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rwest/Profiling_data.txt

Created June 11, 2012 14:51
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Profiling data for RMG-Py/examples/rmg/methylformate
Raw
profile.dot
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Display the source blob
Display the rendered blob
Raw
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<!-- 30&#45;&gt;239 -->
<g id="edge10" class="edge"><title>30&#45;&gt;239</title>
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<g id="node33" class="node"><title>276</title>
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<!-- 613&#45;&gt;276 -->
<g id="edge42" class="edge"><title>613&#45;&gt;276</title>
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<g id="edge58" class="edge"><title>1734&#45;&gt;28</title>
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<!-- 138 -->
<g id="node17" class="node"><title>138</title>
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<!-- 239&#45;&gt;138 -->
<g id="edge16" class="edge"><title>239&#45;&gt;138</title>
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<!-- 239&#45;&gt;187 -->
<g id="edge22" class="edge"><title>239&#45;&gt;187</title>
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<!-- 244 -->
<g id="node24" class="node"><title>244</title>
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<!-- 239&#45;&gt;244 -->
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<!-- 375 -->
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<g id="edge12" class="edge"><title>32&#45;&gt;308</title>
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<!-- 308&#45;&gt;749 -->
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<!-- 187&#45;&gt;802 -->
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<!-- 244&#45;&gt;621 -->
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<!-- 621&#45;&gt;620 -->
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<!-- 749&#45;&gt;340 -->
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<!-- 312&#45;&gt;174 -->
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<!-- 324&#45;&gt;918 -->
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<g id="node47" class="node"><title>381</title>
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Raw
Profiling_data.txt
================================================================================
Profiling Data
================================================================================
Sorted by internal time
Sat Jun 9 08:56:38 2012 /Users/rwest/Code/rmgpy/RMG-Py/examples/rmg/methylformate/RMG.profile
47278589233 function calls (47165643959 primitive calls) in 61955.711 seconds
Ordered by: internal time
List reduced from 1953 to 25 due to restriction <25>
ncalls tottime percall cumtime percall filename:lineno(function)
160 38084.212 238.026 41975.686 262.348 model.py:1250(updateUnimolecularReactionNetworks)
474 13635.259 28.766 14360.285 30.296 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects}
44812899017/44812898898 2558.555 0.000 2558.555 0.000 {len}
4440958 672.306 0.000 739.050 0.000 {method 'getFormula' of 'rmgpy.molecule.Molecule' objects}
6583 510.899 0.078 539.453 0.082 {method 'getDensityOfStates' of 'rmgpy.statmech.StatesModel' objects}
60664755 477.120 0.000 477.120 0.000 {method 'fill' of 'numpy.ndarray' objects}
58157971 468.948 0.000 468.948 0.000 {method 'isSubgraphIsomorphic' of 'rmgpy.molecule.Molecule' objects}
48518 452.011 0.009 453.035 0.009 model.py:1198(addReactionToUnimolecularNetworks)
160 423.102 2.644 46219.335 288.871 model.py:504(enlarge)
23629270 251.363 0.000 251.363 0.000 {method 'isIsomorphic' of 'rmgpy.molecule.Molecule' objects}
2103290 181.808 0.000 181.808 0.000 {method 'isIsomorphic' of 'rmgpy.reaction.Reaction' objects}
99625699/1497813 146.698 0.000 361.583 0.000 copy.py:145(deepcopy)
106455 139.558 0.001 139.558 0.001 {method 'calculateSymmetryNumber' of 'rmgpy.molecule.Molecule' objects}
5935007 128.783 0.000 486.764 0.000 base.py:1060(isMoleculeForbidden)
27943382/27311530 124.204 0.000 435.671 0.000 base.py:766(matchNodeToStructure)
5239099 117.762 0.000 117.762 0.000 {method 'copy' of 'rmgpy.molecule.Molecule' objects}
615487 102.656 0.000 125.205 0.000 {method 'getURL' of 'rmgpy.reaction.Reaction' objects}
2425271 100.699 0.000 123.501 0.000 {method 'getURL' of 'rmgpy.molecule.Molecule' objects}
843211 99.444 0.000 215.174 0.000 {method '__residual' of 'rmgpy.thermo.Wilhoit' objects}
365542800 95.054 0.000 95.054 0.000 {isinstance}
615487 83.319 0.000 103.001 0.000 {method 'toHTML' of 'rmgpy.kinetics.KineticsModel' objects}
60642609 77.400 0.000 625.811 0.000 numeric.py:65(zeros_like)
66173 74.445 0.001 375.871 0.006 optimize.py:967(fminbound)
60642609 71.400 0.000 71.400 0.000 {numpy.core.multiarray.empty_like}
59140 68.393 0.001 68.416 0.001 model.py:1020(addReactionToEdge)
Ordered by: internal time
List reduced from 1953 to 25 due to restriction <25>
Function was called by...
