strange simulation results
Summary
When the attached simple model is simulated with dune_copasi_md, the concentrations do not change.
Steps to reproduce
Simulate model
What is the current bug behaviour?
Concentrations do not change
What is the expected correct behaviour?
Concentrations change during the simulation
Relevant logs, screenshots, files...?
Anything that helps reproducing the bug
Expand to see logs
00:00:00.000 Captured DebugStream dgrave 00:00:00.000 Configuration: backend=default level=critical line_buffered=true 00:00:00.000 Captured DebugStream derr 00:00:00.000 Configuration: backend=default level=error line_buffered=true 00:00:00.000 Captured DebugStream dwarn 00:00:00.000 Configuration: backend=default level=warning line_buffered=true 00:00:00.000 Captured DebugStream dinfo 00:00:00.000 Configuration: backend=default level=notice line_buffered=true 00:00:00.000 Captured DebugStream dverb 00:00:00.000 Configuration: backend=default level=detail line_buffered=true 00:00:00.000 Captured DebugStream dvverb 00:00:00.000 Configuration: backend=default level=debug line_buffered=true 00:00:00.000 Logging system initialized at Mon 2020-09-28 20:50:59 CEST 00:00:00.000 Starting dune-copasi(md) at Mon 2020-09-28 20:50:59 CEST 00:00:00.000 Reading configuration file: 'dune.ini' 00:00:00.000 ---- 00:00:00.000 [ grid ] 00:00:00.000 dimension = "2" 00:00:00.000 file = "grid.msh" 00:00:00.000 initial_level = "0" 00:00:00.000 [ logging ] 00:00:00.000 [ logging.default ] 00:00:00.000 level = "trace" 00:00:00.000 sinks = "stdout" 00:00:00.000 [ logging.sinks ] 00:00:00.000 [ logging.sinks.stdout ] 00:00:00.000 level = "trace" 00:00:00.000 [ model ] 00:00:00.000 order = "1" 00:00:00.000 [ model.compartments ] 00:00:00.000 cyt = "1" 00:00:00.000 cyt_kern_membrane = "2" 00:00:00.000 kern = "0" 00:00:00.000 [ model.cyt ] 00:00:00.000 [ model.cyt.diffusion ] 00:00:00.000 B = "0.0100000000000000002" 00:00:00.000 [ model.cyt.initial ] 00:00:00.000 B = "1" 00:00:00.000 [ model.cyt.reaction ] 00:00:00.000 B = "B*-0.0001" 00:00:00.000 [ model.cyt.reaction.jacobian ] 00:00:00.000 dB__dB = "-0.0001" 00:00:00.000 [ model.cyt_kern_membrane ] 00:00:00.000 [ model.cyt_kern_membrane.diffusion ] 00:00:00.000 A = "0" 00:00:00.000 B = "0" 00:00:00.000 [ model.cyt_kern_membrane.initial ] 00:00:00.000 A = "1" 00:00:00.000 B = "1" 00:00:00.000 [ model.cyt_kern_membrane.reaction ] 00:00:00.000 A = "A*-0.1" 00:00:00.000 B = "A*0.1" 00:00:00.000 [ model.cyt_kern_membrane.reaction.jacobian ] 00:00:00.000 dA__dA = "-0.1" 00:00:00.000 dA__dB = "0" 00:00:00.000 dB__dA = "0.1" 00:00:00.000 dB__dB = "0" 00:00:00.000 [ model.kern ] 00:00:00.000 [ model.kern.diffusion ] 00:00:00.000 A = "0.0100000000000000002" 00:00:00.000 [ model.kern.initial ] 00:00:00.000 A = "1" 00:00:00.000 [ model.kern.reaction ] 00:00:00.000 A = "1e-05" 00:00:00.000 [ model.kern.reaction.jacobian ] 00:00:00.000 dA__dA = "0" 00:00:00.000 [ model.time_stepping ] 00:00:00.000 begin = "0" 00:00:00.000 decrease_factor = "0.5" 00:00:00.000 end = "100" 00:00:00.000 increase_factor = "1.5" 00:00:00.000 initial_step = "0.100000000000000006" 00:00:00.000 max_step = "10000" 00:00:00.000 min_step = "1.00000000000000004e-10" 00:00:00.000 rk_method = "alexander_2" 00:00:00.000 [ model.writer ] 00:00:00.000 file_path = "vtk" 00:00:00.000 ---- 00:00:00.000 Reading grid file: 'grid.msh' 00:00:00.000 Reading 2d Gmsh grid... 00:00:00.000 version 2.2 Gmsh file detected 00:00:00.000 file contains 121 nodes 00:00:00.000 file contains 197 elements 00:00:00.000 number of real vertices = 121 00:00:00.000 number of boundary elements = 0 00:00:00.000 number of elements = 197 00:00:00.001 Creating multidomain grid from host grid 00:00:00.001 Creating multidomain sub-domains 00:00:00.001 Cell 0 added to subdomain 0 00:00:00.001 Cell 1 added to subdomain 0 00:00:00.001 Cell 2 added to subdomain 0 00:00:00.001 Cell 3 added to subdomain 0 00:00:00.001 Cell 4 added to subdomain 0 00:00:00.001 Cell 5 added to subdomain 0 00:00:00.001 Cell 6 added to subdomain 0 00:00:00.001 Cell 7 added to subdomain 0 00:00:00.001 Cell 8 added to subdomain 0 00:00:00.001 Cell 9 added to subdomain 0 00:00:00.001 Cell 10 added to subdomain 0 00:00:00.001 Cell 11 added to subdomain 0 00:00:00.001 Cell 12 added to subdomain 0 00:00:00.001 Cell 13 added to subdomain 0 00:00:00.001 Cell 14 added to subdomain 0 00:00:00.002 Cell 15 added to subdomain 0 00:00:00.002 Cell 16 added to subdomain 0 00:00:00.002 Cell 17 added to subdomain 0 00:00:00.002 Cell 18 added to subdomain 0 00:00:00.002 Cell 19 added to subdomain 0 00:00:00.002 Cell 20 added to subdomain 0 00:00:00.002 Cell 21 added to subdomain 0 00:00:00.002 Cell 22 added to subdomain 0 00:00:00.002 Cell 23 added to subdomain 0 00:00:00.002 Cell 24 added to subdomain 0 00:00:00.002 Cell 25 added to subdomain 0 00:00:00.002 Cell 26 added to subdomain 0 00:00:00.002 Cell 27 added to subdomain 0 00:00:00.002 Cell 28 added to subdomain 0 00:00:00.002 Cell 29 added to subdomain 0 00:00:00.002 Cell 30 added to subdomain 0 00:00:00.002 Cell 31 added to subdomain 0 00:00:00.002 Cell 32 added to subdomain 0 00:00:00.002 Cell 33 added to subdomain 0 00:00:00.002 Cell 34 added to subdomain 0 00:00:00.002 Cell 35 added to subdomain 0 00:00:00.002 Cell 36 added to subdomain 0 00:00:00.002 Cell 37 added to subdomain 0 00:00:00.002 Cell 38 added to subdomain 0 00:00:00.002 Cell 39 added to subdomain 1 00:00:00.002 Cell 40 added to subdomain 1 00:00:00.002 Cell 41 added to subdomain 1 00:00:00.002 Cell 42 added to subdomain 1 00:00:00.002 Cell 43 added to subdomain 1 00:00:00.002 Cell 44 added to subdomain 1 00:00:00.002 Cell 45 added to subdomain 1 00:00:00.002 Cell 46 added to subdomain 1 00:00:00.002 Cell 47 added to subdomain 1 00:00:00.002 Cell 48 added to subdomain 1 00:00:00.002 Cell 49 added to subdomain 1 00:00:00.002 Cell 50 added to subdomain 1 00:00:00.002 Cell 51 added to subdomain 1 00:00:00.002 Cell 52 added to subdomain 1 00:00:00.002 Cell 53 added to subdomain 1 00:00:00.002 Cell 54 added to subdomain 1 00:00:00.002 Cell 55 added to subdomain 1 00:00:00.002 Cell 56 added to subdomain 1 00:00:00.002 Cell 57 added to subdomain 1 00:00:00.002 Cell 58 added to subdomain 1 00:00:00.002 Cell 59 added to subdomain 1 00:00:00.002 Cell 60 added to subdomain 1 00:00:00.002 Cell 61 added to subdomain 1 00:00:00.002 Cell 62 added to subdomain 1 00:00:00.002 Cell 63 added to subdomain 1 00:00:00.002 Cell 64 added to subdomain 1 00:00:00.002 Cell 65 added to subdomain 1 00:00:00.002 Cell 66 added to subdomain 1 00:00:00.002 Cell 67 added to subdomain 1 00:00:00.002 Cell 68 added to subdomain 1 00:00:00.002 Cell 69 added to subdomain 1 00:00:00.002 Cell 70 added to subdomain 1 00:00:00.002 Cell 71 added to subdomain 1 00:00:00.002 Cell 72 added to subdomain 1 00:00:00.002 Cell 73 added to subdomain 1 00:00:00.002 Cell 74 added to subdomain 1 00:00:00.002 Cell 75 added to subdomain 1 00:00:00.002 Cell 76 added to subdomain 1 00:00:00.002 Cell 77 added to subdomain 1 00:00:00.002 Cell 78 added to subdomain 1 00:00:00.002 Cell 79 added to subdomain 1 00:00:00.002 Cell 80 added to subdomain 1 00:00:00.002 Cell 81 added to subdomain 1 00:00:00.002 Cell 82 added to subdomain 1 00:00:00.002 Cell 83 added to subdomain 1 00:00:00.002 Cell 84 added to subdomain 1 00:00:00.002 Cell 85 added to subdomain 1 00:00:00.002 Cell 86 added to subdomain 1 00:00:00.002 Cell 87 added to subdomain 1 00:00:00.002 Cell 88 added to subdomain 1 00:00:00.002 Cell 89 added to subdomain 1 00:00:00.002 Cell 90 added to subdomain 1 00:00:00.002 Cell 91 added to subdomain 1 00:00:00.002 Cell 92 added to subdomain 1 00:00:00.002 Cell 93 added to subdomain 1 00:00:00.002 Cell 94 added to subdomain 1 00:00:00.002 Cell 95 added to subdomain 1 00:00:00.002 Cell 96 added to subdomain 1 00:00:00.002 Cell 97 added to subdomain 1 00:00:00.002 Cell 98 added to subdomain 1 00:00:00.002 Cell 99 added to subdomain 1 00:00:00.002 Cell 100 added to subdomain 1 00:00:00.002 Cell 101 added to subdomain 1 00:00:00.002 Cell 102 added to subdomain 1 00:00:00.002 Cell 103 added to subdomain 1 00:00:00.002 Cell 104 added to subdomain 1 00:00:00.002 Cell 105 added to subdomain 1 00:00:00.002 Cell 106 added to subdomain 1 00:00:00.002 Cell 107 added to subdomain 1 00:00:00.002 Cell 108 added to subdomain 1 00:00:00.002 Cell 109 added to subdomain 1 00:00:00.002 Cell 110 added to subdomain 1 00:00:00.002 Cell 111 added to subdomain 1 00:00:00.002 Cell 112 added to subdomain 1 00:00:00.002 Cell 113 added to subdomain 1 00:00:00.002 Cell 114 added to subdomain 1 00:00:00.002 Cell 115 added to subdomain 1 00:00:00.002 Cell 116 added to subdomain 1 00:00:00.002 Cell 117 added to subdomain 1 00:00:00.002 Cell 118 added to subdomain 1 00:00:00.002 Cell 119 added to subdomain 1 00:00:00.002 Cell 120 added to subdomain 1 00:00:00.002 Cell 121 added to subdomain 1 00:00:00.002 Cell 122 added to subdomain 1 00:00:00.002 Cell 123 added to subdomain 1 00:00:00.002 Cell 124 added to subdomain 1 00:00:00.002 Cell 125 added to subdomain 1 00:00:00.002 Cell 126 added to subdomain 1 00:00:00.002 Cell 127 added to subdomain 1 00:00:00.002 Cell 128 added to subdomain 1 00:00:00.002 Cell 129 added to subdomain 1 00:00:00.002 Cell 130 added to subdomain 1 00:00:00.002 Cell 131 added to subdomain 1 00:00:00.002 Cell 132 