def func(param, return_oofunvalue=False):
num = len(param["Substrate"])
p, s = oovars(2, size = num)
equations = [
(0==-param["Protein"]+(ones(num)+param['k1']*s)*p)(tol=tolerence),
(0==-param['Substrate']+(ones(num)+param['k1']*p)*s)(tol=tolerence),
]
startpoint = {p:param["Protein"], s:param['Substrate']}
system = SNLE(equations, startpoint, iprint = -100)
if local_constrained:
# Slow but works when not close
system.constraints = [
p > zeros(num), s > zeros(num),
p < param['Protein'], s < param['Substrate']
]
solutions = system.solve('nssolve')
else:
# Fast and good if close
solutions = system.solve('scipy_fsolve')
P, S = p(solutions), s(solutions)
return param['s']*(param['k1'])*P*S/param['Substrate']
def calcScatteringPlaneTilt (h1, h2, UBmatrix, wavelength,stars):
"Calculates the chi and phi for the scattering plane defined by h1 and h2. Used with calcIdealAngles2."
#Accepts two scattering plane vectors, h1 and h2, the UB matrix, and the wavelength
h1p = N.dot(UBmatrix, h1)
h2p = N.dot(UBmatrix, h2)
x0 = [0.0, 0.0, 0.0, 0.0]
q = calcq (h1[0], h1[1], h1[2], stars)
twotheta1 = 2.0 * N.arcsin(wavelength * q / 4.0 / N.pi)
q = calcq (h2[0], h2[1], h2[2], stars)
twotheta2 = 2.0 * N.arcsin(wavelength * q / 4.0 / N.pi)
s1='before NLSP\n'
genout(s1)
p0 = SNLE(scatteringEquationsTilt, x0, args=(h1p, h2p, wavelength, twotheta1, twotheta2))
s1=s1+'after NLSP\n'
genout(s1)
p0.xtol=1e-8
p0.ftol=1e-8
r0 = p0.solve('nlp:ralg')
s1=s1+'after solve\n'
genout(s1)
upper = N.degrees(r0.xf[0]) #xf is the final array, xf[0] = chi
lower = N.degrees(r0.xf[1]) # xf[1] = phi
return lower,upper
def calcIdealAngles(self, desiredh, chi, phi, UBmatrix, stars, ubcalc):
"Calculates the twotheta, theta, and omega values for a desired h vector. Uses chi and phi from calcScatteringPlane."
#Accepts the desired h vector, chi, phi, the UB matrix, the wavelength, and the stars dictionary
desiredhp = np.dot(UBmatrix, desiredh[0:3])
#Old code (scipy.optimize.fsolve) produced inaccurate results with far-off estimates
#solutions = scipy.optimize.fsolve(equations, x0, args=(h1p, h2p, wavelength))
q = calcq(desiredh[0], desiredh[1], desiredh[2], stars)
#twotheta = 2.0 * np.arcsin(wavelength * q / 4.0 / np.pi)
ei = desiredh[3]
ef = desiredh[4]
#q=calc_q_inelastic(ei,ef,desiredh[0],desiredh[1],desiredh[2])
twotheta = calc_tth_inelastic(ei, ef, q)
x0 = [0.0]
p = SNLE(self.secondequations,
x0,
args=(desiredhp, chi, phi, ei, twotheta, ubcalc))
r = p.solve('nlp:ralg')
omega = r.xf[0]
#theta = twotheta/2.0 + omega # ------ ALTERNATE SOLUTION FOR THETA ------
#theta=calc_th_inelastic(ei,ef,np.radians(twotheta))
theta = twotheta / 2.0 + omega
#theta = r.xf[1] # ------ SOLVER POTENTIALLY INACCURATE FOR THETA ------
solutions = [twotheta, theta, omega]
return solutions #% 360
def func(param, return_oofunvalue=False):
#print traits
#ImportOld.calltimes += 1
#print x
#print "I have been called: " + str(ImportOld.calltimes) + " times"
num = len(param["x"])
p = oovar(size=num)
d = oovar(size=num)
equations = [
(0 == -param["x"] + (ones(num) + param['k1'] * d) * p)(tol=1e-8),
(0 == -param['NCPconc'] + (ones(num) + param['k1'] * p) * d)(tol=1e-8)
]
startpoint = {p: param['x'], d: param['NCPconc']}
system = SNLE(equations, startpoint, iprint=10)
if Data.constrained:
# Slow but works when not close
system.constraints = [
p > zeros(num), d > zeros(num), p < param['x'],
d < param['NCPconc']
]
solutions = system.solve('nssolve')
else:
# Fast and good if close
solutions = system.solve('scipy_fsolve')
P, D = p(solutions), d(solutions)
return param['s'] * (
param['k1']) * P * D / param['NCPconc'] + param['offset']
def calcIdealAngles(self,desiredh, chi, phi, UBmatrix, stars,ubcalc):
"Calculates the twotheta, theta, and omega values for a desired h vector. Uses chi and phi from calcScatteringPlane."
