def trikap(run):
# Only execute if plotting
if run.no_plot:
return
print("Plotting scan of triangularity vs elongation...")
Nfile = len(run.fnames)
# Init arrays of data used in scan.
full_lingrowth = [dict() for ifile in range(Nfile)]
# Get lingrowth data from .dat file.
for ifile in range(Nfile):
datfile_name = run.work_dir + run.dirs[ifile] + run.out_dir + run.files[ifile] + '.lingrowth.dat'
with open(datfile_name,'rb') as datfile:
full_lingrowth[ifile] = pickle.load(datfile)
nakx = len(full_lingrowth[0]['kx'])
for ifile in range(Nfile):
if len(full_lingrowth[ifile]['kx']) != nakx:
quit("Error - number of kx values should be constant across all items in the scan - Exiting...")
tri,kap = np.zeros(Nfile),np.zeros(Nfile)
for ifile in range(Nfile):
tri[ifile] = full_lingrowth[ifile]['tri']
kap[ifile] = full_lingrowth[ifile]['kap']
tris = sorted(list(set(tri)))
kaps = sorted(list(set(kap)))
print("Triangularity values: " + str(tris))
print("Elongation values: " + str(kaps))
if len(tris) * len(kaps) != Nfile:
quit("Incorrect number of files added to populate the scan - exiting")
gammas = np.zeros((len(tris), len(kaps), nakx))
kymax = np.zeros((len(tris), len(kaps), nakx))
for ifile in range(Nfile):
gamma = full_lingrowth[ifile]['gamma']
ky = full_lingrowth[ifile]['ky']
kx = full_lingrowth[ifile]['kx']
# Limits search to ITG.
ikymax = int((np.abs(ky-1.0)).argmin())
for itri in range(len(tris)):
for ikap in range(len(kaps)):
if tri[ifile] == tris[itri] and kap[ifile] == kaps[ikap]:
for ikx in range(len(kx)):
gammas[itri,ikap,ikx] = np.nanmax(gamma[:ikymax,ikx])
kymax[itri,ikap,ikx] = ky[np.nanargmax(gamma[:ikymax,ikx])]
pdflist = []
tmp_pdf_id=0
for ikx in range(nakx):
gplot.plot_2d(gammas,tris,kaps,np.min(gammas[:,:,ikx]),np.max(gammas[:,:,ikx]),cmp='Reds',xlab='$\delta$',ylab='$\kappa$',title='$\gamma a/v_t: k_x$ = ' + str(full_lingrowth[0]['kx'][ikx]))
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run)
pdflist.append(tmp_pdfname)
tmp_pdf_id += 1
merged_pdfname = 'tri_kap_scan'
gplot.merge_pdfs(pdflist, merged_pdfname, run)
def plot(self, ifile, run, mytime, myfields, mytxt):
write_correlation_times(mytxt, self)
tmp_pdf_id = 1
pdflist = []
plot_timecorrfnc_nonzonal(self)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
plot_timecorrfnc_zonal(self)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
plot_timecorrfnc_gyrozonal(self)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
plot_nonzonal_freq_spectrum(mytime, myfields)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
plot_zonal_power_spectrum(mytime, myfields, self)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
gfields.plot_power_spectrum(myfields, mytime)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
merged_pdfname = 'time_correlation'
gplot.merge_pdfs(pdflist, merged_pdfname, run, ifile)
def plot_along_tube(ifile,run,mytime,mydict):
kperp2_theta_x_y = mydict['kperp2']
gds2 = mydict['gds2' ]
gds21 = mydict['gds21']
gds22 = mydict['gds22']
gbdrift = mydict['gbdrift']
gbdrift0 = mydict['gbdrift0']
cvdrift = mydict['cvdrift']
cvdrift0 = mydict['cvdrift0']
bmag = mydict['bmag']
pdflist = []
tmp_pdf_id = 0
write = False
if bmag is not None:
gplot.plot_1d(mydict['theta'],bmag, '$\\theta$', title = 'bmag', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if gds2 is not None:
gplot.plot_1d(mydict['theta'],gds2, '$\\theta$', title = 'gds2', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if gds21 is not None:
gplot.plot_1d(mydict['theta'],gds21, '$\\theta$', title = 'gds21', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if gds22 is not None:
gplot.plot_1d(mydict['theta'],gds22, '$\\theta$', title = 'gds22', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if kperp2_theta_x_y is not None:
