def massLossRate(dat):
js =2
je = dat.Nx-1
ie = dat.Nz-1
ist = 2
ro = dat.dd[:,js]*dat.Dsc
# outer x boundary
mout1 = zeros(dat.Nz)
mout1[:] = 2.*pi* dat.Rsc*dat.x[je]* dat.u2[:, je]*dat.Usc* ro
mout1[:]=[0. if x<0. else x for x in mout1 ]
mdotTot1 = trapz(mout1, dat.z*dat.Rsc)
mout2 = zeros(dat.Nx)
# upper z boundary
mout2[:] = 2.*pi* dat.Rsc*dat.x[:]* dat.u1[ie, :]*dat.Usc* dat.dd[ie,:]*dat.Dsc
mdotTotUp = trapz(mout2, dat.x*dat.Rsc)
mout2[:] = 0.
# lower z boundary
mout2[:] = -2.*pi* dat.Rsc*dat.x[:]* dat.u1[ist, :]*dat.Usc* dat.dd[ist,:]*dat.Dsc
mdotTotBot = trapz(mout2, dat.x*dat.Rsc)
return(mdotTot1, mdotTotUp, mdotTotBot )
def turbulent_power_curve(self):
'''post processes the power curve for 10 minute average points in a class 3A turbulent environment to IEC standard'''
# Number of points in distribution
n = 10
# iec standard values for class A
I_ref = 0.16
b = 5.6
x = np.linspace(stats.norm.ppf(0.05), stats.norm.ppf(0.95), n) # linear spacing between 5th and 95th percentile
x0 = x
pdf = stats.norm.pdf(x)
powers = []
for v_w in self.v_ws_at_h_ref:
# calculating sigma of 90th quantile from IEC
sig = (I_ref * (.75 * v_w + b))
x = x0 * (sig / x0[-1])
x_ea = x + v_w
# calculates all the powers at the different points
y_ea = np.array(interp(x_ea, self.v_ws_at_h_ref, self.powers))
av = trapz(y_ea * pdf, x_ea) / trapz(pdf, x_ea)
powers.append(av)
self.powers_turb = powers
def is_up_major(self, iatom, anglars=['s', 'p', 'd']):
up_angs = [a + '+' for a in anglars]
down_angs = [a + '-' for a in anglars]
up_dos = [self.site_dos(iatom, s) for s in up_angs]
up_dos_sum = []
for di in up_dos:
x = np.array([self.energy, di])
e = x[0][x[0] < 0]
d = x[1][x[0] < 0]
up_dos_sum.append(trapz(d, x=e))
self.up_tot_dos = sum(up_dos_sum)
down_dos = [self.site_dos(iatom, s) for s in down_angs]
down_dos_sum = []
for di in down_dos:
x = np.array([self.energy, di])
e = x[0][x[0] < 0]
d = x[1][x[0] < 0]
down_dos_sum.append(trapz(d, x=e))
self.down_tot_dos = sum(down_dos_sum)
if self.up_tot_dos < self.down_tot_dos:
print('Warning: up down reversed so that up is major ')
return self.up_tot_dos > self.down_tot_dos
def get_major_minor_dos(self, iatom, anglars=['s', 'p', 'd']):
"""
return the DOS_major, DOS_minor.
Args:
iatom: index of atom or symnum.
anglars: orbital names without up/down. eg. ['s','p'] or [dxy,dxz]
"""
up_angs = [a + '+' for a in anglars]
down_angs = [a + '-' for a in anglars]
up_dos = [self.site_dos(iatom, s) for s in up_angs]
up_dos_sum = []
for di in up_dos:
x = np.array([self.energy, di])
e = x[0][x[0] < 0]
d = x[1][x[0] < 0]
up_dos_sum.append(trapz(d, x=e))
self.up_tot_dos = sum(up_dos_sum)
down_dos = [self.site_dos(iatom, s) for s in down_angs]
down_dos_sum = []
for di in down_dos:
x = np.array([self.energy, di])
e = x[0][x[0] < 0]
d = x[1][x[0] < 0]
down_dos_sum.append(trapz(d, x=e))
self.down_tot_dos = sum(down_dos_sum)
print(('up: %s, down: %s' % (self.up_tot_dos, self.down_tot_dos)))
if self.up_tot_dos > self.down_tot_dos:
return up_dos, down_dos
else:
return down_dos, up_dos
def X_binding(par, qw):
"""Computation of the exciton binding energy given the electron and hole
wave function and the variational parameter par
Defined in Eq. 15(b) of Mares and Chuang, J. Appl. Phys. 74, 1388 (1993)
Keyword arguments:
par -- variational parameter in [nm]
qw -- Object containing the electronic structure related magnitudes. See QW.
"""
lam = par * 1.0E-9
Ry = spc.physical_constants['Rydberg constant times hc in eV'][0]
R0 = Ry*qw.mu/qw.eps_r**2
aB = spc.physical_constants['Bohr radius'][0]
ax = aB*qw.eps_r/qw.mu
beta = ax/lam
C0 = R0*beta**2
C1 = -R0*4.0*beta
Ze = sp.zeros([1,qw.grid.shape[0]])
Ze[0,:] = qw.grid[:]
Zh = sp.zeros([qw.grid.shape[0],1])
Zh[:,0] = qw.grid[:]
X = 2.0*sp.absolute(Ze-Zh)/par
Fe = sp.zeros([1,qw.grid.shape[0]])
Fe[0,:] = qw.Elec.wf[:]**2
Fh = sp.zeros([qw.grid.shape[0],1])
Fh[:,0] = qw.Hole.wf[:]**2
Int = Fe * Fh * G_int(X)
Val = sp.trapz( sp.trapz(Int, Ze.flatten() ), Zh.flatten())
return C0 + C1 * Val
def Data_processing_python(data_name, R_int, R_out, W, X0):
import numpy as np
import scipy as sp
Max_elements = np.genfromtxt(data_name,
usecols=(0),
skip_header=0,
skip_footer=-1,
dtype=float,
unpack=True)
data = np.genfromtxt(data_name,
usecols=(0, 1),
skip_header=1,
skip_footer=Max_elements[0])
np.matrix(data)
g = np.genfromtxt(data_name,
usecols=(0),
skip_header=int(Max_elements[0] + 1.),
dtype=float,
unpack=True)
from scipy.interpolate import LinearNDInterpolator
f_cart = sp.interpolate.LinearNDInterpolator(data, g, rescale=False)
r = np.linspace(R_int, R_out, 4000)
o = np.linspace(-W * np.pi, W * np.pi, 4000)
x = np.linspace(X0, X0, 4000)
f = f_cart(r[:, np.newaxis] * np.cos(o[np.newaxis, :]) + x[:, np.newaxis],
r[:, np.newaxis] * np.sin(o[np.newaxis, :])) * (r[:,
np.newaxis])
