248 lines
9.0 KiB
Python
248 lines
9.0 KiB
Python
## Implementation of a mesh based force solver
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import numpy as np
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import matplotlib.pyplot as plt
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from scipy import fft
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import logging
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logger = logging.getLogger(__name__)
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#### Version 1 - keeping the derivative of phi
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def mesh_forces(particles: np.ndarray, G: float, n_grid: int, mapping: callable) -> np.ndarray:
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"""
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Computes the gravitational force acting on a set of particles using a mesh-based approach.
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Assumes that the particles array has the following columns: x, y, z, m.
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"""
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if particles.shape[1] != 4:
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raise ValueError("Particles array must have 4 columns: x, y, z, m")
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logger.debug(f"Computing forces for {particles.shape[0]} particles using mesh [mapping={mapping.__name__}, {n_grid=}]")
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mesh, axis = to_mesh(particles, n_grid, mapping)
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spacing = np.abs(axis[1] - axis[0])
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logger.debug(f"Using mesh spacing: {spacing}")
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# we want a density mesh:
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cell_volume = spacing**3
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rho = mesh / cell_volume
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if logger.isEnabledFor(logging.DEBUG):
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show_mesh_information(mesh, "Density mesh")
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# compute the potential and its gradient
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phi_grad = mesh_poisson(rho, G, spacing)
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if logger.isEnabledFor(logging.DEBUG):
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logger.debug(f"Got phi_grad with: {phi_grad.shape}, {np.max(phi_grad)}")
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show_mesh_information(phi_grad[0], "Potential gradient (x-direction)")
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# compute the particle forces from the mesh potential
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forces = np.zeros_like(particles[:, :3])
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for i, p in enumerate(particles):
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ijk = np.digitize(p, axis) - 1
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logger.debug(f"Particle {p} maps to cell {ijk}")
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# this gives 4 entries since p[3] the mass is digitized as well -> this is meaningless and we discard it
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# logger.debug(f"Particle {p} maps to cell {ijk}")
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forces[i] = - p[3] * phi_grad[..., ijk[0], ijk[1], ijk[2]]
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return forces
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def mesh_poisson(mesh: np.ndarray, G: float, spacing: float) -> np.ndarray:
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"""
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Solves the poisson equation for the mesh using the FFT.
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Returns the derivative of the potential - grad phi
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"""
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rho_hat = fft.fftn(mesh)
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k = fft.fftfreq(mesh.shape[0], spacing)
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# shift the zero frequency to the center
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k = fft.fftshift(k)
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kx, ky, kz = np.meshgrid(k, k, k)
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k_vec = np.stack([kx, ky, kz], axis=0)
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k_sr = kx**2 + ky**2 + kz**2
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if logger.isEnabledFor(logging.DEBUG):
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logger.debug(f"Got k_square with: {k_sr.shape}, {np.max(k_sr)} {np.min(k_sr)}")
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logger.debug(f"Count of ksquare zeros: {np.sum(k_sr == 0)}")
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show_mesh_information(np.abs(k_sr), "k_square")
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k_sr[k_sr == 0] = np.inf
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k_inv = k_vec / k_sr # allows for element-wise division
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logger.debug(f"Proceeding to poisson equation with {rho_hat.shape=}, {k_inv.shape=}")
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grad_phi_hat = - 4 * np.pi * G * rho_hat * k_inv * 1j
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# nabla^2 phi => -i * k * nabla phi = 4 pi G rho => nabla phi = - i * rho * k / k^2
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# todo: check minus
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grad_phi = np.real(fft.ifftn(grad_phi_hat))
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return grad_phi
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#### Version 2 - only storing the scalar potential
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def mesh_forces_v2(particles: np.ndarray, G: float, n_grid: int, mapping: callable) -> np.ndarray:
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"""
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Computes the gravitational force acting on a set of particles using a mesh-based approach.
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Assumes that the particles array has the following columns: x, y, z, m.
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"""
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if particles.shape[1] != 4:
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raise ValueError("Particles array must have 4 columns: x, y, z, m")
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logger.debug(f"Computing forces for {particles.shape[0]} particles using mesh [mapping={mapping.__name__}, {n_grid=}]")
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mesh, axis = to_mesh(particles, n_grid, mapping)
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spacing = np.abs(axis[1] - axis[0])
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logger.debug(f"Using mesh spacing: {spacing}")
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# we want a density mesh:
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cell_volume = spacing**3
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rho = mesh / cell_volume
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if logger.isEnabledFor(logging.DEBUG):
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show_mesh_information(mesh, "Density mesh")
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# compute the potential and its gradient
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phi = mesh_poisson_v2(rho, G, spacing)
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logger.debug(f"Got phi with: {phi.shape}, {np.max(phi)}")
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phi_grad = np.stack(np.gradient(phi, spacing), axis=0)
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if logger.isEnabledFor(logging.DEBUG):
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logger.debug(f"Got phi_grad with: {phi_grad.shape}, {np.max(phi_grad)}")
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show_mesh_information(phi, "Potential mesh")
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show_mesh_information(phi_grad[0], "Potential gradient (x-direction)")
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# compute the particle forces from the mesh potential
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forces = np.zeros_like(particles[:, :3])
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for i, p in enumerate(particles):
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ijk = np.digitize(p, axis) - 1
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# this gives 4 entries since p[3] the mass is digitized as well -> this is meaningless and we discard it
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# logger.debug(f"Particle {p} maps to cell {ijk}")
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forces[i] = - p[3] * phi_grad[..., ijk[0], ijk[1], ijk[2]]
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# TODO remove factor of 10
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# TODO could also index phi_grad the other way around?
