default=0)
options, args = parser.parse_args()
mode_type = args[0]
if mode_type == 'Imode':
efit_file_name = 'g_901_901_1415_q'
p_file_name = 'p1120907032.01012'
elif mode_type == 'Hmode':
efit_file_name = 'g1120815027.01075_001'
p_file_name = 'p1120815027.01075_001'
plot_EFIT = options.plot_EFIT
plot_pfile = options.plot_pfile
shift_Ti = options.shift_Ti
### read EFIT file
psip_n, Rgrid, Zgrid, F, p, ffprime, pprime, psirz, qpsi, rmag, zmag, nw, psiax, psisep = read_EFIT_file(
efit_file_name)
### find conversion relation from psi_pol to rhot_n
### rho_tor_spl takes psi_pol (not normalized) and calculates rhot (normalized)
rho_tor_spl, rhot_n = calc_rho_tor(psip_n, psiax, psisep, qpsi, nw)
f = open('q_profile.dat', 'w')
f.write('#1.rhot_n 2.q\n')
np.savetxt(f, np.column_stack((rhot_n, qpsi)))
f.close()
if plot_EFIT:
### plot pressure vs rhot_n
plt.plot(rhot_n, p, 'x', label='EFIT')
plt.xlabel('rhot_n')
plt.ylabel('P')
import re
from interp import *
from finite_differences import *
from read_EFIT_file import *
import math
e = 1.6 * 10**(-19)
a = 2.6863997038399379E-01
parser = op.OptionParser()
options, args = parser.parse_args()
lores_efit_file_name = args[0]
hires_efit_file_name = args[1]
### read EFIT file
psip_n_lores, Rgrid_lores, Zgrid_lores, F_lores, p_lores, ffprime_lores, pprime_lores, psirz_lores, qpsi_lores, rmag_lores, zmag_lores, nw_lores, psiax_lores, psisep_lores, Bctr_lores = read_EFIT_file(
lores_efit_file_name)
psip_n_hires, Rgrid_hires, Zgrid_hires, F_hires, p_hires, ffprime_hires, pprime_hires, psirz_hires, qpsi_hires, rmag_hires, zmag_hires, nw_hires, psiax_hires, psisep_hires, Bctr_hires = read_EFIT_file(
hires_efit_file_name)
rho_tor_spl_lores, rhot_n_lores = calc_rho_tor(psip_n_lores, psiax_lores,
psisep_lores, qpsi_lores,
nw_lores)
uni_rhot_lores = np.linspace(rhot_n_lores[0], rhot_n_lores[-1], 1000)
q_unirhot_lores = interp(rhot_n_lores, qpsi_lores, uni_rhot_lores)
shat_lores = fd_d1_o4(q_unirhot_lores,
uni_rhot_lores) * uni_rhot_lores / q_unirhot_lores
rho_tor_spl_hires, rhot_n_hires = calc_rho_tor(psip_n_hires, psiax_hires,
psisep_hires, qpsi_hires,
dummy = raw_input("WARNING: profile file must have rho_poloidal as second column! Press any key to continue.\n")
dummy = raw_input("Assuming ion charge is 1 and reference mass is deuterium (press any key to continue).\n")
rhot = data[:,0]
psi = data[:,1]**2
Ti = data[:,2]
ni = data[:,3]
mi = 1.673e-27
ee = 1.602e-19
mref = 2.0*mi
Z = 1.0
Lref, Bref, R_major, q0 = get_dimpar_pars(efit_file_name,0.9)
psip_n, Rgrid, Zgrid, F, p, ffprime, pprime, psirz, qpsi, rmag, zmag, nw,psiax,psisep = read_EFIT_file(efit_file_name)
print "R_major",R_major
print "Bref",Bref
print "psisep",psisep
print "psiax",psiax
psisep0 = psisep-psiax
print "psisep0",psisep0
#Get everything on the same even psi grid
psi0 = np.linspace(0.0,1.0,num=3000)
#interopolate rho_tor, n, T, qpsi
ni0 = interp(psi,ni,psi0)
Ti0 = interp(psi,Ti,psi0)
Ti0J = Ti0*1000.0*ee
