def actionsFreqs(self,*args,**kwargs):
"""
NAME:
actionsFreqs
PURPOSE:
evaluate the actions and frequencies (jr,lz,jz,Omegar,Omegaphi,Omegaz)
INPUT:
Either:
a) R,vR,vT,z,vz
b) Orbit instance: initial condition used if that's it, orbit(t)
if there is a time given as well
scipy.integrate.quadrature keywords
OUTPUT:
(jr,lz,jz,Omegar,Omegaphi,Omegaz)
HISTORY:
2013-08-28 - Written - Bovy (IAS)
"""
if ((self._c and not (kwargs.has_key('c') and not kwargs['c']))\
or (ext_loaded and ((kwargs.has_key('c') and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R,vR,vT, z, vz= args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R,vR,vT, z, vz, phi= args
else:
meta= actionAngle(*args)
R= meta._R
vR= meta._vR
vT= meta._vT
z= meta._z
vz= meta._vz
if isinstance(R,float):
R= nu.array([R])
vR= nu.array([vR])
vT= nu.array([vT])
z= nu.array([z])
vz= nu.array([vz])
Lz= R*vT
if self._useu0:
#First calculate u0
if kwargs.has_key('u0'):
u0= kwargs['u0']
else:
E= nu.array([evaluatePotentials(R[ii],z[ii],self._pot) +vR[ii]**2./2.+vz[ii]**2./2.+vT[ii]**2./2. for ii in range(len(R))])
u0= actionAngleStaeckel_c.actionAngleStaeckel_calcu0(E,Lz,
self._pot,
self._delta)[0]
if kwargs.has_key('u0'): kwargs.pop('u0')
else:
u0= None
jr, jz, Omegar, Omegaphi, Omegaz, err= actionAngleStaeckel_c.actionAngleFreqStaeckel_c(\
self._pot,self._delta,R,vR,vT,z,vz,u0=u0)
if err == 0:
return (jr,Lz,jz,Omegar,Omegaphi,Omegaz)
else:
raise RuntimeError("C-code for calculation actions failed; try with c=False")
else:
if kwargs.has_key('c') and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning)
raise NotImplementedError("actionsFreqs with c=False not implemented")
def __init__(self,*args,**kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleAdiabatic object
INPUT:
pot= potential or list of potentials (planarPotentials)
gamma= (default=1.) replace Lz by Lz+gamma Jz in effective potential
OUTPUT:
HISTORY:
2012-07-26 - Written - Bovy (IAS@MPIA)
"""
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleAxi")
self._pot= kwargs['pot']
if self._pot == MWPotential:
warnings.warn("Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if ext_loaded and 'c' in kwargs and kwargs['c']:
self._c= _check_c(self._pot)
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning) #pragma: no cover
else:
self._c= False
self._gamma= kwargs.get('gamma',1.)
return None
def __init__(self,*args,**kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleAdiabatic object
INPUT:
pot= potential or list of potentials (planarPotentials)
gamma= (default=1.) replace Lz by Lz+gamma Jz in effective potential
OUTPUT:
HISTORY:
2012-07-26 - Written - Bovy (IAS@MPIA)
"""
if not kwargs.has_key('pot'): #pragma: no cover
raise IOError("Must specify pot= for actionAngleAxi")
self._pot= kwargs['pot']
if ext_loaded and kwargs.has_key('c') and kwargs['c']:
self._c= _check_c(self._pot)
if kwargs.has_key('c') and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning) #pragma: no cover
else:
self._c= False
if kwargs.has_key('gamma'):
self._gamma= kwargs['gamma']
else:
self._gamma= 1.
return None
def __init__(self, *args, **kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleStaeckel object
INPUT:
pot= potential or list of potentials (3D)
delta= focus (can be Quantity)
useu0 - use u0 to calculate dV (NOT recommended)
c= if True, always use C for calculations
order= (10) number of points to use in the Gauss-Legendre numerical integration of the relevant action, frequency, and angle integrals
ro= distance from vantage point to GC (kpc; can be Quantity)
vo= circular velocity at ro (km/s; can be Quantity)
OUTPUT:
instance
HISTORY:
2012-11-27 - Written - Bovy (IAS)
"""
actionAngle.__init__(self,
ro=kwargs.get('ro', None),
vo=kwargs.get('vo', None))
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleStaeckel")
self._pot = kwargs['pot']
if self._pot == MWPotential:
warnings.warn(
"Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if not 'delta' in kwargs: #pragma: no cover
raise IOError("Must specify delta= for actionAngleStaeckel")
if ext_loaded and (('c' in kwargs and kwargs['c'])
or not 'c' in kwargs):
self._c = _check_c(self._pot)
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning) #pragma: no cover
else:
self._c = False
self._useu0 = kwargs.get('useu0', False)
self._delta = kwargs['delta']
self._order = kwargs.get('order', 10)
if _APY_LOADED and isinstance(self._delta, units.Quantity):
self._delta = self._delta.to(units.kpc).value / self._ro
# Check the units
self._check_consistent_units()
return None
def _integrateROrbit(vxvv,pot,t,method,dt):
"""
NAME:
_integrateROrbit
PURPOSE:
integrate an orbit in a Phi(R) potential in the R-plane
INPUT:
vxvv - array with the initial conditions stacked like
[R,vR,vT]; vR outward!
pot - Potential instance
t - list of times at which to output (0 has to be in this!)
method - 'odeint' or 'leapfrog'
dt - if set, force the integrator to use this basic stepsize; must be an integer divisor of output stepsize
OUTPUT:
[:,3] array of [R,vR,vT] at each t
HISTORY:
2010-07-20 - Written - Bovy (NYU)
"""
#First check that the potential has C
if '_c' in method:
if not _check_c(pot):
if ('leapfrog' in method or 'symplec' in method):
method= 'leapfrog'
else:
method= 'odeint'
warnings.warn("Cannot use C integration because some of the potentials are not implemented in C (using %s instead)" % (method), galpyWarning)
if method.lower() == 'leapfrog':
#We hack this by putting in a dummy phi
this_vxvv= nu.zeros(len(vxvv)+1)
this_vxvv[0:len(vxvv)]= vxvv
tmp_out, msg= _integrateOrbit(this_vxvv,pot,t,method,dt)
#tmp_out is (nt,4)
out= tmp_out[:,0:3]
elif method.lower() == 'leapfrog_c' or method.lower() == 'rk4_c' \
or method.lower() == 'rk6_c' or method.lower() == 'symplec4_c' \
or method.lower() == 'symplec6_c' or method.lower() == 'dopr54_c':
#We hack this by putting in a dummy phi
this_vxvv= nu.zeros(len(vxvv)+1)
this_vxvv[0:len(vxvv)]= vxvv
tmp_out, msg= _integrateOrbit(this_vxvv,pot,t,method,dt)
#tmp_out is (nt,4)
out= tmp_out[:,0:3]
elif method.lower() == 'odeint':
l= vxvv[0]*vxvv[2]
l2= l**2.
init= [vxvv[0],vxvv[1]]
intOut= integrate.odeint(_REOM,init,t,args=(pot,l2),
rtol=10.**-8.)#,mxstep=100000000)
out= nu.zeros((len(t),3))
out[:,0]= intOut[:,0]
out[:,1]= intOut[:,1]
out[:,2]= l/out[:,0]
msg= 0
#post-process to remove negative radii
neg_radii= (out[:,0] < 0.)
out[neg_radii,0]= -out[neg_radii,0]
_parse_warnmessage(msg)
return (out,msg)
def __init__(self,*args,**kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleStaeckel object
INPUT:
pot= potential or list of potentials (3D)
delta= focus (can be Quantity)
useu0 - use u0 to calculate dV (NOT recommended)
c= if True, always use C for calculations
ro= distance from vantage point to GC (kpc; can be Quantity)
vo= circular velocity at ro (km/s; can be Quantity)
OUTPUT:
instance
HISTORY:
2012-11-27 - Written - Bovy (IAS)
"""
actionAngle.__init__(self,
ro=kwargs.get('ro',None),vo=kwargs.get('vo',None))
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleStaeckel")
self._pot= kwargs['pot']
if self._pot == MWPotential:
warnings.warn("Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if not 'delta' in kwargs: #pragma: no cover
raise IOError("Must specify delta= for actionAngleStaeckel")
if ext_loaded and (('c' in kwargs and kwargs['c'])
or not 'c' in kwargs):
self._c= _check_c(self._pot)
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning) #pragma: no cover
else:
self._c= False
self._useu0= kwargs.get('useu0',False)
self._delta= kwargs['delta']
if _APY_LOADED and isinstance(self._delta,units.Quantity):
self._delta= self._delta.to(units.kpc).value/self._ro
# Check the units
self._check_consistent_units()
return None
def __init__(self, *args, **kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleTorus object
INPUT:
pot= potential or list of potentials (3D)
tol= default tolerance to use when fitting tori (|dJ|/J)
dJ= default action difference when computing derivatives (Hessian or Jacobian)
OUTPUT:
instance
HISTORY:
2015-08-07 - Written - Bovy (UofT)
"""
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleTorus")
self._pot = kwargs['pot']
if _isNonAxi(self._pot):
raise RuntimeError(
"actionAngleTorus for non-axisymmetric potentials is not supported"
)
if self._pot == MWPotential:
warnings.warn(
"Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if ext_loaded:
self._c = _check_c(self._pot)
if not self._c:
raise RuntimeError(
'The given potential is not fully implemented in C; using the actionAngleTorus code is not supported in pure Python'
)
else: # pragma: no cover
raise RuntimeError(
'actionAngleTorus instances cannot be used, because the actionAngleTorus_c extension failed to load'
)
self._tol = kwargs.get('tol', 0.001)
self._dJ = kwargs.get('dJ', 0.001)
return None
def __init__(self, *args, **kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleAdiabatic object
INPUT:
pot= potential or list of potentials (planarPotentials)
gamma= (default=1.) replace Lz by Lz+gamma Jz in effective potential
ro= distance from vantage point to GC (kpc; can be Quantity)
vo= circular velocity at ro (km/s; can be Quantity)
OUTPUT:
instance
HISTORY:
2012-07-26 - Written - Bovy (IAS@MPIA)
"""
actionAngle.__init__(self,
ro=kwargs.get('ro', None),
vo=kwargs.get('vo', None))
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleAxi")
self._pot = flatten_potential(kwargs['pot'])
if self._pot == MWPotential:
warnings.warn(
"Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if ext_loaded and 'c' in kwargs and kwargs['c']:
self._c = _check_c(self._pot)
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning) #pragma: no cover
else:
self._c = False
self._gamma = kwargs.get('gamma', 1.)
