Merge
This commit is contained in:
Guilhem Lavaux
commit
025cdba6a9
@ -1,7 +1,7 @@
|
||||
from cpython cimport bool
|
||||
from cython cimport view
|
||||
from cython.parallel import prange, parallel
|
||||
from libc.math cimport sin, cos, abs, floor, sqrt
|
||||
from libc.math cimport sin, cos, abs, floor, round, sqrt
|
||||
import numpy as np
|
||||
cimport numpy as npx
|
||||
cimport cython
|
||||
@ -45,13 +45,6 @@ cdef int interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
|
||||
ry -= iy
|
||||
rz -= iz
|
||||
|
||||
while ix < 0:
|
||||
ix += Ngrid
|
||||
while iy < 0:
|
||||
iy += Ngrid
|
||||
while iz < 0:
|
||||
iz += Ngrid
|
||||
|
||||
jx = (ix+1)%Ngrid
|
||||
jy = (iy+1)%Ngrid
|
||||
jz = (iz+1)%Ngrid
|
||||
@ -89,6 +82,69 @@ cdef int interp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
|
||||
|
||||
return 0
|
||||
|
||||
@cython.boundscheck(False)
|
||||
@cython.cdivision(True)
|
||||
cdef int ngp3d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
|
||||
DTYPE_t z,
|
||||
DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval) nogil:
|
||||
|
||||
cdef int Ngrid = d.shape[0]
|
||||
cdef DTYPE_t inv_delta = Ngrid/Lbox
|
||||
cdef int ix, iy, iz
|
||||
cdef DTYPE_t f[2][2][2]
|
||||
cdef DTYPE_t rx, ry, rz
|
||||
cdef int jx, jy, jz
|
||||
|
||||
rx = (inv_delta*x)
|
||||
ry = (inv_delta*y)
|
||||
rz = (inv_delta*z)
|
||||
|
||||
ix = int(round(rx))
|
||||
iy = int(round(ry))
|
||||
iz = int(round(rz))
|
||||
|
||||
|
||||
ix = ix%Ngrid
|
||||
iy = iy%Ngrid
|
||||
iz = iz%Ngrid
|
||||
|
||||
retval[0] = d[ix ,iy ,iz ]
|
||||
|
||||
return 0
|
||||
|
||||
|
||||
@cython.boundscheck(False)
|
||||
@cython.cdivision(True)
|
||||
cdef int ngp3d_INTERNAL(DTYPE_t x, DTYPE_t y,
|
||||
DTYPE_t z,
|
||||
DTYPE_t[:,:,:] d, DTYPE_t Lbox, DTYPE_t *retval) nogil:
|
||||
|
||||
cdef int Ngrid = d.shape[0]
|
||||
cdef DTYPE_t inv_delta = Ngrid/Lbox
|
||||
cdef int ix, iy, iz
|
||||
cdef DTYPE_t f[2][2][2]
|
||||
cdef DTYPE_t rx, ry, rz
|
||||
cdef int jx, jy, jz
|
||||
|
||||
rx = (inv_delta*x)
|
||||
ry = (inv_delta*y)
|
||||
rz = (inv_delta*z)
|
||||
|
||||
ix = int(round(rx))
|
||||
iy = int(round(ry))
|
||||
iz = int(round(rz))
|
||||
|
||||
if (ix < 0 or ix >= Ngrid):
|
||||
return -1
|
||||
if (iy < 0 or iy >= Ngrid):
|
||||
return -2
|
||||
if (iz < 0 or iz >= Ngrid):
|
||||
return -3
|
||||
|
||||
retval[0] = d[ix ,iy ,iz ]
|
||||
|
||||
return 0
|
||||
|
||||
|
||||
@cython.boundscheck(False)
|
||||
@cython.cdivision(True)
|
||||
@ -152,8 +208,8 @@ cdef int interp3d_INTERNAL(DTYPE_t x, DTYPE_t y,
|
||||
def interp3d(x not None, y not None,
|
||||
z not None,
|
||||
npx.ndarray[DTYPE_t, ndim=3] d not None, DTYPE_t Lbox,
|
||||
bool periodic=False, bool centered=True):
|
||||
""" interp3d(x,y,z,d,Lbox,periodic=False) -> interpolated values
|
||||
bool periodic=False, bool centered=True, bool ngp=False):
|
||||
""" interp3d(x,y,z,d,Lbox,periodic=False,centered=True,ngp=False) -> interpolated values