import re from interp import * from finite_differences import * from read_EFIT_file import * import math e = 1.6*10**(-19) a = 2.6863997038399379E-01 parser = op.OptionParser() options,args = parser.parse_args() lores_efit_file_name = args[0] hires_efit_file_name = args[1] ### read EFIT file psip_n_lores, Rgrid_lores, Zgrid_lores, F_lores, p_lores, ffprime_lores, pprime_lores, psirz_lores, qpsi_lores, rmag_lores, zmag_lores, nw_lores, psiax_lores, psisep_lores, Bctr_lores = read_EFIT_file(lores_efit_file_name) psip_n_hires, Rgrid_hires, Zgrid_hires, F_hires, p_hires, ffprime_hires, pprime_hires, psirz_hires, qpsi_hires, rmag_hires, zmag_hires, nw_hires, psiax_hires, psisep_hires, Bctr_hires = read_EFIT_file(hires_efit_file_name) rho_tor_spl_lores, rhot_n_lores = calc_rho_tor(psip_n_lores, psiax_lores, psisep_lores, qpsi_lores, nw_lores) uni_rhot_lores = np.linspace(rhot_n_lores[0],rhot_n_lores[-1],1000) q_unirhot_lores = interp(rhot_n_lores,qpsi_lores,uni_rhot_lores) shat_lores = fd_d1_o4(q_unirhot_lores,uni_rhot_lores)*uni_rhot_lores/q_unirhot_lores rho_tor_spl_hires, rhot_n_hires = calc_rho_tor(psip_n_hires, psiax_hires, psisep_hires, qpsi_hires, nw_hires) uni_rhot_hires = np.linspace(rhot_n_hires[0],rhot_n_hires[-1],1000) q_unirhot_hires = interp(rhot_n_hires,qpsi_hires,uni_rhot_hires) shat_hires = fd_d1_o4(q_unirhot_hires,uni_rhot_hires)*uni_rhot_hires/q_unirhot_hires
def fields_fs_upper(efit_file_name,flux_surface,ngrid_r,ngrid_z,extra_r,extra_z):
fs = float(flux_surface)
psip_n, Rgrid, Zgrid, F, p, ffprime, pprime, psirz, qpsi, rmag, zmag, nw, psiax, psisep = read_EFIT_file(efit_file_name)
Z_fs = np.empty(0)
R_fs_out_grid = np.empty(0)
B_pol_fs_out = np.empty(0)
B_tor_fs_out = np.empty(0)
R_fs_in_grid = np.empty(0)
B_pol_fs_in = np.empty(0)
B_tor_fs_in = np.empty(0)
Z0_ind = np.argmin(abs(Zgrid-zmag))
#decrease Z from midplane until the lowest psip at that Z is larger than fs
while (np.min((psirz[Z0_ind,:]-psiax)/(psisep-psiax))<fs):
psi_pol = psirz[Z0_ind,:]
#Rmag_ind is the position of lowest psip at that Z
Rmag_ind = np.argmin(abs(psi_pol))
#R_fs_ind_out is the index of psip_n_temp that is on fs
psi_pol_out = psi_pol[Rmag_ind:].copy()
psip_n_temp = (psi_pol_out-psiax)/(psisep-psiax)
R_fs_ind_out = np.argmin(abs(psip_n_temp-fs))
#unif_R_out is a fine grid of Rgrid on the outer
unif_R_out = np.linspace(Rgrid[Rmag_ind],Rgrid[-1],nw*10)
psip_n_unifR_out = interp(Rgrid[Rmag_ind:],psip_n_temp,unif_R_out)
#psifs_ind_out is the postition of psip_n = fs
psifs_ind_out = np.argmin(abs(psip_n_unifR_out-fs))
#psip_n_fs_out is the local grid of psip_n around fs
psip_n_fs_out = psip_n_unifR_out[psifs_ind_out-ngrid_r:psifs_ind_out+ngrid_r].copy()
#R_fs_out is the local grid of R around fs
R_fs_out = unif_R_out[psifs_ind_out-ngrid_r:psifs_ind_out+ngrid_r].copy()
#B_pol_Z_out is the z component of B_pol at fs, B_pol_Z = 1/R d psip /d R
B_pol_Z_out = fd_d1_o4(psip_n_fs_out*(psisep-psiax)+psiax,R_fs_out)/R_fs_out
#B_tor = F/R
F_out = interp(psip_n,F,psip_n_fs_out)
B_tor_out = F_out/R_fs_out
#psi_pol_z selects ngrid_z points above and below (R_fs,Z0) from psirz
psi_pol_z = psirz[Z0_ind-ngrid_z:Z0_ind+ngrid_z,R_fs_ind_out+Rmag_ind]
#unif_z is a local fine grid of Z
unif_z = np.linspace(Zgrid[Z0_ind-ngrid_z],Zgrid[Z0_ind+ngrid_z],10*ngrid_z)
#psi_pol_unifz is a local grid of psi_pol
psi_pol_unifz = interp(Zgrid[Z0_ind-ngrid_z:Z0_ind+ngrid_z],psi_pol_z,unif_z)
#B_pol_R_out is the R component of B_pol at fs, B_pol_R = 1/R d psip/d Z
B_pol_R_out = fd_d1_o4(psi_pol_unifz,unif_z)/R_fs_out[ngrid_r]
#z_fs_ind is the position of Z0_ind in the newly constructed array unif_z
z_fs_ind=np.argmin(abs(unif_z-Zgrid[Z0_ind]))
#B_pol_out is the total B_pol field at psip=fs
B_pol_out = np.sqrt(B_pol_Z_out[ngrid_r]**2+B_pol_R_out[z_fs_ind]**2)
#similar procedure at inner side
