/Applications/BioNetGen/Perl2/BNG2.pl BioNetGen version 2.0.48 readFile::Reading from file toy-jim.bngl Read 16 parameters. Read 5 species. Adding P as allowed state of component Y of molecule K Read 8 reaction rule(s). Read 9 observable(s). WARNING: Removing old network file toy-jim.net. Iteration 0: 5 species 0 rxns 0.00e+00 CPU s Iteration 1: 8 species 3 rxns 0.00e+00 CPU s Iteration 2: 12 species 12 rxns 2.00e-02 CPU s Iteration 3: 17 species 29 rxns 6.00e-02 CPU s Iteration 4: 18 species 51 rxns 1.40e-01 CPU s Iteration 5: 24 species 58 rxns 4.00e-02 CPU s Iteration 6: 25 species 97 rxns 1.60e-01 CPU s Iteration 7: 25 species 101 rxns 1.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 8 reactions 4.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 2: 20 reactions 1.20e-01 CPU s 6.00e-03 CPU s/rxn Rule 3: 36 reactions 1.20e-01 CPU s 3.33e-03 CPU s/rxn Rule 4: 28 reactions 8.00e-02 CPU s 2.86e-03 CPU s/rxn Rule 5: 1 reactions 1.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 6: 1 reactions 1.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 7: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 8: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 101 reactions 3.90e-01 CPU s 3.86e-03 CPU s/rxn Wrote network to toy-jim.net. CPU TIME: generate_network 0.5 s. Network simulation using ODEs Wrote network to toy-jim_equil.net. Running run_network on Steve-2.home full command: "/Applications/BioNetGen/bin/run_network" -o "toy-jim_equil" -e -p cvode -a 1e-10 -r 1e-08 -b -c -g "toy-jim_equil.net" "toy-jim_equil.net" 100 10 run_network 1.5 Read 16 parameters Read 25 species Read 101 reaction(s) 101 reaction(s) have nonzero rate Read 9 group(s) from toy-jim_equil.net Initialization took 0.00 CPU seconds Propagating with cvode using GMRES time n_steps n_deriv_calls 100.00 199 462 RMS change in concentrations=3.6e-02. 200.00 211 494 RMS change in concentrations=8.4e-11. Steady state reached. Time course of concentrations written to file toy-jim_equil.cdat. Time course of groups written to file toy-jim_equil.gdat. Propagation took 0.00e+00 CPU seconds Final network file written to toy-jim_equil_end.net Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from toy-jim_equil.cdat CPU TIME: simulate_ode 0.0 s. Set concentration of species L(r) to value 1 Wrote SBML to toy-jim.xml. CPU TIME: writeSBML 0.0 s. Wrote M-file toy-jim.m. CPU TIME: writeMfile 0.0 s. Network simulation using ODEs Wrote network to toy-jim_kinetics.net. Running run_network on Steve-2.home full command: "/Applications/BioNetGen/bin/run_network" -o "toy-jim_kinetics" -e -p cvode -a 1e-10 -r 1e-08 -g "toy-jim_kinetics.net" "toy-jim_kinetics.net" 1 120 run_network 1.5 Read 16 parameters Read 25 species Read 101 reaction(s) 101 reaction(s) have nonzero rate Read 9 group(s) from toy-jim_kinetics.net Initialization took 0.00 CPU seconds Propagating with cvode using dense LU time n_steps n_deriv_calls 1.00 38 75 2.00 49 90 3.00 60 101 4.00 70 136 5.00 78 145 6.00 85 152 7.00 92 159 8.00 99 166 9.00 104 172 10.00 109 177 11.00 114 182 12.00 118 186 13.00 122 216 14.00 125 219 15.00 128 222 16.00 131 225 17.00 133 228 18.00 135 230 19.00 137 232 20.00 139 234 21.00 141 236 22.00 143 238 23.00 145 240 24.00 147 242 25.00 149 244 26.00 151 246 27.00 153 249 28.00 154 250 29.00 155 251 30.00 157 253 31.00 158 254 32.00 159 255 33.00 161 257 34.00 162 258 35.00 163 259 36.00 165 261 37.00 166 262 38.00 167 263 39.00 169 265 40.00 170 266 41.00 171 267 42.00 173 294 43.00 174 296 44.00 174 296 45.00 175 297 46.00 176 298 47.00 177 299 48.00 178 300 49.00 179 301 50.00 180 302 51.00 181 303 52.00 182 304 53.00 182 304 54.00 183 305 55.00 184 306 56.00 185 307 57.00 186 308 58.00 187 309 59.00 188 310 60.00 189 311 61.00 189 311 62.00 190 312 63.00 191 313 64.00 192 314 65.00 193 315 66.00 194 316 67.00 194 316 68.00 195 318 69.00 196 319 70.00 196 319 71.00 197 320 72.00 197 320 73.00 198 321 74.00 198 321 75.00 199 322 76.00 200 323 77.00 200 323 78.00 201 324 79.00 201 324 80.00 202 325 81.00 203 326 82.00 203 326 83.00 204 327 84.00 204 327 85.00 205 328 86.00 206 329 87.00 206 329 88.00 207 330 89.00 207 330 90.00 208 331 91.00 208 331 92.00 209 332 93.00 210 333 94.00 210 333 95.00 211 334 96.00 211 334 97.00 212 336 98.00 212 336 99.00 212 336 100.00 213 337 101.00 213 337 102.00 213 337 103.00 214 338 104.00 214 338 105.00 215 339 106.00 215 339 107.00 215 339 108.00 216 340 109.00 216 340 110.00 217 341 111.00 217 341 112.00 217 341 113.00 218 342 114.00 218 342 115.00 218 342 116.00 219 343 117.00 219 343 118.00 220 344 119.00 220 344 120.00 220 344 Time course of concentrations written to file toy-jim_kinetics.cdat. Time course of groups written to file toy-jim_kinetics.gdat. Propagation took 1.00e-02 CPU seconds Final network file written to toy-jim_kinetics_end.net Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from toy-jim_kinetics.cdat CPU TIME: simulate_ode 0.1 s. Finished processing file toy-jim.bngl CPU TIME: total 0.7 s.