def copy_run(src,dst):
if not os.path.isdir(dst):
os.mkdir(dst)
cp(src+'/adapted0.smb',dst+'/adapted0.smb')
cp(src+'/batch_slurm',dst+'/batch_slurm')
cp(src+'/batch_torque',dst+'/batch_torque')
cp(src+'/C1input',dst+'/C1input')
cp(src+'/coil.dat',dst+'/coil.dat')
cp(src+'/current.dat',dst+'/current.dat')
cp(src+'/diiid0.020.smb',dst+'/diiid0.020.smb')
cp(src+'/diiid0.02.smd',dst+'/diiid0.02.smd')
cp(src+'/diiid0.02.sms',dst+'/diiid0.02.sms')
cp(src+'/diiid0.02.txt',dst+'/diiid0.02.txt')
cp(src+'/geqdsk',dst+'/geqdsk')
cp(src+'/profile_ne',dst+'/profile_ne')
cp(src+'/profile_te',dst+'/profile_te')
cp(src+'/profile_omega',dst+'/profile_omega')
cp(src+'/rmp_coil.dat',dst+'/rmp_coil.dat')
cp(src+'/rmp_current.dat',dst+'/rmp_current.dat')
cp(src+'/sizefieldParam',dst+'/sizefieldParam')
return
def extract_profiles(machine="DIII-D", profile="all"):
if machine in ["DIII-D", "NSTX-U"]:
profile = "all"
print "Extracting all profiles from single file"
if len(glob(r"m3dc1_profiles_*.txt")) != 0:
mysh.cp(r"m3dc1_profiles_*.txt", "m3dc1_profiles_0.txt")
prof = "m3dc1_profiles_0.txt"
elif len(glob(r"p*.*")) != 0:
mysh.cp(r"p*.*", "p0.0")
prof = "p0.0"
else:
print "Error: EFIT profiles file not found"
return
# extract profiles using Nate's utility
call(["extract_profiles.sh", prof])
if prof == "p0.0":
# extact the Carbon toroidal rotation from the p-file
with open("p0.0", "r") as fin:
iprint = False
for line in fin:
if not iprint:
if "psinorm omeg" in line:
iprint = True
fout = open("profile_omega.Ctor", "w")
else:
if "psinorm" not in line:
fout.write(line)
else:
iprint = False
fout.close()
os.remove(prof)
elif machine in ["AUG"]:
print "Extracting profile " + profile
if profile in ["all", "ne"]:
if len(glob(r"neprof_*.asc")) != 0:
mysh.cp(r"neprof_*.asc", "neprof_0.asc")
prof = "neprof_0.asc"
ne = np.loadtxt("neprof_0.asc")
ne[:, 0] = ne[:, 0] ** 2
ne[:, 1] = ne[:, 1] * 1e-20
ne = ne[ne[:, 0] <= 1.0]
np.savetxt("profile_ne", ne, fmt="%.6e", delimiter=" ")
os.remove(prof)
if profile in ["all", "te", "Te"]:
if len(glob(r"Teprof_*.asc")) != 0:
mysh.cp(r"Teprof_*.asc", "Teprof_0.asc")
prof = "Teprof_0.asc"
Te = np.loadtxt("Teprof_0.asc")
Te[:, 0] = Te[:, 0] ** 2
Te[:, 1] = Te[:, 1] * 1e-3
Te = Te[Te[:, 0] <= 1.0]
np.savetxt("profile_te", Te, fmt="%.6e", delimiter=" ")
os.remove(prof)
if profile in ["all", "vt", "vtor"]:
if len(glob(r"vtprof_*.asc")) != 0:
mysh.cp(r"vtprof_*.asc", "vtprof_0.asc")
prof = "vtprof_0.asc"
vt = np.loadtxt("vtprof_0.asc")
vt[:, 0] = vt[:, 0] ** 2
vt[:, 1] = vt[:, 1] * 1e-3
vt = vt[vt[:, 0] <= 1.0]
np.savetxt("profile_omega.Btor", vt, fmt="%.6e", delimiter=" ")
os.remove(prof)
mysh.cp(r"profile_omega.Btor", "profile_omega")
if profile in ["all", "omgeb", "ExB"]:
if len(glob(r"omgeb_*.asc")) != 0:
mysh.cp(r"omgeb_*.asc", "omgeb_0.asc")
prof = "omgeb_0.asc"
omgeb = np.loadtxt("omgeb_0.asc")
omgeb[:, 0] = omgeb[:, 0] ** 2
