mirror of
https://github.com/Richard-Sti/csiborgtools.git
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Forward model fields to RSP (#66)
* Add radial velocity field * Add overdensity plot * Flip velocities too * Add field calculations * Add RSP mapping * Add potential in RSP * Add projected field plotting
This commit is contained in:
Richard Stiskalek
GitHub
parent
f7b8b782a0
commit
63b6cdbe72
@ -18,7 +18,8 @@ try:
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import MAS_library as MASL # noqa
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from .density import DensityField, PotentialField, VelocityField # noqa
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from .interp import evaluate_cartesian, evaluate_sky, make_sky # noqa
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from .interp import (evaluate_cartesian, evaluate_sky, field2rsp, # noqa
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make_sky)
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from .utils import nside2radec, smoothen_field # noqa
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except ImportError:
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warn("MAS_library not found, `DensityField` will not be available", UserWarning) # noqa
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@ -20,8 +20,10 @@ TODO:
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"""
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from abc import ABC
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import MAS_library as MASL
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import numpy
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import MAS_library as MASL
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from numba import jit
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from tqdm import trange
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from ..read.utils import real2redshift
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@ -220,6 +222,36 @@ class VelocityField(BaseField):
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self.box = box
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self.MAS = MAS
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@staticmethod
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@jit(nopython=True)
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def radial_velocity(rho_vel):
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"""
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Calculate the radial velocity field around the observer in the centre
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of the box.
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Parameters
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----------
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rho_vel : 4-dimensional array of shape `(3, grid, grid, grid)`.
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Velocity field along each axis.
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Returns
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-------
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radvel : 3-dimensional array of shape `(grid, grid, grid)`.
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Radial velocity field.
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"""
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grid = rho_vel.shape[1]
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radvel = numpy.zeros((grid, grid, grid), dtype=numpy.float32)
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for i in range(grid):
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px = i - 0.5 * (grid - 1)
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for j in range(grid):
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py = j - 0.5 * (grid - 1)
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for k in range(grid):
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pz = k - 0.5 * (grid - 1)
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vx, vy, vz = rho_vel[:, i, j, k]
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radvel[i, j, k] = ((px * vx + py * vy + pz * vz)
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/ numpy.sqrt(px**2 + py**2 + pz**2))
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return radvel
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def __call__(self, parts, grid, mpart, flip_xz=True, nbatch=30,
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verbose=True):
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"""
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@ -245,7 +277,7 @@ class VelocityField(BaseField):
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Returns
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-------
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rho_vel : 3-dimensional array of shape `(3, grid, grid, grid)`.
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rho_vel : 4-dimensional array of shape `(3, grid, grid, grid)`.
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Velocity field along each axis.
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References
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@ -272,6 +304,7 @@ class VelocityField(BaseField):
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mass = force_single_precision(mass, "particle_mass")
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if flip_xz:
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pos[:, [0, 2]] = pos[:, [2, 0]]
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vel[:, [0, 2]] = vel[:, [2, 0]]
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vel *= mass.reshape(-1, 1) / mpart
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for i in range(3):
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@ -17,9 +17,11 @@ Tools for interpolating 3D fields at arbitrary positions.
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"""
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import MAS_library as MASL
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import numpy
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from numba import jit
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from scipy.ndimage import gaussian_filter
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from tqdm import trange
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from ..read.utils import radec_to_cartesian
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from ..read.utils import radec_to_cartesian, real2redshift
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from .utils import force_single_precision
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@ -137,3 +139,99 @@ def make_sky(field, angpos, dist, box, volume_weight=True, verbose=True):
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evaluate_sky(field, pos=dir_loop, box=box, isdeg=True))
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out *= dx
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return out
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@jit(nopython=True)
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def divide_nonzero(field0, field1):
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"""
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Divide two fields where the second one is not zero. If the second field
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is zero, the first one is left unchanged. Operates in-place.
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Parameters
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----------
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field0 : 3-dimensional array of shape `(grid, grid, grid)`
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Field to be divided.
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field1 : 3-dimensional array of shape `(grid, grid, grid)`
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Field to divide by.
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Returns
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-------
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field0 : 3-dimensional array of shape `(grid, grid, grid)`
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Field divided by the second one.
