def file_read():
tolerance = 0.5
crs = []
for i in range(0, 53):
crs.append(open("The_3_fluxes_vs.angle_%d.txt" % (i), "r"))
#for i in range(0,24):
#next(crs[i])
angle = []
eq_fl = []
tur_fl = []
for i in range(0, 53):
for columns in (raw.strip().split() for raw in crs[i]):
angle.append(float(columns[0]))
eq_fl.append(float(columns[1]))
tur_fl.append(float(columns[2]))
excl_val = []
excl_val_2 = []
for elem in np.where(
np.isnan(eq_fl))[0][:]: #filter out nan values from fluxes
excl_val_2.append(elem)
for elem in sorted(excl_val_2, reverse=True):
del angle[elem]
del eq_fl[elem]
del tur_fl[elem]
excl_val_3 = []
for elem in np.where(np.isnan(tur_fl))[0][:]:
excl_val_3.append(elem)
for elem in sorted(excl_val_3, reverse=True):
del angle[elem]
del eq_fl[elem]
del tur_fl[elem]
for i in range(0, len(angle) - 1): #remove duplicates in angle
for j in range(i + 1, len(angle) - 1):
diff = abs(angle[i] - angle[j])
if (diff < tolerance) or (diff > 360 - tolerance):
excl_val.append(j)
for elem in sorted(excl_val, reverse=True):
del angle[elem]
del eq_fl[elem]
del tur_fl[elem]
excl_val = []
print(angle)
nul_pos = angle.index(min(angle)) #start all values from zero angle
#for i in range(0,len(angle)):
#if angle[i]<0.8:
#nul_pos = i
angle = np.roll(angle, -nul_pos)
eq_fl = np.roll(eq_fl, -nul_pos)
tur_fl = np.roll(tur_fl, -nul_pos)
print(angle)
plt.xlabel("angle")
plt.ylabel("fluxes")
plt.plot(angle[:], eq_fl[:], 'b-', angle[:], tur_fl[:], 'r-')
plt.show()
return angle, eq_fl, tur_fl
def file_read(verbose = False):
'''Reads all the files and joins the values in lists. Then, it filters duplicates and nans.'''
tolerance = 0.5
crs = []
for i in range(0,77): #ti253-IFS(0,61)/ti255-separatrix (0,60)
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_mag_fluxes_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_diamag_fluxes_vs.angle_%d.txt" %(i),"r"))
crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti262_mag_fluxes_vs.angle_%d.txt" %(i),"r"))
for i in range(0,77):
next(crs[i])
angle = []
mag_fl = []
R_value = []
Z_value = []
for i in range(0,77):
for columns in ( raw.strip().split() for raw in crs[i] ):
angle.append(float(columns[0]))
mag_fl.append(float(columns[1]))
R_value.append(float(columns[2]))
Z_value.append(float(columns[3]))
#filter out nan values from fluxes
excl_val_2 = []
for elem in np.where(np.isnan(mag_fl))[0][:]:
excl_val_2.append(elem)
for elem in sorted(excl_val_2,reverse=True):
del angle[elem]
del mag_fl[elem]
del R_value[elem]
del Z_value[elem]
#Keeping only one entry per angle, filtering out all others.
B = []
for i in range(0,len(angle)):
B.append(int(angle[i]))
for i in range(0,len(B)-1):
excl_val = []
for j in range(i+1,len(B)):
diff = abs(B[i]-B[j])
if (diff<tolerance) or (diff>360-tolerance):
excl_val.append(j)
if len(excl_val)>0:
for elem in sorted(excl_val,reverse=True):
del B[elem]
del angle[elem]
del mag_fl[elem]
del R_value[elem]
del Z_value[elem]
#start all values from zero angle.
nul_pos = angle.index(min(angle))
angle = np.roll(angle,-nul_pos)
mag_fl = np.roll(mag_fl,-nul_pos)
R_value = np.roll(R_value,-nul_pos)
Z_value = np.roll(Z_value,-nul_pos)
print(angle)
#returning the R-distance for the integral function.