G_theta = sp.trapz(sp.trapz(f, o[np.newaxis, :], axis=1), r, axis=0)
return G_theta
def __init__(self, xvals, yvals):
# if order is reversed, flip it
if xvals[0] > xvals[-1]:
xvals = xvals[::-1]
yvals = yvals[::-1]
# number of intervals to partition our range
nsamp = options['pdf']['numpart']
# for pdfs with tails, set the range for sampling
_range = options['pdf']['range']
range = [(1.0 - _range)/2.0, (1.0 + _range)/2.0]
self.x = xvals
self.cdfy = np.append([0.0], np.cumsum((np.diff(yvals)/2.0 + yvals[:-1])*np.diff(xvals)))
self.cdfy /= self.cdfy[-1]
# Trim tails that have grown to 10% of the range of the PDF
resample = False
mmin, mmax = self.ppf([0, 1])
dist = mmax - mmin
#print "range of pdf = [%s - %s]" % (mmin, mmax)
#print "range of PDF = [%s - %s]" % (xvals[0], xvals[-1])
#print "dist=%s" % dist
#print "proposed range = [%s - %s]" % (self.ppf(range[0]), self.ppf(range[1]))
#print "[%s , %s]" % ((mmin - self.ppf(range[0]))/dist, (mmax - self.ppf(range[1]))/dist)
if np.isnan(mmin) or abs((mmin - self.ppf(range[0])) / dist) > .1:
mmin = self.ppf(range[0])
resample = True
else:
mmin = xvals[0]
if np.isnan(mmax) or abs((mmax - self.ppf(range[1])) / dist) > .1:
mmax = self.ppf(range[1])
resample = True
else:
mmax = xvals[-1]
# resample if not even spacing
if not resample:
resample = not np.allclose(np.diff(xvals)[0], np.diff(xvals))
# resample if number of intervals is 10% too large or small
if not resample:
resample = np.abs(len(xvals) - nsamp) > (nsamp * .1)
if resample:
self.x = np.linspace(mmin, mmax, nsamp)
self.y = np.interp(self.x, xvals, yvals)
self.y = np.abs(self.y / trapz(self.y, self.x))
self.cdfy = np.append([0.0], np.cumsum((np.diff(self.y)/2.0 + self.y[:-1])*np.diff(self.x)))
else:
# normalize (integral must be 1.0)
self.y = yvals / trapz(yvals, self.x)
self.mean = trapz(self.x * self.y, self.x)
self.dev = np.sqrt(np.abs(trapz(self.y * (self.x - self.mean)**2, self.x)))
def diffraction_efficiency(str_gmsh_path, nm, lambda0, theta, d, eps_sub,
eps_sup, npt_integ, nb_slice, N_d_order):
decalage = 0
No_ordre = np.linspace(-N_d_order + decalage, N_d_order + decalage,
2 * N_d_order + 1)
x_slice = sc.linspace(-d / 2, d / 2, npt_integ)
k_sub = 2 * pi * sc.sqrt(eps_sub) / lambda0
k_sup = 2 * pi * sc.sqrt(eps_sup) / lambda0
alpha_sup = k_sup * sc.sin(theta)
beta_sup = sc.sqrt(k_sup**2 - alpha_sup**2)
beta_sub = sc.sqrt(k_sub**2 - alpha_sup**2)
s_t = sc.zeros((1, (2 * N_d_order + 1)), complex)[0, :]
s_r = sc.zeros((1, (2 * N_d_order + 1)), complex)[0, :]
Aeff_t = sc.zeros((nb_slice, 2 * N_d_order + 1), complex)
Aeff_r = sc.zeros((nb_slice, 2 * N_d_order + 1), complex)
Ez_diff_t = np.loadtxt('./Views/sub_field_cuts.out', usecols=[
8
]) + 1j * np.loadtxt('./Views/sub_field_cuts.out', usecols=[9])
Ez_diff_r = np.loadtxt('./Views/sup_field_cuts.out', usecols=[
8
]) + 1j * np.loadtxt('./Views/sup_field_cuts.out', usecols=[9])
Ez_diff_t = np.transpose(Ez_diff_t.reshape(npt_integ, nb_slice, order="F"))
Ez_diff_r = np.transpose(Ez_diff_r.reshape(npt_integ, nb_slice, order="F"))
for m1 in range(0, nb_slice):
slice_t = Ez_diff_t[m1, :]
slice_r = Ez_diff_r[m1, :]
alphat_t = alpha_sup + 2 * pi / (d) * No_ordre
alphat_r = alpha_sup + 2 * pi / (d) * No_ordre
betat_sup = sc.sqrt(k_sup**2 - alphat_r**2)
betat_sub = sc.sqrt(k_sub**2 - alphat_t**2)
for k in range(0, 2 * N_d_order + 1):
expalpha_t = sc.exp(-1j * alphat_t[k] * x_slice)
expalpha_r = sc.exp(-1j * alphat_r[k] * x_slice)
s_t[k] = sc.trapz(slice_t * expalpha_t, x=x_slice) / d
s_r[k] = sc.trapz(slice_r * expalpha_r, x=x_slice) / d
Aeff_t[m1, :] = (np.abs(s_t))**2 * betat_sub / beta_sup
Aeff_r[m1, :] = (np.abs(s_r))**2 * betat_sup / beta_sup
Rordre = np.mean(Aeff_r, axis=0)
Tordre = np.mean(Aeff_t, axis=0)
R = np.mean(np.sum(Aeff_r.real, axis=1))
T = np.mean(np.sum(Aeff_t.real, axis=1))
Q_lamel_in = np.loadtxt('./Views/temp-Q_lamel_in.txt')[1]
#[bit[1] for bit in [map(float, line.split()) for line in file('./Views/temp-Q_lamel_in.txt')]][0]
print('\n******************')
print('* ENERGY BALANCE *')
print('******************')
print('R = ', "%0.6f" % R, ' (standard dev slice2slice=',
sc.std(np.sum(Aeff_r.real, axis=1)), ')')
print('T = ', "%0.6f" % T, ' (standard dev slice2slice=',
sc.std(np.sum(Aeff_t.real, axis=1)), ')')
print('Q_lamel_in = ', "%0.6f" % Q_lamel_in)
print('------------------------')
print('TOTAL = ', "%0.6f" % (T + R + Q_lamel_in))
return [Rordre, Tordre, R, T, Q_lamel_in]
def rmse(self, individual, *f_args):
y = self.trajectory(individual, *f_args)
# 2/NT * ∫y0^2 dt from 0 to N*T.
ampl_ = np.sqrt(scipy.trapz(y[0, :]**2, x=self.x) * 2.0 / self.NT)
# 2/NTA^2 * ∫y1^2 dt from 0 to N*T.
omega_ = np.sqrt(
scipy.trapz(y[1, :]**2, x=self.x) * 2.0 / (self.NT * ampl_**2))
rmse_ampl = utils.numeric.rmse(self.ampl, ampl_)
rmse_omega = utils.numeric.rmse(self.omega, omega_)
