace_eFrom_ps_Norm(1e-2,False))
|
||||
def test_appPhs1en3(self):self.assertTrue(appResPhsHalfspace_eFrom_ps_Norm(1e-3,False))
|
||||
if __name__ == '__main__':
|
||||
unittest.main()
|
||||
@@ -121,4 +121,8 @@ def plotMT1DModelData(problem,models,symList=None):
|
||||
for ax in [axM,axR,axP]:
|
||||
ax.xaxis.set_tick_params(labelsize=fontSize)
|
||||
ax.yaxis.set_tick_params(labelsize=fontSize)
|
||||
return fig
|
||||
return fig
|
||||
|
||||
def printTime():
|
||||
import time
|
||||
print time.strftime("%a, %d %b %Y %H:%M:%S +0000", time.localtime())
|
||||
Reference in New Issue
Block a user