Merge
This commit is contained in:
Guilhem Lavaux
commit
d31d1245c2
@ -47,31 +47,7 @@ find_program(CYTHON cython)
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find_package(Boost 1.53)
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if (ENABLE_SHARP)
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SET(SHARP_SOURCE ${CMAKE_SOURCE_DIR}/external/sharp)
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SET(DEP_BUILD ${CMAKE_SOURCE_DIR}/external/sharp/auto)
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ExternalProject_Add(sharp
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SOURCE_DIR ${SHARP_SOURCE}
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BUILD_IN_SOURCE 1
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CONFIGURE_COMMAND ${SHARP_SOURCE}/configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD}
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BUILD_COMMAND ${CMAKE_MAKE_PROGRAM}
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INSTALL_COMMAND echo "No install"
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)
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SET(CUTILS_LIBRARY ${DEP_BUILD}/lib/libc_utils.a)
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SET(FFTPACK_LIBRARY ${DEP_BUILD}/lib/libfftpack.a)
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SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a)
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SET(SHARP_LIBRARIES ${SHARP_LIBRARY} ${FFTPACK_LIBRARY} ${CUTILS_LIBRARY})
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SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include)
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endif (ENABLE_SHARP)
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SET(OMPTL_BUILD_DIR ${CMAKE_BINARY_DIR}/omptl-prefix/src/omptl)
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ExternalProject_Add(omptl
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URL ${CMAKE_SOURCE_DIR}/external/omptl-20120422.tar.bz2
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CONFIGURE_COMMAND echo "No configure"
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BUILD_COMMAND echo "No build"
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INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${OMPTL_BUILD_DIR} ${CMAKE_BINARY_DIR}/external/stage/include/omptl
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)
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include_directories(${OMPTL_BUILD_DIR}/..)
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include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
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set(HDF5_FIND_COMPONENTS HL CXX)
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if(HDF5_ROOTDIR)
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29
external/external_build.cmake
vendored
Normal file
29
external/external_build.cmake
vendored
Normal file
@ -0,0 +1,29 @@
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if (ENABLE_SHARP)
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SET(SHARP_SOURCE ${CMAKE_SOURCE_DIR}/external/sharp)
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SET(DEP_BUILD ${CMAKE_SOURCE_DIR}/external/sharp/auto)
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ExternalProject_Add(sharp
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SOURCE_DIR ${SHARP_SOURCE}
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BUILD_IN_SOURCE 1
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CONFIGURE_COMMAND ${SHARP_SOURCE}/configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD}
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BUILD_COMMAND ${CMAKE_MAKE_PROGRAM}
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INSTALL_COMMAND echo "No install"
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)
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SET(CUTILS_LIBRARY ${DEP_BUILD}/lib/libc_utils.a)
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SET(FFTPACK_LIBRARY ${DEP_BUILD}/lib/libfftpack.a)
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SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a)
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SET(SHARP_LIBRARIES ${SHARP_LIBRARY} ${FFTPACK_LIBRARY} ${CUTILS_LIBRARY})
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SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include)
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endif (ENABLE_SHARP)
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SET(OMPTL_BUILD_DIR ${CMAKE_BINARY_DIR}/omptl-prefix/src/omptl)
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ExternalProject_Add(omptl
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URL ${CMAKE_SOURCE_DIR}/external/omptl-20120422.tar.bz2
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CONFIGURE_COMMAND echo "No configure"
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BUILD_COMMAND echo "No build"
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INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${OMPTL_BUILD_DIR} ${CMAKE_BINARY_DIR}/external/stage/include/omptl
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)
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include_directories(${OMPTL_BUILD_DIR}/..)