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"""
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assert field0.shape == field1.shape
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imax, jmax, kmax = field0.shape
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for i in range(imax):
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for j in range(jmax):
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for k in range(kmax):
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if field1[i, j, k] != 0:
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field0[i, j, k] /= field1[i, j, k]
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def field2rsp(field, parts, box, nbatch=30, flip_partsxz=True, init_value=0.,
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verbose=True):
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"""
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Forward model real space scalar field to redshift space. Attaches field
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values to particles, those are then moved to redshift space and from their
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positions reconstructs back the field on a regular grid by NGP
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interpolation. This by definition produces a discontinuous field.
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Parameters
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----------
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field : 3-dimensional array of shape `(grid, grid, grid)`
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Real space field to be evolved to redshift space.
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parts_pos : 2-dimensional array of shape `(n_parts, 3)`
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Particle positions in real space.
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parts_vel : 2-dimensional array of shape `(n_parts, 3)`
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Particle velocities in real space.
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box : :py:class:`csiborgtools.read.CSiBORGBox`
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The simulation box information and transformations.
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nbatch : int, optional
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Number of batches to use when moving particles to redshift space.
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Particles are assumed to be lazily loaded to memory.
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flip_partsxz : bool, optional
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Whether to flip the x and z coordinates of the particles. This is
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because of a BORG bug.
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init_value : float, optional
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Initial value of the RSP field on the grid.
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verbose : bool, optional
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Verbosity flag.
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Returns
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-------
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rsp_fields : (list of) 3-dimensional array of shape `(grid, grid, grid)`
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"""
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rsp_field = numpy.full(field.shape, init_value, dtype=numpy.float32)
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cellcounts = numpy.zeros(rsp_field.shape, dtype=numpy.float32)
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# We iterate over the fields and in the inner loop over the particles. This
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# is slower than iterating over the particles and in the inner loop over
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# the fields, but it is more memory efficient. Typically we will only have
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# one field.
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nparts = parts.shape[0]
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batch_size = nparts // nbatch
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start = 0
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for k in trange(nbatch + 1) if verbose else range(nbatch + 1):
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end = min(start + batch_size, nparts)
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pos = parts[start:end]
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pos, vel = pos[:, :3], pos[:, 3:6]
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if flip_partsxz:
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pos[:, [0, 2]] = pos[:, [2, 0]]
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vel[:, [0, 2]] = vel[:, [2, 0]]
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# Evaluate the field at the particle positions in real space.
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values = evaluate_cartesian(field, pos=pos)
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# Move particles to redshift space.
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rsp_pos = real2redshift(pos, vel, [0.5, 0.5, 0.5], box,
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in_box_units=True, periodic_wrap=True,
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make_copy=True)
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# Assign particles' values to the grid.
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MASL.MA(rsp_pos, rsp_field, 1., "NGP", W=values)
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# Count the number of particles in each grid cell.
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MASL.MA(rsp_pos, cellcounts, 1., "NGP")
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if end == nparts:
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break
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start = end
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# Finally divide by the number of particles in each cell and smooth.
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divide_nonzero(rsp_field, cellcounts)
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return rsp_field
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@ -363,7 +363,8 @@ class Paths:
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Parameters
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----------
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kind : str
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Field type. Must be one of: `density`, `velocity`, `potential`.
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Field type. Must be one of: `density`, `velocity`, `potential`,
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`radvel`.
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MAS : str
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Mass-assignment scheme.
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grid : int
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@ -378,7 +379,7 @@ class Paths:
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path : str
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"""
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fdir = join(self.postdir, "environment")
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assert kind in ["density", "velocity", "potential"]
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assert kind in ["density", "velocity", "potential", "radvel"]
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if not isdir(fdir):
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makedirs(fdir)
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warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
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@ -1,78 +0,0 @@
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# Copyright (C) 2022 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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MPI script to calculate density field-derived fields in the CSiBORG
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simulations' final snapshot.
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"""
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from argparse import ArgumentParser
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from datetime import datetime
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from distutils.util import strtobool
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import numpy
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from mpi4py import MPI
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try:
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import csiborgtools
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except ModuleNotFoundError:
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import sys
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sys.path.append("../")
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import csiborgtools
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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nproc = comm.Get_size()
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verbose = nproc == 1
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parser = ArgumentParser()
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parser.add_argument("--ics", type=int, nargs="+", default=None,
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help="IC realisations. If `-1` processes all simulations.")
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parser.add_argument("--kind", type=str, choices=["potential", "velocity"],
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help="What derived field to calculate?")
