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Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,603 @@ ================================================================================ Profiling Data ================================================================================ Sorted by internal time Wed Jun 13 22:29:04 2012 /Users/rwest/Code/rmgpy/RMG-Py/examples/rmg/methylformate/RMG.profile 3411174244 function calls (3298217272 primitive calls) in 20996.773 seconds Ordered by: internal time List reduced from 1956 to 25 due to restriction <25> ncalls tottime percall cumtime percall filename:lineno(function) 477 13698.314 28.718 14425.269 30.242 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} 4476062 711.038 0.000 775.896 0.000 {method 'getFormula' of 'rmgpy.molecule.Molecule' objects} 6582 483.001 0.073 511.423 0.078 {method 'getDensityOfStates' of 'rmgpy.statmech.StatesModel' objects} 61150916 482.258 0.000 482.258 0.000 {method 'fill' of 'numpy.ndarray' objects} 58158075 454.974 0.000 454.974 0.000 {method 'isSubgraphIsomorphic' of 'rmgpy.molecule.Molecule' objects} 161 422.137 2.622 5150.083 31.988 model.py:504(enlarge) 23638617 239.754 0.000 239.754 0.000 {method 'isIsomorphic' of 'rmgpy.molecule.Molecule' objects} 2103290 174.274 0.000 174.274 0.000 {method 'isIsomorphic' of 'rmgpy.reaction.Reaction' objects} 99629385/1497821 145.742 0.000 360.856 0.000 copy.py:145(deepcopy) 106455 138.394 0.001 138.394 0.001 {method 'calculateSymmetryNumber' of 'rmgpy.molecule.Molecule' objects} 5935007 124.366 0.000 467.417 0.000 base.py:1060(isMoleculeForbidden) 27943498/27311544 122.039 0.000 426.909 0.000 base.py:766(matchNodeToStructure) 5239099 109.854 0.000 109.854 0.000 {method 'copy' of 'rmgpy.molecule.Molecule' objects} 620264 103.157 0.000 125.721 0.000 {method 'getURL' of 'rmgpy.reaction.Reaction' objects} 2444097 101.314 0.000 123.973 0.000 {method 'getURL' of 'rmgpy.molecule.Molecule' objects} 843410 97.948 0.000 210.886 0.000 {method '__residual' of 'rmgpy.thermo.Wilhoit' objects} 310848 85.114 0.000 85.114 0.000 {method 'flush' of 'file' objects} 620264 83.797 0.000 103.486 0.000 {method 'toHTML' of 'rmgpy.kinetics.KineticsModel' objects} 61128764 73.827 0.000 627.712 0.000 numeric.py:65(zeros_like) 1147676289/1147676170 73.103 0.000 73.103 0.000 {len} 66173 71.761 0.001 366.232 0.006 optimize.py:967(fminbound) 61128764 71.733 0.000 71.733 0.000 {numpy.core.multiarray.empty_like} 59140 67.178 0.001 67.196 0.001 model.py:1024(addReactionToEdge) 3681639 66.193 0.000 66.821 0.000 statesfit.py:332(hinderedRotor_heatCapacity) 6834737 62.477 0.000 63.556 0.000 statesfit.py:321(harmonicOscillator_d_heatCapacity_d_freq) Ordered by: internal time List reduced from 1956 to 25 due to restriction <25> Function was called by... ncalls tottime cumtime {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} <- 477 13698.314 14425.269 main.py:309(execute) {method 'getFormula' of 'rmgpy.molecule.Molecule' objects} <- 4264890 670.160 730.976 chemkin.py:763(getSpeciesIdentifier) 178085 33.402 36.879 model.py:222(checkForExistingSpecies) 33087 7.477 8.042 model.py:252(makeNewSpecies) {method 'getDensityOfStates' of 'rmgpy.statmech.StatesModel' objects} <- 6582 483.001 511.423 network.py:372(calculateDensitiesOfStates) {method 'fill' of 'numpy.ndarray' objects} <- 61128764 482.152 482.152 numeric.py:65(zeros_like) 22152 0.106 0.106 numeric.py:1791(ones) {method 'isSubgraphIsomorphic' of 'rmgpy.molecule.Molecule' objects} <- 20966393 184.436 184.436 base.py:766(matchNodeToStructure) 37191682 270.538 270.538 base.py:1060(isMoleculeForbidden) model.py:504(enlarge) <- 2 0.266 99.883 main.py:212(initialize) 159 421.870 5050.200 main.py:309(execute) {method 'isIsomorphic' of 'rmgpy.molecule.Molecule' objects} <- 1369406 13.195 13.195 chemkin.py:893(writeKineticsEntry) 3276 0.022 0.022 kinetics.py:688(speciesMatch) 1059187 1.037 1.037 kinetics.py:2304(__createReaction) 4619882 30.757 30.757 kinetics.py:2471(__generateReactions) 2206508 9.957 9.957 model.py:222(checkForExistingSpecies) 14380358 184.786 184.786 thermo.py:589(getThermoDataFromLibrary) {method 'isIsomorphic' of 'rmgpy.reaction.Reaction' objects} <- 2103290 174.274 174.274 kinetics.py:2717(getKineticsFromDepository) copy.py:145(deepcopy) <- 640 0.004 0.145 compiler.py:136(copy) 4741/4337 