clusters: Move units.py and cosmology.py to utils

5 files changed, 6 insertions, 291 deletions

diff --git a/fg21sim/extragalactic/clusters/cosmology.py b/fg21sim/extragalactic/clusters/cosmology.py
deleted file mode 100644
index 12e581a..0000000
--- a/fg21sim/extragalactic/clusters/cosmology.py
+++ /dev/null
@@ -1,215 +0,0 @@
-# Copyright (c) 2016-2017 Weitian LI <liweitianux@live.com>
-# MIT license
-
-"""
-Flat ΛCDM cosmological model.
-"""
-
-import numpy as np
-from scipy import integrate
-from astropy.cosmology import FlatLambdaCDM
-
-from .units import (UnitConversions as AUC, Constants as AC)
-
-
-class Cosmology:
-    """
-    Flat ΛCDM cosmological model.
-
-    Attributes
-    ----------
-    H0 : float
-        Hubble parameter at present day (z=0)
-    Om0 : float
-        Density parameter of (dark and baryon) matter at present day
-    Ob0 : float
-        Density parameter of baryon at present day
-    Ode0 : float
-        Density parameter of dark energy at present day
-    sigma8 : float
-        Present-day rms density fluctuation on a scale of 8 h^-1 Mpc.
-
-    References
-    ----------
-    [1] https://astro.uni-bonn.de/~pavel/WIKIPEDIA/Lambda-CDM_model.html
-    [2] https://en.wikipedia.org/wiki/Lambda-CDM_model
-    [3] Randall, Sarazin & Ricker 2002, ApJ, 577, 579
-        http://adsabs.harvard.edu/abs/2002ApJ...577..579R
-        Sec.(2)
-    """
-    def __init__(self, H0=71.0, Om0=0.27, Ob0=0.046, sigma8=0.834):
-        self.H0 = H0  # [km/s/Mpc]
-        self.Om0 = Om0
-        self.Ob0 = Ob0
-        self.Ode0 = 1.0 - Om0
-        self.sigma8 = sigma8
-        self._cosmo = FlatLambdaCDM(H0=H0, Om0=Om0, Ob0=Ob0)
-
-    @property
-    def h(self):
-        """
-        Dimensionless/reduced Hubble parameter
-        """
-        return self.H0 / 100.0
-
-    @property
-    def M8(self):
-        """
-        Mass contained in a sphere of radius of 8 h^-1 Mpc.
-        Unit: [Msun]
-        """
-        r = 8 * AUC.Mpc2cm / self.h  # [cm]
-        M8 = (4*np.pi/3) * r**3 * self.rho_crit(0)  # [g]
-        M8 *= AUC.g2Msun  # [Msun]
-        return M8
-
-    def E(self, z):
-        """
-        Redshift evolution factor.
-        """
-        return np.sqrt(self.Om0 * (1+z)**3 + self.Ode0)
-
-    def H(self, z):
-        """
-        Hubble parameter at redshift z.
-        """
-        return self.H0 * self.E(z)
-
-    @property
-    def hubble_time(self):
-        """
-        Hubble time.
-        Unit: [Gyr]
-        """
-        uconv = AUC.Mpc2km * AUC.s2Gyr
-        t_H = (1.0/self.H0) * uconv  # [Gyr]
-        return t_H
-
-    def age(self, z):
-        """
-        Cosmic time (age) at redshift z.
-
-        Parameters
-        ----------
-        z : float
-            Redshift
-
-        Returns
-        -------
-        age : float
-            Age of the universe (cosmic time) at the given redshift.
-            Unit: [Gyr]
-
-        References
-        ----------
-        [1] Thomas & Kantowski 2000, Physical Review D, 62, 103507
-            http://adsabs.harvard.edu/abs/2000PhRvD..62j3507T
-            Eq.(18)
-        """
-        t_H = self.hubble_time
-        t = (t_H * (2/3/np.sqrt(1-self.Om0)) *
-             np.arcsinh(np.sqrt((1/self.Om0 - 1) / (1+z)**3)))
-        return t
-
-    @property
-    def age0(self):
-        """