ncalls tottime cumtime
model.py:1250(updateUnimolecularReactionNetworks) <- 160 38084.212 41975.686 model.py:504(enlarge)
{method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} <- 474 13635.259 14360.285 main.py:309(execute)
{len} <- 318 0.000 0.000 <template>:5(root)
2198 0.000 0.000 BIFFRecords.py:23(add_str)
471 0.000 0.000 BIFFRecords.py:66(get_biff_record)
2198 0.000 0.000 BIFFRecords.py:133(_save_atom)
2198 0.000 0.000 BIFFRecords.py:140(_save_splitted)
25905 0.002 0.002 BIFFRecords.py:180(get_rec_header)
25748 0.003 0.003 BIFFRecords.py:187(get)
157 0.000 0.000 BIFFRecords.py:274(__init__)
1099 0.000 0.000 BIFFRecords.py:724(__init__)
157 0.000 0.000 BIFFRecords.py:790(__init__)
314 0.000 0.000 BIFFRecords.py:1105(__init__)
157 0.000 0.000 BIFFRecords.py:1483(__init__)
157 0.000 0.000 BIFFRecords.py:1906(__init__)
157 0.000 0.000 BIFFRecords.py:1933(__init__)
12560 0.001 0.001 Cell.py:171(_get_cells_biff_data_mul)
471 0.000 0.000 CompoundDoc.py:44(__build_directory)
157 0.000 0.000 CompoundDoc.py:123(__build_sat)
471 0.000 0.000 CompoundDoc.py:208(__build_header)
471 0.000 0.000 CompoundDoc.py:250(save)
1099 0.000 0.000 Row.py:233(write)
942 0.000 0.000 Style.py:92(_add_style)
1570 0.000 0.000 UnicodeUtils.py:45(upack2)
1413 0.000 0.000 UnicodeUtils.py:92(upack1)
157 0.000 0.000 Utils.py:183(valid_sheet_name)
157 0.000 0.000 Workbook.py:323(add_sheet)
157 0.000 0.000 Workbook.py:497(__tabid_rec)
157 0.000 0.000 Workbook.py:525(__boundsheets_rec)
157 0.000 0.000 Workbook.py:550(__all_links_rec)
1413 0.000 0.000 Workbook.py:587(get_biff_data)
157 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)
122671 0.022 0.022 __init__.py:1594(info)
194884 0.035 0.035 __init__.py:1602(debug)
536581 0.081 0.081 __init__.py:1610(log)
16967 0.001 0.001 base.py:347(__loadTree)
4480 0.000 0.000 base.py:410(<lambda>)
8685796 1.109 1.109 base.py:831(descendTree)
623341 0.120 0.120 basic.py:19(solve)
26119620 3.075 3.075 chemkin.py:763(getSpeciesIdentifier)
161159 0.014 0.014 chemkin.py:818(writeThermoEntry)
1236662 0.160 0.160 chemkin.py:893(writeKineticsEntry)
19 0.000 0.000 collections.py:237(namedtuple)
2544 0.000 0.000 compiler.py:1212(visit_Output)
2999689 0.377 0.377 copy.py:234(_deepcopy_tuple)
7546625 1.002 1.002 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)
1958588 0.192 0.192 kinetics.py:1896(getRateRule)
44 0.000 0.000 kinetics.py:2019(getRootTemplate)
726098 0.067 0.067 kinetics.py:2031(fillKineticsRulesByAveragingUp)
2099500 0.196 0.196 kinetics.py:2120(applyRecipe)
1395782 0.198 0.198 kinetics.py:2236(__generateProductStructures)
2499720 0.233 0.233 kinetics.py:2304(__createReaction)
654044 0.085 0.085 kinetics.py:2346(__matchReactantToTemplate)
29061 0.003 0.003 kinetics.py:2365(generateReactions)
215974 0.017 0.017 kinetics.py:2445(calculateDegeneracy)
11671821 0.982 0.982 kinetics.py:2471(__generateReactions)
492027 0.040 0.040 kinetics.py:2630(getReactionPairs)
