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Added more timing. Fixed whitification.

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This commit is contained in:
Guilhem Lavaux 2014-06-12 09:45:46 +02:00
parent 401ddc8a8b
commit a6b08dfe8f
7 changed files with 95 additions and 30 deletions
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2
python/cosmotool/__init__.py
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@ -4,4 +4,4 @@ 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 timeit
from timing import timeit, timeit_quiet

13
python/cosmotool/timing.py
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@ -13,3 +13,16 @@ def timeit(method):
return timed
def timeit_quiet(method):
def timed(*args, **kw):
ts = time.time()
result = method(*args, **kw)
te = time.time()
print '%r %2.2f sec' % \
(method.__name__, te-ts)
return result
return timed

37
python_sample/icgen/borgadaptor.py
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@ -6,15 +6,50 @@ def fourier_analysis(borg_vol):
return np.fft.rfftn(borg_vol.density)*(L/N)**3, L, N
def borg_upgrade_sampling(dhat, supersample):
N = dhat.shape[0]
N2 = N * supersample
dhat_new = np.zeros((N2, N2, N2/2+1), dtype=np.complex128)
hN = N/2
dhat_new[:hN, :hN, :hN+1] = dhat[:hN, :hN, :]
dhat_new[:hN, (N2-hN):N2, :hN+1] = dhat[:hN, hN:, :]
dhat_new[(N2-hN):N2, (N2-hN):N2, :hN+1] = dhat[hN:, hN:, :]
dhat_new[(N2-hN):N2, :hN, :hN+1] = dhat[hN:, :hN, :]
return dhat_new, N2
def half_pixel_shift(borg, doshift=False):
dhat,L,N = fourier_analysis(borg)
if not doshift:
return dhat, L
return bare_half_pixel_shift(dhat, L, N)
def bare_half_pixel_shift(dhat, L, N, doshift=False):
# dhat_new,N2 = borg_upgrade_sampling(dhat, 2)
# d = (np.fft.irfftn(dhat_new)*(N2/L)**3)[1::2,1::2,1::2]
# del dhat_new
# dhat = np.fft.rfftn(d)*(L/N)**3
# return dhat, L
# dhat2 = np.zeros((N,N,N),dtype=np.complex128)
# dhat2[:,:,:N/2+1] = dhat
# dhat2[N:0:-1, N:0:-1, N:N/2:-1] = np.conj(dhat[1:,1:,1:N/2])
# dhat2[0, N:0:-1, N:N/2:-1] = np.conj(dhat[0, 1:, 1:N/2])
# dhat2[N:0:-1, 0, N:N/2:-1] = np.conj(dhat[1:, 0, 1:N/2])
# dhat2[0,0,N:N/2:-1] = np.conj(dhat[0, 0, 1:N/2])
ik = np.fft.fftfreq(N,d=L/N)*2*np.pi
phi = 0.5*L/N*(ik[:,None,None]+ik[None,:,None]+ik[None,None,:(N/2+1)])
# phi %= 2*np.pi
phase = np.cos(phi)+1j*np.sin(phi)
dhat = dhat*phase
dhat[N/2,:,:] = 0
dhat[:,N/2,:] = 0
dhat[:,:,N/2] = 0
return dhat*phase, L
return dhat, L

