https://github.com/JoeMcEwen/FAST-PT
Tip revision: 68c2df21063d59bb39d5a1e5f1747e463ba00d29 authored by Jonathan Blazek on 21 September 2016, 01:19:09 UTC
updated arxiv number
updated arxiv number
Tip revision: 68c2df2
RG_RK4_filt.py
'''
This RG flow method usese a digital filter to smooth out the instabilities that develop at
high k. This is a good integrator to use when k_max is greater than 1 and the grid
is sparsely sampled.
J. E. McEwen (c) 2016
mcewen.24@osu.edu
'''
import numpy as np
from matter_power_spt import one_loop
import matplotlib.pyplot as plt
from fastpt_extr import p_window
from scipy.signal import butter, lfilter, filtfilt, lfilter_zi
import time
import sys
import FASTPT
def RG_RK4_filt(name,k,P,d_lambda,max,n_pad,P_window,C_window):
x=max/d_lambda-int(max/d_lambda)
if ( x !=0.0 ):
raise ValueError('You need to send a d_lambda step so that max/d_lambda has no remainder to reach Lambda=max')
#save name
name='RG_RK4_filt_'+name
# The spacing in log(k)
Delta=np.log(k[1])-np.log(k[0])
# This window function tapers the edge of the power spectrum.
# It is applied to each Runge-Kutta step.
# You could change it here.
W=p_window(k,P_window[0],P_window[1])
#W=1
t1=time.time()
# windowed initial power spectrum
P_0=P*W
nu=-2
fastpt=FASTPT.FASTPT(k,nu=nu,n_pad=n_pad)
P_spt=fastpt.one_loop(P_0,C_window=C_window)
P_spt=P_0+P_spt
# initial lambda
Lambda=0
d_out=np.zeros((3,k.size+1))
d_out[0,1:]=k
d_out[2,1:]=P_0
d_out[1,1:]=P_spt
# filtering specific
k_start=1; k_end=5
id1=np.where( k > k_end)[0]
id2=np.where( k <= k_end)[0]
id3=np.where( k > k_start)[0]
#id4=np.where( k <= k_start)[0]
id4=np.where( (k > k_start) & ( k<= k_end))[0]
order=6; wn=.1
B,A=butter(order,wn, btype='low', analog=False)
theta=np.linspace(1,0,id4.size)
W_fad=theta - 1/2./np.pi*np.sin(2*np.pi*theta)
filt_pad=id3.size
# end filtering specific
def filt_zp(k,P_filt):
def zero_phase(sig):
sig=np.pad(sig,(filt_pad,filt_pad), 'constant', constant_values=(0, 0))
#zi=lfilter_zi(B,A)
#x,_=lfilter(B,A,sig, zi=zi*sig[0])
x=lfilter(B,A,sig)
#y,_=lfilter(B,A,x,zi=zi*x[0])
y=lfilter(B,A,x[::-1])
y=y[::-1]
#return y
return y[filt_pad:id3.size+filt_pad]
P_smoothed=zero_phase(P_filt[id3])
P_patch=P_filt[id4]*W_fad
P_filt[id3]=P_smoothed
P_filt[id4]=P_patch+(1-W_fad)*P_filt[id4]
return P_filt
i=0
while Lambda <= max:
k1=fastpt.one_loop(P,C_window=C_window)
k1=filt_zp(k,k1)
k2=fastpt.one_loop(k1*d_lambda/2.+ P,C_window=C_window)
k2=filt_zp(k,k2)
k3=fastpt.one_loop(k2*d_lambda/2. +P,C_window=C_window)
k3=filt_zp(k,k3)
k4=fastpt.one_loop(k3*d_lambda +P,C_window=C_window)
k4=filt_zp(k,k4)
# full Runge-Kutta step
P=P+1/6.*(k1+2*k2+2*k3+k4)*d_lambda
# check for failure.
if (np.any(np.isnan(P))):
print('RG flow has failed. It could be that you have not chosen a step size well.')
print('You may want to consider a smaller step size.')
print('Failure at lambda =', Lambda)
sys.exit()
if (np.any(np.isinf(P))):
print('RG flow has failed. It could be that you have not chosen a step size well.')
print('You may want to consider a smaller step size.')
print('Failure at lambda =', Lambda)
sys.exit()
#update lambda and the iteration
i=i+1
Lambda+=d_lambda
# update data for saving
d_update=np.append(Lambda,P)
d_out=np.row_stack((d_out,d_update))
if(False):
ax=plt.subplot(111)
ax.set_xscale('log')
ax.set_yscale('log')
ax.set_xlabel('k')
ax.plot(k,P)
ax.plot(k,P_0, color='red')
plt.grid()
plt.show()
# save the data
t2=time.time()
print('time to run seconds', t2-t1)
print('time to run minutes', (t2-t1)/60.)
print('number of iterations and output shape', i, d_out.shape)
np.save(name,d_out)
return P
if __name__ == "__main__":
V=sys.version_info[0]
if (V < 3):
from ConfigParser import SafeConfigParser
if (V >=3 ):
from configparser import SafeConfigParser
parser = SafeConfigParser()
name='kmax10_example.ini'
parser.read(name)
k_max=parser.getfloat('floats', 'k_max')
k_min=parser.getfloat('floats', 'k_min')
step=parser.getfloat('floats', 'step')
max=parser.getfloat('floats', 'max')
P_right=parser.getfloat('floats', 'P_w_right')
P_left=parser.getfloat('floats', 'P_w_left')
C_window=parser.getfloat('floats', 'C_window')
n_pad=parser.getint('integers', 'n_pad')
down_sample=parser.getint('integers', 'down_sample')
read_name=parser.get('files', 'in_file')
name=parser.get('files', 'out_file')
d=np.loadtxt(read_name) # load data
k=d[:,0]
P=d[:,1]
id=np.where( (k >= k_min) & (k <= k_max) )[0]
k=k[id]
P=P[id]
k=k[::down_sample]
P=P[::down_sample]
# if your array is not even in size, FAST-PT will not work-
# trim if so.
if (k.size % 2 != 0):
k=k[:-1]
P=P[:-1]
print('Details of run.')
print('save name :', name)
print('k min and max:', k_min, k_max )
print('step size : ', step)
print('grid size : ', k.size)
print('d log k: ', np.log(k[1])-np.log(k[0]) )
print('down sample factor:', down_sample)
P_window=np.array([P_left,P_right])
P_rg=RG_RK4_filt(name,k,P,step,max,n_pad,P_window,C_window)
ax=plt.subplot(111)
ax.set_xscale('log')
ax.set_yscale('log')
ax.set_xlabel('k')
ax.set_ylabel(r'$P(k)$', size=30)
ax.set_xlabel(r'$k$', size=30)
ax.plot(k,P, label='linear power')
ax.plot(k,P_rg, label='RG' )
plt.legend(loc=3)
plt.grid()
plt.show()