lattices.py using now the c module
Former-commit-id: 52cecb23a8757726bcac796417ebade8242d687a
This commit is contained in:
Marek Nečada
parent
796c7d7289
commit
e2a2100b57
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@ -6,7 +6,7 @@ nx = np.newaxis
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import time
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import scipy
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import sys
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from qpms_c import get_mn_y # TODO be explicit about what is imported
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from qpms_c import get_mn_y, trans_calculator # TODO be explicit about what is imported
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from .qpms_p import cart2sph, nelem2lMax, Ã, B̃ # TODO be explicit about what is imported
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def _time_b(active = True, name = None, step = None):
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@ -83,6 +83,7 @@ class Scattering(object):
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self.N = positions.shape[0]
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self.k_0 = k_0
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self.lMax = lMax if lMax else nelem2lMax(TMatrices.shape[-1])
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self.tc = trans_calculator(lMax)
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nelem = lMax * (lMax + 2) #!
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self.nelem = nelem #!
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self.prepared = False
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@ -91,7 +92,7 @@ class Scattering(object):
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def prepare(self, keep_interaction_matrix = False, verbose=False):
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btime = _time_b(verbose)
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if not self.prepared:
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if not self.interaction_matrix:
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if self.interaction_matrix is None:
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self.build_interaction_matrix(verbose=verbose)
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self.lupiv = scipy.linalg.lu_factor(self.interaction_matrix,overwrite_a = not keep_interaction_matrix)
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if not keep_interaction_matrix:
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@ -106,6 +107,7 @@ class Scattering(object):
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nelem = len(my)
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leftmatrix = np.zeros((N,2,nelem,N,2,nelem), dtype=complex)
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sbtime = _time_b(verbose, step = 'Calculating interparticle translation coefficients')
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"""
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for i in range(N):
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for j in range(N):
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for yi in range(nelem):
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@ -118,6 +120,20 @@ class Scattering(object):
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leftmatrix[j,1,yj,i,1,yi] = a
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leftmatrix[j,0,yj,i,1,yi] = b
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leftmatrix[j,1,yj,i,0,yi] = b
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"""
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kdji = cart2sph(self.positions[:,nx,:] - self.positions[nx,:,:])
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kdji[:,:,0] *= self.k_0
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# get_AB array structure: [j,yj,i,yi]
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a, b = self.tc.get_AB(my[nx,:,nx,nx],ny[nx,:,nx,nx],my[nx,nx,nx,:],ny[nx,nx,nx,:],
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(kdji[:,:,0])[:,nx,:,nx], (kdji[:,:,1])[:,nx,:,nx], (kdji[:,:,2])[:,nx,:,nx],
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False,self.J_scat)
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mask = np.broadcast_to(np.eye(N,dtype=bool)[:,nx,:,nx],(N,nelem,N,nelem))
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a[mask] = 0 # no self-translations
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b[mask] = 0
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leftmatrix[:,0,:,:,0,:] = a
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leftmatrix[:,1,:,:,1,:] = a
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leftmatrix[:,0,:,:,1,:] = b
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leftmatrix[:,1,:,:,0,:] = b
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_time_e(sbtime, verbose, step = 'Calculating interparticle translation coefficients')
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# at this point, leftmatrix is the translation matrix
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n2id = np.identity(2*nelem)
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@ -199,6 +215,7 @@ class Scattering_2D_zsym(Scattering):
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self.my, self.ny = get_mn_y(self.lMax)
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self.TE_NMz = (self.my + self.ny) % 2
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self.TM_NMz = 1 - self.TE_NMz
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self.tc = trans_calculator(lMax)
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# TODO možnost zadávat T-matice rovnou ve zhuštěné podobě
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TMatrices_TE = TMatrices[...,self.TE_NMz[:,nx],self.TE_yz[:,nx],self.TE_NMz[nx,:],self.TE_yz[nx,:]]
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TMatrices_TM = TMatrices[...,self.TM_NMz[:,nx],self.TM_yz[:,nx],self.TM_NMz[nx,:],self.TM_yz[nx,:]]
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@ -216,13 +233,13 @@ class Scattering_2D_zsym(Scattering):
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btime = _time_b(verbose)
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if (TE_or_TM == 0): #TE
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if not self.prepared_TE:
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if not self.interaction_matrix_TE:
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if self.interaction_matrix_TE is None:
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self.build_interaction_matrix(0, verbose)
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self.lupiv_TE = scipy.linalg.lu_factor(self.interaction_matrix_TE, overwrite_a = not keep_interaction_matrix)
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self.prepared_TE = True
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if (TE_or_TM == 1): #TM
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if not self.prepared_TM:
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if not self.interaction_matrix_TM:
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if self.interaction_matrix_TM is None:
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self.build_interaction_matrix(1, verbose)
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self.lupiv_TM = scipy.linalg.lu_factor(self.interaction_matrix_TM, overwrite_a = not keep_interaction_matrix)