# Alternative measure.
# rmse_ampl = utils.numeric.rmse(self.ampl * np.sin(self.omega * self.x), y[0, :])
# rmse_omega = utils.numeric.rmse(self.ampl * self.omega * np.cos(self.omega * self.x), y[1, :])
return assessment.replace_nan((rmse_ampl, rmse_omega))
def testConversion(self):
#loadFiles()
readerSIG = HarmonieReader(os.path.join(parentdir, "test.SIG"))
print("Saving a copy in the BDF format...")
readerSIG.saveAsEDF(os.path.join(parentdir, "test.bdf"),
"BDF",
annotationFileName=os.path.join(
parentdir, "test Annotations.bdf"))
print("Reading the saved BDF file...")
readerEDF = EDFReader(os.path.join(parentdir, "test.BDF"),
annotationFileName=os.path.join(
parentdir, "test Annotations.bdf"))
channelListSig = readerSIG.getChannelLabels()
channelListEdf = readerEDF.getChannelLabels()
# For each pages, verify that the signals in reader and readerEDF
# are essentially the same by verifying their signal-to-noise ratio
for noPage in range(readerSIG.getNbRecords()):
# We test only complete pages since incomplete pages will be
# different for the two formats, the EDF format padding zeros
# at the end of the page to make complete records.
if readerSIG.getInfoRecords(noPage + 1).isComplete:
pageSIG = readerSIG.readRecord(channelListSig, noPage + 1)
pageEDF = readerEDF.readRecord(channelListEdf, noPage + 1)
for channelSig, channelEdf in zip(channelListSig,
channelListEdf):
Y1 = pageSIG.getSignal(channelSig)
Y2 = pageEDF.getSignal(channelEdf)
SNR = 10.0 * log10(trapz(Y1**2) / trapz((Y1 - Y2)**2))
print(("noPage=", noPage + 1, "(of ",
readerSIG.getNbRecords(), ")", "channel=",
channelSig, "SNR=", SNR))
if channelSig != "Mic-Mic" and SNR < 50.0:
import pylab
pylab.plot(list(range(len(Y1))), Y1)
pylab.plot(list(range(len(Y2))), Y2)
pylab.show()
self.failIf(channelSig != "Mic-Mic" and SNR < 50.0)
else:
print(("Skiping incomplete page " + str(noPage + 1)))
def bandpower(signal, fs, fmin, fmax):
'''
This function calculates the bandpower of a selected frequency range.
Parameters
----------
signal : array (1-dim)
Signal for which the bandpower is calculated.
fs : float or int
Sampling rate of the input signal [Hz].
fmin : float or int
Lower limiting frequency of the power band [Hz].
fmax : float or int
Upper limiting frequency of the power band [Hz].
Returns
-------
float
Bandpower of the choosen frequency range.
'''
f, Pxx = scipy.signal.periodogram(
signal, fs=fs) # Pxx has units of V**2/Hz if x is measured in V
ind_min = scipy.argmax(f > fmin) - 1 # get lower limiting frequency index
ind_max = scipy.argmax(f > fmax) - 1 # get upper limiting frequency index
return scipy.trapz(Pxx[ind_min:ind_max], f[ind_min:ind_max]
) # integrate selected power densitiy spectrum & return
def calc(x, fmin, fmax, fs=sample_freq):
x = np.asarray(x, dtype=np.float64)
f, Pxx = periodogram(x, fs=fs)
ind_min = scipy.argmax(f > fmin) - 1
ind_max = scipy.argmax(f > fmax) - 1
y = scipy.trapz(Pxx[ind_min: ind_max], f[ind_min: ind_max])
return y
def bandpower(f, Pxx, fmin, fmax):
""" integrate the power spectral density between fmin and fmax
using the trapezoidal method
"""
ind_min = scipy.argmax(f > fmin) - 1
ind_max = scipy.argmax(f > fmax) - 1
return scipy.trapz(Pxx[ind_min: ind_max], f[ind_min: ind_max])
def compute_baseline(path,animal,trials):
BASELINE_INDEX = []
for trial in trials:
data = '{}/{}/{}_TRACES.csv'.format(path,trial,animal)
trace = np.genfromtxt(data,delimiter='').reshape((16,3,-1))
CHARGES = []
for i in range(trace.shape[0]):
sinus = trace[i,2,:]
clean_trace = sinus[np.logical_not(np.isnan(sinus))]
#Discard empty trials
if len(clean_trace) == 0:
continue
else:
charge = trapz(clean_trace,dx=0.0001)
CHARGES.append(charge)
BASELINE_INDEX.append(np.nanmean(CHARGES))
return [np.nanmean(BASELINE_INDEX), np.nanstd(BASELINE_INDEX),
np.nanstd(BASELINE_INDEX)/np.sqrt(len(BASELINE_INDEX))]
def compute_timecourse(path,animal,trials):
TIMECOURSE = []
for trial in trials:
data = '{}/{}/{}_TRACES.csv'.format(path,trial,animal)
trace = np.genfromtxt(data,delimiter='').reshape((16,3,-1))
CHARGES = []
for i in range(trace.shape[0]):
sinus = trace[i,2,:]
clean_trace = sinus[np.logical_not(np.isnan(sinus))]
#Discard empty trials
if len(clean_trace) == 0:
continue
else:
charge = trapz(clean_trace,dx=0.0001)
CHARGES.append(charge)
TIMECOURSE.append(np.nanmean(CHARGES))
return TIMECOURSE
def exchange(a, b, grid, end_point=-1):
abc, asc, al, aj = a # radial and angular for a
bbc, bsc, bl, bj = b # radial and angular for b
jmax, jmin = max(aj, bj), min(aj, bj)
ro, w, h = grid # radial grid and weights
end_ind = end_point < 0 and len(ro) or (sc.where(ro > end_point)[0][0]+1)
cabc = abc[:end_ind]
casc = asc[:end_ind]
cbbc = bbc[:end_ind]
cbsc = bsc[:end_ind]
cro = ro[:end_ind]
cw = w[:end_ind]
k = jmax - jmin
if (k+al+bl) % 2 != 0:
k += 1
dens0 = cabc*cbbc+casc*cbsc
dens_kg = dens0/cro**(k+1)
dens_kl = dens0*cro**k
res = 0e0
while (k <= (jmax+jmin)):
dens_g_int = cumtrapz(dens_kg*cw, initial=0e0)*h
# внешнее интегрирование от r до бесконечности
dens_g_int = dens_g_int[-1] - dens_g_int
dens_l_int = cumtrapz(dens_kl*cw, initial=0e0)*h
res_k = sc.trapz((dens_kg*dens_l_int+dens_kl*dens_g_int)*cw)*h
res += res_k*w3js0[(jmax, jmin, k)]
k += 2
dens_kg = dens_kg/cro**2
dens_kl = dens_kl*cro**2
return res
def bandpower(f, Pxx, fmin, fmax):
""" integrate the power spectral density between fmin and fmax
using the trapezoidal method
"""
ind_min = scipy.argmax(f > fmin) - 1
ind_max = scipy.argmax(f > fmax) - 1
return scipy.trapz(Pxx[ind_min: ind_max], f[ind_min: ind_max])
def compute(specter, lines):
h = 6.62606957 * 10**-34
c = 3 * 10**8
kb = 1.3806488 * 10**-23
temp = []
z = []
for row, spec in enumerate(np.transpose(specter)):
tempData = []
for key, line in enumerate(lines):
intLine = sp.trapz(spec[line[0]:line[1]])
#print(intLine)
lambdaNist = line[2]
Aki = line[3]
Ek = line[4]
g = line[5]
if intLine > 0:
nkgk = np.log(intLine / ((h * c * Aki * g) / lambdaNist))
tempData.append((Ek, nkgk))
if len(tempData) > 0:
tempArray = np.array(tempData)
print(tempArray)
koef = np.polyfit(tempArray[:, 0], tempArray[:, 1], 1)
temp.append(koef[0])
z.append(row)
print(temp)
plt.plot(z, temp)
plt.show()
def calc(x, fmin, fmax, fs):
x = np.asarray(x, dtype=np.float64)
f, Pxx = periodogram(x, fs=fs)
ind_min = argmax(f > fmin) - 1
ind_max = argmax(f > fmax) - 1
y = trapz(Pxx[ind_min: ind_max], f[ind_min: ind_max])
return y
def bandpower(seq, sampling_frequency, frequency_band, window_sec=None):
low, high = frequency_band
nperseg = (2 / low) * sampling_frequency
# f, Pxx = scipy.signal.periodogram(seq, fs=sampling_frequency)
f, Pxx = welch(seq, sampling_frequency, nperseg=nperseg)
ind_min = scipy.argmax(f > frequency_band[0]) - 1
ind_max = scipy.argmax(f > frequency_band[1]) - 1
return scipy.trapz(Pxx[ind_min:ind_max], f[ind_min:ind_max])
def sampleDerAlleles(phi, xx, ssize):
sf = np.zeros(ssize + 1)
for ii in xrange(0, 668): # int( ssize*0.01) ): # ssize+1
# binomial distribution
binomDist = lambda i, q: scipy.stats.binom.pmf(i, ssize, q)
biomd = binomDist(ii, xx)
sf[ii] = scipy.trapz(biomd * phi, xx)
return np.nan_to_num(sf)
def getSOC(power):
P=power
Voc = 400
R = 0.1
c=90 #in kwh
I = (Voc - math.sqrt(math.Voc** - 4*R*P))/2*R
SOC = np.trapz(Voc*I)/(c*3600*1000)
soc_percent = SOC*100
return soc_percent
def __convolveSphinx(self,star):
'''
Convolve the Sphinx output with the SPIRE resolution. The convolution
is done in wave number (cm^-1).
@param star: The Star() object for which Sphinx profiles are loaded
@type star: Star()
'''
#- Get sphinx model output and merge, for all star models in star_grid
if not self.resolution:
print '* Resolution is undefined. Cannot convolve Sphinx.'
return
print '* Reading Sphinx model and merging.'
sphinx_wav,sphinx_flux = star['LAST_GASTRONOOM_MODEL'] \
and self.mergeSphinx(star) \
or [[],[]]
if not sphinx_wav:
print '* No Sphinx data found.'
return
sphinx_wav = 1./array(sphinx_wav)*10**(4)
sphinx_flux = array(sphinx_flux)
sphinx_wav = sphinx_wav[::-1]
sphinx_flux = sphinx_flux[::-1]
#-- eliminate some of the zeroes in the grid to reduce calculation time
# (can reduce the array by a factor up to 100!!)
s = self.sigma
lcs = array(sorted([1./line.wavelength
for line in star['GAS_LINES']]))
new_wav, new_flux = [sphinx_wav[0]],[sphinx_flux[0]]
for w,f in zip(sphinx_wav[1:],sphinx_flux[1:]):
if f != 0 or (w < 5*s+lcs[argmin(abs(lcs-w))] \
and w > lcs[argmin(abs(lcs-w))]-5*s):
new_wav.append(w)
new_flux.append(f)
new_wav, new_flux = array(new_wav), array(new_flux)
#-- convolve the model fluxes with a gaussian and constant sigma(spire)
print '* Convolving Sphinx model for SPIRE.'
convolution = Data.convolveArray(new_wav,new_flux,s)
for data_wav,fn in zip(self.data_wave_list,self.data_filenames):
rebinned = []
#-- Convert wavelengths to wave number for integration, and reverse
data_cm = data_wav[::-1]
data_cm = 1./data_cm*10**4
rebinned = [trapz(y=convolution[abs(new_wav-wavi)<=self.resolution/self.oversampling],\
x=new_wav[abs(new_wav-wavi)<=self.resolution/self.oversampling])\
/(self.resolution/self.oversampling)
for wavi in data_cm]
#-- Reverse the rebinned fluxes so they match up with the
# wavelength grid.
rebinned = array(rebinned)[::-1]
self.sphinx_convolution[star['LAST_SPIRE_MODEL']][fn] = rebinned
def __convolveSphinx(self, star):
'''
Convolve the Sphinx output with the SPIRE resolution. The convolution
is done in wave number (cm^-1).
@param star: The Star() object for which Sphinx profiles are loaded
@type star: Star()
'''
#- Get sphinx model output and merge, for all star models in star_grid
if not self.resolution:
print '* Resolution is undefined. Cannot convolve Sphinx.'
return
print '* Reading Sphinx model and merging.'
sphinx_wav,sphinx_flux = star['LAST_GASTRONOOM_MODEL'] \
and self.mergeSphinx(star) \
or [[],[]]
if not sphinx_wav:
print '* No Sphinx data found.'
return
sphinx_wav = 1. / array(sphinx_wav) * 10**(4)
sphinx_flux = array(sphinx_flux)
sphinx_wav = sphinx_wav[::-1]
sphinx_flux = sphinx_flux[::-1]
#-- eliminate some of the zeroes in the grid to reduce calculation time
# (can reduce the array by a factor up to 100!!)
s = self.sigma
lcs = array(
sorted([1. / line.wavelength for line in star['GAS_LINES']]))
new_wav, new_flux = [sphinx_wav[0]], [sphinx_flux[0]]
for w, f in zip(sphinx_wav[1:], sphinx_flux[1:]):
if f != 0 or (w < 5*s+lcs[argmin(abs(lcs-w))] \
and w > lcs[argmin(abs(lcs-w))]-5*s):
new_wav.append(w)
new_flux.append(f)
new_wav, new_flux = array(new_wav), array(new_flux)
#-- convolve the model fluxes with a gaussian and constant sigma(spire)
print '* Convolving Sphinx model for SPIRE.'
convolution = Data.convolveArray(new_wav, new_flux, s)
for data_wav, fn in zip(self.data_wave_list, self.data_filenames):
rebinned = []
#-- Convert wavelengths to wave number for integration, and reverse
data_cm = data_wav[::-1]
data_cm = 1. / data_cm * 10**4
rebinned = [trapz(y=convolution[abs(new_wav-wavi)<=self.resolution/self.oversampling],\
x=new_wav[abs(new_wav-wavi)<=self.resolution/self.oversampling])\
/(self.resolution/self.oversampling)
for wavi in data_cm]
#-- Reverse the rebinned fluxes so they match up with the
# wavelength grid.
rebinned = array(rebinned)[::-1]
self.sphinx_convolution[star['LAST_SPIRE_MODEL']][fn] = rebinned
def _bandwidth(data, N=None, MIN=None, MAX=None):
'''
An implementation of the kde bandwidth selection method outlined in:
Z. I. Botev, J. F. Grotowski, and D. P. Kroese. Kernel density
estimation via diffusion. The Annals of Statistics, 38(5):2916-2957, 2010.
Based on the implementation in Matlab by Zdravko Botev.
Daniel B. Smith, PhD
https://github.com/Daniel-B-Smith/KDE-for-SciPy/blob/master/kde.py
Updated 1-23-2013
'''
# Parameters to set up the mesh on which to calculate
N = 2**14 if N is None else int(2**sp.ceil(sp.log2(N)))
if MIN is None or MAX is None:
minimum = min(data)
maximum = max(data)
Range = maximum - minimum
MIN = minimum - Range / 10 if MIN is None else MIN
MAX = maximum + Range / 10 if MAX is None else MAX
# Range of the data
R = MAX - MIN
# Histogram the data to get a crude first approximation of the density
M = len(data)
DataHist, bins = sp.histogram(data, bins=N, range=(MIN, MAX))
DataHist = DataHist / M
DCTData = scipy.fftpack.dct(DataHist, norm=None)
I = [iN * iN for iN in range(1, N)]
SqDCTData = (DCTData[1:] / 2)**2
# The fixed point calculation finds the bandwidth = t_star
guess = 0.1
try:
t_star = scipy.optimize.brentq(__fixed_point,
0,
guess,
args=(M, I, SqDCTData))
except ValueError:
print('Oops!')
return None
# Smooth the DCTransformed data using t_star
SmDCTData = DCTData * sp.exp(-sp.arange(N)**2 * sp.pi**2 * t_star / 2)
# Inverse DCT to get density
density = scipy.fftpack.idct(SmDCTData, norm=None) * N / R
mesh = [(bins[i] + bins[i + 1]) / 2 for i in range(N)]
bandwidth = sp.sqrt(t_star) * R
density = density / sp.trapz(density, mesh)
# return bandwidth, mesh, density
return bandwidth
def Lookback_Time(self, zt):
lenzt = len(zt)
th = 1 / self.Ho
E_zt = np.zeros(lenzt)
tL = np.zeros(lenzt)
t = np.zeros(lenzt)
for n in range(lenzt):
E_zt[n] = np.sqrt(omega_M * np.power((1.0 + zt[n]), 3) + omega_K * np.power((1.0 + zt[n]), 2) + omega_L)
integrating_quantity = (1.0 + zt[0:n]) * E_zt[0:n]
tL[n] = th * sp.trapz((1.0 / integrating_quantity), zt[0:n])
return tL / th
def get_fe_v1(df):
"""
计算总负载里程
"""
measdate = []
s_total = 0
if not df.empty:
measdate = df.index[0] # 时间
s_total = scipy.trapz(np.abs(df.speed)) * df.dt # 总里程
return measdate, s_total
def get_fe_v2(df):
"""
通过压力模式计算负载、空载里程指标
"""
measdate = []
s_total = 0
s_in_operation = 0
if not df.empty:
measdate = df.index[0] # 时间
idx = (df.in_force_control == 1)
re_iter = com_util.Reg.finditer(idx, 0.5 *
df.num_per_sec) # 负载时间大于0.5秒计入
s_total = scipy.trapz(np.abs(df.speed)) * df.dt # 总里程
for i in re_iter:
[stidx, edidx] = i.span()
s_in_operation += scipy.trapz(np.abs(
df.speed[stidx:edidx])) * df.dt # 负载里程
return measdate, s_total, s_in_operation, max(0,
s_total - s_in_operation)
def bandpower(x, fs, fmin, fmax):
if any(np.isnan(x)):
try:
x = interp_nans(x)
except:
print("except!")