Rnorm = []
for r,z in zip(R_value,Z_value):
Rnorm.append(r**2 + z**2)
R = R_value + core.Rmaj
#Plotting option
if verbose == True:
plt.xlabel("angle")
plt.ylabel("fluxes")
plt.plot(angle[:], mag_fl[:],'b-')
plt.show()
#new_file = open("DiaMag_flux_20_smoothes.txt",'a')
#new_file.write("angle"+"\t"+"DiaMagnetic"+"\t"+"R"+"\t"+"Z"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(mag_fl[i])+"\t"+str(R_value[i])+"\t"+str(Z_value[i])+"\n")
#new_file.close()
new_file = open("ti262_Mag_flux.txt",'a')
new_file.write("angle"+"\t"+"Magnetic"+"\t"+"R"+"\t"+"Z"+"\n")
for i in range(0,len(angle)):
new_file.write(str(angle[i])+"\t"+str(mag_fl[i])+"\t"+str(R_value[i])+"\t"+str(Z_value[i])+"\n")
new_file.close()
return angle, mag_fl, Rnorm, R
def file_read(verbose=True):
tolerance = 0.5
crs = []
for i in range(
0, 60
): #ti253-separatrix(0,60)/ti253-IFS(0,61)/ti255-separatrix (0,60)/ti262 (0,78)
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_temperatures_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_densities_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_turbulence_strength_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_magnetic_field_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_geom_magnetic_drift_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_ion_temperatures_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_magnetic_field_comp_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_magnetic_drifts_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_density_perturbation_strength_vs.angle_%d.txt" %(i),"r"))
crs.append(
open("/global/homes/g/giannos/xgc_python_dir/Check_%d.txt" % (i),
"r"))
#for i in range(0,60):
#next(crs[i])
angle = []
#gradBR = []
#gradBZ = []
#curvR = []
#curvZ = []
#Br = []
#Bz = []
#T_perp = []
#E_par = []
#geom = []
#Bp = []
#Bm = []
#den=[]
#te = []
#ti = []
#den_str = []
R = []
Z = []
for i in range(0, 60):
for columns in (raw.strip().split() for raw in crs[i]):
angle.append(float(columns[0]))
R.append(float(columns[1]))
Z.append(float(columns[2]))
#den_str.append(float(columns[1]))
#gradBR.append(float(columns[1]))
#gradBZ.append(float(columns[2]))
#curvR.append(float(columns[3]))
#curvZ.append(float(columns[4]))
#Br.append(float(columns[1]))
#Bz.append(float(columns[2]))
#T_perp.append(float(columns[1]))
#E_par.append(float(columns[2]))
#geom.append(float(columns[1]))
#Bp.append(float(columns[1]))
#Bm.append(float(columns[2]))
#den.append(float(columns[1]))
#ti.append(float(columns[1]))
#te.append(float(columns[2]))
excl_val_2 = []
for elem in np.where(
np.isnan(R))[0][:]: #filter out nan values from fluxes
excl_val_2.append(elem)
for elem in sorted(excl_val_2, reverse=True):
del angle[elem]
del R[elem]
del Z[elem]
#del den_str[elem]
#del gradBR[elem]
#del gradBZ[elem]
#del curvR[elem]
#del curvZ[elem]
#del Br[elem]
#del Bz[elem]
#del Bzeta[elem]
#del T_perp[elem]
#del E_par[elem]
#del geom[elem]
#del Bp[elem]
#del Bm[elem]
#del den[elem]
#del ti[elem]
#del te[elem]
excl_val_3 = []
for elem in np.where(np.isnan(Z))[0][:]:
excl_val_3.append(elem)
for elem in sorted(excl_val_3, reverse=True):
del angle[elem]
del R[elem]
del Z[elem]
#del gradBR[elem]
#del gradBZ[elem]
#del curvR[elem]
#del curvZ[elem]
#del Br[elem]
#del Bz[elem]
#del Bzeta[elem]
#del T_perp[elem]
#del E_par[elem]
#del Bp[elem]
#del Bm[elem]
#del ti[elem]
#del te[elem]
#excl_val_4 = []
#for elem in np.where(np.isnan())[0][:]:
#excl_val_4.append(elem)
#for elem in sorted(excl_val_4,reverse=True):
#del angle[elem]
#del Br[elem]
#del Bz[elem]
#del Bzeta[elem]
B = [] #Keeping only one entry per angle, filtering out all others.