229798 0.041 0.041 kinetics.py:2752(getKinetics)
102226 0.012 0.012 kinetics.py:2806(__getAverageKinetics)
1320031 0.139 0.139 kinetics.py:2830(estimateKineticsUsingRateRules)
292048 0.028 0.028 kinetics.py:2877(filterReactions)
623341 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)
159 0.000 0.000 lexer.py:548(tokeniter)
4735656 0.593 0.593 linalg.py:127(_to_native_byte_order)
4735656 0.665 0.665 linalg.py:139(_fastCopyAndTranspose)
9471312 0.757 0.757 linalg.py:151(_assertRank2)
3854020 0.581 0.581 linalg.py:244(solve)
881636 0.156 0.156 linalg.py:1680(lstsq)
158 0.000 0.000 main.py:608(saveChemkinFile)
99257 0.015 0.015 model.py:68(generateThermoData)
33087 0.007 0.007 model.py:252(makeNewSpecies)
715477 0.073 0.073 model.py:309(checkForExistingReaction)
213135 0.036 0.036 model.py:384(makeNewReaction)
972411704 55.998 55.998 model.py:504(enlarge)
725 0.000 0.000 model.py:779(printEnlargeSummary)
1276 0.000 0.000 model.py:1031(getModelSize)
2 0.000 0.000 model.py:1086(addSeedMechanismToCore)
4 0.000 0.000 model.py:1127(addReactionLibraryToEdge)
84749 0.013 0.013 model.py:1198(addReactionToUnimolecularNetworks)
43678774188 2486.316 2486.316 model.py:1250(updateUnimolecularReactionNetworks)
1078 0.000 0.000 molecule_draw.py:117(render)
5638 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)
1254 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)
1381 0.000 0.000 molecule_draw.py:1111(drawMolecule)
13772 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 0.006 0.006 network.py:674(calculateCollisionModel)
66180 0.006 0.006 network.py:725(setConditions)
62040 0.011 0.011 network.py:775(applyModifiedStrongCollisionMethod)
2590 0.000 0.000 network.py:817(calculateRateCoefficients)
378 0.000 0.000 nodes.py:62(__new__)
72822 0.009 0.009 nodes.py:126(__init__)
7 0.000 0.000 nonlin.py:1429(_nonlin_wrapper)
132346 0.018 0.018 optimize.py:46(is_array_scalar)
18654 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)
10335 0.001 0.001 parser.py:468(parse_concat)
1272 0.000 0.000 parser.py:688(parse_subscript)
20543956 1.562 1.562 pdep.py:98(getLeakCoefficient)
763 0.000 0.000 pdep.py:128(getMaximumLeakSpecies)
425 0.000 0.000 pdep.py:231(merge)
31953985 2.283 2.283 pdep.py:293(updateConfigurations)
6505068 0.476 0.476 pdep.py:352(update)
2 0.000 0.000 posixpath.py:80(split)
187 0.000 0.000 posixpath.py:118(dirname)
38 0.000 0.000 re.py:226(_compile)
1231133 0.221 0.221 runtime.py:270(__init__)
264692 0.033 0.033 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)
5721 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)
98773 0.023 0.023 statesfit.py:383(evaluate)
184000 0.023 0.023 statesfit.py:424(evaluate)
3000 0.001 0.001 statesfit.py:474(evaluate)
2646202 0.329 0.329 thermo.py:775(__addThermoData)
1 0.000 0.000 utils.py:460(__setitem__)
{method 'getFormula' of 'rmgpy.molecule.Molecule' objects} <- 4229733 631.140 693.277 chemkin.py:763(getSpeciesIdentifier)