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parser.add_argument("--MAS", type=str, choices=["NGP", "CIC", "TSC", "PCS"])
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parser.add_argument("--grid", type=int, help="Grid resolution.")
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parser.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
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help="Calculate from the RSP density field?")
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args = parser.parse_args()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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if args.ics is None or args.ics[0] == -1:
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ics = paths.get_ics("csiborg")
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else:
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ics = args.ics
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for i in csiborgtools.fits.split_jobs(len(ics), nproc)[rank]:
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nsim = ics[i]
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if verbose:
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print(f"{datetime.now()}: rank {rank} working on simulation {nsim}.",
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flush=True)
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nsnap = max(paths.get_snapshots(nsim))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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density_gen = csiborgtools.field.DensityField(box, args.MAS)
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rho = numpy.load(paths.field("density", args.MAS, args.grid, nsim,
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args.in_rsp))
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rho = density_gen.overdensity_field(rho)
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if args.kind == "potential":
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gen = csiborgtools.field.PotentialField(box, args.MAS)
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else:
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raise RuntimeError(f"Field {args.kind} is not implemented yet.")
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field = gen(rho)
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fout = paths.field("potential", args.MAS, args.grid, nsim,
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args.in_rsp)
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print(f"{datetime.now()}: rank {rank} saving output to `{fout}`.")
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numpy.save(fout, field)
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169
scripts/field_prop.py
Normal file
169
scripts/field_prop.py
Normal file
@ -0,0 +1,169 @@
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# Copyright (C) 2022 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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MPI script to calculate density field-derived fields in the CSiBORG
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simulations' final snapshot.
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"""
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from argparse import ArgumentParser
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from datetime import datetime
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from distutils.util import strtobool
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import numpy
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from mpi4py import MPI
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try:
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import csiborgtools
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except ModuleNotFoundError:
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import sys
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sys.path.append("../")
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import csiborgtools
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from taskmaster import work_delegation
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from utils import get_nsims
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###############################################################################
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# Density field #
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###############################################################################
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def density_field(nsim, parser_args):
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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parts = csiborgtools.read.read_h5(paths.particles(nsim))["particles"]
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gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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field = gen(parts, parser_args.grid, in_rsp=parser_args.in_rsp,
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verbose=parser_args.verbose)
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fout = paths.field("density", parser_args.MAS, parser_args.grid,
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nsim, parser_args.in_rsp)
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print(f"{datetime.now()}: saving output to `{fout}`.")
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numpy.save(fout, field)
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###############################################################################
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# Velocity field #
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###############################################################################
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def velocity_field(nsim, parser_args):
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if parser_args.in_rsp:
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raise NotImplementedError("Velocity field in RSP is not implemented.")
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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mpart = 1.1641532e-10 # Particle mass in CSiBORG simulations.
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nsnap = max(paths.get_snapshots(nsim))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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parts = csiborgtools.read.read_h5(paths.particles(nsim))["particles"]
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gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
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field = gen(parts, parser_args.grid, mpart, verbose=parser_args.verbose)
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fout = paths.field("velocity", parser_args.MAS, parser_args.grid,
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nsim, in_rsp=False)
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print(f"{datetime.now()}: saving output to `{fout}`.")
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numpy.save(fout, field)
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###############################################################################
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# Potential field #
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###############################################################################
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def potential_field(nsim, parser_args):
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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# Load the real space overdensity field
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density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
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rho = numpy.load(paths.field("density", parser_args.MAS, parser_args.grid,
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nsim, in_rsp=False))
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rho = density_gen.overdensity_field(rho)
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# Calculate the real space potentiel field
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gen = csiborgtools.field.PotentialField(box, parser_args.MAS)
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field = gen(rho)
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if parser_args.in_rsp:
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parts = csiborgtools.read.read_h5(paths.particles(nsim))["particles"]
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field = csiborgtools.field.field2rsp(field, parts=parts, box=box,
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verbose=parser_args.verbose)
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fout = paths.field(parser_args.kind, parser_args.MAS, parser_args.grid,
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nsim, parser_args.in_rsp)
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print(f"{datetime.now()}: saving output to `{fout}`.")
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numpy.save(fout, field)
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###############################################################################
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# Radial velocity field #
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###############################################################################
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def radvel_field(nsim, parser_args):
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if parser_args.in_rsp:
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raise NotImplementedError("Radial vel. field in RSP not implemented.")