# Average over kx,ky.
kperp2_theta_x = kperp2_theta_x_y.mean(axis=2)
kperp2_theta = kperp2_theta_x.mean(axis=1)
gplot.plot_1d(mydict['theta'],kperp2_theta,'$\\theta$', title='$k_\perp^2$', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if gbdrift is not None:
gplot.plot_1d(mydict['theta'],gbdrift, '$\\theta$', title = 'gbdrift', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if gbdrift0 is not None:
gplot.plot_1d(mydict['theta'],gbdrift0, '$\\theta$', title = 'gbdrift0', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if cvdrift is not None:
gplot.plot_1d(mydict['theta'],cvdrift, '$\\theta$', title = 'cvdrift', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if cvdrift0 is not None:
gplot.plot_1d(mydict['theta'],cvdrift0, '$\\theta$', title = 'cvdrift0', rads = True, grid="x")
tmp_pdfname = 'tmp'+str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id+1
write = True
if write:
print(run.scan_name)
merged_pdfname = 'along_tube' + run.scan_name
gplot.merge_pdfs(pdflist, merged_pdfname, run, ifile)
def plot(self, ifile, run, myout, mygrids, mytime):
print()
print("producing time-dependent zonal flow plots...",end='')
tmp_pdf_id = 1
pdflist = []
plot_zonal_phi_kx_vs_t(mygrids, mytime, np.real(self.zonal_phi))
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
if (mygrids.nx > 1):
# plot flow and flow shear vs (kx,t) and vs (x,t)
title='$| J_{0}(k_{x}\\rho)k_{x}\\rho\Phi_{zf}(k_{x},t) |^2$'
plot_zonal_vs_kxt(mygrids.kx,mytime.time,self.flow_gyro,title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
title='$| J_0(k_x\\rho)k_{x}^2\\rho^2\Phi_{zf}(k_{x},t) |^2$'
plot_zonal_vs_kxt(mygrids.kx,mytime.time,self.shear_gyro,title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
title='$\left< \partial_x \Phi_{zf} (x,t) \\right> $'
plot_zonal_vs_xt(mygrids.xgrid,mytime.time,self.flow_gyro_xt,title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
title='$\left<\partial_x^2 \Phi_{zf}(x,t)\\right>$'
plot_zonal_vs_xt(mygrids.xgrid,mytime.time,self.shear_gyro_xt,title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
if myout['ntot_igomega_by_mode_present']:
for ispec in range(myout['nspec']):
stitle=str(ispec+1) + ',zf} (x,t)$'
title = '$\delta n_{' + stitle
plot_zonal_vs_xt(mygrids.xgrid,mytime.time,self.dens_xt[:,ispec,:],title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
if myout['upar_igomega_by_mode_present']:
for ispec in range(myout['nspec']):
stitle=str(ispec+1) + ',zf} (x,t)$'
title = '$\delta u_{\parallel' + stitle
plot_zonal_vs_xt(mygrids.xgrid,mytime.time,self.upar_xt[:,ispec,:],title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
if myout['tpar_igomega_by_mode_present']:
for ispec in range(myout['nspec']):
stitle=str(ispec+1) + ',zf} (x,t)$'
title = '$\delta T_{\parallel' + stitle
plot_zonal_vs_xt(mygrids.xgrid,mytime.time,self.tpar_xt[:,ispec,:],title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
if myout['tperp_igomega_by_mode_present']:
for ispec in range(myout['nspec']):
stitle=str(ispec+1) + ',zf} (x,t)$'
title = '$\delta T_{\perp' + stitle
plot_zonal_vs_xt(mygrids.xgrid,mytime.time,self.tperp_xt[:,ispec,:],title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
# save plots
merged_pdfname = 'zonal_vs_time'
gplot.merge_pdfs(pdflist, merged_pdfname, run, ifile)
print('complete')
if (mygrids.nx > 1):
print()
print("producing time-averaged zonal flow plots...",end='')
tmp_pdf_id = 1
pdflist = []
title = '$| J_{0}(k_{x}\\rho)k_{x}\\rho\Phi_{zf}(k_{x}) |^2$'
plot_zonal_vs_kx(mygrids.kx,self.flow_gyro_avg,title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
title = '$| J_0(k_x\\rho)k_{x}^2\\rho^2\Phi_{zf}(k_{x}) |^2$'
plot_zonal_vs_kx(mygrids.kx,self.shear_gyro_avg,title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
title = '$\left< \partial_x \Phi_{zf} (x) \\right> $'
plot_zonal_vs_x(mygrids.xgrid,self.flow_gyro_xt_avg,title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
tmp_pdf_id = tmp_pdf_id+1
title = '$\left<\partial_x^2 \Phi_{zf}(x)\\right>$'
plot_zonal_vs_x(mygrids.xgrid,self.shear_gyro_xt_avg,title)
tmp_pdfname = 'tmp'+tmp_pdf_id
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdf_name)
# save plots
merged_pdfname = 'zonal_steady'
gplot.merge_pdfs(pdflist, merged_pdfname, run, ifile)
print('complete')
print()
def task_scan(run, full_space):
# Start comparing simulations at time-step it_start = N_start*Tfloquet/dt
# ie after N_start Floquet oscillations
# Normalise sum_phi2 by sum_phi2[it_start] for each run
N_start = 2
sum_phi2 = []
t = []
delt = np.zeros(len(run.fnames))
dkx = np.zeros(len(run.fnames))
slope = np.zeros(len(run.fnames))
if not run.no_plot:
for ifile in range(len(run.fnames)):
Tf = full_space[ifile]['floquet'].Tf
delt[ifile] = full_space[ifile]['floquet'].delt
dkx[ifile] = full_space[ifile]['floquet'].dkx
nwrite = full_space[ifile]['floquet'].nwrite
it_start = int(round((N_start*Tf/delt[ifile])/nwrite))
sum_phi2_tmp = np.zeros(len(full_space[ifile]['floquet'].sum_phi2_chain)-it_start)
for it in range(sum_phi2_tmp.size):
