mirror of
https://github.com/wassname/simpeg.git
synced 2026-06-27 18:25:42 +08:00
Merge branch 'startupScripts' of https://github.com/simpeg/simpeg into develop
This commit is contained in:
rowanc1
@@ -0,0 +1,470 @@
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#!/usr/bin/python
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"""
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Input and output functions.
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"""
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import os as _os
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import errno as _errno
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import sys as _sys
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import numpy as _np
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from petsc4py import PETSc as _PETSc
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import fileinput as _fl
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def vecToArray(obj):
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""" Converts a PETSc vector to a numpy array, available on *all* MPI nodes.
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Args:
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obj (petsc4py.PETSc.Vec): input vector.
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Returns:
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numpy.array :
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"""
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# scatter vector 'obj' to all processes
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comm = obj.getComm()
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scatter, obj0 = _PETSc.Scatter.toAll(obj)
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scatter.scatter(obj, obj0, False, _PETSc.Scatter.Mode.FORWARD)
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return _np.asarray(obj0)
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# deallocate
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comm.barrier()
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scatter.destroy()
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obj0.destroy()
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def vecToArray0(obj):
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""" Converts a PETSc vector to a numpy array available on MPI node 0.
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Args:
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obj (petsc4py.PETSc.Vec): input vector.
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Returns:
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numpy.array :
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"""
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# scatter vector 'obj' to process 0
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comm = obj.getComm()
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rank = comm.getRank()
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scatter, obj0 = _PETSc.Scatter.toZero(obj)
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scatter.scatter(obj, obj0, False, _PETSc.Scatter.Mode.FORWARD)
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if rank == 0: return _np.asarray(obj0)
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# deallocate
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comm.barrier()
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scatter.destroy()
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obj0.destroy()
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def arrayToVec(vecArray):
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""" Converts a (global) array to a PETSc vector over :attr:`petsc4py.PETSc.COMM_WORLD`.
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Args:
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vecArray (array or numpy.array): input vector.
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Returns:
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petsc4py.PETSc.Vec() :
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"""
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vec = _PETSc.Vec().create(comm=_PETSc.COMM_WORLD)
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vec.setSizes(len(vecArray))
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vec.setUp()
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(Istart,Iend) = vec.getOwnershipRange()
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return vec.createWithArray(vecArray[Istart:Iend],
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comm=_PETSc.COMM_WORLD)
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vec.destroy()
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def arrayToMat(matArray):
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""" Converts a (global) 2D array to a PETSc matrix over :attr:`petsc4py.PETSc.COMM_WORLD`.
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Args:
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matArray (array or numpy.array): input square array.
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:rtype: petsc4py.PETSc.Mat()
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.. important::
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Requires `SciPy <http://www.scipy.org>`_.
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"""
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try:
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import scipy.sparse as sparse
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except:
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print '\nERROR: loading matrices from txt files requires Scipy!'
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return
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matSparse =matArray
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mat = _PETSc.Mat().createAIJ(size=matSparse.shape,comm=_PETSc.COMM_WORLD)
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(Istart,Iend) = mat.getOwnershipRange()
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ai = matSparse.indptr[Istart:Iend+1] - matSparse.indptr[Istart]
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aj = matSparse.indices[matSparse.indptr[Istart]:matSparse.indptr[Iend]]
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av = matSparse.data[matSparse.indptr[Istart]:matSparse.indptr[Iend]]
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mat.setValuesCSR(ai,aj,av)
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mat.assemble()
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return mat
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mat.destroy()
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def matToSparse(mat):
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""" Converts a PETSc matrix to a (global) sparse matrix.
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Args:
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mat (petsc4py.PETSc.Mat): input PETSc matrix.
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:rtype: scipy.sparse.csr_matrix
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.. important::
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Requires `SciPy <http://www.scipy.org>`_.