omgeb[:, 1] = omgeb[:, 1] * 1e-3
omgeb = omgeb[omgeb[:, 0] <= 1.0]
# interpolate profile omega onto Te grid
if len(glob(r"profile_te")) != 0:
Te = np.loadtxt("profile_te")
Pte = Te[:, 0]
O = interp1d(omgeb[:, 0], omgeb[:, 1], fill_value="extrapolate")
om2 = O(Pte)
omgeb = np.transpose(np.array([Pte, om2]))
np.savetxt("profile_omega.ExB", omgeb, fmt="%.6e", delimiter=" ")
os.remove(prof)
mysh.cp(r"profile_omega.ExB", "profile_omega")
return
def autoC1(task='all',machine='DIII-D',C1inputs=None,
interactive=True, OMFIT=False, calcs=[(0,0,0)]):
if task == 'all':
task = 'setup'
if OMFIT:
interactive = False
template = os.environ.get('AUTOC1_HOME')+'/templates/'+ machine + '/'
if machine is 'DIII-D':
rot = 'eb1'
elif machine is 'NSTX-U':
rot = 'eb1'
elif machine is 'AUG':
rot = 'eb1'
else:
rot = 'eb1'
C1arch = os.environ.get('M3DC1_ARCH')
if C1arch == 'sunfire.r6':
submit_batch = ['sbatch','batch_slurm']
elif C1arch == 'saturn':
submit_batch = ['qsub','batch_torque']
else:
print 'Error: autoC1 does not support M3DC1_ARCH = '+C1arch
return
if task == 'setup':
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'Setting up equilibrium files in efit/'
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print
os.chdir('efit/')
if not OMFIT:
mysh.cp(r'g*.*','geqdsk')
extract_profiles(machine=machine)
if machine in ['DIII-D','NSTX-U']:
fc = open('current.dat','w')
mysh.cp(r'a*.*','a0.0')
call(['a2cc', 'a0.0'], stdout=fc)
fc.close()
os.remove('a0.0')
if interactive:
next = '-'
while next not in ['Y','N']:
next = raw_input('>>> Would you like to extend profile_ne and profile_te? (Y/N) ')
if next == 'Y':
print "Trying: extend_profile('profile_ne',minval=1e-2,psimax=1.1,psimin=0.95,center=0.98,width=0.01,smooth=None)"
loop_extprof('profile_ne',minval=1e-2,psimax=1.1,psimin=0.95,
center=0.98,width=0.01,smooth=None)
os.rename('profile_ne.extpy','profile_ne')
print "Trying: extend_profile('profile_te',minval=1e-4,psimax=1.1,psimin=0.95,center=0.98,width=0.01,smooth=None)"
loop_extprof('profile_te',minval=1e-4,psimax=1.1,psimin=0.95,
center=0.98,width=0.01,smooth=None)
os.rename('profile_te.extpy','profile_te')
print
print 'Using extended profiles'
print
elif next == 'N':
print 'Using default profiles'
else:
print '*** Improper response ***'
os.chdir('..')
task = 'efit'
print
print
else:
print 'Skipping setup of equilibrium files'
print
if task == 'efit':
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'Calculating EFIT equilibrium in uni_efit/'
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print
if not os.path.isdir('uni_efit/'):
sh.copytree(template+'uni_efit/','uni_efit')
load_equil('efit/','uni_efit/')
os.chdir('uni_efit/')
mod_C1input(C1inputs)
call(submit_batch)
print
if machine in ['AUG']:
while not os.path.exists('time_000.h5'):
sleep(10)
call("\idl -e '@get_aug_currents'",shell=True)
os.chdir('..')