#Accepts the desired h vector, chi, phi, the UB matrix, the wavelength, and the stars dictionary
desiredhp = np.dot(UBmatrix, desiredh[0:3])
#Old code (scipy.optimize.fsolve) produced inaccurate results with far-off estimates
#solutions = scipy.optimize.fsolve(equations, x0, args=(h1p, h2p, wavelength))
q = calcq (desiredh[0], desiredh[1], desiredh[2], stars)
#twotheta = 2.0 * np.arcsin(wavelength * q / 4.0 / np.pi)
ei=desiredh[3]
ef=desiredh[4]
#q=calc_q_inelastic(ei,ef,desiredh[0],desiredh[1],desiredh[2])
twotheta=calc_tth_inelastic(ei,ef,q)
x0 = [0.0]
p = SNLE(self.secondequations, x0, args=(desiredhp, chi, phi, ei, twotheta,ubcalc))
r = p.solve('nlp:ralg')
omega = r.xf[0]
#theta = twotheta/2.0 + omega # ------ ALTERNATE SOLUTION FOR THETA ------
#theta=calc_th_inelastic(ei,ef,np.radians(twotheta))
theta=twotheta/2.0+omega
#theta = r.xf[1] # ------ SOLVER POTENTIALLY INACCURATE FOR THETA ------
solutions = [twotheta, theta, omega]
return solutions #% 360
def solve_gamma_3D(gammas): #y={eta_fixed, mu_fixed, nu_fixed}
gamma_array = []
sol_1_array = []
sol_2_array = []
sol_3_array = []
sol_4_array = []
eta, mu, nu = oovars(3)
start_point = {eta:3.0, mu:0.7, nu:0.20}
for gamma in gammas:
# gamma = gamma.tolist()
global alpha, beta, tau_l, tau_k, Lambda, delta, A, N, phi_k, phi_l, theta
# Set equations
L = N * (mu * (1-mu/2) + theta * (1-mu))
f_1 = -nu - delta + N * mu * beta / (1 + beta) * ((1 - tau_l) * (1 - mu / 2) * (1 - alpha) * A * L**(-alpha) *eta ** (alpha - 1) - gamma)
f_2 = mu * phi_k * alpha * (1-alpha)*A* L**(1-alpha) *eta**alpha / (alpha*A*L**(1-alpha)*eta**(alpha-1) + N*mu*gamma) + (1-mu)*phi_l* (tau_l*(1-alpha)**2*A*L**(-alpha)*eta**alpha + tau_k*alpha*(1-alpha)*A*L**(1-alpha)*eta**alpha-1) / (tau_l*(1-alpha)*A*L**(-alpha)*eta**(alpha-1) + tau_k*(alpha*A*L**(1-alpha)*eta**(alpha-1)+N*mu*gamma)-eta**(-1))
c_yk = 1/(1+beta) * ( (1-tau_l)* (1-mu)* (1-alpha)* A* eta**(alpha-1)* L**(-alpha) - gamma)
c_ok = beta * (1-tau_k) * (1+alpha*A*eta**(alpha-1)*L**(1-alpha) - delta) / (1+beta) * ( (1-tau_l)* (1-mu)* (1-alpha)* A* eta**(alpha-1)* L**(-alpha) - gamma)
c_yl = (1-tau_l)* theta * (1-alpha)* A* eta**(alpha-1)* L**(-alpha)
c_ol = 1/(N*(1-mu)) * (tau_l*(1-alpha)*A*eta**(alpha-1)*L**(1-alpha) + tau_k* (alpha*A*eta**(alpha-1)*L**(1-alpha) +N*mu*gamma) - eta**(-1))
U_k = c_yk * c_ok**beta
U_l = c_yl * c_ol**beta
f3 = U_k-U_l
equations = (f_1 == 0, f_2 == 0, f3 == 0)
p = SNLE(equations, start_point)
cons_1 = Lambda * A * eta ** alpha + tau_k * mu * gamma * eta - 1
cons_2 = eta - ((1 - alpha) * A) ** (-1 / alpha)
cons_3 = (1 - tau_l) * (1 - mu) * (1 - alpha) * A * eta ** (alpha - 1) - gamma
p.constraints = [0 < mu, mu < 1, cons_1 > 0, cons_2 > 0, cons_3 >=0, nu>0]
r = p.solve('nssolve')
sol_1, sol_2, sol_3 = r(eta, mu, nu)
sol_4 = N * (sol_2 * (1-sol_2/2) + theta * (1-sol_2))
print('Solution: eta=%f, mu=%f, nu=%f, L=%f' % (sol_1, sol_2, sol_3, sol_4))
if r.stopcase>0:
gamma_array.append(gamma)
sol_1_array.append(sol_1)
sol_2_array.append(sol_2)
sol_3_array.append(sol_3)
sol_4_array.append(sol_4)
return gamma_array, sol_1_array, sol_2_array, sol_3_array, sol_4_array
def calcScatteringPlane(self, h1, h2, UBmatrix, ei, stars):
"Returns the chi and phi for the scattering plane defined by h1 and h2. Used with calcIdealAngles2."
#Accepts two scattering plane vectors, h1 and h2, the UB matrix, and the wavelength
#Should we allow the scattering plane to be defined by two vectors at different energies?
#For now, I say NoN
h1p = np.dot(UBmatrix, h1)
h2p = np.dot(UBmatrix, h2)
x0 = [0.0, 0.0, 0.0, 0.0]
wavelength = e_to_wavelength(ei)
q1 = calcq(h1[0], h1[1], h1[2], stars)
twotheta1 = np.degrees(2.0 * np.arcsin(wavelength * q1 / 4.0 / np.pi))
q2 = calcq(h2[0], h2[1], h2[2], stars)
twotheta2 = np.degrees(2.0 * np.arcsin(wavelength * q2 / 4.0 / np.pi))
if 1:
#original openopt
#outp=self.scatteringEquations([45,90,-90,0],h1p, h2p, q1, q2,wavelength,twotheta1/2,twotheta2/2)
p0 = SNLE(self.scatteringEquations,
x0,
args=(h1p, h2p, q1, q2),
contol=1e-15,
ftol=1e-15,
maxFunEvals=1e8,
maxIter=1e5)
r0 = p0.solve('nlp:ralg')
#outp=self.scatteringEquations(r0.xf,h1p, h2p, q1, q2,wavelength,twotheta1/2,twotheta2/2)
chi = r0.xf[0] #xf is the final array, xf[0] = chi
phi = r0.xf[1] # xf[1] = phi
if 0:
import bumps
from bumps.fitters import FIT_OPTIONS, FitDriver, DreamFit, StepMonitor, ConsoleMonitor
import bumps.modelfn, bumps.fitproblem
fn = lambda chi, phi, omega1, omega2: np.linalg.norm(
self.scatteringEquations([chi, phi, omega1, omega2], h1p, h2p,
q1, q2))
print fn(chi=45, phi=72.4, omega1=-90, omega2=0)
M = bumps.modelfn.ModelFunction(fn,
chi=0.0,
phi=0.0,
omega1=0.0,
omega2=0.0)
M._parameters['chi'].range(30, 60.)
M._parameters['phi'].range(0, 90.)
M._parameters['omega1'].range(-90, 90.)
M._parameters['omega2'].range(-90, 90.)