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsnap = max(paths.get_snapshots(nsim))
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box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
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vel = numpy.load(paths.field("velocity", parser_args.MAS, parser_args.grid,
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nsim, parser_args.in_rsp))
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gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
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field = gen.radial_velocity(vel)
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fout = paths.field("radvel", parser_args.MAS, parser_args.grid,
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nsim, parser_args.in_rsp)
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print(f"{datetime.now()}: saving output to `{fout}`.")
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numpy.save(fout, field)
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###############################################################################
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# Command line interface #
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###############################################################################
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--nsims", type=int, nargs="+", default=None,
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help="IC realisations. `-1` for all simulations.")
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parser.add_argument("--kind", type=str,
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choices=["density", "velocity", "radvel", "potential"],
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help="What derived field to calculate?")
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parser.add_argument("--MAS", type=str,
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choices=["NGP", "CIC", "TSC", "PCS"])
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parser.add_argument("--grid", type=int, help="Grid resolution.")
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parser.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
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help="Calculate in RSP?")
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parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
|
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help="Verbosity flag for reading in particles.")
|
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parser_args = parser.parse_args()
|
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comm = MPI.COMM_WORLD
|
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
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nsims = get_nsims(parser_args, paths)
|
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|
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def main(nsim):
|
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if parser_args.kind == "density":
|
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density_field(nsim, parser_args)
|
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elif parser_args.kind == "velocity":
|
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velocity_field(nsim, parser_args)
|
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elif parser_args.kind == "radvel":
|
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radvel_field(nsim, parser_args)
|
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elif parser_args.kind == "potential":
|
||||
potential_field(nsim, parser_args)
|
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else:
|
||||
raise RuntimeError(f"Field {parser_args.kind} is not implemented.")
|
||||
|
||||
work_delegation(main, nsims, comm, master_verbose=True)
|
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@ -162,29 +162,73 @@ def plot_hmf(pdf=False):
|
||||
plt.close()
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Sky distribution #
|
||||
###############################################################################
|
||||
|
||||
@cache_to_disk(7)
|
||||
def load_field(kind, nsim, grid, MAS, in_rsp=False):
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
print(paths.field(kind, MAS, grid, nsim, in_rsp=in_rsp))
|
||||
return numpy.load(paths.field(kind, MAS, grid, nsim, in_rsp=in_rsp))
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Projected field #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def plot_projected_field(kind, nsim, grid, in_rsp, MAS="PCS", pdf=False):
|
||||
print(f"Plotting projected field `{kind}`. ", flush=True)
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
nsnap = max(paths.get_snapshots(nsim))
|
||||
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
|
||||
|
||||
if kind == "overdensity":
|
||||
field = load_field("density", nsim, grid, MAS=MAS, in_rsp=in_rsp)
|
||||
density_gen = csiborgtools.field.DensityField(box, MAS)
|
||||
field = density_gen.overdensity_field(field) + 2
|
||||
else:
|
||||
field = load_field(kind, nsim, grid, MAS=MAS, in_rsp=in_rsp)
|
||||
|
||||
print(field)
|
||||
|
||||
with plt.style.context(utils.mplstyle):
|
||||
fig, ax = plt.subplots(figsize=(3.5 * 2, 2.625), ncols=3, sharey=True,
|
||||
sharex=True)
|
||||
fig.subplots_adjust(hspace=0, wspace=0)
|
||||
for i in range(3):
|
||||
ax[i].imshow(numpy.sum(field, axis=i))
|
||||
|
||||
fig.tight_layout(h_pad=0, w_pad=0)
|
||||
for ext in ["png"] if pdf is False else ["png", "pdf"]:
|
||||
fout = join(utils.fout, f"field_{kind}_{nsim}_rsp{in_rsp}.{ext}")
|
||||
print(f"Saving to `{fout}`.")
