Merge branch 'master' of bitbucket.org:glavaux/cosmotool
This commit is contained in:
Guilhem Lavaux
commit
e698201f38
@ -1,11 +1,12 @@
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from cpython cimport bool
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from cython cimport view
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from cython.parallel import prange, parallel
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from openmp cimport omp_get_max_threads, omp_get_thread_num
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from libc.math cimport sin, cos, abs, floor, sqrt
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import numpy as np
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cimport numpy as npx
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cimport cython
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from copy cimport *
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from openmp cimport omp_get_max_threads, omp_get_thread_num
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ctypedef npx.float64_t DTYPE_t
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DTYPE=np.float64
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@ -297,8 +298,7 @@ cdef void INTERNAL_project_cic_no_mass(npx.ndarray[DTYPE_t, ndim=3] g,
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cdef double half_Box = 0.5*Lbox
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cdef double delta_Box = Ngrid/Lbox
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cdef int i
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cdef double a[3]
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cdef double c[3]
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cdef double a[3], c[3]
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cdef int b[3]
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cdef int do_not_put
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@ -334,10 +334,8 @@ cdef void INTERNAL_project_cic_no_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g,
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cdef double half_Box = 0.5*Lbox
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cdef double delta_Box = Ngrid/Lbox
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cdef int i
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cdef double a[3]
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cdef double c[3]
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cdef int b[3]
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cdef int b1[3]
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cdef double a[3], c[3]
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cdef int b[3], b1[3]
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cdef int do_not_put
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for i in range(x.shape[0]):
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@ -375,8 +373,7 @@ cdef void INTERNAL_project_cic_with_mass(npx.ndarray[DTYPE_t, ndim=3] g,
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cdef double half_Box = 0.5*Lbox
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cdef double delta_Box = Ngrid/Lbox
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cdef int i
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cdef double a[3]
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cdef double c[3]
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cdef double a[3], c[3]
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cdef DTYPE_t m0
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cdef int b[3]
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@ -413,10 +410,8 @@ cdef void INTERNAL_project_cic_with_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g
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cdef double half_Box = 0.5*Lbox, m0
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cdef double delta_Box = Ngrid/Lbox
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cdef int i
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cdef double a[3]
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cdef double c[3]
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cdef int b[3]
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cdef int b1[3]
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cdef double a[3], c[3]
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cdef int b[3], b1[3]
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for i in range(x.shape[0]):
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@ -537,23 +532,10 @@ cdef DTYPE_t cube_integral(DTYPE_t u[3], DTYPE_t u0[3], int r[1]) nogil:
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@cython.boundscheck(False)
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@cython.cdivision(True)
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cdef DTYPE_t mysum(DTYPE_t *v, int q) nogil:
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cdef int i
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cdef DTYPE_t s
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s = 0
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for i in xrange(q):
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s += v[i]
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return s
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@cython.boundscheck(False)