sum_phi2_tmp[it] = full_space[ifile]['floquet'].sum_phi2_chain[it_start+it]
sum_phi2_tmp = sum_phi2_tmp/sum_phi2_tmp[0]
sum_phi2.append(sum_phi2_tmp)
t_tmp = np.zeros(len(full_space[ifile]['floquet'].t)-it_start)
for it in range(t_tmp.size):
t_tmp[it] = full_space[ifile]['floquet'].t[it_start+it]
t.append(t_tmp)
[a,dummy] = leastsq_lin(t_tmp,np.log(sum_phi2_tmp))
slope[ifile] = a
idxsort = np.argsort(delt)
delt = delt[idxsort]
dkx = dkx[idxsort]
slope = slope[idxsort]
pdflist = []
plt.figure(figsize=(12,8))
plt.xlabel('$t$')
plt.ylabel('$\\ln \\left(\\sum_{K_x}\\vert \\langle\\phi\\rangle_\\theta \\vert ^2\\right)$')
plt.title('Sum along a single ballooning mode')
plt.grid(True)
my_legend = []
my_colorlist = plt.cm.plasma(np.linspace(0,1,len(run.fnames)))
for ifile in range(len(run.fnames)):
#my_legend.append('$\\Delta t =$'+str(full_space[ifile]['floquet'].delt))
my_legend.append('$\\Delta k_x =$'+str(full_space[ifile]['floquet'].dkx))
plt.plot(t[ifile], np.log(sum_phi2[ifile]), color=my_colorlist[ifile], linewidth=3.0)
plt.legend(my_legend)
axes = plt.gca()
axes.set_ylim([-0.5, 13.75])
pdfname = 'tmp_1'
gplots.save_plot(pdfname, run, ifile)
pdflist.append(pdfname)
plt.clf()
plt.cla()
#plt.xlabel('$\\Delta t$')
plt.xlabel('$\\Delta k_x$')
plt.ylabel('$\\langle \\gamma \\rangle_t$')
plt.title('Time averaged growth-rate')
plt.grid(True)
print('Slopes : ',end='')
print(slope)
#plt.plot(delt, slope, marker='o', \
# markersize=12, markerfacecolor='none', markeredgecolor=gplots.myblue, linewidth=3.0)
plt.plot(dkx, slope, marker='o', \
markersize=12, markerfacecolor='none', markeredgecolor=gplots.myblue, linewidth=3.0)
pdfname = 'tmp_2'
gplots.save_plot(pdfname, run, ifile)
pdflist.append(pdfname)
plt.clf()
plt.cla()
outname = run.scan_name
gplots.merge_pdfs(pdflist,outname,run,ifile)
plt.close()
def plot_task_single(ifile, run, my_vars, my_it, my_iky, my_dmid, make_movies):
Nf = my_vars['Nf']
t = my_vars['t']
delt = my_vars['delt']
kx = my_vars['kx']
nakx = my_vars['nakx']
kx_bar = my_vars['kx_bar']
dkx = my_vars['dkx']
bloonang_chain = my_vars['bloonang_chain']
phi2 = my_vars['phi2']
phi2bloon_chain = my_vars['phi2bloon_chain']
sum_phi2_chain = my_vars['sum_phi2_chain']
gamma_mid = my_vars['gamma_mid']
gamma_chain = my_vars['gamma_chain']
phi_t_present = my_vars['phi_t_present']
Tf = Nf*delt
nt = t.size
plt.figure(figsize=(12,8))
# plot sum of phi2 along chain vs time
plt.xlabel('$t$')
plt.ylabel('$\\ln \\left(\\sum_{K_x}\\vert \\langle \\phi \\rangle_\\theta \\vert ^2\\right)$')
plt.title('Sum along a single ballooning mode')
plt.grid(True)
# NDCTEST: shorten time trace
#plt.plot(t[0:600], np.log(sum_phi2_chain[0:600]), color=gplots.myblue, linewidth=3.0)
plt.plot(t, np.log(sum_phi2_chain), color=gplots.myblue, linewidth=3.0)
# endNDCTEST
pdfname = 'floquet_vs_t'
pdfname = run.out_dir + pdfname + '_' + run.fnames[ifile] + '_iky_' + str(my_iky) + '_dmid_' + str(my_dmid) + '.pdf'
plt.savefig(pdfname)
plt.clf()
plt.cla()
# plot phi2 of chosen chain vs ballooning angle at chosen time
if (phi_t_present):
for it in my_it:
plt.xlabel('$\\theta -\\theta_0$')
plt.ylabel('$\\vert \\phi \\vert ^2$')
plt.title('$t=$ '+str(t[it]))
plt.grid(True)
plt.gca().set_xlim(np.min(bloonang_chain[it]),np.max(bloonang_chain[it]))
plt.gca().yaxis.set_major_formatter(FormatStrFormatter('%.1E'))
plt.plot(bloonang_chain[it], phi2bloon_chain[it], marker='o', \
markersize=12, markerfacecolor='none', markeredgecolor=gplots.myblue, linewidth=3.0)
pdfname = 'balloon_it_' + str(it)
pdfname = run.out_dir + pdfname + '_' + run.fnames[ifile] + '_iky_' + str(my_iky) + '_dmid_' + str(my_dmid) + '.pdf'
plt.savefig(pdfname)
plt.clf()
plt.cla()
# make movie of phi2 vs ballooning angle over time
if (make_movies and phi_t_present):
moviename = run.out_dir + 'phi_bloon_' + run.fnames[ifile] + '_iky_' + str(my_iky) + '_dmid_' + str(my_dmid) + '.mp4'
images = []
# find global min and max of ballooning angle
bloonang_min = 0.
bloonang_max = 0.
# NDCTEST: to shorten movie
#for it in range(401):
for it in range(nt):
if np.min(bloonang_chain[it]) < bloonang_min:
bloonang_min = np.min(bloonang_chain[it])
if np.max(bloonang_chain[it]) > bloonang_max:
bloonang_max = np.max(bloonang_chain[it])
print("\ncreating movie of phi vs ballooning angle ...")
# NDCTEST: to shorten movie
#for it in range(401):
for it in range(nt):
sys.stdout.write("\r{0}".format("\tFrame : "+str(it)+"/"+str(nt-1)))
plt.xlabel('$\\theta -\\theta_0$')
plt.ylabel('$\\vert \\phi \\vert ^2$')
plt.title('$t=$ '+str(t[it]))
plt.grid(True)
plt.gca().set_xlim(bloonang_min,bloonang_max)
plt.gca().yaxis.set_major_formatter(FormatStrFormatter('%.1E'))
plt.plot(bloonang_chain[it], phi2bloon_chain[it], marker='o', \
markersize=12, markerfacecolor='none', markeredgecolor=gplots.myblue, linewidth=3.0)
pngname = run.out_dir + 'tmp_image.png'
plt.savefig(pngname)
images.append(imageio.imread(pngname))
os.system('rm -rf ' + pngname)
plt.clf()
plt.cla()
sys.stdout.flush()
imageio.mimsave(moviename, images, format='FFMPEG')
print("\n... movie completed.")