# Check the units
self._check_consistent_units()
return None
def __init__(self,*args,**kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleAdiabatic object
INPUT:
pot= potential or list of potentials (planarPotentials)
gamma= (default=1.) replace Lz by Lz+gamma Jz in effective potential
ro= distance from vantage point to GC (kpc; can be Quantity)
vo= circular velocity at ro (km/s; can be Quantity)
OUTPUT:
instance
HISTORY:
2012-07-26 - Written - Bovy (IAS@MPIA)
"""
actionAngle.__init__(self,
ro=kwargs.get('ro',None),vo=kwargs.get('vo',None))
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleAxi")
self._pot= flatten_potential(kwargs['pot'])
if self._pot == MWPotential:
warnings.warn("Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if ext_loaded and 'c' in kwargs and kwargs['c']:
self._c= _check_c(self._pot)
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning) #pragma: no cover
else:
self._c= False
self._gamma= kwargs.get('gamma',1.)
# Check the units
self._check_consistent_units()
return None
def __init__(self,*args,**kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleTorus object
INPUT:
pot= potential or list of potentials (3D)
tol= default tolerance to use when fitting tori (|dJ|/J)
dJ= default action difference when computing derivatives (Hessian or Jacobian)
OUTPUT:
instance
HISTORY:
2015-08-07 - Written - Bovy (UofT)
"""
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleTorus")
self._pot= kwargs['pot']
if _isNonAxi(self._pot):
raise RuntimeError("actionAngleTorus for non-axisymmetric potentials is not supported")
if self._pot == MWPotential:
warnings.warn("Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if ext_loaded:
self._c= _check_c(self._pot)
if not self._c:
raise RuntimeError('The given potential is not fully implemented in C; using the actionAngleTorus code is not supported in pure Python')
else:# pragma: no cover
raise RuntimeError('actionAngleTorus instances cannot be used, because the actionAngleTorus_c extension failed to load')
self._tol= kwargs.get('tol',0.001)
self._dJ= kwargs.get('dJ',0.001)
return None
def __init__(self, *args, **kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleStaeckel object
INPUT:
pot= potential or list of potentials (3D)
delta= focus
useu0 - use u0 to calculate dV (NOT recommended)
c= if True, always use C for calculations
OUTPUT:
HISTORY:
2012-11-27 - Written - Bovy (IAS)
"""
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleStaeckel")
self._pot = kwargs['pot']
if self._pot == MWPotential:
warnings.warn(
"Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if not 'delta' in kwargs: #pragma: no cover
raise IOError("Must specify delta= for actionAngleStaeckel")
if ext_loaded and (('c' in kwargs and kwargs['c'])
or not 'c' in kwargs):
self._c = _check_c(self._pot)
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning) #pragma: no cover
else:
self._c = False
self._useu0 = kwargs.get('useu0', False)
self._delta = kwargs['delta']
return None
def __init__(self,*args,**kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleStaeckel object
INPUT:
pot= potential or list of potentials (3D)
delta= focus
useu0 - use u0 to calculate dV (NOT recommended)
c= if True, always use C for calculations
OUTPUT:
HISTORY:
2012-11-27 - Written - Bovy (IAS)
"""
if not kwargs.has_key('pot'):
raise IOError("Must specify pot= for actionAngleStaeckel")
self._pot= kwargs['pot']
if not kwargs.has_key('delta'):
raise IOError("Must specify delta= for actionAngleStaeckel")
if ext_loaded and ((kwargs.has_key('c') and kwargs['c'])
or not kwargs.has_key('c')):
self._c= _check_c(self._pot)
if kwargs.has_key('c') and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning)
else:
self._c= False
if kwargs.has_key('useu0') and kwargs['useu0']:
self._useu0= True
else:
self._useu0= False
self._delta= kwargs['delta']
return None
def __init__(self,*args,**kwargs):
"""
NAME:
__init__
PURPOSE:
initialize an actionAngleStaeckel object
INPUT:
pot= potential or list of potentials (3D)
delta= focus
useu0 - use u0 to calculate dV (NOT recommended)
c= if True, always use C for calculations
OUTPUT:
HISTORY:
2012-11-27 - Written - Bovy (IAS)
"""
if not 'pot' in kwargs: #pragma: no cover
raise IOError("Must specify pot= for actionAngleStaeckel")
self._pot= kwargs['pot']
if self._pot == MWPotential:
warnings.warn("Use of MWPotential as a Milky-Way-like potential is deprecated; galpy.potential.MWPotential2014, a potential fit to a large variety of dynamical constraints (see Bovy 2015), is the preferred Milky-Way-like potential in galpy",
galpyWarning)
if not 'delta' in kwargs: #pragma: no cover
raise IOError("Must specify delta= for actionAngleStaeckel")
if ext_loaded and (('c' in kwargs and kwargs['c'])
or not 'c' in kwargs):
self._c= _check_c(self._pot)
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning) #pragma: no cover
else:
self._c= False
self._useu0= kwargs.get('useu0',False)
self._delta= kwargs['delta']
return None
def _evaluate(self, *args, **kwargs):
"""
NAME:
__call__ (_evaluate)
PURPOSE:
evaluate the actions (jr,lz,jz)
INPUT:
Either:
a) R,vR,vT,z,vz[,phi]:
1) floats: phase-space value for single object (phi is optional) (each can be a Quantity)
2) numpy.ndarray: [N] phase-space values for N objects (each can be a Quantity)
b) Orbit instance: initial condition used if that's it, orbit(t) if there is a time given as well as the second argument
delta= (object-wide default) can be used to override the object-wide focal length; can also be an array with length N to allow different delta for different phase-space points
u0= (None) if object-wide option useu0 is set, u0 to use (if useu0 and useu0 is None, a good value will be computed)
c= (object-wide default, bool) True/False to override the object-wide setting for whether or not to use the C implementation
order= (object-wide default, int) number of points to use in the Gauss-Legendre numerical integration of the relevant action integrals
When not using C:
fixed_quad= (False) if True, use Gaussian quadrature (scipy.integrate.fixed_quad instead of scipy.integrate.quad)
scipy.integrate.fixed_quad or .quad keywords
OUTPUT:
(jr,lz,jz)
HISTORY:
2012-11-27 - Written - Bovy (IAS)
2017-12-27 - Allowed individual delta for each point - Bovy (UofT)
"""
delta = kwargs.pop('delta', self._delta)
order = kwargs.get('order', self._order)
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R, vR, vT, z, vz = args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R, vR, vT, z, vz, phi = args
else:
self._parse_eval_args(*args)
R = self._eval_R
vR = self._eval_vR
vT = self._eval_vT
z = self._eval_z
vz = self._eval_vz
if isinstance(R, float):
R = nu.array([R])
vR = nu.array([vR])
vT = nu.array([vT])
z = nu.array([z])
vz = nu.array([vz])
Lz = R * vT
if self._useu0:
#First calculate u0
if 'u0' in kwargs:
u0 = nu.asarray(kwargs['u0'])
else:
E = nu.array([
_evaluatePotentials(self._pot, R[ii], z[ii]) +
vR[ii]**2. / 2. + vz[ii]**2. / 2. + vT[ii]**2. / 2.
for ii in range(len(R))
])
u0= actionAngleStaeckel_c.actionAngleStaeckel_calcu0(\
E,Lz,self._pot,delta)[0]
kwargs.pop('u0', None)
else:
u0 = None
jr, jz, err= actionAngleStaeckel_c.actionAngleStaeckel_c(\
self._pot,delta,R,vR,vT,z,vz,u0=u0,order=order)
if err == 0:
return (jr, Lz, jz)
else: #pragma: no cover
raise RuntimeError(
"C-code for calculation actions failed; try with c=False")
else:
if 'c' in kwargs and kwargs['c'] and not self._c: #pragma: no cover
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning)
kwargs.pop('c', None)
if (len(args) == 5 or len(args) == 6) \
and isinstance(args[0],nu.ndarray):
ojr = nu.zeros((len(args[0])))
olz = nu.zeros((len(args[0])))
ojz = nu.zeros((len(args[0])))
for ii in range(len(args[0])):
if len(args) == 5:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii])
elif len(args) == 6:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii], args[5][ii])
tkwargs = copy.copy(kwargs)
try:
tkwargs['delta'] = delta[ii]
except TypeError:
tkwargs['delta'] = delta
tjr, tlz, tjz = self(*targs, **tkwargs)
ojr[ii] = tjr
ojz[ii] = tjz
olz[ii] = tlz
return (ojr, olz, ojz)
else:
#Set up the actionAngleStaeckelSingle object
aASingle = actionAngleStaeckelSingle(*args,
pot=self._pot,
delta=delta)
return (aASingle.JR(**copy.copy(kwargs)),
aASingle._R * aASingle._vT,
aASingle.Jz(**copy.copy(kwargs)))
def _uminumaxvmin(self, *args, **kwargs):
"""
NAME:
_uminumaxvmin
PURPOSE:
evaluate u_min, u_max, and v_min
INPUT:
Either:
a) R,vR,vT,z,vz
b) Orbit instance: initial condition used if that's it, orbit(t)
if there is a time given as well
c= True/False; overrides the object's c= keyword to use C or not
OUTPUT:
(umin,umax,vmin)
HISTORY:
2017-12-12 - Written - Bovy (UofT)
"""
delta = kwargs.pop('delta', self._delta)
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R, vR, vT, z, vz = args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R, vR, vT, z, vz, phi = args
else:
self._parse_eval_args(*args)
R = self._eval_R
vR = self._eval_vR
vT = self._eval_vT
z = self._eval_z
vz = self._eval_vz
if isinstance(R, float):
R = nu.array([R])
vR = nu.array([vR])
vT = nu.array([vT])
z = nu.array([z])
vz = nu.array([vz])
Lz = R * vT
if self._useu0:
#First calculate u0
if 'u0' in kwargs:
u0 = nu.asarray(kwargs['u0'])
else:
E = nu.array([
_evaluatePotentials(self._pot, R[ii], z[ii]) +
vR[ii]**2. / 2. + vz[ii]**2. / 2. + vT[ii]**2. / 2.