added to subdomain 1 00:00:00.002 Cell 133 added to subdomain 1 00:00:00.002 Cell 134 added to subdomain 1 00:00:00.002 Cell 135 added to subdomain 1 00:00:00.002 Cell 136 added to subdomain 1 00:00:00.002 Cell 137 added to subdomain 1 00:00:00.002 Cell 138 added to subdomain 1 00:00:00.002 Cell 139 added to subdomain 1 00:00:00.002 Cell 140 added to subdomain 1 00:00:00.002 Cell 141 added to subdomain 1 00:00:00.002 Cell 142 added to subdomain 1 00:00:00.002 Cell 143 added to subdomain 1 00:00:00.002 Cell 144 added to subdomain 1 00:00:00.002 Cell 145 added to subdomain 1 00:00:00.002 Cell 146 added to subdomain 1 00:00:00.002 Cell 147 added to subdomain 1 00:00:00.002 Cell 148 added to subdomain 1 00:00:00.002 Cell 149 added to subdomain 1 00:00:00.002 Cell 150 added to subdomain 1 00:00:00.002 Cell 151 added to subdomain 1 00:00:00.002 Cell 152 added to subdomain 1 00:00:00.002 Cell 153 added to subdomain 1 00:00:00.002 Cell 154 added to subdomain 1 00:00:00.002 Cell 155 added to subdomain 1 00:00:00.002 Cell 156 added to subdomain 1 00:00:00.002 Cell 157 added to subdomain 1 00:00:00.002 Cell 158 added to subdomain 1 00:00:00.002 Cell 159 added to subdomain 1 00:00:00.002 Cell 160 added to subdomain 1 00:00:00.002 Cell 161 added to subdomain 1 00:00:00.002 Cell 162 added to subdomain 1 00:00:00.002 Cell 163 added to subdomain 1 00:00:00.002 Cell 164 added to subdomain 1 00:00:00.002 Cell 165 added to subdomain 1 00:00:00.002 Cell 166 added to subdomain 1 00:00:00.002 Cell 167 added to subdomain 1 00:00:00.002 Cell 168 added to subdomain 1 00:00:00.002 Cell 169 added to subdomain 1 00:00:00.002 Cell 170 added to subdomain 1 00:00:00.002 Cell 171 added to subdomain 1 00:00:00.002 Cell 172 added to subdomain 1 00:00:00.002 Cell 173 added to subdomain 1 00:00:00.002 Cell 174 added to subdomain 1 00:00:00.002 Cell 175 added to subdomain 1 00:00:00.002 Cell 176 added to subdomain 1 00:00:00.002 Cell 177 added to subdomain 1 00:00:00.002 Cell 178 added to subdomain 1 00:00:00.002 Cell 179 added to subdomain 1 00:00:00.002 Cell 180 added to subdomain 1 00:00:00.002 Cell 181 added to subdomain 1 00:00:00.002 Cell 0 added to subdomain 2 00:00:00.002 Cell 1 added to subdomain 2 00:00:00.002 Cell 2 added to subdomain 2 00:00:00.002 Cell 3 added to subdomain 2 00:00:00.002 Cell 4 added to subdomain 2 00:00:00.002 Cell 5 added to subdomain 2 00:00:00.002 Cell 6 added to subdomain 2 00:00:00.002 Cell 7 added to subdomain 2 00:00:00.002 Cell 8 added to subdomain 2 00:00:00.002 Cell 9 added to subdomain 2 00:00:00.002 Cell 10 added to subdomain 2 00:00:00.002 Cell 11 added to subdomain 2 00:00:00.002 Cell 12 added to subdomain 2 00:00:00.002 Cell 13 added to subdomain 2 00:00:00.002 Cell 14 added to subdomain 2 00:00:00.002 Grid info 00:00:00.002 => Dune::mdgrid::MultiDomainGrid, Dune::mdgrid::DynamicSubDomainCountTraits<2, 1ul, Dune::mdgrid::AllCodims> > const (dim=2, dimworld=2) 00:00:00.002 level 0 codim[0]=197 codim[1]=317 codim[2]=121 00:00:00.002 leaf codim[0]=197 codim[1]=317 codim[2]=121 00:00:00.002 leaf dim=2 types=((simplex, 2)[0]=182,(cube, 2)[0]=15,(simplex, 1)[1]=317,(simplex, 0)[2]=121) 00:00:00.002 Subdomain 0 info 00:00:00.002 => Dune::mdgrid::subdomain::SubDomainGrid, Dune::mdgrid::DynamicSubDomainCountTraits<2, 1ul, Dune::mdgrid::AllCodims> > > const (dim=2, dimworld=2) 00:00:00.002 level 0 codim[0]=39 codim[1]=66 codim[2]=28 00:00:00.002 leaf codim[0]=39 codim[1]=66 codim[2]=28 00:00:00.002 leaf dim=2 types=((simplex, 2)[0]=39,(cube, 2)[0]=0,(simplex, 1)[1]=66,(simplex, 0)[2]=28) 00:00:00.002 Subdomain 1 info 00:00:00.002 => Dune::mdgrid::subdomain::SubDomainGrid, Dune::mdgrid::DynamicSubDomainCountTraits<2, 1ul, Dune::mdgrid::AllCodims> > > const (dim=2, dimworld=2) 00:00:00.002 level 0 codim[0]=143 codim[1]=236 codim[2]=93 00:00:00.002 leaf codim[0]=143 codim[1]=236 codim[2]=93 00:00:00.002 leaf dim=2 types=((simplex, 2)[0]=143,(cube, 2)[0]=0,(simplex, 1)[1]=236,(simplex, 0)[2]=93) 00:00:00.002 Subdomain 2 info 00:00:00.002 => Dune::mdgrid::subdomain::SubDomainGrid, Dune::mdgrid::DynamicSubDomainCountTraits<2, 1ul, Dune::mdgrid::AllCodims> > > const (dim=2, dimworld=2) 00:00:00.002 level 0 codim[0]=15 codim[1]=45 codim[2]=30 00:00:00.002 leaf codim[0]=15 codim[1]=45 codim[2]=30 00:00:00.002 leaf dim=2 types=((simplex, 2)[0]=0,(cube, 2)[0]=15,(simplex, 1)[1]=45,(simplex, 0)[2]=30) 00:00:00.002 Stopped redirection of std::cout 00:00:00.002 Applying refinement of level: 0 00:00:00.002 ModelBase constructed 00:00:00.002 Setting up multi-compartment diffusion-reaction model 00:00:00.002 Setup grid function space 00:00:00.002 Create a sub model for compartment 0 00:00:00.002 ModelBase constructed 00:00:00.002 Setting up diffusion-reaction model for kern compartment 00:00:00.002 Setup domain grid function space 00:00:00.002 Create a finite element map 00:00:00.002 Setup grid function space for component A 00:00:00.002 Setup domian power grid function space 00:00:00.002 No. of components 1 00:00:00.002 ModelDiffusionReaction constructed 00:00:00.002 ModelDiffusionReaction deconstructed 00:00:00.002 ModelBase deconstructed 00:00:00.002 Create a sub model for compartment 1 00:00:00.002 ModelBase constructed 00:00:00.002 Setting up diffusion-reaction model for cyt compartment 00:00:00.002 Setup domain grid function space 00:00:00.002 Create a finite element map 00:00:00.002 Setup grid function space for component B 00:00:00.002 Setup domian power grid function space 00:00:00.002 No. of components 1 00:00:00.002 ModelDiffusionReaction constructed 00:00:00.002 ModelDiffusionReaction deconstructed 00:00:00.002 ModelBase deconstructed 00:00:00.002 Create a sub model for compartment 2 00:00:00.002 ModelBase constructed 00:00:00.002 Setting up diffusion-reaction model for cyt_kern_membrane compartment 00:00:00.002 Setup domain grid function space 00:00:00.002 Create a finite element map 00:00:00.002 Setup grid function space for component B 00:00:00.002 Create a finite element map 00:00:00.002 Setup grid function space for component A 00:00:00.002 Setup domian power grid function space 00:00:00.002 No. of components 2 00:00:00.002 ModelDiffusionReaction constructed 00:00:00.002 ModelDiffusionReaction deconstructed 00:00:00.002 ModelBase deconstructed 00:00:00.002 Setup coefficient vector 00:00:00.002 initialize parser with constant variables 00:00:00.002 ExpressionToGridFunctionAdapter constructed 00:00:00.002 initialize parser with constant variables 00:00:00.002 ExpressionToGridFunctionAdapter constructed 00:00:00.002 initialize parser with constant variables 00:00:00.002 ExpressionToGridFunctionAdapter constructed 00:00:00.002 initialize parser with constant variables 00:00:00.002 ExpressionToGridFunctionAdapter constructed 00:00:00.003 compile expression: 1 00:00:00.003 compile expression: 1 00:00:00.003 compile expression: 1 00:00:00.003 compile expression: 1 00:00:00.003 Set initial state from grid functions 00:00:00.003 ExpressionToGridFunctionAdapter deconstructed 00:00:00.003 ExpressionToGridFunctionAdapter deconstructed 00:00:00.003 ExpressionToGridFunctionAdapter deconstructed 00:00:00.003 ExpressionToGridFunctionAdapter deconstructed 00:00:00.003 Setup base constraints 00:00:00.003 Setup power constraints 00:00:00.003 Assemble constraints 00:00:00.003 Constrained dofs: 0 of 151 00:00:00.003 Setup local operator 00:00:00.003 Create spatial local operator 00:00:00.003 creating pattern and grid function expressions 00:00:00.003 initialize parser with constant variables 00:00:00.003 compile expression: 0.0100000000000000002 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: A 00:00:00.003 compile expression: 1e-05 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: A 00:00:00.003 compile expression: 0 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 pattern <0,0> 00:00:00.003 creating pattern and grid function expressions 00:00:00.003 initialize parser with constant variables 00:00:00.003 compile expression: 0.0100000000000000002 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: A 00:00:00.003 compile expression: 1e-05 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: A 00:00:00.003 compile expression: 0 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 pattern <0,0> 00:00:00.003 creating pattern and grid function expressions 00:00:00.003 initialize parser with constant variables 00:00:00.003 compile expression: 0.0100000000000000002 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: B 00:00:00.003 compile expression: B*-0.0001 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: B 00:00:00.003 compile expression: -0.0001 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 pattern <0,0> 00:00:00.003 creating pattern and grid function expressions 00:00:00.003 initialize parser with constant variables 00:00:00.003 compile expression: 0.0100000000000000002 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: B 00:00:00.003 compile expression: B*-0.0001 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: B 00:00:00.003 compile expression: -0.0001 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 pattern <0,0> 00:00:00.003 creating pattern and grid function expressions 00:00:00.003 initialize parser with constant variables 00:00:00.003 compile expression: 0 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.003 initialize parser