def inc_normal(self, D, weight, var):
# probability being normal
A = abs(self.D - D) - 0.5
B = A + 1
probability = 0.5 * (utils.erf(B / var / math.sqrt(2)) -
utils.erf(A / var / math.sqrt(2)))
self.prd_support += probability * weight
def phig(y):
"""
Modified error function
erf(y) - chandrasekhar(y)
"""
return erf(y) - chandrasekhar(y)
def chandrasekhar(y):
""" Chandrasekhar function for dynamical friction
"""
if abs(y) < 1e-3:
return (2./sqrt(pi)) * y/3.
return (erf(y) - (2./sqrt(pi))*y*exp(-y*y)) / (2.*y*y)
def inverse(self, x):
#print('sigma:' + str(self.sig))
#print('inner_erf:', x/(np.sqrt(2)*self.sig))
#print('erf:',utils.erf( x/(np.sqrt(2)*self.sig) ))
#print('inverse:',-(1/self.lambd) * np.log( 0.5 - 0.5 * utils.erf( x/(np.sqrt(2)*self.sig) ) ))
res = np.maximum(
-(1 / self.lambd) *
np.log(0.5 - 0.5 * utils.erf(x / (np.sqrt(2) * self.sig)) + 1e-14),
0)
return np.nan_to_num(res)
def expected_improvement(self, t):
"""Computes the expected improvement at position ``t`` under the current
GP model.
Reference "current best" is the observed ``t`` with minimal posterior
mean."""
assert isinstance(t, (float, np.float32, np.float64))
# Find the observation with minimal posterior mean, if it has not yet been
# computed by a previous call to this method
if self.min_obs is None:
self.min_obs = min(self.mu(tt) for tt in self.ts)
# Compute posterior mean and variance at t
m, v = self.mu(t), self.V(t)
# Compute the two terms in the formula for EI and return the sum
t1 = 0.5 * (self.min_obs-m) * (1 + erf((self.min_obs-m)/np.sqrt(2.*v)))
t2 = np.sqrt(0.5*v/np.pi) * np.exp(-0.5*(self.min_obs-m)**2/v)
return t1 + t2
def inc_normal(self, D, weight, var):
# probability being normal
A = abs(self.D - D) - 0.5
B = A + 1
probability = 0.5 * (utils.erf(B / var / math.sqrt(2)) - utils.erf(A / var / math.sqrt(2)))
self.prd_support += probability * weight
def viscosity(surf, spec, vmax=5., nv=500, colldamping=0.):
"""
Neoclassical viscosity calculation
Parameters
----------
surf = Flux surface object (see equilibrium.py)
.aspectRatio = aspect ratio a/R
.Bsqav() # < B^2 > flux-surface average
.average( func(theta) )
.deriv( func(theta) )
.B(theta)
.Bp(theta)
spec = list of Species
Optional inputs
---------------
vmax (=5.) Maximum velocity to consider (units of vth)
nv (=500) Number of velocity grid points
colldamping (=0.) determines collisional suppression:
]0,1[ Collisional suppression
None Shiang's result that a=1 experiences no collisional suppression
"""
conl = connectionLength(surf)
ft = trappedFraction(surf)
Bsq = surf.Bsqav() # < B^2 > flux-surface average
# < (dB/dl)^2 Bp^2 / B^2 >
dotav = surf.average(lambda x: ( surf.deriv(surf.B)(x) * surf.Bp(x) / surf.B(x) )**2 )
ns = size(spec) # Number of species
nv = 500 # Number of velocity points
dv=vmax/(nv-1.)
vd = zeros([ns, nv])
vt = zeros([ns, nv])
vtot = zeros([ns, nv])
# Calculate collision times
coltau = collisionTimes(spec)
# Populate velocity mesh values
# This code really needs some love
for i, si in enumerate(spec):
vtha = si.Vth # Thermal speed
omta = vtha / conl
vsttau = 8./(3.*pi) * ft*omta*Bsq / (dotav * vtha**2)
for n in range(nv):
vv = (n+0.5)*dv
for j, sj in enumerate(spec):
y = vv * si.Vth / sj.Vth
vdij = phig(y) / (coltau[i,j]*vv**3)
vd[i,n] += vdij
vtij = (((erf(y) - 3.*chandrasekhar(y)) / vv**3) + 4.*(si.T/sj.T + (si.Vth/sj.Vth)**2)*chandrasekhar(y)/vv)/coltau[i,j]
vt[i,n] += vtij
vd[i,n] *= 3.*sqrt(pi)/4.
vt[i,n] *= 3.*sqrt(pi)/4.
if colldamping == None:
# Shiang's result
fac1=1.+(1.- surf.aspectRatio**2)*vsttau*vd[i,n]/vv
fac2=1.+5.*pi*vt[i,n]/(8.*vv*omta)
else:
fac1=1.+colldamping*vsttau*vd[i,n]/vv
fac2=1.+colldamping*5.*pi*vt[i,n]/(8.*vv*omta)
vtot[i,n] = vd[i,n] / (fac1 * fac2)
# perform velocity integrals to calculate k's
# No need to store vd,vt,vtot arrays
rk11 = zeros(ns)
rk12 = zeros(ns)
rk22 = zeros(ns)
vis = zeros([ns, 3])
for i, si in enumerate(spec):
for n in range(nv):
vv = (n+0.5)*dv
arg=(vv**4)*exp(-vv**2)*vtot[i,n]*dv
rk11[i] += arg
rk12[i] += arg*vv**2
rk22[i] += arg*vv**4
rk11[i] *= ft*8./(3.*(1.-ft)*sqrt(pi))
rk12[i] *= ft*8./(3.*(1.-ft)*sqrt(pi))
rk22[i] *= ft*8./(3.*(1.-ft)*sqrt(pi))
print "viscosity: ", rk11[i], rk12[i], rk22[i]
vis[i,0] = rk11[i]*si.density*si.mass
vis[i,1] = (rk12[i] - 2.5*rk11[i])*si.density*si.mass
vis[i,2] = (rk22[i] - 5.*rk12[i] + 6.25*rk11[i])*si.density*si.mass
return vis
def inverse(self, x):
return np.sqrt(2) * self.s * utils.inv_erf(
0.5 + 0.5 * utils.erf(x / (np.sqrt(2) * self.sig)))