def read_upar(self, lab_frame=False):
"""
Read the parallel velocity.
"""
self.upar_i = field.get_field(self.cdf_file, 'upar_igomega_by_mode', 0)
self.upar_e = field.get_field(self.cdf_file, 'upar_igomega_by_mode', 1)
if lab_frame:
for ix in range(self.nkx):
for iy in range(self.nky):
self.upar_i[:,ix,iy] = self.upar_i[:,ix,iy]* \
np.exp(1j * self.n0 * iy * \
self.omega * self.t)
self.upar_e[:,ix,iy] = self.upar_e[:,ix,iy]* \
np.exp(1j * self.n0 * iy * \
self.omega * self.t)
self.upar_i = field.field_to_real_space(self.upar_i)*self.rho_star
self.upar_e = field.field_to_real_space(self.upar_e)*self.rho_star
def read_tperp(self, lab_frame):
"""
Read the perpendicular temperature.
"""
self.tperp_i = field.get_field(self.cdf_file, 'tperp_igomega_by_mode', 0)
self.tperp_e = field.get_field(self.cdf_file, 'tperp_igomega_by_mode', 1)
if lab_frame:
for ix in range(self.nkx):
for iy in range(self.nky):
self.tperp_i[:,ix,iy] = self.tperp_i[:,ix,iy]* \
np.exp(1j * self.n0 * iy * \
self.omega * self.t)
self.tperp_e[:,ix,iy] = self.terp_e[:,ix,iy]* \
np.exp(1j * self.n0 * iy * \
self.omega * self.t)
# Convert to real space
self.tperp_i = field.field_to_real_space(self.tperp_i)*self.rho_star
self.tperp_e = field.field_to_real_space(self.tperp_e)*self.rho_star
def read_ntot(self, lab_frame=False):
"""
Read the 2D density fluctuations from the NetCDF file.
"""
self.ntot_i = field.get_field(self.cdf_file, 'ntot_igomega_by_mode', 0)
self.ntot_e = field.get_field(self.cdf_file, 'ntot_igomega_by_mode', 1)
if lab_frame:
for ix in range(self.nkx):
for iy in range(self.nky):
self.ntot_i[:,ix,iy] = self.ntot_i[:,ix,iy]* \
np.exp(1j * self.n0 * iy * \
self.omega * self.t)
self.ntot_e[:,ix,iy] = self.ntot_e[:,ix,iy]* \
np.exp(1j * self.n0 * iy * \
self.omega * self.t)
# Convert to real space
self.ntot_i = field.field_to_real_space(self.ntot_i)*self.rho_star
self.ntot_e = field.field_to_real_space(self.ntot_e)*self.rho_star
def calculate_zf_shear(self):
"""
Calculate the max rms zonal flow shear.
"""
phi_k = field.get_field(self.cdf_file, 'phi_igomega_by_mode', None)
self.kxfac = abs(self.qinp)/self.rhoc/abs(self.drho_dpsi)
zf_shear = 0.5 * self.kxfac * (- phi_k[:, :, 0]*self.kx[np.newaxis, :]**2).real * self.rho_star / self.rhoref
self.zf_shear_max = np.sqrt(np.mean(np.max(np.abs(zf_shear), axis=1)**2))
self.zf_shear_rms = np.sqrt(np.mean(zf_shear**2))
def calculate_zf_shear(self):
"""
Calculate the shear in the zonal flow velocity as a function of radius
and time.
"""
phi_k = field.get_field(self.cdf_file, 'phi_igomega_by_mode', None)
self.kxfac = abs(self.qinp)/self.rhoc/abs(self.drho_dpsi)
self.zf_shear = 0.5 * self.kxfac * \
np.fft.ifft(- phi_k[:, :, 0]*self.kx[np.newaxis, :]**2,
axis=1).real * \
self.nx * self.rho_star / self.rhoref
def read_phi(self, lab_frame=False):
"""
Read the electrostatic potenential from the NetCDF file.
"""
self.phi = field.get_field(self.cdf_file, 'phi_igomega_by_mode', None)
if lab_frame:
for ix in range(self.nkx):
for iy in range(self.nky):
self.phi[:,ix,iy] = self.phi[:,ix,iy]* \
np.exp(1j * self.n0 * iy * \
self.omega * self.t)
self.phi = field.field_to_real_space(self.phi)*self.rho_star
def calculate_v_zf(self, add_mean_flow=False):
"""
Calculate the zonal flow velocity as a function of radius and time.
The velocity is in units of vth.
"""
phi_k = field.get_field(self.cdf_file, 'phi_igomega_by_mode', None)
self.kxfac = abs(self.qinp)/self.rhoc/abs(self.drho_dpsi)
self.v_zf = 0.5 * self.kxfac * \
np.fft.ifft(-phi_k[:, :, 0] * self.kx[np.newaxis, :],
axis=1).imag * self.nx * self.rho_star
if add_mean_flow:
self.v_zf += self.r * self.g_exb / self.amin
def calculate_v_exb(self, lab_frame=False):
"""
Calculates the radial ExB velocity in real space in units of v_th,i.
"""
phi_k = field.get_field(self.cdf_file, 'phi_igomega_by_mode', None)
self.v_exb = 1j*self.ky*phi_k
if lab_frame:
for ix in range(self.nkx):
for iy in range(self.nky):
self.v_exb[:,ix,iy] = self.v_exb[:,ix,iy]* \
np.exp(1j * self.n0 * iy * \
self.omega * self.t)
self.v_exb = field.field_to_real_space(self.v_exb)* \
self.rho_star*self.vth
def calculate_q(self):
"""
Calculate the local heat flux Q(x, y) for the ion species.
"""
# Need phi as a function of kx, ky so read directly from netcdf file
self.phi = field.get_field(self.cdf_file, 'phi_igomega_by_mode', None)
self.read_ntot()
self.read_tperp()
self.read_tpar()
# Convert to real space
v_exb = field.field_to_real_space(1j*self.ky*self.phi)
ntot_i = self.ntot_i/self.rho_star
tperp_i = self.tperp_i/self.rho_star
tpar_i = self.tpar_i/self.rho_star
self.q = ((tperp_i + tpar_i/2 + 3/2*ntot_i)*v_exb).real/2
dnorm = self.dtheta/self.bmag/self.gradpar
wgt = np.sum(dnorm*self.grho)
self.q = self.q * dnorm[int(self.nth/2)] / wgt