for i in range(0, len(angle)):
B.append(int(angle[i]))
for i in range(0, len(B) - 1):
excl_val = []
for j in range(i + 1, len(B)):
diff = abs(B[i] - B[j])
if (diff < tolerance) or (diff > 360 - tolerance):
excl_val.append(j)
if len(excl_val) > 0:
for elem in sorted(excl_val, reverse=True):
del B[elem]
del angle[elem]
del R[elem]
del Z[elem]
#del den_str[elem]
#del gradBR[elem]
#del gradBZ[elem]
#del curvR[elem]
#del curvZ[elem]
#del Br[elem]
#del Bz[elem]
#del Bzeta[elem]
#del T_perp[elem]
#del E_par[elem]
#del geom[elem]
#del Bp[elem]
#del Bm[elem]
#del den[elem]
#del ti[elem]
#del te[elem]
nul_pos = angle.index(min(angle)) #start all values from zero angle
angle = np.roll(angle, -nul_pos)
R = np.roll(R, -nul_pos)
Z = np.roll(Z, -nul_pos)
#den_str = np.roll(den_str,-nul_pos)
#gradBR = np.roll(gradBR,-nul_pos)
#gradBZ = np.roll(gradBZ,-nul_pos)
#curvR = np.roll(curvR,-nul_pos)
#curvZ = np.roll(curvZ,-nul_pos)
#Br = np.roll(Br,-nul_pos)
#Bz = np.roll(Bz,-nul_pos)
#Bzeta = np.roll(Bzeta,-nul_pos)
#T_perp = np.roll(T_perp,-nul_pos)
#E_par = np.roll(E_par,-nul_pos)
#geom = np.roll(geom,-nul_pos)
#Bp = np.roll(Bp,-nul_pos)
#Bm = np.roll(Bm,-nul_pos)
#den = np.roll(den,-nul_pos)
#ti = np.roll(ti,-nul_pos)
#te = np.roll(te,-nul_pos)
print(angle)
#new_file = open("Sep_temperatures.txt",'a')
#new_file.write("angle"+"\t"+"t_i"+"\t"+"t_e"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(ti[i])+"\t"+str(te[i])+"\n")
#new_file.close()
#new_file = open("Sep_densities.txt",'a')
#new_file.write("angle"+"\t"+"den"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(den[i])+"\n")
#new_file.close()
#new_file = open("Sep_turbulence_strength.txt",'a')
#new_file.write("angle"+"\t"+"rms(dphi)/<phi>"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(den[i])+"\n")
#new_file.close()
#new_file = open("Sep_Mag_field.txt",'a')
#new_file.write("angle"+"\t"+"B_p"+"\t"+"B"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(Bp[i])+"\t"+str(Bm[i])+"\n")
#new_file.close()
#new_file = open("Sep_Mag_geom.txt",'a')
#new_file.write("angle"+"\t"+"geom"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(geom[i])+"\n")
#new_file.close()
#new_file = open("Ion_temperatures.txt",'a')
#new_file.write("angle"+"\t"+"T_perp"+"\t"+"E_para"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(T_perp[i])+"\t"+str(E_par[i])+"\n")
#new_file.close()
#new_file = open("Mag_components.txt",'a')
#new_file.write("angle"+"\t"+"Br"+"\t"+"Bz"+"\t"+"Bzeta"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(Br[i])+"\t"+str(Bz[i])+"\n")
#new_file.close()
#new_file = open("Mag_curv_drifts.txt",'a')
#new_file.write("angle"+"\t"+"curvR"+"\t"+"curvZ"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(curvR[i])+"\t"+str(curvZ[i])+"\n")
#new_file.close()
#new_file = open("Den_pert_str.txt",'a')
#new_file.write("angle"+"\t"+"dn"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(den_str[i])+"\n")
#new_file.close()
new_file = open("Check.txt", 'a')
new_file.write("angle" + "\t" + "R" + "\t" + "Z" + "\n")
for i in range(0, len(angle)):
new_file.write(