problem = bumps.fitproblem.FitProblem(M)
fitdriver = FitDriver(DreamFit, problem=problem, burn=1000)
best, fbest = fitdriver.fit()
print best, fbest
print 'done'
print 'chi, phi', chi, phi
return chi, phi
def solve_eqn_np(theta, gamma, N): #y={eta_fixed, mu_fixed, nu_fixed}
nu, eta, mu, = oovars(3)
# start_point = {nu:0.08, eta:4, mu:0.8}
# start_point = {nu:0.2, eta:3.4, mu:0.55} #Cololado
# start_point = {nu:0.15, eta:2.5, mu:0.55} # Alabama not feasible
start_point = {nu:0.2, eta:2.5, mu:0.55}
global alpha, beta, tau_l, tau_k, Lambda, delta, A
L = N*(mu*(1-mu/2)+(1-mu)*theta)
f_1 = -nu - delta + N * mu * beta / (1 + beta) * ((1 - tau_l) * (1 - mu / 2) * (1 - alpha) * A * L**(-alpha) *eta ** (alpha - 1) - gamma)
Log = log(((1-tau_l)*(1-mu)*(1-alpha)*A*L**(-alpha)*eta**(alpha-1) -gamma)/ ((1-tau_l)*(1-alpha)*A*L**(-alpha)*eta**(alpha-1)) -gamma)
dV_yk = (1-alpha)*mu*eta - gamma/((1-tau_l)*A*L**(-alpha)*eta**(alpha-2))*Log
dV_yl = (1-mu)*(1-alpha)*eta
dV_ok = beta* mu * alpha * (1-alpha)*A* L**(1-alpha) *eta**alpha / (alpha*A*L**(1-alpha)*eta**(alpha-1) + N*mu*gamma)
dV_ol = beta * (1-mu)* (tau_l*(1-alpha)**2*A*L**(-alpha)*eta**alpha + tau_k*alpha*(1-alpha)*A*L**(1-alpha)*eta**alpha-1) / (tau_l*(1-alpha)*A*L**(-alpha)*eta**(alpha-1) + tau_k*(alpha*A*L**(1-alpha)*eta**(alpha-1)+N*mu*gamma)-eta**(-1))
f_2 = dV_yk + dV_yl + dV_ok + dV_ol
c_yk = 1/(1+beta) * ( (1-tau_l)* (1-mu)* (1-alpha)* A* eta**(alpha-1)* L**(-alpha) - gamma)
c_ok = beta * (1-tau_k) * (1+alpha*A*eta**(alpha-1)*L**(1-alpha) - delta) / (1+beta) * ( (1-tau_l)* (1-mu)* (1-alpha)* A* eta**(alpha-1)* L**(-alpha) - gamma)
c_yl = (1-tau_l)* theta * (1-alpha)* A* eta**(alpha-1)* L**(-alpha)
c_ol = 1/(N*(1-mu)) * (tau_l*(1-alpha)*A*eta**(alpha-1)*L**(1-alpha) + tau_k* (alpha*A*eta**(alpha-1)*L**(1-alpha) +N*mu*gamma) - eta**(-1))
U_k = c_yk * c_ok**beta
U_l = c_yl * c_ol**beta
f_3 = U_k-U_l
equations = (f_1 == 0, f_2 == 0, f_3==0)
p = SNLE(equations, start_point)
# cons_1 = Lambda * A * eta ** alpha + tau_k * mu * gamma * eta - 1
# cons_2 = eta - ((1 - alpha) * A) ** (-1 / alpha)
cons_3 = (1 - tau_l) * (1 - mu) * (1 - alpha) * A * eta ** (alpha - 1) - gamma
p.constraints = [nu>0, eta>0, 0< mu, mu < 1, cons_3 >0]
# cons_1>=0, cons_2 >=0,
r = p.solve('nssolve')
nu_s, eta_s, mu_s = r(nu, eta, mu)
print('Solution: x1=%f, x2=%f, x3=%f' %(nu_s, eta_s, mu_s))
L = N*(mu_s*(1-mu_s/2)+(1-mu_s)*theta)
Y_K_ratio = A*eta_s**(alpha-1)*L**(1-alpha)
return nu_s, Y_K_ratio, eta_s, mu_s, L
def func(param, return_oofunvalue=False, snle_style=False):
#print traits
#ImportOld.calltimes += 1
#print x
#print "I have been called: " + str(ImportOld.calltimes) + " times"
num = len(param["x"])
p = oovar(size=num)
print param
# equations = [
# (0.0 == param["x"] - p * (ones(num) + param['k1'] * s * (ones(num) + 2.0 * param['k2'] * p)))(tol=1e-12),
# (0.0 == param["Substrate"] - s * (ones(num) + param['k1'] * p * (ones(num) + param['k2'] * p)))(tol=1e-12),
# ]
# m == k2/k1
#
s = param["N"]
equations = [
(0.0 == param['od'] * param["x"] - p *
(ones(num) + param['k1'] * s *
(ones(num) + 2.0 * param['k1'] * param['m'] * p)))(tol=1e-12)
]
#startpoint = {p:param['x']/2.0, s:param['Substrate']/2.0}
startpoint = {p: param['x']}
#startpoint = {p:zeros(num), s:zeros(num)}
system = SNLE(equations, startpoint, iprint=1000)
if Data.local_constrained:
# Slow but works when not close
constraints = [
p > zeros(num), s > zeros(num), p < param['x'],
s < param['Substrate'], p > param['x'] - 2 * param['Substrate']
]
system.constraints = constraints
#solutions = system.solve('interalg')
if Data.local_constrained:
solutions = system.solve('nssolve')
else:
# Fast and good if close
solutions = system.solve('scipy_fsolve')
P = p(solutions)
print "Protein:"
print P
return s * (ones(num) + param['k1'] * P *
(ones(num) + param['k1'] * param['m'] * P)) / param['od']
def solve_eqn(nu, eta, phi_k, phi_l, tau_k, tau_l): #y={eta_fixed, mu_fixed, nu_fixed}
theta, mu, gamma = oovars(3)
start_point = {theta:0.5, mu:0.8, gamma:0.2}
global alpha, beta, delta, A
Lambda = alpha * tau_k + (1 - alpha) * tau_l
# Set equations
L = 1
N = L / (mu*(1-mu/2)+(1-mu)*theta)
f_1 = -nu - delta + N * mu * beta / (1 + beta) * ((1 - tau_l) * (1 - mu / 2) * (1 - alpha) * A * L**(-alpha) *eta ** (alpha - 1) - gamma)
f_2 = mu * phi_k * alpha * (1-alpha)*A* L**(1-alpha) *eta**alpha / (alpha*A*L**(1-alpha)*eta**(alpha-1) + N*mu*gamma) + (1-mu)*phi_l* (tau_l*(1-alpha)**2*A*L**(-alpha)*eta**alpha + tau_k*alpha*(1-alpha)*A*L**(1-alpha)*eta**alpha-1) / (tau_l*(1-alpha)*A*L**(-alpha)*eta**(alpha-1) + tau_k*(alpha*A*L**(1-alpha)*eta**(alpha-1)+N*mu*gamma)-eta**(-1))
c_yk = 1/(1+beta) * ( (1-tau_l)* (1-mu)* (1-alpha)* A* eta**(alpha-1)* L**(-alpha) - gamma)
c_ok = beta * (1-tau_k) * (1+alpha*A*eta**(alpha-1)*L**(1-alpha) - delta) / (1+beta) * ( (1-tau_l)* (1-mu)* (1-alpha)* A* eta**(alpha-1)* L**(-alpha) - gamma)
c_yl = (1-tau_l)* theta * (1-alpha)* A* eta**(alpha-1)* L**(-alpha)
c_ol = 1/(N*(1-mu)) * (tau_l*(1-alpha)*A*eta**(alpha-1)*L**(1-alpha) + tau_k* (alpha*A*eta**(alpha-1)*L**(1-alpha) +N*mu*gamma) - eta**(-1))
U_k = c_yk * c_ok**beta
U_l = c_yl * c_ol**beta
f_3 = U_k-U_l
equations = (f_1 == 0, f_2 == 0, f_3==0)
p = SNLE(equations, start_point)
cons_1 = Lambda * A * eta ** alpha + tau_k * mu * gamma * eta - 1
cons_2 = eta - ((1 - alpha) * A) ** (-1 / alpha)
cons_3 = (1 - tau_l) * (1 - mu) * (1 - alpha) * A * eta ** (alpha - 1) - gamma
p.constraints = [0 < mu, mu < 1, cons_1 > 0, cons_2 > 0, cons_3 >=0, N>1, gamma > 0, theta>0, theta<1 ]
r = p.solve('nssolve')
theta_s, mu_s, gamma_s = r(theta, mu, gamma)
print('Solution: x1=%f, x2=%f, x3=%f' %(theta_s, mu_s, gamma_s))
# theta = ( 1/N - mu_s*( 1 - mu_s/2) )/(1 - mu_s)
N = 1 / (mu_s*(1-mu_s/2)+(1-mu_s)*theta_s)
return theta_s, mu_s, gamma_s, N, eta
def calcScatteringPlane(self,h1, h2, UBmatrix, ei,stars):
"Returns the chi and phi for the scattering plane defined by h1 and h2. Used with calcIdealAngles2."