# NDCTEST: plotting mutliple times together
#plt.xlabel('$\\theta -\\theta_0$')
#plt.ylabel('$\\vert \\phi \\vert ^2$')
#plt.grid(True)
#plt.gca().yaxis.set_major_formatter(FormatStrFormatter('%.1E'))
#line2, = plt.plot(bloonang_chain[210], phi2bloon_chain[210], marker='None', linestyle='--', linewidth=4.0, color=gplots.oxbluel)
#line3, = plt.plot(bloonang_chain[310], phi2bloon_chain[310], marker='None', linestyle=':', linewidth=3.0, color=gplots.oxbluell)
#line1, = plt.plot(bloonang_chain[110], phi2bloon_chain[110], marker='None', linewidth=5.0, color=gplots.oxblue)
#plt.legend([line1,line2,line3], ['$t=$ '+"{:.1f}".format(t[110]),'$t=$ '+"{:.1f}".format(t[210]),'$t=$ '+"{:.1f}".format(t[310])])
#plt.savefig('two_times_floquet.pdf')
#plt.clf()
#plt.cla()
# endNDCTEST
# plot instantaneous growthrate at mid-plane vs kx
pdflist = []
for ifloq in range((nt-1)//Nf):
plt.xlabel('$k_x$')
plt.ylabel('$\\gamma$')
plt.title('Growthrate at $\\theta = 0$ and $t='+str(t[ifloq*Nf])+'$')
plt.grid(True)
plt.plot(kx[ifloq*Nf,my_iky,:], gamma_mid[ifloq*Nf,:], color=gplots.myblue)
pdfname = 'tmp_' + str(ifloq)
gplots.save_plot(pdfname, run, ifile)
plt.clf()
plt.cla()
pdflist.append(pdfname)
outname = 'growth_mid'
outname = outname + '_iky_' + str(my_iky) + '_dmid_' + str(my_dmid)
gplots.merge_pdfs(pdflist,outname,run,ifile)
# make movie of growthrate at mid-plane vs kx over time
#if (make_movies and phi_t_present):
#
# moviename = run.out_dir + 'growth_mid_' + run.fnames[ifile] + '_iky_' + str(my_iky) + '_dmid_' + str(my_dmid) + '.mp4'
# images = []
# # find global min and max of kx
# kx_min = 0.
# kx_max = 0.
# for it in range(nt):
# for ikx in range(nakx):
# if np.min(kx[it,my_iky,ikx]) < kx_min:
# kx_min = np.min(kx[it,my_iky,ikx])
# if np.max(kx[it,my_iky,ikx]) > kx_max:
# kx_max = np.max(kx[it,my_iky,ikx])
#
# print("\ncreating movie of growthrate at mid-plane vs kx ...")
# for it in range(nt):
#
# sys.stdout.write("\r{0}".format("\tFrame : "+str(it)+"/"+str(nt-1)))
#
# plt.xlabel('$k_x$')
# plt.ylabel('$\\gamma (\\theta=0)$')
# plt.title('$t=$ '+str(t[it]))
# plt.grid(True)
# plt.gca().set_xlim(kx_min,kx_max)
# plt.gca().set_ylim(bottom=-0.5)
# plt.gca().set_ylim(top=0.5)
# plt.gca().yaxis.set_major_formatter(FormatStrFormatter('%.1E'))
# plt.plot(kx[it,my_iky,:], gamma_mid[it,:], marker='o', \
# markersize=12, markerfacecolor='none', markeredgecolor=gplots.myblue, linewidth=3.0)
# pngname = run.out_dir + 'tmp_image.png'
# plt.savefig(pngname)
#
# images.append(imageio.imread(pngname))
# os.system('rm -rf ' + pngname)
# plt.clf()
# plt.cla()
# sys.stdout.flush()
#
# imageio.mimsave(moviename, images, format='FFMPEG')
# print("\n... movie completed.")
# plot growthrate vs theta-theta0 at time t[my_it]
for it in my_it:
plt.xlabel('$\\theta - \\theta_0$')
plt.ylabel('$\\gamma$')
plt.title('Growthrate at $t='+str(t[it])+'$')
plt.grid(True)
plt.plot(bloonang_chain[it], gamma_chain[it][:], color=gplots.myblue)
pdfname = 'growth_bloon_it_'+str(it)
pdfname = run.out_dir + pdfname + '_' + run.fnames[ifile] + '_iky_' + str(my_iky) + '_dmid_' + str(my_dmid) + '.pdf'
plt.savefig(pdfname)
plt.clf()
plt.cla()
# make movie of growthrate vs ballooning angle over time
#if (make_movies and phi_t_present):
#
# moviename = run.out_dir + 'growth_bloon_' + run.fnames[ifile] + '_iky_' + str(my_iky) + '_dmid_' + str(my_dmid) + '.mp4'
