# public fuentesdt /UQGenPolyChaos forked from ImageGuidedTherapyLab/UQGenPolyChaos

### Subversion checkout URL

You can clone with HTTPS or Subversion.

Fetching contributors…

Cannot retrieve contributors at this time

file 139 lines (136 sloc) 5.957 kb
 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 [exec]work_dir = dog1scratch_dir = /dev/shmphysics = AddPennesSDASystem;physics = AddPennesRFSystem;physics = AddPennesDeltaPSystem[dakota];responselevels [ (variable # , response list) ,(variable # , response list) , ... ] ;responselevels = [(0,[42.0,57.0,90.0]),(1,[0.5,0.8,1.0]),(3,[10.0,100.0,1000.0])]responselevels = [("u0",[42.0,57.0,90.0]),("d0",[0.5,0.8,1.0])]probabilitylevels = [0.01,0.02275,0.05,0.5,0.95,0.97725,0.99]reliabilitylevels = [0.15,0.59][pre_run]#mesh_files = [clusterVesselDistance0.150000Diameter10.000000.e,clusterVesselDistance4.000000Diameter5.000000.e]mesh_files = [meshTemplateFull3.e][timestep]acquisitiontime = 6.00nsubstep = 6powerhistory = [[19,28,46,78,119],[0.0,4.0,0.0,9.0,0.0]]#powerhistory = [[1],[9.0]][initial_condition]u_init = 34.3[material]rho = 1045specific_heat = 3600[perfusion]; linearity is superset of nonlinearityw_0_healthy = 6.0; CRC Handbook Thermal Engineering 2000w_0_healthy_gpc = {'type':'uniform_uncertain','quadrature_order':4,'lower_bound':0,'upper_bound':9}w_1_coag_gpc = {'type':'uniform_uncertain','quadrature_order':4,'lower_bound':0,'upper_bound':3}c_blood = 3840[thermal_conductivity]k_0_healthy = 0.527; Duck Physical Properties of Tissue 1990 ; CRC Handbook Thermal Engineering 2000k_0_healthy_gpc = {'type':'uniform_uncertain','quadrature_order':4,'lower_bound':.49,'upper_bound':.58}[optical]; Yaroslavsky optical properties of human brain tissues 2002; wavelength: 980mm; white matter native scattering 30 - 40 1/mm; white matter native absorption .09-.15 1/mm; grey matter native scattering 5 - 6 1/mm; grey matter native absorption .02-.08 1/mm; white matter coagulated scattering 30 - 40 1/mm; white matter coagulated absorption .10-.25 1/mm; grey matter coagulated scattering 15 - 20 1/mm; grey matter coagulated absorption .1 -.2 1/mm; Welch optical-thermal response of laser irradiate tissue 1995 ; wavelength: 1064mm; white matter native scattering 469 \pm 34 1/cm; white matter native absorption 3.2 \pm .4 1/cm; grey matter native scattering 134 \pm 14 1/cm; grey matter native absorption 5.0 \pm .5 1/cm ; ; welch does not have coagulated values; to 'estimate' the corresponding coagulated values of welch; lets assume that the ratio of the difference is constant between yaro and welch, ; ie; ; coag - native coag - native; ------------- = ------------- ; native native ;; white matter coagulated scattering [((30.- 30.)/30.)*435.+435.,((40. - 40.)/ 40.)*503.+503.] = [435.0, 503.0] 1/cm; white matter coagulated absorption [((.1 - .09)/.09)*2.8 +2.8 ,((.250 -.150)/.150)*3.6 +3.6 ] = [3.1 , 6.0 ] 1/cm; grey matter coagulated scattering [((15.- 5. )/5. )*120.+120.,((20. - 6. )/6.) *148.+148.] = [360.0, 493.3] 1/cm; grey matter coagulated absorption [((.1 - .02)/.02)*4.5 +4.5 ,((.2 - .08)/ .08)*5.5 +5.5 ] = [22.5 , 13.75] 1/cm; grey matter coagulated absorption [((.1 - .02)/.1 )*4.5 +4.5 ,((.2 - .08)/ .2 )*5.5 +5.5 ] = [8.1 , 8.8 ] 1/cm;mu_s_healthy = 14000.mu_s_healthy_gpc = {'type':'uniform_uncertain','quadrature_order':4,'lower_bound':5000,'upper_bound':50000}mu_s_coag_gpc = {'type':'uniform_uncertain','quadrature_order':4,'lower_bound':30000,'upper_bound':50000} ; linearity is superset of nonlinearitymu_a_healthy = 500.mu_a_healthy_gpc = {'type':'uniform_uncertain','quadrature_order':4,'lower_bound':50,'upper_bound':600} mu_a_coag_gpc = {'type':'uniform_uncertain','quadrature_order':4,'lower_bound':300,'upper_bound':600} anfact = 0.88e0[bc]; node set 1 will be treated as dirichlet bc;u_dirichlet = 1 4u_dirichlet = 1 [probe]domain = 2applicatordomain = 1;tip;x_0 = .2069;y_0 = .245;x_0 = -.0345;centerx_0 = .206y_0 = .289z_0 = -.0215## # handle perfusion specially for agar## DataSetParams['default_perfusion'] = '6.0'## if (options.data_set == "dog1"):## DataSetParams['acquisitionTime'] = 6.00## DataSetParams['nsubstep'] = 6## DataSetParams['u_init'] = 34.3## DataSetParams['powerHistory'] = [[19,28,46,78,119],[0.0,4.0,0.0,9.0,0.0]]## elif (options.data_set == "dog2"):## DataSetParams['acquisitionTime'] = 6.00## DataSetParams['nsubstep'] = 6## DataSetParams['u_init'] = 35.9## DataSetParams['powerHistory'] = [[14,16,27,39,41,46,52,55,59,74,82,86,90,95,122],[0.0,6.0,0.0,10.05,0.0,11.25,0.0,11.25,0.0,11.25,0.0,13.2,0.0,12.0,0.0]]## elif (options.data_set == "dog3"):## DataSetParams['acquisitionTime'] = 6.00## DataSetParams['nsubstep'] = 6## DataSetParams['u_init'] = 33.9## DataSetParams['powerHistory'] = [[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]]## elif (options.data_set == "dog4"):## DataSetParams['acquisitionTime'] = 5.00## DataSetParams['nsubstep'] = 5## DataSetParams['u_init'] = 34.3## DataSetParams['powerHistory'] = [[20,31,61],[0.0,15.0,0.0]]## elif (options.data_set == "human0"):## DataSetParams['acquisitionTime'] = 5.00## DataSetParams['nsubstep'] = 5## DataSetParams['u_init'] = 36.7## DataSetParams['powerHistory'] = [ [17,27,39,69,128],[0.0,4.05,0.0,10.05,0.0] ]## # handle perfusion specially for human brain## DataSetParams['default_perfusion'] = '9.0'## elif (options.data_set == "agar0"):## DataSetParams['acquisitionTime'] = 5.00## DataSetParams['nsubstep'] = 5## DataSetParams['u_init'] = 21.0## DataSetParams['powerHistory'] = [[5,75,150],[0.0,5.0,0.0]]## # handle perfusion specially for agar## DataSetParams['default_perfusion'] = '0.0'## elif (options.data_set == "tmp"):## DataSetParams['acquisitionTime'] = 5.00## DataSetParams['nsubstep'] = 5## DataSetParams['u_init'] = 37.0## DataSetParams['powerHistory'] = [[20,31,61],[0.0,15.0,0.0]]## elif(options.run_queue == None):## raise RuntimeError("data set not chosen")
Something went wrong with that request. Please try again.