#Accepts two scattering plane vectors, h1 and h2, the UB matrix, and the wavelength
#Should we allow the scattering plane to be defined by two vectors at different energies?
#For now, I say NoN
h1p = np.dot(UBmatrix, h1)
h2p = np.dot(UBmatrix, h2)
x0 = [0.0, 0.0, 0.0, 0.0]
wavelength=e_to_wavelength(ei)
q1 = calcq (h1[0], h1[1], h1[2], stars)
twotheta1 = np.degrees(2.0 * np.arcsin(wavelength * q1 / 4.0 / np.pi))
q2 = calcq (h2[0], h2[1], h2[2], stars)
twotheta2 = np.degrees(2.0 * np.arcsin(wavelength * q2 / 4.0 / np.pi))
if 1:
#original openopt
#outp=self.scatteringEquations([45,90,-90,0],h1p, h2p, q1, q2,wavelength,twotheta1/2,twotheta2/2)
p0 = SNLE(self.scatteringEquations, x0, args=(h1p, h2p, q1, q2),contol=1e-15, ftol=1e-15,maxFunEvals=1e8,maxIter=1e5)
r0 = p0.solve('nlp:ralg')
#outp=self.scatteringEquations(r0.xf,h1p, h2p, q1, q2,wavelength,twotheta1/2,twotheta2/2)
chi = r0.xf[0] #xf is the final array, xf[0] = chi
phi = r0.xf[1] # xf[1] = phi
if 0:
import bumps
from bumps.fitters import FIT_OPTIONS, FitDriver, DreamFit, StepMonitor, ConsoleMonitor
import bumps.modelfn, bumps.fitproblem
fn=lambda chi,phi,omega1,omega2: np.linalg.norm(self.scatteringEquations([chi,phi,omega1,omega2], h1p, h2p,q1,q2))
print fn(chi=45, phi=72.4, omega1=-90, omega2=0)
M=bumps.modelfn.ModelFunction(fn,chi=0.0,phi=0.0,omega1=0.0,omega2=0.0)
M._parameters['chi'].range(30,60.)
M._parameters['phi'].range(0,90.)
M._parameters['omega1'].range(-90,90.)
M._parameters['omega2'].range(-90,90.)
problem=bumps.fitproblem.FitProblem(M)
fitdriver = FitDriver(DreamFit, problem=problem, burn=1000)
best, fbest = fitdriver.fit()
print best,fbest
print 'done'
print 'chi, phi', chi, phi
return chi, phi
def func(param, return_oofunvalue=False):
#print param
#ImportOld.calltimes += 1
#print "I have been called: " + str(ImportOld.calltimes) + " times"
num = len(param["x"])
p = oovar(size=num)
d = oovar(size=num)
n = oovar(size=num)
equations = [
(0 == (ones(num) + param['k1'] * d + param['k2'] * n +
param['k2'] * param['k4'] * d * n) * p -
exp(param['x']))(tol=1e-8),
(0 == (ones(num) + param['k1'] * p + param['k2'] * param['k4'] * p * n)
* d - param['dnaconc'])(tol=1e-8),
(0 == (ones(num) + param['k2'] * p + param['k2'] * param['k4'] * p * d)
* n - param['nconc'])(tol=1e-8)
]
startpoint = {p: param['x'], d: param['dnaconc'], n: param['nconc']}
system = SNLE(equations, startpoint, iprint=-1)
if Data.constrained:
# Slow but works when not close
system.constraints = [
p > zeros(num), d > zeros(num), n > zeros(num), p < param['x'],
d < param['dnaconc'], n < param['nconc']
]
solutions = system.solve('nssolve')
else:
# Fast and good if close
solutions = system.solve('scipy_fsolve')
P, D, N = p(solutions), d(solutions), n(solutions)
#print "P: " + str(P)
#print "D: " + str(D)
#print "N: " + str(N)
return log(param['s']) + log(
(1.0 + param['k1'] * param['A'] * param['k2'] * param['k4'] *
N)) - log(param['k1']) + log(P) + log(D) - log(param['dnaconc'])
def calcIdealAngles(self, desiredh, chi, phi, UBmatrix, stars, ubcalc):
"Calculates the twotheta, theta, and omega values for a desired h vector. Uses chi and phi from calcScatteringPlane."
#Accepts the desired h vector, chi, phi, the UB matrix, the wavelength, and the stars dictionary
desiredhp = np.dot(UBmatrix, desiredh[0:3])
#Old code (scipy.optimize.fsolve) produced inaccurate results with far-off estimates
#solutions = scipy.optimize.fsolve(equations, x0, args=(h1p, h2p, wavelength))
q = calcq(desiredh[0], desiredh[1], desiredh[2], stars)
#twotheta = 2.0 * np.arcsin(wavelength * q / 4.0 / np.pi)
ei = desiredh[3]
ef = desiredh[4]
#q=calc_q_inelastic(ei,ef,desiredh[0],desiredh[1],desiredh[2])
twotheta = calc_tth_inelastic(ei, ef, q)
x0 = [0.0]
p = SNLE(self.secondequations,
x0,
args=(desiredhp, chi, phi, ei, twotheta, ubcalc))
df[1, 0] = 1
df[1, 1] = -0.5
df[2, 0] = 1
df[2, 2] = -sin(x[2])
return df
x0 = [8, 15, 80]
#w/o gradient:
#p = SNLE(f, x0)
p = SNLE(f,
x0,
df=df,
maxFunEvals=1e5,
iprint=10,
plot=1,
ftol=1e-8,
contol=1e-15)
#optional: user-supplied gradient check:
#p.checkdf()
#optional: graphical output, requires matplotlib installed
#p.plot = 1
#set some constraints
p.lb, p.ub = [-inf] * 3, [inf] * 3
p.lb[2], p.ub[2] = 145, 150
# you could try also comment/uncomment nonlinear constraints:
def calcRefineUB(self, observations, stars_dict):
#observations are an array of dictionaries for each observed reflection
#These can be taken at different energies, but should be elastic
hvectors = []
Uv = []
omt = []
for i in range(0, len(observations)):
h = np.array([
observations[i]['h'], observations[i]['k'],
observations[i]['l']
], 'Float64')
hvectors.append(h)
'''
sys.stderr.write('i %3.4f \n'%(observations[i]['h'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['k'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['l'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['twotheta'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['theta'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['chi'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['phi'],))
'''
theta = (observations[i]['theta']
) #For us, theta is theta measured (or Lumsden's 's')
chi = (observations[i]['chi'])
phi = (observations[i]['phi'])
twotheta = (observations[i]['twotheta'])
ei = observations[i]['ei']
ef = observations[i]['ei'] #reflections are elastic!!!!