str(angle[i]) + "\t" + str(R[i]) + "\t" + str(Z[i]) + "\n")
new_file.close()
#plt.style.use('ggplot')
#plt.xlabel(r"angle$^{\circ}$")
#plt.ylabel(r"T (eV)")
#plt.xlim([0.0,360.0])
#plt.plot(angle[:], ti[:],'b',marker='o',label=r'$T_i$')
#plt.plot(angle[:], te[:],'r',marker='o',label=r'$T_e$')
#plt.legend()
#plt.show()
#plt.style.use('ggplot')
#plt.xlabel(r"angle$^{\circ}$")
#plt.ylabel(r"n ($m^{-3}$)")
#plt.xlim([0.0,360.0])
#plt.plot(angle[:], den[:],'b',marker='o')
#plt.legend()
#plt.show()
return angle
def file_read(verbose=True):
tolerance = 0.5
crs = []
for i in range(
0, 60
): #ti253-separatrix(0,60)/ti253-IFS(0,61)/ti255-separatrix (0,60)
crs.append(
open(
"/global/homes/g/giannos/xgc_python_dir/ti255_analysis/Reynolds/Re_tur_pol_files_%d.txt"
% (i), "r"))
for i in range(0, 60):
next(crs[i])
angle = []
R_value = []
Z_value = []
Re = []
for i in range(0, 60):
try:
for columns in (raw.strip().split() for raw in crs[i]):
angle.append(float(columns[0]))
R_value.append(float(columns[1]))
Z_value.append(float(columns[2]))
Re.append(float(columns[3]))
except ValueError:
print("error on file", i)
excl_val_2 = []
for elem in np.where(
np.isnan(Re))[0][:]: #filter out nan values from shear
#for elem in np.where(shear < 1e2)[0][:]:
excl_val_2.append(elem)
#print(np.where(shear == 0.0))
for elem in sorted(excl_val_2, reverse=True):
del angle[elem]
del R_value[elem]
del Z_value[elem]
del Re[elem]
B = [] #Keeping only one entry per angle, filtering out all others.
for i in range(0, len(angle)):
B.append(int(angle[i]))
for i in range(0, len(B) - 1):
excl_val = []
for j in range(i + 1, len(B)):
diff = abs(B[i] - B[j])
if (diff < tolerance) or (diff > 360 - tolerance):
excl_val.append(j)
if len(excl_val) > 0:
for elem in sorted(excl_val, reverse=True):
del B[elem]
del angle[elem]
del Re[elem]
del R_value[elem]
del Z_value[elem]
nul_pos = angle.index(min(angle)) #start all values from zero angle
angle = np.roll(angle, -nul_pos)
Re = np.roll(Re, -nul_pos)
R_value = np.roll(R_value, -nul_pos)
Z_value = np.roll(Z_value, -nul_pos)
#print(angle)
Rnorm = [] #returning the R-distance for the integral function.
for r, z in zip(R_value, Z_value):
Rnorm.append(r**2 + z**2)
R = R_value + core.Rmaj
if verbose == True: # Plotting option
#new_angle = smooth(angle)
fig, ax = plt.subplots()
ax.yaxis.set_major_formatter(mtick.FormatStrFormatter('%.2e'))
ax.set_xlim([0, 360])
ax.set_xlabel("angle")
ax.set_ylabel("Reynolds Turbulent Poloidal Force")
ax.plot(angle[50:], Re[50:], 'b-')
ax.plot(angle[0:50], Re[0:50], 'b-')
ax.plot(np.unique(angle),
np.poly1d(np.polyfit(angle, Re, 18))(np.unique(angle)), 'r')
plt.show()
new_file = open(
"/global/homes/g/giannos/xgc_python_dir/ti255_analysis/Reynolds/Re_tur_pol_f_total.txt",
'a')
new_file.write("angle" + "\t" + "Re_pol_f" + "\t" + "R" + "\t" + "Z" +
"\n")
for i in range(0, len(angle)):
new_file.write(
str(angle[i]) + "\t" + str(Re[i]) + "\t" + str(R_value[i]) + "\t" +
str(Z_value[i]) + "\n")
new_file.close()
return angle, Re, Rnorm, R
def file_read(verbose=True):
tolerance = 0.5
crs = []
for i in range(
0, 60
