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Box units conversion (#3)
* linting * fix long line * rename nb * rename import * add group catalog * move imports out of functions * add array_to_structured * add references * fix subsampling * fix coord bug * add 2M++ dists * save nb * fix comment * add snapshot path * add snapshot path * add read_info * Move transforms * add import radec * expand docs * Move flipcols * update nb * add flip_cols * create file * add blank line * Move units transfs * add blank line * add units import * rm imports * add import * add box_units * add comments
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Richard Stiskalek
GitHub
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18 changed files with 6730 additions and 1574 deletions
18
galomatch/units/__init__.py
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18
galomatch/units/__init__.py
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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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from .transforms import (cartesian_to_radec, convert_mass_cols, # noqa
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convert_position_cols) # noqa
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from .box_units import BoxUnits # noqa
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166
galomatch/units/box_units.py
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166
galomatch/units/box_units.py
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# Copyright (C) 2022 Richard Stiskalek, Deaglan Bartlett
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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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Simulation box unit transformations.
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"""
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from astropy.cosmology import LambdaCDM
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from astropy import (constants, units)
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from ..io import read_info
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# Conversion factors
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MSUNCGS = constants.M_sun.cgs.value
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KPC_TO_CM = 3.08567758149137e21
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PI = 3.1415926535897932384626433
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class BoxUnits:
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"""
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Box units class for converting between box and physical units.
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Paramaters
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----------
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Nsnap : int
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Snapshot index.
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simpath : str
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Path to the simulation where its snapshot index folders are stored.
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"""
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def __init__(self, Nsnap, simpath):
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"""
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Read in the snapshot info file and set the units from it.
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"""
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info = read_info(Nsnap, simpath)
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pars = ["boxlen", "time", "aexp", "H0",
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"omega_m", "omega_l", "omega_k", "omega_b",
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"unit_l", "unit_d", "unit_t"]
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for par in pars:
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setattr(self, par, float(info[par]))
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self.h = self.H0 / 100
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self.cosmo = LambdaCDM(H0=self.H0, Om0=self.omega_m, Ode0=self.omega_l,
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Tcmb0=2.725 * units.K, Ob0=self.omega_b)
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# Constants in box units
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self.G = constants.G.cgs.value * (self.unit_d * self.unit_t ** 2)
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self.H0 = self.H0 * 1e5 / (1e3 * KPC_TO_CM) * self.unit_t
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self.c = constants.c.cgs.value * self.unit_t / self.unit_l
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self.rho_crit = 3 * self.H0 ** 2 / (8 * PI * self.G)
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def box2kpc(self, length):
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r"""
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Convert length from box units to :math:`\mathrm{kpc}`.
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Parameters
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----------
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length : float
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Length in box units.
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Returns
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-------
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length : foat
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Length in :math:`\mathrm{kpc}`
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"""
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return length * self.unit_l / KPC_TO_CM
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def kpc2box(self, length):
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r"""
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Convert length from :math:`\mathrm{kpc}` to box units.
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Parameters
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----------
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length : float
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Length in :math:`\mathrm{kpc}`
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Returns
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-------
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length : foat
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Length in box units.
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"""
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return length / self.unit_l * KPC_TO_CM
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def solarmass2box(self, mass):
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r"""
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Convert mass from :math:`M_\odot` to box units.
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Parameters
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----------
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mass : float
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Mass in :math:`M_\odot`.
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Returns
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-------
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mass : float
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Mass in box units.
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"""
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m = mass * MSUNCGS # In cgs
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unit_m = self.unit_d * self.unit_l ** 3
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return m / unit_m
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def box2solarmass(self, mass):
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r"""
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Convert mass from box units to :math:`M_\odot`.
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TODO: check this.
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Parameters
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----------
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mass : float
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Mass in box units.
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Returns
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-------
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mass : float
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Mass in :math:`M_\odot`.
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"""
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unit_m = self.unit_d * self.unit_l**3
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m = mass * unit_m # In cgs
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m = m / MSUNCGS
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return m
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def box2dens(self, density):
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r"""
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Convert density from box units to :math:`M_\odot / \mathrm{pc}^3`.
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TODO: check this.
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Parameters
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----------
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density : float
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Density in box units.
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box : `BoxConstants`
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Simulation box class with units.
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Returns
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-------
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density : float
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Density in :math:`M_\odot / \mathrm{pc}^3`.
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"""
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rho = density * self.unit_d # In cgs
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rho = rho * (KPC_TO_CM * 1e-3)**3 # In g/pc^3
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rho = rho / MSUNCGS
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return rho
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def dens2box(self, density):
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r"""
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Convert density from M_sun / pc^3
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TODO: check this and write documentation.
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"""
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rho = density * MSUNCGS
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rho = rho / (KPC_TO_CM * 1e-3)**3 # In g/cm^3
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rho = rho / self.unit_d
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return rho
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110
galomatch/units/transforms.py
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110
galomatch/units/transforms.py
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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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Various coordinate transformations.
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"""
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import numpy
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little_h = 0.705
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BOXSIZE = 677.7 / little_h # Mpc. Otherwise positions in [0, 1].
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BOXMASS = 3.749e19 # Msun
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def cartesian_to_radec(arr, xpar="peak_x", ypar="peak_y", zpar="peak_z"):
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r"""
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Extract `x`, `y`, and `z` coordinates from a record array `arr` and
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calculate the radial distance :math:`r` in coordinate units, right
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ascension :math:`\mathrm{RA} \in [0, 360)` degrees and declination
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:math:`\delta \in [-90, 90]` degrees.
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Parameters
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----------
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arr : record array
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Record array with the Cartesian coordinates.
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xpar : str, optional
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Name of the x coordinate in the record array.
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ypar : str, optional
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Name of the y coordinate in the record array.
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zpar : str, optional
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Name of the z coordinate in the record array.
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Returns
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-------
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dist : 1-dimensional array
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Radial distance.
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ra : 1-dimensional array
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Right ascension.
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dec : 1-dimensional array
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Declination.
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"""
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x, y, z = arr[xpar], arr[ypar], arr[zpar]
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dist = numpy.sqrt(x**2 + y**2 + z**2)
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dec = numpy.rad2deg(numpy.arcsin(z/dist))
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ra = numpy.rad2deg(numpy.arctan2(y, x))
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# Make sure RA in the correct range
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ra[ra < 0] += 360
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return dist, ra, dec
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def convert_mass_cols(arr, cols):
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r"""
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Convert mass columns from box units to :math:`M_{\odot}`. `arr` is passed
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by reference and is not explicitly returned back.
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Parameters
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----------
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arr : structured array
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The array whose columns are to be converted.
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cols : str or list of str
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The mass columns to be converted.
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Returns
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-------
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None
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"""
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cols = [cols] if isinstance(cols, str) else cols
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for col in cols:
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arr[col] *= BOXMASS
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def convert_position_cols(arr, cols, zero_centered=True):
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r"""
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Convert position columns from box units to :math:`\mathrm{Mpc}`. `arr` is
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passed by reference and is not explicitly returned back.
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Parameters
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----------
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arr : structured array
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The array whose columns are to be converted.
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cols : str or list of str
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The mass columns to be converted.
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zero_centered : bool, optional
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Whether to translate the well-resolved origin in the centre of the
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simulation to the :math:`(0, 0 , 0)` point. By default `True`.
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Returns
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-------
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None
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"""
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cols = [cols] if isinstance(cols, str) else cols
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for col in cols:
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arr[col] *= BOXSIZE
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if zero_centered:
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arr[col] -= BOXSIZE / 2
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