#omega = theta - twotheta/2.0 #diffraction...
omega = calc_om_elastic(h[0], h[1], h[2], ei, theta, stars_dict)
#omega=calc_om_inelastic(ei,ef,twotheta)
u1_phi = self.calc_u_phi(omega, chi, phi)
u1p, u2p, u3p = u1_phi
omt.append(omega)
#u1p = np.cos(omega)*np.cos(chi)*np.cos(phi) - np.sin(omega)*np.sin(phi)
#u2p = np.cos(omega)*np.cos(chi)*np.sin(phi) + np.sin(omega)*np.cos(phi)
#u3p = np.cos(omega)*np.sin(chi)
#reflections are elastic
q = calc_q_inelastic(ei, ei, twotheta)
#uv1p=q*u1p
#uv2p=q*u2p
#uv3p=q*u3p
#uv1p = 2.0*np.sin(twotheta/2) / wavelength * u1p
#uv2p = 2.0*np.sin(twotheta/2) / wavelength * u2p
#uv3p = 2.0*np.sin(twotheta/2) / wavelength * u3p
uv1p = (q / (2 * np.pi)) * u1p
uv2p = (q / (2 * np.pi)) * u2p
uv3p = (q / (2 * np.pi)) * u3p
#h1p[0] - (q1/(2*np.pi)) * u1[0]
Uv.append(uv1p)
Uv.append(uv2p)
Uv.append(uv3p)
x0 = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
p = SNLE(
self.UBRefinementEquations, x0,
args=(hvectors,
Uv)) #,contol=1e-15, ftol=1e-15,maxFunEvals=1e8,maxIter=1e5)
r = p.solve('nlp:ralg')
a = r.xf[0]
b = r.xf[1]
c = r.xf[2]
d = r.xf[3]
e = r.xf[4]
f = r.xf[5]
g = r.xf[6]
h = r.xf[7]
j = r.xf[8]
UB = 2 * np.pi * np.array([[a, b, c], [d, e, f], [g, h, j]], 'Float64')
return UB
for i in range(n):
no_a_i = no_a[i]
Aeq.append([0.] * actagg[i] + [1.] * no_a_i + [0.] *
(total_no_a - actagg[i] - no_a_i))
x0 = x0 + [1.0 / no_a_i] * no_a_i
actagg.append(actagg[i] + no_a_i)
#multiplies the vectors strat and Delta(strat); this product has to be 0 in equilibrium
def product(x):
strat = []
for i in range(n):
strat.append(x[actagg[i]:actagg[i + 1]])
return np.dot(x, Delta(strat))
p = SNLE(product, x0, lb=lb, ub=ub, Aeq=Aeq, beq=beq)
p.iprint = -1
r = p.solve('nssolve')
if r.stopcase == 1:
print 'there is an equilibrium in which '
for i in range(n):
out = [round(item, 3) for item in r.xf[actagg[i]:actagg[i + 1]]]
print 'player', i, 'uses the mixed strategy', out
else:
print 'Error: solver cannot find an equilibrium'
print("--- %s seconds ---" % (time.time() - start_time))
# Let's solve some parametrized problems
from FuncDesigner import *
from openopt import NLP, SNLE
# let's create parameterized triangle :
a,b,c = oovars(3)
T = Triangle((1,2,a),(2,b,4),(c,6.5,7))
# let's create an initial estimation to the problems below
startValues = {a:1, b:0.5, c:0.1} # you could mere set any, but sometimes a good estimation matters
# let's find an a,b,c values wrt r = 1.5 with required tolerance 10^-5, R = 4.2 and tol 10^-4, a+c == 2.5 wrt tol 10^-7
# if no tol is provided, p.contol is used (default 10^-6)
equations = [(T.r == 1.5)(tol=1e-5) , (T.R == 4.2)(tol=1e-4), (a+c == 2.5)(tol=1e-7)]
prob = SNLE(equations, startValues)
result = prob.solve('nssolve', iprint = 0) # nssolve is name of the solver involved
print('\nsolution has%s been found' % ('' if result.stopcase > 0 else ' not'))
print('values:' + str(result(a, b, c))) # [1.5773327492140974, -1.2582702179532217, 0.92266725078590239]
print('triangle sides: '+str(T.sides(result))) # [8.387574299361475, 7.0470774415247455, 4.1815836020856336]
print('orthocenter of the triangle: ' + str(T.H(result))) # [ 0.90789867 2.15008869 1.15609611]
# let's find minimum inscribed radius subjected to the constraints a<1.5, a>-1, b<0, a+2*c<4, log(1-b)<2] :
objective = T.r
prob = NLP(objective, startValues, constraints = [a<1.5, a>-1, b<0, a+2*c<4, log(1-b)<2])
result1 = prob.minimize('ralg', iprint = 0) # ralg is name of the solver involved, see http://openopt.org/ralg for details
print('\nminimal inscribed radius: %0.3f' % T.r(result1)) # 1.321
print('optimal values:' + str(result1(a, b, c))) # [1.4999968332804028, 2.7938728907900973e-07, 0.62272481283890913]
#let's find minimum outscribed radius subjected to the constraints a<1.5, a>-1, b<0, a+2*c<4, log(1-b)<2] :
prob = NLP(T.R, startValues, constraints = (a<1.5, a>-1, b<0, (a+2*c<4)(tol=1e-7), log(1-b)<2))
f = (lambda x: x[0]**3 + x[1]**3 - 9, lambda x: x[0] - 0.5 * x[1],
lambda x: cos(x[2]) + x[0] - 1.5)
# Python list, numpy.array are allowed as well:
#f = lambda x: [x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5]
#or f = lambda x: asfarray((x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5))
# start point
x0 = [8, 15, 80]
#optional: gradient
df = (lambda x: [3 * x[0]**2, 3 * x[1]**2, 0], lambda x: [1, -0.5, 0],
lambda x: [1, 0, -sin(x[2])])
#w/o gradient:
#p = NLSP(f, x0)
p = SNLE(f, x0, df=df)
#optional: user-supplied gradient check:
#p.checkdf()
#optional: graphical output, requires matplotlib installed
p.plot = 1
p.maxFunEvals = 1e5
p.iprint = 10
#r = p.solve('scipy_fsolve')
#r = p.solve('nssolve')
#or using converter nlsp2nlp, try to minimize sum(f_i(x)^2):
r = p.solve('nlp:ralg', plot=1)
f = (lambda x: x[0]**3 + x[1]**3 - 9, lambda x: x[0] - 0.5 * x[1],
lambda x: cos(x[2]) + x[0] - 1.5)
# Python list, numpy.array are allowed as well:
#f = lambda x: [x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5]
#or f = lambda x: asfarray((x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5))
