[visualase]
visualase_file = mlat.dat
override = False
visualase_dir = /tmp
override_power = 0.0

[perfusion]
w_0_probe = 48.35e0
w_n_lb =  4.0e0 
w_2_lb =  1.0e-1
w_i = 0.000000
w_i_ub =  1.0e2 
w_d_ub =  4.0e0 
w_d_lb =  0.0e0 
w_0_ub =  50.0e0
w_0_healthy = 3.000000
w_ni = 305.000000
w_0_lb =  6.0e0 
w_nid_ub = 335.0e0
w_i_lb = 20.0e0 
w_n = 0.000000
w_nid_lb = 300.0e0
w_id = 315.000000
w_d = 0.000000
w_2_ub =  10.0e0
w_n_ub = 20.0e0 
w_nid_md = 315.0e0
w_2 = 0.000000

[kalman]
magiy = 65
magix = 65

[thermal_conductivity]
k_3_lb = 305.0e0
k_1_lb = 0.0e0  
k_0_ub = 0.720000
k_1 = 0.000000
k_0_lb = 0.40e0 
k_3 = 0.000000
k_2 = 0.000000
k_2_lb = 1.0e-2 
k_0_probe = .5e0
k_0_healthy = 0.527000
k_2_ub = 10.0e0 
k_1_ub = 0.330000
k_3_ub = 325.0e0

[timestep]
isteps_per_ideal = 6
ideal_dt = 6.0e0

[probe]
z_0 = -0.033500
domain = 2
x_0 = 0.233500
y_0 = 0.234000

[mrti]
img_sizefile = mrtiimg.size
dictionary = $ITK_SOURCE/Utilities/gdcm/Dicts/GEMS.dic
exampath = /FUS4/data2/BioTex/Brain_PhaseII/061113_BrainDog2_Treat/e351850
filein = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat/dog2_980/dog2_98000/mrivis/temperature.%04d.vtk
uncertaintyin = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat/dog2_980/dog2_98000/mrivis/snr.%04d.vtk
dirid = 353172
ntime = 122

[qoi_0]
init_time_window = [0,122]
noptsteps = 1
optimize_k_2 = False
optimize_k_3 = False
optimize_k_0 = False
optimize_k_1 = False
noffset = 0
plotoptsolve = true
numideal = 0
optimize_w_0 = False
optimize_pow = False
optimize_mu_a = False
ideal_ntime_init = 122
ideal_nzero_init = 0
optimize_mu_s = False

[bc]
u_dirichletid = 1
newton_coeff = 0.000000
newton_coeff_ub = 112.0e0
u_flux_lb = 0.1e0
u_flux = 0.000000
u_flux_ub = 112.0e0
newton_coeff_lb = 0.1e0

[avs]
femvis_sizefile = ucdvis.size
mrtivis_sizefile = mrtivis.size

[field]
w_0_field = False
k_0_field = False

[optical]
mu_a_healthy = 500.000000
mu_a_tumor = 2.38e2
mu_a_probe = 0.0195e0
mu_s_probe = 100.0e0
mu_s_healthy = 14000.000000
anfact = 0.880000
mu_s_tumor = 3.5e2

[compexec]
a21 = 1.0
executable = dddas
comphost = scripvl5
a11 = 0.0
a10 = -0.10452846326765347
a12 = -0.99452189536827329
a02 = -0.10452846326765347
a00 = 0.99452189536827329
a22 = 0.0
jobid = dog2verif980
execcode = cd /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat/dog2verif980/dog2verif98005 ; mpirun -n 1 $WORK/exec/dddas_$COMPILER-$MPI_VERSION-cxx-$METHOD  -snes_ls basic -info  -info_exclude null,vec,mat,pc,ksp,snes -ksp_rtol 1.e-9 -pc_type bjacobi  -snes_monitor -snes_rtol 1.e-6 -snes_converged_reason -tao_max_funcs 0  
workdir = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat
b0 = .2335
b1 = .234
b2 = -.0335
profileid = dog2verif98005
numproc = 1
runtime_options = -snes_ls basic -info  -info_exclude null,vec,mat,pc,ksp,snes -ksp_rtol 1.e-9 -pc_type bjacobi  -snes_monitor -snes_rtol 1.e-6 -snes_converged_reason -tao_max_funcs 0
method = opt
meshdata = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/generic-mesh/meshTemplate.e

[registration]
createbackupmesh = createboxmesh.py
transform_script = LBIE_2_hp3d.py 1 1
subsamplefactorx = 2
subsamplefactorz = 1
registration_exe = RigidRegistration
dicomconvert = DicomSeriesConvert
subsamplevolume = SubsampleNoFilter
registration = False
interop_dicom_dir = 
subsamplefactory = 2

[output]
femgmv = False
compwritefem = femvis/
mrtiavs = False
fem_filename = fem
computefinalobjective = false
mriavs = False
femraw = False
femavs = False
compwritemri = mrivis/
mrirawiv = False
mrtirawiv = False

[source_laser]
mu_s_ub = 2820.0e+2
pow_ub = 15.0e0
pow_lb = -0.1e0
mu_s_lb = 2.0e+2
anfact_ub = 1.0e0
mu_a_ub = 0.60e+2
mu_a_lb = 0.30e+2
anfact_lb = 0.6e0
anfact = 0.71e0

[method]
pde = 1
qoi = 4

[initial_condition]
u_init = 35.9
z_init = 7.431e4
probe_init = 34.3