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return forces
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def mesh_poisson_v2(mesh: np.ndarray, G: float, spacing: float) -> np.ndarray:
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"""
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Solves the poisson equation for the mesh using the FFT.
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Returns the scalar potential.
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"""
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rho_hat = fft.fftn(mesh)
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k = fft.fftfreq(mesh.shape[0], spacing)
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# shift the zero frequency to the center
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k = fft.fftshift(k)
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kx, ky, kz = np.meshgrid(k, k, k)
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k_sr = kx**2 + ky**2 + kz**2
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if logger.isEnabledFor(logging.DEBUG):
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logger.debug(f"Got k_square with: {k_sr.shape}, {np.max(k_sr)} {np.min(k_sr)}")
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logger.debug(f"Count of ksquare zeros: {np.sum(k_sr == 0)}")
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show_mesh_information(np.abs(k_sr), "k_square")
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# avoid division by zero
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# TODO: review this
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k_sr[k_sr == 0] = np.inf
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logger.debug(f"Proceeding to poisson equation with {rho_hat.shape=}, {k_sr.shape=}")
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phi_hat = - 4 * np.pi * G * rho_hat / k_sr
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# - comes from i squared
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# TODO: 4pi stays since the backtransform removes the 1/2pi factor
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phi = np.real(fft.ifftn(phi_hat))
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return phi
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#### Helper functions for star mapping
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def to_mesh(particles: np.ndarray, n_grid: int, mapping: callable) -> tuple[np.ndarray, np.ndarray]:
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"""
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Maps a list of particles to a of mesh of size n_grid x n_grid x n_grid.
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Assumes that the particles array has the following columns: x, y, z, ..., m.
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Uses the mapping function to detemine the contribution to each cell.
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"""
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if particles.shape[1] < 4:
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raise ValueError("Particles array must have at least 4 columns: x, y, z, m")
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# axis provide an easy way to map the particles to the mesh
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max_pos = np.max(particles[:, :3])
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axis = np.linspace(-max_pos, max_pos, n_grid)
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mesh_grid = np.meshgrid(axis, axis, axis)
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mesh = np.zeros_like(mesh_grid[0])
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for p in particles:
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m = p[-1]
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# spread the star onto cells through the shape function, taking into account the mass
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ijks, weights = mapping(p, axis)
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for ijk, weight in zip(ijks, weights):
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mesh[ijk[0], ijk[1], ijk[2]] += weight * m
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return mesh, axis
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def particle_to_cells_nn(particle, axis):
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# find the single cell that contains the particle
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ijk = np.digitize(particle, axis) - 1
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# the weight is obviously 1
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return [ijk], [1]
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bbox = np.array([
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[1, 0, 0],
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[-1, 0, 0],
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[1, 1, 0],
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[-1, -1, 0],
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[1, 1, 1],
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[-1, -1, 1],
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[1, 1, -1],
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[-1, -1, -1]
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])
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def particle_to_cells_cic(particle, axis, width):
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# create a virtual cell around the particle and check the intersections
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bounding_cell = particle + width * bbox
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# find all the cells that intersect with the virtual cell
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ijks = []
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weights = []
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for b in bounding_cell:
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# TODO: this is not the correct weight
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w = np.linalg.norm(particle - b)
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ijk = np.digitize(b, axis) - 1
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ijks.append(ijk)
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weights.append(w)
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# ensure that the weights sum to 1
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weights = np.array(weights)
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weights /= np.sum(weights)
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return ijks, weights
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#### Helper functions for mesh plotting
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def show_mesh_information(mesh: np.ndarray, name: str):
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logger.info(f"Mesh information for {name}")
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logger.info(f"Total mapped mass: {np.sum(mesh):.0f}")
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logger.info(f"Max cell value: {np.max(mesh)}")
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logger.info(f"Min cell value: {np.min(mesh)}")
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logger.info(f"Mean cell value: {np.mean(mesh)}")
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mesh_plot_3d(mesh, name)
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mesh_plot_2d(mesh, name)
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def mesh_plot_3d(mesh: np.ndarray, name: str):
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fig = plt.figure()
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fig.suptitle(f"{name} - {mesh.shape}")
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ax = fig.add_subplot(111, projection='3d')
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sc = ax.scatter(*np.where(mesh), c=mesh[np.where(mesh)], cmap='viridis')
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plt.colorbar(sc, ax=ax, label='Density')
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plt.show()
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def mesh_plot_2d(mesh: np.ndarray, name: str, only_z: bool = False):
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fig = plt.figure()
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fig.suptitle(f"{name} - {mesh.shape}")
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if only_z:
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plt.imshow(np.sum(mesh, axis=2), cmap='viridis', origin='lower')
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else:
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axs = fig.subplots(1, 3)
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axs[0].imshow(np.sum(mesh, axis=0), origin='lower')
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axs[0].set_title("Flattened in x")
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axs[1].imshow(np.sum(mesh, axis=1), origin='lower')
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axs[1].set_title("Flattened in y")
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axs[2].imshow(np.sum(mesh, axis=2), origin='lower')
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axs[2].set_title("Flattened in z")
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plt.show()
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