178138 33.886 37.921 model.py:222(checkForExistingSpecies)
33087 7.280 7.853 model.py:252(makeNewSpecies)
{method 'getDensityOfStates' of 'rmgpy.statmech.StatesModel' objects} <- 6583 510.899 539.453 network.py:372(calculateDensitiesOfStates)
{method 'fill' of 'numpy.ndarray' objects} <- 60642609 477.011 477.011 numeric.py:65(zeros_like)
22146 0.109 0.109 numeric.py:1791(ones)
{method 'isSubgraphIsomorphic' of 'rmgpy.molecule.Molecule' objects} <- 20966289 188.371 188.371 base.py:766(matchNodeToStructure)
37191682 280.577 280.577 base.py:1060(isMoleculeForbidden)
model.py:1198(addReactionToUnimolecularNetworks) <- 48518 452.011 453.035 model.py:649(processNewReactions)
model.py:504(enlarge) <- 2 0.268 104.060 main.py:212(initialize)
158 422.833 46115.275 main.py:309(execute)
{method 'isIsomorphic' of 'rmgpy.molecule.Molecule' objects} <- 1360198 13.542 13.542 chemkin.py:893(writeKineticsEntry)
3276 0.023 0.023 kinetics.py:688(speciesMatch)
1059187 1.081 1.081 kinetics.py:2304(__createReaction)
4619836 31.520 31.520 kinetics.py:2471(__generateReactions)
2206416 10.712 10.712 model.py:222(checkForExistingSpecies)
14380357 194.484 194.484 thermo.py:589(getThermoDataFromLibrary)
{method 'isIsomorphic' of 'rmgpy.reaction.Reaction' objects} <- 2103290 181.808 181.808 kinetics.py:2717(getKineticsFromDepository)
copy.py:145(deepcopy) <- 636 0.004 0.144 compiler.py:136(copy)
4719/4315 0.011 0.225 copy.py:226(_deepcopy_list)
11989572/10482612 30.098 312.744 copy.py:234(_deepcopy_tuple)
72541824/72535960 86.215 141.387 copy.py:253(_deepcopy_dict)
13591771/1498699 23.296 335.470 copy.py:306(_reconstruct)
300 0.001 0.033 kinetics.py:1928(addKineticsRulesFromTrainingSet)
14639 0.075 4.302 kinetics.py:2717(getKineticsFromDepository)
102420 0.529 24.718 kinetics.py:2830(estimateKineticsUsingRateRules)
1728 0.010 0.636 kinetics.py:3132(generateReactionsFromLibrary)
180 0.001 0.048 thermo.py:589(getThermoDataFromLibrary)
1377910 6.456 331.702 thermo.py:793(__getGroupThermoData)
{method 'calculateSymmetryNumber' of 'rmgpy.molecule.Molecule' objects} <- 106455 139.558 139.558 thermo.py:635(estimateThermoViaGroupAdditivity)
base.py:1060(isMoleculeForbidden) <- 4112915 90.195 342.281 kinetics.py:2236(__generateProductStructures)
1822092 38.588 144.484 kinetics.py:2304(__createReaction)
base.py:766(matchNodeToStructure) <- 27311530 116.875 435.671 base.py:831(descendTree)
630688/626921 7.312 24.887 base.py:903(matchToStructure)
1164 0.018 0.035 base.py:937(matchToStructure)
{method 'copy' of 'rmgpy.molecule.Molecule' objects} <- 1378157 44.080 44.080 kinetics.py:2120(applyRecipe)
2402499 54.568 54.568 kinetics.py:2304(__createReaction)
1406697 16.680 16.680 kinetics.py:2471(__generateReactions)
100 0.000 0.000 molecule_draw.py:558(findBackbone)
51646 2.434 2.434 thermo.py:635(estimateThermoViaGroupAdditivity)
{method 'getURL' of 'rmgpy.reaction.Reaction' objects} <- 615487 102.656 125.205 runtime.py:163(call)