with constant variables 00:00:00.003 define extra variable: A 00:00:00.003 define extra variable: B 00:00:00.003 compile expression: A*-0.1 00:00:00.003 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: -0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: A*0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 pattern <0,0> 00:00:00.004 pattern <1,0> 00:00:00.004 pattern <1,1> 00:00:00.004 creating pattern and grid function expressions 00:00:00.004 initialize parser with constant variables 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: A*-0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: -0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: A*0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 pattern <0,0> 00:00:00.004 pattern <1,0> 00:00:00.004 pattern <1,1> 00:00:00.004 Create temporal local operator 00:00:00.004 creating pattern and grid function expressions 00:00:00.004 initialize parser with constant variables 00:00:00.004 compile expression: 0.0100000000000000002 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 compile expression: 1e-05 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 pattern <0,0> 00:00:00.004 creating pattern and grid function expressions 00:00:00.004 initialize parser with constant variables 00:00:00.004 compile expression: 0.0100000000000000002 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: B*-0.0001 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: -0.0001 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 pattern <0,0> 00:00:00.004 creating pattern and grid function expressions 00:00:00.004 initialize parser with constant variables 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: A*-0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: -0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: A*0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0.1 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 initialize parser with constant variables 00:00:00.004 define extra variable: A 00:00:00.004 define extra variable: B 00:00:00.004 compile expression: 0 00:00:00.004 ExpressionToGridFunctionAdapter constructed 00:00:00.004 pattern <0,0> 00:00:00.004 pattern <1,0> 00:00:00.004 pattern <1,1> 00:00:00.004 Setup grid operator 00:00:00.004 Create spatial grid operator 00:00:00.004 Create temporal grid operator 00:00:00.004 Create instationary grid operator 00:00:00.004 Create jacobian operator 00:00:00.004 Setup VTK writer 00:00:00.004 ModelMultiDomainDiffusionReaction constructed 00:00:00.004 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.004 Writing solution for 0.00s time stamp 00:00:00.004 Writing vtu file: 'vtk-kern/vtk-kern-00000.vtu' 00:00:00.005 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.005 Writing vtu file: 'vtk-cyt/vtk-cyt-00000.vtu' 00:00:00.005 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.005 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00000.vtu' 00:00:00.005 Increase factor: 1.5 00:00:00.005 Decrease factor: 0.5 00:00:00.005 Runge-Kutta method: alexander_2 00:00:00.005 Setting up time stepper 00:00:00.005 Stepper methd: Alexander (order 2) 00:00:00.005 Evolving system: 0.00s -> 100.00s 00:00:00.005 Trying step: 0.00s + 0.10s -> 0.10s 00:00:00.005 Get non-linear operator 00:00:00.005 Get one step operator 00:00:00.005 TIME STEP [Alexander (order 2)] 1 time (from): 0.0000e+00 dt: 1.0000e-01 time (to): 1.0000e-01 00:00:00.005 STAGE 1 time (to): 2.9289e-02. 00:00:00.009 Newton converged after 0 iterations. Reduction: 1.0000e+00 (2.6163e-03s) 00:00:00.009 STAGE 2 time (to): 1.0000e-01. 00:00:00.012 Newton converged after 0 iterations. Reduction: 1.0000e+00 (1.4905e-03s) 00:00:00.012 ::: timesteps 1 (1) 00:00:00.012 ::: nl iterations 0 (0) 00:00:00.012 ::: lin iterations 0 (0) 00:00:00.012 ::: assemble time 0.0000e+00 (0.0000e+00) 00:00:00.012 ::: lin solve time 0.0000e+00 (0.0000e+00) 00:00:00.012 Time Step: 0.00s + 0.10s -> 0.10s 00:00:00.012 Stopped redirection of std::cout 00:00:00.012 Increasing step size: 0.10s -> 0.15s 00:00:00.012 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.012 Writing solution for 0.10s time stamp 00:00:00.012 Writing vtu file: 'vtk-kern/vtk-kern-00001.vtu' 00:00:00.018 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.018 Writing vtu file: 'vtk-cyt/vtk-cyt-00001.vtu' 00:00:00.018 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.018 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00001.vtu' 00:00:00.019 Trying step: 0.10s + 0.15s -> 0.25s 00:00:00.019 TIME STEP [Alexander (order 2)] 2 time (from): 1.0000e-01 dt: 1.5000e-01 time (to): 2.5000e-01 00:00:00.019 STAGE 1 time (to): 1.4393e-01. 00:00:00.020 Newton converged after 0 iterations. Reduction: 1.0000e+00 (8.6520e-04s) 00:00:00.020 STAGE 2 time (to): 2.5000e-01. 00:00:00.022 Newton converged after 0 iterations. Reduction: 1.0000e+00 (8.9120e-04s) 00:00:00.022 ::: timesteps 2 (2) 00:00:00.022 ::: nl iterations 0 (0) 00:00:00.022 ::: lin iterations 0 (0) 00:00:00.022 ::: assemble time 0.0000e+00 (0.0000e+00) 00:00:00.022 ::: lin solve time 0.0000e+00 (0.0000e+00) 00:00:00.022 Time Step: 0.10s + 0.15s -> 0.25s 00:00:00.022 Stopped redirection of std::cout 00:00:00.022 Increasing step size: 0.15s -> 0.23s 00:00:00.022 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.022 Writing solution for 0.25s time stamp 00:00:00.022 Writing vtu file: 'vtk-kern/vtk-kern-00002.vtu' 00:00:00.022 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.022 Writing vtu file: 'vtk-cyt/vtk-cyt-00002.vtu' 00:00:00.022 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.022 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00002.vtu' 00:00:00.023 Trying step: 0.25s + 0.23s -> 0.48s 00:00:00.023 TIME STEP [Alexander (order 2)] 3 time (from): 2.5000e-01 dt: 2.2500e-01 time (to): 4.7500e-01 00:00:00.023 STAGE 1 time (to): 3.1590e-01. 00:00:00.025 Newton converged after 0 iterations. Reduction: 1.0000e+00 (1.1758e-03s) 00:00:00.025 STAGE 2 time (to): 4.7500e-01. 00:00:00.027 Newton converged after 0 iterations. Reduction: 1.0000e+00 (1.1686e-03s) 00:00:00.027 ::: timesteps 3 (3) 00:00:00.027 ::: nl iterations 0 (0) 00:00:00.027 ::: lin iterations 0 (0) 00:00:00.027 ::: assemble time 0.0000e+00 (0.0000e+00) 00:00:00.027 ::: lin solve time 0.0000e+00 (0.0000e+00) 00:00:00.027 Time Step: 0.25s + 0.23s -> 0.48s 00:00:00.027 Stopped redirection of std::cout 00:00:00.027 Increasing step size: 0.23s -> 0.34s 00:00:00.027 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.027 Writing solution for 0.48s time stamp 00:00:00.027 Writing vtu file: 'vtk-kern/vtk-kern-00003.vtu' 00:00:00.027 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.027 Writing vtu file: 'vtk-cyt/vtk-cyt-00003.vtu' 00:00:00.028 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.028 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00003.vtu' 00:00:00.028 Trying step: 0.48s + 0.34s -> 0.81s 00:00:00.028 TIME STEP [Alexander (order 2)] 4 time (from): 4.7500e-01 dt: 3.3750e-01 time (to): 8.1250e-01 00:00:00.028 STAGE 1 time (to): 5.7385e-01. 00:00:00.030 Newton converged after 0 iterations. Reduction: 1.0000e+00 (1.1871e-03s) 00:00:00.030 STAGE 2 time (to): 8.1250e-01. 00:00:00.032 === Dune::BiCGSTABSolver 00:00:00.033 === rate=0.7287, T=0.0006936, TIT=2.89e-05, IT=24 00:00:00.034 Newton converged after 1 iterations. Reduction: 6.5436e-01 (3.2584e-03s) 00:00:00.034 ::: timesteps 4 (4) 00:00:00.034 ::: nl iterations 1 (1) 00:00:00.034 ::: lin iterations 24 (24) 00:00:00.034 ::: assemble time 8.3213e-04 (8.3213e-04) 00:00:00.034 ::: lin solve time 6.9903e-04 (6.9903e-04) 00:00:00.034 Time Step: 0.48s + 0.34s -> 0.81s 00:00:00.034 Stopped redirection of std::cout 00:00:00.034 Increasing step size: 0.34s -> 0.51s 00:00:00.034 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.034 Writing solution for 0.81s time stamp 00:00:00.034 Writing vtu file: 'vtk-kern/vtk-kern-00004.vtu' 00:00:00.034 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.034 Writing vtu file: 'vtk-cyt/vtk-cyt-00004.vtu' 00:00:00.034 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.034 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00004.vtu' 00:00:00.034 Trying step: 0.81s + 0.51s -> 1.32s 00:00:00.034 TIME STEP [Alexander (order 2)] 5 time (from): 8.1250e-01 dt: 5.0625e-01 time (to): 1.3188e+00 00:00:00.034 STAGE 1 time (to): 9.6078e-01. 00:00:00.037 === Dune::BiCGSTABSolver 00:00:00.037 === rate=0.6764, T=0.0006011, TIT=2.732e-05, IT=22 00:00:00.038 Newton converged after 1 iterations. Reduction: 3.7907e-01 (3.1718e-03s) 00:00:00.038 STAGE 2 time (to): 1.3188e+00. 00:00:00.041 === Dune::BiCGSTABSolver 00:00:00.041 === rate=0.6102, T=0.0005611, TIT=2.806e-05, IT=20 00:00:00.042 Newton converged after 1 iterations. Reduction: 4.0064e-01 (3.1185e-03s) 00:00:00.042 ::: timesteps 5 (5) 00:00:00.042 ::: nl iterations 3 (3) 00:00:00.042 ::: lin iterations 66 (66) 00:00:00.042 ::: assemble time 2.4820e-03 (2.4820e-03) 00:00:00.042 ::: lin solve time 1.8697e-03 (1.8697e-03) 00:00:00.042 Time Step: 0.81s + 0.51s -> 1.32s 00:00:00.042 Stopped redirection of std::cout 00:00:00.042 Increasing step size: 0.51s -> 0.76s 00:00:00.042 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.042 Writing solution for 1.32s time stamp 00:00:00.042 Writing vtu file: 'vtk-kern/vtk-kern-00005.vtu' 00:00:00.043 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.043 Writing vtu file: 'vtk-cyt/vtk-cyt-00005.vtu' 00:00:00.043 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.043 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00005.vtu' 00:00:00.043 Trying step: 1.32s + 0.76s -> 2.08s 00:00:00.043 TIME STEP [Alexander (order 2)] 6 time (from): 1.3188e+00 dt: 7.5938e-01 time (to): 2.0781e+00 00:00:00.043 STAGE 1 time (to): 1.5412e+00. 