psi_pol_in = psi_pol[:Rmag_ind].copy()
psip_n_temp = (psi_pol_in-psiax)/(psisep-psiax)
R_fs_ind_in = np.argmin(abs(psip_n_temp-fs))
unif_R_in = np.linspace(Rgrid[0],Rgrid[Rmag_ind],nw*10)
psip_n_unifR_in = interp(Rgrid[:Rmag_ind],psip_n_temp,unif_R_in)
psifs_ind_in = np.argmin(abs(psip_n_unifR_in-fs))
psip_n_fs_in = psip_n_unifR_in[psifs_ind_in-ngrid_r:psifs_ind_in+ngrid_r].copy()
R_fs_in = unif_R_in[psifs_ind_in-ngrid_r:psifs_ind_in+ngrid_r].copy()
B_pol_Z_in = fd_d1_o4(psip_n_fs_in*(psisep-psiax)+psiax,R_fs_in)/R_fs_in
F_in = interp(psip_n,F,psip_n_fs_in)
B_tor_in = F_in/R_fs_in
psi_pol_z = psirz[Z0_ind-ngrid_z:Z0_ind+ngrid_z,R_fs_ind_in]
psi_pol_unifz = interp(Zgrid[Z0_ind-ngrid_z:Z0_ind+ngrid_z],psi_pol_z,unif_z)
B_pol_R_in = fd_d1_o4(psi_pol_unifz,unif_z)/R_fs_in[ngrid_r]
B_pol_in = np.sqrt(B_pol_Z_in[ngrid_r]**2+B_pol_R_in[z_fs_ind]**2)
Z_fs = np.append(Z_fs,Zgrid[Z0_ind])
R_fs_out_grid = np.append(R_fs_out_grid,R_fs_out[ngrid_r])
B_pol_fs_out = np.append(B_pol_fs_out,B_pol_out)
B_tor_fs_out = np.append(B_tor_fs_out,B_tor_out[ngrid_r])
R_fs_in_grid = np.append(R_fs_in_grid,R_fs_in[ngrid_r])
B_pol_fs_in = np.append(B_pol_fs_in,B_pol_in)
B_tor_fs_in = np.append(B_tor_fs_in,B_tor_in[ngrid_r])
Z0_ind = Z0_ind-1
extra_Rgrid = np.linspace(R_fs_in[ngrid_r],R_fs_out[ngrid_r],extra_r)
extra_Zgrid = np.linspace(Zgrid[Z0_ind],Zgrid[Z0_ind+3],extra_z)
Zgrid_frame = Zgrid[Z0_ind-ngrid_z:Z0_ind+1+ngrid_z]
psip_extra_frame = np.empty([1+2*ngrid_z,extra_r])
psip_extra = np.empty([extra_z,extra_r])
for i in arange(0,2*ngrid_z+1):
psi_pol = psirz[Z0_ind-ngrid_z+i,:]
psip_extra_frame[i,:] = interp(Rgrid,psi_pol,extra_Rgrid)
#plt.plot(extra_Rgrid,psip_extra[i,:])
#plt.show()
for i in arange(0,extra_r):
psip_z_frame = psip_extra_frame[:,i]
psip_extra[:,i]=interp(Zgrid_frame,psip_z_frame,extra_Zgrid)
#plt.plot(extra_Zgrid,psip_extra[:,i],'.')
#plt.show()
B_pol_bottom_out = np.empty(0)
B_tor_bottom_out = np.empty(0)
R_bottom_out = np.empty(0)
B_pol_bottom_in = np.empty(0)
B_tor_bottom_in = np.empty(0)
R_bottom_in = np.empty(0)
for i in arange(0,extra_z):
psip_n_extra = (psip_extra[i,:]-psiax)/(psisep-psiax)
r_ind = np.argmin(psip_n_extra)
psip_n_extra_out = psip_n_extra[r_ind:].copy()
extra_r_ind_out = np.argmin(psip_n_extra_out-fs)
B_pol_Z_extra_out = \
fd_d1_o4(psip_n_extra_out*(psisep-psiax)+psiax,extra_Rgrid[r_ind:])/extra_Rgrid[r_ind:]
F_extra_out = interp(psip_n,F,psip_n_extra_out)
B_tor_extra_out = F_extra_out/extra_Rgrid[r_ind:]
B_pol_R_extra_out = \
fd_d1_o4(psip_extra[:,r_ind+extra_r_ind_out],extra_Zgrid)/extra_Rgrid[r_ind+extra_r_ind_out]
this_B_pol = np.sqrt(B_pol_R_extra_out[i]**2+B_pol_Z_extra_out[extra_r_ind_out]**2)
if this_B_pol>1.E-3 :
B_pol_bottom_out = np.append(B_pol_bottom_out,this_B_pol)
R_bottom_out = np.append(R_bottom_out,extra_Rgrid[r_ind+extra_r_ind_out])
B_tor_bottom_out = np.append(B_tor_bottom_out,B_tor_extra_out[extra_r_ind_out])
psip_n_extra_in = psip_n_extra[:r_ind].copy()
extra_r_ind_in = np.argmin(psip_n_extra_in-fs)
B_pol_Z_extra_in = \
fd_d1_o4(psip_n_extra_in*(psisep-psiax)+psiax,extra_Rgrid[:r_ind])/extra_Rgrid[:r_ind]
F_extra_in = interp(psip_n,F,psip_n_extra_in)
B_tor_extra_in = F_extra_in/extra_Rgrid[:r_ind]
B_pol_R_extra_in = \
fd_d1_o4(psip_extra[:,extra_r_ind_in],extra_Zgrid)/extra_Rgrid[extra_r_ind_in]
this_B_pol = np.sqrt(B_pol_R_extra_in[i]**2+B_pol_Z_extra_in[extra_r_ind_in]**2)
if this_B_pol>1.E-3 :