{method 'getURL' of 'rmgpy.molecule.Molecule' objects} <- 2425271 100.699 123.501 runtime.py:163(call)
{method '__residual' of 'rmgpy.thermo.Wilhoit' objects} <- 843211 99.444 215.174 optimize.py:967(fminbound)
{isinstance} <- 1099 0.000 0.000 BIFFRecords.py:66(get_biff_record)
89019 0.011 0.011 Cell.py:171(_get_cells_biff_data_mul)
12560 0.001 0.001 Row.py:40(__init__)
261562 0.072 0.072 Row.py:233(write)
1570 0.001 0.001 UnicodeUtils.py:45(upack2)
1413 0.001 0.001 UnicodeUtils.py:92(upack1)
157 0.000 0.000 Workbook.py:323(add_sheet)
4 0.000 0.000 __init__.py:49(normalize_encoding)
4 0.000 0.000 __init__.py:71(search_function)
157 0.000 0.000 __init__.py:98(__init__)
310824 0.112 0.112 __init__.py:311(getMessage)
310824 0.138 0.138 __init__.py:834(emit)
536581 0.074 0.074 __init__.py:1188(log)
2425271 0.953 0.953 _native.py:39(soft_unicode)
2 0.000 0.000 abc.py:105(register)
10094 0.002 0.002 base.py:347(__loadTree)
85365240 28.800 28.800 base.py:766(matchNodeToStructure)
630688 0.272 0.272 base.py:903(matchToStructure)
5725287 1.121 1.121 base.py:916(getPossibleStructures)
2328 0.001 0.001 base.py:937(matchToStructure)
17889 0.003 0.003 chemkin.py:818(writeThermoEntry)
8773940 2.944 2.944 chemkin.py:893(writeKineticsEntry)
19 0.000 0.000 collections.py:237(namedtuple)
159 0.000 0.000 compiler.py:57(generate)
20193 0.005 0.005 compiler.py:1212(visit_Output)
3180 0.001 0.001 compiler.py:1380(visit_Const)
1272 0.000 0.000 compiler.py:1491(visit_Getitem)
15093886 3.377 3.377 copy.py:306(_reconstruct)
101 0.000 0.000 dimensionality.py:15(assert_isinstance)
159 0.000 0.000 environment.py:453(compile)
5983248 5.332 5.332 fromnumeric.py:1379(sum)
1 0.000 0.000 function_base.py:1685(_get_nargs)
1 0.000 0.000 function_base.py:1815(__init__)
2 0.000 0.000 glob.py:49(glob1)
6 0.000 0.000 input.py:54(database)
7 0.000 0.000 inspect.py:67(ismethod)
7 0.000 0.000 inspect.py:142(isfunction)
7 0.000 0.000 inspect.py:209(iscode)
698515 0.386 0.386 kinetics.py:202(__apply)
857075 0.312 0.312 kinetics.py:1287(getReactionTemplate)
66 0.000 0.000 kinetics.py:1801(generateProductTemplate)
50 0.000 0.000 kinetics.py:1928(addKineticsRulesFromTrainingSet)
1992158 0.716 0.716 kinetics.py:2120(applyRecipe)
3237409 1.014 1.014 kinetics.py:2346(__matchReactantToTemplate)
81102 0.014 0.014 kinetics.py:2445(calculateDegeneracy)
1406697 0.587 0.587 kinetics.py:2471(__generateReactions)
14639 0.003 0.003 kinetics.py:2717(getKineticsFromDepository)
1 0.000 0.000 kinetics.py:2966(loadFamilies)
81090 0.032 0.032 lexer.py:548(tokeniter)
255 0.000 0.000 main.py:309(execute)
99260 0.065 0.065 model.py:68(generateThermoData)
436009 0.111 0.111 model.py:252(makeNewSpecies)
2473876 0.314 0.314 model.py:309(checkForExistingReaction)
94911 0.010 0.010 model.py:384(makeNewReaction)
187790 0.049 0.049 model.py:504(enlarge)
93432 0.019 0.019 model.py:703(generateKinetics)
48518 0.016 0.016 model.py:1198(addReactionToUnimolecularNetworks)