0.011 0.189 copy.py:226(_deepcopy_list) 11989628/10482664 29.987 310.121 copy.py:234(_deepcopy_tuple) 72544888/72539024 85.605 139.958 copy.py:253(_deepcopy_dict) 13592307/1498711 23.147 332.545 copy.py:306(_reconstruct) 300 0.001 0.034 kinetics.py:1928(addKineticsRulesFromTrainingSet) 14720 0.072 4.328 kinetics.py:2717(getKineticsFromDepository) 102343 0.509 24.632 kinetics.py:2830(estimateKineticsUsingRateRules) 1728 0.010 0.594 kinetics.py:3132(generateReactionsFromLibrary) 180 0.001 0.047 thermo.py:589(getThermoDataFromLibrary) 1377910 6.394 331.075 thermo.py:793(__getGroupThermoData) {method 'calculateSymmetryNumber' of 'rmgpy.molecule.Molecule' objects} <- 106455 138.394 138.394 thermo.py:635(estimateThermoViaGroupAdditivity) base.py:1060(isMoleculeForbidden) <- 4112915 87.369 327.896 kinetics.py:2236(__generateProductStructures) 1822092 36.997 139.521 kinetics.py:2304(__createReaction) base.py:766(matchNodeToStructure) <- 27311544 114.585 426.909 base.py:831(descendTree) 630790/627023 7.438 25.324 base.py:903(matchToStructure) 1164 0.017 0.033 base.py:937(matchToStructure) {method 'copy' of 'rmgpy.molecule.Molecule' objects} <- 1378157 37.151 37.151 kinetics.py:2120(applyRecipe) 2402499 53.876 53.876 kinetics.py:2304(__createReaction) 1406697 16.434 16.434 kinetics.py:2471(__generateReactions) 100 0.000 0.000 molecule_draw.py:558(findBackbone) 51646 2.391 2.391 thermo.py:635(estimateThermoViaGroupAdditivity) {method 'getURL' of 'rmgpy.reaction.Reaction' objects} <- 620264 103.157 125.721 runtime.py:163(call) {method 'getURL' of 'rmgpy.molecule.Molecule' objects} <- 2444097 101.314 123.973 runtime.py:163(call) {method '__residual' of 'rmgpy.thermo.Wilhoit' objects} <- 843410 97.948 210.886 optimize.py:967(fminbound) {method 'flush' of 'file' objects} <- 310848 85.114 85.114 __init__.py:827(flush) {method 'toHTML' of 'rmgpy.kinetics.KineticsModel' objects} <- 620264 83.797 103.486 runtime.py:163(call) numeric.py:65(zeros_like) <- 38410 0.059 0.242 {method 'getDensityOfStates' of 'rmgpy.statmech.StatesModel' objects} 60944055 73.569 626.912 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} 1480 0.004 0.012 {rmgpy._statmech.convolve} 144819 0.195 0.546 {rmgpy.measure.reaction.calculateMicrocanonicalRateCoefficient} {len} <- 320 0.000 0.000 <template>:5(root) 2212 0.000 0.000 BIFFRecords.py:23(add_str) 474 0.000 0.000 BIFFRecords.py:66(get_biff_record) 2212 0.000 0.000 BIFFRecords.py:133(_save_atom) 2212 0.000 0.000 BIFFRecords.py:140(_save_splitted) 26149 0.002 0.002 BIFFRecords.py:180(get_rec_header) 25991 0.003 0.003 BIFFRecords.py:187(get) 158 0.000 0.000 BIFFRecords.py:274(__init__) 1106 0.000 0.000 BIFFRecords.py:724(__init__) 158 0.000 0.000 BIFFRecords.py:790(__init__) 316 0.000 0.000 BIFFRecords.py:1105(__init__) 158 0.000 0.000 BIFFRecords.py:1483(__init__) 158 0.000 0.000 BIFFRecords.py:1906(__init__) 158 0.000 0.000 BIFFRecords.py:1933(__init__) 12719 0.001 0.001 Cell.py:171(_get_cells_biff_data_mul) 474 0.000 0.000 CompoundDoc.py:44(__build_directory) 158 0.000 0.000 CompoundDoc.py:123(__build_sat) 474 0.000 0.000 CompoundDoc.py:208(__build_header) 474 0.000 0.000 CompoundDoc.py:250(save) 1106 0.000 0.000 Row.py:233(write) 948 0.000 0.000 Style.py:92(_add_style) 1580 0.000 0.000 UnicodeUtils.py:45(upack2) 1422 0.000 0.000 UnicodeUtils.py:92(upack1) 158 0.000 0.000 Utils.py:183(valid_sheet_name) 158 0.000 0.000 Workbook.py:323(add_sheet) 158 0.000 0.000 Workbook.py:497(__tabid_rec) 158 0.000 0.000 Workbook.py:525(__boundsheets_rec) 158 0.000 0.000 Workbook.py:550(__all_links_rec) 1422 0.000 0.000 Workbook.py:587(get_biff_data) 158 0.000 0.000 Worksheet.py:1112(__guts_rec) 5 0.000 0.000 __init__.py:1569(error) 2596 0.000 0.000 __init__.py:1584(warning) 122684 0.024 0.024 __init__.py:1594(info) 194872 0.033 0.033 __init__.py:1602(debug) 536581 0.077 0.077 __init__.py:1610(log) 16967 0.001 0.001 base.py:347(__loadTree) 4480 0.000 0.000 base.py:410(<lambda>) 8685797 1.099 1.099 base.py:831(descendTree) 623189 0.116 0.116 basic.py:19(solve) 26325370 3.073 3.073 chemkin.py:763(getSpeciesIdentifier) 162357 0.014 0.014 chemkin.py:818(writeThermoEntry) 1246252 0.164 0.164 chemkin.py:893(writeKineticsEntry) 19 0.000 0.000 collections.py:237(namedtuple) 2560 0.000 0.000 compiler.py:1212(visit_Output) 2999721 0.376 0.376 copy.py:234(_deepcopy_tuple) 