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"""
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import scipy.sparse as sparse
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data = mat.getValuesCSR()
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(Istart,Iend) = mat.getOwnershipRange()
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columns = mat.getSize()[0]
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sparseSubMat = sparse.csr_matrix(data[::-1],shape=(Iend-Istart,columns))
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comm = _PETSc.COMM_WORLD
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sparseSubMat = comm.tompi4py().allgather(sparseSubMat)
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return sparse.vstack(sparseSubMat)
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def adjToH(adj,d=[0],amp=[0.]):
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""" Creates a 1 particle PETSc-type Hamiltonian matrix from a PETSc adjacency matrix.
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Args:
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adj (petsc4py.PETSc.Mat): input PETSc-type adjacency matrix.
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d (array of ints): an array containing *integers* indicating the nodes
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where diagonal defects are to be placed (e.g. ``d=[0,1,4]``).
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amp (array of floats): an array containing *floats* indicating the diagonal defect
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amplitudes corresponding to each element in ``d`` (e.g. ``amp=[0.5,-1,4.2]``).
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Returns:
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: 1 particle Hamiltonian matrix
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:rtype: petsc4py.PETSc.Mat()
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Warning:
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* The size of ``a`` and ``d`` must be identical
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>>> amp = [0.5,-1.,4.2]
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>>> len(d) == len(amp)
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True
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* Elements of ``d`` can range from :math:`[0,N-1]` where the adjacency matrix is :math:`N\\times N`.
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"""
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(Istart,Iend) = adj.getOwnershipRange()
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diagSum = []
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for i in range(Istart,Iend):
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diagSum.append(_np.sum(adj.getRow(i)[-1]))
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for j,val in enumerate(d):
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if i==val: diagSum[i-Istart] += amp[j]
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mat = _PETSc.Mat().create(comm=_PETSc.COMM_WORLD)
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mat.setSizes(adj.getSize())
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mat.setUp()
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for i in range(Istart,Iend):
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mat.setValue(i,i,diagSum[i-Istart])
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mat.assemble()
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mat.axpy(-1,adj)
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return mat
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mat.destroy()
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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#---------------------- Vec I/O functions ---------------------------
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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def exportVec(vec,filename,filetype):
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""" Export a PETSc vector to a file.
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Args:
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vec (petsc4py.PETSc.Vec): input vector.
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filename (str): path to desired output file.
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filetype (str): the filetype of the exported vector.
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* ``'txt'`` - a column vector in text format.
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* ``'bin'`` - a PETSc binary vector.
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"""
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if _os.path.isabs(filename):
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outDir = _os.path.dirname(filename)
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else:
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outDir = './'+_os.path.dirname(filename)
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# create output directory if it doesn't exist
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try:
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_os.mkdir(outDir)
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except OSError as exception:
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if exception.errno != _errno.EEXIST:
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raise
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if filetype == 'txt':
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# scatter prob to process 0
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comm = vec.getComm()
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rank = comm.getRank()
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scatter, vec0 = _PETSc.Scatter.toZero(vec)
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scatter.scatter(vec, vec0, False, _PETSc.Scatter.Mode.FORWARD)
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# use process 0 to write to text file
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if rank == 0:
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array0 = _np.asarray(vec0)
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with open(filename,'w') as f:
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for i in range(len(array0)):
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f.write('{0: .12e}\n'.format(array0[i]))
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# deallocate
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comm.barrier()
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scatter.destroy()
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vec0.destroy()
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elif filetype == 'bin':
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binSave = _PETSc.Viewer().createBinary(filename, 'w')
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binSave(vec)
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binSave.destroy()
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vec.comm.barrier()
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def loadVec(filename,filetype):
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""" Import a PETSc vector from a file.
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Args:
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filename (str): path to input file.
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filetype (str): the filetype.
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* ``'txt'`` - a column vector in text format.
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* ``'bin'`` - a PETSc binary vector.