for ii in range(len(R))
])
u0= actionAngleStaeckel_c.actionAngleStaeckel_calcu0(\
E,Lz,self._pot,delta)[0]
kwargs.pop('u0', None)
else:
u0 = None
umin, umax, vmin, err= \
actionAngleStaeckel_c.actionAngleUminUmaxVminStaeckel_c(\
self._pot,delta,R,vR,vT,z,vz,u0=u0)
if err == 0:
return (umin, umax, vmin)
else: #pragma: no cover
raise RuntimeError(
"C-code for calculation actions failed; try with c=False")
else:
if 'c' in kwargs and kwargs['c'] and not self._c: #pragma: no cover
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning)
kwargs.pop('c', None)
if (len(args) == 5 or len(args) == 6) \
and isinstance(args[0],nu.ndarray):
oumin = nu.zeros((len(args[0])))
oumax = nu.zeros((len(args[0])))
ovmin = nu.zeros((len(args[0])))
for ii in range(len(args[0])):
if len(args) == 5:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii])
elif len(args) == 6:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii], args[5][ii])
tkwargs = copy.copy(kwargs)
try:
tkwargs['delta'] = delta[ii]
except TypeError:
tkwargs['delta'] = delta
tumin,tumax,tvmin= self._uminumaxvmin(\
*targs,**tkwargs)
oumin[ii] = tumin
oumax[ii] = tumax
ovmin[ii] = tvmin
return (oumin, oumax, ovmin)
else:
#Set up the actionAngleStaeckelSingle object
aASingle = actionAngleStaeckelSingle(*args,
pot=self._pot,
delta=delta)
umin, umax = aASingle.calcUminUmax()
vmin = aASingle.calcVmin()
return (umin, umax, vmin)
def _integrateOrbit_dxdv(vxvv,dxdv,pot,t,method,rectIn,rectOut):
"""
NAME:
_integrateOrbit_dxdv
PURPOSE:
integrate an orbit and area of phase space in a Phi(R) potential
in the (R,phi)-plane
INPUT:
vxvv - array with the initial conditions stacked like
[R,vR,vT,phi]; vR outward!
dxdv - difference to integrate [dR,dvR,dvT,dphi]
pot - Potential instance
t - list of times at which to output (0 has to be in this!)
method - 'odeint' or 'leapfrog'
rectIn= (False) if True, input dxdv is in rectangular coordinates
rectOut= (False) if True, output dxdv (that in orbit_dxdv) is in rectangular coordinates
OUTPUT:
[:,8] array of [R,vR,vT,phi,dR,dvR,dvT,dphi] at each t
error message from integrator
HISTORY:
2010-10-17 - Written - Bovy (IAS)
"""
#First check that the potential has C
if '_c' in method:
allHasC= _check_c(pot) and _check_c(pot,dxdv=True)
if not allHasC and not 'leapfrog' in method and not 'symplec' in method:
method= 'odeint'
warnings.warn("Using odeint because not all used potential have adequate C implementations to integrate phase-space volumes",galpyWarning)
#go to the rectangular frame
this_vxvv= nu.array([vxvv[0]*nu.cos(vxvv[3]),
vxvv[0]*nu.sin(vxvv[3]),
vxvv[1]*nu.cos(vxvv[3])-vxvv[2]*nu.sin(vxvv[3]),
vxvv[2]*nu.cos(vxvv[3])+vxvv[1]*nu.sin(vxvv[3])])
if not rectIn:
this_dxdv= nu.array([nu.cos(vxvv[3])*dxdv[0]
-vxvv[0]*nu.sin(vxvv[3])*dxdv[3],
nu.sin(vxvv[3])*dxdv[0]
+vxvv[0]*nu.cos(vxvv[3])*dxdv[3],
-(vxvv[1]*nu.sin(vxvv[3])
+vxvv[2]*nu.cos(vxvv[3]))*dxdv[3]
+nu.cos(vxvv[3])*dxdv[1]-nu.sin(vxvv[3])*dxdv[2],
(vxvv[1]*nu.cos(vxvv[3])
-vxvv[2]*nu.sin(vxvv[3]))*dxdv[3]
+nu.sin(vxvv[3])*dxdv[1]+nu.cos(vxvv[3])*dxdv[2]])
else:
this_dxdv= dxdv
if 'leapfrog' in method.lower() or 'symplec' in method.lower():
raise TypeError('Symplectic integration for phase-space volume is not possible')
elif method.lower() == 'rk4_c' or method.lower() == 'rk6_c' \
or method.lower() == 'dopr54_c':
warnings.warn("Using C implementation to integrate orbits",galpyWarning)
#integrate
tmp_out, msg= integratePlanarOrbit_dxdv_c(pot,this_vxvv,this_dxdv,
t,method)
elif method.lower() == 'odeint':
init= [this_vxvv[0],this_vxvv[1],this_vxvv[2],this_vxvv[3],
this_dxdv[0],this_dxdv[1],this_dxdv[2],this_dxdv[3]]
#integrate
tmp_out= integrate.odeint(_EOM_dxdv,init,t,args=(pot,),
rtol=10.**-8.)#,mxstep=100000000)
msg= 0
else:
raise NotImplementedError("requested integration method does not exist")
#go back to the cylindrical frame
R= nu.sqrt(tmp_out[:,0]**2.+tmp_out[:,1]**2.)
phi= nu.arccos(tmp_out[:,0]/R)
phi[(tmp_out[:,1] < 0.)]= 2.*nu.pi-phi[(tmp_out[:,1] < 0.)]
vR= tmp_out[:,2]*nu.cos(phi)+tmp_out[:,3]*nu.sin(phi)
vT= tmp_out[:,3]*nu.cos(phi)-tmp_out[:,2]*nu.sin(phi)
cp= nu.cos(phi)
sp= nu.sin(phi)
dR= cp*tmp_out[:,4]+sp*tmp_out[:,5]
dphi= (cp*tmp_out[:,5]-sp*tmp_out[:,4])/R
dvR= cp*tmp_out[:,6]+sp*tmp_out[:,7]+vT*dphi
dvT= cp*tmp_out[:,7]-sp*tmp_out[:,6]-vR*dphi
out= nu.zeros((len(t),8))
out[:,0]= R
out[:,1]= vR
out[:,2]= vT
out[:,3]= phi
if rectOut:
out[:,4:]= tmp_out[:,4:]
else:
out[:,4]= dR
out[:,7]= dphi
out[:,5]= dvR
out[:,6]= dvT
_parse_warnmessage(msg)
return (out,msg)
def _actionsFreqsAngles(self, *args, **kwargs):
"""
NAME:
actionsFreqsAngles (_actionsFreqsAngles)
PURPOSE:
evaluate the actions, frequencies, and angles (jr,lz,jz,Omegar,Omegaphi,Omegaz,angler,anglephi,anglez)
INPUT:
Either:
a) R,vR,vT,z,vz[,phi]:
1) floats: phase-space value for single object (phi is optional) (each can be a Quantity)
2) numpy.ndarray: [N] phase-space values for N objects (each can be a Quantity)
b) Orbit instance: initial condition used if that's it, orbit(t) if there is a time given as well as the second argument
delta= (object-wide default) can be used to override the object-wide focal length; can also be an array with length N to allow different delta for different phase-space points
u0= (None) if object-wide option useu0 is set, u0 to use (if useu0 and useu0 is None, a good value will be computed)
c= (object-wide default, bool) True/False to override the object-wide setting for whether or not to use the C implementation
order= (10) number of points to use in the Gauss-Legendre numerical integration of the relevant action, frequency, and angle integrals
When not using C:
fixed_quad= (False) if True, use Gaussian quadrature (scipy.integrate.fixed_quad instead of scipy.integrate.quad)
scipy.integrate.fixed_quad or .quad keywords
OUTPUT:
(jr,lz,jz,Omegar,Omegaphi,Omegaz,angler,anglephi,anglez)
HISTORY:
2013-08-28 - Written - Bovy (IAS)
"""
delta = kwargs.pop('delta', self._delta)
order = kwargs.get('order', self._order)
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz pragma: no cover
raise IOError("Must specify phi")
elif len(args) == 6: #R,vR.vT, z, vz, phi
R, vR, vT, z, vz, phi = args
else:
self._parse_eval_args(*args)
R = self._eval_R
vR = self._eval_vR
vT = self._eval_vT
z = self._eval_z
vz = self._eval_vz
phi = self._eval_phi
if isinstance(R, float):
R = nu.array([R])
vR = nu.array([vR])
vT = nu.array([vT])
z = nu.array([z])
vz = nu.array([vz])
phi = nu.array([phi])
Lz = R * vT
if self._useu0:
#First calculate u0
if 'u0' in kwargs:
u0 = nu.asarray(kwargs['u0'])
else:
E = nu.array([
_evaluatePotentials(self._pot, R[ii], z[ii]) +
vR[ii]**2. / 2. + vz[ii]**2. / 2. + vT[ii]**2. / 2.
for ii in range(len(R))
])
u0= actionAngleStaeckel_c.actionAngleStaeckel_calcu0(\
E,Lz,self._pot,delta)[0]
kwargs.pop('u0', None)
else:
u0 = None
jr, jz, Omegar, Omegaphi, Omegaz, angler, anglephi,anglez, err= actionAngleStaeckel_c.actionAngleFreqAngleStaeckel_c(\
self._pot,delta,R,vR,vT,z,vz,phi,u0=u0,order=order)
# Adjustements for close-to-circular orbits
indx = nu.isnan(Omegar) * (jr < 10.**-3.) + nu.isnan(Omegaz) * (
jz < 10.**-3.