-        Present age of the universe.
-        """
-        return self.age(0)
-
-    def redshift(self, age):
-        """
-        Invert the above ``self.age(z)`` formula analytically, to calculate
-        the redshift corresponding to the given cosmic time (age).
-
-        Parameters
-        ----------
-        age : float
-            Age of the universe (cosmic time), unit [Gyr]
-
-        Returns
-        -------
-        z : float
-            Redshift corresponding to the specified age.
-        """
-        t_H = self.hubble_time
-        term1 = (1/self.Om0) - 1
-        term2 = np.sinh(3*age*np.sqrt(1-self.Om0) / (2*t_H)) ** 2
-        z = (term1 / term2) ** (1/3) - 1
-        return z
-
-    def rho_crit(self, z):
-        """
-        Critical density at redshift z.
-        Unit: [g/cm^3]
-        """
-        rho = 3 * self.H(z)**2 / (8*np.pi * AC.G)
-        rho *= AUC.km2Mpc**2
-        return rho
-
-    def Om(self, z):
-        """
-        Density parameter of matter at redshift z.
-        """
-        return self.Om0 * (1+z)**3 / self.E(z)**2
-
-    def overdensity_virial(self, z):
-        """
-        Calculate the virial overdensity, which generally used to
-        determine the virial radius of a cluster.
-
-        References
-        ----------
-        [1] Cassano & Brunetti 2005, MNRAS, 357, 1313
-            http://adsabs.harvard.edu/abs/2005MNRAS.357.1313C
-            Eqs.(10,A4)
-        """
-        omega_z = (1 / self.Om(z)) - 1
-        Delta_c = 18*np.pi**2 * (1 + 0.4093 * omega_z**0.9052)
-        return Delta_c
-
-    def overdensity_crit(self, z):
-        """
-        Critical (linear) overdensity for a region to collapse
-        at a redshift z.
-
-        References
-        ----------
-        [1] Randall, Sarazin & Ricker 2002, ApJ, 577, 579
-            http://adsabs.harvard.edu/abs/2002ApJ...577..579R
-            Appendix.A, Eq.(A1)
-        """
-        coef = 3 * (12*np.pi) ** (2/3) / 20
-        D0 = self.growth_factor0
-        D_z = self.growth_factor(z)
-        Om_z = self.Om(z)
-        delta_c = coef * (D0 / D_z) * (1 + 0.0123*np.log10(Om_z))
-        return delta_c
-
-    def growth_factor(self, z):
-        """
-        Growth factor at redshift z.
-
-        References
-        ----------
-        [1] Randall, Sarazin & Ricker 2002, ApJ, 577, 579
-            http://adsabs.harvard.edu/abs/2002ApJ...577..579R
-            Appendix.A, Eq.(A7)
-        """
-        x0 = (2 * self.Ode0 / self.Om0) ** (1/3)
-        x = x0 / (1 + z)
-        coef = np.sqrt(x**3 + 2) / (x**1.5)
-        integral = integrate.quad(lambda y: y**1.5 * (y**3+2)**(-1.5),
-                                  a=0, b=x, epsabs=1e-5, epsrel=1e-5)[0]
-        D = coef * integral
-        return D
-
-    @property
-    def growth_factor0(self):
-        """
-        Present-day (z=0) growth factor.
-        """
-        if not hasattr(self, "_growth_factor0"):
-            self._growth_factor0 = self.growth_factor(0)
-        return self._growth_factor0
diff --git a/fg21sim/extragalactic/clusters/emission.py b/fg21sim/extragalactic/clusters/emission.py
index e71632b..1374b52 100644
--- a/fg21sim/extragalactic/clusters/emission.py
+++ b/fg21sim/extragalactic/clusters/emission.py
@@ -11,7 +11,7 @@ import numpy as np
 import scipy.integrate
 import scipy.special
 