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"""
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if filetype == 'txt':
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try:
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vecArray = _np.loadtxt(filename,dtype=_PETSc.ScalarType)
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return arrayToVec(vecArray)
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except:
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print "\nERROR: input state space file " + filename\
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+ " does not exist or is in an incorrect format"
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_sys.exit()
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elif filetype == 'bin':
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binLoad = _PETSc.Viewer().createBinary(filename, 'r')
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try:
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return _PETSc.Vec().load(binLoad)
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except:
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print "\nERROR: input state space file " + filename\
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+ " does not exist or is in an incorrect format"
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_sys.exit()
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binLoad.destroy()
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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#---------------------- Mat I/O functions ---------------------------
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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def exportMat(mat,filename,filetype,mattype=None):
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""" Export a PETSc matrix to a file.
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||||
Args:
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mat (petsc4py.PETSc.Mat): input matrix.
|
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filename (str): path to desired output file.
|
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filetype (str): the filetype of the exported vector.
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* ``'txt'`` - a 2D matrix array in text format.
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* ``'bin'`` - a PETSc binary matrix.
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mattype (str): (``None``,``'adj'``) - if set to ``adj``, only
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integers ``0`` and ``1`` are written. Note
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that this only applied in ``txt`` mode.
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"""
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rank = _PETSc.Comm.Get_rank(_PETSc.COMM_WORLD)
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||||
|
||||
if _os.path.isabs(filename):
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||||
outDir = _os.path.dirname(filename)
|
||||
else:
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||||
outDir = './'+_os.path.dirname(filename)
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||||
|
||||
# create output directory if it doesn't exist
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||||
try:
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_os.mkdir(outDir)
|
||||
except OSError as exception:
|
||||
if exception.errno != _errno.EEXIST:
|
||||
raise
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||||
|
||||
if filetype == 'txt':
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txtSave = _PETSc.Viewer().createASCII(filename, 'w',
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format=_PETSc.Viewer.Format.ASCII_DENSE, comm=_PETSc.COMM_WORLD)
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txtSave(mat)
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txtSave.destroy()
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|
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if rank == 0:
|
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for line in _fl.FileInput(filename,inplace=1):
|
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if line[2] != 't':
|
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if mattype == 'adj':
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||||
line = line.replace(" i","j")
|
||||
line = line.replace(" -","-")
|
||||
line = line.replace("+-","-")
|
||||
line = line.replace("0000e+01+0.00000e+00j","")
|
||||
line = line.replace(".00000e+00+0.00000e+00j","")
|
||||
line = line.replace(".","")
|
||||
line = line.replace(" -","\t-")
|
||||
line = line.replace(" ","\t")
|
||||
line = line.replace(" ","")
|
||||
line = line.replace("\t"," ")
|
||||
print line,
|
||||
else:
|
||||
line = line.replace(" i","j")
|
||||
line = line.replace(" -","-")
|
||||
line = line.replace("+-","-")
|
||||
print line,
|
||||
|
||||
elif filetype == 'bin':
|
||||
binSave = _PETSc.Viewer().createBinary(filename, 'w', comm=_PETSc.COMM_WORLD)
|
||||
binSave(mat)
|
||||
binSave.destroy()
|
||||
|
||||
mat.comm.barrier()
|
||||
|
||||
def loadMat(filename,filetype,delimiter=None):
|
||||
""" Import a PETSc matrix from a file.
|
||||
|
||||
Args:
|
||||
filename (str): path to input file.
|
||||
filetype (str): the filetype.
|
||||
|
||||
* ``'txt'`` - a 2D matrix array in text format.
|
||||
* ``'bin'`` - a PETSc matrix vector.
|
||||
|
||||
delimiter (str): this is passed to `numpy.genfromtxt\
|
||||
<http://docs.scipy.org/doc/numpy/reference/generated/numpy.genfromtxt.html>`_
|
||||
in the case of strange delimiters in an imported ``txt`` file.