00:00:00.045 === Dune::BiCGSTABSolver 00:00:00.046 === rate=0.7697, T=0.000742, TIT=2.748e-05, IT=27 00:00:00.048 === Dune::BiCGSTABSolver 00:00:00.048 === rate=0.4547, T=0.0002583, TIT=2.87e-05, IT=9 00:00:00.050 === Dune::BiCGSTABSolver 00:00:00.050 === rate=0.1265, T=9.79e-05, TIT=3.263e-05, IT=3 00:00:00.051 Newton converged after 3 iterations. Reduction: 1.2502e-01 (7.0708e-03s) 00:00:00.051 STAGE 2 time (to): 2.0781e+00. 00:00:00.053 === Dune::BiCGSTABSolver 00:00:00.054 === rate=0.7315, T=0.0006331, TIT=2.753e-05, IT=23 00:00:00.056 === Dune::BiCGSTABSolver 00:00:00.056 === rate=0.4461, T=0.0002581, TIT=2.868e-05, IT=9 00:00:00.057 Newton converged after 2 iterations. Reduction: 2.3157e-01 (5.1467e-03s) 00:00:00.057 ::: timesteps 6 (6) 00:00:00.057 ::: nl iterations 8 (8) 00:00:00.057 ::: lin iterations 137 (137) 00:00:00.057 ::: assemble time 6.6194e-03 (6.6194e-03) 00:00:00.057 ::: lin solve time 3.8767e-03 (3.8767e-03) 00:00:00.057 Time Step: 1.32s + 0.76s -> 2.08s 00:00:00.057 Stopped redirection of std::cout 00:00:00.057 Increasing step size: 0.76s -> 1.14s 00:00:00.057 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.057 Writing solution for 2.08s time stamp 00:00:00.057 Writing vtu file: 'vtk-kern/vtk-kern-00006.vtu' 00:00:00.057 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.057 Writing vtu file: 'vtk-cyt/vtk-cyt-00006.vtu' 00:00:00.057 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.057 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00006.vtu' 00:00:00.057 Trying step: 2.08s + 1.14s -> 3.22s 00:00:00.057 TIME STEP [Alexander (order 2)] 7 time (from): 2.0781e+00 dt: 1.1391e+00 time (to): 3.2172e+00 00:00:00.057 STAGE 1 time (to): 2.4117e+00. 00:00:00.059 === Dune::BiCGSTABSolver 00:00:00.060 === rate=0.7859, T=0.0007952, TIT=2.742e-05, IT=29 00:00:00.062 === Dune::BiCGSTABSolver 00:00:00.062 === rate=0.4613, T=0.0002586, TIT=2.873e-05, IT=9 00:00:00.063 Newton converged after 2 iterations. Reduction: 2.2233e-01 (5.3227e-03s) 00:00:00.063 STAGE 2 time (to): 3.2172e+00. 00:00:00.066 === Dune::BiCGSTABSolver 00:00:00.066 === rate=0.7511, T=0.0006597, TIT=2.749e-05, IT=24 00:00:00.068 === Dune::BiCGSTABSolver 00:00:00.068 === rate=0.473, T=0.0002583, TIT=2.87e-05, IT=9 00:00:00.069 Newton converged after 2 iterations. Reduction: 2.3100e-01 (5.1669e-03s) 00:00:00.069 ::: timesteps 7 (7) 00:00:00.069 ::: nl iterations 12 (12) 00:00:00.069 ::: lin iterations 208 (208) 00:00:00.069 ::: assemble time 9.9076e-03 (9.9076e-03) 00:00:00.069 ::: lin solve time 5.8625e-03 (5.8625e-03) 00:00:00.069 Time Step: 2.08s + 1.14s -> 3.22s 00:00:00.069 Stopped redirection of std::cout 00:00:00.069 Increasing step size: 1.14s -> 1.71s 00:00:00.069 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.069 Writing solution for 3.22s time stamp 00:00:00.069 Writing vtu file: 'vtk-kern/vtk-kern-00007.vtu' 00:00:00.069 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.069 Writing vtu file: 'vtk-cyt/vtk-cyt-00007.vtu' 00:00:00.070 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.070 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00007.vtu' 00:00:00.070 Trying step: 3.22s + 1.71s -> 4.93s 00:00:00.070 TIME STEP [Alexander (order 2)] 8 time (from): 3.2172e+00 dt: 1.7086e+00 time (to): 4.9258e+00 00:00:00.070 STAGE 1 time (to): 3.7176e+00. 00:00:00.072 === Dune::BiCGSTABSolver 00:00:00.116 === rate=0.9952, T=0.04437, TIT=2.68e-05, IT=1656 00:00:00.118 === Dune::BiCGSTABSolver 00:00:00.118 === rate=0.0001606, T=1.77e-05, TIT=inf, IT=0 00:00:00.119 Newton converged after 2 iterations. Reduction: 1.2063e-01 (4.8647e-02s) 00:00:00.119 STAGE 2 time (to): 4.9258e+00. 00:00:00.122 === Dune::BiCGSTABSolver 00:00:00.123 === rate=0.8894, T=0.001596, TIT=2.706e-05, IT=59 00:00:00.125 === Dune::BiCGSTABSolver 00:00:00.125 === rate=0.0001752, T=1.709e-05, TIT=inf, IT=0 00:00:00.126 Newton converged after 2 iterations. Reduction: 1.3613e-01 (5.8618e-03s) 00:00:00.126 ::: timesteps 8 (8) 00:00:00.126 ::: nl iterations 16 (16) 00:00:00.126 ::: lin iterations 1923 (1923) 00:00:00.126 ::: assemble time 1.3187e-02 (1.3187e-02) 00:00:00.126 ::: lin solve time 5.1883e-02 (5.1883e-02) 00:00:00.126 Time Step: 3.22s + 1.71s -> 4.93s 00:00:00.126 Stopped redirection of std::cout 00:00:00.126 Increasing step size: 1.71s -> 2.56s 00:00:00.126 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.126 Writing solution for 4.93s time stamp 00:00:00.126 Writing vtu file: 'vtk-kern/vtk-kern-00008.vtu' 00:00:00.126 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.126 Writing vtu file: 'vtk-cyt/vtk-cyt-00008.vtu' 00:00:00.126 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.126 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00008.vtu' 00:00:00.126 Trying step: 4.93s + 2.56s -> 7.49s 00:00:00.126 TIME STEP [Alexander (order 2)] 9 time (from): 4.9258e+00 dt: 2.5629e+00 time (to): 7.4887e+00 00:00:00.126 STAGE 1 time (to): 5.6764e+00. 00:00:00.129 === Dune::BiCGSTABSolver 00:00:00.130 === rate=0.843, T=0.001201, TIT=2.73e-05, IT=44 00:00:00.131 === Dune::BiCGSTABSolver 00:00:00.132 === rate=0.4916, T=0.0002716, TIT=2.716e-05, IT=10 00:00:00.133 Newton converged after 2 iterations. Reduction: 1.2215e-01 (5.7411e-03s) 00:00:00.133 STAGE 2 time (to): 7.4887e+00. 00:00:00.135 === Dune::BiCGSTABSolver 00:00:00.136 === rate=0.6619, T=0.0006198, TIT=2.695e-05, IT=23 00:00:00.138 === Dune::BiCGSTABSolver 00:00:00.138 === rate=0.1086, T=9.762e-05, TIT=3.254e-05, IT=3 00:00:00.139 Newton converged after 2 iterations. Reduction: 1.3899e-01 (4.9638e-03s) 00:00:00.139 ::: timesteps 9 (9) 00:00:00.139 ::: nl iterations 20 (20) 00:00:00.139 ::: lin iterations 2003 (2003) 00:00:00.139 ::: assemble time 1.6469e-02 (1.6469e-02) 00:00:00.139 ::: lin solve time 5.4088e-02 (5.4088e-02) 00:00:00.139 Time Step: 4.93s + 2.56s -> 7.49s 00:00:00.139 Stopped redirection of std::cout 00:00:00.139 Increasing step size: 2.56s -> 3.84s 00:00:00.139 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.139 Writing solution for 7.49s time stamp 00:00:00.139 Writing vtu file: 'vtk-kern/vtk-kern-00009.vtu' 00:00:00.139 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.139 Writing vtu file: 'vtk-cyt/vtk-cyt-00009.vtu' 00:00:00.139 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.139 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00009.vtu' 00:00:00.139 Trying step: 7.49s + 3.84s -> 11.33s 00:00:00.139 TIME STEP [Alexander (order 2)] 10 time (from): 7.4887e+00 dt: 3.8443e+00 time (to): 1.1333e+01 00:00:00.139 STAGE 1 time (to): 8.6147e+00. 00:00:00.141 === Dune::BiCGSTABSolver 00:00:00.143 === rate=0.8969, T=0.001878, TIT=2.683e-05, IT=70 00:00:00.144 Newton converged after 1 iterations. Reduction: 1.0636e-01 (4.4673e-03s) 00:00:00.144 STAGE 2 time (to): 1.1333e+01. 00:00:00.147 === Dune::BiCGSTABSolver 00:00:00.148 === rate=0.8572, T=0.001274, TIT=2.711e-05, IT=47 00:00:00.150 === Dune::BiCGSTABSolver 00:00:00.150 === rate=0.0001574, T=1.716e-05, TIT=inf, IT=0 00:00:00.151 Newton converged after 2 iterations. Reduction: 1.1174e-01 (5.5368e-03s) 00:00:00.151 ::: timesteps 10 (10) 00:00:00.151 ::: nl iterations 23 (23) 00:00:00.151 ::: lin iterations 2120 (2120) 00:00:00.151 ::: assemble time 1.8943e-02 (1.8943e-02) 00:00:00.151 ::: lin solve time 5.7274e-02 (5.7274e-02) 00:00:00.151 Time Step: 7.49s + 3.84s -> 11.33s 00:00:00.151 Stopped redirection of std::cout 00:00:00.151 Increasing step size: 3.84s -> 5.77s 00:00:00.151 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.151 Writing solution for 11.33s time stamp 00:00:00.151 Writing vtu file: 'vtk-kern/vtk-kern-00010.vtu' 00:00:00.151 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.151 Writing vtu file: 'vtk-cyt/vtk-cyt-00010.vtu' 00:00:00.151 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.151 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00010.vtu' 00:00:00.151 Trying step: 11.33s + 5.77s -> 17.10s 00:00:00.151 TIME STEP [Alexander (order 2)] 11 time (from): 1.1333e+01 dt: 5.7665e+00 time (to): 1.7100e+01 00:00:00.151 STAGE 1 time (to): 1.3022e+01. 00:00:00.154 === Dune::BiCGSTABSolver 00:00:00.171 === rate=0.9892, T=0.01766, TIT=2.684e-05, IT=658 00:00:00.173 === Dune::BiCGSTABSolver 00:00:00.173 === rate=0.0002313, T=1.731e-05, TIT=inf, IT=0 00:00:00.174 Newton converged after 2 iterations. Reduction: 5.1464e-02 (2.1968e-02s) 00:00:00.174 STAGE 2 time (to): 1.7100e+01. 