task = 'uni_equil'
print
print
else:
print 'Skipping calculation of EFIT equilibrium'
print
if task == 'uni_equil':
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'Calculating equilibrium with M3D-C1 GS solver in uni_equil/'
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print
if not os.path.isdir('uni_equil/'):
sh.copytree(template+'uni_equil/','uni_equil')
load_equil('efit/','uni_equil/')
os.chdir('uni_equil/')
mod_C1input(C1inputs)
if interactive:
while True:
min_iter = raw_input('>>> Please enter minimum iteration number: ')
try:
min_iter = int(min_iter)
if min_iter < 1:
print '*** min_iter must be greater than or equal to 1 ***'
else:
break
except ValueError:
print '*** min_iter must be an integer ***'
else:
min_iter = 1
iter = 0
for iter in range(1,min_iter):
call(submit_batch)
print
while not os.path.exists('time_000.h5'):
sleep(10)
print '>>> iter '+str(iter)+' time_000.h5 created'
print check_output('grep "Final error in GS solution" C1stdout',shell=True)
os.mkdir('iter_'+str(iter))
move_iter('iter_'+str(iter)+'/')
next = 'Y'
iter += 1
while next != 'N':
call(submit_batch)
print
while not os.path.exists('time_000.h5'):
sleep(10)
print
print '>>> iter '+str(iter)+' time_000.h5 created'
print check_output('grep "Final error in GS solution" C1stdout',shell=True)
os.mkdir('iter_'+str(iter))
move_iter('iter_'+str(iter)+'/')
if interactive:
print '>>> Check the equilibrium match for iter_'+str(iter)
next = '-'
while next not in ['Y','N']:
next = raw_input('>>> Would you like to do another iteration? (Y/N) ')
if next == 'Y':
iter += 1
elif next == 'N':
break
else:
print '*** Improper response ***'
else:
next = 'N'
else:
print '>>> Continuing to mesh adaptation'
print '>>> Check the equilibrium match for iter_'+str(iter)
print
print '>>> Stopped equilibrium iteration after ',iter,' iterations'
os.chdir('..')
if interactive:
next = '-'
while next not in ['Y','N']:
next = raw_input('>>> Would you like to continue onto mesh adaptation? (Y/N) ')
if next == 'Y':
mysh.cp('uni_equil/iter_'+str(iter)+'/current.dat','uni_equil/current.dat.good')
continue
elif next == 'N':
return
else:
print '*** Improper response ***'
else:
f = plt.figure(figsize=(16,5))
gs= gridspec.GridSpec(1,4,width_ratios=[4,5,5,5])
fs = 0.5
ax = plt.subplot(gs[0])
C1py.plot_shape(folder=['uni_efit/','uni_equil/iter_1/'],
rrange=[1.0,2.5],zrange=[-1.25,1.25],
fs=fs,ax=ax,title='Shape')
leg = ax.legend(fontsize=24*fs,frameon=True,loc=[0.6,0.85])
leg.get_frame().set_facecolor('white')
plts = [('ne',r'$n_e$',plt.subplot(gs[1])),
('te',r'$T_e$',plt.subplot(gs[2])),
('ti',r'$T_i$',plt.subplot(gs[3]))]
for field,title,ax in plts:
C1py.plot_field(field,filename='uni_equil/iter_1/C1.h5',
slice=-1,rrange=[1.0,2.5],zrange=[-1.25,1.25],
lcfs=True,range=[-1,1],fs=fs,ax=ax,
title=title,palette='coolwarm')
f.tight_layout()
plt.show()
f.savefig('equil_check.pdf')
mysh.cp('uni_equil/iter_'+str(iter)+'/current.dat','uni_equil/current.dat.good')
task = 'adapt'
print
print
else:
print 'Skipping calculation of equilibrium with M3D-C1 GS solver'
print
if task == 'adapt':
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'Adapting mesh to equilibrium in rw1_adapt/'
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print
if not os.path.isdir('rw1_adapt/'):
sh.copytree(template+'rw1_adapt/','rw1_adapt')
load_equil('efit/','rw1_adapt/')
mysh.cp('uni_equil/current.dat.good', 'rw1_adapt/current.dat')
os.chdir('rw1_adapt/')
mod_C1input(C1inputs)
call(submit_batch)
print
print '>>> Wait for adapted0.smb to be created'
while not os.path.exists('adapted0.smb'):
sleep(10)
print '>>> Mesh adaptation complete'
os.chdir('..')