B_pol_bottom_in = np.append(B_pol_bottom_in,this_B_pol)
R_bottom_in = np.append(R_bottom_in,extra_Rgrid[extra_r_ind_in])
B_tor_bottom_in = np.append(B_tor_bottom_in,B_tor_extra_in[extra_r_ind_in])
R_bottom_out_r = np.flipud(R_bottom_out)
B_pol_bottom_out_r = np.flipud(B_pol_bottom_out)
B_tor_bottom_out_r = np.flipud(B_tor_bottom_out)
B_tot_bottom_out_r = np.sqrt(B_tor_bottom_out_r**2+B_pol_bottom_out_r**2)
B_tot_bottom_in = np.sqrt(B_tor_bottom_in**2+B_pol_bottom_in**2)
R_fs_out_grid_r = np.flipud(R_fs_out_grid)
B_pol_fs_out_r = np.flipud(B_pol_fs_out)
B_tor_fs_out_r = np.flipud(B_tor_fs_out)
B_tot_fs_out_r = np.sqrt(B_tor_fs_out_r**2+B_pol_fs_out_r**2)
B_tot_fs_in = np.sqrt(B_tor_fs_in**2+B_pol_fs_in**2)
#theta_out_r = np.arctan(abs(Z_fs)/R_fs_out_grid_r)
#theta_in = -np.arctan(abs(Z_fs)/R_fs_in_grid)+np.pi
R_fs = np.concatenate([R_fs_in_grid,R_bottom_in,R_bottom_out_r,R_fs_out_grid_r])
B_pol = np.concatenate([B_pol_fs_in,B_pol_bottom_in,B_pol_bottom_out_r,B_pol_fs_out_r])
B_tor = np.concatenate([B_tor_fs_in,B_tor_bottom_in,B_tor_bottom_out_r,B_tor_fs_out_r])
B_tot = np.concatenate([B_tot_fs_in,B_tot_bottom_in,B_tot_bottom_out_r,B_tot_fs_out_r])
#theta_fs = np.concatenate([theta_in,theta_out_r])
#f=open('fs_'+efit_file_name+'.dat','w')
#f.write('# R B_pol B_tor B_tot theta\n')
#np.savetxt(f,np.column_stack((R_fs,B_pol,B_tor,B_tot,theta_fs)))
#f.close()
return R_fs, B_pol, B_tor, B_tot
def fields_fs_lower(efit_file_name,flux_surface,ngrid_r,ngrid_z):
fs = float(flux_surface)
psip_n, Rgrid, Zgrid, F, p, ffprime, pprime, psirz, qpsi, rmag, zmag, nw, psiax, psisep = read_EFIT_file(efit_file_name)
Z_fs = np.empty(0)
R_fs_out_grid = np.empty(0)
B_pol_fs_out = np.empty(0)
B_tor_fs_out = np.empty(0)
R_fs_in_grid = np.empty(0)
B_pol_fs_in = np.empty(0)
B_tor_fs_in = np.empty(0)
Z0_ind = np.argmin(abs(Zgrid-zmag))
#decrease Z from midplane until the lowest psip at that Z is larger than fs
while (np.min((psirz[Z0_ind,:]-psiax)/(psisep-psiax))<fs):
psi_pol = psirz[Z0_ind,:]
#Rmag_ind is the position of lowest psip at that Z
Rmag_ind = np.argmin(abs(psi_pol))
psi_pol_out = psi_pol[Rmag_ind:].copy()
psip_n_temp = (psi_pol_out-psiax)/(psisep-psiax)
R_fs_ind_out = np.argmin(abs(psip_n_temp-fs))
#print ((psirz[Z0_ind,Rmag_ind+R_fs_ind_out]-psiax)/(psisep-psiax)-fs)/fs
unif_R_out = np.linspace(Rgrid[Rmag_ind],Rgrid[-1],nw*10)
psip_n_unifR_out = interp(Rgrid[Rmag_ind:],psip_n_temp,unif_R_out)
#psifs_ind_out is the postition of psip_n = fs
psifs_ind_out = np.argmin(abs(psip_n_unifR_out-fs))
#psip_n_fs_out is the local grid of psip_n around fs
psip_n_fs_out = psip_n_unifR_out[psifs_ind_out-ngrid_r:psifs_ind_out+ngrid_r].copy()
#R_fs_out is the local grid of R around fs
R_fs_out = unif_R_out[psifs_ind_out-ngrid_r:psifs_ind_out+ngrid_r].copy()
#B_pol_Z_out is the z component of B_pol at fs, B_pol_Z = 1/R d psip /d R
B_pol_Z_out = fd_d1_o4(psip_n_fs_out*(psisep-psiax)+psiax,R_fs_out)/R_fs_out
F_out = interp(psip_n,F,psip_n_fs_out)
B_tor_out = F_out/R_fs_out
# psi_pol_z selects ngrid_z points above and below Z0 and R_fs from psirz
psi_pol_z = psirz[Z0_ind-ngrid_z:Z0_ind+ngrid_z,R_fs_ind_out+Rmag_ind]
unif_z = np.linspace(Zgrid[Z0_ind-ngrid_z],Zgrid[Z0_ind+ngrid_z],10*ngrid_z)
psi_pol_unifz = interp(Zgrid[Z0_ind-ngrid_z:Z0_ind+ngrid_z],psi_pol_z,unif_z)
###plt.plot(Zgrid[Z0_ind-ngrid_z:Z0_ind+ngrid_z],psi_pol_z,'x')
###plt.plot(unif_z,psi_pol_unifz,'.')