-from .units import (Units as AU, Constants as AC)
+from ...utils.units import (Units as AU, Constants as AC)
 
 
 logger = logging.getLogger(__name__)
diff --git a/fg21sim/extragalactic/clusters/formation.py b/fg21sim/extragalactic/clusters/formation.py
index f8c6d3a..1f48433 100644
--- a/fg21sim/extragalactic/clusters/formation.py
+++ b/fg21sim/extragalactic/clusters/formation.py
@@ -20,8 +20,8 @@ import scipy.integrate
 import scipy.special
 import scipy.optimize
 
-from .cosmology import Cosmology
 from .mergertree import MergerTree
+from ...utils.cosmology import Cosmology
 
 
 logger = logging.getLogger(__name__)
diff --git a/fg21sim/extragalactic/clusters/halo.py b/fg21sim/extragalactic/clusters/halo.py
index a6d5a20..02bd74b 100644
--- a/fg21sim/extragalactic/clusters/halo.py
+++ b/fg21sim/extragalactic/clusters/halo.py
@@ -18,10 +18,12 @@ import scipy.interpolate
 import scipy.integrate
 import scipy.optimize
 
-from .cosmology import Cosmology
 from .formation import ClusterFormation
 from .solver import FokkerPlanckSolver
-from .units import (Units as AU, UnitConversions as AUC, Constants as AC)
+from ...utils.cosmology import Cosmology
+from ...utils.units import (Units as AU,
+                            UnitConversions as AUC,
+                            Constants as AC)
 
 
 logger = logging.getLogger(__name__)
diff --git a/fg21sim/extragalactic/clusters/units.py b/fg21sim/extragalactic/clusters/units.py
deleted file mode 100644
index a7e4ef5..0000000
--- a/fg21sim/extragalactic/clusters/units.py
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright (c) 2017 Weitian LI <liweitianux@live.com>
-# MIT license
-
-"""
-Commonly used units and their conversions relations, as well as constants.
-
-Astropy's units system is very powerful, but also very slow,
-and may even be the speed bottleneck of the program.
-
-This module provides commonly used units conversions by holding
-them directly in a class, thus avoid repeated/unnecessary calculations.
-"""
-
-import astropy.units as au
-import astropy.constants as ac
-
-
-class Units:
-    """
-    Commonly used units, especially in the CGS unit system.
-    """
-    # Unit for electron momentum (p), thus its value is the Lorentz factor
-    mec = ac.m_e.cgs.value*ac.c.cgs.value  # [g cm / s]
-
-
-class UnitConversions:
-    """
-    Commonly used units conversion relations.
-
-    Hold the conversion relations directly to avoid repeated/unnecessary
-    calculations.
-    """
-    # Mass
-    Msun2g = au.solMass.to(au.g)
-    g2Msun = au.g.to(au.solMass)
-    # Time
-    Gyr2s = au.Gyr.to(au.s)
-    s2Gyr = au.s.to(au.Gyr)
-    # Length
-    kpc2cm = au.kpc.to(au.cm)
-    cm2kpc = au.cm.to(au.kpc)
-    Mpc2cm = au.Mpc.to(au.cm)
-    cm2Mpc = au.cm.to(au.Mpc)
-    Mpc2km = au.Mpc.to(au.km)
-    km2Mpc = au.km.to(au.Mpc)
-    kpc2km = au.kpc.to(au.km)
-    km2kpc = au.km.to(au.kpc)
-    km2cm = au.km.to(au.cm)
-    # Energy
-    keV2erg = au.keV.to(au.erg)
-
-
-class Constants:
-    """
-    Commonly used constants, especially in the CGS unit system.
-
-    Astropy's constants are stored in SI units by default.
-    When request a constant in CGS unit system, additional (and slow)
-    conversions required.
-    """
-    # Speed of light
-    c = ac.c.cgs.value  # [cm/s]
-    # Atomic mass unit (i.e., a.m.u.)
-    u = ac.u.cgs.value  # [g]
-    # Gravitational constant
-    G = ac.G.cgs.value  # [cm^3/g/s^2]
-    # Electron charge
-    e = ac.e.gauss.value  # [Fr] = [esu]
-
-    # Mean molecular weight
-    # Ref.: Ettori et al, 2013, Space Science Review, 177, 119-154, Eq.(6)
-    mu = 0.6