def sink_radius(IC):
"""
Determine a reasonable sink radius for the star particles depending on
the star system type (e.g., single star, binary, etc...)
Parameters
----------
IC : IC object
Returns
-------
r_sink : SimArray
Sink radius for star particles
"""
# Set up the sink radius
starMode = IC.settings.physical.starMode.lower()
if starMode == 'binary':
binsys = IC.settings.physical.binsys
#Set Sink Radius to be mass-weighted average of Roche lobes of two stars
r1 = AddBinary.calcRocheLobe(binsys.m1/binsys.m2,binsys.a)
r2 = AddBinary.calcRocheLobe(binsys.m2/binsys.m1,binsys.a)
p = strip_units(binsys.m1/(binsys.m1 + binsys.m2))
r_sink = (r1*p) + (r2*(1.0-p))
else:
r_sink = IC.pos.r.min()
return r_sink
def sink_radius(IC):
"""
Determine a reasonable sink radius for the star particles depending on
the star system type (e.g., single star, binary, etc...)
Parameters
----------
IC : IC object
Returns
-------
r_sink : SimArray
Sink radius for star particles
"""
# Set up the sink radius
starMode = IC.settings.physical.starMode.lower()
if starMode == 'binary':
binsys = IC.settings.physical.binsys
#Set Sink Radius to be mass-weighted average of Roche lobes of two stars
r1 = AddBinary.calcRocheLobe(binsys.m1/binsys.m2,binsys.a)
r2 = AddBinary.calcRocheLobe(binsys.m2/binsys.m1,binsys.a)
p = strip_units(binsys.m1/(binsys.m1 + binsys.m2))
r_sink = (r1*p) + (r2*(1.0-p))
else:
r_sink = IC.pos.r.min()
return r_sink
def snapshot_gen(ICobj):
"""
Generates a tipsy snapshot from the initial conditions object ICobj.
Returns snapshot, param
snapshot: tipsy snapshot
param: dictionary containing info for a .param file
Note: Code has been edited (dflemin3) such that now it returns a snapshot for a circumbinary disk
where initial conditions generated assuming star at origin of mass M. After gas initialized, replaced
star at origin with binary system who's center of mass lies at the origin and who's mass m1 +m2 = M
"""
print 'Generating snapshot...'
# Constants
G = SimArray(1.0,'G')
# ------------------------------------
# Load in things from ICobj
# ------------------------------------
print 'Accessing data from ICs'
settings = ICobj.settings
# snapshot file name
snapshotName = settings.filenames.snapshotName
paramName = settings.filenames.paramName
# particle positions
r = ICobj.pos.r
xyz = ICobj.pos.xyz
# Number of particles
nParticles = ICobj.pos.nParticles
# molecular mass
m = settings.physical.m
# star mass
m_star = settings.physical.M.copy()
# disk mass
m_disk = ICobj.sigma.m_disk.copy()
m_disk = match_units(m_disk, m_star)[0]
# mass of the gas particles
m_particles = m_disk / float(nParticles)
# re-scale the particles (allows making of low-mass disk)
m_particles *= settings.snapshot.mScale
# -------------------------------------------------
# Assign output
# -------------------------------------------------
print 'Assigning data to snapshot'
# Get units all set up
m_unit = m_star.units
pos_unit = r.units
if xyz.units != r.units:
xyz.convert_units(pos_unit)
# time units are sqrt(L^3/GM)
t_unit = np.sqrt((pos_unit**3)*np.power((G*m_unit), -1)).units
# velocity units are L/t
v_unit = (pos_unit/t_unit).ratio('km s**-1')
# Make it a unit, save value for future conversion
v_unit_vel = v_unit
#Ensure v_unit_vel is the same as what I assume it is.
assert(np.fabs(AddBinary.VEL_UNIT-v_unit_vel)<AddBinary.SMALL),"VEL_UNIT not equal to ChaNGa unit! Why??"