7546905 1.007 1.007 copy.py:306(_reconstruct) 1 0.000 0.000 fnmatch.py:45(filter) 1 0.000 0.000 fnmatch.py:81(translate) 3 0.000 0.000 input.py:103(simpleReactor) 296642 0.027 0.027 kinetics.py:1287(getReactionTemplate) 22 0.000 0.000 kinetics.py:1632(load) 43 0.000 0.000 kinetics.py:1801(generateProductTemplate) 1960630 0.193 0.193 kinetics.py:1896(getRateRule) 44 0.000 0.000 kinetics.py:2019(getRootTemplate) 726098 0.071 0.071 kinetics.py:2031(fillKineticsRulesByAveragingUp) 2099500 0.205 0.205 kinetics.py:2120(applyRecipe) 1395782 0.183 0.183 kinetics.py:2236(__generateProductStructures) 2499720 0.243 0.243 kinetics.py:2304(__createReaction) 654044 0.083 0.083 kinetics.py:2346(__matchReactantToTemplate) 29061 0.003 0.003 kinetics.py:2365(generateReactions) 215976 0.017 0.017 kinetics.py:2445(calculateDegeneracy) 11671711 0.979 0.979 kinetics.py:2471(__generateReactions) 492027 0.041 0.041 kinetics.py:2630(getReactionPairs) 229798 0.042 0.042 kinetics.py:2752(getKinetics) 102149 0.013 0.013 kinetics.py:2806(__getAverageKinetics) 1321130 0.138 0.138 kinetics.py:2830(estimateKineticsUsingRateRules) 292048 0.029 0.029 kinetics.py:2877(filterReactions) 623189 0.057 0.057 lapack.py:45(find_best_lapack_type) 2 0.000 0.000 lexer.py:16(<module>) 26 0.000 0.000 lexer.py:132(<lambda>) 3 0.000 0.000 lexer.py:186(compile_rules) 160 0.000 0.000 lexer.py:548(tokeniter) 4735855 0.586 0.586 linalg.py:127(_to_native_byte_order) 4735855 0.642 0.642 linalg.py:139(_fastCopyAndTranspose) 9471710 0.760 0.760 linalg.py:151(_assertRank2) 3854020 0.634 0.634 linalg.py:244(solve) 881835 0.158 0.158 linalg.py:1680(lstsq) 159 0.000 0.000 main.py:611(saveChemkinFile) 99257 0.017 0.017 model.py:68(generateThermoData) 33087 0.006 0.006 model.py:252(makeNewSpecies) 715147 0.074 0.074 model.py:309(checkForExistingReaction) 213135 0.036 0.036 model.py:384(makeNewReaction) 979707545 56.315 56.315 model.py:504(enlarge) 729 0.000 0.000 model.py:780(printEnlargeSummary) 1284 0.000 0.000 model.py:1035(getModelSize) 2 0.000 0.000 model.py:1090(addSeedMechanismToCore) 4 0.000 0.000 model.py:1131(addReactionLibraryToEdge) 85276 0.012 0.012 model.py:1202(addReactionToUnimolecularNetworks) 7292607 0.520 0.520 model.py:1265(updateUnimolecularReactionNetworks) 1078 0.000 0.000 molecule_draw.py:117(render) 5656 0.001 0.001 molecule_draw.py:267(renderAtom) 1641 0.000 0.000 molecule_draw.py:539(findLongestPath) 1083 0.000 0.000 molecule_draw.py:558(findBackbone) 670 0.000 0.000 molecule_draw.py:607(generateCoordinates) 396 0.000 0.000 molecule_draw.py:700(generateStraightChainCoordinates) 1256 0.000 0.000 molecule_draw.py:768(generateNeighborCoordinates) 72 0.000 0.000 molecule_draw.py:847(generateRingSystemCoordinates) 34 0.000 0.000 molecule_draw.py:989(generateFunctionalGroupCoordinates) 1382 0.000 0.000 molecule_draw.py:1111(drawMolecule) 13765 0.002 0.002 network.py:372(calculateDensitiesOfStates) 1554 0.000 0.000 network.py:456(calculateGroundStateEnergies) 518 0.000 0.000 network.py:474(calculateFirstReactiveEnergies) 12411 0.002 0.002 network.py:488(mapDensitiesOfStates) 16548 0.002 0.002 network.py:508(calculateMicrocanonicalRates) 4136 0.001 0.001 network.py:626(calculateDeltaEDown) 19112 0.003 0.003 network.py:651(calculateEquilibriumRatios) 41360 0.005 0.005 network.py:674(calculateCollisionModel) 66180 0.006 0.006 network.py:725(setConditions) 62040 0.010 0.010 network.py:775(applyModifiedStrongCollisionMethod) 2590 0.001 0.001 network.py:817(calculateRateCoefficients) 378 0.000 0.000 nodes.py:62(__new__) 73280 0.009 0.009 nodes.py:126(__init__) 7 0.000 0.000 nonlin.py:1429(_nonlin_wrapper) 132346 0.020 0.020 optimize.py:46(is_array_scalar) 18651 0.002 0.002 output.py:64(writeStates) 8359 0.002 0.002 output.py:138(writeSpecies) 518 0.000 0.000 output.py:235(writeFile) 10400 0.001 0.001 parser.py:468(parse_concat) 1280 0.000 0.000 parser.py:688(parse_subscript) 20732080 1.553 1.553 pdep.py:98(getLeakCoefficient) 782 0.000 0.000 pdep.py:128(getMaximumLeakSpecies) 425 0.000 0.000 pdep.py:231(merge) 30470319 2.247 2.247 pdep.py:293(updateConfigurations) 6530802 0.502 0.502 pdep.py:352(update) 2 0.000 0.000 posixpath.py:80(split) 188 0.000 0.000 posixpath.py:118(dirname) 38 0.000 0.000 re.py:226(_compile) 1240688 0.222 0.222 runtime.py:270(__init__) 264692 0.034 0.034 shape_base.py:6(atleast_1d) 