csiborgtools/notebooks/plot_galaxy_distribution.ipynb
Richard Stiskalek 5dd8c668fa
Gaussian smoothing of density fields (#33)
* Simplify smoothing support and looping over nonzero

* Simplify comments

* add now()

* add cat length

* add smoothed calculation

* add smoothing

* Add sorting

* Edit what is ignored

* Move notebooks

* Add nonsymmetric smoothed overlap

* Update NB

* Add support for reading in the smoothed overlap

* Switch to the true overlap definition

* Reader of the true overlap

* rem occups

* Import moved to a class

* Move definition

* Edit submission script

* Update to account for the new definition

* backup nb

* Switch back to properly initialising arrays

* Fix addition bug

* Update NB

* Fix little bug

* Update nb
2023-03-27 09:22:03 +01:00

1.1 MiB

Open In Colab

In [8]:
!pip install --quiet git+https://github.com/DifferentiableUniverseInitiative/JaxPM.git
In [1]:
%pylab inline

import jax
import jax.numpy as jnp
import jax_cosmo as jc

from jax.experimental.ode import odeint

from jaxpm.painting import cic_paint
from jaxpm.pm import linear_field, lpt, make_ode_fn
Populating the interactive namespace from numpy and matplotlib
In [7]:
mesh_shape= [256, 256, 256]
box_size  = [256.,256.,256.]
snapshots = jnp.linspace(0.1,1.,2)

@jax.jit
def run_simulation(omega_c, sigma8):
    # Create a small function to generate the matter power spectrum
    k = jnp.logspace(-4, 1, 128)
    pk = jc.power.linear_matter_power(jc.Planck15(Omega_c=omega_c, sigma8=sigma8), k)
    pk_fn = lambda x: jc.scipy.interpolate.interp(x.reshape([-1]), k, pk).reshape(x.shape)

    # Create initial conditions
    initial_conditions = linear_field(mesh_shape, box_size, pk_fn, seed=jax.random.PRNGKey(0))

    # Create particles
    particles = jnp.stack(jnp.meshgrid(*[jnp.arange(s) for s in mesh_shape]),axis=-1).reshape([-1,3])

    cosmo = jc.Planck15(Omega_c=omega_c, sigma8=sigma8)
    
    # Initial displacement
    dx, p, f = lpt(cosmo, initial_conditions, particles, 0.1)
    
    # Evolve the simulation forward
    res = odeint(make_ode_fn(mesh_shape), [particles+dx, p], snapshots, cosmo, rtol=1e-5, atol=1e-5)
    
    # Return the simulation volume at requested 
    return res[0]
In [10]:
res = run_simulation(0.25, 0.8)
%timeit res = run_simulation(0.25, 0.8)
1 loop, best of 5: 29.2 s per loop
In [11]:
figure(figsize=[10,5])
subplot(121)
imshow(cic_paint(jnp.zeros(mesh_shape), res[0]).sum(axis=0),cmap='gist_stern')
subplot(122)
imshow(cic_paint(jnp.zeros(mesh_shape), res[1]).sum(axis=0),cmap='gist_stern')
Out[11]:
<matplotlib.image.AxesImage at 0x7f3502382c90>
No description has been provided for this image
In [ ]: