diff --git a/jaxpm/kernels.py b/jaxpm/kernels.py index dad13ba..b4303fc 100644 --- a/jaxpm/kernels.py +++ b/jaxpm/kernels.py @@ -1,5 +1,3 @@ -from enum import Enum - import jax.numpy as jnp import jax_cosmo as jc import numpy as np @@ -45,16 +43,18 @@ def interpolate_power_spectrum(input, k, pk, sharding=None): def gradient_kernel(kvec, direction, order=1): """ Computes the gradient kernel in the requested direction - Parameters: + + Parameters ----------- - kvec: array - Array of k values in Fourier space + kvec: list + List of wave-vectors in Fourier space direction: int - Index of the direction in which to take the gradient - Returns: + Index of the direction in which to take the gradient + + Returns -------- wts: array - Complex kernel + Complex kernel values """ if order == 0: wts = 1j * kvec[direction] @@ -69,37 +69,43 @@ def gradient_kernel(kvec, direction, order=1): return wts -def laplace_kernel(kvec): +def invlaplace_kernel(kvec): """ - Compute the Laplace kernel from a given K vector - Parameters: + Compute the inverse Laplace kernel + + Parameters ----------- - kvec: array - Array of k values in Fourier space - Returns: + kvec: list + List of wave-vectors + + Returns -------- wts: array - Complex kernel + Complex kernel values """ kk = sum(ki**2 for ki in kvec) - wts = jnp.where(kk == 0, 1., 1. / kk) - return wts + kk_nozeros = jnp.where(kk==0, 1, kk) + return - jnp.where(kk==0, 0, 1 / kk_nozeros) def longrange_kernel(kvec, r_split): """ - Computes a long range kernel - Parameters: - ----------- - kvec: array - Array of k values in Fourier space - r_split: float + Computes a long range kernel + + Parameters + ----------- + kvec: list + List of wave-vectors + r_split: float + Splitting radius + + Returns + -------- + wts: array + Complex kernel values + TODO: @modichirag add documentation - Returns: - -------- - wts: array - kernel - """ + """ if r_split != 0: kk = sum(ki**2 for ki in kvec) return np.exp(-kk * r_split**2) @@ -109,15 +115,21 @@ def longrange_kernel(kvec, r_split): def cic_compensation(kvec): """ - Computes cic compensation kernel. - Adapted from https://github.com/bccp/nbodykit/blob/a387cf429d8cb4a07bb19e3b4325ffdf279a131e/nbodykit/source/mesh/catalog.py#L499 - Itself based on equation 18 (with p=2) of - `Jing et al 2005 `_ - Args: - kvec: array of k values in Fourier space - Returns: - v: array of kernel - """ + Computes cic compensation kernel. + Adapted from https://github.com/bccp/nbodykit/blob/a387cf429d8cb4a07bb19e3b4325ffdf279a131e/nbodykit/source/mesh/catalog.py#L499 + Itself based on equation 18 (with p=2) of + [Jing et al 2005](https://arxiv.org/abs/astro-ph/0409240) + + Parameters: + ----------- + kvec: list + List of wave-vectors + + Returns: + -------- + wts: array + Complex kernel values + """ kwts = [np.sinc(kvec[i] / (2 * np.pi)) for i in range(3)] wts = (kwts[0] * kwts[1] * kwts[2])**(-2) return wts @@ -125,20 +137,22 @@ def cic_compensation(kvec): def PGD_kernel(kvec, kl, ks): """ - Computes the PGD kernel - Parameters: - ----------- - kvec: array - Array of k values in Fourier space - kl: float - initial long range scale parameter - ks: float - initial dhort range scale parameter - Returns: - -------- - v: array - kernel - """ + Computes the PGD kernel + + Parameters: + ----------- + kvec: list + List of wave-vectors + kl: float + Initial long range scale parameter + ks: float + Initial dhort range scale parameter + + Returns: + -------- + v: array + Complex kernel values + """ kk = sum(ki**2 for ki in kvec) kl2 = kl**2 ks4 = ks**4 diff --git a/jaxpm/pm.py b/jaxpm/pm.py index f78a765..3b18d48 100644 --- a/jaxpm/pm.py +++ b/jaxpm/pm.py @@ -9,7 +9,7 @@ from jaxpm.distributed import (autoshmap, fft3d, get_local_shape, ifft3d, normal_field) from jaxpm.growth import (dGf2a, dGfa, growth_factor, growth_factor_second, growth_rate, growth_rate_second) -from jaxpm.kernels import (PGD_kernel, fftk, gradient_kernel, laplace_kernel, +from jaxpm.kernels import (PGD_kernel, fftk, gradient_kernel, invlaplace_kernel, longrange_kernel) from jaxpm.painting import cic_paint, cic_paint_dx, cic_read, cic_read_dx @@ -29,18 +29,20 @@ def pm_forces(positions, mesh_shape = delta.shape if delta is None: - delta_k = fft3d( - cic_paint_dx(positions, halo_size=halo_size, sharding=sharding)) - else: + field = cic_paint_dx(positions, halo_size=halo_size, sharding=sharding) + delta_k = fft3d(field) + elif jnp.isrealobj(delta): delta_k = fft3d(delta) + else: + delta_k = delta kvec = fftk(delta_k) # Computes gravitational potential - pot_k = delta_k * laplace_kernel(kvec) * longrange_kernel(kvec, + pot_k = delta_k * invlaplace_kernel(kvec) * longrange_kernel(kvec, r_split=r_split) # Computes gravitational forces forces = jnp.stack([ - cic_read_dx(ifft3d(gradient_kernel(kvec, i) * pot_k), + cic_read_dx(ifft3d( - gradient_kernel(kvec, i) * pot_k), halo_size=halo_size, sharding=sharding) for i in range(3) ], @@ -49,44 +51,10 @@ def pm_forces(positions, return forces -def lpt2_source(mesh_size, initial_conditions): - - kvec = fftk(mesh_size) - # TODO : this has already been done for LPT1, we should reuse it - delta_k = fft3d(initial_conditions) - - source = jnp.zeros_like(delta_k) - - D1 = [1, 2, 0] - D2 = [2, 0, 1] - - # laplace_kernel should be actually inv laplace_kernel - # adding a minus sign here that will be negated when computing forces - # because F = -grad(phi) - # and phi = -laplace_kernel(delta_k) - pot_k = delta_k * laplace_kernel(delta_k) - - nabla_i_nabla_i = [ - ifft3d(gradient_kernel(kvec, i)**2 * pot_k) for i in range(3) - ] - # for diagonal terms - source += nabla_i_nabla_i[D1[0]] * nabla_i_nabla_i[D2[0]] - source += nabla_i_nabla_i[D1[1]] * nabla_i_nabla_i[D2[1]] - source += nabla_i_nabla_i[D1[2]] * nabla_i_nabla_i[D2[2]] - - # off diag terms - for i in range(3): - nabla_i_nabla_j = gradient_kernel(kvec, D1[i]) * gradient_kernel( - kvec, D2[i]) - phi = ifft3d(nabla_i_nabla_j * pot_k) - source -= phi**2 - - return source - - -def lpt(cosmo, initial_conditions, a, halo_size=0, sharding=None): +def lpt(cosmo, initial_conditions, a, halo_size=0, sharding=None,order=1): """ - Computes first order LPT