600 0.000 0.000 sre_compile.py:32(_compile) 54 0.000 0.000 sre_compile.py:207(_optimize_charset) 140 0.000 0.000 sre_compile.py:361(_compile_info) 434 0.000 0.000 sre_parse.py:126(__len__) 1796 0.000 0.000 sre_parse.py:182(__next) 5 0.000 0.000 sre_parse.py:225(_class_escape) 103 0.000 0.000 sre_parse.py:257(_escape) 126 0.000 0.000 sre_parse.py:301(_parse_sub) 103 0.000 0.000 sre_parse.py:379(_parse) 5725 0.001 0.001 states.py:305(getStatesData) 2780 0.000 0.000 statesfit.py:80(fitStatesToHeatCapacity) 1244 0.000 0.000 statesfit.py:141(fitStatesDirect) 92 0.000 0.000 statesfit.py:197(fitStatesPseudoRotors) 6 0.000 0.000 statesfit.py:248(fitStatesPseudo) 99982 0.020 0.020 statesfit.py:383(evaluate) 184000 0.024 0.024 statesfit.py:424(evaluate) 3000 0.001 0.001 statesfit.py:474(evaluate) 2646202 0.351 0.351 thermo.py:775(__addThermoData) 1 0.000 0.000 utils.py:460(__setitem__) optimize.py:967(fminbound) <- 66173 71.761 366.232 {rmgpy.thermo.convertThermoModel} {numpy.core.multiarray.empty_like} <- 61128764 71.733 71.733 numeric.py:65(zeros_like) model.py:1024(addReactionToEdge) <- 56111 63.478 63.495 model.py:650(processNewReactions) 107 0.000 0.000 model.py:1131(addReactionLibraryToEdge) 2922 3.700 3.701 pdep.py:352(update) statesfit.py:332(hinderedRotor_heatCapacity) <- 3044639 54.634 55.170 statesfit.py:383(evaluate) 598000 10.854 10.942 statesfit.py:424(evaluate) 39000 0.705 0.710 statesfit.py:474(evaluate) statesfit.py:321(harmonicOscillator_d_heatCapacity_d_freq) <- 3142737 28.981 29.521 statesfit.py:383(evaluate) 3575000 32.424 32.944 statesfit.py:424(evaluate) 117000 1.072 1.091 statesfit.py:474(evaluate) Sorted by cumulative time Wed Jun 13 22:29:04 2012 /Users/rwest/Code/rmgpy/RMG-Py/examples/rmg/methylformate/RMG.profile 3411174244 function calls (3298217272 primitive calls) in 20996.773 seconds Ordered by: cumulative time List reduced from 1956 to 25 due to restriction <25> ncalls tottime percall cumtime percall filename:lineno(function) 1 1.067 1.067 21045.764 21045.764 main.py:309(execute) 477 13698.314 28.718 14425.269 30.242 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} 161 422.137 2.622 5150.083 31.988 model.py:504(enlarge) 33087 1.352 0.000 1518.681 0.046 model.py:68(generateThermoData) 161 23.627 0.147 1451.735 9.017 model.py:1265(updateUnimolecularReactionNetworks) 159 0.002 0.000 1438.330 9.046 main.py:449(saveEverything) 3262419 39.644 0.000 1395.055 0.000 pdep.py:352(update) 33087 0.287 0.000 1110.090 0.034 thermo.py:534(getThermoData) 11095 0.087 0.000 1067.530 0.096 model.py:484(react) 15551 0.052 0.000 1067.410 0.069 kinetics.py:3110(generateReactions) 15551 0.599 0.000 1007.516 0.065 kinetics.py:3156(generateReactionsFromFamilies) 342122 7.396 0.000 1006.843 0.003 kinetics.py:2365(generateReactions) 160 1.455 0.009 977.753 6.111 output.py:52(saveOutputHTML) 159 0.017 0.000 977.703 6.149 main.py:603(saveOutputHTML) 160 0.002 0.000 956.267 5.977 environment.py:879(render) 9921 5.734 0.001 956.266 0.096 {method 'join' of 'unicode' objects} 32907 0.941 0.000 914.002 0.028 thermo.py:604(getThermoDataFromGroups) 106455/54809 11.182 0.000 910.379 0.017 thermo.py:635(estimateThermoViaGroupAdditivity) 1251658/1240528 41.599 0.000 901.041 0.001 chemkin.py:893(writeKineticsEntry) 724756 21.271 0.000 869.526 0.001 kinetics.py:2471(__generateReactions) 9850306 12.937 0.000 842.625 0.000 runtime.py:163(call) 9891390 33.711 0.000 814.549 0.000 chemkin.py:763(getSpeciesIdentifier) 518 5.011 0.010 810.478 1.565 network.py:817(calculateRateCoefficients) 4476062 711.038 0.000 775.896 0.000 {method 'getFormula' of 'rmgpy.molecule.Molecule' objects} 1956275 19.395 0.000 713.145 0.000 thermo.py:793(__getGroupThermoData) Ordered by: cumulative time List reduced from 1956 to 25 due to restriction <25> Function was called by... ncalls tottime cumtime main.py:309(execute) <- 1 1.067 21045.764 <string>:1(<module>) {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} <- 477 13698.314 14425.269 main.py:309(execute) model.py:504(enlarge) <- 2 0.266 99.883 main.py:212(initialize) 159 421.870 5050.200 main.py:309(execute) model.py:68(generateThermoData) <- 16 0.001 0.174 main.py:212(initialize) 33018 1.349 1517.613 model.py:504(enlarge) 38 0.001 0.705 model.py:1090(addSeedMechanismToCore) 15 0.001 0.190 