|
||||
|
||||
Compute the tri-linear interpolation of the given field (d) at the given position (x,y,z). It assumes that they are box-centered coordinates. So (x,y,z) == (0,0,0) is equivalent to the pixel at (Nx/2,Ny/2,Nz/2) with Nx,Ny,Nz = d.shape. If periodic is set, it assumes the box is periodic
|
||||
"""
|
||||
@ -164,10 +220,11 @@ def interp3d(x not None, y not None,
|
||||
cdef DTYPE_t retval
|
||||
cdef long i
|
||||
cdef long Nelt
|
||||
cdef int myperiodic
|
||||
cdef int myperiodic, myngp
|
||||
cdef DTYPE_t shifter
|
||||
|
||||
myperiodic = periodic
|
||||
myngp = ngp
|
||||
|
||||
if centered:
|
||||
shifter = Lbox/2
|
||||
@ -193,26 +250,46 @@ def interp3d(x not None, y not None,
|
||||
in_slice = d
|
||||
Nelt = ax.size
|
||||
with nogil:
|
||||
if not myngp:
|
||||
if myperiodic:
|
||||
for i in xrange(Nelt):
|
||||
for i in prange(Nelt):
|
||||
if interp3d_INTERNAL_periodic(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i]) < 0:
|
||||
with gil:
|
||||
raise ierror
|
||||
else:
|
||||
for i in xrange(Nelt):
|
||||
for i in prange(Nelt):
|
||||
if interp3d_INTERNAL(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i]) < 0:
|
||||
with gil:
|
||||
raise ierror
|
||||
|
||||
else:
|
||||
if myperiodic:
|
||||
for i in prange(Nelt):
|
||||
if ngp3d_INTERNAL_periodic(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i]) < 0:
|
||||
with gil:
|
||||
raise ierror
|
||||
else:
|
||||
for i in prange(Nelt):
|
||||
if ngp3d_INTERNAL(shifter+ax[i], shifter+ay[i], shifter+az[i], in_slice, Lbox, &out_slice[i]) < 0:
|
||||
with gil:
|
||||
raise ierror
|
||||
return out
|
||||
else:
|
||||
if not myngp:
|
||||
if periodic:
|
||||
if interp3d_INTERNAL_periodic(shifter+x, shifter+y, shifter+z, d, Lbox, &retval) < 0:
|
||||
raise ierror
|
||||
else:
|
||||
if interp3d_INTERNAL(shifter+x, shifter+y, shifter+z, d, Lbox, &retval) < 0:
|
||||
raise ierror
|
||||
else:
|
||||
if periodic:
|
||||
if ngp3d_INTERNAL_periodic(shifter+x, shifter+y, shifter+z, d, Lbox, &retval) < 0:
|
||||
raise ierror
|
||||
else:
|
||||
if ngp3d_INTERNAL(shifter+x, shifter+y, shifter+z, d, Lbox, &retval) < 0:
|
||||
raise ierror
|
||||
return retval
|
||||
|
||||
@cython.boundscheck(False)
|
||||
@cython.cdivision(True)
|
||||
cdef DTYPE_t interp2d_INTERNAL_periodic(DTYPE_t x, DTYPE_t y,
|
||||
@ -376,12 +453,17 @@ cdef void INTERNAL_project_cic_no_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g,
|
||||
cdef double a[3], c[3]
|
||||
cdef int b[3], b1[3]
|
||||
cdef int do_not_put
|
||||
cdef DTYPE_t[:,:] ax
|
||||
cdef DTYPE_t[:,:,:] ag
|
||||
|
||||
ax = x
|
||||
ag = g
|
||||
|
||||
for i in range(x.shape[0]):
|
||||
|
||||
do_not_put = 0
|
||||
for j in range(3):
|
||||
a[j] = (x[i,j]+half_Box)*delta_Box
|
||||
a[j] = (ax[i,j]+half_Box)*delta_Box
|
||||
b[j] = int(floor(a[j]))
|
||||
b1[j] = (b[j]+1) % Ngrid
|
||||
|
||||
@ -390,18 +472,15 @@ cdef void INTERNAL_project_cic_no_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g,
|
||||
|
||||
b[j] %= Ngrid
|
||||
|
||||
assert b[j] >= 0 and b[j] < Ngrid
|
||||
assert b1[j] >= 0 and b1[j] < Ngrid
|
||||
ag[b[0],b[1],b[2]] += c[0]*c[1]*c[2]
|
||||
ag[b1[0],b[1],b[2]] += a[0]*c[1]*c[2]
|
||||
ag[b[0],b1[1],b[2]] += c[0]*a[1]*c[2]
|
||||
ag[b1[0],b1[1],b[2]] += a[0]*a[1]*c[2]
|
||||
|
||||
g[b[0],b[1],b[2]] += c[0]*c[1]*c[2]
|
||||
g[b1[0],b[1],b[2]] += a[0]*c[1]*c[2]
|
||||
g[b[0],b1[1],b[2]] += c[0]*a[1]*c[2]
|
||||
g[b1[0],b1[1],b[2]] += a[0]*a[1]*c[2]
|
||||
|
||||
g[b[0],b[1],b1[2]] += c[0]*c[1]*a[2]
|
||||
g[b1[0],b[1],b1[2]] += a[0]*c[1]*a[2]
|
||||
g[b[0],b1[1],b1[2]] += c[0]*a[1]*a[2]
|
||||
g[b1[0],b1[1],b1[2]] += a[0]*a[1]*a[2]
|
||||
ag[b[0],b[1],b1[2]] += c[0]*c[1]*a[2]
|
||||
ag[b1[0],b[1],b1[2]] += a[0]*c[1]*a[2]
|
||||
ag[b[0],b1[1],b1[2]] += c[0]*a[1]*a[2]
|
||||
ag[b1[0],b1[1],b1[2]] += a[0]*a[1]*a[2]
|
||||
|
||||
|
||||
@cython.boundscheck(False)
|
||||
|
||||
@ -1,7 +1,12 @@
|
||||
from _cosmotool import *
|
||||
from _project import *
|
||||
from grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
|
||||
from borg import read_borg_vol
|
||||
from cic import cicParticles
|
||||
from simu import loadRamsesAll, simpleWriteGadget, SimulationBare
|
||||
from timing import time_block, timeit, timeit_quiet
|
||||
from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
|
||||
from .borg import read_borg_vol
|
||||
from .cic import cicParticles
|
||||
from .simu import loadRamsesAll, simpleWriteGadget, SimulationBare
|
||||
from .timing import time_block, timeit, timeit_quiet
|
||||
|
||||
try:
|
||||
from .fftw import CubeFT
|
||||
except ImportError:
|
||||
print("No FFTW support")
|
||||
|
||||
36
python/cosmotool/fftw.py
Normal file
36
python/cosmotool/fftw.py
Normal file
@ -0,0 +1,36 @@
|
||||
import pyfftw
|
||||
import multiprocessing
|
||||
import numpy as np
|
||||
import numexpr as ne
|
||||
|
||||
class CubeFT(object):
|
||||
def __init__(self, L, N, max_cpu=-1):
|
||||
|
||||
self.N = N
|
||||
self.align = pyfftw.simd_alignment
|
||||
self.L = L
|
||||
self.max_cpu = multiprocessing.cpu_count() if max_cpu < 0 else max_cpu
|
||||
self._dhat = pyfftw.n_byte_align_empty((self.N,self.N,self.N/2+1), self.align, dtype='complex64')
|
||||
self._density = pyfftw.n_byte_align_empty((self.N,self.N,self.N), self.align, dtype='float32')
|
||||
self._irfft = pyfftw.FFTW(self._dhat, self._density, axes=(0,1,2), direction='FFTW_BACKWARD', threads=self.max_cpu, normalize_idft=False)
|
||||
self._rfft = pyfftw.FFTW(self._density, self._dhat, axes=(0,1,2), threads=self.max_cpu, normalize_idft=False)
|
||||
|
||||
def rfft(self):
|
||||
return ne.evaluate('c*a', out=self._dhat, local_dict={'c':self._rfft(normalise_idft=False),'a':(self.L/self.N)**3}, casting='unsafe')
|
||||
|
||||
def irfft(self):
|
||||
return ne.evaluate('c*a', out=self._density, local_dict={'c':self._irfft(normalise_idft=False),'a':(1/self.L)**3}, casting='unsafe')
|
||||
|
||||
def get_dhat(self):
|