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self.prepared_TM = True
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@ -249,9 +266,29 @@ class Scattering_2D_zsym(Scattering):
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EoMl = (1,)
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elif (TE_or_TM is None):
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EoMl = (0,1)
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sbtime = _time_b(verbose, step = 'Calculating interparticle translation coefficients')
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kdji = cart2sph(self.positions[:,nx,:] - self.positions[nx,:,:])
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kdji[:,:,0] *= self.k_0
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# get_AB array structure: [j,yj,i,yi]
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# FIXME I could save some memory by calculating only half of these coefficients
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a, b = self.tc.get_AB(my[nx,:,nx,nx],ny[nx,:,nx,nx],my[nx,nx,nx,:],ny[nx,nx,nx,:],
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(kdji[:,:,0])[:,nx,:,nx], (kdji[:,:,1])[:,nx,:,nx], (kdji[:,:,2])[:,nx,:,nx],
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False,self.J_scat)
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mask = np.broadcast_to(np.eye(N,dtype=bool)[:,nx,:,nx],(N,nelem,N,nelem))
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a[mask] = 0 # no self-translations
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b[mask] = 0
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print(np.isnan(np.min(a)))
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_time_e(sbtime, verbose, step = 'Calculating interparticle translation coefficients')
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for EoM in EoMl:
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leftmatrix = np.zeros((N,nelem,N,nelem), dtype=complex)
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sbtime = _time_b(verbose, step = 'Calculating interparticle translation coefficients, T%s part' % ('M' if EoM else 'E'))
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y = np.arange(nelem)
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yi = y[nx,nx,nx,:]
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yj = y[nx,:,nx,nx]
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mask = np.broadcast_to((((yi - yj) % 2) == 0),(N,nelem,N,nelem))
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leftmatrix[mask] = a[mask]
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mask = np.broadcast_to((((yi - yj) % 2) != 0),(N,nelem,N,nelem))
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leftmatrix[mask] = b[mask]
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""" # we use to calculate the AB coefficients here
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for i in range(N):
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for j in range(i):
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for yi in range(nelem):
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@ -264,6 +301,7 @@ class Scattering_2D_zsym(Scattering):
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leftmatrix[j,yj,i,yi] = tr
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leftmatrix[i,yi,j,yj] = tr if (0 == (my[yj]+my[yi]) % 2) else -tr
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_time_e(sbtime, verbose, step = 'Calculating interparticle translation coefficients, T%s part' % ('M' if EoM else 'E'))
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"""
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for j in range(N):
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leftmatrix[j] = - np.tensordot(self.TMatrices_TM[j] if EoM else self.TMatrices_TE[j],leftmatrix[j],
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axes = ([-1],[0]))
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@ -273,6 +311,8 @@ class Scattering_2D_zsym(Scattering):
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self.interaction_matrix_TE = leftmatrix
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if EoM == 1:
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self.interaction_matrix_TM = leftmatrix
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a = None
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b = None
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_time_e(btime, verbose)
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def scatter_partial(self, TE_or_TM, pq_0, verbose = False):
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@ -5,6 +5,8 @@ import numpy as np
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cimport numpy as np
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cimport cython
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from cython.parallel cimport parallel, prange
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#cimport openmp
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#openmp.omp_set_dynamic(1)
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## Auxillary function for retrieving the "meshgrid-like" indices; inc. nmax
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@cython.boundscheck(False)
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@ -371,10 +373,65 @@ cdef void trans_calculator_loop_E_C_DD_iiiidddii_As_lllldddbl_DD(char **args, np
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# FIXME ERROR HANDLING!!! requires correct import and different data passed (see scipy's generated ufuncs)
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# sf_error.check_fpe(func_name)
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@cython.boundscheck(False)
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@cython.wraparound(False)
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cdef void trans_calculator_parallel_loop_E_C_DD_iiiidddii_As_lllldddbl_DD(char **args, np.npy_intp *dims, np.npy_intp *steps, void *data) nogil:
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# E stands for error value (int), C for qpms_trans_calculator*
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cdef np.npy_intp i, n = dims[0]
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cdef void *func = (<trans_calculator_get_X_data_t*>data)[0].cmethod
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#cdef complex double (*func)(qpms_trans_calculator*, double complex *, double complex *, int, int, int, int, double, double, double, int, int) nogil = (<trans_calculator_get_X_data_t*>data)[0].cmethod
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cdef qpms_trans_calculator* c = (<trans_calculator_get_X_data_t*>data)[0].c
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#cdef char *func_name= <char*>(<void**>data)[1] # i am not using this, nor have I saved func_name to data
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cdef char *ip0
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cdef char *ip1
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cdef char *ip2
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cdef char *ip3
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cdef char *ip4
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cdef char *ip5
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cdef char *ip6
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cdef char *ip7