model.py:1131(addReactionLibraryToEdge) model.py:1265(updateUnimolecularReactionNetworks) <- 161 23.627 1451.735 model.py:504(enlarge) main.py:449(saveEverything) <- 159 0.002 1438.330 main.py:309(execute) pdep.py:352(update) <- 3262419 39.644 1395.055 model.py:1265(updateUnimolecularReactionNetworks) thermo.py:534(getThermoData) <- 33087 0.287 1110.090 model.py:68(generateThermoData) model.py:484(react) <- 10395 0.082 1017.308 model.py:504(enlarge) 700 0.006 50.223 pdep.py:185(exploreIsomer) kinetics.py:3110(generateReactions) <- 15551 0.052 1067.410 model.py:484(react) kinetics.py:3156(generateReactionsFromFamilies) <- 15551 0.599 1007.516 kinetics.py:3110(generateReactions) kinetics.py:2365(generateReactions) <- 342122 7.396 1006.843 kinetics.py:3156(generateReactionsFromFamilies) output.py:52(saveOutputHTML) <- 1 0.011 0.081 main.py:212(initialize) 159 1.444 977.672 main.py:603(saveOutputHTML) main.py:603(saveOutputHTML) <- 159 0.017 977.703 main.py:449(saveEverything) environment.py:879(render) <- 160 0.002 956.267 output.py:52(saveOutputHTML) {method 'join' of 'unicode' objects} <- 9760 0.004 0.004 compiler.py:1212(visit_Output) 160 5.731 956.262 environment.py:879(render) 1 0.000 0.000 utils.py:10(<module>) thermo.py:604(getThermoDataFromGroups) <- 32907 0.941 914.002 thermo.py:534(getThermoData) thermo.py:635(estimateThermoViaGroupAdditivity) <- 54809 3.398 910.379 thermo.py:604(getThermoDataFromGroups) 51646 7.784 736.581 thermo.py:635(estimateThermoViaGroupAdditivity) chemkin.py:893(writeKineticsEntry) <- 11130 0.254 1.125 chemkin.py:893(writeKineticsEntry) 620264 21.043 446.158 chemkin.py:1075(saveChemkinFile) 620264 20.302 454.883 {method 'toChemkin' of 'rmgpy.reaction.Reaction' objects} kinetics.py:2471(__generateReactions) <- 682203 17.068 619.766 kinetics.py:2365(generateReactions) 42553 4.204 249.760 kinetics.py:2445(calculateDegeneracy) runtime.py:163(call) <- 9850306 12.937 842.625 <template>:5(root) chemkin.py:763(getSpeciesIdentifier) <- 18022 0.069 1.937 chemkin.py:818(writeThermoEntry) 9837324 33.500 808.713 chemkin.py:893(writeKineticsEntry) 18022 0.071 1.936 chemkin.py:1065(saveSpeciesDictionary) 18022 0.070 1.962 chemkin.py:1075(saveChemkinFile) network.py:817(calculateRateCoefficients) <- 518 5.011 810.478 pdep.py:352(update) {method 'getFormula' of 'rmgpy.molecule.Molecule' objects} <- 4264890 670.160 730.976 chemkin.py:763(getSpeciesIdentifier) 178085 33.402 36.879 model.py:222(checkForExistingSpecies) 33087 7.477 8.042 model.py:252(makeNewSpecies) thermo.py:793(__getGroupThermoData) <- 1956275 19.395 713.145 thermo.py:635(estimateThermoViaGroupAdditivity) Ordered by: cumulative time List reduced from 1956 to 25 due to restriction <25> Function called... ncalls tottime cumtime main.py:309(execute) -> 158 0.001 0.002 __init__.py:98(__init__) 158 0.000 0.004 __init__.py:366(get_memory_info) 1745 0.005 0.205 __init__.py:1594(info) 158 0.001 0.034 genericpath.py:15(exists) 1 0.007 113.826 main.py:212(initialize) 159 0.002 1438.330 main.py:449(saveEverything) 158 0.113 4.056 main.py:646(saveExecutionStatistics) 159 421.870 5050.200 model.py:504(enlarge) 158 0.000 0.001 model.py:1035(getModelSize) 151 0.001 0.014 pdep.py:128(getMaximumLeakSpecies) 158 0.001 0.001 posixpath.py:60(join) 256 0.000 0.000 {isinstance} 1362 0.000 0.000 {method 'append' of 'list' objects} 2170059 0.683 0.683 {method 'extend' of 'list' objects} 477 12.069 12.069 {method 'items' of 'dict' objects} 477 13698.314 14425.269 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} 158 0.000 0.000 {posix.getpid} 158 0.001 0.001 {time.gmtime} 158 0.001 0.001 {time.strftime} 158 0.000 0.000 {time.time} {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} -> 2047 0.006 0.238 __init__.py:1594(info) 2512390 2.256 38.507 fromnumeric.py:683(argmax) 1256195 2.956 12.917 fromnumeric.py:1379(sum) 60944055 73.569 626.912 numeric.py:65(zeros_like) 954 0.005 0.076 numeric.py:1791(ones) 9834300 20.052 48.304 pdep.py:98(getLeakCoefficient) model.py:504(enlarge) -> 753 0.003 0.103 __init__.py:1594(info) 110 0.000 0.000 display.py:36(do_nothing) 33018 1.349 1517.613 model.py:68(generateThermoData) 10395 0.082 1017.308 model.py:484(react) 811 32.820 247.401 model.py:650(processNewReactions) 93432 0.544 317.296 model.py:704(generateKinetics) 160 0.166 8.419 model.py:780(printEnlargeSummary) 111 19.453 26.280 