00:00:00.176 === Dune::BiCGSTABSolver 00:00:00.180 === rate=0.9397, T=0.00405, TIT=2.682e-05, IT=151 00:00:00.181 Newton converged after 1 iterations. Reduction: 1.0400e-01 (6.6073e-03s) 00:00:00.181 ::: timesteps 11 (11) 00:00:00.181 ::: nl iterations 26 (26) 00:00:00.181 ::: lin iterations 2929 (2929) 00:00:00.181 ::: assemble time 2.1434e-02 (2.1434e-02) 00:00:00.181 ::: lin solve time 7.9014e-02 (7.9014e-02) 00:00:00.181 Time Step: 11.33s + 5.77s -> 17.10s 00:00:00.181 Stopped redirection of std::cout 00:00:00.181 Increasing step size: 5.77s -> 8.65s 00:00:00.181 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.181 Writing solution for 17.10s time stamp 00:00:00.181 Writing vtu file: 'vtk-kern/vtk-kern-00011.vtu' 00:00:00.182 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.182 Writing vtu file: 'vtk-cyt/vtk-cyt-00011.vtu' 00:00:00.182 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.182 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00011.vtu' 00:00:00.182 Trying step: 17.10s + 8.65s -> 25.75s 00:00:00.182 TIME STEP [Alexander (order 2)] 12 time (from): 1.7100e+01 dt: 8.6498e+00 time (to): 2.5749e+01 00:00:00.182 STAGE 1 time (to): 1.9633e+01. 00:00:00.184 === Dune::BiCGSTABSolver 00:00:00.204 === rate=0.9893, T=0.01996, TIT=2.683e-05, IT=744 00:00:00.206 === Dune::BiCGSTABSolver 00:00:00.206 === rate=0.0001965, T=1.748e-05, TIT=inf, IT=0 00:00:00.207 Newton converged after 2 iterations. Reduction: 2.8275e-02 (2.4221e-02s) 00:00:00.207 STAGE 2 time (to): 2.5749e+01. 00:00:00.209 === Dune::BiCGSTABSolver 00:00:00.211 === rate=0.9008, T=0.001891, TIT=2.702e-05, IT=70 00:00:00.212 Newton converged after 1 iterations. Reduction: 3.8945e-02 (4.4481e-03s) 00:00:00.212 ::: timesteps 12 (12) 00:00:00.212 ::: nl iterations 29 (29) 00:00:00.212 ::: lin iterations 3743 (3743) 00:00:00.212 ::: assemble time 2.3896e-02 (2.3896e-02) 00:00:00.212 ::: lin solve time 1.0089e-01 (1.0089e-01) 00:00:00.212 Time Step: 17.10s + 8.65s -> 25.75s 00:00:00.212 Stopped redirection of std::cout 00:00:00.212 Increasing step size: 8.65s -> 12.97s 00:00:00.212 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.212 Writing solution for 25.75s time stamp 00:00:00.212 Writing vtu file: 'vtk-kern/vtk-kern-00012.vtu' 00:00:00.212 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.212 Writing vtu file: 'vtk-cyt/vtk-cyt-00012.vtu' 00:00:00.213 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.213 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00012.vtu' 00:00:00.213 Trying step: 25.75s + 12.97s -> 38.72s 00:00:00.213 TIME STEP [Alexander (order 2)] 13 time (from): 2.5749e+01 dt: 1.2975e+01 time (to): 3.8724e+01 00:00:00.213 STAGE 1 time (to): 2.9549e+01. 00:00:00.215 === Dune::BiCGSTABSolver 00:00:00.349 === rate=1.007, T=0.134, TIT=2.68e-05, IT=5000 00:00:00.349 Step failed (NewtonError) 00:00:00.349 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:00.349 Stopped redirection of std::cout 00:00:00.349 Reducing step size: 12.974633789062501s -> 6.487316894531251s 00:00:00.349 Trying step: 25.75s + 6.49s -> 32.24s 00:00:00.349 TIME STEP [Alexander (order 2)] 13 time (from): 2.5749e+01 dt: 6.4873e+00 time (to): 3.2237e+01 00:00:00.349 STAGE 1 time (to): 2.7649e+01. 00:00:00.351 === Dune::BiCGSTABSolver 00:00:00.485 === rate=1.007, T=0.1342, TIT=2.685e-05, IT=5000 00:00:00.485 Step failed (NewtonError) 00:00:00.485 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:00.485 Stopped redirection of std::cout 00:00:00.485 Reducing step size: 6.487316894531251s -> 3.2436584472656254s 00:00:00.485 Trying step: 25.75s + 3.24s -> 28.99s 00:00:00.485 TIME STEP [Alexander (order 2)] 13 time (from): 2.5749e+01 dt: 3.2437e+00 time (to): 2.8993e+01 00:00:00.485 STAGE 1 time (to): 2.6699e+01. 00:00:00.488 === Dune::BiCGSTABSolver 00:00:00.489 === rate=0.7651, T=0.0007942, TIT=2.738e-05, IT=29 00:00:00.489 Newton converged after 1 iterations. Reduction: 1.6897e-01 (3.3546e-03s) 00:00:00.489 STAGE 2 time (to): 2.8993e+01. 00:00:00.492 === Dune::BiCGSTABSolver 00:00:00.493 === rate=0.6718, T=0.000553, TIT=2.765e-05, IT=20 00:00:00.494 Newton converged after 1 iterations. Reduction: 1.2317e-01 (3.1122e-03s) 00:00:00.494 ::: timesteps 13 (15) 00:00:00.494 ::: nl iterations 31 (31) 00:00:00.494 ::: lin iterations 3792 (13792) 00:00:00.494 ::: assemble time 2.5536e-02 (2.7177e-02) 00:00:00.494 ::: lin solve time 1.0225e-01 (3.7052e-01) 00:00:00.494 Time Step: 25.75s + 3.24s -> 28.99s 00:00:00.494 Stopped redirection of std::cout 00:00:00.494 Increasing step size: 3.24s -> 4.87s 00:00:00.494 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.494 Writing solution for 28.99s time stamp 00:00:00.494 Writing vtu file: 'vtk-kern/vtk-kern-00013.vtu' 00:00:00.494 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.494 Writing vtu file: 'vtk-cyt/vtk-cyt-00013.vtu' 00:00:00.494 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.494 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00013.vtu' 00:00:00.494 Trying step: 28.99s + 4.87s -> 33.86s 00:00:00.494 TIME STEP [Alexander (order 2)] 14 time (from): 2.8993e+01 dt: 4.8655e+00 time (to): 3.3858e+01 00:00:00.494 STAGE 1 time (to): 3.0418e+01. 00:00:00.496 === Dune::BiCGSTABSolver 00:00:00.497 === rate=0.6138, T=0.000618, TIT=2.809e-05, IT=22 00:00:00.498 Newton converged after 1 iterations. Reduction: 7.0272e-02 (3.1805e-03s) 00:00:00.498 STAGE 2 time (to): 3.3858e+01. 00:00:00.500 === Dune::BiCGSTABSolver 00:00:00.501 === rate=0.7573, T=0.0007757, TIT=2.77e-05, IT=28 00:00:00.502 Newton converged after 1 iterations. Reduction: 1.5464e-01 (3.3273e-03s) 00:00:00.502 ::: timesteps 14 (16) 00:00:00.502 ::: nl iterations 33 (33) 00:00:00.502 ::: lin iterations 3842 (13842) 00:00:00.502 ::: assemble time 2.7174e-02 (2.8815e-02) 00:00:00.502 ::: lin solve time 1.0365e-01 (3.7192e-01) 00:00:00.502 Time Step: 28.99s + 4.87s -> 33.86s 00:00:00.502 Stopped redirection of std::cout 00:00:00.502 Increasing step size: 4.87s -> 7.30s 00:00:00.502 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.502 Writing solution for 33.86s time stamp 00:00:00.502 Writing vtu file: 'vtk-kern/vtk-kern-00014.vtu' 00:00:00.502 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.502 Writing vtu file: 'vtk-cyt/vtk-cyt-00014.vtu' 00:00:00.503 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.503 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00014.vtu' 00:00:00.503 Trying step: 33.86s + 7.30s -> 41.16s 00:00:00.503 TIME STEP [Alexander (order 2)] 15 time (from): 3.3858e+01 dt: 7.2982e+00 time (to): 4.1157e+01 00:00:00.503 STAGE 1 time (to): 3.5996e+01. 00:00:00.505 === Dune::BiCGSTABSolver 00:00:00.520 === rate=0.9864, T=0.01465, TIT=2.683e-05, IT=546 00:00:00.521 === Dune::BiCGSTABSolver 00:00:00.521 === rate=0.0001588, T=1.743e-05, TIT=inf, IT=0 00:00:00.522 Newton converged after 2 iterations. Reduction: 6.8660e-02 (1.8927e-02s) 00:00:00.522 STAGE 2 time (to): 4.1157e+01. 00:00:00.525 === Dune::BiCGSTABSolver 00:00:00.659 === rate=1.005, T=0.134, TIT=2.68e-05, IT=5000 00:00:00.659 Step failed (NewtonError) 00:00:00.659 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:00.659 Stopped redirection of std::cout 00:00:00.659 Reducing step size: 7.298231506347657s -> 3.6491157531738283s 00:00:00.659 Trying step: 33.86s + 3.65s -> 37.51s 00:00:00.659 TIME STEP [Alexander (order 2)] 15 time (from): 3.3858e+01 dt: 3.6491e+00 time (to): 3.7508e+01 00:00:00.659 STAGE 1 time (to): 3.4927e+01. 00:00:00.661 === Dune::BiCGSTABSolver 00:00:00.662 === rate=0.7649, T=0.0007003, TIT=2.693e-05, IT=26 00:00:00.663 Newton converged after 1 iterations. Reduction: 3.3797e-01 (3.2529e-03s) 00:00:00.663 STAGE 2 time (to): 3.7508e+01. 00:00:00.665 === Dune::BiCGSTABSolver 00:00:00.666 === rate=0.7945, T=0.001035, TIT=2.724e-05, IT=38 00:00:00.668 === Dune::BiCGSTABSolver 00:00:00.668 === rate=0.1356, T=9.749e-05, TIT=3.25e-05, IT=3 00:00:00.669 Newton converged after 2 iterations. Reduction: 1.5501e-01 (5.3701e-03s) 00:00:00.669 ::: timesteps 15 (18) 00:00:00.669 ::: nl iterations 36 (38) 00:00:00.669 ::: lin iterations 3909 (19455) 00:00:00.669 ::: assemble time 2.9634e-02 (3.3740e-02) 00:00:00.669 ::: lin solve time 1.0549e-01 (5.2247e-01) 00:00:00.669 Time Step: 33.86s + 3.65s -> 37.51s 00:00:00.669 Stopped redirection of std::cout 00:00:00.669 Increasing step size: 3.65s -> 5.47s 00:00:00.669 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.669 Writing solution for 37.51s time stamp 00:00:00.669 Writing vtu file: 'vtk-kern/vtk-kern-00015.vtu' 00:00:00.669 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.669 Writing vtu file: 'vtk-cyt/vtk-cyt-00015.vtu' 00:00:00.669 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.669 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00015.vtu' 00:00:00.670 Trying step: 37.51s + 5.47s -> 42.98s 00:00:00.670 TIME STEP [Alexander (order 2)] 16 time (from): 3.7508e+01 dt: 5.4737e+00 time (to): 4.2981e+01 00:00:00.670 STAGE 1 time (to): 3.9111e+01. 00:00:00.672 === Dune::BiCGSTABSolver 00:00:00.790 === rate=0.9984, T=0.1184, TIT=2.679e-05, IT=4419 00:00:00.792 === Dune::BiCGSTABSolver 00:00:00.792 === rate=0.0002375, T=1.791e-05, TIT=inf, IT=0 00:00:00.793 Newton converged after 2 iterations. Reduction: 8.0052e-02 (1.2265e-01s) 00:00:00.793 STAGE 2 time (to): 4.2981e+01. 00:00:00.795 === Dune::BiCGSTABSolver 00:00:00.929 === rate=1.004, T=0.1339, TIT=2.679e-05, IT=5000 00:00:00.929 Step failed (NewtonError) 00:00:00.929 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:00.929 Stopped redirection of std::cout 00:00:00.929 Reducing step size: 5.473673629760743s -> 2.7368368148803714s 00:00:00.929 Trying step: 37.51s + 2.74s -> 40.24s 00:00:00.929 TIME STEP [Alexander (order 2)] 16 time (from): 3.7508e+01 dt: 2.7368e+00 time (to): 4.0244e+01 00:00:00.929 STAGE 1 time (to): 3.8309e+01. 