) #Close-to-circular and close-to-the-plane orbits
if nu.sum(indx) > 0:
Omegar[indx] = [
epifreq(self._pot, r, use_physical=False) for r in R[indx]
]
Omegaphi[indx] = [
omegac(self._pot, r, use_physical=False) for r in R[indx]
]
Omegaz[indx] = [
verticalfreq(self._pot, r, use_physical=False)
for r in R[indx]
]
if err == 0:
return (jr, Lz, jz, Omegar, Omegaphi, Omegaz, angler, anglephi,
anglez)
else:
raise RuntimeError(
"C-code for calculation actions failed; try with c=False"
) #pragma: no cover
else: #pragma: no cover
if 'c' in kwargs and kwargs['c'] and not self._c: #pragma: no cover
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning)
raise NotImplementedError(
"actionsFreqs with c=False not implemented")
def __call__(self, *args, **kwargs):
"""
NAME:
__call__
PURPOSE:
evaluate the actions (jr,lz,jz)
INPUT:
Either:
a) R,vR,vT,z,vz
b) Orbit instance: initial condition used if that's it, orbit(t)
if there is a time given as well
c= True/False; overrides the object's c= keyword to use C or not
scipy.integrate.quadrature keywords
OUTPUT:
(jr,lz,jz)
HISTORY:
2012-11-27 - Written - Bovy (IAS)
"""
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R, vR, vT, z, vz = args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R, vR, vT, z, vz, phi = args
else:
meta = actionAngle(*args)
R = meta._R
vR = meta._vR
vT = meta._vT
z = meta._z
vz = meta._vz
if isinstance(R, float):
R = nu.array([R])
vR = nu.array([vR])
vT = nu.array([vT])
z = nu.array([z])
vz = nu.array([vz])
Lz = R * vT
if self._useu0:
#First calculate u0
if 'u0' in kwargs:
u0 = nu.asarray(kwargs['u0'])
else:
E = nu.array([
evaluatePotentials(R[ii], z[ii], self._pot) +
vR[ii]**2. / 2. + vz[ii]**2. / 2. + vT[ii]**2. / 2.
for ii in range(len(R))
])
u0 = actionAngleStaeckel_c.actionAngleStaeckel_calcu0(
E, Lz, self._pot, self._delta)[0]
kwargs.pop('u0', None)
else:
u0 = None
jr, jz, err= actionAngleStaeckel_c.actionAngleStaeckel_c(\
self._pot,self._delta,R,vR,vT,z,vz,u0=u0)
if err == 0:
return (jr, Lz, jz)
else: #pragma: no cover
raise RuntimeError(
"C-code for calculation actions failed; try with c=False")
else:
if 'c' in kwargs and kwargs['c'] and not self._c: #pragma: no cover
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning)
kwargs.pop('c', None)
if (len(args) == 5 or len(args) == 6) \
and isinstance(args[0],nu.ndarray):
ojr = nu.zeros((len(args[0])))
olz = nu.zeros((len(args[0])))
ojz = nu.zeros((len(args[0])))
for ii in range(len(args[0])):
if len(args) == 5:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii])
elif len(args) == 6:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii], args[5][ii])
tjr, tlz, tjz = self(*targs, **copy.copy(kwargs))
ojr[ii] = tjr
ojz[ii] = tjz
olz[ii] = tlz
return (ojr, olz, ojz)
else:
#Set up the actionAngleStaeckelSingle object
aASingle = actionAngleStaeckelSingle(*args,
pot=self._pot,
delta=self._delta)
return (aASingle.JR(**copy.copy(kwargs)),
aASingle._R * aASingle._vT,
aASingle.Jz(**copy.copy(kwargs)))
def _integrateFullOrbit(vxvv, pot, t, method, dt):
"""
NAME:
_integrateFullOrbit
PURPOSE:
integrate an orbit in a Phi(R,z,phi) potential
INPUT:
vxvv - array with the initial conditions stacked like
[R,vR,vT,z,vz,phi]; vR outward!
pot - Potential instance
t - list of times at which to output (0 has to be in this!)
method - 'odeint' or 'leapfrog'
dt - if set, force the integrator to use this basic stepsize; must be an integer divisor of output stepsize
OUTPUT:
[:,5] array of [R,vR,vT,z,vz,phi] at each t
HISTORY:
2010-08-01 - Written - Bovy (NYU)
"""
#First check that the potential has C
if '_c' in method:
if not ext_loaded or not _check_c(pot):
if ('leapfrog' in method or 'symplec' in method):
method = 'leapfrog'
else:
method = 'odeint'
if not ext_loaded: # pragma: no cover
warnings.warn(
"Cannot use C integration because C extension not loaded (using %s instead)"
% (method), galpyWarning)
else:
warnings.warn(
"Cannot use C integration because some of the potentials are not implemented in C (using %s instead)"
% (method), galpyWarning)
if method.lower() == 'leapfrog':
#go to the rectangular frame
this_vxvv = nu.array([
vxvv[0] * nu.cos(vxvv[5]), vxvv[0] * nu.sin(vxvv[5]), vxvv[3],
vxvv[1] * nu.cos(vxvv[5]) - vxvv[2] * nu.sin(vxvv[5]),
vxvv[2] * nu.cos(vxvv[5]) + vxvv[1] * nu.sin(vxvv[5]), vxvv[4]
])
#integrate
out = symplecticode.leapfrog(_rectForce,
this_vxvv,
t,
args=(pot, ),
rtol=10.**-8)
#go back to the cylindrical frame
R = nu.sqrt(out[:, 0]**2. + out[:, 1]**2.)
phi = nu.arccos(out[:, 0] / R)
phi[(out[:, 1] < 0.)] = 2. * nu.pi - phi[(out[:, 1] < 0.)]
vR = out[:, 3] * nu.cos(phi) + out[:, 4] * nu.sin(phi)
vT = out[:, 4] * nu.cos(phi) - out[:, 3] * nu.sin(phi)
out[:, 3] = out[:, 2]
out[:, 4] = out[:, 5]
out[:, 0] = R
out[:, 1] = vR
out[:, 2] = vT
out[:, 5] = phi
elif ext_loaded and \
(method.lower() == 'leapfrog_c' or method.lower() == 'rk4_c' \
or method.lower() == 'rk6_c' or method.lower() == 'symplec4_c' \
or method.lower() == 'symplec6_c' or method.lower() == 'dopr54_c'):
warnings.warn("Using C implementation to integrate orbits",
galpyWarningVerbose)
#go to the rectangular frame
this_vxvv = nu.array([
vxvv[0] * nu.cos(vxvv[5]), vxvv[0] * nu.sin(vxvv[5]), vxvv[3],
vxvv[1] * nu.cos(vxvv[5]) - vxvv[2] * nu.sin(vxvv[5]),
vxvv[2] * nu.cos(vxvv[5]) + vxvv[1] * nu.sin(vxvv[5]), vxvv[4]
])
#integrate
tmp_out, msg = integrateFullOrbit_c(pot, this_vxvv, t, method, dt=dt)
#go back to the cylindrical frame
R = nu.sqrt(tmp_out[:, 0]**2. + tmp_out[:, 1]**2.)
phi = nu.arccos(tmp_out[:, 0] / R)
phi[(tmp_out[:, 1] < 0.)] = 2. * nu.pi - phi[(tmp_out[:, 1] < 0.)]
vR = tmp_out[:, 3] * nu.cos(phi) + tmp_out[:, 4] * nu.sin(phi)
vT = tmp_out[:, 4] * nu.cos(phi) - tmp_out[:, 3] * nu.sin(phi)
out = nu.zeros((len(t), 6))
out[:, 0] = R
out[:, 1] = vR
out[:, 2] = vT
out[:, 5] = phi
out[:, 3] = tmp_out[:, 2]
out[:, 4] = tmp_out[:, 5]
elif method.lower() == 'odeint' or not ext_loaded:
vphi = vxvv[2] / vxvv[0]
init = [vxvv[0], vxvv[1], vxvv[5], vphi, vxvv[3], vxvv[4]]
intOut = integrate.odeint(_FullEOM,
init,
t,
args=(pot, ),
rtol=10.**-8.) #,mxstep=100000000)
out = nu.zeros((len(t), 6))
out[:, 0] = intOut[:, 0]
out[:, 1] = intOut[:, 1]
out[:, 2] = out[:, 0] * intOut[:, 3]
out[:, 3] = intOut[:, 4]
out[:, 4] = intOut[:, 5]
out[:, 5] = intOut[:, 2]
#post-process to remove negative radii
neg_radii = (out[:, 0] < 0.)