###plt.show()
#B_pol_R_out is the R component of B_pol at fs, B_pol_R = 1/R d psip/d Z
B_pol_R_out = fd_d1_o4(psi_pol_unifz,unif_z)/R_fs_out[ngrid_r]
#z_fs_ind is the position of Z0_ind in the newly constructed array unif_z
z_fs_ind=np.argmin(abs(unif_z-Zgrid[Z0_ind]))
#B_pol_out is the total B_pol field at psip=fs
B_pol_out = np.sqrt(B_pol_Z_out[ngrid_r]**2+B_pol_R_out[z_fs_ind]**2)
#similar procedure at inner side
psi_pol_in = psi_pol[:Rmag_ind].copy()
psip_n_temp = (psi_pol_in-psiax)/(psisep-psiax)
R_fs_ind_in = np.argmin(abs(psip_n_temp-fs))
unif_R_in = np.linspace(Rgrid[0],Rgrid[Rmag_ind],nw*10)
psip_n_unifR_in = interp(Rgrid[:Rmag_ind],psip_n_temp,unif_R_in)
psifs_ind_in = np.argmin(abs(psip_n_unifR_in-fs))
psip_n_fs_in = psip_n_unifR_in[psifs_ind_in-ngrid_r:psifs_ind_in+ngrid_r].copy()
R_fs_in = unif_R_in[psifs_ind_in-ngrid_r:psifs_ind_in+ngrid_r].copy()
B_pol_Z_in = fd_d1_o4(psip_n_fs_in*(psisep-psiax)+psiax,R_fs_in)/R_fs_in
F_in = interp(psip_n,F,psip_n_fs_in)
B_tor_in = F_in/R_fs_in
psi_pol_z = psirz[Z0_ind-ngrid_z:Z0_ind+ngrid_z,R_fs_ind_in]
psi_pol_unifz = interp(Zgrid[Z0_ind-ngrid_z:Z0_ind+ngrid_z],psi_pol_z,unif_z)
B_pol_R_in = fd_d1_o4(psi_pol_unifz,unif_z)/R_fs_in[ngrid_r]
B_pol_in = np.sqrt(B_pol_Z_in[ngrid_r]**2+B_pol_R_in[z_fs_ind]**2)
Z_fs = np.append(Z_fs,Zgrid[Z0_ind])
R_fs_out_grid = np.append(R_fs_out_grid,R_fs_out[ngrid_r])
B_pol_fs_out = np.append(B_pol_fs_out,B_pol_out)
B_tor_fs_out = np.append(B_tor_fs_out,B_tor_out[ngrid_r])
R_fs_in_grid = np.append(R_fs_in_grid,R_fs_in[ngrid_r])
B_pol_fs_in = np.append(B_pol_fs_in,B_pol_in)
B_tor_fs_in = np.append(B_tor_fs_in,B_tor_in[ngrid_r])
Z0_ind = Z0_ind+1
R_fs_out_grid_r = np.flipud(R_fs_out_grid)
B_pol_fs_out_r = np.flipud(B_pol_fs_out)
B_tor_fs_out_r = np.flipud(B_tor_fs_out)
B_tot_fs_out_r = np.sqrt(B_tor_fs_out_r**2+B_pol_fs_out_r**2)
B_tot_fs_in = np.sqrt(B_tor_fs_in**2+B_pol_fs_in**2)
theta_out_r = np.arctan(abs(Z_fs)/R_fs_out_grid_r)
theta_in = -np.arctan(abs(Z_fs)/R_fs_in_grid)+np.pi
R_fs = np.concatenate([R_fs_in_grid,R_fs_out_grid_r])
B_pol = np.concatenate([B_pol_fs_in,B_pol_fs_out_r])
B_tor = np.concatenate([B_tor_fs_in,B_tor_fs_out_r])
B_tot = np.concatenate([B_tot_fs_in,B_tot_fs_out_r])
theta_fs = np.concatenate([theta_in,theta_out_r])
f=open('fs_'+efit_file_name+'.dat','w')
f.write('# R B_pol B_tor B_tot theta\n')
np.savetxt(f,np.column_stack((R_fs,B_pol,B_tor,B_tot,theta_fs)))
f.close()
return R_fs, B_pol, B_tor, B_tot
def fields_fs_lower(efit_file_name, flux_surface, ngrid_r, ngrid_z):
fs = float(flux_surface)
psip_n, Rgrid, Zgrid, F, p, ffprime, pprime, psirz, qpsi, rmag, zmag, nw, psiax, psisep = read_EFIT_file(
efit_file_name
)
Z_fs = np.empty(0)
R_fs_out_grid = np.empty(0)
B_pol_fs_out = np.empty(0)
B_tor_fs_out = np.empty(0)
R_fs_in_grid = np.empty(0)
B_pol_fs_in = np.empty(0)
B_tor_fs_in = np.empty(0)
Z0_ind = np.argmin(abs(Zgrid - zmag))
# decrease Z from midplane until the lowest psip at that Z is larger than fs
while np.min((psirz[Z0_ind, :] - psiax) / (psisep - psiax)) < fs:
psi_pol = psirz[Z0_ind, :]
# Rmag_ind is the position of lowest psip at that Z
Rmag_ind = np.argmin(abs(psi_pol))
psi_pol_out = psi_pol[Rmag_ind:].copy()
psip_n_temp = (psi_pol_out - psiax) / (psisep - psiax)
R_fs_ind_out = np.argmin(abs(psip_n_temp - fs))
# print ((psirz[Z0_ind,Rmag_ind+R_fs_ind_out]-psiax)/(psisep-psiax)-fs)/fs
unif_R_out = np.linspace(Rgrid[Rmag_ind], Rgrid[-1], nw * 10)
psip_n_unifR_out = interp(Rgrid[Rmag_ind:], psip_n_temp, unif_R_out)
# psifs_ind_out is the postition of psip_n = fs
psifs_ind_out = np.argmin(abs(psip_n_unifR_out - fs))
# psip_n_fs_out is the local grid of psip_n around fs
psip_n_fs_out = psip_n_unifR_out[psifs_ind_out - ngrid_r : psifs_ind_out + ngrid_r].copy()
# R_fs_out is the local grid of R around fs
R_fs_out = unif_R_out[psifs_ind_out - ngrid_r : psifs_ind_out + ngrid_r].copy()
# B_pol_Z_out is the z component of B_pol at fs, B_pol_Z = 1/R d psip /d R
B_pol_Z_out = fd_d1_o4(psip_n_fs_out * (psisep - psiax) + psiax, R_fs_out) / R_fs_out
F_out = interp(psip_n, F, psip_n_fs_out)
B_tor_out = F_out / R_fs_out
# psi_pol_z selects ngrid_z points above and below Z0 and R_fs from psirz
psi_pol_z = psirz[Z0_ind - ngrid_z : Z0_ind + ngrid_z, R_fs_ind_out + Rmag_ind]
unif_z = np.linspace(Zgrid[Z0_ind - ngrid_z], Zgrid[Z0_ind + ngrid_z], 10 * ngrid_z)
psi_pol_unifz = interp(Zgrid[Z0_ind - ngrid_z : Z0_ind + ngrid_z], psi_pol_z, unif_z)
###plt.plot(Zgrid[Z0_ind-ngrid_z:Z0_ind+ngrid_z],psi_pol_z,'x')
###plt.plot(unif_z,psi_pol_unifz,'.')