||||
return self._dhat
|
||||
def set_dhat(self, in_dhat):
|
||||
self._dhat[:] = in_dhat
|
||||
dhat = property(get_dhat, set_dhat, None)
|
||||
|
||||
def get_density(self):
|
||||
return self._density
|
||||
def set_density(self, d):
|
||||
self._density[:] = d
|
||||
density = property(get_density, set_density, None)
|
||||
|
||||
|
||||
@ -103,7 +103,7 @@ def run_generation(input_borg, a_borg, a_ic, cosmo, supersample=1, do_lpt2=True,
|
||||
|
||||
|
||||
@ct.timeit_quiet
|
||||
def whitify(density, L, cosmo, supergenerate=1, func='HU_WIGGLES'):
|
||||
def whitify(density, L, cosmo, supergenerate=1, zero_fill=False, func='HU_WIGGLES'):
|
||||
|
||||
N = density.shape[0]
|
||||
p = ct.CosmologyPower(**cosmo)
|
||||
@ -141,6 +141,10 @@ def whitify(density, L, cosmo, supergenerate=1, func='HU_WIGGLES'):
|
||||
if supergenerate > 1:
|
||||
|
||||
cond=np.isnan(density_hat_super)
|
||||
if zero_fill:
|
||||
density_hat_super[cond] = 0
|
||||
else:
|
||||
|
||||
print np.where(np.isnan(density_hat_super))[0].size
|
||||
Nz = np.count_nonzero(cond)
|
||||
density_hat_super.real[cond] = np.random.randn(Nz)
|
||||
@ -166,8 +170,8 @@ def write_icfiles(*generated_ic, **kwargs):
|
||||
"""Write the initial conditions from the tuple returned by run_generation"""
|
||||
|
||||
supergenerate=1
|
||||
if 'supergenerate' in kwargs:
|
||||
supergenerate=kwargs['supergenerate']
|
||||
supergenerate=kwargs.get('supergenerate', 1)
|
||||
zero_fill=kwargs.get('zero_fill', False)
|
||||
posx,vel,density,N,L,a_ic,cosmo = generated_ic
|
||||
|
||||
ct.simpleWriteGadget("Data/borg.gad", posx, velocities=vel, boxsize=L, Hubble=cosmo['h'], Omega_M=cosmo['omega_M_0'], time=a_ic)
|
||||
@ -176,7 +180,7 @@ def write_icfiles(*generated_ic, **kwargs):
|
||||
|
||||
ct.writeGrafic("Data/ic_deltab", density, L, a_ic, **cosmo)
|
||||
|
||||
ct.writeWhitePhase("Data/white.dat", whitify(density, L, cosmo, supergenerate=supergenerate))
|
||||
ct.writeWhitePhase("Data/white.dat", whitify(density, L, cosmo, supergenerate=supergenerate,zero_fill=zero_fill))
|
||||
|
||||
with file("Data/white_params", mode="w") as f:
|
||||
f.write("4\n%lg, %lg, %lg\n" % (cosmo['omega_M_0'], cosmo['omega_lambda_0'], 100*cosmo['h']))
|
||||
|
||||
@ -9,10 +9,11 @@ cosmo['omega_B_0']=0.049
|
||||
cosmo['SIGMA8']=0.8344
|
||||
cosmo['ns']=0.9624
|
||||
|
||||
supergen=1
|
||||
supergen=2
|
||||
zstart=50
|
||||
astart=1/(1.+zstart)
|
||||
astart=1/69.#1/(1.+zstart)
|
||||
halfPixelShift=False
|
||||
zero_fill=True
|
||||
|
||||
if __name__=="__main__":
|
||||
bic.write_icfiles(*bic.run_generation("initial_density_988.dat", 0.001, astart, cosmo, supersample=1, shiftPixel=halfPixelShift, do_lpt2=False), supergenerate=supergen)
|
||||
bic.write_icfiles(*bic.run_generation("initial_density_1380.dat", 0.001, astart, cosmo, supersample=1, shiftPixel=halfPixelShift, do_lpt2=False), supergenerate=supergen, zero_fill=zero_fill)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user