out[neg_radii, 0] = -out[neg_radii, 0]
out[neg_radii, 5] += m.pi
return out
def _evaluate(self, *args, **kwargs):
"""
NAME:
_evaluate
PURPOSE:
evaluate the actions (jr,lz,jz)
INPUT:
Either:
a) R,vR,vT,z,vz
b) Orbit instance: initial condition used if that's it, orbit(t)
if there is a time given as well
scipy.integrate.quadrature keywords
_justjr, _justjz= if True, only calculate the radial or vertical action (internal use)
OUTPUT:
(jr,lz,jz), where jr=[jr,jrerr], and jz=[jz,jzerr]
HISTORY:
2012-07-26 - Written - Bovy (IAS@MPIA)
"""
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R, vR, vT, z, vz = args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R, vR, vT, z, vz, phi = args
else:
self._parse_eval_args(*args)
R = self._eval_R
vR = self._eval_vR
vT = self._eval_vT
z = self._eval_z
vz = self._eval_vz
if isinstance(R, float):
R = nu.array([R])
vR = nu.array([vR])
vT = nu.array([vT])
z = nu.array([z])
vz = nu.array([vz])
Lz = R * vT
jr, jz, err= actionAngleAdiabatic_c.actionAngleAdiabatic_c(\
self._pot,self._gamma,R,vR,vT,z,vz)
if err == 0:
return (jr, Lz, jz)
else: #pragma: no cover
raise RuntimeError(
"C-code for calculation actions failed; try with c=False")
else:
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning) #pragma: no cover
kwargs.pop('c', None)
if (len(args) == 5 or len(args) == 6) \
and isinstance(args[0],nu.ndarray):
ojr = nu.zeros((len(args[0])))
olz = nu.zeros((len(args[0])))
ojz = nu.zeros((len(args[0])))
for ii in range(len(args[0])):
if len(args) == 5:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii])
elif len(args) == 6:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii], args[5][ii])
tjr, tlz, tjz = self(*targs, **copy.copy(kwargs))
ojr[ii] = tjr
ojz[ii] = tjz
olz[ii] = tlz
return (ojr, olz, ojz)
else:
#Set up the actionAngleAxi object
self._parse_eval_args(*args)
if isinstance(self._pot, list):
thispot = [p.toPlanar() for p in self._pot]
else:
thispot = self._pot.toPlanar()
if isinstance(self._pot, list):
thisverticalpot = [
p.toVertical(self._eval_R) for p in self._pot
]
else:
thisverticalpot = self._pot.toVertical(self._eval_R)
aAAxi = actionAngleAxi(*args,
pot=thispot,
verticalPot=thisverticalpot,
gamma=self._gamma)
if kwargs.get('_justjr', False):
kwargs.pop('_justjr')
return (aAAxi.JR(**kwargs), nu.nan, nu.nan)
elif kwargs.get('_justjz', False):
kwargs.pop('_justjz')
return (nu.nan, nu.nan, aAAxi.Jz(**kwargs))
else:
return (aAAxi.JR(**kwargs), aAAxi._R * aAAxi._vT,
aAAxi.Jz(**kwargs))
def _EccZmaxRperiRap(self, *args, **kwargs):
"""
NAME:
EccZmaxRperiRap (_EccZmaxRperiRap)
PURPOSE:
evaluate the eccentricity, maximum height above the plane, peri- and apocenter in the adiabatic approximation
INPUT:
Either:
a) R,vR,vT,z,vz[,phi]:
1) floats: phase-space value for single object (phi is optional) (each can be a Quantity)
2) numpy.ndarray: [N] phase-space values for N objects (each can be a Quantity)
b) Orbit instance: initial condition used if that's it, orbit(t) if there is a time given as well as the second argument
c= (object-wide default, bool) True/False to override the object-wide setting for whether or not to use the C implementation
OUTPUT:
(e,zmax,rperi,rap)
HISTORY:
2017-12-21 - Written - Bovy (UofT)
"""
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R, vR, vT, z, vz = args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R, vR, vT, z, vz, phi = args
else:
self._parse_eval_args(*args)
R = self._eval_R
vR = self._eval_vR
vT = self._eval_vT
z = self._eval_z
vz = self._eval_vz
if isinstance(R, float):
R = nu.array([R])
vR = nu.array([vR])
vT = nu.array([vT])
z = nu.array([z])
vz = nu.array([vz])
rperi,Rap,zmax, err= actionAngleAdiabatic_c.actionAngleRperiRapZmaxAdiabatic_c(\
self._pot,self._gamma,R,vR,vT,z,vz)
if err == 0:
rap = nu.sqrt(Rap**2. + zmax**2.)
ecc = (rap - rperi) / (rap + rperi)
return (ecc, zmax, rperi, rap)
else: #pragma: no cover
raise RuntimeError(
"C-code for calculation actions failed; try with c=False")
else:
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning) #pragma: no cover
kwargs.pop('c', None)
if (len(args) == 5 or len(args) == 6) \
and isinstance(args[0],nu.ndarray):
oecc = nu.zeros((len(args[0])))
orperi = nu.zeros((len(args[0])))
orap = nu.zeros((len(args[0])))
ozmax = nu.zeros((len(args[0])))
for ii in range(len(args[0])):
if len(args) == 5:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii])
elif len(args) == 6:
targs = (args[0][ii], args[1][ii], args[2][ii],
args[3][ii], args[4][ii], args[5][ii])
tecc, tzmax, trperi,trap= self._EccZmaxRperiRap(\
*targs,**copy.copy(kwargs))
oecc[ii] = tecc
ozmax[ii] = tzmax
orperi[ii] = trperi
orap[ii] = trap
return (oecc, ozmax, orperi, orap)
else:
#Set up the actionAngleAxi object
self._parse_eval_args(*args)
if isinstance(self._pot, list):
thispot = [p.toPlanar() for p in self._pot]
else:
thispot = self._pot.toPlanar()
if isinstance(self._pot, list):
thisverticalpot = [
p.toVertical(self._eval_R) for p in self._pot
]
else:
thisverticalpot = self._pot.toVertical(self._eval_R)
aAAxi = actionAngleAxi(*args,
pot=thispot,
verticalPot=thisverticalpot,
gamma=self._gamma)
rperi, Rap = aAAxi.calcRapRperi(**kwargs)
zmax = aAAxi.calczmax(**kwargs)
rap = nu.sqrt(Rap**2. + zmax**2.)
return ((rap - rperi) / (rap + rperi), zmax, rperi, rap)
def _EccZmaxRperiRap(self,*args,**kwargs):
"""
NAME:
EccZmaxRperiRap (_EccZmaxRperiRap)
PURPOSE:
evaluate the eccentricity, maximum height above the plane, peri- and apocenter in the adiabatic approximation
INPUT:
Either:
a) R,vR,vT,z,vz[,phi]:
1) floats: phase-space value for single object (phi is optional) (each can be a Quantity)
2) numpy.ndarray: [N] phase-space values for N objects (each can be a Quantity)
b) Orbit instance: initial condition used if that's it, orbit(t) if there is a time given as well as the second argument
c= (object-wide default, bool) True/False to override the object-wide setting for whether or not to use the C implementation
OUTPUT:
(e,zmax,rperi,rap)
HISTORY:
2017-12-21 - Written - Bovy (UofT)
"""
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R,vR,vT, z, vz= args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R,vR,vT, z, vz, phi= args
else:
self._parse_eval_args(*args)
R= self._eval_R
vR= self._eval_vR
vT= self._eval_vT
z= self._eval_z
vz= self._eval_vz
if isinstance(R,float):
R= nu.array([R])
vR= nu.array([vR])
vT= nu.array([vT])
z= nu.array([z])
vz= nu.array([vz])
rperi,Rap,zmax, err= actionAngleAdiabatic_c.actionAngleRperiRapZmaxAdiabatic_c(\
self._pot,self._gamma,R,vR,vT,z,vz)
if err == 0:
rap= nu.sqrt(Rap**2.+zmax**2.)
ecc= (rap-rperi)/(rap+rperi)
return (ecc,zmax,rperi,rap)
else: #pragma: no cover
raise RuntimeError("C-code for calculation actions failed; try with c=False")
else:
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning) #pragma: no cover
kwargs.pop('c',None)
if (len(args) == 5 or len(args) == 6) \
and isinstance(args[0],nu.ndarray):
oecc= nu.zeros((len(args[0])))
orperi= nu.zeros((len(args[0])))
orap= nu.zeros((len(args[0])))
ozmax= nu.zeros((len(args[0])))
for ii in range(len(args[0])):
if len(args) == 5:
targs= (args[0][ii],args[1][ii],args[2][ii],
args[3][ii],args[4][ii])
elif len(args) == 6:
targs= (args[0][ii],args[1][ii],args[2][ii],
args[3][ii],args[4][ii],args[5][ii])
tecc, tzmax, trperi,trap= self._EccZmaxRperiRap(\
*targs,**copy.copy(kwargs))
oecc[ii]= tecc
ozmax[ii]= tzmax
orperi[ii]= trperi
orap[ii]= trap
return (oecc,ozmax,orperi,orap)
else:
#Set up the actionAngleAxi object
self._parse_eval_args(*args)
if isinstance(self._pot,list):
thispot= [p.toPlanar() for p in self._pot]
else:
thispot= self._pot.toPlanar()
if isinstance(self._pot,list):
thisverticalpot= [p.toVertical(self._eval_R) for p in self._pot]
else:
thisverticalpot= self._pot.toVertical(self._eval_R)
aAAxi= actionAngleAxi(*args,pot=thispot,
verticalPot=thisverticalpot,
gamma=self._gamma)
rperi,Rap= aAAxi.calcRapRperi(**kwargs)
zmax= aAAxi.calczmax(**kwargs)
rap= nu.sqrt(Rap**2.+zmax**2.)