): #ti253-separatrix(0,60)/ti253-IFS(0,61)/ti255-separatrix (0,60)
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti253_analysis/ti253_sep_flux/flux_data_new/ti253_sep_The_fluxes_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti253_analysis/ti253_IFS_flux/ti253_IFS_The_fluxes_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_analysis/sep_flux/long_run/ti255_The_fluxes_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_analysis/sep_flux/short_run/ti255_sep_short_The_fluxes_vs.angle_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_analysis/sep_flux/shorter_run/ti255_sep_short_The_fluxes_vs.angle_%d.txt" %(i),"r"))
crs.append(
open(
"/global/homes/g/giannos/xgc_python_dir/ti255_sep_short_All_fluxes_vs.angle_%d.txt"
% (i), "r"))
for i in range(0, 60):
next(crs[i])
angle = []
eq_fl = []
mean_fl = []
tur_fl = []
ttf = []
total = []
check = []
R_value = []
Z_value = []
for i in range(0, 60):
for columns in (raw.strip().split() for raw in crs[i]):
angle.append(float(columns[0]))
eq_fl.append(float(columns[1]))
mean_fl.append(float(columns[2]))
tur_fl.append(float(columns[3]))
ttf.append(float(columns[4]))
total.append(float(columns[5]))
check.append(float(columns[6]))
R_value.append(float(columns[7]))
Z_value.append(float(columns[8]))
excl_val_2 = []
for elem in np.where(
np.isnan(eq_fl))[0][:]: #filter out nan values from fluxes
excl_val_2.append(elem)
for elem in sorted(excl_val_2, reverse=True):
del angle[elem]
del eq_fl[elem]
del mean_fl[elem]
del tur_fl[elem]
del ttf[elem]
del total[elem]
del check[elem]
del R_value[elem]
del Z_value[elem]
excl_val_3 = []
for elem in np.where(np.isnan(tur_fl))[0][:]:
excl_val_3.append(elem)
for elem in sorted(excl_val_3, reverse=True):
del angle[elem]
del eq_fl[elem]
del mean_fl[elem]
del tur_fl[elem]
del ttf[elem]
del total[elem]
del check[elem]
del R_value[elem]
del Z_value[elem]
B = [] #Keeping only one entry per angle, filtering out all others.
for i in range(0, len(angle)):
B.append(int(angle[i]))
for i in range(0, len(B) - 1):
excl_val = []
for j in range(i + 1, len(B)):
diff = abs(B[i] - B[j])
if (diff < tolerance) or (diff > 360 - tolerance):
excl_val.append(j)
if len(excl_val) > 0:
for elem in sorted(excl_val, reverse=True):
del angle[elem]
del eq_fl[elem]
del mean_fl[elem]
del tur_fl[elem]
del ttf[elem]
del total[elem]
del check[elem]
del R_value[elem]
del Z_value[elem]
del B[elem]
nul_pos = angle.index(min(angle)) #start all values from zero angle
angle = np.roll(angle, -nul_pos)
eq_fl = np.roll(eq_fl, -nul_pos)
mean_fl = np.roll(eq_fl, -nul_pos)
tur_fl = np.roll(tur_fl, -nul_pos)
ttf_fl = np.roll(eq_fl, -nul_pos)
total_fl = np.roll(eq_fl, -nul_pos)
check_fl = np.roll(eq_fl, -nul_pos)
R_value = np.roll(R_value, -nul_pos)
Z_value = np.roll(Z_value, -nul_pos)
#print(angle)
Rnorm = [
] #returning the R-distance for the integral function. This is the r-distance from the center of the tokamak to the flux point.
for r, z in zip(R_value, Z_value):
Rnorm.append(r**2 + z**2)
#Returning the distance from the axis of the tokamak for the R dzeta part of the integral.