# images = []
# # find global min and max of ballooning angle
# bloonang_min = 0.
# bloonang_max = 0.
# for it in range(nt):
# if np.min(bloonang_chain[it]) < bloonang_min:
# bloonang_min = np.min(bloonang_chain[it])
# if np.max(bloonang_chain[it]) > bloonang_max:
# bloonang_max = np.max(bloonang_chain[it])
#
# print("\ncreating movie of growthrate vs ballooning angle ...")
# for it in range(nt):
#
# sys.stdout.write("\r{0}".format("\tFrame : "+str(it)+"/"+str(nt-1)))
#
# plt.xlabel('$\\theta -\\theta_0$')
# plt.ylabel('$\\gamma$')
# plt.title('$t=$ '+str(t[it]))
# plt.grid(True)
# plt.gca().set_xlim(bloonang_min,bloonang_max)
# plt.gca().set_ylim(bottom=-0.5)
# plt.gca().set_ylim(top=0.5)
# plt.gca().yaxis.set_major_formatter(FormatStrFormatter('%.1E'))
# plt.plot(bloonang_chain[it], gamma_chain[it], marker='o', \
# markersize=12, markerfacecolor='none', markeredgecolor=gplots.myblue, linewidth=3.0)
# pngname = run.out_dir + 'tmp_image.png'
# plt.savefig(pngname)
#
# images.append(imageio.imread(pngname))
# os.system('rm -rf ' + pngname)
# plt.clf()
# plt.cla()
# sys.stdout.flush()
#
# imageio.mimsave(moviename, images, format='FFMPEG')
# print("\n... movie completed.")
# plot phi2 vs t for each kx
plt.xlabel('$$t\\ [r_r/v_{thr}]$$')
my_ylabel = '$\\ln \\left(\\vert \\langle \\phi \\rangle_\\theta \\vert ^2\\right)$'
plt.ylabel(my_ylabel)
plt.grid(True)
my_colorlist = plt.cm.plasma(np.linspace(0,1,kx_bar.size))
my_legend = []
for ikx in range(kx_bar.size):
plt.plot(t, np.log(phi2[:,1,ikx]), color=my_colorlist[ikx])
my_legend.append('$\\rho_i\\bar{k}_x = '+str(kx_bar[ikx])+'$')
plt.legend(my_legend)
pdfname = 'phi2_by_kx'
pdfname = run.out_dir + pdfname + '_' + run.fnames[ifile] + '.pdf'
plt.savefig(pdfname)
plt.clf()
plt.cla()
plt.close()
def my_task_single(ifile, run, myin, myout, mygrids):
if not run.only_plot:
#######################
### User parameters ###
#######################
# Choose which Fourier components to plot
it_start_list = [0, 0]
ikx_start_list = [3, 4] # ikxmax=126 for nx=192
iky_list = [1, 1]
###########################
### End user parameters ###
###########################
# Check parameters make sense
size_check = (len(it_start_list) == len(ikx_start_list) ==
len(iky_list))
if not size_check:
print('potential.py: size mismatch in user parameters')
sys.exit()
# Number of Fourier components to plot
Nplot = len(it_start_list)
# Copy relevant quantities and make monotonous in kx
t = myout['t']
delt = myin['knobs']['delt']
nwrite = myin['gs2_diagnostics_knobs']['nwrite']
kxgrid = mygrids.kx # this version is monotonous
dkx = kxgrid[1] - kxgrid[0]
kygrid = mygrids.ky
g_exb = myin['dist_fn_knobs']['g_exb']
sgn_g = int(np.sign(g_exb))
phi2_by_mode = myout['phi2_by_mode']
phi2_by_mode = np.concatenate(
(phi2_by_mode[:, :,
mygrids.nxmid:], phi2_by_mode[:, :, :mygrids.nxmid]),
axis=2)
# Arrays to store values for each (it,ikx,iky) chosen by the user
kx_full = []
ky_full = []
t_plot_full = []
t_zero_full = []
t_outgrid_full = []
it_drop_full = []
phi2_kxky_full = []
# Loop over (it,ikx,iky) chosen by the user
for iplot in range(Nplot):
# Time against which we plot
t_plot = []
t_plot.append(t[it_start_list[iplot]])
# My ky
iky = iky_list[iplot]
ky = kygrid[iky]
# Period of ExB remapping
Tshift = abs(dkx / (g_exb * ky))
# Time dependent radial wavenumber in lab frame
kxstar = []
# Grid point closest to kxstar
kxbar = []
# Starting at ...
kxbar.append(kxgrid[ikx_start_list[iplot]])
# ... which corresponds to the following wavenumber in shearing frame:
kx = kxbar[0] + int(
round(g_exb * ky * t[it_start_list[iplot]] / dkx)) * dkx
# ... and to the following time dependent wavenumber in lab frame:
kxstar.append(kx - g_exb * ky * t[it_start_list[iplot]])
# Mod. sq. of Fourier component phi(kx,ky):
phi2_kxky = []
phi2_kxky.append(phi2_by_mode[it_start_list[iplot], iky,
ikx_start_list[iplot]])
# At what time was this Fourier coefficient included in the sim ?
if kx >= kxgrid.min() and kx <= kxgrid.max(
): # Already in at the start
t_ingrid = 0.
else:
if g_exb > 0.: # Enters from high kx end
t_ingrid = (kx - (kxgrid.max() + 0.5 * dkx)) / (g_exb * ky)
if g_exb < 0.: # Enters from low ky end
t_ingrid = (kx - (kxgrid.min() - 0.5 * dkx)) / (g_exb * ky)
# At what time was this Fourier coefficient dropped from the sim ?
if g_exb > 0.: # Leaves through low kx end
t_outgrid = (kx - (kxgrid.min() - 0.5 * dkx)) / (g_exb * ky)
if g_exb < 0.: # Leaves through high ky end
t_outgrid = (kx - (kxgrid.max() + 0.5 * dkx)) / (g_exb * ky)