# start point
x0 = [8, 15, 80]
#optional: gradient
df = (lambda x: [3 * x[0]**2, 3 * x[1]**2, 0], lambda x: [1, -0.5, 0],
lambda x: [1, 0, -sin(x[2])])
#w/o gradient:
#p = SNLE(f, x0)
p = SNLE(f, x0, df=df)
#optional: user-supplied gradient check:
#p.checkdf()
#optional: graphical output, requires matplotlib installed
p.plot = 1
#r = p.solve('scipy_fsolve')
r = p.solve('nssolve')
#or using converter to nlp, try to minimize sum(f_i(x)^2):
#r = p.solve('nlp:ralg')
print('solution: %s' % r.xf)
print('max residual: %e' % r.ff)
###############################
#f = lambda x: (x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5)
# or:
f = (lambda x: x[0]**3+x[1]**3-9, lambda x: x[0]-0.5*x[1], lambda x: cos(x[2])+x[0]-1.5)
# Python list, numpy.array are allowed as well:
#f = lambda x: [x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5]
#or f = lambda x: asfarray((x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5))
# start point
x0 = [8,15, 80]
#optional: gradient
df = (lambda x: [3*x[0]**2, 3*x[1]**2, 0], lambda x: [1, -0.5, 0], lambda x:[1, 0, -sin(x[2])])
#w/o gradient:
#p = NLSP(f, x0)
p = SNLE(f, x0, df = df)
#optional: user-supplied gradient check:
#p.checkdf()
#optional: graphical output, requires matplotlib installed
p.plot = 1
p.maxFunEvals = 1e5
p.iprint = 10
#r = p.solve('scipy_fsolve')
#r = p.solve('nssolve')
#or using converter nlsp2nlp, try to minimize sum(f_i(x)^2):
r = p.solve('nlp:ralg', plot=1)
## df[2,2] = cosh(x[2])
## return df
N = 100
desired_ftol = 1e-6
assert desired_ftol - noise*len(x0) > 1e-7
#w/o gradient:
scipy_fsolve_failed, fs = 0, []
print '----------------------------------'
print 'desired ftol:', desired_ftol, 'objFunc noise:', noise
############################################################################
print '---------- fsolve fails ----------'
t = time()
print 'N log10(MaxResidual) MaxResidual'
for i in xrange(N):
p = SNLE(f, x0, ftol = desired_ftol - noise*len(x0), iprint = -1, maxFunEvals = int(1e7))
r = p.solve('scipy_fsolve')
v = fvn(r.xf)
fs.append(log10(v))
if v > desired_ftol:
scipy_fsolve_failed += 1
print i+1, ' %0.2f ' % log10(v), v
else:
print i+1, 'OK'
print 'fsolve time elapsed', time()-t
#print 'fsolve_failed number:', scipy_fsolve_failed , '(from', N, '),', 100.0*scipy_fsolve_failed / N, '%'
print 'counters:', count1, count2, count3
############################################################################
count1 = count2 = count3 = 0
t = time()
print '---------- nssolve fails ---------'
from numpy import arange
x, y, z = oovars(3)
n = 5000
equations = (
x + 2 * y + 1 == 3 * z, # n equations
#x[i] + x[i+1] + y[i] + log(z[i]^2+15) = i+1, i = 0, 1, ..., n-1
x + hstack(
(x[1:n], x[0])) + y + log(z**2 + 15) == arange(1,
n + 1), # n equations
z + 2 * x + 5 * y == 100 # n equations
)
# you can use equations with custom tolerances
# equations = (x**3 + y**3 - 9==0, (x - 0.5*y==0)(tol=1e-9), (cos(z) + x == 1.5) (tol=1e-9))
# if no tol is assigned for an equation, p.ftol (default 10^-6) will be used for that one
startPoint = {x: [0] * n, y: [0] * n, z: [0] * n}
p = SNLE(equations, startPoint)
# for some OpenOpt SNLE solvers we can set some constraints
# p.constraints = [z<70, z>50, z + sin(x) < 60]
r = p.solve('matlab_fsolve', matlab='/usr/local/MATLAB/R2012a/bin/matlab')
# Notebook Intel Atom 1.6 GHz:
# Solver: Time Elapsed = 189.23 (MATLAB preload time ~ 30 sec)
# peak memory consumption for n = 5000 (thus 15000 variables) 160 MB
#f = lambda x: (x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5)
# or:
f = (lambda x: x[0]**3+x[1]**3-9, lambda x: x[0]-0.5*x[1], lambda x: cos(x[2])+x[0]-1.5)
# Python list, numpy.array are allowed as well:
#f = lambda x: [x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5]
#or f = lambda x: asfarray((x[0]**3+x[1]**3-9, x[0]-0.5*x[1], cos(x[2])+x[0]-1.5))
# start point
x0 = [8,15, 80]
#optional: gradient
df = (lambda x: [3*x[0]**2, 3*x[1]**2, 0], lambda x: [1, -0.5, 0], lambda x:[1, 0, -sin(x[2])])
#w/o gradient:
#p = SNLE(f, x0)
p = SNLE(f, x0, df = df)
#optional: user-supplied gradient check:
#p.checkdf()
#optional: graphical output, requires matplotlib installed
p.plot = 1
#r = p.solve('scipy_fsolve')
r = p.solve('nssolve')
#or using converter to nlp, try to minimize sum(f_i(x)^2):
#r = p.solve('nlp:ralg')
print('solution: %s' % r.xf)
print('max residual: %e' % r.ff)
###############################
def datafit(self,
event,
paramlinks,
groups=[],
ssrresult=None,
timeresult=None,
Main=False):
def errfunc(fit_params,
x=None,
y=None,
yerr=None,
consts=None,
traits=None,
groups=None,
snle_style=False):
fitrun = fitfunc(fit_params,
x,
consts,
traits,
groups,
return_oofunvalue=True,
snle_style=snle_style)
#print "Fit Params: " + str(fitrun)
#print "Bad Fit Adjust: " + str(ssr_mod_for_bad_fit[0])
if snle_style:
try:
if fitrun[0]:
fitrun[2].append(0 == ((fitrun[1] - y) /
(array(yerr) + 1.0))**2.0)
return [fitrun[2], fitrun[3], fitrun[4]]
except:
if fitrun[0]:
fitrun[2].append(0 == ((fitrun[1] - y) /
(array(yerr) + 1.0))**2.0)