00:00:00.932 === Dune::BiCGSTABSolver 00:00:00.938 === rate=0.9645, T=0.006192, TIT=2.692e-05, IT=230 00:00:00.939 Newton converged after 1 iterations. Reduction: 3.0898e-01 (8.7500e-03s) 00:00:00.939 STAGE 2 time (to): 4.0244e+01. 00:00:00.941 === Dune::BiCGSTABSolver 00:00:00.943 === rate=0.8433, T=0.00117, TIT=2.72e-05, IT=43 00:00:00.944 Newton converged after 1 iterations. Reduction: 2.7578e-01 (3.7314e-03s) 00:00:00.944 ::: timesteps 16 (20) 00:00:00.944 ::: nl iterations 38 (42) 00:00:00.944 ::: lin iterations 4182 (29147) 00:00:00.944 ::: assemble time 3.1279e-02 (3.7845e-02) 00:00:00.944 ::: lin solve time 1.1286e-01 (7.8221e-01) 00:00:00.944 Time Step: 37.51s + 2.74s -> 40.24s 00:00:00.944 Stopped redirection of std::cout 00:00:00.944 Increasing step size: 2.74s -> 4.11s 00:00:00.944 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.944 Writing solution for 40.24s time stamp 00:00:00.944 Writing vtu file: 'vtk-kern/vtk-kern-00016.vtu' 00:00:00.944 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.944 Writing vtu file: 'vtk-cyt/vtk-cyt-00016.vtu' 00:00:00.944 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.944 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00016.vtu' 00:00:00.944 Trying step: 40.24s + 4.11s -> 44.35s 00:00:00.944 TIME STEP [Alexander (order 2)] 17 time (from): 4.0244e+01 dt: 4.1053e+00 time (to): 4.4350e+01 00:00:00.944 STAGE 1 time (to): 4.1447e+01. 00:00:00.946 === Dune::BiCGSTABSolver 00:00:00.948 === rate=0.8835, T=0.00154, TIT=2.702e-05, IT=57 00:00:00.949 Newton converged after 1 iterations. Reduction: 1.3623e-01 (4.1013e-03s) 00:00:00.949 STAGE 2 time (to): 4.4350e+01. 00:00:00.951 === Dune::BiCGSTABSolver 00:00:00.959 === rate=0.9759, T=0.007776, TIT=2.69e-05, IT=289 00:00:00.961 === Dune::BiCGSTABSolver 00:00:00.961 === rate=0.4957, T=0.0002854, TIT=2.854e-05, IT=10 00:00:00.962 Newton converged after 2 iterations. Reduction: 1.4870e-01 (1.2307e-02s) 00:00:00.962 ::: timesteps 17 (21) 00:00:00.962 ::: nl iterations 41 (45) 00:00:00.962 ::: lin iterations 4538 (29503) 00:00:00.962 ::: assemble time 3.3738e-02 (4.0305e-02) 00:00:00.962 ::: lin solve time 1.2248e-01 (7.9182e-01) 00:00:00.962 Time Step: 40.24s + 4.11s -> 44.35s 00:00:00.962 Stopped redirection of std::cout 00:00:00.962 Increasing step size: 4.11s -> 6.16s 00:00:00.962 Overriding time sequence file: 'vtk-kern.pvd' 00:00:00.962 Writing solution for 44.35s time stamp 00:00:00.962 Writing vtu file: 'vtk-kern/vtk-kern-00017.vtu' 00:00:00.962 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:00.962 Writing vtu file: 'vtk-cyt/vtk-cyt-00017.vtu' 00:00:00.962 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:00.962 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00017.vtu' 00:00:00.963 Trying step: 44.35s + 6.16s -> 50.51s 00:00:00.963 TIME STEP [Alexander (order 2)] 18 time (from): 4.4350e+01 dt: 6.1579e+00 time (to): 5.0508e+01 00:00:00.963 STAGE 1 time (to): 4.6153e+01. 00:00:00.965 === Dune::BiCGSTABSolver 00:00:01.099 === rate=0.9997, T=0.1339, TIT=2.678e-05, IT=5000 00:00:01.099 Step failed (NewtonError) 00:00:01.099 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:01.099 Stopped redirection of std::cout 00:00:01.099 Reducing step size: 6.157882833480835s -> 3.0789414167404177s 00:00:01.099 Trying step: 44.35s + 3.08s -> 47.43s 00:00:01.099 TIME STEP [Alexander (order 2)] 18 time (from): 4.4350e+01 dt: 3.0789e+00 time (to): 4.7429e+01 00:00:01.099 STAGE 1 time (to): 4.5251e+01. 00:00:01.101 === Dune::BiCGSTABSolver 00:00:01.102 === rate=0.7182, T=0.0005668, TIT=2.699e-05, IT=21 00:00:01.102 Newton converged after 1 iterations. Reduction: 3.0242e-01 (3.1354e-03s) 00:00:01.102 STAGE 2 time (to): 4.7429e+01. 00:00:01.105 === Dune::BiCGSTABSolver 00:00:01.109 === rate=0.947, T=0.003419, TIT=2.692e-05, IT=127 00:00:01.109 Newton converged after 1 iterations. Reduction: 2.6635e-01 (5.9846e-03s) 00:00:01.109 ::: timesteps 18 (23) 00:00:01.109 ::: nl iterations 43 (47) 00:00:01.109 ::: lin iterations 4686 (34651) 00:00:01.109 ::: assemble time 3.5392e-02 (4.2779e-02) 00:00:01.109 ::: lin solve time 1.2647e-01 (9.2971e-01) 00:00:01.109 Time Step: 44.35s + 3.08s -> 47.43s 00:00:01.109 Stopped redirection of std::cout 00:00:01.109 Increasing step size: 3.08s -> 4.62s 00:00:01.109 Overriding time sequence file: 'vtk-kern.pvd' 00:00:01.109 Writing solution for 47.43s time stamp 00:00:01.109 Writing vtu file: 'vtk-kern/vtk-kern-00018.vtu' 00:00:01.110 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:01.110 Writing vtu file: 'vtk-cyt/vtk-cyt-00018.vtu' 00:00:01.110 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:01.110 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00018.vtu' 00:00:01.110 Trying step: 47.43s + 4.62s -> 52.05s 00:00:01.110 TIME STEP [Alexander (order 2)] 19 time (from): 4.7429e+01 dt: 4.6184e+00 time (to): 5.2047e+01 00:00:01.110 STAGE 1 time (to): 4.8781e+01. 00:00:01.112 === Dune::BiCGSTABSolver 00:00:01.113 === rate=0.7389, T=0.0007235, TIT=2.783e-05, IT=26 00:00:01.114 Newton converged after 1 iterations. Reduction: 1.3346e-01 (3.2940e-03s) 00:00:01.114 STAGE 2 time (to): 5.2047e+01. 00:00:01.117 === Dune::BiCGSTABSolver 00:00:01.123 === rate=0.967, T=0.006235, TIT=2.687e-05, IT=232 00:00:01.124 === Dune::BiCGSTABSolver 00:00:01.125 === rate=0.484, T=0.0002715, TIT=2.715e-05, IT=10 00:00:01.126 Newton converged after 2 iterations. Reduction: 1.4548e-01 (1.0761e-02s) 00:00:01.126 ::: timesteps 19 (24) 00:00:01.126 ::: nl iterations 46 (50) 00:00:01.126 ::: lin iterations 4954 (34919) 00:00:01.126 ::: assemble time 3.7862e-02 (4.5248e-02) 00:00:01.126 ::: lin solve time 1.3371e-01 (9.3695e-01) 00:00:01.126 Time Step: 47.43s + 4.62s -> 52.05s 00:00:01.126 Stopped redirection of std::cout 00:00:01.126 Increasing step size: 4.62s -> 6.93s 00:00:01.126 Overriding time sequence file: 'vtk-kern.pvd' 00:00:01.126 Writing solution for 52.05s time stamp 00:00:01.126 Writing vtu file: 'vtk-kern/vtk-kern-00019.vtu' 00:00:01.126 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:01.126 Writing vtu file: 'vtk-cyt/vtk-cyt-00019.vtu' 00:00:01.126 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:01.126 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00019.vtu' 00:00:01.126 Trying step: 52.05s + 6.93s -> 58.97s 00:00:01.126 TIME STEP [Alexander (order 2)] 20 time (from): 5.2047e+01 dt: 6.9276e+00 time (to): 5.8975e+01 00:00:01.126 STAGE 1 time (to): 5.4076e+01. 00:00:01.128 === Dune::BiCGSTABSolver 00:00:01.262 === rate=1.002, T=0.1339, TIT=2.678e-05, IT=5000 00:00:01.262 Step failed (NewtonError) 00:00:01.262 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:01.262 Stopped redirection of std::cout 00:00:01.262 Reducing step size: 6.92761818766594s -> 3.46380909383297s 00:00:01.262 Trying step: 52.05s + 3.46s -> 55.51s 00:00:01.262 TIME STEP [Alexander (order 2)] 20 time (from): 5.2047e+01 dt: 3.4638e+00 time (to): 5.5511e+01 00:00:01.262 STAGE 1 time (to): 5.3062e+01. 00:00:01.265 === Dune::BiCGSTABSolver 00:00:01.266 === rate=0.839, T=0.001091, TIT=2.727e-05, IT=40 00:00:01.267 Newton converged after 1 iterations. Reduction: 3.0109e-01 (3.6561e-03s) 00:00:01.267 STAGE 2 time (to): 5.5511e+01. 00:00:01.269 === Dune::BiCGSTABSolver 00:00:01.271 === rate=0.8581, T=0.001415, TIT=2.722e-05, IT=52 00:00:01.272 Newton converged after 1 iterations. Reduction: 2.6306e-01 (3.9697e-03s) 00:00:01.272 ::: timesteps 20 (26) 00:00:01.272 ::: nl iterations 48 (52) 00:00:01.272 ::: lin iterations 5046 (40011) 00:00:01.272 ::: assemble time 3.9513e-02 (4.7725e-02) 00:00:01.272 ::: lin solve time 1.3622e-01 (1.0734e+00) 00:00:01.272 Time Step: 52.05s + 3.46s -> 55.51s 00:00:01.272 Stopped redirection of std::cout 00:00:01.272 Increasing step size: 3.46s -> 5.20s 00:00:01.272 Overriding time sequence file: 'vtk-kern.pvd' 00:00:01.272 Writing solution for 55.51s time stamp 00:00:01.272 Writing vtu file: 'vtk-kern/vtk-kern-00020.vtu' 00:00:01.272 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:01.272 Writing vtu file: 'vtk-cyt/vtk-cyt-00020.vtu' 00:00:01.272 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:01.272 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00020.vtu' 00:00:01.272 Trying step: 55.51s + 5.20s -> 60.71s 00:00:01.272 TIME STEP [Alexander (order 2)] 21 time (from): 5.5511e+01 dt: 5.1957e+00 time (to): 6.0706e+01 00:00:01.272 STAGE 1 time (to): 5.7033e+01. 00:00:01.274 === Dune::BiCGSTABSolver 00:00:01.275 === rate=0.749, T=0.0006616, TIT=2.757e-05, IT=24 00:00:01.277 === Dune::BiCGSTABSolver 00:00:01.277 === rate=0.0002082, T=1.71e-05, TIT=inf, IT=0 00:00:01.278 Newton converged after 2 iterations. Reduction: 6.7105e-02 (4.9427e-03s) 00:00:01.278 STAGE 2 time (to): 6.0706e+01. 00:00:01.280 === Dune::BiCGSTABSolver 00:00:01.412 === rate=0.9986, T=0.1312, TIT=2.682e-05, IT=4891 00:00:01.421 Step failed (NewtonError) 00:00:01.421 NewtonLineSearchError [line_search:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:703]: NewtonLineSearch::line_search(): line search failed, max iteration count reached, defect did not improve enough 00:00:01.421 Stopped redirection of std::cout 00:00:01.421 Reducing step size: 5.195713640749455s -> 2.5978568203747274s 00:00:01.421 Trying step: 55.51s + 2.60s -> 58.11s 00:00:01.421 TIME STEP [Alexander (order 2)] 21 time (from): 5.5511e+01 dt: 2.5979e+00 time (to): 5.8109e+01 00:00:01.421 STAGE 1 time (to): 5.6272e+01. 