v_unit = pynbody.units.Unit('{0} km s**-1'.format(v_unit))
# Other settings
metals = settings.snapshot.metals
star_metals = metals
# Generate snapshot
# Note that empty pos, vel, and mass arrays are created in the snapshot
snapshot = pynbody.new(star=1,gas=nParticles)
snapshot['vel'].units = v_unit
snapshot['eps'] = 0.01*SimArray(np.ones(nParticles+1, dtype=np.float32), pos_unit)
snapshot['metals'] = SimArray(np.zeros(nParticles+1, dtype=np.float32))
snapshot['rho'] = SimArray(np.zeros(nParticles+1, dtype=np.float32))
snapshot.gas['pos'] = xyz
snapshot.gas['temp'] = ICobj.T(r)
snapshot.gas['mass'] = m_particles
snapshot.gas['metals'] = metals
snapshot.star['pos'] = SimArray([[ 0., 0., 0.]],pos_unit)
snapshot.star['vel'] = SimArray([[ 0., 0., 0.]], v_unit)
snapshot.star['mass'] = m_star
snapshot.star['metals'] = SimArray(star_metals)
# Estimate the star's softening length as the closest particle distance
#snapshot.star['eps'] = r.min()
# Make param file
param = make_param(snapshot, snapshotName)
param['dMeanMolWeight'] = m
gc.collect()
# CALCULATE VELOCITY USING calc_velocity.py. This also estimates the
# gravitational softening length eps
print 'Calculating circular velocity'
preset = settings.changa_run.preset
max_particles = global_settings['misc']['max_particles']
calc_velocity.v_xy(snapshot, param, changa_preset=preset, max_particles=max_particles)
gc.collect()
# -------------------------------------------------
# Estimate time step for changa to use
# -------------------------------------------------
# Save param file
configsave(param, paramName, 'param')
# Save snapshot
snapshot.write(filename=snapshotName, fmt=pynbody.tipsy.TipsySnap)
# est dDelta
dDelta = ICgen_utils.est_time_step(paramName, preset)
param['dDelta'] = dDelta
# -------------------------------------------------
# Create director file
# -------------------------------------------------
# largest radius to plot
r_director = float(0.9 * r.max())
# Maximum surface density
sigma_min = float(ICobj.sigma(r_director))
# surface density at largest radius
sigma_max = float(ICobj.sigma.input_dict['sigma'].max())
# Create director dict
director = make_director(sigma_min, sigma_max, r_director, filename=param['achOutName'])
## Save .director file
#configsave(director, directorName, 'director')
#Now that velocities and everything are all initialized for gas particles, create new snapshot to return in which
#single star particle is replaced by 2, same units as above
snapshotBinary = pynbody.new(star=2,gas=nParticles)
snapshotBinary['eps'] = 0.01*SimArray(np.ones(nParticles+2, dtype=np.float32), pos_unit)
snapshotBinary['metals'] = SimArray(np.zeros(nParticles+2, dtype=np.float32))
snapshotBinary['vel'].units = v_unit
snapshotBinary['pos'].units = pos_unit
snapshotBinary['mass'].units = snapshot['mass'].units
snapshotBinary['rho'] = SimArray(np.zeros(nParticles+2, dtype=np.float32))
#Assign gas particles with calculated/given values from above
snapshotBinary.gas['pos'] = snapshot.gas['pos']
snapshotBinary.gas['vel'] = snapshot.gas['vel']
snapshotBinary.gas['temp'] = snapshot.gas['temp']
snapshotBinary.gas['rho'] = snapshot.gas['rho']
snapshotBinary.gas['eps'] = snapshot.gas['eps']
snapshotBinary.gas['mass'] = snapshot.gas['mass']
snapshotBinary.gas['metals'] = snapshot.gas['metals']
#Load Binary system obj to initialize system
binsys = ICobj.settings.physical.binsys
x1,x2,v1,v2 = binsys.generateICs()
#Put velocity in sim units
#!!! Note: v_unit_vel will always be 29.785598165 km/s when m_unit = Msol and r_unit = 1 AU in kpc!!!
#conv = v_unit_vel #km/s in sim units
#v1 /= conv
#v2 /= conv
#Assign position, velocity assuming CCW orbit
snapshotBinary.star[0]['pos'] = SimArray(x1,pos_unit)
snapshotBinary.star[0]['vel'] = SimArray(v1,v_unit)
snapshotBinary.star[1]['pos'] = SimArray(x2,pos_unit)
snapshotBinary.star[1]['vel'] = SimArray(v2,v_unit)
#Set stellar masses
#Set Mass units
#Create simArray for mass, convert units to simulation mass units
priMass = SimArray(binsys.m1,m_unit)
secMass = SimArray(binsys.m2,m_unit)
snapshotBinary.star[0]['mass'] = priMass
snapshotBinary.star[1]['mass'] = secMass
snapshotBinary.star['metals'] = SimArray(star_metals)
#Estimate stars' softening length as fraction of distance to COM
d = np.sqrt(AddBinary.dotProduct(x1-x2,x1-x2))
snapshotBinary.star[0]['eps'] = SimArray(math.fabs(d)/4.0,pos_unit)
snapshotBinary.star[1]['eps'] = SimArray(math.fabs(d)/4.0,pos_unit)
print 'Wrapping up'