###plt.show()
# B_pol_R_out is the R component of B_pol at fs, B_pol_R = 1/R d psip/d Z
B_pol_R_out = fd_d1_o4(psi_pol_unifz, unif_z) / R_fs_out[ngrid_r]
# z_fs_ind is the position of Z0_ind in the newly constructed array unif_z
z_fs_ind = np.argmin(abs(unif_z - Zgrid[Z0_ind]))
# B_pol_out is the total B_pol field at psip=fs
B_pol_out = np.sqrt(B_pol_Z_out[ngrid_r] ** 2 + B_pol_R_out[z_fs_ind] ** 2)
# similar procedure at inner side
psi_pol_in = psi_pol[:Rmag_ind].copy()
psip_n_temp = (psi_pol_in - psiax) / (psisep - psiax)
R_fs_ind_in = np.argmin(abs(psip_n_temp - fs))
unif_R_in = np.linspace(Rgrid[0], Rgrid[Rmag_ind], nw * 10)
psip_n_unifR_in = interp(Rgrid[:Rmag_ind], psip_n_temp, unif_R_in)
psifs_ind_in = np.argmin(abs(psip_n_unifR_in - fs))
psip_n_fs_in = psip_n_unifR_in[psifs_ind_in - ngrid_r : psifs_ind_in + ngrid_r].copy()
R_fs_in = unif_R_in[psifs_ind_in - ngrid_r : psifs_ind_in + ngrid_r].copy()
B_pol_Z_in = fd_d1_o4(psip_n_fs_in * (psisep - psiax) + psiax, R_fs_in) / R_fs_in
F_in = interp(psip_n, F, psip_n_fs_in)
B_tor_in = F_in / R_fs_in
psi_pol_z = psirz[Z0_ind - ngrid_z : Z0_ind + ngrid_z, R_fs_ind_in]
psi_pol_unifz = interp(Zgrid[Z0_ind - ngrid_z : Z0_ind + ngrid_z], psi_pol_z, unif_z)
B_pol_R_in = fd_d1_o4(psi_pol_unifz, unif_z) / R_fs_in[ngrid_r]
B_pol_in = np.sqrt(B_pol_Z_in[ngrid_r] ** 2 + B_pol_R_in[z_fs_ind] ** 2)
Z_fs = np.append(Z_fs, Zgrid[Z0_ind])
R_fs_out_grid = np.append(R_fs_out_grid, R_fs_out[ngrid_r])
B_pol_fs_out = np.append(B_pol_fs_out, B_pol_out)
B_tor_fs_out = np.append(B_tor_fs_out, B_tor_out[ngrid_r])
R_fs_in_grid = np.append(R_fs_in_grid, R_fs_in[ngrid_r])
B_pol_fs_in = np.append(B_pol_fs_in, B_pol_in)
B_tor_fs_in = np.append(B_tor_fs_in, B_tor_in[ngrid_r])
Z0_ind = Z0_ind + 1
R_fs_out_grid_r = np.flipud(R_fs_out_grid)
B_pol_fs_out_r = np.flipud(B_pol_fs_out)
B_tor_fs_out_r = np.flipud(B_tor_fs_out)
B_tot_fs_out_r = np.sqrt(B_tor_fs_out_r ** 2 + B_pol_fs_out_r ** 2)
B_tot_fs_in = np.sqrt(B_tor_fs_in ** 2 + B_pol_fs_in ** 2)
theta_out_r = np.arctan(abs(Z_fs) / R_fs_out_grid_r)
theta_in = -np.arctan(abs(Z_fs) / R_fs_in_grid) + np.pi
R_fs = np.concatenate([R_fs_in_grid, R_fs_out_grid_r])
B_pol = np.concatenate([B_pol_fs_in, B_pol_fs_out_r])
B_tor = np.concatenate([B_tor_fs_in, B_tor_fs_out_r])
B_tot = np.concatenate([B_tot_fs_in, B_tot_fs_out_r])
theta_fs = np.concatenate([theta_in, theta_out_r])
f = open("fs_" + efit_file_name + ".dat", "w")
f.write("# R B_pol B_tor B_tot theta\n")
np.savetxt(f, np.column_stack((R_fs, B_pol, B_tor, B_tot, theta_fs)))
f.close()
return R_fs, B_pol, B_tor, B_tot
def fields_fs_upper(efit_file_name, flux_surface, ngrid_r, ngrid_z, extra_r, extra_z):
fs = float(flux_surface)
psip_n, Rgrid, Zgrid, F, p, ffprime, pprime, psirz, qpsi, rmag, zmag, nw, psiax, psisep = read_EFIT_file(
efit_file_name
)
Z_fs = np.empty(0)
R_fs_out_grid = np.empty(0)
B_pol_fs_out = np.empty(0)
B_tor_fs_out = np.empty(0)
R_fs_in_grid = np.empty(0)
B_pol_fs_in = np.empty(0)
B_tor_fs_in = np.empty(0)
Z0_ind = np.argmin(abs(Zgrid - zmag))
# decrease Z from midplane until the lowest psip at that Z is larger than fs
while np.min((psirz[Z0_ind, :] - psiax) / (psisep - psiax)) < fs:
psi_pol = psirz[Z0_ind, :]
# Rmag_ind is the position of lowest psip at that Z
Rmag_ind = np.argmin(abs(psi_pol))
# R_fs_ind_out is the index of psip_n_temp that is on fs
psi_pol_out = psi_pol[Rmag_ind:].copy()
psip_n_temp = (psi_pol_out - psiax) / (psisep - psiax)
R_fs_ind_out = np.argmin(abs(psip_n_temp - fs))