displacement + Computes first and second order LPT displacement and momentum, + e.g. Eq. 2 and 3 [Jenkins2010](https://arxiv.org/pdf/0910.0258) """ gpu_mesh = sharding.mesh if sharding is not None else None spec = sharding.spec if sharding is not None else P() @@ -99,48 +67,48 @@ def lpt(cosmo, initial_conditions, a, halo_size=0, sharding=None): out_specs=spec)() # yapf: disable + a = jnp.atleast_1d(a) + E = jnp.sqrt(jc.background.Esqr(cosmo, a)) + delta_k = fft3d(initial_conditions) initial_force = pm_forces(displacement, - delta=initial_conditions, + delta=delta_k, halo_size=halo_size, sharding=sharding) - a = jnp.atleast_1d(a) dx = growth_factor(cosmo, a) * initial_force - p = a**2 * growth_rate(cosmo, a) * jnp.sqrt(jc.background.Esqr(cosmo, - a)) * dx - f = a**2 * jnp.sqrt(jc.background.Esqr(cosmo, a)) * dGfa(cosmo, - a) * initial_force - return dx, p, f + p = a**2 * growth_rate(cosmo, a) * E * dx + f = a**2 * E * dGfa(cosmo,a) * initial_force + if order == 2: + kvec = fftk(delta_k) + pot_k = delta_k * invlaplace_kernel(kvec) + delta2 = 0 + shear_acc = 0 + # for i, ki in enumerate(kvec): + for i in range(3): + # Add products of diagonal terms = 0 + s11*s00 + s22*(s11+s00)... + # shear_ii = jnp.fft.irfftn(- ki**2 * pot_k) + nabla_i_nabla_i = gradient_kernel(kvec, i)**2 + shear_ii = jnp.fft.irfftn(nabla_i_nabla_i * pot_k) + delta2 += shear_ii * shear_acc + shear_acc += shear_ii -# @Credit Hugo Simon https://github.com/hsimonfroy/montecosmo -def lpt2(cosmo, initial_conditions, dx, p, f, a, halo_size=0): + # for kj in kvec[i+1:]: + for j in range(i+1, 3): + # Substract squared strict-up-triangle terms + # delta2 -= jnp.fft.irfftn(- ki * kj * pot_k)**2 + nabla_i_nabla_j = gradient_kernel(kvec, i) * gradient_kernel(kvec, j) + delta2 -= jnp.fft.irfftn(nabla_i_nabla_j * pot_k)**2 + + delta_k2 = fft3d(delta2) + init_force2 = pm_forces(displacement, delta=delta_k2,halo_size=halo_size,sharding=sharding) + # NOTE: growth_factor_second is renormalized: - D2 = 3/7 * growth_factor_second + dx2 = 3/7 * growth_factor_second(cosmo, a) * init_force2 + p2 = a**2 * growth_rate_second(cosmo, a) * E * dx2 + f2 = a**2 * E * dGf2a(cosmo, a) * init_force2 - mesh_size = initial_conditions.shape - local_mesh_shape = (*get_local_shape(initial_conditions.shape), 3) - # TODO - # Displacements have been created in the previous step - # find a way to reuse them - displacement = autoshmap( - partial(jnp.zeros, shape=(local_mesh_shape), dtype='float32'), - in_specs=(), - out_specs=P('x', 'y'))() # yapf: disable - - lpt2_delta = lpt2_source(mesh_size, initial_conditions) - delta2_k = fft3d(lpt2_delta) - - lpt2_forces = pm_forces(displacement, - mesh_size, - delta_k=delta2_k, - halo_size=halo_size) - dx2 = 3 / 7 * growth_factor_second(cosmo, a) * lpt2_forces - p2 = a**2 * growth_rate_second(cosmo, a) * jnp.sqrt( - jc.background.Esqr(cosmo, a)) * dx2 - f2 = a**2 * jnp.sqrt(jc.background.Esqr(cosmo, a)) * dGf2a(cosmo, - a) * lpt2_forces - - dx += dx2 - p += p2 - f += f2 + dx += dx2 + p += p2 + f += f2 return dx, p, f @@ -185,10 +153,33 @@ def