return [fitrun[2], fitrun[3]]
else:
return ((fitrun - y) / (array(yerr) + 1.0))**2.0
#*(1.0+ssr_mod_for_bad_fit)
def fitfunc(fit_params,
x,
consts=None,
traits=None,
groups=None,
return_oofunvalue=False,
snle_style=False):
reload(self.Parent.Parent.model)
tempparam = OrderedDict()
k = 0
m = 0
templist = list()
for j in range(len(paramlinks.keys())):
key = paramlinks.keys()[j]
if (paramlinks[key][2].IsChecked()):
tempparam[key] = fit_params[k]
k += 1
elif (Main == True
and self.use_individual_fit_params[key].GetValue()):
tempparam[key] = list()
for group in groups:
tempparam[key].append(
list(
float(self.individualparamentrylinks[group]
[key][1].GetValue()) *
ones(len(Data.currentdata.x(groups=group)))))
tempparam[key] = array(sum(tempparam[key], []))
else:
try:
tempparam[key] = consts[m]
m += 1
except:
pass
tempparam["x"] = x
tempparam.update(traits)
#print "Fit Params: "+str(fit_params)
#print "x values: "+str(x)
#print "consts: "+str(consts)
#print "traits: "+str(traits)
#print "Results:" +str(self.Parent.Parent.model.func(x, tempparam, traits))
return self.Parent.Parent.model.func(
tempparam,
return_oofunvalue=return_oofunvalue,
snle_style=snle_style)
# Find Current Params
params = OrderedDict()
for param in paramlinks.keys():
params[param] = float(paramlinks[param][1].GetValue())
# Check for empty groups
if groups == []:
return False
#from scipy.optimize import leastsq
t = time()
#results = fitting.solve('nlp:scipy_slsqp', iprint = 1)
#results = fitting.solve('nlp:lincher', iprint = 1)
print_level = 10
# Best so far
if Data.constrained and Data.snle:
#fitting = NLLSP(
p0 = list()
consts = list()
ibounds = list()
sp = OrderedDict()
# Setup fitted params and consts
for j in range(len(params.keys())):
key = params.keys()[j]
value = params.values()[j]
if paramlinks[key][2].IsChecked():
try:
point = oovar(size=len(value))
except TypeError:
point = oovar()
p0.append(point)
sp[point] = value
ibounds.append(Data.param_upper_bounds[key] > p0[-1] >
Data.param_lower_bounds[key])
else:
consts.append(array(value))
equations = []
startpoint = []
equations = errfunc(p0,
y=Data.currentdata.y(groups=groups),
yerr=Data.currentdata.yerr(groups=groups),
consts=consts,
traits=Data.currentdata.traits(groups=groups),
x=Data.currentdata.x(groups=groups),
groups=groups,
snle_style=True)
startpoint = equations[1]
startpoint.update(sp)
print startpoint
fitting = SNLE(
equations[0],
startpoint,
ftol=1e-10,
)
equations[2].extend(ibounds)
fitting.constraints = equations[2]
#results = fitting.solve('nlp:ralg', iprint=print_level)
results = fitting.solve('nssolve', iprint=print_level, maxIter=1e8)
p1 = results.xf
for key in p1:
try:
params[key]
params[key] = p1[key]
except:
pass
elif (not Data.constrained) and (not Data.snle):
p0 = list()
consts = list()
ub = list()
lb = list()
# Setup fitted params and consts
for j in range(len(params.keys())):
key = params.keys()[j]
value = params.values()[j]
if paramlinks[key][2].IsChecked():
p0.append(array(value))
ub.append(Data.param_upper_bounds[key])
lb.append(Data.param_lower_bounds[key])
else:
consts.append(array(value))
equations = partial(
errfunc,
y=Data.currentdata.y(groups=groups),
yerr=Data.currentdata.yerr(groups=groups),
consts=consts,
traits=Data.currentdata.traits(groups=groups),
x=Data.currentdata.x(groups=groups),
groups=groups,
snle_style=False,
)
fitting = NLP(
equations,
p0,
)
results = fitting.solve('scipy_leastsq',
iprint=print_level,
maxIter=1e8)
p1 = results.xf
i = 0
for j in range(len(params.keys())):
key = params.keys()[j]
if paramlinks[key][2].IsChecked():
params[key] = p1[i]
i += 1
elif (Data.constrained) and (not Data.snle):
p0 = list()
consts = list()
ub = list()
lb = list()
# Setup fitted params and consts
for j in range(len(params.keys())):
key = params.keys()[j]
value = params.values()[j]
if paramlinks[key][2].IsChecked():
p0.append(array(value))
ub.append(Data.param_upper_bounds[key])
lb.append(Data.param_lower_bounds[key])
else:
consts.append(array(value))
fitting = NLP(
partial(
errfunc,
y=Data.currentdata.y(groups=groups),
yerr=Data.currentdata.yerr(groups=groups),
consts=consts,
traits=Data.currentdata.traits(groups=groups),
x=Data.currentdata.x(groups=groups),
groups=groups,
snle_style=False,
),
p0,
ub=ub,
lb=lb,
ftol=1e-16,
)
results = fitting.solve('ralg', iprint=print_level, maxIter=1e8)
#results = fitting.solve('nssolve', iprint = print_level, maxIter = 1e8)
p1 = results.xf
i = 0
for j in range(len(params.keys())):
key = params.keys()[j]
if paramlinks[key][2].IsChecked():
params[key] = p1[i]
i += 1
# Good if close
#results = fitting.solve('nlp:scipy_cobyla', iprint = 1)
#print('solution: '+str(results.xf)+'\n||residuals||^2 = '+str(results.ff)+'\nresiduals: ')
if not Main:
#print groups
#print p1
#print Data.param_individual["3"].keys()
#print Data.param
try:
i = 0
for key in params.keys():
if paramlinks[key][2].IsChecked():
Data.param_individual[groups][key] = p1[i]
i += 1
except:
print "More than one group was passed, when there should have been only one."