model.py:825(addSpeciesToCore) 161 23.627 1451.735 model.py:1265(updateUnimolecularReactionNetworks) 700 0.008 50.343 pdep.py:185(exploreIsomer) 3874912 22.631 27.723 pdep.py:293(updateConfigurations) 21467 0.369 0.369 {delattr} 21467 0.008 0.008 {hasattr} 187795 0.047 0.047 {isinstance} 979707545 56.315 56.315 {len} 94 0.000 0.000 {method 'append' of 'list' objects} 11028 0.007 0.007 {method 'extend' of 'list' objects} 93432 0.967 1.893 {method 'fixBarrierHeight' of 'rmgpy.reaction.Reaction' objects} 111 0.001 0.001 {method 'format' of 'str' objects} 248 5.085 5.085 {method 'items' of 'dict' objects} model.py:68(generateThermoData) -> 33086 0.090 2.167 __init__.py:1610(log) 33086 0.046 0.175 fromnumeric.py:1379(sum) 33087 0.287 1110.090 thermo.py:534(getThermoData) 99260 0.064 0.064 {isinstance} 99257 0.017 0.017 {len} 33086 0.011 0.011 {math.sqrt} 33084 5.001 5.001 {method 'countInternalRotors' of 'rmgpy.molecule.Molecule' objects} 33086 0.245 0.245 {method 'format' of 'str' objects} 33087 0.027 0.027 {method 'getEnthalpy' of 'rmgpy.thermo.Wilhoit' objects} 66172 3.246 5.022 {method 'getHeatCapacities' of 'rmgpy.thermo.ThermoModel' objects} 33084 3.556 3.556 {method 'isLinear' of 'rmgpy.molecule.Molecule' objects} 55010 1.004 1.004 {method 'makeHydrogensExplicit' of 'rmgpy.molecule.Molecule' objects} 55008 0.748 0.748 {method 'makeHydrogensImplicit' of 'rmgpy.molecule.Molecule' objects} 33086 0.336 0.336 {numpy.core.multiarray.array} 66173 11.993 388.825 {rmgpy.thermo.convertThermoModel} 33087 0.039 0.039 {zip} model.py:1265(updateUnimolecularReactionNetworks) -> 8 0.000 0.001 __init__.py:1584(warning) 226 0.001 0.036 __init__.py:1594(info) 32 0.000 0.000 __init__.py:1602(debug) 65 0.004 0.004 pdep.py:231(merge) 3262419 39.644 1395.055 pdep.py:352(update) 3908841 0.791 0.791 {isinstance} 7292607 0.520 0.520 {len} 3262418 0.273 0.273 {method 'append' of 'list' objects} 266 0.001 0.001 {method 'format' of 'str' objects} 1170 0.014 0.014 {method 'getEquilibriumConstant' of 'rmgpy.reaction.Reaction' objects} 2340 0.163 0.163 {method 'getRateCoefficient' of 'rmgpy.reaction.Reaction' objects} 5439 7.451 18.972 {method 'index' of 'list' objects} 335 0.000 0.000 {method 'insert' of 'list' objects} 483 12.079 12.079 {method 'items' of 'dict' objects} 985 0.108 0.108 {method 'remove' of 'list' objects} 731548 0.090 0.090 {sum} main.py:449(saveEverything) -> 159 0.017 977.703 main.py:603(saveOutputHTML) 159 0.017 460.626 main.py:611(saveChemkinFile) pdep.py:352(update) -> 17 0.000 0.003 __init__.py:1584(warning) 17 0.000 0.001 __init__.py:1594(info) 3262419 19.267 25.677 main.py:109(copy) 518 0.005 6.831 main.py:183(saveInput) 3420 0.013 464.537 model.py:121(generateStatesData) 3999 0.013 0.077 model.py:455(makeNewPDepReaction) 1077 1.341 1.342 model.py:1012(addReactionToCore) 2922 3.700 3.701 model.py:1024(addReactionToEdge) 518 0.063 1.562 network.py:257(printSummary) 518 5.011 810.478 network.py:817(calculateRateCoefficients) 3999 0.014 0.014 pdep.py:57(__init__) 3262419 18.448 23.011 pdep.py:293(updateConfigurations) 518 0.003 0.004 posixpath.py:60(join) 7998 0.002 0.002 {all} 12088 0.003 0.003 {isinstance} 6530802 0.502 0.502 {len} 3999 0.001 0.001 {method 'append' of 'list' objects} 1551 0.001 0.001 {method 'extend' of 'list' objects} 552 0.003 0.003 {method 'format' of 'str' objects} 569 0.009 0.009 {method 'getEquilibriumConstant' of 'rmgpy.reaction.Reaction' objects} 950 0.002 0.002 {method 'getRateCoefficient' of 'rmgpy.kinetics.Arrhenius' objects} 50178 0.056 0.056 {method 'hasTemplate' of 'rmgpy.reaction.Reaction' objects} 517 0.001 0.001 {method 'index' of 'list' objects} 81485 0.012 0.012 {method 'isIsomerization' of 'rmgpy.reaction.Reaction' objects} 3267945 0.379 0.379 {method 'isPressureDependent' of 'rmgpy.kinetics.Arrhenius' objects} 517 0.000 0.000 {range} 5446 15.896 17.200 {rmgpy.measure.reaction.fitInterpolationModel} 6044 0.002 0.002 {sum} thermo.py:534(getThermoData) -> 99070 10.940 195.802 thermo.py:589(getThermoDataFromLibrary) 32907 0.941 914.002 thermo.py:604(getThermoDataFromGroups) model.py:484(react) -> 15551 0.052 1067.410 kinetics.py:3110(generateReactions) 30118 0.015 0.015 {method 'clearLabeledAtoms' of 'rmgpy.molecule.Molecule' objects} 15551 0.005 0.005 {method 'extend' of 'list' objects} 30118 0.013 0.013 {method 