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@cython.cdivision(True)
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cdef DTYPE_t cube_integral_trilin(DTYPE_t u[3], DTYPE_t u0[3], int r[1], DTYPE_t vertex_value[8], int err[1]) nogil:
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cdef DTYPE_t cube_integral_trilin(DTYPE_t u[3], DTYPE_t u0[3], int r[1], DTYPE_t vertex_value[8]) nogil:
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cdef DTYPE_t alpha_max
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cdef DTYPE_t I, tmp_a
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cdef DTYPE_t v[3]
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cdef DTYPE_t term[4]
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cdef DTYPE_t v[3], term[4]
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cdef int i, j, q
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alpha_max = 10.0 # A big number
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@ -571,11 +553,7 @@ cdef DTYPE_t cube_integral_trilin(DTYPE_t u[3], DTYPE_t u0[3], int r[1], DTYPE_t
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if tmp_a < alpha_max:
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alpha_max = tmp_a
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j = i
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if (u0[i] >= 0 || u0[i] <= 1)
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err[0] = 1
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return 0
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I = compute_projection(vertex_value, u, u0, alpha_max)
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for i in xrange(3):
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@ -589,7 +567,7 @@ cdef DTYPE_t cube_integral_trilin(DTYPE_t u[3], DTYPE_t u0[3], int r[1], DTYPE_t
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@cython.boundscheck(False)
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cdef DTYPE_t integrator0(DTYPE_t[:,:,:] density,
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DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1], int err[1]) nogil:
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DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1]) nogil:
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cdef DTYPE_t d
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d = density[iu0[0], iu0[1], iu0[2]]
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@ -598,24 +576,15 @@ cdef DTYPE_t integrator0(DTYPE_t[:,:,:] density,
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@cython.boundscheck(False)
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cdef DTYPE_t integrator1(DTYPE_t[:,:,:] density,
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DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1], int err[1]) nogil:
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DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1]) nogil:
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cdef DTYPE_t vertex_value[8]
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cdef DTYPE_t d
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cdef int a[3][2]
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cdef int i
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cdef int a[3][2], i
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for i in xrange(3):
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# if u[i] < 0:
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# a[i][0] = iu0[i]-1
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# a[i][1] = iu0[i]
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# else:
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a[i][0] = iu0[i]
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a[i][1] = iu0[i]+1
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with gil:
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assert a[i][0] >= 0
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assert a[i][1] < density.shape[i]
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vertex_value[0 + 2*0 + 4*0] = density[a[0][0], a[1][0], a[2][0]]
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vertex_value[1 + 2*0 + 4*0] = density[a[0][1], a[1][0], a[2][0]]
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vertex_value[0 + 2*1 + 4*0] = density[a[0][0], a[1][1], a[2][0]]
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@ -626,8 +595,7 @@ cdef DTYPE_t integrator1(DTYPE_t[:,:,:] density,
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vertex_value[0 + 2*1 + 4*1] = density[a[0][0], a[1][1], a[2][1]]
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vertex_value[1 + 2*1 + 4*1] = density[a[0][1], a[1][1], a[2][1]]
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# return cube_integral(u, u0, jumper)*d
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return cube_integral_trilin(u, u0, jumper, vertex_value, err)
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return cube_integral_trilin(u, u0, jumper, vertex_value)
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@ -635,15 +603,11 @@ cdef DTYPE_t integrator1(DTYPE_t[:,:,:] density,
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cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
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DTYPE_t a_u[3],
