Commit 9dbac28d authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

Add the NFW + Myamoto-Nagai isolated galaxy to the main repository

parent 3467c9d8
# Example to test the external NFW + MN external potential implementation.
# The gas disc is initialized so that the particles are in cicular orbit with that of the NFW + MN potential.
# The initial thickness of the gaseous disk is arbitrarius, so that it readjust while runnig the simulation.
# Parameters of the MN disk should be self-explanatory from the parameter file.
tested with the following options:
./configure --with-hydro=gadget2 --with-ext-potential=nfw_mn --disable-hand-vec
###############################################################################
# This file is part of SWIFT.
# Copyright (c) 2019 Alejandro Benitez-Llambay (alejandro.b.llambay@durham.ac.uk)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
##############################################################################
import numpy as np
from scipy import special
import matplotlib.pyplot as plt
import h5py
G = 4.299e-6
def mcum(r, c):
a = np.log(1+c*r)-c*r/(1.0+c*r)
b = np.log(1+c)-c/(1.0+c)
return a/b
def MN_Vcirc(R, z, Rd=4.0, Md=3e10, Zd=0.4):
return np.sqrt(G*Md*R**2/(R**2+(Rd+np.sqrt(z**2+Zd**2))**2)**(3./2.))
def get_vcirc_expo(R, Mgas=3e10, Rd=4.0):
sigma0 = Mgas/(2.0*np.pi*Rd**2)
sigma = sigma0*np.exp(-R/Rd)
y = R/(2.0*Rd)
I0 = special.i0(y)
K0 = special.k0(y)
I1 = special.i1(y)
K1 = special.k1(y)
return np.sqrt(4.0*np.pi*G*sigma0*Rd*y**2*(I0*K0-I1*K1))
def dP1(x):
return x*np.exp(-x)
def dP2(x):
return 1.0/np.cosh(x)**2
hlittle = 0.704
rhoc = 2.775e2 * hlittle**2
#halo mass and concentration
#-------------------
m200 = 1.5e12 #Msun
c = 10.0
r200 = (m200/(200*rhoc*4./3.*np.pi))**(1./3.)
#-------------------
#Gaseous disk
#-----------------
npart = int(1e5) #This controls the resolution
md = 7e8
rd = 0.02*r200
zd = 0.1*rd
#-----------------
#MN parameters
#-----------------
MN_Md = 3e10 #Msun
MN_Rd = 4.0 #kpc
MN_Zd = 0.4 #kpc
#-----------------
#Outputfile
#------------------------
outputfile = 'MN_ICs.hdf5' #Output file for SWIFT
#------------------------
x = []
y = []
z = []
phi = []
while(len(x) <= npart):
n = int(4.5e5)
rmin = 0
rmax = 8
zmin = -6
zmax = 6
r0 = rmin+(rmax-rmin)*np.random.rand(n)
z0 = zmin+(zmax-zmin)*np.random.rand(n)
ymin = 0
ymax1 = np.max(dP1(r0))
ymax2 = np.max(dP2(z0))
y1 = ymin+(ymax1-ymin)*np.random.rand(n)
y2 = ymin+(ymax2-ymin)*np.random.rand(n)
k, = np.where( (y1 <= dP1(r0)) & (y2 <= dP2(z0) ) )
phi0 = 2*np.pi*np.random.rand(len(k))
phi.extend(phi0)
x.extend(r0[k]*np.cos(phi0))
y.extend(r0[k]*np.sin(phi0))
z.extend(z0[k])
sample = np.random.randint(0,len(x), npart)
x = np.asarray(x)[:npart]
y = np.asarray(y)[:npart]
z = np.asarray(z)[:npart]
phi = np.asarray(phi)[:npart]
r = np.sqrt(x**2+y**2+z**2)
#Set positions
pgas = np.ones([npart,3])
pgas[:,0] = x*rd
pgas[:,1] = y*rd
pgas[:,2] = z*zd
vgas = np.zeros([npart,3])
rhogas = np.zeros(npart)
ugas = np.ones(npart)*0
mgas = np.ones(npart)*md/npart*1e-10
#Set velocities
Rgas = np.sqrt(pgas[:,0]**2+pgas[:,1]**2)
ksort = np.argsort(Rgas)
vcirc_gas = get_vcirc_expo(Rgas, Mgas=md, Rd=rd) #Approximate the velocity of the disk (better than spherical)
vcirc_dm = np.sqrt(G*mcum(Rgas/r200,c)*m200/(Rgas))
vcirc_MN = MN_Vcirc(Rgas, pgas[:,2], Md=MN_Md, Rd=MN_Rd, Zd=MN_Zd)
vcirc_tot = np.sqrt(vcirc_dm**2+vcirc_gas**2+vcirc_MN**2)
vgas[:,0] = vcirc_tot*np.sin(phi)
vgas[:,1] = -vcirc_tot*np.cos(phi)
boxsize = 400.0 #Boxsize for SWIFT
for i in range(3):
pgas[:,i] += 200
with h5py.File(outputfile,'w') as snap:
header = snap.create_group('Header')
particles = snap.create_group('PartType0')
particles.create_dataset('Coordinates',data=pgas,dtype=np.float32)
particles.create_dataset('Velocities',data=vgas,dtype=np.float32)
particles.create_dataset('InternalEnergy',data=ugas,dtype=np.float32)