|
||||
fig.savefig(fout, dpi=utils.dpi, bbox_inches="tight")
|
||||
plt.close()
|
||||
|
||||
###############################################################################
|
||||
# Sky distribution #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def get_sky_label(kind, volume_weight):
|
||||
if volume_weight:
|
||||
if kind == "density":
|
||||
label = r"$\log \int_{0}^{R} r^2 \delta(r, \mathrm{RA}, \mathrm{dec}) \mathrm{d} r$" # noqa
|
||||
label = r"$\log \int_{0}^{R} r^2 \rho(r, \mathrm{RA}, \mathrm{dec}) \mathrm{d} r$" # noqa
|
||||
if kind == "overdensity":
|
||||
label = r"$\log \int_{0}^{R} r^2 \left[\delta(r, \mathrm{RA}, \mathrm{dec}) + 2\right] \mathrm{d} r$" # noqa
|
||||
elif kind == "potential":
|
||||
label = r"$\int_{0}^{R} r^2 \phi(r, \mathrm{RA}, \mathrm{dec}) \mathrm{d} r$" # noqa
|
||||
elif kind == "radvel":
|
||||
label = r"$\int_{0}^{R} r^2 v_r(r, \mathrm{RA}, \mathrm{dec}) \mathrm{d} r$" # noqa
|
||||
else:
|
||||
label = None
|
||||
else:
|
||||
if kind == "density":
|
||||
label = r"$\log \int_{0}^{R} \delta(r, \mathrm{RA}, \mathrm{dec}) \mathrm{d} r$" # noqa
|
||||
label = r"$\log \int_{0}^{R} \rho(r, \mathrm{RA}, \mathrm{dec}) \mathrm{d} r$" # noqa
|
||||
if kind == "overdensity":
|
||||
label = r"$\log \int_{0}^{R} \left[\delta(r, \mathrm{RA}, \mathrm{dec}) + 2\right] \mathrm{d} r$" # noqa
|
||||
elif kind == "potential":
|
||||
label = r"$\int_{0}^{R} \phi(r, \mathrm{RA}, \mathrm{dec}) \mathrm{d} r$" # noqa
|
||||
elif kind == "radvel":
|
||||
label = r"$\int_{0}^{R} v_r(r, \mathrm{RA}, \mathrm{dec}) \mathrm{d} r$" # noqa
|
||||
else:
|
||||
label = None
|
||||
return label
|
||||
@ -200,7 +244,12 @@ def plot_sky_distribution(kind, nsim, grid, nside, MAS="PCS", plot_groups=True,
|
||||
nsnap = max(paths.get_snapshots(nsim))
|
||||
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
|
||||
|
||||
field = load_field(kind, nsim, grid, MAS=MAS, in_rsp=False)
|
||||
if kind == "overdensity":
|
||||
field = load_field("density", nsim, grid, MAS=MAS, in_rsp=False)
|
||||
density_gen = csiborgtools.field.DensityField(box, MAS)
|
||||
field = density_gen.overdensity_field(field) + 2
|
||||
else:
|
||||
field = load_field(kind, nsim, grid, MAS=MAS, in_rsp=False)
|
||||
|
||||
angpos = csiborgtools.field.nside2radec(nside)
|
||||
dist = numpy.linspace(dmin, dmax, 500)
|
||||
@ -209,7 +258,7 @@ def plot_sky_distribution(kind, nsim, grid, nside, MAS="PCS", plot_groups=True,
|
||||
|
||||
with plt.style.context(utils.mplstyle):
|
||||
label = get_sky_label(kind, volume_weight)
|
||||
if kind == "density":
|
||||
if kind in ["density", "overdensity"]:
|
||||
out = numpy.log10(out)
|
||||
healpy.mollview(out, fig=0, title="", unit=label)
|
||||
|
||||
@ -248,7 +297,7 @@ if __name__ == "__main__":
|
||||
parser.add_argument('-c', '--clean', action='store_true')
|
||||
args = parser.parse_args()
|
||||
|
||||
cached_funcs = []
|
||||
cached_funcs = ["load_field"]
|
||||
if args.clean:
|
||||
for func in cached_funcs:
|
||||
print(f"Cleaning cache for function {func}.")
|
||||
@ -258,6 +307,8 @@ if __name__ == "__main__":
|
||||
# plot_mass_vs_normcells(7444 + 24 * 4, pdf=False)
|
||||
# plot_mass_vs_ncells(7444, pdf=True)
|
||||
# plot_hmf(pdf=True)
|
||||
plot_sky_distribution("potential", 7444, 256, nside=64, plot_groups=False,
|
||||
dmin=50, dmax=100, plot_halos=5e13,
|
||||
volume_weight=True)
|
||||
# plot_sky_distribution("radvel", 7444, 256, nside=64,
|
||||
# plot_groups=False, dmin=50, dmax=100,
|
||||
# plot_halos=5e13, volume_weight=False)
|
||||
|
||||
plot_projected_field("potential", 7444, 256, in_rsp=True)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user