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DTYPE_t min_distance,
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DTYPE_t max_distance, DTYPE_t[:] shifter, int integrator_id, int out_err[1]) nogil:
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DTYPE_t max_distance, DTYPE_t[:] shifter, int integrator_id) nogil except? 0:
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cdef DTYPE_t u[3]
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cdef DTYPE_t ifu0[3]
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cdef DTYPE_t u0[3]
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cdef DTYPE_t utot[3]
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cdef DTYPE_t u[3], ifu0[3], u0[3], utot[3]
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cdef int u_delta[3]
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cdef int iu0[3]
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cdef int err[1]
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cdef int i
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cdef int N = density.shape[0]
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cdef int half_N = density.shape[0]/2
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@ -652,10 +616,8 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
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cdef int jumper[1]
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cdef DTYPE_t (*integrator)(DTYPE_t[:,:,:],
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DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1], int err[1]) nogil
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DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1]) nogil
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out_err[0] = 0
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if integrator_id == 0:
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integrator = integrator0
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else:
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@ -673,12 +635,12 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
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u0[i] = ifu0[i]-iu0[i]
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u_delta[i] = 1 if iu0[i] > 0 else -1
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if (not ((iu0[i]>= 0) and (iu0[i] < N))):
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out_err[0] = 1
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return 0
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with gil:
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raise RuntimeError("iu0[%d] = %d !!" % (i,iu0[i]))
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if (not (u0[i]>=0 and u0[i]<=1)):
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out_err[0] = 1
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return 0
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with gil:
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raise RuntimeError("u0[%d] = %g !" % (i,u0[i]))
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completed = 0
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if ((iu0[0] >= N) or (iu0[0] <= 0) or
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@ -689,12 +651,8 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
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I0 = 0
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jumper[0] = 0
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while completed == 0:
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err[0] = 0
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I0 += integrator(density, u, u0, u_delta, iu0, jumper, err)
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if err[0] == 1:
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out_err[0] = 1
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return 0
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I0 += integrator(density, u, u0, u_delta, iu0, jumper)
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if u[jumper[0]] < 0:
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iu0[jumper[0]] -= 1
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@ -711,7 +669,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
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else:
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dist2 = 0
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for i in range(3):
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delta = iu0[i]+u0[i]-half_N
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delta = iu0[i]+u0[i]-half_N-shifter[i]
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dist2 += delta*delta
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if (dist2 > max_distance2):
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@ -727,24 +685,19 @@ def line_of_sight_projection(DTYPE_t[:,:,:] density not None,
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DTYPE_t min_distance,
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DTYPE_t max_distance, DTYPE_t[:] shifter not None, int integrator_id=0):
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cdef DTYPE_t u[3]
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cdef int out_err[1]
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cdef DTYPE_t v