214354576 41.754 41.754 model.py:1250(updateUnimolecularReactionNetworks)
1514157 0.335 0.335 nodes.py:163(iter_child_nodes)
158205 0.033 0.033 nodes.py:183(find_all)
46 0.000 0.000 numeric.py:1574(isscalar)
5 0.000 0.000 numerictypes.py:608(obj2sctype)
615487 0.143 0.143 output.py:52(saveOutputHTML)
32191 0.011 0.011 output.py:64(writeStates)
1440 0.000 0.000 output.py:200(writePDepReaction)
1272 0.001 0.001 parser.py:844(subparse)
12088 0.003 0.003 pdep.py:352(update)
160 0.000 0.000 posixpath.py:312(normpath)
1 0.000 0.000 posixpath.py:341(abspath)
70 0.000 0.000 quantity.py:19(validate_unit_quantity)
170 0.000 0.000 quantity.py:31(validate_dimensionality)
35 0.000 0.000 quantity.py:118(__new__)
50 0.000 0.000 quantity.py:200(astype)
217 0.000 0.000 quantity.py:217(__array_prepare__)
217 0.000 0.000 quantity.py:240(__array_wrap__)
38 0.000 0.000 re.py:226(_compile)
9774438 5.110 5.110 runtime.py:163(call)
76 0.000 0.000 sre_compile.py:474(isstring)
949 0.000 0.000 sre_parse.py:130(__getitem__)
837 0.000 0.000 states.py:305(getStatesData)
1491418 0.746 0.746 thermo.py:793(__getGroupThermoData)
159 0.000 0.000 utils.py:81(_encode_filename)
202884 0.048 0.048 visitor.py:58(generic_visit)
{method 'toHTML' of 'rmgpy.kinetics.KineticsModel' objects} <- 615487 83.319 103.001 runtime.py:163(call)
numeric.py:65(zeros_like) <- 38456 0.064 0.253 {method 'getDensityOfStates' of 'rmgpy.statmech.StatesModel' objects}
60457854 77.131 624.981 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects}
1480 0.005 0.014 {rmgpy._statmech.convolve}
144819 0.200 0.563 {rmgpy.measure.reaction.calculateMicrocanonicalRateCoefficient}
optimize.py:967(fminbound) <- 66173 74.445 375.871 {rmgpy.thermo.convertThermoModel}
{numpy.core.multiarray.empty_like} <- 60642609 71.400 71.400 numeric.py:65(zeros_like)
model.py:1020(addReactionToEdge) <- 56111 64.626 64.648 model.py:649(processNewReactions)
107 0.000 0.000 model.py:1127(addReactionLibraryToEdge)
2922 3.767 3.768 pdep.py:352(update)
Sorted by cumulative time
Sat Jun 9 08:56:38 2012 /Users/rwest/Code/rmgpy/RMG-Py/examples/rmg/methylformate/RMG.profile
47278589233 function calls (47165643959 primitive calls) in 61955.711 seconds
Ordered by: cumulative time
List reduced from 1953 to 25 due to restriction <25>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.026 0.026 62005.562 62005.562 main.py:309(execute)
160 423.102 2.644 46219.335 288.871 model.py:504(enlarge)
160 38084.212 238.026 41975.686 262.348 model.py:1250(updateUnimolecularReactionNetworks)
474 13635.259 28.766 14360.285 30.296 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects}
44812899017/44812898898 2558.555 0.000 2558.555 0.000 {len}
33087 1.468 0.000 1552.777 0.047 model.py:68(generateThermoData)
158 0.002 0.000 1407.628 8.909 main.py:446(saveEverything)
3289804 40.901 0.000 1361.483 0.000 pdep.py:352(update)
33087 0.312 0.000 1133.450 0.034 thermo.py:534(getThermoData)
11095 0.093 0.000 1111.334 0.100 model.py:484(react)