00:00:01.423 === Dune::BiCGSTABSolver 00:00:01.424 === rate=0.8051, T=0.0008754, TIT=2.736e-05, IT=32 00:00:01.425 Newton converged after 1 iterations. Reduction: 4.1156e-01 (3.4511e-03s) 00:00:01.425 STAGE 2 time (to): 5.8109e+01. 00:00:01.428 === Dune::BiCGSTABSolver 00:00:01.428 === rate=0.705, T=0.0006333, TIT=2.754e-05, IT=23 00:00:01.430 === Dune::BiCGSTABSolver 00:00:01.430 === rate=0.1721, T=0.0001109, TIT=2.774e-05, IT=4 00:00:01.431 Newton converged after 2 iterations. Reduction: 2.0936e-01 (4.9932e-03s) 00:00:01.431 ::: timesteps 21 (28) 00:00:01.431 ::: nl iterations 51 (57) 00:00:01.431 ::: lin iterations 5105 (44985) 00:00:01.431 ::: assemble time 4.1978e-02 (5.2648e-02) 00:00:01.431 ::: lin solve time 1.3785e-01 (1.2069e+00) 00:00:01.431 Time Step: 55.51s + 2.60s -> 58.11s 00:00:01.431 Stopped redirection of std::cout 00:00:01.431 Increasing step size: 2.60s -> 3.90s 00:00:01.431 Overriding time sequence file: 'vtk-kern.pvd' 00:00:01.431 Writing solution for 58.11s time stamp 00:00:01.431 Writing vtu file: 'vtk-kern/vtk-kern-00021.vtu' 00:00:01.431 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:01.431 Writing vtu file: 'vtk-cyt/vtk-cyt-00021.vtu' 00:00:01.432 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:01.432 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00021.vtu' 00:00:01.432 Trying step: 58.11s + 3.90s -> 62.01s 00:00:01.432 TIME STEP [Alexander (order 2)] 22 time (from): 5.8109e+01 dt: 3.8968e+00 time (to): 6.2005e+01 00:00:01.432 STAGE 1 time (to): 5.9250e+01. 00:00:01.434 === Dune::BiCGSTABSolver 00:00:01.503 === rate=0.9972, T=0.06948, TIT=2.687e-05, IT=2586 00:00:01.506 === Dune::BiCGSTABSolver 00:00:01.507 === rate=0.8427, T=0.001118, TIT=2.727e-05, IT=41 00:00:01.508 Newton converged after 2 iterations. Reduction: 5.7156e-02 (7.5739e-02s) 00:00:01.508 STAGE 2 time (to): 6.2005e+01. 00:00:01.511 === Dune::BiCGSTABSolver 00:00:01.515 === rate=0.953, T=0.003909, TIT=2.696e-05, IT=145 00:00:01.515 Newton converged after 1 iterations. Reduction: 1.5047e-01 (6.4626e-03s) 00:00:01.515 ::: timesteps 22 (29) 00:00:01.515 ::: nl iterations 54 (60) 00:00:01.515 ::: lin iterations 7877 (47757) 00:00:01.515 ::: assemble time 4.4444e-02 (5.5114e-02) 00:00:01.515 ::: lin solve time 2.1238e-01 (1.2814e+00) 00:00:01.515 Time Step: 58.11s + 3.90s -> 62.01s 00:00:01.515 Stopped redirection of std::cout 00:00:01.515 Increasing step size: 3.90s -> 5.85s 00:00:01.516 Overriding time sequence file: 'vtk-kern.pvd' 00:00:01.516 Writing solution for 62.01s time stamp 00:00:01.516 Writing vtu file: 'vtk-kern/vtk-kern-00022.vtu' 00:00:01.516 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:01.516 Writing vtu file: 'vtk-cyt/vtk-cyt-00022.vtu' 00:00:01.516 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:01.516 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00022.vtu' 00:00:01.516 Trying step: 62.01s + 5.85s -> 67.85s 00:00:01.516 TIME STEP [Alexander (order 2)] 23 time (from): 6.2005e+01 dt: 5.8452e+00 time (to): 6.7851e+01 00:00:01.516 STAGE 1 time (to): 6.3717e+01. 00:00:01.518 === Dune::BiCGSTABSolver 00:00:01.520 === rate=0.8983, T=0.001877, TIT=2.682e-05, IT=70 00:00:01.522 === Dune::BiCGSTABSolver 00:00:01.522 === rate=0.0001561, T=1.741e-05, TIT=inf, IT=0 00:00:01.523 Newton converged after 2 iterations. Reduction: 1.0487e-01 (6.1607e-03s) 00:00:01.523 STAGE 2 time (to): 6.7851e+01. 00:00:01.525 === Dune::BiCGSTABSolver 00:00:01.527 === rate=0.8328, T=0.001101, TIT=2.685e-05, IT=41 00:00:01.528 === Dune::BiCGSTABSolver 00:00:01.529 === rate=0.5038, T=0.0002848, TIT=2.848e-05, IT=10 00:00:01.529 Newton converged after 2 iterations. Reduction: 1.2729e-01 (5.6345e-03s) 00:00:01.529 ::: timesteps 23 (30) 00:00:01.529 ::: nl iterations 58 (64) 00:00:01.529 ::: lin iterations 7998 (47878) 00:00:01.529 ::: assemble time 4.7722e-02 (5.8392e-02) 00:00:01.529 ::: lin solve time 2.1567e-01 (1.2847e+00) 00:00:01.529 Time Step: 62.01s + 5.85s -> 67.85s 00:00:01.529 Stopped redirection of std::cout 00:00:01.529 Increasing step size: 5.85s -> 8.77s 00:00:01.529 Overriding time sequence file: 'vtk-kern.pvd' 00:00:01.529 Writing solution for 67.85s time stamp 00:00:01.529 Writing vtu file: 'vtk-kern/vtk-kern-00023.vtu' 00:00:01.530 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:01.530 Writing vtu file: 'vtk-cyt/vtk-cyt-00023.vtu' 00:00:01.530 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:01.530 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00023.vtu' 00:00:01.530 Trying step: 67.85s + 8.77s -> 76.62s 00:00:01.530 TIME STEP [Alexander (order 2)] 24 time (from): 6.7851e+01 dt: 8.7678e+00 time (to): 7.6618e+01 00:00:01.530 STAGE 1 time (to): 7.0419e+01. 00:00:01.532 === Dune::BiCGSTABSolver 00:00:01.533 === rate=0.7651, T=0.000723, TIT=2.781e-05, IT=26 00:00:01.535 === Dune::BiCGSTABSolver 00:00:01.535 === rate=0.0001586, T=1.746e-05, TIT=inf, IT=0 00:00:01.536 Newton converged after 2 iterations. Reduction: 8.3012e-02 (4.9829e-03s) 00:00:01.536 STAGE 2 time (to): 7.6618e+01. 00:00:01.538 === Dune::BiCGSTABSolver 00:00:01.672 === rate=1.004, T=0.134, TIT=2.68e-05, IT=5000 00:00:01.672 Step failed (NewtonError) 00:00:01.672 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:01.672 Stopped redirection of std::cout 00:00:01.672 Reducing step size: 8.767766768764705s -> 4.383883384382353s 00:00:01.672 Trying step: 67.85s + 4.38s -> 72.23s 00:00:01.672 TIME STEP [Alexander (order 2)] 24 time (from): 6.7851e+01 dt: 4.3839e+00 time (to): 7.2234e+01 00:00:01.672 STAGE 1 time (to): 6.9135e+01. 00:00:01.675 === Dune::BiCGSTABSolver 00:00:01.774 === rate=0.9974, T=0.09949, TIT=2.683e-05, IT=3708 00:00:01.779 === Dune::BiCGSTABSolver 00:00:01.780 === rate=0.8031, T=0.0008742, TIT=2.732e-05, IT=32 00:00:01.781 Newton converged after 2 iterations. Reduction: 2.5456e-01 (1.0808e-01s) 00:00:01.781 STAGE 2 time (to): 7.2234e+01. 00:00:01.784 === Dune::BiCGSTABSolver 00:00:01.785 === rate=0.8673, T=0.001345, TIT=2.69e-05, IT=50 00:00:01.786 Newton converged after 1 iterations. Reduction: 1.9161e-01 (3.8986e-03s) 00:00:01.786 ::: timesteps 24 (32) 00:00:01.786 ::: nl iterations 61 (69) 00:00:01.786 ::: lin iterations 11788 (56694) 00:00:01.786 ::: assemble time 5.0188e-02 (6.3317e-02) 00:00:01.786 ::: lin solve time 3.1739e-01 (1.5212e+00) 00:00:01.786 Time Step: 67.85s + 4.38s -> 72.23s 00:00:01.786 Stopped redirection of std::cout 00:00:01.786 Increasing step size: 4.38s -> 6.58s 00:00:01.786 Overriding time sequence file: 'vtk-kern.pvd' 00:00:01.786 Writing solution for 72.23s time stamp 00:00:01.786 Writing vtu file: 'vtk-kern/vtk-kern-00024.vtu' 00:00:01.786 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:01.786 Writing vtu file: 'vtk-cyt/vtk-cyt-00024.vtu' 00:00:01.786 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:01.786 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00024.vtu' 00:00:01.786 Trying step: 72.23s + 6.58s -> 78.81s 00:00:01.786 TIME STEP [Alexander (order 2)] 25 time (from): 7.2234e+01 dt: 6.5758e+00 time (to): 7.8810e+01 00:00:01.786 STAGE 1 time (to): 7.4161e+01. 00:00:01.789 === Dune::BiCGSTABSolver 00:00:01.819 === rate=0.9934, T=0.02984, TIT=2.684e-05, IT=1112 00:00:01.819 Newton converged after 1 iterations. Reduction: 7.8438e-02 (3.2411e-02s) 00:00:01.819 STAGE 2 time (to): 7.8810e+01. 00:00:01.822 === Dune::BiCGSTABSolver 00:00:01.956 === rate=1.005, T=0.134, TIT=2.681e-05, IT=5000 00:00:01.956 Step failed (NewtonError) 00:00:01.956 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:01.956 Stopped redirection of std::cout 00:00:01.956 Reducing step size: 6.575825076573529s -> 3.2879125382867644s 00:00:01.956 Trying step: 72.23s + 3.29s -> 75.52s 00:00:01.956 TIME STEP [Alexander (order 2)] 25 time (from): 7.2234e+01 dt: 3.2879e+00 time (to): 7.5522e+01 00:00:01.956 STAGE 1 time (to): 7.3197e+01. 00:00:01.958 === Dune::BiCGSTABSolver 00:00:01.961 === rate=0.9388, T=0.00296, TIT=2.715e-05, IT=109 00:00:01.962 Newton converged after 1 iterations. Reduction: 4.1679e-01 (5.5239e-03s) 00:00:01.962 STAGE 2 time (to): 7.5522e+01. 00:00:01.965 === Dune::BiCGSTABSolver 00:00:01.966 === rate=0.7291, T=0.000654, TIT=2.725e-05, IT=24 00:00:01.967 === Dune::BiCGSTABSolver 00:00:01.968 === rate=0.4918, T=0.0002737, TIT=2.737e-05, IT=10 00:00:01.968 Newton converged after 2 iterations. Reduction: 1.5788e-01 (5.1714e-03s) 00:00:01.968 ::: timesteps 25 (34) 00:00:01.968 ::: nl iterations 64 (73) 00:00:01.968 ::: lin iterations 11931 (62949) 00:00:01.968 ::: assemble time 5.2646e-02 (6.7421e-02) 00:00:01.968 ::: lin solve time 3.2129e-01 (1.6890e+00) 00:00:01.968 Time Step: 72.23s + 3.29s -> 75.52s 00:00:01.968 Stopped redirection of std::cout 00:00:01.968 Increasing step size: 3.29s -> 4.93s 00:00:01.968 Overriding time sequence file: 'vtk-kern.pvd' 00:00:01.968 Writing solution for 75.52s time stamp 00:00:01.968 Writing vtu file: 'vtk-kern/vtk-kern-00025.vtu' 00:00:01.969 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:01.969 Writing vtu file: 'vtk-cyt/vtk-cyt-00025.vtu' 00:00:01.969 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:01.969 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00025.vtu' 00:00:01.969 Trying step: 75.52s + 4.93s -> 80.45s 00:00:01.969 TIME STEP [Alexander (order 2)] 26 time (from): 7.5522e+01 dt: 4.9319e+00 time (to): 8.0454e+01 00:00:01.969 STAGE 1 time (to): 7.6967e+01. 