return 0
f, Pxx = periodogram(x, fs=fs, nfft=len(x) * 10)
ind_min = argmax(f > fmin) - 1
ind_max = argmax(f > fmax) - 1
return trapz(Pxx[ind_min:ind_max], f[ind_min:ind_max])
def Lookback_Time(self, zt):
lenzt = len(zt)
th = 1 / self.Ho
E_zt = np.zeros(lenzt)
tL = np.zeros(lenzt)
t = np.zeros(lenzt)
for n in range(lenzt):
E_zt[n] = np.sqrt(omega_M * np.power((1. + zt[n]), 3) +
omega_K * np.power((1. + zt[n]), 2) + omega_L)
integrating_quantity = (1. + zt[0:n]) * E_zt[0:n]
tL[n] = th * sp.trapz((1. / integrating_quantity), zt[0:n])
return tL / th
def bandpower(x, fs, fmin, fmax):
'''
Taken (and adapted -- to not miss indexes) from the internet:
https://stackoverflow.com/questions/44547669/python-numpy-equivalent-of-bandpower-from-matlab
Based on the matlab function (bandpower)
INPUT:
x - time series
fs - sample rate to return the power in a specified frequency band
fmin - lower band of the frequency range
fmax - upper band of the frequency range
Return the average power in the frequency range
'''
f, Pxx = signal.periodogram(x, fs=fs)
ind_min = sp.argmax(f > fmin) - 1
ind_max = sp.argmax(f > fmax) - 1
if ind_max != 0:
var = sp.trapz(Pxx[ind_min:ind_max + 1], f[ind_min:ind_max + 1])
elif ind_max == 0:
var = sp.trapz(Pxx[ind_min:], f[ind_min:])
return var
def calculate_abspower(self, data, times, s_rate):
channel_num = len(data[0])
baseline_band_mat = []
for c in range(channel_num):
data = np.array(data)
# Welch- method for computing power spectral density
f, power = periodogram(
data[:, c], s_rate
) # is doing FFM, f is mask and power the power for every frequence in channel c
# f = frequencies (0-62,5)
# indices for alpha and theta freq
fmin_theta = 4
fmax_theta = 8
ind_min_theta = argmax(f > fmin_theta) - 1
ind_max_theta = argmax(f > fmax_theta) - 1
fmin_alpha = 8
fmax_alpha = 13
ind_min_alpha = argmax(f > fmin_alpha) - 1
ind_max_alpha = argmax(f > fmax_alpha) - 1
# calculate bandpower via integration
bandpower_alpha = trapz(power[ind_min_alpha:ind_max_alpha],
f[ind_min_alpha:ind_max_alpha])
bandpower_theta = trapz(power[ind_min_theta:ind_max_theta],
f[ind_min_theta:ind_max_theta])
abs_band = np.zeros(self.n_bands)
abs_band[0] = bandpower_theta
abs_band[1] = bandpower_alpha
# append for each channel
baseline_band_mat.append(abs_band)
return baseline_band_mat
def transform(F):
diff=Abel.diff(F)
nx = len(F)
x=np.arange(nx)
integral = sp.zeros(nx, dtype=float)
for i in range(0, nx-1):
divisor = sp.sqrt(x[i:nx]**2 - x[i]**2)
integrand = diff[i:nx] / divisor
integrand[0] = integrand[1] # deal with the singularity at x=r
integral[i] = - sp.trapz(integrand, x[i:nx]) / sp.pi
return(integral)
def transform(F):
diff = Abel.diff(F)
nx = len(F)
x = np.arange(nx)
integral = sp.zeros(nx, dtype=float)
for i in range(0, nx - 1):
divisor = sp.sqrt(x[i:nx]**2 - x[i]**2)
integrand = diff[i:nx] / divisor
integrand[0] = integrand[1] # deal with the singularity at x=r
integral[i] = -sp.trapz(integrand, x[i:nx]) / sp.pi
return (integral)
def bandpower_Pxx(Pxx, f, fmin, fmax):
'''
Adapted from (see below) to read directly the power spectrum
Taken (and adapted -- to not miss indexes) from the internet:
https://stackoverflow.com/questions/44547669/python-numpy-equivalent-of-bandpower-from-matlab
Based on the matlab function (bandpower)
INPUT:
Pxx - power spectrum
f - fequencies from the power spectrum
fmin - lower band of the frequency range
fmax - upper band of the frequency range
Return the average power in the frequency range by integrating
the power spectral density (PSD) estimate, pxx (usingthe trapezoidal rule)
'''
ind_min = sp.argmax(f > fmin) - 1
ind_max = sp.argmax(f > fmax) - 1
if ind_max != -1:
var = sp.trapz(Pxx[ind_min:ind_max + 1], f[ind_min:ind_max + 1])
elif ind_max == -1:
var = sp.trapz(Pxx[ind_min:], f[ind_min:])
return var
def integrate_evoked(evoked, axis=-1):
"""Integrate a peristumulus timecourse.
Parameters
----------
evoked : list of 2D arrays or 2D array
values of evoked datapoints
Returns
-------
int_evoked : squeezed array
evoked values integrated over the time dimension
"""
return sp.trapz(evoked, axis=axis)
def integrate_evoked(evoked, axis=-1):
"""Integrate a peristumulus timecourse.
Parameters
----------
evoked : list of 2D arrays or 2D array
values of evoked datapoints
Returns
-------
int_evoked : squeezed array
evoked values integrated over the time dimension
"""
return sp.trapz(evoked, axis=axis)
def coulumb(a, b, grid, end_point=-1):
abc, asc, al, aj = a # radial and angular for a
bbc, bsc, bl, bj = b # radial and angular for b
ro, w, h = grid # radial grid and weights
end_ind = end_point < 0 and len(ro) or (sc.where(ro > end_point)[0][0]+1)
cro = ro[:end_ind]
cw = w[:end_ind]
cabc = abc[:end_ind]
casc = asc[:end_ind]
cbbc = bbc[:end_ind]
cbsc = bsc[:end_ind]
bdens = cbbc**2 + cbsc**2
inner = 1./cro*cumtrapz(bdens*cw, initial=0e0)*h
outer = cumtrapz(bdens/cro*cw, initial=0e0)*h
outer = outer[-1] - outer # внешнее интегрирование от r до бесконечности
adens = cabc**2 + casc**2
res = sc.trapz(adens*(inner+outer)*cw)*h
return res
def Comoving_Distance(self, z):
# print self.Ho, "is Ho. \n"
Dh = self.Dh
E_z = np.zeros(len(z))
Dc = np.zeros(len(z))
for n in range(len(z)):
E_z[n] = np.sqrt(omega_M * np.power((1.0 + z[n]), 3.0) + omega_K * np.power((1.0 + z[n]), 2.0) + omega_L)
Dc[n] = Dh * sp.trapz((1.0 / E_z[0:n]), z[0:n])
# Dc[n]=Dh*sp.integrate.simps( (1.E_z[0:n]) , z[0:n] ,dx=666,axis=-1,even='avg')
if omega_K > 0:
Dm = Dh * (1.0 / np.sqrt(omega_K)) * np.sinh(np.sqrt(omega_K) * (Dc / Dh))
print "Omega k > 0 \n"
if omega_K == 0:
Dm = Dc
# print "Omega k = 0 \n"
if omega_K < 0:
Dm = Dh * (1.0 / np.sqrt(abs(omega_K))) * np.sin(np.sqrt(abs(omega_K)) * (Dc / Dh))
print "Omega k < 0 \n"
return Dm
def kde(data, N=None, MIN=None, MAX=None):
# Parameters to set up the mesh on which to calculate
N = 2**12 if N is None else int(2**sci.ceil(sci.log2(N)))
if MIN is None or MAX is None:
minimum = min(data)
maximum = max(data)
Range = maximum - minimum
MIN = minimum - Range/10 if MIN is None else MIN
MAX = maximum + Range/10 if MAX is None else MAX
# Range of the data
R = MAX-MIN
# Histogram the data to get a crude first approximation of the density
M = len(data)
DataHist, bins = sci.histogram(data, bins=N, range=(MIN,MAX))
DataHist = DataHist/M
DCTData = scipy.fftpack.dct(DataHist, norm=None)
I = [iN*iN for iN in range(1, N)]
SqDCTData = (DCTData[1:]/2)**2
# The fixed point calculation finds the bandwidth = t_star
guess = 0.1
try:
t_star = scipy.optimize.brentq(fixed_point, 0, guess,
args=(M, I, SqDCTData))
except ValueError:
print('Oops!')