#print Data.param_individual
"""
Cleanup and redraw
"""
for key in paramlinks.keys():
paramlinks[key][1].SetValue(str(params[key]))
self.Parent.Parent.plotpanel.Update()
self.xrange = Data.currentdata.x(groups=groups)
currentfitvalues = fitfunc(
p1,
Data.currentdata.x(groups=groups),
consts=consts,
traits=Data.currentdata.traits(groups=groups),
groups=groups)
#ssr = sum((currentfitvalues - Data.currentdata.y(groups=groups)) ** 2)
ssr = sum(
map(lambda x: x**2, currentfitvalues -
Data.currentdata.y(groups=groups))) / len(currentfitvalues)
#print "SSR:" + str(ssr)
Data.param = params
ssrresult.SetLabel("SSR: " + str(ssr))
timeresult.SetLabel("Time Elapsed: %f" % (time() - t))
self.Parent.Parent.plotpanel.Update()
beq = [1.]*n#dito
x0 = []
actagg = [0]
for i in range(n):
no_a_i = no_a[i]
Aeq.append([0.]*actagg[i] + [1.]*no_a_i + [0.]*(total_no_a-actagg[i]-no_a_i))
x0 = x0 + [1.0/no_a_i]*no_a_i
actagg.append(actagg[i]+no_a_i)
#multiplies the vectors strat and Delta(strat); this product has to be 0 in equilibrium
def product(x):
strat = []
for i in range(n):
strat.append(x[actagg[i]:actagg[i+1]])
return np.dot(x,Delta(strat))
p = SNLE(product,x0,lb=lb,ub=ub,Aeq=Aeq,beq=beq)
p.iprint = -1
r = p.solve('nssolve')
if r.stopcase==1:
print 'there is an equilibrium in which '
for i in range(n):
out = [round(item,3) for item in r.xf[actagg[i]:actagg[i+1]]]
print 'player',i,'uses the mixed strategy',out
else:
print 'Error: solver cannot find an equilibrium'
print("--- %s seconds ---" % (time.time() - start_time))
def calcRefineUB(self,observations,stars_dict):
#observations are an array of dictionaries for each observed reflection
#These can be taken at different energies, but should be elastic
hvectors = []
Uv = []
omt=[]
for i in range(0, len(observations)):
h = np.array([observations[i]['h'], observations[i]['k'], observations[i]['l']],'Float64')
hvectors.append(h)
'''
sys.stderr.write('i %3.4f \n'%(observations[i]['h'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['k'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['l'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['twotheta'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['theta'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['chi'],))
sys.stderr.write('i %3.4f \n'%(observations[i]['phi'],))
'''
theta =(observations[i]['theta']) #For us, theta is theta measured (or Lumsden's 's')
chi = (observations[i]['chi'])
phi = (observations[i]['phi'])
twotheta = (observations[i]['twotheta'])
ei=observations[i]['ei']
ef=observations[i]['ei'] #reflections are elastic!!!!
#omega = theta - twotheta/2.0 #diffraction...
omega=calc_om_elastic(h[0],h[1],h[2],ei,theta,stars_dict)
#omega=calc_om_inelastic(ei,ef,twotheta)
u1_phi=self.calc_u_phi(omega,chi,phi)
u1p,u2p,u3p=u1_phi
omt.append(omega)
#u1p = np.cos(omega)*np.cos(chi)*np.cos(phi) - np.sin(omega)*np.sin(phi)
#u2p = np.cos(omega)*np.cos(chi)*np.sin(phi) + np.sin(omega)*np.cos(phi)
#u3p = np.cos(omega)*np.sin(chi)
#reflections are elastic
q=calc_q_inelastic(ei,ei,twotheta)
#uv1p=q*u1p
#uv2p=q*u2p
#uv3p=q*u3p
#uv1p = 2.0*np.sin(twotheta/2) / wavelength * u1p
#uv2p = 2.0*np.sin(twotheta/2) / wavelength * u2p
#uv3p = 2.0*np.sin(twotheta/2) / wavelength * u3p
uv1p=(q/(2*np.pi))*u1p
uv2p=(q/(2*np.pi))*u2p
uv3p=(q/(2*np.pi))*u3p
#h1p[0] - (q1/(2*np.pi)) * u1[0]
Uv.append(uv1p)
Uv.append(uv2p)
Uv.append(uv3p)
x0 = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
p = SNLE(self.UBRefinementEquations, x0, args=(hvectors, Uv))#,contol=1e-15, ftol=1e-15,maxFunEvals=1e8,maxIter=1e5)
r = p.solve('nlp:ralg')
a = r.xf[0]
b = r.xf[1]
c = r.xf[2]
d = r.xf[3]
e = r.xf[4]
f = r.xf[5]
g = r.xf[6]
h = r.xf[7]
j = r.xf[8]
UB = 2*np.pi*np.array([[a, b, c], [d, e, f], [g, h, j]],'Float64')
return UB
def df(x):
df = zeros((3,3))
df[0,0] = 3*x[0]**2
df[0,1] = 3*x[1]**2
df[1,0] = 1
df[1,1] = -0.5
df[2,0] = 1
df[2,2] = -sin(x[2])
return df
x0 = [8,15, 80]
#w/o gradient:
#p = SNLE(f, x0)
p = SNLE(f, x0, df = df, maxFunEvals = 1e5, iprint = 10, plot=1, ftol = 1e-8, contol=1e-15)
#optional: user-supplied gradient check:
#p.checkdf()
#optional: graphical output, requires matplotlib installed
#p.plot = 1
#set some constraints
p.lb, p.ub = [-inf]*3, [inf]*3
p.lb[2], p.ub[2] = 145, 150
# you could try also comment/uncomment nonlinear constraints:
p.c = lambda x: (x[2] - 146)**2-1.5
# optional: gradient
p.dc = lambda x: asfarray((0, 0, 2*(x[2]-146)))
N = 100
desired_ftol = 1e-6
assert desired_ftol - noise * len(x0) > 1e-7
#w/o gradient:
scipy_fsolve_failed, fs = 0, []
print '----------------------------------'
print 'desired ftol:', desired_ftol, 'objFunc noise:', noise
############################################################################
print '---------- fsolve fails ----------'
t = time()
print 'N log10(MaxResidual) MaxResidual'
for i in xrange(N):
p = SNLE(f,
x0,
ftol=desired_ftol - noise * len(x0),
iprint=-1,
maxFunEvals=int(1e7))
r = p.solve('scipy_fsolve')
v = fvn(r.xf)
fs.append(log10(v))
if v > desired_ftol:
scipy_fsolve_failed += 1
print i + 1, ' %0.2f ' % log10(v), v
else:
print i + 1, 'OK'
print 'fsolve time elapsed', time() - t
#print 'fsolve_failed number:', scipy_fsolve_failed , '(from', N, '),', 100.0*scipy_fsolve_failed / N, '%'
print 'counters:', count1, count2, count3
############################################################################
count1 = count2 = count3 = 0
from numpy import arange
x, y, z = oovars(3)
n = 5000
equations = (
x + 2* y + 1 == 3*z, # n equations
#x[i] + x[i+1] + y[i] + log(z[i]^2+15) = i+1, i = 0, 1, ..., n-1
x+hstack((x[1:n], x[0])) + y + log(z**2 + 15) == arange(1, n+1), # n equations
z + 2*x + 5*y == 100 # n equations
)
# you can use equations with custom tolerances
# equations = (x**3 + y**3 - 9==0, (x - 0.5*y==0)(tol=1e-9), (cos(z) + x == 1.5) (tol=1e-9))
# if no tol is assigned for an equation, p.ftol (default 10^-6) will be used for that one
startPoint = {x:[0]*n, y:[0]*n, z:[0]*n}
p = SNLE(equations, startPoint)
# for some OpenOpt SNLE solvers we can set some constraints
# p.constraints = [z<70, z>50, z + sin(x) < 60]
r = p.solve('matlab_fsolve', matlab='/usr/local/MATLAB/R2012a/bin/matlab')
# Notebook Intel Atom 1.6 GHz:
# Solver: Time Elapsed = 189.23 (MATLAB preload time ~ 30 sec)
# peak memory consumption for n = 5000 (thus 15000 variables) 160 MB
