[method]
pde = 1
;qoi = 4
qoi = 1
[qoi_0]
init_time_window = [0,74]
noffset =  0
numideal =  0
plotoptsolve = true
[perfusion]
w_0_probe = 48.35e0
;w_0_healthy = 6.0;12.0;18.0;24.0;30.0;42.0;54.0;66.0;72.0;84.0
;w_0_healthy = 6.0;18.0;30.0;42.0
w_0_healthy = 0.0;3.0;6.0;12.0
w_n = 0.0e0
w_i = 0.0e0
w_d = 0.0e0
w_2 = 0.0e0
w_ni = 305.0e0
w_id = 315.0e0
[thermal_conductivity]
k_0_probe = .5e0
k_0_healthy = .527e0
k_1 = 0.0e0
k_2 = 0.0e0
k_3 = 0.0e0
[compexec]
;meshdata=s129226-files/s129226_smooth.e
;meshdata = s129226-files/s129226_cooledTip.e
;meshdata = generic-mesh/tumorTemplateLoRes.e
;meshdata = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/generic-mesh/meshTemplate.e
meshdata = /work/00131/fuentes/data/mdacc/canine_feb07/generic-mesh/meshTemplateLowerRes.e;/work/00131/fuentes/data/mdacc/canine_feb07/generic-mesh/meshTemplateLoRes.e;/work/00131/fuentes/data/mdacc/canine_feb07/generic-mesh/meshTemplateNormRes.e;/work/00131/fuentes/data/mdacc/canine_feb07/generic-mesh/meshTemplateHiRes.e
;meshfile=/org/groups/oden/fuentes/DDDAS/data/mdacc/canine_oct08/canine_feb07/s129226-files/s129226_2d.e
;>>> .97 * 12
;11.640000000000001
;>>> .80 * 12
;9.6000000000000014
;>>> .34 * 12
;4.0800000000000001
powerdata = [9,13,17,22,23,24,39,46,74]@[0.0,4.2,0.0,14.54,0.0,14.54,0.0,12.0,0.0]
;executable = image
executable = dddas
;meshrefine = 1
jobid = dog3fem980
;numproc = 1
numproc = 16;16;32;48
solver = superlu_dist
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
b0 = .209
b1 = .2625
b2 = -.0247
; FIRST R1 rotation Then R3 rotation.... (not commutative) 
;-90deg  R1  --->  -8deg R3 rotation  (NEGATIVE OF PARAVIEW)
; |  cos \theta   sin \theta   0 |    | 1        0            0      |   
; | -sin \theta   cos \theta   0 |    | 0    cos \gamma   sin \gamma |   
; |       0            0       1 |    | 0   -sin \gamma   cos \gamma |   
;
; |  cos \theta   sin \theta   0 |    | 1        0            0      |   
; | -sin \theta   cos \theta   0 |    | 0        0           -1      |   
; |       0            0       1 |    | 0        1            0      |   
;
; |  cos \theta  0  -sin \theta  |    
; | -sin \theta  0  -cos \theta  |
; |       0      1      0        |
;
a11 = 0.0
a22 = 0.0
;>>> cos(pi/180.*8.)
;0.99026806874157036
;>>> sin(pi/180.*8.)
;0.13917310096006544
a00 =  0.99026806874157036
a02 =  0.13917310096006544
a10 =  0.13917310096006544
a12 = -0.99026806874157036
a21 =  1.0
[bc]
u_dirichletid = 1
u_flux = 0.0
newton_coeff = 0.0
[optical]
mu_a_healthy = 5.0e2
mu_a_tumor = 2.38e2
mu_a_probe = 0.0195e0
mu_s_healthy = 140.0e2
mu_s_tumor = 3.5e2
mu_s_probe = 100.0e0
anfact = 0.88e0
[initial_condition]
z_init = 7.431e4
probe_init = 21.0;33.9
u_init = 33.9
[output]
;writeinterval = 1
[probe]
domain = 2;10
;center
x_0 = .209
y_0 = .2625
z_0 = -.0247
[timestep]
isteps_per_ideal = 6
ideal_dt = 6.0e0
[mrti]
filein = /work/00131/fuentes/data/mdacc/canine_feb07/980brainStat/dog3_980/dog3_98000/mrivis/temperature.%04d.vtk
uncertaintyin = /work/00131/fuentes/data/mdacc/canine_feb07/980brainStat/dog3_980/dog3_98000/mrivis/tmapstd.%04d.vtk
;filein = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat/dog3_980/dog3_98000/mrivis/temperature.%04d.vtk
;uncertaintyin = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat/dog3_980/dog3_98000/mrivis/tmapstd.%04d.vtk
ntime = 74
dictionary = $ITK_SOURCE/Utilities/gdcm/Dicts/GEMS.dic
exampath = /FUS4/data2/BioTex/Brain_PhaseII/070205_BrainDog3_Treat/e126515
dirid =    128475
;ixlo = 90  
;ixhi = 140 
;iylo = 125
;iyhi = 175
ixlo = 132 
ixhi = 152 
iylo = 118
iyhi = 142
[kalman]
method = 2
roi = [0,255,0,255]
magix = 65
magiy = 65