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cdef char *ip8
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cdef char *op0
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cdef char *op1
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cdef int errval
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for i in prange(n): # iterating over dimensions
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ip0 = args[0] + i * steps[0]
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ip1 = args[1] + i * steps[1]
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ip2 = args[2] + i * steps[2]
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ip3 = args[3] + i * steps[3]
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ip4 = args[4] + i * steps[4]
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ip5 = args[5] + i * steps[5]
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ip6 = args[6] + i * steps[6]
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ip7 = args[7] + i * steps[7]
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ip8 = args[8] + i * steps[8]
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op0 = args[9] + i * steps[9]
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op1 = args[10] + i * steps[10]
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#errval = func(
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errval = (<int(*)(qpms_trans_calculator*, double complex *, double complex *, int, int, int, int, double, double, double, int, int) nogil>func)(
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c,
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<cdouble *> op0,
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<cdouble *> op1,
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<int>(<np.npy_long*>ip0)[0],
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<int>(<np.npy_long*>ip1)[0],
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<int>(<np.npy_long*>ip2)[0],
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<int>(<np.npy_long*>ip3)[0],
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<double>(<np.npy_double*>ip4)[0],
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<double>(<np.npy_double*>ip5)[0],
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<double>(<np.npy_double*>ip6)[0],
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<int>(<np.npy_bool*>ip7)[0],
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<int>(<np.npy_long*>ip8)[0],
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)
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# TODO if (errval != 0): ...
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# FIXME ERROR HANDLING!!! requires correct import and different data passed (see scipy's generated ufuncs)
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# sf_error.check_fpe(func_name)
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cdef np.PyUFuncGenericFunction trans_calculator_get_X_loop_funcs[1]
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trans_calculator_get_X_loop_funcs[0] = trans_calculator_loop_D_Ciiiidddii_As_D_lllldddbl
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cdef np.PyUFuncGenericFunction trans_calculator_get_AB_loop_funcs[1]
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#trans_calculator_get_AB_loop_funcs[0] = trans_calculator_parallel_loop_E_C_DD_iiiidddii_As_lllldddbl_DD
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trans_calculator_get_AB_loop_funcs[0] = trans_calculator_loop_E_C_DD_iiiidddii_As_lllldddbl_DD
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cdef void *trans_calculator_get_AB_elementwise_funcs[1]
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trans_calculator_get_AB_elementwise_funcs[0] = <void *>qpms_trans_calculator_get_AB_p_ext
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@ -419,6 +419,10 @@ complex double qpms_trans_calculator_get_A_buf(const qpms_trans_calculator *c,
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bool r_ge_d, qpms_bessel_t J,
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complex double *bessel_buf, double *legendre_buf) {
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if (r_ge_d) J = QPMS_BESSEL_REGULAR;
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if (0 == kdlj.r && J != QPMS_BESSEL_REGULAR)
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// TODO warn?
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return NAN+I*NAN;
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switch(c->normalization) {
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case QPMS_NORMALIZATION_TAYLOR:
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{
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@ -451,6 +455,9 @@ complex double qpms_trans_calculator_get_B_buf(const qpms_trans_calculator *c,
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bool r_ge_d, qpms_bessel_t J,
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complex double *bessel_buf, double *legendre_buf) {
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if (r_ge_d) J = QPMS_BESSEL_REGULAR;
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if (0 == kdlj.r && J != QPMS_BESSEL_REGULAR)
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// TODO warn?
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return NAN+I*NAN;
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switch(c->normalization) {
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case QPMS_NORMALIZATION_TAYLOR:
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{
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@ -486,6 +493,12 @@ int qpms_trans_calculator_get_AB_buf_p(const qpms_trans_calculator *c,
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bool r_ge_d, qpms_bessel_t J,
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complex double *bessel_buf, double *legendre_buf) {
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if (r_ge_d) J = QPMS_BESSEL_REGULAR;
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if (0 == kdlj.r && J != QPMS_BESSEL_REGULAR) {
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*Adest = NAN+I*NAN;
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*Bdest = NAN+I*NAN;
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// TODO warn? different return value?
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return 0;
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}
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switch(c->normalization) {
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case QPMS_NORMALIZATION_TAYLOR:
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{
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2
setup.py
2
setup.py
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@ -23,7 +23,7 @@ qpms_c = Extension('qpms_c',
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extra_compile_args=['-std=c99','-ggdb','-O3',
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'-DDISABLE_NDEBUG', # uncomment to enable assertions in the modules
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],
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libraries=['gsl', 'blas'],
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libraries=['gsl', 'blas', 'omp'],
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runtime_library_dirs=os.environ['LD_LIBRARY_PATH'].split(':')
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)
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