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@ -7,7 +7,7 @@ import borgadaptor as ba
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def gen_posgrid(N, L):
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""" Generate an ordered lagrangian grid"""
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ix = np.arange(N)*L/N
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ix = (np.arange(N)*L/N).astype(np.float32)
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x = ix[:,None,None].repeat(N, axis=1).repeat(N, axis=2)
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y = ix[None,:,None].repeat(N, axis=0).repeat(N, axis=2)
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@ -95,7 +95,9 @@ def run_generation(input_borg, a_borg, a_ic, cosmo, supersample=1, do_lpt2=True,
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print("velmul=%lg" % (cosmo['h']*velmul))
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density = cgrowth.D(1)/cgrowth.D(a_borg)*np.fft.irfftn(lpt.dhat)*(supersample*N/L)**3
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lpt.cube.dhat = lpt.dhat
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density = lpt.cube.irfft()
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density *= (cgrowth.D(1)/cgrowth.D(a_borg))
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return posx,vel,density,N*supersample,L,a_ic,cosmo
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@ -117,7 +119,9 @@ def whitify(density, L, cosmo, supergenerate=1, func='HU_WIGGLES'):
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Pk = build_Pk()
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Pk[0,0,0]=1
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density_hat = np.fft.rfftn(density)*(L/N)**3
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cube = CubeFT(N, L)
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cube.density = density
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density_hat = cube.rfft()
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density_hat /= np.sqrt(Pk)
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Ns = N*supergenerate
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@ -152,6 +156,8 @@ def whitify(density, L, cosmo, supergenerate=1, func='HU_WIGGLES'):
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print np.where(np.isnan(density_hat_super))[0].size
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cube = CubeFT(Ns, L)
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cube.dhat = density_hat_super
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return np.fft.irfftn(density_hat_super)*Ns**1.5
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@ -1,7 +1,40 @@
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import multiprocessing
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import pyfftw
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import weakref
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import numpy as np
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import cosmolopy as cpy
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class CubeFT(object):
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def __init__(self, L, N, max_cpu=-1):
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self.N = N
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self.align = pyfftw.simd_alignment
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self.L = L
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self.max_cpu = multiprocessing.cpu_count() if max_cpu < 0 else max_cpu
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self._dhat = pyfftw.n_byte_align_empty((self.N,self.N,self.N/2+1), self.align, dtype='complex64')
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self._density = pyfftw.n_byte_align_empty((self.N,self.N,self.N), self.align, dtype='float32')
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self.irfft = pyfftw.FFTW(self._dhat, self._density, axes=(0,1,2), direction='FFTW_BACKWARD', threads=self.max_cpu, normalize_idft=False)
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self.rfft = pyfftw.FFTW(self._density, self._dhat, axes=(0,1,2), threads=self.max_cpu, normalize_idft=False)
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def rfft(self):
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return self.rfft()*(self.L/self.N)**3
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def irfft(self):
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return self.irfft()/self.L**3
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def get_dhat(self):
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return self._dhat
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def set_dhat(self, in_dhat):
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self._dhat[:] = in_dhat
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dhat = property(get_dhat, set_dhat, None)
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def get_density(self):
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return self._density
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def set_density(self, d):
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self._density[:] = d
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density = property(get_density, set_density, None)
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class CosmoGrowth(object):
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def __init__(self, **cosmo):
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@ -42,11 +75,20 @@ class CosmoGrowth(object):
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class LagrangianPerturbation(object):
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def __init__(self,density,L, fourier=False, supersample=1):
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def __init__(self,density,L, fourier=False, supersample=1, max_cpu=-1):
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self.L = L
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self.N = density.shape[0]
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self.dhat = np.fft.rfftn(density)*(L/self.N)**3 if not fourier else density
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self.max_cpu = max_cpu
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self.cube = CubeFT(self.L, self.N, max_cpu=max_cpu)
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if not fourier:
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self.cube.density = density
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self.dhat = self.cube.rfft().copy()
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else:
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self.dhat = density.copy()
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if supersample > 1:
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self.upgrade_sampling(supersample)
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self.ik = np.fft.fftfreq(self.N, d=L/self.N)*2*np.pi
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@ -65,9 +107,11 @@ class LagrangianPerturbation(object):
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self.dhat = dhat_new
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self.N = N2
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self.cube = CubeFT(self.L, self.N, max_cpu=self.max_cpu)
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def _gradient(self, phi, direction):
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return np.fft.irfftn(self._kdir(direction)*1j*phi)*(self.N/self.L)**3
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self.cube.dhat = self._kdir(direction)*1j*phi
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return self.cube.irfft()
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def lpt1(self, direction=0):
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k2 = self._get_k2()
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@ -96,6 +140,14 @@ class LagrangianPerturbation(object):
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self.cache['k2'] = k2
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return k2
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def _do_irfft(self, array):
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self.cube.dhat = array
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return self.cube.irfft()
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def _do_rfft(self, array):
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self.cube.density = array
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return self.cube.rfft()
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def lpt2(self, direction=0):
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k2 = self._get_k2()
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k2[0,0,0] = 1
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@ -104,14 +156,14 @@ class LagrangianPerturbation(object):
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print("Rebuilding potential...")
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div_phi2 = np.zeros((self.N,self.N,self.N), dtype=np.float64)
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for j in xrange(3):
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q = np.fft.irfftn( self._kdir(j)**2*self.dhat / k2 )
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q = self._do_irfft( self._kdir(j)**2*self.dhat / k2 ).copy()
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for i in xrange(j+1, 3):
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div_phi2 += q * np.fft.irfftn( self._kdir(i)**2*self.dhat / k2 )
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div_phi2 -= (np.fft.irfftn( self._kdir(j)*self._kdir(i)*self.dhat / k2 ))**2
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div_phi2 += q * self._do_irfft( self._kdir(i)**2*self.dhat / k2 )
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div_phi2 -= (self._do_irfft(self._kdir(j)*self._kdir(i)*self.dhat / k2 ) )**2
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div_phi2 *= (self.N/self.L)**6
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phi2_hat = -np.fft.rfftn(div_phi2) * ((self.L/self.N)**3) / k2
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self.cache['lpt2_potential'] = phi2_hat
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div_phi2 *= 1/self.L**6
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phi2_hat = -self._do_rfft(div_phi2) / k2
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#self.cache['lpt2_potential'] = phi2_hat
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del div_phi2
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else:
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phi2_hat = self.cache['lpt2_potential']
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