15551 0.060 0.000 1111.206 0.071 kinetics.py:3110(generateReactions)
15551 0.634 0.000 1047.278 0.067 kinetics.py:3156(generateReactionsFromFamilies)
342122 7.535 0.000 1046.575 0.003 kinetics.py:2365(generateReactions)
159 1.491 0.009 962.205 6.052 output.py:52(saveOutputHTML)
158 0.017 0.000 962.161 6.090 main.py:600(saveOutputHTML)
159 0.002 0.000 936.790 5.892 environment.py:879(render)
9859 5.947 0.001 936.788 0.095 {method 'join' of 'unicode' objects}
32907 1.029 0.000 926.686 0.028 thermo.py:604(getThermoDataFromGroups)
106455/54809 11.604 0.000 922.808 0.017 thermo.py:635(estimateThermoViaGroupAdditivity)
724756 21.731 0.000 906.665 0.001 kinetics.py:2471(__generateReactions)
1242034/1230974 42.027 0.000 864.437 0.001 chemkin.py:893(writeKineticsEntry)
518 5.415 0.010 844.083 1.630 network.py:817(calculateRateCoefficients)
9774438 13.182 0.000 822.427 0.000 runtime.py:163(call)
9815271 34.537 0.000 777.777 0.000 chemkin.py:763(getSpeciesIdentifier)
4440958 672.306 0.000 739.050 0.000 {method 'getFormula' of 'rmgpy.molecule.Molecule' objects}
Ordered by: cumulative time
List reduced from 1953 to 25 due to restriction <25>
Function was called by...
ncalls tottime cumtime
main.py:309(execute) <- 1 0.026 62005.562 <string>:1(<module>)
model.py:504(enlarge) <- 2 0.268 104.060 main.py:212(initialize)
158 422.833 46115.275 main.py:309(execute)
model.py:1250(updateUnimolecularReactionNetworks) <- 160 38084.212 41975.686 model.py:504(enlarge)
{method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} <- 474 13635.259 14360.285 main.py:309(execute)
{len} <- 318 0.000 0.000 <template>:5(root)
2198 0.000 0.000 BIFFRecords.py:23(add_str)
471 0.000 0.000 BIFFRecords.py:66(get_biff_record)
2198 0.000 0.000 BIFFRecords.py:133(_save_atom)
2198 0.000 0.000 BIFFRecords.py:140(_save_splitted)
25905 0.002 0.002 BIFFRecords.py:180(get_rec_header)
25748 0.003 0.003 BIFFRecords.py:187(get)
157 0.000 0.000 BIFFRecords.py:274(__init__)
1099 0.000 0.000 BIFFRecords.py:724(__init__)
157 0.000 0.000 BIFFRecords.py:790(__init__)
314 0.000 0.000 BIFFRecords.py:1105(__init__)
157 0.000 0.000 BIFFRecords.py:1483(__init__)
157 0.000 0.000 BIFFRecords.py:1906(__init__)
157 0.000 0.000 BIFFRecords.py:1933(__init__)
12560 0.001 0.001 Cell.py:171(_get_cells_biff_data_mul)
471 0.000 0.000 CompoundDoc.py:44(__build_directory)
157 0.000 0.000 CompoundDoc.py:123(__build_sat)
471 0.000 0.000 CompoundDoc.py:208(__build_header)
471 0.000 0.000 CompoundDoc.py:250(save)
1099 0.000 0.000 Row.py:233(write)
942 0.000 0.000 Style.py:92(_add_style)
1570 0.000 0.000 UnicodeUtils.py:45(upack2)
1413 0.000 0.000 UnicodeUtils.py:92(upack1)
157 0.000 0.000 Utils.py:183(valid_sheet_name)
157 0.000 0.000 Workbook.py:323(add_sheet)
157 0.000 0.000 Workbook.py:497(__tabid_rec)
157 0.000 0.000 Workbook.py:525(__boundsheets_rec)
157 0.000 0.000 Workbook.py:550(__all_links_rec)
1413 0.000 0.000 Workbook.py:587(get_biff_data)