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u[0] = a_u[0]
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u[1] = a_u[1]
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u[2] = a_u[2]
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v = C_line_of_sight_projection(density,
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C_line_of_sight_projection(density,
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u,
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min_distance,
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max_distance, shifter, integrator_id, out_err)
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if out_err[0] == 1:
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raise RuntimeError("Error occured during integration")
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return v
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max_distance, shifter, integrator_id)
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cdef double _spherical_projloop(double theta, double phi, DTYPE_t[:,:,:] density,
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double min_distance, double max_distance,
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DTYPE_t[:] shifter, int integrator_id, int out_err[1]) nogil:
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DTYPE_t[:] shifter, int integrator_id) nogil:
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cdef DTYPE_t u0[3]
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stheta = sin(theta)
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@ -752,19 +705,7 @@ cdef double _spherical_projloop(double theta, double phi, DTYPE_t[:,:,:] density
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u0[1] = sin(phi)*stheta
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u0[2] = cos(theta)
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return C_line_of_sight_projection(density, u0, min_distance, max_distance, shifter, integrator_id, out_err)
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@cython.boundscheck(False)
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cdef npx.uint64_t _mysum(int[:] jobs) nogil:
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cdef npx.uint64_t s
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cdef npx.uint64_t N
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cdef int i
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s = 0
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N = jobs.shape[0]
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for i in xrange(N):
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s += jobs[i]
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return s
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return C_line_of_sight_projection(density, u0, min_distance, max_distance, shifter, integrator_id)
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@cython.boundscheck(False)
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@ -781,9 +722,9 @@ def spherical_projection(int Nside,
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cdef DTYPE_t[:] outm
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cdef int[:] job_done
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cdef npx.ndarray[DTYPE_t, ndim=1] outm_array
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cdef long N
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cdef long N, N0
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cdef double stheta
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cdef int out_err[1]
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cdef int tid
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if shifter is None:
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shifter = view.array(shape=(3,), format=FORMAT_DTYPE, itemsize=sizeof(DTYPE_t))
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@ -797,20 +738,22 @@ def spherical_projection(int Nside,
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p = pb.ProgressBar(maxval=outm.size,widgets=[pb.Bar(), pb.ETA()]).start()
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N = omp_get_max_threads()
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N0 = outm.size
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if booster < 0:
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booster = 1000
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job_done = view.array(shape=(N,), format="i", itemsize=sizeof(int))
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job_done[:] = 0
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theta,phi = hp.pix2ang(Nside, np.arange(outm.size))
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if booster <= 0:
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booster = density.size / 100 / N
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theta,phi = hp.pix2ang(Nside, np.arange(N0))
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with nogil, parallel():
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for i in prange(N):
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if omp_get_thread_num() == 0 and progress != 0 and (i%booster) == 0:
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tid = omp_get_thread_num()
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for i in prange(N0):