return None
# Smooth the DCTransformed data using t_star
SmDCTData = DCTData*sci.exp(-sci.arange(N)**2*sci.pi**2*t_star/2)
# Inverse DCT to get density
density = scipy.fftpack.idct(SmDCTData, norm=None)*N/R
mesh = [(bins[i]+bins[i+1])/2 for i in range(N)]
bandwidth = sci.sqrt(t_star)*R
density = density/sci.trapz(density, mesh)
cdf = np.cumsum(density)*(mesh[1]-mesh[0])
return bandwidth, mesh, density, cdf
def exchange_melem(a, b, c, grid, end_point=-1):
abc, asc, al, aj = a # radial and angular for a
bbc, bsc, bl, bj = b # radial and angular for b
cbc, csc, cl, cj = c # radial and angular for c
if (cj != bj or cl != bl):
return 0e0 # only angle-diagonal elements are nonzero
jmax, jmin = max(aj, bj), min(aj, bj)
ro, w, h = grid # radial grid and weights
end_ind = end_point < 0 and len(ro) or (sc.where(ro > end_point)[0][0]+1)
cabc = abc[:end_ind]
casc = asc[:end_ind]
cbbc = bbc[:end_ind]
cbsc = bsc[:end_ind]
ccbc = cbc[:end_ind]
ccsc = csc[:end_ind]
cro = ro[:end_ind]
cw = w[:end_ind]
k = jmax - jmin
if (k+al+bl) % 2 != 0:
k += 1
dens0b = cabc*cbbc+casc*cbsc
dens0c = cabc*ccbc+casc*ccsc
dens_kgb = dens0b/cro**(k+1)
dens_klb = dens0b*cro**k
dens_kgc = dens0c/cro**(k+1)
dens_klc = dens0c*cro**k
res = 0e0
while (k <= (jmax+jmin)):
dens_g_int = cumtrapz(dens_kgc*cw, initial=0e0)*h
# внешнее интегрирование от r до бесконечности
dens_g_int = dens_g_int[-1] - dens_g_int
dens_l_int = cumtrapz(dens_klc*cw, initial=0e0)*h
res_k = sc.trapz((dens_kgb*dens_l_int+dens_klb*dens_g_int)*cw)*h
res += res_k*w3js0[(jmax, jmin, k)]
k += 2
dens_kgb = dens_kgb/cro**2
dens_klb = dens_klb*cro**2
dens_kgc = dens_kgc/cro**2
dens_klc = dens_klc*cro**2
return res
def coulumb_melem(a, b, c, grid, end_point=-1):
abc, asc, al, aj = a # radial and angular for a
bbc, bsc, bl, bj = b # radial and angular for b
cbc, csc, cl, cj = c # radial and angular for c
if (cl != bl or cj != bj):
return 0e0 # operator diagonal for angular variables
ro, w, h = grid # radial grid and weights
end_ind = end_point < 0 and len(ro) or (sc.where(ro > end_point)[0][0]+1)
cro = ro[:end_ind]
cw = w[:end_ind]
cabc = abc[:end_ind]
casc = asc[:end_ind]
cbbc = bbc[:end_ind]
cbsc = bsc[:end_ind]
ccbc = cbc[:end_ind]
ccsc = csc[:end_ind]
bdens = cbbc*ccbc + ccsc*cbsc
inner = 1./cro*cumtrapz(bdens*cw, initial=0e0)*h
outer = cumtrapz(bdens/cro*cw, initial=0e0)*h
outer = outer[-1] - outer # внешнее интегрирование от r до бесконечности
adens = cabc**2 + casc**2
res = sc.trapz(adens*(inner+outer)*cw)*h
return res
def compute(specter,lines):
h=6.62606957*10**-34
c=3*10**8
kb=1.3806488*10**-23
temp=[]
z=[]
for row, spec in enumerate(np.transpose(specter)):
tempData=[]
for key, line in enumerate(lines):
intLine = sp.trapz(spec[line[0]:line[1]])
#print(intLine)
lambdaNist=line[2]
Aki=line[3]
Ek=line[4]
g=line[5]
if intLine>0:
nkgk=np.log(intLine/((h*c*Aki*g)/lambdaNist))
tempData.append((Ek,nkgk))
if len(tempData)>0:
tempArray=np.array(tempData)
print(tempArray)
koef=np.polyfit(tempArray[:,0], tempArray[:,1], 1)
temp.append(koef[0])
z.append(row)
print(temp)
plt.plot(z,temp)
plt.show()
def energy(x, u):
return scipy.trapz(abs(u)**2, x)
def __init__(self, xvals, yvals):
# if order is reversed, flip it
if xvals[0] > xvals[-1]:
xvals = xvals[::-1]
yvals = yvals[::-1]
# number of intervals to partition our range
nsamp = options['pdf']['numpart']
# for pdfs with tails, set the range for sampling
_range = options['pdf']['range']
range = [(1.0 - _range)/2.0, (1.0 + _range)/2.0]
self.x = xvals
if len(xvals) == 1 or xvals[0] == xvals[-1]:
self.x = [xvals[0]]
self.y = [1]
self.cdfy = [1]
self.mean = xvals[0]
self.dev = 0
return
self.cdfy = np.append([0.0], np.cumsum((np.diff(yvals)/2.0 + yvals[:-1])*np.diff(xvals)))
self.cdfy /= self.cdfy[-1]
# Trim tails that have grown to 10% of the range of the PDF
resample = False
mmin, mmax = self.ppf([0, 1])
dist = mmax - mmin
if dist == 0.0:
self.x = [xvals[0]]
self.y = [1]
self.cdfy = [1]
self.mean = xvals[0]
self.dev = 0
return
# print "range of pdf = [%s - %s]" % (mmin, mmax)
# print "range of PDF = [%s - %s]" % (xvals[0], xvals[-1])
# print "dist=%s" % (dist)
# print "proposed range = [%s - %s]" % (self.ppf(range[0]), self.ppf(range[1]))
if np.isnan(mmin) or abs((mmin - self.ppf(range[0])) / dist) > .1:
mmin = self.ppf(range[0])
resample = True
else:
mmin = xvals[0]
if np.isnan(mmax) or abs((mmax - self.ppf(range[1])) / dist) > .1:
mmax = self.ppf(range[1])