'makeHydrogensImplicit' of 'rmgpy.molecule.Molecule' objects} kinetics.py:3110(generateReactions) -> 15551 0.086 59.834 kinetics.py:3121(generateReactionsFromLibraries) 15551 0.599 1007.516 kinetics.py:3156(generateReactionsFromFamilies) 31102 0.007 0.007 {method 'extend' of 'list' objects} kinetics.py:3156(generateReactionsFromFamilies) -> 342122 7.396 1006.843 kinetics.py:2365(generateReactions) 342122 0.068 0.068 {method 'extend' of 'list' objects} 15551 0.006 0.006 {method 'iteritems' of 'dict' objects} kinetics.py:2365(generateReactions) -> 148271 0.479 0.479 kinetics.py:130(__init__) 42553 1.293 258.239 kinetics.py:2445(calculateDegeneracy) 682203 17.068 619.766 kinetics.py:2471(__generateReactions) 148271 0.687 0.950 kinetics.py:2630(getReactionPairs) 148271 0.218 102.926 kinetics.py:2695(getReactionTemplate) 29061 1.449 16.932 kinetics.py:2877(filterReactions) 119210 0.125 0.125 {hasattr} 29061 0.003 0.003 {len} 148271 0.027 0.027 {method 'append' of 'list' objects} output.py:52(saveOutputHTML) -> 1 0.002 0.026 __init__.py:28(<module>) 160 0.002 0.007 environment.py:217(__init__) 160 0.001 6.409 environment.py:763(from_string) 160 0.002 956.267 environment.py:879(render) 18022 0.015 0.279 genericpath.py:15(exists) 160 0.000 0.004 genericpath.py:38(isdir) 73760 0.014 0.014 kinetics.py:114(getSource) 451133 0.086 0.086 kinetics.py:141(getSource) 1 0.000 0.000 molecule_draw.py:86(<module>) 148 0.015 0.610 molecule_draw.py:1111(drawMolecule) 18182 0.039 0.055 posixpath.py:60(join) 160 0.000 0.001 posixpath.py:118(dirname) 160 0.000 0.003 posixpath.py:341(abspath) 320 0.000 0.002 re.py:188(compile) 620264 0.141 0.141 {isinstance} 160 0.417 0.417 {method 'close' of 'file' objects} 18022 0.034 0.034 {method 'format' of 'str' objects} 160 0.000 0.000 {method 'keys' of 'dict' objects} 18022 0.011 0.011 {method 'search' of '_sre.SRE_Pattern' objects} 160 0.000 0.000 {method 'sort' of 'list' objects} 160 11.774 11.774 {method 'write' of 'file' objects} 160 0.159 0.159 {open} main.py:603(saveOutputHTML) -> 159 0.000 0.013 __init__.py:1594(info) 159 1.444 977.672 output.py:52(saveOutputHTML) 159 0.001 0.001 posixpath.py:60(join) environment.py:879(render) -> 160 0.000 0.003 environment.py:920(new_context) 160 5.731 956.262 {method 'join' of 'unicode' objects} {method 'join' of 'unicode' objects} -> 67973 0.503 10.128 <template>:5(root) 1 0.000 0.000 utils.py:47(_test_gen_bug) thermo.py:604(getThermoDataFromGroups) -> 54809 3.398 910.379 thermo.py:635(estimateThermoViaGroupAdditivity) 54809 0.012 0.012 {method 'append' of 'list' objects} 32907 0.072 0.072 {method 'argsort' of 'numpy.ndarray' objects} 54809 0.074 0.074 {method 'clearLabeledAtoms' of 'rmgpy.molecule.Molecule' objects} 54809 1.018 1.018 {method 'getEnthalpy' of 'rmgpy.thermo.ThermoData' objects} 54809 0.015 0.015 {method 'makeHydrogensExplicit' of 'rmgpy.molecule.Molecule' objects} 54809 1.098 1.098 {method 'updateAtomTypes' of 'rmgpy.molecule.Molecule' objects} 32907 0.370 0.370 {numpy.core.multiarray.array} 32907 0.023 0.023 {zip} thermo.py:635(estimateThermoViaGroupAdditivity) -> 51646 7.784 736.581 thermo.py:635(estimateThermoViaGroupAdditivity) 1323101 34.078 39.189 thermo.py:775(__addThermoData) 1956275 19.395 713.145 thermo.py:793(__getGroupThermoData) 158101 0.118 0.118 {math.log} 284830 0.148 0.148 {method 'addAtom' of 'rmgpy.molecule.Molecule' objects} 340568 0.152 0.152 {method 'addBond' of 'rmgpy.molecule.Molecule' objects} 114546 0.024 0.024 {method 'append' of 'list' objects} 106455 138.394 138.394 {method 'calculateSymmetryNumber' of 'rmgpy.molecule.Molecule' objects} 51646 2.391 2.391 {method 'copy' of 'rmgpy.molecule.Molecule' objects} 229092 0.042 0.042 {method 'decrementRadical' of 'rmgpy.molecule.Atom' objects} 111476 0.025 0.025 {method 'getBond' of 'rmgpy.molecule.Molecule' objects} 54809 2.452 2.452 {method 'getSmallestSetOfSmallestRings' of 'rmgpy.graph.Graph' objects} 200980 0.045 0.045 {method 'hasBond' of 'rmgpy.molecule.Molecule' objects} 114546 0.023 0.023 {method 'incrementRadical' of 'rmgpy.molecule.Atom' objects} 863381 0.150 0.150 {method 'isNonHydrogen' of 'rmgpy.molecule.Atom' objects} 106455 0.038 0.038 {method 'makeHydrogensExplicit' of 'rmgpy.molecule.Molecule' objects} 114546 0.263 0.263 {method 'removeAtom' of 'rmgpy.molecule.Molecule' objects} 114546 0.060 0.060 {method 'removeBond' of 'rmgpy.molecule.Molecule' objects} 158101 0.675 0.675 {method 'sortVertices' of 'rmgpy.graph.Graph' objects} 51646 0.927 0.927 {method 'updateAtomTypes' of 'rmgpy.molecule.Molecule' objects} 161848 0.703 0.703 {method 'updateConnectivityValues' of 'rmgpy.graph.Graph' objects} 818284 0.178 0.178 {range} 106455 0.055 0.055 {sum} chemkin.py:893(writeKineticsEntry) -> 9837324 33.500 808.713 chemkin.py:763(getSpeciesIdentifier) 11130 0.254 1.125 chemkin.py:893(writeKineticsEntry) 11130 0.038 0.038 kinetics.py:102(__init__) 1259536 0.204 0.204 {any} 199964 0.245 0.245 {hasattr} 8841034 3.040 3.040 {isinstance} 1246252 0.164 0.164 {len} 190742 0.436 0.436 {method 'copy' of 'numpy.ndarray' objects} 17347300 28.884 29.151 {method 'format' of 'str' objects} 1369406 13.195 13.195 {method 'isIsomorphic' of 'rmgpy.molecule.Molecule' objects} 1040882 0.245 0.245 {method 'isPressureDependent' of 'rmgpy.kinetics.Arrhenius' objects} 190742 0.049 0.049 {method 'isPressureDependent' of 'rmgpy.kinetics.Chebyshev' objects} 9222 0.002 0.002 {method 'isPressureDependent' of 'rmgpy.kinetics.PDepArrhenius' objects} 5406 0.002 0.002 {method 'isPressureDependent' of 'rmgpy.kinetics.ThirdBody' objects} 5406 0.002 0.002 {method 'iteritems' of 'dict' objects} 4629892 1.585 1.585 {method 'join' of 'str' objects} 1049786 1.713 1.713 {method 'split' of 'str' objects} 1335194 0.637 0.637 {range} 9222 0.023 0.023 {zip} kinetics.py:2471(__generateReactions) -> 698369 12.661 471.503 kinetics.py:2236(__generateProductStructures) 628925 11.262 230.767 kinetics.py:2304(__createReaction) 1297151 3.809 35.815 kinetics.py:2346(__matchReactantToTemplate) 1406697 0.621 0.621 {isinstance} 11671711 0.979 0.979 {len} 628361 0.145 0.145 {method 'append' of 'list' objects} 1406697 16.434 16.434 {method 'copy' of 'rmgpy.molecule.Molecule' objects} 570137 50.074 50.074 {method 'generateResonanceIsomers' of 'rmgpy.molecule.Molecule' objects} 4619882 30.757 30.757 {method 'isIsomorphic' of 'rmgpy.molecule.Molecule' objects} 730384 0.418 0.418 {method 'lower' of 'str' objects} 1406697 9.344 9.344 {method 'makeHydrogensExplicit' of 'rmgpy.molecule.Molecule' objects} 316908 0.108 0.108 {method 'remove' of 'list' objects} 730384 0.406 0.406 {method 'startswith' of 'str' objects} 2131453 0.883 0.883 {range} runtime.py:163(call) -> 368800 0.128 0.128 kinetics.py:114(getSource) 2255665 0.813 0.813 kinetics.py:141(getSource) 476855 0.198 0.198 pdep.py:61(getSource) 9303960 6.788 6.788 {getattr} 9850306 5.142 5.142 {isinstance} 2444097 5.549 5.549 {method 'getMolecularWeight' of 'rmgpy.molecule.Molecule' objects} 2444097 101.314 123.973 {method 'getURL' of 'rmgpy.molecule.Molecule' objects} 620264 103.157 125.721 {method 'getURL' of 'rmgpy.reaction.Reaction' objects} 620264 3.007 457.890 {method 'toChemkin' of 'rmgpy.reaction.Reaction' objects} 620264 83.797 103.486 {method 'toHTML' of 'rmgpy.kinetics.KineticsModel' objects} chemkin.py:763(getSpeciesIdentifier) -> 9889323 8.092 34.343 re.py:139(search) 26325370 3.073 3.073 {len} 12169090 12.446 12.446 {method 'format' of 'str' objects} 4264890 670.160 730.976 {method 'getFormula' of 'rmgpy.molecule.Molecule' objects} network.py:817(calculateRateCoefficients) -> 518 0.001 0.080 __init__.py:1594(info) 7079 0.008 0.019 __init__.py:1602(debug) 20680 0.051 0.100 __init__.py:1610(log) 1036 0.001 0.005 fromnumeric.py:1774(amax) 1036 0.001 0.010 fromnumeric.py:1836(amin) 518 0.007 512.440 network.py:702(initialize) 20681 0.715 84.150 network.py:725(setConditions) 20680 0.356 208.446 network.py:775(applyModifiedStrongCollisionMethod) 2590 0.001 0.001 {len} 6562 0.039 0.040 {method 'format' of 'str' objects} 20680 0.022 0.022 {method 'lower' of 'str' objects} 518 0.005 0.005 {numpy.core.multiarray.zeros} 370360 0.149 0.149 {range} {method 'getFormula' of 'rmgpy.molecule.Molecule' objects} -> 4476062 5.049 11.567 openbabel.py:2246(__init__) 4476062 5.476 12.008 pybel.py:195(__init__) 4476062 3.869 41.282 pybel.py:222(formula) thermo.py:793(__getGroupThermoData) -> 1956275 8.429 359.320 base.py:831(descendTree) 1377910 6.394 331.075 copy.py:145(deepcopy) 1491418 0.745 0.745 {isinstance} 1377910 1.506 1.506 {method 'format' of 'str' objects} 113508 1.104 1.104 {method 'values' of 'dict' objects} -
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