|
||||
"""
|
||||
if filetype == 'txt':
|
||||
try:
|
||||
try:
|
||||
if delimiter is None:
|
||||
matArray = _np.genfromtxt(filename,dtype=_PETSc.ScalarType)
|
||||
else:
|
||||
matArray = _np.genfromtxt(filename,dtype=_PETSc.ScalarType,delimiter=delimiter)
|
||||
except:
|
||||
filefix = []
|
||||
for line in _fl.FileInput(filename,inplace=0):
|
||||
if line[2] != 't':
|
||||
line = line.replace(" i","j")
|
||||
line = line.replace(" -","-")
|
||||
line = line.replace("+-","-")
|
||||
filefix.append(line)
|
||||
|
||||
matArray = _np.genfromtxt(filefix,dtype=_PETSc.ScalarType)
|
||||
|
||||
return arrayToMat(matArray)
|
||||
except:
|
||||
print "\nERROR: input state space file " + filename\
|
||||
+ " does not exist or is in an incorrect format"
|
||||
_sys.exit()
|
||||
|
||||
elif filetype == 'bin':
|
||||
binLoad = _PETSc.Viewer().createBinary(filename, 'r')
|
||||
try:
|
||||
return _PETSc.Mat().load(binLoad)
|
||||
except:
|
||||
print "\nERROR: input state space file " + filename\
|
||||
+ " does not exist or is in an incorrect format"
|
||||
_sys.exit()
|
||||
binLoad.destroy()
|
||||
|
||||
def exportVecToMat(vec,filename,filetype):
|
||||
""" Export a :math:`N^2` element PETSc vector as a :math:`N\\times N` matrix.
|
||||
|
||||
This is useful when wanting to view the full statespace of a 2 particle
|
||||
quantum walk.
|
||||
|
||||
Args:
|
||||
vec (petsc4py.PETSc.Vec): input :math:`N^2` element vector.
|
||||
filename (str): path to desired output file.
|
||||
filetype (str): the filetype of the exported vector.
|
||||
|
||||
* ``'txt'`` - an :math:`N\\times N` 2D matrix array in text format.
|
||||
* ``'bin'`` - an :math:`N\\times N` PETSc binary matrix.
|
||||
"""
|
||||
rank = _PETSc.Comm.Get_rank(_PETSc.COMM_WORLD)
|
||||
|
||||
if _os.path.isabs(filename):
|
||||
outDir = _os.path.dirname(filename)
|
||||
else:
|
||||
outDir = './'+_os.path.dirname(filename)
|
||||
|
||||
# create output directory if it doesn't exist
|
||||
try:
|
||||
_os.mkdir(outDir)
|
||||
except OSError as exception:
|
||||
if exception.errno != _errno.EEXIST:
|
||||
raise
|
||||
|
||||
vecArray = vecToArray(vec)
|
||||
matArray = vecArray.reshape([_np.sqrt(vecArray.size),_np.sqrt(vecArray.size)])
|
||||
|
||||
if filetype == 'txt':
|
||||
#if rank == 0: _np.savetxt(filename,matArray)
|
||||
txtSave = _PETSc.Viewer().createASCII(filename, 'w',
|
||||
format=_PETSc.Viewer.Format.ASCII_DENSE, comm=_PETSc.COMM_WORLD)
|
||||
txtSave(arrayToMat(matArray))
|
||||
txtSave.destroy()
|
||||
|
||||
if rank == 0:
|
||||
for line in _fl.FileInput(filename,inplace=1):
|
||||
if line[2] != 't':
|
||||
line = line.replace(" i","j")
|
||||
line = line.replace(" -","-")
|
||||
line = line.replace("+-","-")
|
||||
print line,
|
||||
|
||||
elif filetype == 'bin':
|
||||
binSave = _PETSc.Viewer().createBinary(filename, 'w', comm=_PETSc.COMM_WORLD)
|
||||
binSave(arrayToMat(matArray))
|
||||
binSave.destroy()
|
||||
vec.comm.barrier()
|
||||
|
||||
|
||||
def loadMatToVec(filename,filetype):
|
||||
""" Load a :math:`N\\times N` matrix as a :math:`N^2` element PETSc vector.