R = R_value + core.Rmaj
check2 = eq_fl - mean_fl - ttf
if verbose == True: # Plotting option
fig, ax = plt.subplots()
plt.xlabel("angle")
plt.ylabel("fluxes")
ax.plot(angle[:], eq_fl[:], 'b-', label='Equilibrium')
ax.plot(angle[:], tur_fl[:], 'r-', label='Turbulent')
ax.plot(angle[:], mean_fl[:], 'g-', label='Mean Field')
ax.plot(angle[:], total[:], 'k-', label='Total')
legend = ax.legend()
#plt.plot(angle[:], check[:],'b-',angle[:], tur_fl[:],'r-')
plt.show()
fig, ax = plt.subplots()
ax.plot(angle[:], check[:], 'b-', label='check')
ax.plot(angle[:], tur_fl[:], 'r-', label='turbulent')
legend = ax.legend()
plt.show()
fig, ax = plt.subplots()
ax.plot(angle[:], eq_fl[:], 'b-', label='Equilibrium')
ax.plot(angle[:], mean_fl[:], 'r-', label='Mean Field')
ax.plot(angle[:], mean_fl[:] - ttf[:], 'g', label='check')
legend = ax.legend()
plt.show()
new_file = open("All_new_fluxes_total.txt", 'a')
new_file.write("angle" + "\t" + "Equilibrium" + "\t" + "Mean Field" +
"\t" + "Turbulent" + "\t" + "ttf" + "\t" + "Total" +
"\t" + "check" + "\t" + "R" + "\t" + "Z" + "\n")
for i in range(0, len(angle)):
new_file.write(
str(angle[i]) + "\t" + str(eq_fl[i]) + "\t" + str(mean_fl[i]) +
"\t" + str(tur_fl[i]) + "\t" + str(ttf[i]) + "\t" +
str(total[i]) + "\t" + str(check[i]) + "\t" + str(R_value[i]) +
"\t" + str(Z_value[i]) + "\n")
new_file.close()
def file_read(verbose=False):
tolerance = 0.5
crs = []
for i in range(
0, 60
): #ti253-separatrix(0,60)/ti253-IFS(0,61)/ti255-separatrix (0,60)/ti262 (0,78)
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_Scale_lengths_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_temperatures_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_densities_%d.txt" %(i),"r"))
#crs.append(open("/global/homes/g/giannos/xgc_python_dir/ti255_phis_vs.angle_%d.txt" %(i),"r"))
crs.append(
open(
"/global/homes/g/giannos/xgc_python_dir/ti255_magnetic_field_vs.angle_%d.txt"
% (i), "r"))
for i in range(0, 60):
next(crs[i])
angle = []
Bp = []
B_mag = []
#phi = []
#dphi = []
#den = []
#lte = []
#lti = []
#ln = []
#R_value = []
#Z_value = []
for i in range(0, 60):
for columns in (raw.strip().split() for raw in crs[i]):
angle.append(float(columns[0]))
Bp.append(float(columns[1]))
B_mag.append(float(columns[2]))
#phi.append(float(columns[1]))
#dphi.append(float(columns[2]))
#den.append(float(columns[1]))
#lte.append(float(columns[1]))
#lti.append(float(columns[2]))
#ln.append(float(columns[3]))
#R_value.append(float(columns[4]))
#Z_value.append(float(columns[5]))
excl_val_2 = []
for elem in np.where(
np.isnan(Bp))[0][:]: #filter out nan values from fluxes
excl_val_2.append(elem)
for elem in sorted(excl_val_2, reverse=True):
del angle[elem]
del Bp[elem]
del B_mag[elem]
#del phi[elem]
#del dphi[elem]
#del den[elem]
#del lte[elem]
#del lti[elem]
#del ln[elem]
#del R_value[elem]
#del Z_value[elem]
excl_val_3 = []
for elem in np.where(np.isnan(B_mag))[0][:]:
excl_val_3.append(elem)
for elem in sorted(excl_val_3, reverse=True):
del angle[elem]
del Bp[elem]
del B_mag[elem]
#del phi[elem]
#del dphi[elem]
#del lte[elem]
#del lti[elem]
#del ln[elem]
#del R_value[elem]
#del Z_value[elem]
#excl_val_4 = []
#for elem in np.where(np.isnan(ln))[0][:]:
#excl_val_4.append(elem)
#for elem in sorted(excl_val_4,reverse=True):
#del angle[elem]
#del lte[elem]
#del lti[elem]
#del ln[elem]
#del R_value[elem]
#del Z_value[elem]
B = [] #Keeping only one entry per angle, filtering out all others.