return ((rap-rperi)/(rap+rperi),zmax,rperi,rap)
def _evaluate(self,*args,**kwargs):
"""
NAME:
_evaluate
PURPOSE:
evaluate the actions (jr,lz,jz)
INPUT:
Either:
a) R,vR,vT,z,vz
b) Orbit instance: initial condition used if that's it, orbit(t)
if there is a time given as well
scipy.integrate.quadrature keywords
_justjr, _justjz= if True, only calculate the radial or vertical action (internal use)
OUTPUT:
(jr,lz,jz), where jr=[jr,jrerr], and jz=[jz,jzerr]
HISTORY:
2012-07-26 - Written - Bovy (IAS@MPIA)
"""
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R,vR,vT, z, vz= args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R,vR,vT, z, vz, phi= args
else:
self._parse_eval_args(*args)
R= self._eval_R
vR= self._eval_vR
vT= self._eval_vT
z= self._eval_z
vz= self._eval_vz
if isinstance(R,float):
R= nu.array([R])
vR= nu.array([vR])
vT= nu.array([vT])
z= nu.array([z])
vz= nu.array([vz])
Lz= R*vT
jr, jz, err= actionAngleAdiabatic_c.actionAngleAdiabatic_c(\
self._pot,self._gamma,R,vR,vT,z,vz)
if err == 0:
return (jr,Lz,jz)
else: #pragma: no cover
raise RuntimeError("C-code for calculation actions failed; try with c=False")
else:
if 'c' in kwargs and kwargs['c'] and not self._c:
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning) #pragma: no cover
kwargs.pop('c',None)
if (len(args) == 5 or len(args) == 6) \
and isinstance(args[0],nu.ndarray):
ojr= nu.zeros((len(args[0])))
olz= nu.zeros((len(args[0])))
ojz= nu.zeros((len(args[0])))
for ii in range(len(args[0])):
if len(args) == 5:
targs= (args[0][ii],args[1][ii],args[2][ii],
args[3][ii],args[4][ii])
elif len(args) == 6:
targs= (args[0][ii],args[1][ii],args[2][ii],
args[3][ii],args[4][ii],args[5][ii])
tjr,tlz,tjz= self(*targs,**copy.copy(kwargs))
ojr[ii]= tjr
ojz[ii]= tjz
olz[ii]= tlz
return (ojr,olz,ojz)
else:
#Set up the actionAngleAxi object
self._parse_eval_args(*args)
if isinstance(self._pot,list):
thispot= [p.toPlanar() for p in self._pot]
else:
thispot= self._pot.toPlanar()
if isinstance(self._pot,list):
thisverticalpot= [p.toVertical(self._eval_R) for p in self._pot]
else:
thisverticalpot= self._pot.toVertical(self._eval_R)
aAAxi= actionAngleAxi(*args,pot=thispot,
verticalPot=thisverticalpot,
gamma=self._gamma)
if kwargs.get('_justjr',False):
kwargs.pop('_justjr')
return (aAAxi.JR(**kwargs),nu.nan,nu.nan)
elif kwargs.get('_justjz',False):
kwargs.pop('_justjz')
return (nu.nan,nu.nan,aAAxi.Jz(**kwargs))
else:
return (aAAxi.JR(**kwargs),aAAxi._R*aAAxi._vT,aAAxi.Jz(**kwargs))
def _integrateOrbit(vxvv, pot, t, method, dt):
"""
NAME:
_integrateOrbit
PURPOSE:
integrate an orbit in a Phi(R) potential in the (R,phi)-plane
INPUT:
vxvv - array with the initial conditions stacked like
[R,vR,vT,phi]; vR outward!
pot - Potential instance
t - list of times at which to output (0 has to be in this!)
method - 'odeint' or 'leapfrog'
dt- if set, force the integrator to use this basic stepsize; must be an integer divisor of output stepsize
OUTPUT:
[:,4] array of [R,vR,vT,phi] at each t
HISTORY:
2010-07-20 - Written - Bovy (NYU)
"""
#First check that the potential has C
if '_c' in method:
if not _check_c(pot):
if ('leapfrog' in method or 'symplec' in method):
method = 'leapfrog'
else:
method = 'odeint'
warnings.warn(
"Cannot use C integration because some of the potentials are not implemented in C (using %s instead)"
% (method), galpyWarning)
if method.lower() == 'leapfrog':
#go to the rectangular frame
this_vxvv = nu.array([
vxvv[0] * nu.cos(vxvv[3]), vxvv[0] * nu.sin(vxvv[3]),
vxvv[1] * nu.cos(vxvv[3]) - vxvv[2] * nu.sin(vxvv[3]),
vxvv[2] * nu.cos(vxvv[3]) + vxvv[1] * nu.sin(vxvv[3])
])
#integrate
tmp_out = symplecticode.leapfrog(_rectForce,
this_vxvv,
t,
args=(pot, ),
rtol=10.**-8)
#go back to the cylindrical frame
R = nu.sqrt(tmp_out[:, 0]**2. + tmp_out[:, 1]**2.)
phi = nu.arccos(tmp_out[:, 0] / R)
phi[(tmp_out[:, 1] < 0.)] = 2. * nu.pi - phi[(tmp_out[:, 1] < 0.)]
vR = tmp_out[:, 2] * nu.cos(phi) + tmp_out[:, 3] * nu.sin(phi)
vT = tmp_out[:, 3] * nu.cos(phi) - tmp_out[:, 2] * nu.sin(phi)
out = nu.zeros((len(t), 4))
out[:, 0] = R
out[:, 1] = vR
out[:, 2] = vT
out[:, 3] = phi
msg = 0
elif method.lower() == 'leapfrog_c' or method.lower() == 'rk4_c' \
or method.lower() == 'rk6_c' or method.lower() == 'symplec4_c' \
or method.lower() == 'symplec6_c' or method.lower() == 'dopr54_c':
warnings.warn("Using C implementation to integrate orbits",
galpyWarningVerbose)
#go to the rectangular frame
this_vxvv = nu.array([
vxvv[0] * nu.cos(vxvv[3]), vxvv[0] * nu.sin(vxvv[3]),
vxvv[1] * nu.cos(vxvv[3]) - vxvv[2] * nu.sin(vxvv[3]),
vxvv[2] * nu.cos(vxvv[3]) + vxvv[1] * nu.sin(vxvv[3])
])
#integrate
tmp_out, msg = integratePlanarOrbit_c(pot, this_vxvv, t, method, dt=dt)
#go back to the cylindrical frame
R = nu.sqrt(tmp_out[:, 0]**2. + tmp_out[:, 1]**2.)
phi = nu.arccos(tmp_out[:, 0] / R)
phi[(tmp_out[:, 1] < 0.)] = 2. * nu.pi - phi[(tmp_out[:, 1] < 0.)]
vR = tmp_out[:, 2] * nu.cos(phi) + tmp_out[:, 3] * nu.sin(phi)
vT = tmp_out[:, 3] * nu.cos(phi) - tmp_out[:, 2] * nu.sin(phi)
out = nu.zeros((len(t), 4))
out[:, 0] = R
out[:, 1] = vR
out[:, 2] = vT
out[:, 3] = phi
elif method.lower() == 'odeint':
vphi = vxvv[2] / vxvv[0]
init = [vxvv[0], vxvv[1], vxvv[3], vphi]
intOut = integrate.odeint(_EOM, init, t, args=(pot, ),
rtol=10.**-8.) #,mxstep=100000000)
out = nu.zeros((len(t), 4))
out[:, 0] = intOut[:, 0]
out[:, 1] = intOut[:, 1]
out[:, 3] = intOut[:, 2]
out[:, 2] = out[:, 0] * intOut[:, 3]
msg = 0
else:
raise NotImplementedError(
"requested integration method does not exist")
#post-process to remove negative radii
neg_radii = (out[:, 0] < 0.)
out[neg_radii, 0] = -out[neg_radii, 0]
out[neg_radii, 3] += m.pi
_parse_warnmessage(msg)
return (out, msg)
def _actionsFreqsAngles(self,*args,**kwargs):
"""
NAME:
_actionsFreqsAngles
PURPOSE:
evaluate the actions, frequencies, and angles
(jr,lz,jz,Omegar,Omegaphi,Omegaz,angler,anglephi,anglez)
INPUT:
Either:
a) R,vR,vT,z,vz,phi (MUST HAVE PHI)
b) Orbit instance: initial condition used if that's it, orbit(t)
if there is a time given as well
scipy.integrate.quadrature keywords
OUTPUT:
(jr,lz,jz,Omegar,Omegaphi,Omegaz,angler,anglephi,anglez)
HISTORY:
2013-08-28 - Written - Bovy (IAS)
"""
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz pragma: no cover
raise IOError("Must specify phi")
elif len(args) == 6: #R,vR.vT, z, vz, phi
R,vR,vT, z, vz, phi= args
else:
self._parse_eval_args(*args)
R= self._eval_R
vR= self._eval_vR
vT= self._eval_vT
z= self._eval_z
vz= self._eval_vz
phi= self._eval_phi
if isinstance(R,float):
R= nu.array([R])
vR= nu.array([vR])
vT= nu.array([vT])
z= nu.array([z])
vz= nu.array([vz])
phi= nu.array([phi])
Lz= R*vT
if self._useu0:
#First calculate u0
if 'u0' in kwargs:
u0= nu.asarray(kwargs['u0'])
else:
E= nu.array([_evaluatePotentials(self._pot,R[ii],z[ii])
+vR[ii]**2./2.+vz[ii]**2./2.+vT[ii]**2./2. for ii in range(len(R))])
u0= actionAngleStaeckel_c.actionAngleStaeckel_calcu0(E,Lz,
self._pot,
self._delta)[0]
kwargs.pop('u0',None)
else:
u0= None
jr, jz, Omegar, Omegaphi, Omegaz, angler, anglephi,anglez, err= actionAngleStaeckel_c.actionAngleFreqAngleStaeckel_c(\
self._pot,self._delta,R,vR,vT,z,vz,phi,u0=u0)
# Adjustements for close-to-circular orbits
indx= nu.isnan(Omegar)*(jr < 10.**-3.)+nu.isnan(Omegaz)*(jz < 10.**-3.) #Close-to-circular and close-to-the-plane orbits
if nu.sum(indx) > 0:
Omegar[indx]= [epifreq(self._pot,r,use_physical=False) for r in R[indx]]
Omegaphi[indx]= [omegac(self._pot,r,use_physical=False) for r in R[indx]]
Omegaz[indx]= [verticalfreq(self._pot,r,use_physical=False) for r in R[indx]]
if err == 0:
return (jr,Lz,jz,Omegar,Omegaphi,Omegaz,angler,anglephi,anglez)
else:
raise RuntimeError("C-code for calculation actions failed; try with c=False") #pragma: no cover
else: #pragma: no cover
if 'c' in kwargs and kwargs['c'] and not self._c: #pragma: no cover
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning)
raise NotImplementedError("actionsFreqs with c=False not implemented")
def _integrateOrbit(vxvv,pot,t,method,dt):
"""
NAME:
_integrateOrbit
PURPOSE:
integrate an orbit in a Phi(R) potential in the (R,phi)-plane
INPUT:
vxvv - array with the initial conditions stacked like
[R,vR,vT,phi]; vR outward!