# unif_R_out is a fine grid of Rgrid on the outer
unif_R_out = np.linspace(Rgrid[Rmag_ind], Rgrid[-1], nw * 10)
psip_n_unifR_out = interp(Rgrid[Rmag_ind:], psip_n_temp, unif_R_out)
# psifs_ind_out is the postition of psip_n = fs
psifs_ind_out = np.argmin(abs(psip_n_unifR_out - fs))
# psip_n_fs_out is the local grid of psip_n around fs
psip_n_fs_out = psip_n_unifR_out[psifs_ind_out - ngrid_r : psifs_ind_out + ngrid_r].copy()
# R_fs_out is the local grid of R around fs
R_fs_out = unif_R_out[psifs_ind_out - ngrid_r : psifs_ind_out + ngrid_r].copy()
# B_pol_Z_out is the z component of B_pol at fs, B_pol_Z = 1/R d psip /d R
B_pol_Z_out = fd_d1_o4(psip_n_fs_out * (psisep - psiax) + psiax, R_fs_out) / R_fs_out
# B_tor = F/R
F_out = interp(psip_n, F, psip_n_fs_out)
B_tor_out = F_out / R_fs_out
# psi_pol_z selects ngrid_z points above and below (R_fs,Z0) from psirz
psi_pol_z = psirz[Z0_ind - ngrid_z : Z0_ind + ngrid_z, R_fs_ind_out + Rmag_ind]
# unif_z is a local fine grid of Z
unif_z = np.linspace(Zgrid[Z0_ind - ngrid_z], Zgrid[Z0_ind + ngrid_z], 10 * ngrid_z)
# psi_pol_unifz is a local grid of psi_pol
psi_pol_unifz = interp(Zgrid[Z0_ind - ngrid_z : Z0_ind + ngrid_z], psi_pol_z, unif_z)
# B_pol_R_out is the R component of B_pol at fs, B_pol_R = 1/R d psip/d Z
B_pol_R_out = fd_d1_o4(psi_pol_unifz, unif_z) / R_fs_out[ngrid_r]
# z_fs_ind is the position of Z0_ind in the newly constructed array unif_z
z_fs_ind = np.argmin(abs(unif_z - Zgrid[Z0_ind]))
# B_pol_out is the total B_pol field at psip=fs
B_pol_out = np.sqrt(B_pol_Z_out[ngrid_r] ** 2 + B_pol_R_out[z_fs_ind] ** 2)
# similar procedure at inner side
psi_pol_in = psi_pol[:Rmag_ind].copy()
psip_n_temp = (psi_pol_in - psiax) / (psisep - psiax)
R_fs_ind_in = np.argmin(abs(psip_n_temp - fs))
unif_R_in = np.linspace(Rgrid[0], Rgrid[Rmag_ind], nw * 10)
psip_n_unifR_in = interp(Rgrid[:Rmag_ind], psip_n_temp, unif_R_in)
psifs_ind_in = np.argmin(abs(psip_n_unifR_in - fs))
psip_n_fs_in = psip_n_unifR_in[psifs_ind_in - ngrid_r : psifs_ind_in + ngrid_r].copy()
R_fs_in = unif_R_in[psifs_ind_in - ngrid_r : psifs_ind_in + ngrid_r].copy()
B_pol_Z_in = fd_d1_o4(psip_n_fs_in * (psisep - psiax) + psiax, R_fs_in) / R_fs_in
F_in = interp(psip_n, F, psip_n_fs_in)
B_tor_in = F_in / R_fs_in
psi_pol_z = psirz[Z0_ind - ngrid_z : Z0_ind + ngrid_z, R_fs_ind_in]
psi_pol_unifz = interp(Zgrid[Z0_ind - ngrid_z : Z0_ind + ngrid_z], psi_pol_z, unif_z)
B_pol_R_in = fd_d1_o4(psi_pol_unifz, unif_z) / R_fs_in[ngrid_r]
B_pol_in = np.sqrt(B_pol_Z_in[ngrid_r] ** 2 + B_pol_R_in[z_fs_ind] ** 2)
Z_fs = np.append(Z_fs, Zgrid[Z0_ind])
R_fs_out_grid = np.append(R_fs_out_grid, R_fs_out[ngrid_r])
B_pol_fs_out = np.append(B_pol_fs_out, B_pol_out)
B_tor_fs_out = np.append(B_tor_fs_out, B_tor_out[ngrid_r])
R_fs_in_grid = np.append(R_fs_in_grid, R_fs_in[ngrid_r])
B_pol_fs_in = np.append(B_pol_fs_in, B_pol_in)
B_tor_fs_in = np.append(B_tor_fs_in, B_tor_in[ngrid_r])
Z0_ind = Z0_ind - 1
extra_Rgrid = np.linspace(R_fs_in[ngrid_r], R_fs_out[ngrid_r], extra_r)
extra_Zgrid = np.linspace(Zgrid[Z0_ind], Zgrid[Z0_ind + 3], extra_z)
Zgrid_frame = Zgrid[Z0_ind - ngrid_z : Z0_ind + 1 + ngrid_z]
psip_extra_frame = np.empty([1 + 2 * ngrid_z, extra_r])
psip_extra = np.empty([extra_z, extra_r])
for i in arange(0, 2 * ngrid_z + 1):
psi_pol = psirz[Z0_ind - ngrid_z + i, :]
psip_extra_frame[i, :] = interp(Rgrid, psi_pol, extra_Rgrid)
# plt.plot(extra_Rgrid,psip_extra[i,:])
# plt.show()
for i in arange(0, extra_r):
psip_z_frame = psip_extra_frame[:, i]
psip_extra[:, i] = interp(Zgrid_frame, psip_z_frame, extra_Zgrid)