make_ode_fn(mesh_shape, halo_size=0, sharding=None): return nbody_ode +def get_ode_fn(cosmo, mesh_shape, halo_size=0, sharding=None): + + def nbody_ode(a, state, args): + """ + State is an array [position, velocities] + + Compatible with [Diffrax API](https://docs.kidger.site/diffrax/) + """ + pos, vel = state + forces = pm_forces(pos, mesh_shape, halo_size=halo_size, sharding=sharding) * 1.5 * cosmo.Omega_m + + # Computes the update of position (drift) + dpos = 1. / (a**3 * jnp.sqrt(jc.background.Esqr(cosmo, a))) * vel + + # Computes the update of velocity (kick) + dvel = 1. / (a**2 * jnp.sqrt(jc.background.Esqr(cosmo, a))) * forces + + return jnp.stack([dpos, dvel]) + + return nbody_ode + def pgd_correction(pos, mesh_shape, params): """ - improve the short-range interactions of PM-Nbody simulations with potential gradient descent method, based on https://arxiv.org/abs/1804.00671 + improve the short-range interactions of PM-Nbody simulations with potential gradient descent method, + based on https://arxiv.org/abs/1804.00671 + args: pos: particle positions [npart, 3] params: [alpha, kl, ks] pgd parameters @@ -197,24 +188,20 @@ def pgd_correction(pos, mesh_shape, params): delta = cic_paint(jnp.zeros(mesh_shape), pos) alpha, kl, ks = params delta_k = jnp.fft.rfftn(delta) - PGD_range = PGD_kernel(kvec, kl, ks) - - pot_k_pgd = (delta_k * laplace_kernel(kvec)) * PGD_range - - forces_pgd = jnp.stack([ - cic_read(jnp.fft.irfftn(gradient_kernel(kvec, i) * pot_k_pgd), pos) - for i in range(3) - ], - axis=-1) - - dpos_pgd = forces_pgd * alpha + PGD_range=PGD_kernel(kvec, kl, ks) + + pot_k_pgd=(delta_k * invlaplace_kernel(kvec))*PGD_range + forces_pgd= jnp.stack([cic_read(jnp.fft.irfftn(- gradient_kernel(kvec, i)*pot_k_pgd), pos) + for i in range(3)],axis=-1) + + dpos_pgd = forces_pgd*alpha + return dpos_pgd def make_neural_ode_fn(model, mesh_shape): - - def neural_nbody_ode(state, a, cosmo, params): + def neural_nbody_ode(state, a, cosmo:Cosmology, params): """ state is a tuple (position, velocities) """ @@ -226,19 +213,15 @@ def make_neural_ode_fn(model, mesh_shape): delta_k = jnp.fft.rfftn(delta) # Computes gravitational potential - pot_k = delta_k * laplace_kernel(kvec) * longrange_kernel(kvec, - r_split=0) + pot_k = delta_k * invlaplace_kernel(kvec) * longrange_kernel(kvec, r_split=0) # Apply a correction filter - kk = jnp.sqrt(sum((ki / jnp.pi)**2 for ki in kvec)) - pot_k = pot_k * (1. + model.apply(params, kk, jnp.atleast_1d(a))) + kk = jnp.sqrt(sum((ki/jnp.pi)**2 for ki in kvec)) + pot_k = pot_k *(1. + model.apply(params, kk, jnp.atleast_1d(a))) # Computes gravitational forces - forces = jnp.stack([ - cic_read(jnp.fft.irfftn(gradient_kernel(kvec, i) * pot_k), pos) - for i in range(3) - ], - axis=-1) + forces = jnp.stack([cic_read(jnp.fft.irfftn(- gradient_kernel(kvec, i)*pot_k), pos) + for i in range(3)],axis=-1) forces = forces * 1.5 * cosmo.Omega_m @@ -249,5 +232,4 @@ def make_neural_ode_fn(model, mesh_shape): dvel = 1. / (a**2 * jnp.sqrt(jc.background.Esqr(cosmo, a))) * forces return dpos, dvel - return neural_nbody_ode