|
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if progress != 0 and (i%booster) == 0:
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with gil:
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p.update(_mysum(job_done))
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outm[i] = _spherical_projloop(theta[i], phi[i], density_view, min_distance, max_distance, shifter, integrator_id, out_err)
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job_done[omp_get_thread_num()] = i
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outm[i] = _spherical_projloop(theta[i], phi[i], density_view, min_distance, max_distance, shifter, integrator_id)
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job_done[tid] += 1
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if progress:
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p.finish()
|
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|
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22
python/copy.pxd
Normal file
22
python/copy.pxd
Normal file
@ -0,0 +1,22 @@
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cimport cython
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cimport numpy as npx
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ctypedef fused sum_type:
|
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cython.int
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cython.float
|
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npx.uint64_t
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npx.uint32_t
|
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|
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@cython.boundscheck(False)
|
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cdef inline sum_type _mysum(sum_type[:] jobs) nogil:
|
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cdef sum_type s
|
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cdef npx.uint64_t N
|
||||
cdef int i
|
||||
|
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s = 0
|
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N = jobs.shape[0]
|
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for i in xrange(N):
|
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s += jobs[i]
|
||||
return s
|
||||
|
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|
||||
@ -7,6 +7,8 @@
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#include <H5Cpp.h>
|
||||
#include "hdf5_array.hpp"
|
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#include <iostream>
|
||||
#include <boost/format.hpp>
|
||||
#include <boost/bind.hpp>
|
||||
|
||||
using namespace std;
|
||||
using namespace CosmoTool;
|
||||
@ -17,8 +19,13 @@ struct VCoord{
|
||||
float v[3];
|
||||
};
|
||||
|
||||
template<int i>
|
||||
ComputePrecision getVelocity(const VCoord& v)
|
||||
using boost::format;
|
||||
using boost::str;
|
||||
typedef boost::multi_array<float, 2> array_type;
|
||||
typedef boost::multi_array<float, 3> array3_type;
|
||||
typedef boost::multi_array<float, 4> array4_type;
|
||||
|
||||
ComputePrecision getVelocity(const VCoord& v, int i)
|
||||
{
|
||||
return v.v[i];
|
||||
}
|
||||
@ -32,11 +39,51 @@ typedef SPHSmooth<VCoord> MySmooth;
|
||||
typedef MySmooth::SPHTree MyTree;
|
||||
typedef MyTree::Cell MyCell;
|
||||
|
||||
template<typename FuncT>
|
||||
void computeInterpolatedField(MyTree *tree1, double boxsize, int Nres, double cx, double cy, double cz,
|
||||
array3_type& bins, array3_type& arr, FuncT func, double rLimit2)
|
||||
{
|
||||
#pragma omp parallel
|
||||
{
|
||||
MySmooth smooth1(tree1, N_SPH);
|
||||
|
||||
#pragma omp for schedule(dynamic)
|
||||
for (int rz = 0; rz < Nres; rz++)
|
||||
{
|
||||
double pz = (rz)*boxsize/Nres-cz;
|
||||
|
||||
cout << format("[%d] %d / %d") % omp_get_thread_num() % rz % Nres << endl;
|
||||
for (int ry = 0; ry < Nres; ry++)
|
||||
{
|
||||
double py = (ry)*boxsize/Nres-cy;
|
||||
for (int rx = 0; rx < Nres; rx++)
|
||||
{
|
||||
double px = (rx)*boxsize/Nres-cx;
|
||||
|
||||
MyTree::coords c = { px, py, pz };
|
||||
|
||||
double r2 = c[0]*c[0]+c[1]*c[1]+c[2]*c[2];
|
||||
if (r2 > rLimit2)
|
||||
{
|
||||
arr[rx][ry][rz] = 0;
|
||||
continue;
|
||||
}
|
||||
|
||||
uint32_t numInCell = bins[rx][ry][rz];
|
||||
if (numInCell > N_SPH)
|
||||
smooth1.fetchNeighbours(c, numInCell);
|
||||
else
|
||||
smooth1.fetchNeighbours(c);
|
||||
|
||||
arr[rx][ry][rz] = smooth1.computeSmoothedValue(c, func);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
typedef boost::multi_array<float, 2> array_type;
|
||||
typedef boost::multi_array<float, 3> array3_type;
|
||||
typedef boost::multi_array<float, 4> array4_type;
|
||||
|
||||
char *fname1, *fname2;
|
||||
double rLimit, boxsize, rLimit2, cx, cy, cz;
|
||||
@ -105,8 +152,6 @@ int main(int argc, char **argv)
|
||||
|
||||
cout << "Creating smoothing filter..." << endl;
|
||||
|
||||
array3_type out_den_1(boost::extents[Nres][Nres][Nres]);
|
||||
array4_type out_v3d_1(boost::extents[Nres][Nres][Nres][3]);
|
||||
// array3_type out_rad_1(boost::extents[Nres][Nres][Nres]);
|
||||
|
||||
cout << "Weighing..." << endl;
|
||||
@ -149,55 +194,18 @@ int main(int argc, char **argv)
|
||||
}
|
||||
|
||||
cout << "Interpolating..." << endl;
|
||||
#pragma omp parallel
|
||||
{
|
||||
MySmooth smooth1(&tree1, N_SPH);
|
||||
|
||||
#pragma omp for schedule(dynamic)
|
||||