task = 'calculation'
print
print
else:
print 'Skipping mesh adaptation'
print
if interactive:
calcs = None
else:
ncalc = 0
opts = {'0':'exit',
'1':'equilibrium',
'2':'stability',
'3':'response',
'4':'examine'}
while True:
if task == 'calculation':
if interactive:
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print
print '>>> What kind of calculation would you like to perform?'
print '>>> 1) Equilibrium'
print '>>> 2) Linear stability'
print '>>> 3) Linear 3D response'
print '>>> 4) Examine results with IDL'
print
option = '-'
while option not in opts:
option = raw_input('>>> Please enter the desired option (1-4, 0 to exit): ')
if option not in opts:
print '*** Improper response ***'
print
task = opts[option]
else:
if ncalc == len(calcs):
task = exit
else:
option, ntor, nflu = calcs[ncalc]
task = opts[option]
print task + ' calculation'
if ntor is not None:
print ' n='+ntor
if nflu is not None:
print ' '+nflu+'-fluid'
print
if task == 'exit':
print 'Exiting'
return
elif task == 'equilibrium':
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'Calculate equilibrium with adapted mesh'
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print
if not os.path.isdir('rw1_equil/'):
sh.copytree(template+'rw1_equil/','rw1_equil')
load_equil('rw1_adapt/','rw1_equil/')
mysh.cp('rw1_adapt/adapted0.smb', 'rw1_equil/adapted0.smb')
os.chdir('rw1_equil/')
mod_C1input(C1inputs)
call(submit_batch)
print
print '>>> Job m3dc1_equil submitted'
if interactive:
print '>>> You can do other calculations in the meantime'
raw_input('>>> Press <ENTER> twice to start another calculation')
raw_input('>>> Press <ENTER> again to proceed')
os.chdir('..')
print
print
elif task == 'stability':
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'Calculate linear stability'
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print
if interactive:
while True:
ntor = raw_input('>>> Please enter the desired ntor: ')
try:
int(ntor)
break
except ValueError:
print '*** ntor must be an integer ***'
nflu = ''
while nflu not in ['1','2']:
nflu = raw_input('>>> How many fluids? (1 or 2) ')
if nflu not in ['1','2']:
print '*** Improper response ***'
print
print 'Calculating stability for '+nflu+'F and ntor = ' + ntor
ndir = 'n='+ntor+'/'
if not os.path.isdir(ndir):
os.mkdir(ndir)
os.chdir(ndir)
stab = rot+'_'+nflu+'f_stab/'
if not os.path.isdir(stab):
sh.copytree(template+'n=/'+stab,stab)
load_equil('../rw1_adapt/',stab)
mysh.cp('../rw1_adapt/adapted0.smb', stab+'adapted0.smb')
os.chdir(stab)
mod_C1input(C1inputs)
for line in fileinput.input('C1input',inplace=1):
print re.sub(r'ntor = ','ntor = '+ntor,line.rstrip('\n'))
call(submit_batch)
print
print '>>> Job m3dc1_stab submitted'
if interactive:
print '>>> You can do other calculations in the meantime'
raw_input('>>> Press <ENTER> twice to start another calculation')
raw_input('>>> Press <ENTER> again to proceed')
os.chdir('../..')