# At what time is kxstar=0 ?
if kx * g_exb < 0:
t_zero = np.nan # will never cross zero
else:
t_zero = kx / (g_exb * ky)
# Compute corresponding it_drop (might be larger than t.size if it does not drop within simulation time)
if t_outgrid < t.max():
it_drop = int(
np.ceil((t_outgrid + 0.5 * delt) / (nwrite * delt))
) # add delt/2 because first step in GS2 uses dt/2
else:
it_drop = -1
# Continue filling phi2_kxky by following it as it moves across kxgrid
ikxgrid = ikx_start_list[iplot]
if it_drop > 0:
it_max = it_drop
else:
it_max = t.size
for it in range(it_start_list[iplot] + 1, it_max):
t_plot.append(t[it])
# Compute new kxstar
kxstar.append(kx - g_exb * ky * t[it])
# Check if we now have a new nearest neighbour
if abs(kxstar[-1] - kxbar[-1]) > 0.5 * dkx:
kxbar.append(kxbar[-1] - sgn_g * dkx)
# In GS2, ExB remapping has shifted our Fourier coefficient -> update ikxgrid
ikxgrid = int(ikxgrid - sgn_g)
else:
kxbar.append(kxbar[-1])
phi2_kxky.append(phi2_by_mode[it, iky, ikxgrid])
# End of t loop
# Append computed quantities to _full arrays
kx_full.append(kx)
ky_full.append(ky)
t_plot_full.append(t_plot)
t_zero_full.append(t_zero)
t_outgrid_full.append(t_outgrid)
it_drop_full.append(it_drop)
phi2_kxky_full.append(phi2_kxky)
# End of iplot loop
# Save quantities to a dat-file
datfile_name = run.work_dir + run.dirs[
ifile] + run.out_dir + run.files[ifile] + '.potential.dat'
mydict = {
'g_exb': g_exb,
'kx_full': kx_full,
'ky_full': ky_full,
't_plot_full': t_plot_full,
't_zero_full': t_zero_full,
't_outgrid_full': t_outgrid_full,
'it_drop_full': it_drop_full,
'phi2_kxky_full': phi2_kxky_full
}
with open(datfile_name, 'wb') as datfile:
pickle.dump(mydict, datfile)
# End if not only_plot
################
### Plotting ###
################
if not run.no_plot:
# If only plot, read quantities from dat-file
if run.only_plot:
datfile_name = run.work_dir + run.dirs[
ifile] + run.out_dir + run.files[ifile] + '.potential.dat'
with open(datfile_name, 'rb') as datfile:
mydict = pickle.load(datfile)
g_exb = mydict['g_exb']
kx_full = mydict['kx_full']
ky_full = mydict['ky_full']
t_plot_full = mydict['t_plot_full']
t_zero_full = mydict['t_zero_full']
t_outgrid_full = mydict['t_outgrid_full']
it_drop_full = mydict['it_drop_full']
phi2_kxky_full = mydict['phi2_kxky_full']
Nplot = len(kx_full)
# Start pdf list to merge at the end
tmp_pdf_id = 1
pdflist = []
for iplot in range(Nplot):
# Pick iplot elements from the _full arrays
kx = kx_full[iplot]
ky = ky_full[iplot]
t_plot = t_plot_full[iplot]
t_zero = t_zero_full[iplot]
t_outgrid = t_outgrid_full[iplot]
it_drop = it_drop_full[iplot]
phi2_kxky = phi2_kxky_full[iplot]
fig = plt.figure(figsize=(12, 8))
# Plot phi_kxky vs t
title = '$(k_x=' + '{:4.2f}'.format(
kx) + ',k_y=' + '{:4.2f}'.format(
ky) + ')$ from $t=' + '{:4.2f}'.format(t_plot[0]) + '$'
xlab = '$t (a/v_{t})$'
ylab = '$\\langle\\vert\\hat{\\varphi}_{k}\\vert ^2\\rangle_{\\theta}$'
plt.semilogy(t_plot, phi2_kxky, linewidth=2)
plt.xlabel(xlab)
plt.ylabel(ylab)
plt.title(title)
plt.grid(True)
#ax = plt.gca() # NDCDEL
#ax.set_ylim([0.01, 1.5]) # NDCDEL
# Draw vertical line where kxstar=0
props = dict(boxstyle='square',
facecolor='white',
edgecolor='white')
if t_zero >= min(t_plot) and t_zero <= max(t_plot):
plt.axvline(x=t_zero, color='k', linestyle='--', linewidth=2)
# Add textbox
ax = plt.gca()
xmin, xmax = ax.get_xlim()
txt_ypos = 0.05 # Place text boxes at bottom
txt_xpos = 0.5 * (1. - (max(t_plot) - min(t_plot)) /
(xmax - xmin)) + (t_zero - min(t_plot)) / (xmax -
xmin)
txt_str = '$k_x^*=0$'
ax.text(txt_xpos,
txt_ypos,
txt_str,
transform=ax.transAxes,
fontsize=20,
bbox=props,
horizontalalignment='center')
# Draw vertical line where kx is dropped from the sim
if it_drop > 0:
plt.axvline(x=t_outgrid,
color='k',
linestyle='--',
linewidth=2)
# Add textbox
txt_xpos = 0.5 * (1. - (max(t_plot) - min(t_plot)) /
(xmax - xmin)) + (t_outgrid -
min(t_plot)) / (xmax - xmin)
if g_exb > 0.:
txt_str = '$k_x^*=\\min(k_{x,GS2})$'
if g_exb < 0.:
txt_str = '$k_x^*=\\max(k_{x,GS2})$'
ax.text(txt_xpos,
txt_ypos,
txt_str,
transform=ax.transAxes,
fontsize=20,
bbox=props,
horizontalalignment='right')
# Save tmp plot and append to list for merge
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
# End of iplot loop
# Merge pdfs
merged_pdfname = 'potential'
gplot.merge_pdfs(pdflist, merged_pdfname, run, ifile)
def plot_fluxes(ifile, run, mytime, mydict):
islin = mydict['islin']
has_flowshear = mydict['has_flowshear']
# t grid
time = mytime.time
time_steady = mytime.time_steady
it_min = mytime.it_min
it_max = mytime.it_max
# k grids
nx = mydict['nx']
ny = mydict['ny']
naky = mydict['naky']
nakx = mydict['nakx']
kx = mydict['kx']
ky = mydict['ky']
# species
nspec = mydict['nspec']
spec_names = mydict['spec_names']
# fluxes vs t
pflx = mydict['pflx']
qflx = mydict['qflx']
vflx = mydict['vflx']
pioq = mydict['pioq']
# fluxes vs (kx,ky)
pflx_kxky_tavg = mydict['pflx_kxky_tavg']
qflx_kxky_tavg = mydict['qflx_kxky_tavg']
vflx_kxky_tavg = mydict['vflx_kxky_tavg']
# potential
phi2_avg = mydict['phi2_avg']
phi2_by_ky = mydict['phi2_by_ky']
phi2_kxky_tavg = mydict['phi2_kxky_tavg']
print()
print(">>> producing plots of fluxes vs time...")