for (int rz = 0; rz < Nres; rz++)
|
||||
{
|
||||
double pz = (rz)*boxsize/Nres-cz;
|
||||
|
||||
cout << rz << " / " << Nres << endl;
|
||||
for (int ry = 0; ry < Nres; ry++)
|
||||
{
|
||||
double py = (ry)*boxsize/Nres-cy;
|
||||
for (int rx = 0; rx < Nres; rx++)
|
||||
{
|
||||
double px = (rx)*boxsize/Nres-cx;
|
||||
|
||||
MyTree::coords c = { px, py, pz };
|
||||
|
||||
double r2 = c[0]*c[0]+c[1]*c[1]+c[2]*c[2];
|
||||
if (r2 > rLimit2)
|
||||
{
|
||||
out_v3d_1[rx][ry][rz][0] = 0;
|
||||
out_v3d_1[rx][ry][rz][1] = 0;
|
||||
out_v3d_1[rx][ry][rz][2] = 0;
|
||||
out_den_1[rx][ry][rz] = 0;
|
||||
//out_rad_1[rx][ry][rz] = -1;
|
||||
continue;
|
||||
}
|
||||
|
||||
uint32_t numInCell = bins[rx][ry][rz];
|
||||
if (numInCell > N_SPH)
|
||||
smooth1.fetchNeighbours(c, numInCell);
|
||||
else
|
||||
smooth1.fetchNeighbours(c);
|
||||
|
||||
//out_rad_1[rx][ry][rz] = smooth1.getSmoothingLen();
|
||||
out_v3d_1[rx][ry][rz][0] = smooth1.computeSmoothedValue(c, getVelocity<0>);
|
||||
out_v3d_1[rx][ry][rz][1] = smooth1.computeSmoothedValue(c, getVelocity<1>);
|
||||
out_v3d_1[rx][ry][rz][2] = smooth1.computeSmoothedValue(c, getVelocity<2>);
|
||||
out_den_1[rx][ry][rz] = smooth1.computeSmoothedValue(c, getUnity);
|
||||
}
|
||||
}
|
||||
}
|
||||
array3_type interpolated(boost::extents[Nres][Nres][Nres]);
|
||||
|
||||
computeInterpolatedField(&tree1, boxsize, Nres, cx, cy, cz,
|
||||
bins, interpolated, getUnity, rLimit2);
|
||||
hdf5_write_array(out_f, "density", interpolated);
|
||||
//out_f.flush();
|
||||
for (int i = 0; i < 3; i++) {
|
||||
computeInterpolatedField(&tree1, boxsize, Nres, cx, cy, cz,
|
||||
bins, interpolated, boost::bind(getVelocity, _1, i), rLimit2);
|
||||
hdf5_write_array(out_f, str(format("p%d") % i), interpolated);
|
||||
}
|
||||
|
||||
//hdf5_write_array(out_f, "radii", out_rad_1);
|
||||
hdf5_write_array(out_f, "velocity", out_v3d_1);
|
||||
hdf5_write_array(out_f, "density", out_den_1);
|
||||
|
||||
|
||||
return 0;
|
||||
};
|
||||
|
||||
@ -82,10 +82,14 @@ namespace CosmoTool
|
||||
return internal.currentCenter;
|
||||
}
|
||||
|
||||
template<typename FuncT>
|
||||
ComputePrecision computeSmoothedValue(const typename SPHTree::coords& c,
|
||||
computeParticleValue fun, SPHState *state = 0);
|
||||
FuncT fun, SPHState *state = 0);
|
||||
|
||||
template<typename FuncT>
|
||||
ComputePrecision computeInterpolatedValue(const typename SPHTree::coords& c,
|
||||
computeParticleValue fun, SPHState *state = 0);
|
||||
FuncT fun, SPHState *state = 0);
|
||||
|
||||
ComputePrecision getMaxDistance(const typename SPHTree::coords& c,
|
||||
SPHNode *node) const;
|
||||
|
||||
@ -101,7 +105,8 @@ namespace CosmoTool
|
||||
}
|
||||
// END
|
||||
|
||||
void runForEachNeighbour(runParticleValue fun, SPHState *state = 0);
|
||||
template<typename FuncT>
|
||||
void runForEachNeighbour(FuncT fun, SPHState *state = 0);
|
||||
void addGridSite(const typename SPHTree::coords& c);
|
||||
|
||||
bool hasNeighbours() const;
|
||||
@ -127,12 +132,15 @@ namespace CosmoTool
|
||||
uint32_t maxNgb;
|
||||
SPHTree *tree;
|
||||
|
||||
template<typename FuncT>
|
||||
ComputePrecision computeWValue(const typename SPHTree::coords & c,
|
||||
SPHCell& cell,
|
||||
CoordType d,
|
||||
computeParticleValue fun, SPHState *state);
|
||||
FuncT fun, SPHState *state);
|
||||
|
||||
template<typename FuncT>
|
||||
void runUnrollNode(SPHNode *node,
|
||||
runParticleValue fun);
|
||||
FuncT fun);
|
||||
};
|
||||
|
||||
template<class ValType1, class ValType2, int Ndims>
|
||||
|
||||
@ -21,10 +21,11 @@ SPHSmooth<ValType,Ndims>::~SPHSmooth()
|
||||
}
|
||||
|
||||
template<typename ValType, int Ndims>
|
||||
template<typename FuncT>
|
||||
ComputePrecision SPHSmooth<ValType,Ndims>::computeWValue(const typename SPHTree::coords& c,
|
||||
SPHCell& cell,
|
||||
CoordType d,
|
||||
computeParticleValue fun, SPHState *state)
|
||||
FuncT fun, SPHState *state)
|
||||
{
|
||||
CoordType weight;
|
||||
|
||||
@ -117,9 +118,10 @@ SPHSmooth<ValType,Ndims>::fetchNeighboursOnVolume(const typename SPHTree::coords
|
||||
}
|
||||
|
||||
template<typename ValType, int Ndims>
|
||||
template<typename FuncT>
|
||||
ComputePrecision
|
||||
SPHSmooth<ValType,Ndims>::computeSmoothedValue(const typename SPHTree::coords& c,
|
||||
computeParticleValue fun, SPHState *state)
|
||||
FuncT fun, SPHState *state)
|
||||
{
|
||||
if (state == 0)
|
||||
state = &internal;
|
||||
@ -144,8 +146,9 @@ ComputePrecision interpolateOne(const ValType& t)
|
||||
|
||||
// WARNING ! Cell's weight must be 1 !!!
|
||||
template<typename ValType, int Ndims>
|
||||
template<typename FuncT>
|
||||
ComputePrecision SPHSmooth<ValType,Ndims>::computeInterpolatedValue(const typename SPHTree::coords& c,
|
||||
computeParticleValue fun, SPHState *state)
|
||||
FuncT fun, SPHState *state)
|
||||
{
|
||||
if (state == 0)
|
||||
state = &internal;
|
||||
@ -164,7 +167,8 @@ ComputePrecision SPHSmooth<ValType,Ndims>::computeInterpolatedValue(const typena
|
||||
}
|
||||
|
||||
template<typename ValType, int Ndims>
|
||||
void SPHSmooth<ValType,Ndims>::runForEachNeighbour(runParticleValue fun, SPHState *state)
|
||||
template<typename FuncT>
|
||||
void SPHSmooth<ValType,Ndims>::runForEachNeighbour(FuncT fun, SPHState *state)
|
||||
{
|
||||
if (state == 0)
|
||||
state = &internal;
|
||||
|
||||
Loading…
Reference in New Issue
Block a user