particles.create_dataset('Densities',data=rhogas,dtype=np.float32)
particles.create_dataset('Masses',data=mgas,dtype=np.float32)
particles.create_dataset('SmoothingLength',data=np.ones(len(mgas)),dtype=np.float32)
particles.create_dataset('ParticleIDs',data=np.arange(len(mgas)),dtype='uint')
header.attrs['NumPart_ThisFile'] = np.array([len(mgas),0,0,0,0,0], dtype='uint')
header.attrs['NumPart_Total'] = np.array([len(mgas),0,0,0,0,0], dtype='uint')
header.attrs['MassTable'] = np.array([0,0,0,0,0,0], dtype='double')
header.attrs['Time'] = 0
header.attrs['Redshift'] = 0
header.attrs['Flag_Entropy_ICs'] = 0
header.attrs['NumFilesPerSnapshot'] = 1
header.attrs['NumPart_Total_HighWord'] = np.array([0,0,0,0,0,0], dtype='int')
header.attrs['BoxSize'] = boxsize
snap.close()
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/IsolatedGalaxies/Isolated_NFW_MN.hdf5
# Define the system of units to use internally.
InternalUnitSystem:
UnitMass_in_cgs: 1.9891E43 # 10^10 solar masses
UnitLength_in_cgs: 3.08567758E21 # 1 kpc
UnitVelocity_in_cgs: 1E5 # km/s
UnitCurrent_in_cgs: 1 # Amperes
UnitTemp_in_cgs: 1 # Kelvin
# Parameters for the self-gravity scheme
Gravity:
eta: 0.025 # Constant dimensionless multiplier for time integration.
theta: 0.7 # Opening angle (Multipole acceptance criterion).
max_physical_baryon_softening: 0.100 # Physical softening length (in internal units).
# Parameters governing the time integration (Set dt_min and dt_max to the same value for a fixed time-step run.)
TimeIntegration:
time_begin: 0. # The starting time of the simulation (in internal units).
time_end: 2. # The end time of the simulation (in internal units).
dt_min: 1e-6 # The minimal time-step size of the simulation (in internal units).
dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
# Parameters governing the snapshots
Snapshots:
basename: output # Common part of the name of output files
time_first: 0. # (Optional) Time of the first output if non-cosmological time-integration (in internal units)
delta_time: 0.001 # Time difference between consecutive outputs (in internal units)
# Parameters governing the conserved quantities statistics
Statistics:
delta_time: 1e-2 # Time between statistics output
time_first: 0. # (Optional) Time of the first stats output if non-cosmological time-integration (in internal units)
Scheduler:
max_top_level_cells: 16
# Parameters related to the initial conditions
InitialConditions:
file_name: Isolated_NFW_MN.hdf5 # The file to read
periodic: 0 # Are we running with periodic ICs?
# Parameters for the hydrodynamics scheme
SPH:
minimal_temperature: 1000. # Minimum allowed gas temperature
resolution_eta: 1.2348 # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
CFL_condition: 0.2 # Courant-Friedrich-Levy condition for time integration.
h_min_ratio: 0.1 # Minimal smoothing in units of softening.
h_max: 100.
#NFWPotential:
NFW_MNPotential:
useabspos: 0 # 0 -> positions based on centre, 1 -> absolute positions
position: [0.,0.,0.] # Location of centre of isothermal potential with respect to centre of the box (if 0) otherwise absolute (if 1) (internal units)
timestep_mult: 0.01 # Dimensionless pre-factor for the time-step condition, basically determines the fraction of the orbital time we use to do the time integration
epsilon: 0.01 # Softening size (internal units)
concentration: 10.0 # concentration of the Halo
M_200: 150.0 # M200 of the galaxy disk
critical_density: 1.37E-8 # Critical density of the Universe in internal units
Mdisk: 3.0 # Disk mass (internal units)
Rdisk: 4.0 # Disk size (internal units)
Zdisk: 0.4704911 # Disk scale-height (internal units)
#!/bin/bash
if [ ! -e Isolated_NFW_MN.hdf5 ]
then
echo "Fetching initial conditions for the isolated galaxy example..."
./getIC.sh
fi
../../swift -g -G -s --threads=16 isolated_galaxy.yml
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