for i in range(0, len(angle)):
B.append(int(angle[i]))
for i in range(0, len(B) - 1):
excl_val = []
for j in range(i + 1, len(B)):
diff = abs(B[i] - B[j])
if (diff < tolerance) or (diff > 360 - tolerance):
excl_val.append(j)
if len(excl_val) > 0:
for elem in sorted(excl_val, reverse=True):
del B[elem]
del angle[elem]
del Bp[elem]
del B_mag[elem]
#del phi[elem]
#del dphi[elem]
#del den[elem]
#del lte[elem]
#del lti[elem]
#del ln[elem]
#del R_value[elem]
#del Z_value[elem]
nul_pos = angle.index(min(angle)) #start all values from zero angle
angle = np.roll(angle, -nul_pos)
Bp = np.roll(Bp, -nul_pos)
B_mag = np.roll(B_mag, -nul_pos)
#phi = np.roll(phi, -nul_pos)
#dphi = np.roll(dphi, -nul_pos)
#den = np.roll(den, -nul_pos)
#lte = np.roll(lte,-nul_pos)
#lti = np.roll(lti,-nul_pos)
#ln = np.roll(ln,-nul_pos)
#R_value = np.roll(R_value,-nul_pos)
#Z_value = np.roll(Z_value,-nul_pos)
print(angle)
#Rnorm = []#returning the R-distance for the integral function. This is the r-distance from the center of the tokamak to the flux point.
#for r,z in zip(R_value,Z_value):
#Rnorm.append(r**2 + z**2)
#Returning the distance from the axis of the tokamak for the R dzeta part of the integral.
#R = R_value + core.Rmaj
#etai = lti/ln
#etae = lte/ln
#new_file = open("etas.txt",'a')
#new_file.write("angle"+"\t"+"eta_e"+"\t"+"eta_i"+"\t"+"R"+"\t"+"Z"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(etae[i])+"\t"+str(etai[i])+"\t"+str(R_value[i])+"\t"+str(Z_value[i])+"\n")
#new_file.close()
#new_file = open("density.txt",'a')
#new_file.write("angle"+"\t"+"density"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(den[i])+"\n")
#new_file.close()
#new_file = open("phis_eq.txt",'a')
#new_file.write("angle"+"\t"+"phi"+"\t"+"dphi"+"\n")
#for i in range(0,len(angle)):
#new_file.write(str(angle[i])+"\t"+str(phi[i])+"\t"+str(dphi[i])+"\n")
#new_file.close()
new_file = open("Sep_Mag_field.txt", 'a')
new_file.write("angle" + "\t" + "Bp" + "\t" + "B" + "\n")
for i in range(0, len(angle)):
new_file.write(
str(angle[i]) + "\t" + str(Bp[i]) + "\t" + str(B_mag[i]) + "\n")
new_file.close()
#plt.style.use('ggplot')
#plt.title("Stability Parameters")
#plt.xlabel("angle")
#plt.ylabel(r"$\eta$")
#plt.xlim([0.0,360.0])
#plt.ylim([0.0,3.0])
#plt.plot(angle[:], etai[:],'b',marker='o',label=r'$\eta_i$')
#plt.plot(angle[:], etae[:],'r',marker='o',label=r'$\eta_e$')
#plt.legend()
#plt.show()
if verbose == True: # Plotting option
plt.style.use('ggplot')
plt.title("Inverse Scale Lenghts")
plt.xlabel("angle")
plt.ylabel(r"$L^{-1}(m)^{-1}$")
plt.xlim([0.0, 360.0])
plt.plot(angle[:], lti[:], 'b', marker='o', label=r'$L^{-1}_{T_i}$')
plt.plot(angle[:], lte[:], 'r', marker='o', label=r'$L^{-1}_{T_e}$')
plt.plot(angle[:], ln[:], 'g', marker='o', label=r'$L^{-1}_{n}$')
plt.legend()
plt.show()
new_file = open("Scale_lengths_2.txt", 'a')
new_file.write("angle" + "\t" + "LTe" + "\t" + "LTi" + "\t" + "Ln" +
"\t" + "R" + "\t" + "Z" + "\n")
for i in range(0, len(angle)):
new_file.write(
str(angle[i]) + "\t" + str(lte[i]) + "\t" + str(lti[i]) +
"\t" + str(ln[i]) + "\t" + str(R_value[i]) + "\t" +
str(Z_value[i]) + "\n")
new_file.close()
return angle #, lte, lti, ln, Rnorm, R