# Now set the star particle's tform to a negative number. This allows
# UW ChaNGa treat it as a sink particle.
snapshotBinary.star['tform'] = -1.0
#Set Sink Radius to be mass-weighted average of Roche lobes of two stars
r1 = AddBinary.calcRocheLobe(binsys.m1/binsys.m2,binsys.a)
r2 = AddBinary.calcRocheLobe(binsys.m2/binsys.m1,binsys.a)
p = strip_units(binsys.m1/(binsys.m1 + binsys.m2))
r_sink = (r1*p) + (r2*(1.0-p))
param['dSinkBoundOrbitRadius'] = r_sink
param['dSinkRadius'] = r_sink
param['dSinkMassMin'] = 0.9 * strip_units(secMass)
param['bDoSinks'] = 1
return snapshotBinary, param, director
def snapshot_gen(ICobj):
"""
Generates a tipsy snapshot from the initial conditions object ICobj.
Returns snapshot, param
snapshot: tipsy snapshot
param: dictionary containing info for a .param file
Note: Code has been edited (dflemin3) such that now it returns a snapshot for a circumbinary disk
where initial conditions generated assuming star at origin of mass M. After gas initialized, replaced
star at origin with binary system who's center of mass lies at the origin and who's mass m1 +m2 = M
"""
print 'Generating snapshot...'
# Constants
G = SimArray(1.0,'G')
# ------------------------------------
# Load in things from ICobj
# ------------------------------------
print 'Accessing data from ICs'
settings = ICobj.settings
# snapshot file name
snapshotName = settings.filenames.snapshotName
paramName = settings.filenames.paramName
# particle positions
r = ICobj.pos.r
xyz = ICobj.pos.xyz
# Number of particles
nParticles = ICobj.pos.nParticles
# molecular mass
m = settings.physical.m
# star mass
m_star = settings.physical.M.copy()
# disk mass
m_disk = ICobj.sigma.m_disk.copy()
m_disk = match_units(m_disk, m_star)[0]
# mass of the gas particles
m_particles = m_disk / float(nParticles)
# re-scale the particles (allows making of low-mass disk)
m_particles *= settings.snapshot.mScale
# -------------------------------------------------
# Assign output
# -------------------------------------------------
print 'Assigning data to snapshot'
# Get units all set up
m_unit = m_star.units
pos_unit = r.units
if xyz.units != r.units:
xyz.convert_units(pos_unit)
# time units are sqrt(L^3/GM)
t_unit = np.sqrt((pos_unit**3)*np.power((G*m_unit), -1)).units
# velocity units are L/t
v_unit = (pos_unit/t_unit).ratio('km s**-1')
# Make it a unit, save value for future conversion
v_unit_vel = v_unit
#Ensure v_unit_vel is the same as what I assume it is.
assert(np.fabs(AddBinary.VEL_UNIT-v_unit_vel)<AddBinary.SMALL),"VEL_UNIT not equal to ChaNGa unit! Why??"
v_unit = pynbody.units.Unit('{0} km s**-1'.format(v_unit))
# Other settings
metals = settings.snapshot.metals
star_metals = metals
# Generate snapshot
# Note that empty pos, vel, and mass arrays are created in the snapshot
snapshot = pynbody.new(star=1,gas=nParticles)
snapshot['vel'].units = v_unit
snapshot['eps'] = 0.01*SimArray(np.ones(nParticles+1, dtype=np.float32), pos_unit)
snapshot['metals'] = SimArray(np.zeros(nParticles+1, dtype=np.float32))
snapshot['rho'] = SimArray(np.zeros(nParticles+1, dtype=np.float32))
snapshot.gas['pos'] = xyz
snapshot.gas['temp'] = ICobj.T(r)
snapshot.gas['mass'] = m_particles
snapshot.gas['metals'] = metals
snapshot.star['pos'] = SimArray([[ 0., 0., 0.]],pos_unit)
snapshot.star['vel'] = SimArray([[ 0., 0., 0.]], v_unit)
snapshot.star['mass'] = m_star
snapshot.star['metals'] = SimArray(star_metals)
# Estimate the star's softening length as the closest particle distance
#snapshot.star['eps'] = r.min()
# Make param file
param = make_param(snapshot, snapshotName)
param['dMeanMolWeight'] = m
gc.collect()
# CALCULATE VELOCITY USING calc_velocity.py. This also estimates the
# gravitational softening length eps
print 'Calculating circular velocity'
preset = settings.changa_run.preset