62
python_sample/icgen/borgicgen.py
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@ -15,7 +15,7 @@ def gen_posgrid(N, L):
return x.reshape((x.size,)), y.reshape((y.size,)), z.reshape((z.size,))
def bin_power(P, L, bins=20, range=(0,1.)):
def bin_power(P, L, bins=20, range=(0,1.), dev=False):
N = P.shape[0]
ik = np.fft.fftfreq(N, d=L/N)*2*np.pi
@ -25,7 +25,10 @@ def bin_power(P, L, bins=20, range=(0,1.)):
H,b = np.histogram(k, bins=bins, range=range)
Hw,b = np.histogram(k, bins=bins, weights=P, range=range)
return Hw/H, 0.5*(b[1:]+b[0:bins])
if dev:
return Hw/(H-1), 0.5*(b[1:]+b[0:bins]), 1.0/np.sqrt(H)
else:
return Hw/(H-1), 0.5*(b[1:]+b[0:bins])
def compute_power_from_borg(input_borg, a_borg, cosmo, bins=10, range=(0,1)):
borg_vol = ct.read_borg_vol(input_borg)
@ -59,9 +62,9 @@ def run_generation(input_borg, a_borg, a_ic, cosmo, supersample=1, do_lpt2=True,
cgrowth = CosmoGrowth(**cosmo)
density_hat, L = ba.half_pixel_shift(borg_vol, doshift=shiftPixel)
density, L = ba.half_pixel_shift(borg_vol, doshift=shiftPixel)
lpt = LagrangianPerturbation(density_hat, L, fourier=True, supersample=supersample)
lpt = LagrangianPerturbation(density, L, fourier=True, supersample=supersample)
# Generate grid
posq = gen_posgrid(N*supersample, L)
@ -73,7 +76,7 @@ def run_generation(input_borg, a_borg, a_ic, cosmo, supersample=1, do_lpt2=True,
D1_0 = D1/cgrowth.D(a_borg)
velmul = cgrowth.compute_velmul(a_ic)
D2 = 3./7 * D1_0**2
D2 = -3./7 * D1_0**2
for j in xrange(3):
# Generate psi_j (displacement along j)
@ -91,23 +94,30 @@ def run_generation(input_borg, a_borg, a_ic, cosmo, supersample=1, do_lpt2=True,
print("velmul=%lg" % (cosmo['h']*velmul))
density = np.fft.irfftn(lpt.dhat*D1_0)*(supersample*N/L)**3
density = cgrowth.D(1)/cgrowth.D(a_borg)*np.fft.irfftn(lpt.dhat)*(supersample*N/L)**3
return posx,vel,density,N*supersample,L,a_ic,cosmo
def whitify(density, L, cosmo, supergenerate=1, func='HU_WIGGLES'):
N = density.shape[0]
ik = np.fft.fftfreq(N, d=L/N)*2*np.pi
k = np.sqrt(ik[:,None,None]**2 + ik[None,:,None]**2 + ik[None,None,:(N/2+1)]**2)
@ct.timeit_quiet
def whitify(density, L, cosmo, supergenerate=1, func='HU_WIGGLES'):
N = density.shape[0]
p = ct.CosmologyPower(**cosmo)
p.setFunction(func)
p.normalize(cosmo['SIGMA8'])
Pk = p.compute(k)*cosmo['h']**3*L**3
@ct.timeit_quiet
def build_Pk():
ik = np.fft.fftfreq(N, d=L/N)*2*np.pi
k = np.sqrt(ik[:,None,None]**2 + ik[None,:,None]**2 + ik[None,None,:(N/2+1)]**2)
return p.compute(k)*cosmo['h']**3*L**3
Pk = build_Pk()
Pk[0,0,0]=1
density_hat = np.fft.rfftn(density)/N**3/np.sqrt(Pk)
density_hat = np.fft.rfftn(density)*(L/N)**3
density_hat /= np.sqrt(Pk)
Ns = N*supergenerate
@ -116,24 +126,28 @@ def whitify(density, L, cosmo, supergenerate=1, func='HU_WIGGLES'):
# Copy density hat in place
hN = N/2
density_hat_super[:hN, :hN, :hN+1] = density_hat[:hN, :hN, :]
density_hat_super[:hN, (Ns-hN):Ns, :hN+1] = density_hat[:hN, hN:, :]
density_hat_super[:hN, :hN, :hN+1] = density_hat[:hN, :hN, :]
density_hat_super[:hN, (Ns-hN):Ns, :hN+1] = density_hat[:hN, hN:, :]
density_hat_super[(Ns-hN):Ns, (Ns-hN):Ns, :hN+1] = density_hat[hN:, hN:, :]
density_hat_super[(Ns-hN):Ns, :hN, :hN+1] = density_hat[hN:, :hN, :]
density_hat_super[(Ns-hN):Ns, :hN, :hN+1] = density_hat[hN:, :hN, :]
# The moved nyquist place is untouched (so loss of "noise") to keep the structure
# now we just add some noise term
cond=np.isnan(density_hat_super)
x = np.random.randn(np.count_nonzero(cond),2)/np.sqrt(2.0)
density_hat_super[cond] = x[:,0] + 1j * x[:,1]
if supergenerate > 1:
cond=np.isnan(density_hat_super)
x = np.random.randn(np.count_nonzero(cond),2)/np.sqrt(2.0)
density_hat_super[cond] = x[:,0] + 1j * x[:,1]
# Now we have to fix the Nyquist plane
hNs = Ns/2
nyquist = density_hat_super[:, :, hNs]
Nplane = nyquist.size
nyquist.flat[:Nplane/2] = np.sqrt(2.0)*nyquist.flat[Nplane:Nplane/2:-1].conj()
return np.fft.irfftn(density_hat_super)*Ns**1.5
# Now we have to fix the Nyquist plane
hNs = Ns/2
nyquist = density_hat_super[:, :, :hNs]
Nplane = nyquist.size
nyquist.flat[:Nplane/2] = nyquist.flat[Nplane:Nplane/2:-1].conj()
return np.fft.irfftn(density_hat_super)
def write_icfiles(*generated_ic, **kwargs):
"""Write the initial conditions from the tuple returned by run_generation"""

2
python_sample/icgen/cosmogrowth.py
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@ -110,7 +110,7 @@ class LagrangianPerturbation(object):
div_phi2 -= (np.fft.irfftn( self._kdir(j)*self._kdir(i)*self.dhat / k2 ))**2
div_phi2 *= (self.N/self.L)**6
phi2_hat = np.fft.rfftn(div_phi2) * ((self.L/self.N)**3) / k2
phi2_hat = -np.fft.rfftn(div_phi2) * ((self.L/self.N)**3) / k2
self.cache['lpt2_potential'] = phi2_hat
del div_phi2
else:

3
python_sample/icgen/gen_ic_from_borg.py
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@ -9,9 +9,10 @@ cosmo['omega_B_0']=0.049
cosmo['SIGMA8']=0.8344
cosmo['ns']=0.9624
supergen=4
zstart=50
astart=1/(1.+zstart)
halfPixelShift=True
if __name__=="__main__":
bic.write_icfiles(*bic.run_generation("initial_condition_borg.dat", 0.001, astart, cosmo, supersample=2, shiftPixel=halfPixelShift, do_lpt2=False))
bic.write_icfiles(*bic.run_generation("initial_condition_borg.dat", 0.001, astart, cosmo, supersample=1, shiftPixel=halfPixelShift, do_lpt2=False), supergenerate=supergen)

2
python_sample/icgen/test_ic_from_borg.py
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@ -51,4 +51,6 @@ Pcic /= D1_0**2
Pdens /= D1_0**2
borg_evolved = ct.read_borg_vol("final_density_1380.dat")
dborg_hat = np.fft.rfftn(borg_evolved.density)*L**3/borg_evolved.density.size
Pborg, bborg = bic.bin_power(np.abs(dborg_hat)**2/L**3, L, range=(0,1.),bins=150)