|
||||
|
||||
This is useful when wanting to import the full statespace of a 2 particle
|
||||
quantum walk to use for propagation.
|
||||
|
||||
Args:
|
||||
filename (str): path to the input file.
|
||||
filetype (str): the filetype
|
||||
|
||||
* ``'txt'`` - an :math:`N\\times N` 2D matrix array in text format.
|
||||
* ``'bin'`` - **Not yet implemented! Please use a txt \
|
||||
format for this type of import**.
|
||||
"""
|
||||
if filetype == 'txt':
|
||||
try:
|
||||
try:
|
||||
matArray = _np.loadtxt(filename,dtype=_PETSc.ScalarType)
|
||||
except:
|
||||
filefix = []
|
||||
for line in _fl.FileInput(filename,inplace=0):
|
||||
if line[2] != 't':
|
||||
line = line.replace(" i","j")
|
||||
line = line.replace(" -","-")
|
||||
line = line.replace("+-","-")
|
||||
filefix.append(line)
|
||||
|
||||
matArray = _np.loadtxt(filefix,dtype=_PETSc.ScalarType)
|
||||
|
||||
vecArray = matArray.reshape(matArray.shape[0]**2)
|
||||
return arrayToVec(vecArray)
|
||||
except:
|
||||
print "\nERROR: input state space file " + filename\
|
||||
+ " does not exist or is in an incorrect format"
|
||||
_sys.exit()
|
||||
|
||||
elif filetype == 'bin':
|
||||
print '\nERROR: only works for txt storage!'
|
||||
_sys.exit()
|
||||
File diff suppressed because one or more lines are too long
Executable
+145
@@ -0,0 +1,145 @@
|
||||
#! /bin/bash
|
||||
|
||||
locale-gen en_US en_US.UTF-8 hu_HU hu_HU.UTF-8 > output.t
|
||||
dpkg-reconfigure locales >> output.t
|
||||
|
||||
sudo apt-get update >> output.t
|
||||
echo " "
|
||||
echo " "
|
||||
echo " ============================================"
|
||||
echo " | Installing packages form package manager |"
|
||||
echo " ============================================"
|
||||
echo " "
|
||||
echo " "
|
||||
|
||||
sudo apt-get -y install aptitude >> output.t
|
||||
|
||||
packages=(gcc gfortran git libopenmpi-dev python-pip python-dev git flex bison cmake vim cython ipython python-scipy python-numpy python-nose python-pip python-matplotlib python-vtk python-h5py libmumps-ptscotch-4.10.0 libmumps-ptscotch-dev libblas-dev liblapack-dev )
|
||||
|
||||
|
||||
for item in ${packages[*]}
|
||||
do
|
||||
printf " %-30s\n" $item
|
||||
|
||||
done
|
||||
|
||||
for item in ${packages[*]}
|
||||
do
|
||||
tput cuu1
|
||||
done
|
||||
|
||||
for item in ${packages[*]}
|
||||
do
|
||||
sudo aptitude -y install $item >> output.t
|
||||
printf " %-30s %-4s\n" $item done
|
||||
done
|
||||
|
||||
|
||||
echo " "
|
||||
echo " "
|
||||
echo " ====================================="
|
||||
echo " | Installing extra Python libraries |"
|
||||
echo " ====================================="
|
||||
echo " "
|
||||
echo " "
|
||||
|
||||
|
||||
pipPackages=(mpi4py pymumps)
|
||||
|
||||
for item in ${pipPackages[*]}
|
||||
do
|
||||
printf " %-30s\n" $item
|
||||
done
|
||||
|
||||
for item in ${pipPackages[*]}
|
||||