print("-- plotting avg(phi2)")
write_fluxes_vs_t = False
tmp_pdf_id = 1
pdflist = []
if phi2_avg is not None:
title = '$\\langle|\phi^{2}|\\rangle_{\\theta,k_x,k_y}$'
if islin:
title = '$\ln$' + title
gplot.plot_1d(time, np.log(phi2_avg), '$t (a/v_{t})$', title)
else:
gplot.plot_1d(time, phi2_avg, '$t (a/v_{t})$', title)
plt.grid(True)
write_fluxes_vs_t = True
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
print("-- plotting particle flux")
if pflx is not None:
title = '$\Gamma_{GS2}$'
plot_flux_vs_t(islin, nspec, spec_names, mytime, pflx, title)
write_fluxes_vs_t = True
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
print("-- plotting heat flux")
if qflx is not None:
title = '$Q_{GS2}$'
plot_flux_vs_t(islin, nspec, spec_names, mytime, qflx, title)
write_fluxes_vs_t = True
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
print("-- plotting momentum flux")
if vflx is not None:
title = '$\Pi_{GS2}$'
plot_flux_vs_t(
islin,
nspec,
spec_names,
mytime,
vflx,
title,
)
write_fluxes_vs_t = True
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
#if myout['es_energy_exchange_present']:
# title = 'energy exchange'
# gplot.plot_1d(mytime.time,self.xchange,"$t (v_t/a)$",title)
# write_fluxes_vs_t = True
# tmp_pdfname = 'tmp'+str(tmp_pdf_id)
# gplot.save_plot(tmp_pdfname, run, ifile)
# pdflist.append(tmp_pdfname)
# tmp_pdf_id = tmp_pdf_id+1
print("-- plotting momentum/heat flux ratio")
if pioq is not None:
title = '$\Pi_{GS2}/Q_{GS2}$'
for idx in range(nspec):
plt.plot(mytime.time_steady,
pioq[it_min:it_max, idx],
label=spec_names[idx])
plt.title(title)
plt.xlabel('$t (a/v_t)$')
plt.legend()
plt.grid(True)
write_fluxes_vs_t = True
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
print("-- plotting phi2 by ky")
if phi2_by_ky is not None:
title = '$\\langle|\phi^{2}|\\rangle_{\\theta,k_x}$'
# Create list of colors
cmap = plt.get_cmap('nipy_spectral')
my_colors = [cmap(i) for i in np.linspace(0, 1, naky - 1)]
if islin:
title = '$\\ln$' + title
plt.semilogy(time,
np.log(phi2_by_ky[:, 0]),
label='ky = ' + '{:5.3f}'.format(ky[0]),
linestyle='dashed',
color='black')
for iky in range(1, naky):
plt.semilogy(time,
np.log(phi2_by_ky[:, iky]),
label='ky = ' + '{:5.3f}'.format(ky[iky]),
color=my_colors[iky - 1])
else:
plt.plot(time,
phi2_by_ky[:, 0],
label='ky = ' + '{:5.3f}'.format(ky[0]),
linestyle='dashed',
color='black')
for iky in range(1, naky):
plt.semilogy(time,
phi2_by_ky[:, iky],
label='ky = ' + '{:5.3f}'.format(ky[iky]),
color=my_colors[iky - 1])
plt.xlabel('$t (a/v_t)$')
plt.title(title)
plt.legend(prop={'size': 11}, ncol=6)
plt.grid(True)
write_fluxes_vs_t = True
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
if naky > 4:
tmp_pdf_id = tmp_pdf_id + 1
title = '$\\langle|\phi^{2}|\\rangle_{\\theta,k_x}$ for low $k_y$'
#plt.figure(figsize=(8,8)) # NDCDEL
if islin:
title = '$\\ln$' + title
plt.semilogy(time,
np.log(phi2_by_ky[:, 0]),
label='ky = ' + '{:5.3f}'.format(ky[0]),
linestyle='dashed',
color='black')
for iky in range(1, 5):
plt.semilogy(time,
np.log(phi2_by_ky[:, iky]),
label='ky = ' + '{:5.3f}'.format(ky[iky]),
color=my_colors[iky - 1])
else:
plt.plot(time[:],
phi2_by_ky[:, 0],
label='ky = ' + '{:5.3f}'.format(ky[0]),
linestyle='dashed',
color='black')
#for iky in range(1,4) :# NDCDEL
for iky in range(1, 5):
plt.semilogy(time[:],
phi2_by_ky[:, iky],
label='ky = ' + '{:5.3f}'.format(ky[iky]),
color=my_colors[iky - 1])
#plt.xlabel('$t$') # NDCDEL
plt.xlabel('$t (a/v_t)$')
#plt.ylabel('$\\langle|\phi^{2}|\\rangle_{\\theta,k_x}$') # NDCDEL
plt.title(title)
plt.legend()
plt.grid(True)
# NDCDEL
#axes = plt.gca()
#axes.set_xlim([0,500])
#plt.savefig('terrific.pdf')
# endNDCDEL
write_fluxes_vs_t = True
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
title = '$\\langle|\phi^{2}|\\rangle_{\\theta,k_x}$ for high $k_y$'
if islin:
title = '$\\ln$' + title
for iky in range(naky - 5, naky):
plt.semilogy(time,
np.log(phi2_by_ky[:, iky]),
label='ky = ' + '{:5.3f}'.format(ky[iky]),
color=my_colors[iky - 1])
else:
for iky in range(naky - 5, naky):
plt.semilogy(time,
phi2_by_ky[:, iky],
label='ky = ' + '{:5.3f}'.format(ky[iky]),
color=my_colors[iky - 1])
plt.xlabel('$t (a/v_t)$')
plt.title(title)
plt.legend()
plt.grid(True)
write_fluxes_vs_t = True
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
if write_fluxes_vs_t:
merged_pdfname = 'fluxes_vs_t'
if ifile == None: # This is the case when we stitch fluxes together
merged_pdfname += '_' + run.scan_name
gplot.merge_pdfs(pdflist, merged_pdfname, run, ifile)
print('complete')
print()
print('producing plots of fluxes vs (kx,ky)...', end='')
write_fluxes_vs_kxky = False
tmp_pdf_id = 1
pdflist = []
# Plot phi2 averaged over t and theta, vs (kx,ky)
plot_phi2_vs_kxky(kx, ky, phi2_kxky_tavg, has_flowshear)
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id += 1
if pflx_kxky_tavg is not None:
title = '$\Gamma_{GS2}$'
for ispec in range(nspec):
plot_flux_vs_kxky(ispec, spec_names, kx, ky, pflx_kxky_tavg, title,
has_flowshear)
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
write_fluxes_vs_kxky = True
if qflx_kxky_tavg is not None:
title = '$Q_{GS2}$'
for ispec in range(nspec):
plot_flux_vs_kxky(ispec, spec_names, kx, ky, qflx_kxky_tavg, title,
has_flowshear)
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
write_fluxes_vs_kxky = True
if vflx_kxky_tavg is not None:
title = '$\Pi_{GS2}$'
for ispec in range(nspec):
plot_flux_vs_kxky(ispec, spec_names, kx, ky, vflx_kxky_tavg, title,
has_flowshear)
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run, ifile)
pdflist.append(tmp_pdfname)
tmp_pdf_id = tmp_pdf_id + 1
write_fluxes_vs_kxky = True
if write_fluxes_vs_kxky:
merged_pdfname = 'fluxes_vs_kxky'
if ifile == None: # This is the case when we stitch fluxes together
merged_pdfname += '_' + run.scan_name
gplot.merge_pdfs(pdflist, merged_pdfname, run, ifile)
print('complete')
def trikap(run):
# Only execute if plotting
if run.no_plot:
return
print("Plotting scan of triangularity vs elongation...")
Nfile = len(run.fnames)
# Init arrays of data used in scan.
full_fluxes = [dict() for ifile in range(Nfile)]
full_time = [dict() for ifile in range(Nfile)]
# Initialize fluxes and grids from .dat files.
for ifile in range(Nfile):
datfile_name = run.work_dir + run.dirs[
ifile] + run.out_dir + run.files[ifile] + '.fluxes.dat'
with open(datfile_name, 'rb') as datfile:
full_fluxes[ifile] = pickle.load(datfile)
datfile_name = run.work_dir + run.dirs[
ifile] + run.out_dir + run.files[ifile] + '.time.dat'
with open(datfile_name, 'rb') as datfile:
full_time[ifile] = pickle.load(datfile)
# Uses nspec from first file. Will quit if not constant between files.
nspec = full_fluxes[0]['nspec']
print("Number of species " + str(nspec))
tri, kap = np.zeros(Nfile), np.zeros(Nfile)
for ifile in range(Nfile):
tri[ifile] = full_fluxes[ifile]['tri']
kap[ifile] = full_fluxes[ifile]['kap']
if full_fluxes[ifile]['nspec'] != nspec:
quit("Number of species varies between files - exiting")
tris = sorted(list(set(tri)))
kaps = sorted(list(set(kap)))
print("Triangularity values: " + str(tris))
print("Elongation values: " + str(kaps))
if len(tris) * len(kaps) != Nfile:
quit("Too few files added to populate the scan - exiting")
qflx = np.zeros((len(tris), len(kaps), nspec))
for itri in range(len(tris)):
for ikap in range(len(kaps)):
for ifile in range(Nfile):
if tri[ifile] == tris[itri] and kap[ifile] == kaps[ikap]:
for ispec in range(nspec):
qflx[itri, ikap, ispec] = full_time[ifile].timeavg(
full_fluxes[ifile]['qflx'][:, ispec])
spec_names = full_fluxes[0]['spec_names']
pdflist = []
tmp_pdf_id = 0
for ispec in range(nspec):
print("Plotting for species: " + spec_names[ispec])
gplot.plot_2d(qflx[:, :, ispec],
tris,
kaps,
np.min(qflx[:, :, ispec]),
np.max(qflx[:, :, ispec]),
cmp='Reds',
xlab='$\delta$',
ylab='$\kappa$',
title='$Q_{GS2}$: ' + spec_names[ispec])
tmp_pdfname = 'tmp' + str(tmp_pdf_id)
gplot.save_plot(tmp_pdfname, run)
pdflist.append(tmp_pdfname)
tmp_pdf_id += 1
merged_pdfname = 'tri_kap_scan'
gplot.merge_pdfs(pdflist, merged_pdfname, run)