print
print
elif task == 'response':
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'Calculate 3D plasma response'
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print
if interactive:
while True:
ntor = raw_input('>>> Please enter the desired ntor: ')
try:
int(ntor)
break
except ValueError:
print '*** ntor must be an integer ***'
nflu = ''
while nflu not in ['1','2']:
nflu = raw_input('>>> How many fluids? (1 or 2) ')
if nflu not in ['1','2']:
print '*** Improper response ***'
print
print 'Calculating '+nflu+'F response for ntor = ' + ntor
ndir = 'n='+ntor+'/'
if not os.path.isdir(ndir):
os.mkdir(ndir)
os.chdir(ndir)
up = rot+'_'+nflu+'f_iu/'
low = rot+'_'+nflu+'f_il/'
if not os.path.isdir(up):
sh.copytree(template+'n=/'+up,up)
load_equil('../rw1_adapt/',up)
mysh.cp('../rw1_adapt/adapted0.smb', up+'adapted0.smb')
os.chdir(up)
mod_C1input(C1inputs)
for line in fileinput.input('C1input',inplace=1):
print re.sub(r'ntor = ','ntor = '+ntor,line.rstrip('\n'))
call(submit_batch)
os.chdir('..')
if not os.path.isdir(low):
sh.copytree(template+'n=/'+low,low)
load_equil('../rw1_adapt/',low)
mysh.cp('../rw1_adapt/adapted0.smb', low+'adapted0.smb')
os.chdir(low)
mod_C1input(C1inputs)
for line in fileinput.input('C1input',inplace=1):
print re.sub(r'ntor = ','ntor = '+ntor,line.rstrip('\n'))
call(submit_batch)
print
print '>>> Jobs m3dc1_iu and m3dc1_il submitted'
if interactive:
print '>>> You can do other calculations in the meantime'
raw_input('>>> Press <ENTER> twice to start another calculation')
raw_input('>>> Press <ENTER> again to proceed')
os.chdir('../..')
print
print
elif task == 'examine':
print '>>> Here are some good things to check:'
print '>>> Is the adapted equilbrium a good shape match?'
print ">>> Is 'jy' a good match to the EFIT?"
print ">>> Does 'ne', 'te', 'ti', or 'p' go negative anywhere?"
print
if interactive:
next = '-'
while next not in ['Y','N']:
next = raw_input('>>> Would you like to check the quality of the equilibrium? (Y/N) ')
if next == 'Y':
print 'Launching IDL for checking quality of the equilibrium'
print 'Recommend the following commands, but modify as need be'
print 'e.g., rw1_equil/ can be replaced by a completed response or stability run in n=2/'
print "plot_shape,['uni_efit/','rw1_equil/']+'C1.h5',rrange=[1.0,2.5],zrange=[-1.25,1.25],thick=3,/iso"
print "plot_flux_average,'jy',-1,file=['uni_efit/','rw1_equil/']+'C1.h5',/mks,/norm,table=39,thick=3,bins=400,points=400"
print "plot_field,'ti',-1,R,Z,file='rw1_equil/C1.h5',/mks,points=400,cutz=0.,/ylog"
print
call(['idl'])
okay = '-'
while okay not in ['Y','N']:
okay = '>>> Is the equilibrium good enough to continue? (Y/N) '
if okay == 'Y':
continue
elif okay == 'N':
return
else:
print '*** Improper response ***'
elif next == 'N':
print 'Continuing, but equilibrium may have problems'
else:
print '*** Improper response ***'
else:
print ">>> In non-interactive mode"
print ">>> Please launch IDL separately"
task = 'calculation'
if not interactive:
ncalc +=1
return
def load_equil(src,dst):
cp(src+'/geqdsk',dst+'/geqdsk')
cp(src+'/profile_ne',dst+'/profile_ne')
cp(src+'/profile_te',dst+'/profile_te')
cp(src+'/profile_omega',dst+'/profile_omega')
cp(src+'/profile_vphi',dst+'/profile_vphi')
cp(src+'/current.dat',dst+'/current.dat')
return