max_particles = global_settings['misc']['max_particles']
calc_velocity.v_xy(snapshot, param, changa_preset=preset, max_particles=max_particles)
gc.collect()
# -------------------------------------------------
# Estimate time step for changa to use
# -------------------------------------------------
# Save param file
configsave(param, paramName, 'param')
# Save snapshot
snapshot.write(filename=snapshotName, fmt=pynbody.tipsy.TipsySnap)
# est dDelta
dDelta = ICgen_utils.est_time_step(paramName, preset)
param['dDelta'] = dDelta
# -------------------------------------------------
# Create director file
# -------------------------------------------------
# largest radius to plot
r_director = float(0.9 * r.max())
# Maximum surface density
sigma_min = float(ICobj.sigma(r_director))
# surface density at largest radius
sigma_max = float(ICobj.sigma.input_dict['sigma'].max())
# Create director dict
director = make_director(sigma_min, sigma_max, r_director, filename=param['achOutName'])
## Save .director file
#configsave(director, directorName, 'director')
#Now that velocities and everything are all initialized for gas particles, create new snapshot to return in which
#single star particle is replaced by 2, same units as above
snapshotBinary = pynbody.new(star=2,gas=nParticles)
snapshotBinary['eps'] = 0.01*SimArray(np.ones(nParticles+2, dtype=np.float32), pos_unit)
snapshotBinary['metals'] = SimArray(np.zeros(nParticles+2, dtype=np.float32))
snapshotBinary['vel'].units = v_unit
snapshotBinary['pos'].units = pos_unit
snapshotBinary['mass'].units = snapshot['mass'].units
snapshotBinary['rho'] = SimArray(np.zeros(nParticles+2, dtype=np.float32))
#Assign gas particles with calculated/given values from above
snapshotBinary.gas['pos'] = snapshot.gas['pos']
snapshotBinary.gas['vel'] = snapshot.gas['vel']
snapshotBinary.gas['temp'] = snapshot.gas['temp']
snapshotBinary.gas['rho'] = snapshot.gas['rho']
snapshotBinary.gas['eps'] = snapshot.gas['eps']
snapshotBinary.gas['mass'] = snapshot.gas['mass']
snapshotBinary.gas['metals'] = snapshot.gas['metals']
#Load Binary system obj to initialize system
binsys = ICobj.settings.physical.binsys
x1,x2,v1,v2 = binsys.generateICs()
#Put velocity in sim units
#!!! Note: v_unit_vel will always be 29.785598165 km/s when m_unit = Msol and r_unit = 1 AU in kpc!!!
#conv = v_unit_vel #km/s in sim units
#v1 /= conv
#v2 /= conv
#Assign position, velocity assuming CCW orbit
snapshotBinary.star[0]['pos'] = SimArray(x1,pos_unit)
snapshotBinary.star[0]['vel'] = SimArray(v1,v_unit)
snapshotBinary.star[1]['pos'] = SimArray(x2,pos_unit)
snapshotBinary.star[1]['vel'] = SimArray(v2,v_unit)
#Set stellar masses
#Set Mass units
#Create simArray for mass, convert units to simulation mass units
priMass = SimArray(binsys.m1,m_unit)
secMass = SimArray(binsys.m2,m_unit)
snapshotBinary.star[0]['mass'] = priMass
snapshotBinary.star[1]['mass'] = secMass
snapshotBinary.star['metals'] = SimArray(star_metals)
#Estimate stars' softening length as fraction of distance to COM
d = np.sqrt(AddBinary.dotProduct(x1-x2,x1-x2))
snapshotBinary.star[0]['eps'] = SimArray(math.fabs(d)/4.0,pos_unit)
snapshotBinary.star[1]['eps'] = SimArray(math.fabs(d)/4.0,pos_unit)
print 'Wrapping up'
# Now set the star particle's tform to a negative number. This allows
# UW ChaNGa treat it as a sink particle.
snapshotBinary.star['tform'] = -1.0
#Set Sink Radius to be mass-weighted average of Roche lobes of two stars
r1 = AddBinary.calcRocheLobe(binsys.m1/binsys.m2,binsys.a)
r2 = AddBinary.calcRocheLobe(binsys.m2/binsys.m1,binsys.a)
p = strip_units(binsys.m1/(binsys.m1 + binsys.m2))
r_sink = (r1*p) + (r2*(1.0-p))
param['dSinkBoundOrbitRadius'] = r_sink
param['dSinkRadius'] = r_sink
param['dSinkMassMin'] = 0.9 * strip_units(secMass)
param['bDoSinks'] = 1
return snapshotBinary, param, director