# plt.plot(extra_Zgrid,psip_extra[:,i],'.')
# plt.show()
B_pol_bottom_out = np.empty(0)
B_tor_bottom_out = np.empty(0)
R_bottom_out = np.empty(0)
B_pol_bottom_in = np.empty(0)
B_tor_bottom_in = np.empty(0)
R_bottom_in = np.empty(0)
for i in arange(0, extra_z):
psip_n_extra = (psip_extra[i, :] - psiax) / (psisep - psiax)
r_ind = np.argmin(psip_n_extra)
psip_n_extra_out = psip_n_extra[r_ind:].copy()
extra_r_ind_out = np.argmin(psip_n_extra_out - fs)
B_pol_Z_extra_out = (
fd_d1_o4(psip_n_extra_out * (psisep - psiax) + psiax, extra_Rgrid[r_ind:]) / extra_Rgrid[r_ind:]
)
F_extra_out = interp(psip_n, F, psip_n_extra_out)
B_tor_extra_out = F_extra_out / extra_Rgrid[r_ind:]
B_pol_R_extra_out = (
fd_d1_o4(psip_extra[:, r_ind + extra_r_ind_out], extra_Zgrid) / extra_Rgrid[r_ind + extra_r_ind_out]
)
this_B_pol = np.sqrt(B_pol_R_extra_out[i] ** 2 + B_pol_Z_extra_out[extra_r_ind_out] ** 2)
if this_B_pol > 1.0e-3:
B_pol_bottom_out = np.append(B_pol_bottom_out, this_B_pol)
R_bottom_out = np.append(R_bottom_out, extra_Rgrid[r_ind + extra_r_ind_out])
B_tor_bottom_out = np.append(B_tor_bottom_out, B_tor_extra_out[extra_r_ind_out])
psip_n_extra_in = psip_n_extra[:r_ind].copy()
extra_r_ind_in = np.argmin(psip_n_extra_in - fs)
B_pol_Z_extra_in = (
fd_d1_o4(psip_n_extra_in * (psisep - psiax) + psiax, extra_Rgrid[:r_ind]) / extra_Rgrid[:r_ind]
)
F_extra_in = interp(psip_n, F, psip_n_extra_in)
B_tor_extra_in = F_extra_in / extra_Rgrid[:r_ind]
B_pol_R_extra_in = fd_d1_o4(psip_extra[:, extra_r_ind_in], extra_Zgrid) / extra_Rgrid[extra_r_ind_in]
this_B_pol = np.sqrt(B_pol_R_extra_in[i] ** 2 + B_pol_Z_extra_in[extra_r_ind_in] ** 2)
if this_B_pol > 1.0e-3:
B_pol_bottom_in = np.append(B_pol_bottom_in, this_B_pol)
R_bottom_in = np.append(R_bottom_in, extra_Rgrid[extra_r_ind_in])
B_tor_bottom_in = np.append(B_tor_bottom_in, B_tor_extra_in[extra_r_ind_in])
R_bottom_out_r = np.flipud(R_bottom_out)
B_pol_bottom_out_r = np.flipud(B_pol_bottom_out)
B_tor_bottom_out_r = np.flipud(B_tor_bottom_out)
B_tot_bottom_out_r = np.sqrt(B_tor_bottom_out_r ** 2 + B_pol_bottom_out_r ** 2)
B_tot_bottom_in = np.sqrt(B_tor_bottom_in ** 2 + B_pol_bottom_in ** 2)
R_fs_out_grid_r = np.flipud(R_fs_out_grid)
B_pol_fs_out_r = np.flipud(B_pol_fs_out)
B_tor_fs_out_r = np.flipud(B_tor_fs_out)
B_tot_fs_out_r = np.sqrt(B_tor_fs_out_r ** 2 + B_pol_fs_out_r ** 2)
B_tot_fs_in = np.sqrt(B_tor_fs_in ** 2 + B_pol_fs_in ** 2)
# theta_out_r = np.arctan(abs(Z_fs)/R_fs_out_grid_r)
# theta_in = -np.arctan(abs(Z_fs)/R_fs_in_grid)+np.pi
R_fs = np.concatenate([R_fs_in_grid, R_bottom_in, R_bottom_out_r, R_fs_out_grid_r])
B_pol = np.concatenate([B_pol_fs_in, B_pol_bottom_in, B_pol_bottom_out_r, B_pol_fs_out_r])
B_tor = np.concatenate([B_tor_fs_in, B_tor_bottom_in, B_tor_bottom_out_r, B_tor_fs_out_r])
B_tot = np.concatenate([B_tot_fs_in, B_tot_bottom_in, B_tot_bottom_out_r, B_tot_fs_out_r])
# theta_fs = np.concatenate([theta_in,theta_out_r])
# f=open('fs_'+efit_file_name+'.dat','w')
# f.write('# R B_pol B_tor B_tot theta\n')
# np.savetxt(f,np.column_stack((R_fs,B_pol,B_tor,B_tot,theta_fs)))
# f.close()
return R_fs, B_pol, B_tor, B_tot