pot - Potential instance
t - list of times at which to output (0 has to be in this!)
method - 'odeint' or 'leapfrog'
dt- if set, force the integrator to use this basic stepsize; must be an integer divisor of output stepsize
OUTPUT:
[:,4] array of [R,vR,vT,phi] at each t
HISTORY:
2010-07-20 - Written - Bovy (NYU)
"""
#First check that the potential has C
if '_c' in method:
if not _check_c(pot):
if ('leapfrog' in method or 'symplec' in method):
method= 'leapfrog'
else:
method= 'odeint'
warnings.warn("Cannot use C integration because some of the potentials are not implemented in C (using %s instead)" % (method), galpyWarning)
if method.lower() == 'leapfrog':
#go to the rectangular frame
this_vxvv= nu.array([vxvv[0]*nu.cos(vxvv[3]),
vxvv[0]*nu.sin(vxvv[3]),
vxvv[1]*nu.cos(vxvv[3])-vxvv[2]*nu.sin(vxvv[3]),
vxvv[2]*nu.cos(vxvv[3])+vxvv[1]*nu.sin(vxvv[3])])
#integrate
tmp_out= symplecticode.leapfrog(_rectForce,this_vxvv,
t,args=(pot,),rtol=10.**-8)
#go back to the cylindrical frame
R= nu.sqrt(tmp_out[:,0]**2.+tmp_out[:,1]**2.)
phi= nu.arccos(tmp_out[:,0]/R)
phi[(tmp_out[:,1] < 0.)]= 2.*nu.pi-phi[(tmp_out[:,1] < 0.)]
vR= tmp_out[:,2]*nu.cos(phi)+tmp_out[:,3]*nu.sin(phi)
vT= tmp_out[:,3]*nu.cos(phi)-tmp_out[:,2]*nu.sin(phi)
out= nu.zeros((len(t),4))
out[:,0]= R
out[:,1]= vR
out[:,2]= vT
out[:,3]= phi
msg= 0
elif method.lower() == 'leapfrog_c' or method.lower() == 'rk4_c' \
or method.lower() == 'rk6_c' or method.lower() == 'symplec4_c' \
or method.lower() == 'symplec6_c' or method.lower() == 'dopr54_c':
warnings.warn("Using C implementation to integrate orbits",galpyWarning)
#go to the rectangular frame
this_vxvv= nu.array([vxvv[0]*nu.cos(vxvv[3]),
vxvv[0]*nu.sin(vxvv[3]),
vxvv[1]*nu.cos(vxvv[3])-vxvv[2]*nu.sin(vxvv[3]),
vxvv[2]*nu.cos(vxvv[3])+vxvv[1]*nu.sin(vxvv[3])])
#integrate
tmp_out, msg= integratePlanarOrbit_c(pot,this_vxvv,
t,method,dt=dt)
#go back to the cylindrical frame
R= nu.sqrt(tmp_out[:,0]**2.+tmp_out[:,1]**2.)
phi= nu.arccos(tmp_out[:,0]/R)
phi[(tmp_out[:,1] < 0.)]= 2.*nu.pi-phi[(tmp_out[:,1] < 0.)]
vR= tmp_out[:,2]*nu.cos(phi)+tmp_out[:,3]*nu.sin(phi)
vT= tmp_out[:,3]*nu.cos(phi)-tmp_out[:,2]*nu.sin(phi)
out= nu.zeros((len(t),4))
out[:,0]= R
out[:,1]= vR
out[:,2]= vT
out[:,3]= phi
elif method.lower() == 'odeint':
vphi= vxvv[2]/vxvv[0]
init= [vxvv[0],vxvv[1],vxvv[3],vphi]
intOut= integrate.odeint(_EOM,init,t,args=(pot,),
rtol=10.**-8.)#,mxstep=100000000)
out= nu.zeros((len(t),4))
out[:,0]= intOut[:,0]
out[:,1]= intOut[:,1]
out[:,3]= intOut[:,2]
out[:,2]= out[:,0]*intOut[:,3]
msg= 0
else:
raise NotImplementedError("requested integration method does not exist")
#post-process to remove negative radii
neg_radii= (out[:,0] < 0.)
out[neg_radii,0]= -out[neg_radii,0]
out[neg_radii,3]+= m.pi
_parse_warnmessage(msg)
return (out,msg)
def _evaluate(self,*args,**kwargs):
"""
NAME:
_evaluate
PURPOSE:
evaluate the actions (jr,lz,jz)
INPUT:
Either:
a) R,vR,vT,z,vz
b) Orbit instance: initial condition used if that's it, orbit(t)
if there is a time given as well
c= True/False; overrides the object's c= keyword to use C or not
scipy.integrate.quadrature keywords
OUTPUT:
(jr,lz,jz)
HISTORY:
2012-11-27 - Written - Bovy (IAS)
"""
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz
R,vR,vT, z, vz= args
elif len(args) == 6: #R,vR.vT, z, vz, phi
R,vR,vT, z, vz, phi= args
else:
self._parse_eval_args(*args)
R= self._eval_R
vR= self._eval_vR
vT= self._eval_vT
z= self._eval_z
vz= self._eval_vz
if isinstance(R,float):
R= nu.array([R])
vR= nu.array([vR])
vT= nu.array([vT])
z= nu.array([z])
vz= nu.array([vz])
Lz= R*vT
if self._useu0:
#First calculate u0
if 'u0' in kwargs:
u0= nu.asarray(kwargs['u0'])
else:
E= nu.array([_evaluatePotentials(self._pot,R[ii],z[ii])
+vR[ii]**2./2.+vz[ii]**2./2.+vT[ii]**2./2. for ii in range(len(R))])
u0= actionAngleStaeckel_c.actionAngleStaeckel_calcu0(E,Lz,
self._pot,
self._delta)[0]
kwargs.pop('u0',None)
else:
u0= None
jr, jz, err= actionAngleStaeckel_c.actionAngleStaeckel_c(\
self._pot,self._delta,R,vR,vT,z,vz,u0=u0)
if err == 0:
return (jr,Lz,jz)
else: #pragma: no cover
raise RuntimeError("C-code for calculation actions failed; try with c=False")
else:
if 'c' in kwargs and kwargs['c'] and not self._c: #pragma: no cover
warnings.warn("C module not used because potential does not have a C implementation",galpyWarning)
kwargs.pop('c',None)
if (len(args) == 5 or len(args) == 6) \
and isinstance(args[0],nu.ndarray):
ojr= nu.zeros((len(args[0])))
olz= nu.zeros((len(args[0])))
ojz= nu.zeros((len(args[0])))
for ii in range(len(args[0])):
if len(args) == 5:
targs= (args[0][ii],args[1][ii],args[2][ii],
args[3][ii],args[4][ii])
elif len(args) == 6:
targs= (args[0][ii],args[1][ii],args[2][ii],
args[3][ii],args[4][ii],args[5][ii])
tjr,tlz,tjz= self(*targs,**copy.copy(kwargs))
ojr[ii]= tjr
ojz[ii]= tjz
olz[ii]= tlz
return (ojr,olz,ojz)
else:
#Set up the actionAngleStaeckelSingle object
aASingle= actionAngleStaeckelSingle(*args,pot=self._pot,
delta=self._delta)
return (aASingle.JR(**copy.copy(kwargs)),
aASingle._R*aASingle._vT,
aASingle.Jz(**copy.copy(kwargs)))
def actionsFreqsAngles(self, *args, **kwargs):
"""
NAME:
actionsFreqsAngles
PURPOSE:
evaluate the actions, frequencies, and angles
(jr,lz,jz,Omegar,Omegaphi,Omegaz,angler,anglephi,anglez)
INPUT:
Either:
a) R,vR,vT,z,vz,phi (MUST HAVE PHI)
b) Orbit instance: initial condition used if that's it, orbit(t)
if there is a time given as well
scipy.integrate.quadrature keywords
OUTPUT:
(jr,lz,jz,Omegar,Omegaphi,Omegaz,angler,anglephi,anglez)
HISTORY:
2013-08-28 - Written - Bovy (IAS)
"""
if ((self._c and not ('c' in kwargs and not kwargs['c']))\
or (ext_loaded and (('c' in kwargs and kwargs['c'])))) \
and _check_c(self._pot):
if len(args) == 5: #R,vR.vT, z, vz pragma: no cover
raise IOError("Must specify phi")
elif len(args) == 6: #R,vR.vT, z, vz, phi
R, vR, vT, z, vz, phi = args
else:
meta = actionAngle(*args)
R = meta._R
vR = meta._vR
vT = meta._vT
z = meta._z
vz = meta._vz
phi = meta._phi
if isinstance(R, float):
R = nu.array([R])
vR = nu.array([vR])
vT = nu.array([vT])
z = nu.array([z])
vz = nu.array([vz])
phi = nu.array([phi])
Lz = R * vT
if self._useu0:
#First calculate u0
if 'u0' in kwargs:
u0 = nu.asarray(kwargs['u0'])
else:
E = nu.array([
evaluatePotentials(R[ii], z[ii], self._pot) +
vR[ii]**2. / 2. + vz[ii]**2. / 2. + vT[ii]**2. / 2.