00:00:01.971 === Dune::BiCGSTABSolver 00:00:01.972 === rate=0.8446, T=0.001169, TIT=2.719e-05, IT=43 00:00:01.973 Newton converged after 1 iterations. Reduction: 1.7378e-01 (3.7315e-03s) 00:00:01.973 STAGE 2 time (to): 8.0454e+01. 00:00:01.976 === Dune::BiCGSTABSolver 00:00:01.999 === rate=0.9891, T=0.0231, TIT=2.683e-05, IT=861 00:00:02.001 === Dune::BiCGSTABSolver 00:00:02.001 === rate=0.07507, T=9.783e-05, TIT=3.261e-05, IT=3 00:00:02.002 Newton converged after 2 iterations. Reduction: 1.5694e-01 (2.7445e-02s) 00:00:02.002 ::: timesteps 26 (35) 00:00:02.002 ::: nl iterations 67 (76) 00:00:02.002 ::: lin iterations 12838 (63856) 00:00:02.002 ::: assemble time 5.5102e-02 (6.9877e-02) 00:00:02.002 ::: lin solve time 3.4567e-01 (1.7133e+00) 00:00:02.002 Time Step: 75.52s + 4.93s -> 80.45s 00:00:02.002 Stopped redirection of std::cout 00:00:02.002 Increasing step size: 4.93s -> 7.40s 00:00:02.002 Overriding time sequence file: 'vtk-kern.pvd' 00:00:02.002 Writing solution for 80.45s time stamp 00:00:02.002 Writing vtu file: 'vtk-kern/vtk-kern-00026.vtu' 00:00:02.002 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:02.002 Writing vtu file: 'vtk-cyt/vtk-cyt-00026.vtu' 00:00:02.002 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:02.002 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00026.vtu' 00:00:02.002 Trying step: 80.45s + 7.40s -> 87.85s 00:00:02.002 TIME STEP [Alexander (order 2)] 27 time (from): 8.0454e+01 dt: 7.3978e+00 time (to): 8.7852e+01 00:00:02.002 STAGE 1 time (to): 8.2621e+01. 00:00:02.005 === Dune::BiCGSTABSolver 00:00:02.006 === rate=0.88, T=0.001793, TIT=2.717e-05, IT=66 00:00:02.007 Newton converged after 1 iterations. Reduction: 1.2616e-01 (4.3529e-03s) 00:00:02.007 STAGE 2 time (to): 8.7852e+01. 00:00:02.010 === Dune::BiCGSTABSolver 00:00:02.011 === rate=0.865, T=0.001315, TIT=2.683e-05, IT=49 00:00:02.013 === Dune::BiCGSTABSolver 00:00:02.018 === rate=0.9553, T=0.005254, TIT=2.694e-05, IT=195 00:00:02.019 Newton converged after 2 iterations. Reduction: 1.3390e-01 (1.0817e-02s) 00:00:02.019 ::: timesteps 27 (36) 00:00:02.019 ::: nl iterations 70 (79) 00:00:02.019 ::: lin iterations 13148 (64166) 00:00:02.019 ::: assemble time 5.7562e-02 (7.2337e-02) 00:00:02.019 ::: lin solve time 3.5404e-01 (1.7217e+00) 00:00:02.019 Time Step: 80.45s + 7.40s -> 87.85s 00:00:02.019 Stopped redirection of std::cout 00:00:02.019 Increasing step size: 7.40s -> 11.10s 00:00:02.019 Overriding time sequence file: 'vtk-kern.pvd' 00:00:02.019 Writing solution for 87.85s time stamp 00:00:02.019 Writing vtu file: 'vtk-kern/vtk-kern-00027.vtu' 00:00:02.019 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:02.019 Writing vtu file: 'vtk-cyt/vtk-cyt-00027.vtu' 00:00:02.020 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:02.020 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00027.vtu' 00:00:02.020 Trying step: 87.85s + 11.10s -> 98.95s 00:00:02.020 TIME STEP [Alexander (order 2)] 28 time (from): 8.7852e+01 dt: 1.1097e+01 time (to): 9.8949e+01 00:00:02.020 STAGE 1 time (to): 9.1102e+01. 00:00:02.022 === Dune::BiCGSTABSolver 00:00:02.156 === rate=1.008, T=0.1342, TIT=2.683e-05, IT=5000 00:00:02.156 Step failed (NewtonError) 00:00:02.156 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:02.156 Stopped redirection of std::cout 00:00:02.156 Reducing step size: 11.09670481671783s -> 5.548352408358915s 00:00:02.156 Trying step: 87.85s + 5.55s -> 93.40s 00:00:02.156 TIME STEP [Alexander (order 2)] 28 time (from): 8.7852e+01 dt: 5.5484e+00 time (to): 9.3400e+01 00:00:02.156 STAGE 1 time (to): 8.9477e+01. 00:00:02.158 === Dune::BiCGSTABSolver 00:00:02.160 === rate=0.8602, T=0.00125, TIT=2.717e-05, IT=46 00:00:02.160 Newton converged after 1 iterations. Reduction: 2.8946e-01 (3.8160e-03s) 00:00:02.161 STAGE 2 time (to): 9.3400e+01. 00:00:02.163 === Dune::BiCGSTABSolver 00:00:02.164 === rate=0.7956, T=0.0008215, TIT=2.738e-05, IT=30 00:00:02.165 Newton converged after 1 iterations. Reduction: 2.1735e-01 (3.3745e-03s) 00:00:02.165 ::: timesteps 28 (38) 00:00:02.165 ::: nl iterations 72 (81) 00:00:02.165 ::: lin iterations 13224 (69242) 00:00:02.165 ::: assemble time 5.9208e-02 (7.4804e-02) 00:00:02.165 ::: lin solve time 3.5612e-01 (1.8580e+00) 00:00:02.165 Time Step: 87.85s + 5.55s -> 93.40s 00:00:02.165 Stopped redirection of std::cout 00:00:02.165 Increasing step size: 5.55s -> 8.32s 00:00:02.165 Overriding time sequence file: 'vtk-kern.pvd' 00:00:02.165 Writing solution for 93.40s time stamp 00:00:02.165 Writing vtu file: 'vtk-kern/vtk-kern-00028.vtu' 00:00:02.165 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:02.165 Writing vtu file: 'vtk-cyt/vtk-cyt-00028.vtu' 00:00:02.165 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:02.165 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00028.vtu' 00:00:02.165 Reduce step to match end time: 8.32s -> 6.60 00:00:02.165 Trying step: 93.40s + 6.60s -> 100.00s 00:00:02.165 TIME STEP [Alexander (order 2)] 29 time (from): 9.3400e+01 dt: 6.5996e+00 time (to): 1.0000e+02 00:00:02.165 STAGE 1 time (to): 9.5333e+01. 00:00:02.168 === Dune::BiCGSTABSolver 00:00:02.302 === rate=1.002, T=0.1341, TIT=2.681e-05, IT=5000 00:00:02.302 Step failed (NewtonError) 00:00:02.302 NewtonLinearSolverError [linearSolve:/home/lkeegan/BIOQUANT/dune/dune-pdelab/dune/pdelab/newton/newton.hh:231]: NewtonSolver::linearSolve(): Linear solver did not converge in 5000 iterations 00:00:02.302 Stopped redirection of std::cout 00:00:02.302 Reducing step size: 6.59957563126882s -> 3.29978781563441s 00:00:02.302 Trying step: 93.40s + 3.30s -> 96.70s 00:00:02.302 TIME STEP [Alexander (order 2)] 29 time (from): 9.3400e+01 dt: 3.2998e+00 time (to): 9.6700e+01 00:00:02.302 STAGE 1 time (to): 9.4367e+01. 00:00:02.304 === Dune::BiCGSTABSolver 00:00:02.305 === rate=0.654, T=0.0006612, TIT=2.755e-05, IT=24 00:00:02.306 Newton converged after 1 iterations. Reduction: 4.4018e-01 (3.2316e-03s) 00:00:02.306 STAGE 2 time (to): 9.6700e+01. 00:00:02.308 === Dune::BiCGSTABSolver 00:00:02.310 === rate=0.8453, T=0.001256, TIT=2.73e-05, IT=46 00:00:02.311 === Dune::BiCGSTABSolver 00:00:02.312 === rate=0.4815, T=0.0002717, TIT=2.717e-05, IT=10 00:00:02.312 Newton converged after 2 iterations. Reduction: 1.7118e-01 (5.7674e-03s) 00:00:02.312 ::: timesteps 29 (40) 00:00:02.312 ::: nl iterations 75 (84) 00:00:02.312 ::: lin iterations 13304 (74322) 00:00:02.312 ::: assemble time 6.1666e-02 (7.8085e-02) 00:00:02.312 ::: lin solve time 3.5832e-01 (1.9943e+00) 00:00:02.312 Time Step: 93.40s + 3.30s -> 96.70s 00:00:02.312 Stopped redirection of std::cout 00:00:02.312 Increasing step size: 3.30s -> 4.95s 00:00:02.312 Overriding time sequence file: 'vtk-kern.pvd' 00:00:02.312 Writing solution for 96.70s time stamp 00:00:02.312 Writing vtu file: 'vtk-kern/vtk-kern-00029.vtu' 00:00:02.313 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:02.313 Writing vtu file: 'vtk-cyt/vtk-cyt-00029.vtu' 00:00:02.313 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:02.313 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00029.vtu' 00:00:02.313 Reduce step to match end time: 4.95s -> 3.30 00:00:02.313 Trying step: 96.70s + 3.30s -> 100.00s 00:00:02.313 TIME STEP [Alexander (order 2)] 30 time (from): 9.6700e+01 dt: 3.2998e+00 time (to): 1.0000e+02 00:00:02.313 STAGE 1 time (to): 9.7667e+01. 00:00:02.315 === Dune::BiCGSTABSolver 00:00:02.316 === rate=0.7444, T=0.0007956, TIT=2.744e-05, IT=29 00:00:02.317 Newton converged after 1 iterations. Reduction: 1.5653e-01 (3.3564e-03s) 00:00:02.317 STAGE 2 time (to): 1.0000e+02. 00:00:02.320 === Dune::BiCGSTABSolver 00:00:02.329 === rate=0.9794, T=0.009374, TIT=2.694e-05, IT=348 00:00:02.331 === Dune::BiCGSTABSolver 00:00:02.331 === rate=0.4804, T=0.0002787, TIT=2.787e-05, IT=10 00:00:02.332 Newton converged after 2 iterations. Reduction: 1.6953e-01 (1.3893e-02s) 00:00:02.332 ::: timesteps 30 (41) 00:00:02.332 ::: nl iterations 78 (87) 00:00:02.332 ::: lin iterations 13691 (74709) 00:00:02.332 ::: assemble time 6.4124e-02 (8.0543e-02) 00:00:02.332 ::: lin solve time 3.6878e-01 (2.0047e+00) 00:00:02.332 Time Step: 96.70s + 3.30s -> 100.00s 00:00:02.332 Stopped redirection of std::cout 00:00:02.332 Increasing step size: 3.30s -> 4.95s 00:00:02.332 Overriding time sequence file: 'vtk-kern.pvd' 00:00:02.332 Writing solution for 100.00s time stamp 00:00:02.332 Writing vtu file: 'vtk-kern/vtk-kern-00030.vtu' 00:00:02.332 Overriding time sequence file: 'vtk-cyt.pvd' 00:00:02.332 Writing vtu file: 'vtk-cyt/vtk-cyt-00030.vtu' 00:00:02.332 Overriding time sequence file: 'vtk-cyt_kern_membrane.pvd' 00:00:02.332 Writing vtu file: 'vtk-cyt_kern_membrane/vtk-cyt_kern_membrane-00030.vtu' 00:00:02.332 ModelMultiDomainDiffusionReaction deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.332 ExpressionToGridFunctionAdapter deconstructed 00:00:02.333 ExpressionToGridFunctionAdapter deconstructed 00:00:02.333 ExpressionToGridFunctionAdapter deconstructed 00:00:02.333 ExpressionToGridFunctionAdapter deconstructed 00:00:02.333 ModelBase deconstructed 00:00:02.333 dune-copasi(md) successfully finished :)
Reproducing input
Do you have input files reproducing the problem? Insert them here:
| Input data | |
|---|---|
| Simulation Case | dune_copasi_md |
| GMSH grid file | grid.msh |
| Run config file | dune.ini |
Ideas how to fix this?
Add them here, if you have any.