cosmotool/python_sample/icgen/borgicgen.py

import cosmotool as ct
import numpy as np
import cosmolopy as cpy
from cosmogrowth import *
import borgadaptor as ba

def gen_posgrid(N, L):
    """ Generate an ordered lagrangian grid"""

    ix = np.arange(N)*L/N

    x = ix[:,None,None].repeat(N, axis=1).repeat(N, axis=2)
    y = ix[None,:,None].repeat(N, axis=0).repeat(N, axis=2)
    z = ix[None,None,:].repeat(N, axis=0).repeat(N, axis=1)

    return x.reshape((x.size,)), y.reshape((y.size,)), z.reshape((z.size,))

def bin_power(P, L, bins=20, range=(0,1.)):

  N = P.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)

  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])

def compute_power_from_borg(input_borg, a_borg, cosmo, bins=10, range=(0,1)):
  borg_vol = ct.read_borg_vol(input_borg)
  N = borg_vol.density.shape[0]

  cgrowth = CosmoGrowth(**cosmo)
  D1 = cgrowth.D(1)
  D1_0 = D1/cgrowth.D(a_borg)
  print("D1_0=%lg" % D1_0)

  density_hat, L = ba.half_pixel_shift(borg_vol)

  return bin_power(D1_0**2*np.abs(density_hat)**2/L**3, L, bins=bins, range=range)
  
def compute_ref_power(L, N, cosmo, bins=10, range=(0,1), func='HU_WIGGLES'):
  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)
  p = ct.CosmologyPower(**cosmo)
  p.setFunction(func)
  p.normalize(cosmo['SIGMA8'])

  return bin_power(p.compute(k)*cosmo['h']**3, L, bins=bins, range=range)

def run_generation(input_borg, a_borg, a_ic, cosmo, supersample=1, do_lpt2=True, shiftPixel=False):
    """ Generate particles and velocities from a BORG snapshot. Returns a tuple of 
    (positions,velocities,N,BoxSize,scale_factor)."""

    borg_vol = ct.read_borg_vol(input_borg)
    N = borg_vol.density.shape[0]

    cgrowth = CosmoGrowth(**cosmo)

    density_hat, L = ba.half_pixel_shift(borg_vol, doshift=shiftPixel)

    lpt = LagrangianPerturbation(density_hat, L, fourier=True, supersample=supersample)

    # Generate grid
    posq = gen_posgrid(N*supersample, L)
    vel= []
    posx = []
    
    # Compute LPT scaling coefficient
    D1 = cgrowth.D(a_ic)
    D1_0 = D1/cgrowth.D(a_borg)
    velmul = cgrowth.compute_velmul(a_ic)
    
    D2 = 3./7 * D1_0**2

    for j in xrange(3):
        # Generate psi_j (displacement along j)
        print("LPT1 axis=%d" % j)
        psi = D1_0*lpt.lpt1(j)
        psi = psi.reshape((psi.size,))
        if do_lpt2:
          print("LPT2 axis=%d" % j)
          psi2 = lpt.lpt2(j)
          psi += D2 * psi2.reshape((psi2.size,))
        # Generate posx
        posx.append(((posq[j] + psi)%L).astype(np.float32))
        # Generate vel
        vel.append((psi*velmul).astype(np.float32)) 

    print("velmul=%lg" % (cosmo['h']*velmul))

    density = np.fft.irfftn(lpt.dhat*D1_0)*(supersample*N/L)**3

    return posx,vel,density,N*supersample,L,a_ic
    
def write_icfiles(*generated_ic, **cosmo):
    """Write the initial conditions from the tuple returned by run_generation"""
    posx,vel,density,N,L,a_ic = generated_ic

    ct.simpleWriteGadget("borg.gad", posx, velocities=vel, boxsize=L, Hubble=cosmo['h'], Omega_M=cosmo['omega_M_0'], time=a_ic) 
    for i,c in enumerate(["x","y","z"]):
        ct.writeGrafic("ic_velc%s" % c, vel[i].reshape((N,N,N)), L, a_ic, **cosmo)
# This used to be necessary. However this has been fixed in writeGrafic now
#        ct.writeGrafic("ic_velc%s" % c, vel[i].reshape((N,N,N)).transpose(), L, a_ic, **cosmo)

    ct.writeGrafic("ic_deltab", density, L, a_ic, **cosmo)
    ct.writeWhitePhase("white.dat", density)