for ii in range(len(R))
])
u0 = actionAngleStaeckel_c.actionAngleStaeckel_calcu0(
E, Lz, self._pot, self._delta)[0]
kwargs.pop('u0', None)
else:
u0 = None
jr, jz, Omegar, Omegaphi, Omegaz, angler, anglephi,anglez, err= actionAngleStaeckel_c.actionAngleFreqAngleStaeckel_c(\
self._pot,self._delta,R,vR,vT,z,vz,phi,u0=u0)
# Adjustements for close-to-circular orbits
indx = nu.isnan(Omegar) * (jr < 10.**-3.) + nu.isnan(Omegaz) * (
jz < 10.**-3.
) #Close-to-circular and close-to-the-plane orbits
if nu.sum(indx) > 0:
Omegar[indx] = [epifreq(self._pot, r) for r in R[indx]]
Omegaphi[indx] = [omegac(self._pot, r) for r in R[indx]]
Omegaz[indx] = [verticalfreq(self._pot, r) for r in R[indx]]
if err == 0:
return (jr, Lz, jz, Omegar, Omegaphi, Omegaz, angler, anglephi,
anglez)
else:
raise RuntimeError(
"C-code for calculation actions failed; try with c=False"
) #pragma: no cover
else: #pragma: no cover
if 'c' in kwargs and kwargs['c'] and not self._c: #pragma: no cover
warnings.warn(
"C module not used because potential does not have a C implementation",
galpyWarning)
raise NotImplementedError(
"actionsFreqs with c=False not implemented")
def _integrateOrbit_dxdv(vxvv, dxdv, pot, t, method, rectIn, rectOut):
"""
NAME:
_integrateOrbit_dxdv
PURPOSE:
integrate an orbit and area of phase space in a Phi(R) potential
in the (R,phi)-plane
INPUT:
vxvv - array with the initial conditions stacked like
[R,vR,vT,phi]; vR outward!
dxdv - difference to integrate [dR,dvR,dvT,dphi]
pot - Potential instance
t - list of times at which to output (0 has to be in this!)
method - 'odeint' or 'leapfrog'
rectIn= (False) if True, input dxdv is in rectangular coordinates
rectOut= (False) if True, output dxdv (that in orbit_dxdv) is in rectangular coordinates
OUTPUT:
[:,8] array of [R,vR,vT,phi,dR,dvR,dvT,dphi] at each t
error message from integrator
HISTORY:
2010-10-17 - Written - Bovy (IAS)
"""
#First check that the potential has C
if '_c' in method:
allHasC = _check_c(pot) and _check_c(pot, dxdv=True)
if not allHasC and not 'leapfrog' in method and not 'symplec' in method:
method = 'odeint'
warnings.warn(
"Using odeint because not all used potential have adequate C implementations to integrate phase-space volumes",
galpyWarning)
#go to the rectangular frame
this_vxvv = nu.array([
vxvv[0] * nu.cos(vxvv[3]), vxvv[0] * nu.sin(vxvv[3]),
vxvv[1] * nu.cos(vxvv[3]) - vxvv[2] * nu.sin(vxvv[3]),
vxvv[2] * nu.cos(vxvv[3]) + vxvv[1] * nu.sin(vxvv[3])
])
if not rectIn:
this_dxdv = nu.array([
nu.cos(vxvv[3]) * dxdv[0] - vxvv[0] * nu.sin(vxvv[3]) * dxdv[3],
nu.sin(vxvv[3]) * dxdv[0] + vxvv[0] * nu.cos(vxvv[3]) * dxdv[3],
-(vxvv[1] * nu.sin(vxvv[3]) + vxvv[2] * nu.cos(vxvv[3])) * dxdv[3]
+ nu.cos(vxvv[3]) * dxdv[1] - nu.sin(vxvv[3]) * dxdv[2],
(vxvv[1] * nu.cos(vxvv[3]) - vxvv[2] * nu.sin(vxvv[3])) * dxdv[3] +
nu.sin(vxvv[3]) * dxdv[1] + nu.cos(vxvv[3]) * dxdv[2]
])
else:
this_dxdv = dxdv
if 'leapfrog' in method.lower() or 'symplec' in method.lower():
raise TypeError(
'Symplectic integration for phase-space volume is not possible')
elif method.lower() == 'rk4_c' or method.lower() == 'rk6_c' \
or method.lower() == 'dopr54_c':
warnings.warn("Using C implementation to integrate orbits",
galpyWarningVerbose)
#integrate
tmp_out, msg = integratePlanarOrbit_dxdv_c(pot, this_vxvv, this_dxdv,
t, method)
elif method.lower() == 'odeint':
init = [
this_vxvv[0], this_vxvv[1], this_vxvv[2], this_vxvv[3],
this_dxdv[0], this_dxdv[1], this_dxdv[2], this_dxdv[3]
]
#integrate
tmp_out = integrate.odeint(_EOM_dxdv,
init,
t,
args=(pot, ),
rtol=10.**-8.) #,mxstep=100000000)
msg = 0
else:
raise NotImplementedError(
"requested integration method does not exist")
#go back to the cylindrical frame
R = nu.sqrt(tmp_out[:, 0]**2. + tmp_out[:, 1]**2.)
phi = nu.arccos(tmp_out[:, 0] / R)
phi[(tmp_out[:, 1] < 0.)] = 2. * nu.pi - phi[(tmp_out[:, 1] < 0.)]
vR = tmp_out[:, 2] * nu.cos(phi) + tmp_out[:, 3] * nu.sin(phi)
vT = tmp_out[:, 3] * nu.cos(phi) - tmp_out[:, 2] * nu.sin(phi)
cp = nu.cos(phi)
sp = nu.sin(phi)
dR = cp * tmp_out[:, 4] + sp * tmp_out[:, 5]
dphi = (cp * tmp_out[:, 5] - sp * tmp_out[:, 4]) / R
dvR = cp * tmp_out[:, 6] + sp * tmp_out[:, 7] + vT * dphi
dvT = cp * tmp_out[:, 7] - sp * tmp_out[:, 6] - vR * dphi
out = nu.zeros((len(t), 8))
out[:, 0] = R
out[:, 1] = vR
out[:, 2] = vT
out[:, 3] = phi
if rectOut:
out[:, 4:] = tmp_out[:, 4:]
else:
out[:, 4] = dR
out[:, 7] = dphi
out[:, 5] = dvR
out[:, 6] = dvT
_parse_warnmessage(msg)
return (out, msg)
def _integrateRZOrbit(vxvv, pot, t, method, dt):
"""
NAME:
_integrateRZOrbit
PURPOSE:
integrate an orbit in a Phi(R,z) potential in the (R,z) plane
INPUT:
vxvv - array with the initial conditions stacked like
[R,vR,vT,z,vz]; vR outward!
pot - Potential instance
t - list of times at which to output (0 has to be in this!)
method - 'odeint' or 'leapfrog'
dt - if set, force the integrator to use this basic stepsize; must be an integer divisor of output stepsize
OUTPUT:
[:,5] array of [R,vR,vT,z,vz] at each t
HISTORY:
2010-04-16 - Written - Bovy (NYU)
"""
#First check that the potential has C
if '_c' in method:
if not ext_loaded or not _check_c(pot):
if ('leapfrog' in method or 'symplec' in method):
method = 'leapfrog'
else:
method = 'odeint'
if not ext_loaded: # pragma: no cover
warnings.warn(
"Cannot use C integration because C extension not loaded (using %s instead)"
% (method), galpyWarning)
else:
warnings.warn(
"Cannot use C integration because some of the potentials are not implemented in C (using %s instead)"
% (method), galpyWarning)
if method.lower() == 'leapfrog' \
or method.lower() == 'leapfrog_c' or method.lower() == 'rk4_c' \
or method.lower() == 'rk6_c' or method.lower() == 'symplec4_c' \
or method.lower() == 'symplec6_c' or method.lower() == 'dopr54_c':
#We hack this by upgrading to a FullOrbit
this_vxvv = nu.zeros(len(vxvv) + 1)
this_vxvv[0:len(vxvv)] = vxvv
tmp_out = _integrateFullOrbit(this_vxvv, pot, t, method, dt)
#tmp_out is (nt,6)
out = tmp_out[:, 0:5]
elif method.lower() == 'odeint':
l = vxvv[0] * vxvv[2]
l2 = l**2.
init = [vxvv[0], vxvv[1], vxvv[3], vxvv[4]]
intOut = integrate.odeint(_RZEOM,
init,
t,
args=(pot, l2),
rtol=10.**-8.) #,mxstep=100000000)
out = nu.zeros((len(t), 5))
out[:, 0] = intOut[:, 0]
out[:, 1] = intOut[:, 1]
out[:, 3] = intOut[:, 2]
out[:, 4] = intOut[:, 3]
out[:, 2] = l / out[:, 0]
#post-process to remove negative radii
neg_radii = (out[:, 0] < 0.)
out[neg_radii, 0] = -out[neg_radii, 0]
return out