do
|
||||
tput cuu1
|
||||
done
|
||||
|
||||
for item in ${pipPackages[*]}
|
||||
do
|
||||
sudo pip install $item >> output.t
|
||||
printf " %-30s %-4s\n" $item done
|
||||
done
|
||||
|
||||
Upgrade=(scipy numpy ipython)
|
||||
|
||||
for item in ${Upgrade[*]}
|
||||
do
|
||||
printf " %-8s%-7s\n" $item upgrade
|
||||
|
||||
done
|
||||
|
||||
for item in ${Upgrade[*]}
|
||||
do
|
||||
tput cuu1
|
||||
done
|
||||
|
||||
for item in ${Upgrade[*]}
|
||||
do
|
||||
sudo pip install $item --upgrade >> output.t
|
||||
printf " %-8s%-7s %-4s\n" $item upgrade done
|
||||
done
|
||||
|
||||
|
||||
|
||||
echo " "
|
||||
echo " "
|
||||
echo " ====================="
|
||||
echo " | Installing SimPEG |"
|
||||
echo " ====================="
|
||||
echo " "
|
||||
echo " "
|
||||
cd ~
|
||||
|
||||
|
||||
git clone https://github.com/simpeg/simpeg.git >> output.t
|
||||
cd simpeg/SimPEG/
|
||||
python setup.py >> output.t
|
||||
cd ~
|
||||
|
||||
mkdir petsc
|
||||
cd petsc
|
||||
|
||||
echo " "
|
||||
echo " "
|
||||
echo " ===================="
|
||||
echo " | Installing PETSc |"
|
||||
echo " ===================="
|
||||
echo " "
|
||||
echo " "
|
||||
wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.4.3.tar.gz
|
||||
|
||||
tar -zxf petsc-3.4.3.tar.gz
|
||||
|
||||
cd petsc-3.4.3
|
||||
|
||||
./configure --with-debugging=no --dowload-mpich=yes --download-blacs=yes --download-f-blas-lapack=yes --download-scalapack=yes --download-mumps=yes --download-ml=yes --download-spooles=yes --download-hypre=yes --dowload-trilinos=yes --download-metis=yes --download-parmetis=yes --download-umfpack=yes --download-ptscotch=yes --download-superlu=yes --download-superlu_dist=yes --download-essl=yes --download-eucild=yes --download-spai=yes --download-mpi4py=yes --download-petsc4py=yes --download-scientificpython=yes
|
||||
|
||||
|
||||
echo "export PETSC_DIR=/home/${USER}/petsc/petsc-3.4.3" >> ~/.bashrc
|
||||
echo "export PETSC_ARCH=arch-linux2-c-opt" >> ~/.bashrc
|
||||
export PETSC_DIR=/home/${USER}/petsc/petsc-3.4.3
|
||||
export PETSC_ARCH=arch-linux2-c-opt
|
||||
. ~/.bashrc
|
||||
|
||||
make PETSC_DIR=/home/${USER}/petsc/petsc-3.4.3 PETSC_ARCH=arch-linux2-c-opt all
|
||||
make PETSC_DIR=/home/${USER}/petsc/petsc-3.4.3 PETSC_ARCH=arch-linux2-c-opt test
|
||||
|
||||
cd ~/petsc
|
||||
echo " "
|
||||
echo " "
|
||||
echo " ======================="
|
||||
echo " | Installing PETSc4PY |"
|
||||
echo " ======================="
|
||||
echo " "
|
||||
echo " "
|
||||
git clone https://bitbucket.org/petsc/petsc4py.git
|
||||
cd petsc4py/
|
||||
python setup.py build >> output.t
|
||||
python setup.py install --prefix=~/petsc >> output.t
|
||||
|
||||
echo "export PYTHONPATH=~/petsc/lib/python2.7/site-packages:/home/$USER/simpeg:${PYTHONPATH}" >> ~/.bashrc
|
||||
|
||||
cd ~
|
||||
source ~/.bashrc
|
||||
Reference in New Issue
Block a user