resample = True
else:
mmax = xvals[-1]
# resample if not even spacing
if not resample:
resample = not np.allclose(np.diff(xvals)[0], np.diff(xvals))
# resample if number of intervals is 10% too large or small
if not resample:
resample = np.abs(len(xvals) - nsamp) > (nsamp * .1)
if resample:
self.x = np.linspace(mmin, mmax, nsamp)
self.y = np.interp(self.x, xvals, yvals)
self.y = np.abs(self.y / trapz(self.y, self.x))
self.cdfy = np.append([0.0], np.cumsum((np.diff(self.y)/2.0 + self.y[:-1])*np.diff(self.x)))
else:
# normalize (integral must be 1.0)
self.y = yvals / trapz(yvals, self.x)
self.mean = trapz(self.x * self.y, self.x)
self.dev = np.sqrt(np.abs(trapz(self.y * (self.x - self.mean)**2, self.x)))
for l in range(1,lmax):
k_star = 2/sp.exp(1)*(1-sp.log(2)/(2*l))*l/x
indices_term1 = (k_star < ks) & (ks < 1./R)
indices_term2 = ks >= 1./R
# if k_star < 1./R:
# indices_term1 = (k_star < ks) & (ks < 1./R)
# factor_term1 = 1
# else:
# indices_term1 = (1/R < ks) & (ks < k_star)
# factor_term1 = -1
integrand_term1 = 1./(ks[indices_term1]*x)**2*Pmk[indices_term1]
integrand_term2 = 1./((ks[indices_term2]*x)**2*(ks[indices_term2]*R))*Pmk[indices_term2]
integral_term1 = sp.trapz(integrand_term1,ks[indices_term1])
integral_term2 = sp.trapz(integrand_term2,ks[indices_term2])
C[l] = H**2*f**2/sp.pi*(integral_term1 + integral_term2)
#
#for l in range(1,lmax):
# C[l] = 4*sp.pi/(2*l+1)*(l*B[l-1]+(l+1)*B[l+1])
#
#
##plt.plot(ks,Pmk)
##plt.xscale('log')
##plt.yscale('log')
##plt.xlabel('$k [Mpc^{-1}]$')
##plt.ylabel('P(k) $[Mpc^{3}]$')
##plt.axis([0.001, 10, 1e-4, 1e5])
#
ls = sp.array(range(1,lmax+1))
# y=mdotOverTime
# ax.plot(timeArr, y)
# ax.plot(timeArr, log10(mdotOverTimeR))
# ax.plot(timeArr, (mdotOverTimeUD))
# set_fonts_etc(ax)
ax.plot(timeArr, log10(abs(mdotAccrAvr)))
show()
exit()
if (plotMassLoss):
mLost = trapz(mdotOverTime, timeArr* 4.8*10**3)
print("mLost=", mLost)
ax.plot(timeArr, (mdotOverTime))
#ax.plot(simTime, mv1)
plt.show()
def integrate(func_vals):
return sc.trapz(func_vals, self.grid)
for n in range(args.num + 1):
eigenvalue = eigenvalues[n]
eigenvector = eigenvectors[:, n]
eigenvector /= scipy.sqrt(util.energy(x, eigenvector))
eigenvectors[:, n] = eigenvector
mode_numbers = scipy.arange(args.num)
coefficients = scipy.zeros((len(t), len(mode_numbers)))
for n in mode_numbers:
eigenvector = eigenvectors[:, n]
for idx, _ in enumerate(t):
state = states[idx, :]
coefficient = scipy.trapz(eigenvector * state, x)
coefficients[idx, n] = abs(coefficient)
# coefficients[coefficients == 0] = None
# coefficients = scipy.log10(coefficients)
estimate = scipy.zeros(len(t))
for n in mode_numbers:
estimate += coefficients[:, n]**2
energy = scipy.zeros(len(t))
for idx, _ in enumerate(t):
energy[idx] = util.energy(x, states[idx, :])
# Sort the modes by maximum value at zero.
def kinEnergyLoss(dat):
i0 = dat.Nz - 3
dEkn = pi* dat.x[:]*dat.Rsc * dat.dd[:,js]*dat.Dsc * (dat.u1[i0, :]*dat.Usc)**3
ekinTot =trapz( 2.*dEkn, dat.x*dat.Rsc)
return(ekinTot)
from source_hfd_python.hfd_dat import Hfd
from scipy import trapz, exp, where
def str2nlj(s):
n = int(s[0])
l = 'spdfgh'.index(s[1])
j = float(s[2:s.find('/')])/2e0
return (n, l, j)
hfd = Hfd()
grid = (hfd.grid, hfd.weights, hfd.h)
nc = where(hfd.grid > 0.5)[0][0]
print(nc)
testgrid = exp(-hfd.grid)
res = trapz(testgrid[:nc]*hfd.weights[:nc])*hfd.h
print("test grid")
print("{} - {} = {}\n".format(res, (1-exp(-0.5)), res-1.0+exp(-0.5)))
rc = 5e-1
csn = sys.argv[1] # core shell
vsns = sys.argv[2:] # valent shells
ncc, lc, jc = str2nlj(csn)
p, q, en = hfd[csn]
print("norm function")
core_orb = (p, q, lc, jc)
norm2rc = trapz((p[:nc]**2+q[:nc]**2)*hfd.weights[:nc])*hfd.h
norm2 = trapz((p**2+q**2)*hfd.weights[:hfd.imax])*hfd.h
print("||{}||^2 = {}\t{}".format(csn, norm2rc, norm2))
v_orbs = []
for v in vsns:
nv, lv, jv = str2nlj(v)
def ctrapz(y, x):
x_shape = x.shape[0]
y_shape = 1
if y.ndim > 1:
y_shape = y.shape[0]
res = np.zeros(y_shape)
C_code = '''
#line 29 "ctrapz.py"
double result=0;
for(int j = 0; j < y_shape; j++){
for(int i = 0; i < x_shape-1; i++){
result += (y(i) + y(i+1)) / 2.0 * (x(i+1) - x(i));
};
res(j) = result;
result=0;
};
'''
weave.inline(C_code, ['x', 'y', 'x_shape', 'y_shape', 'res'], type_converters=weave.converters.blitz, compiler='gcc')
return res
if __name__ == '__main__':
x = np.array([1, 2, 3, 4])
y = np.array([3, 2, 3, 4])
print ctrapz(y, x)
print trapz(y, x)