157 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)
122671 0.022 0.022 __init__.py:1594(info)
194884 0.035 0.035 __init__.py:1602(debug)
536581 0.081 0.081 __init__.py:1610(log)
16967 0.001 0.001 base.py:347(__loadTree)
4480 0.000 0.000 base.py:410(<lambda>)
8685796 1.109 1.109 base.py:831(descendTree)
623341 0.120 0.120 basic.py:19(solve)
26119620 3.075 3.075 chemkin.py:763(getSpeciesIdentifier)
161159 0.014 0.014 chemkin.py:818(writeThermoEntry)
1236662 0.160 0.160 chemkin.py:893(writeKineticsEntry)
19 0.000 0.000 collections.py:237(namedtuple)
2544 0.000 0.000 compiler.py:1212(visit_Output)
2999689 0.377 0.377 copy.py:234(_deepcopy_tuple)
7546625 1.002 1.002 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)
1958588 0.192 0.192 kinetics.py:1896(getRateRule)
44 0.000 0.000 kinetics.py:2019(getRootTemplate)
726098 0.067 0.067 kinetics.py:2031(fillKineticsRulesByAveragingUp)
2099500 0.196 0.196 kinetics.py:2120(applyRecipe)
1395782 0.198 0.198 kinetics.py:2236(__generateProductStructures)
2499720 0.233 0.233 kinetics.py:2304(__createReaction)
654044 0.085 0.085 kinetics.py:2346(__matchReactantToTemplate)
29061 0.003 0.003 kinetics.py:2365(generateReactions)
215974 0.017 0.017 kinetics.py:2445(calculateDegeneracy)
11671821 0.982 0.982 kinetics.py:2471(__generateReactions)
492027 0.040 0.040 kinetics.py:2630(getReactionPairs)
229798 0.041 0.041 kinetics.py:2752(getKinetics)
102226 0.012 0.012 kinetics.py:2806(__getAverageKinetics)
1320031 0.139 0.139 kinetics.py:2830(estimateKineticsUsingRateRules)
292048 0.028 0.028 kinetics.py:2877(filterReactions)
623341 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)
159 0.000 0.000 lexer.py:548(tokeniter)
4735656 0.593 0.593 linalg.py:127(_to_native_byte_order)
4735656 0.665 0.665 linalg.py:139(_fastCopyAndTranspose)
9471312 0.757 0.757 linalg.py:151(_assertRank2)
3854020 0.581 0.581 linalg.py:244(solve)
881636 0.156 0.156 linalg.py:1680(lstsq)
158 0.000 0.000 main.py:608(saveChemkinFile)
99257 0.015 0.015 model.py:68(generateThermoData)
33087 0.007 0.007 model.py:252(makeNewSpecies)
715477 0.073 0.073 model.py:309(checkForExistingReaction)
213135 0.036 0.036 model.py:384(makeNewReaction)
972411704 55.998 55.998 model.py:504(enlarge)
725 0.000 0.000 model.py:779(printEnlargeSummary)
1276 0.000 0.000 model.py:1031(getModelSize)
2 0.000 0.000 model.py:1086(addSeedMechanismToCore)
4 0.000 0.000 model.py:1127(addReactionLibraryToEdge)
84749 0.013 0.013 model.py:1198(addReactionToUnimolecularNetworks)
43678774188 2486.316 2486.316 model.py:1250(updateUnimolecularReactionNetworks)
1078 0.000 0.000 molecule_draw.py:117(render)
5638 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)
1254 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)
1381 0.000 0.000 molecule_draw.py:1111(drawMolecule)
13772 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 0.006 0.006 network.py:674(calculateCollisionModel)
66180 0.006 0.006 network.py:725(setConditions)
62040 0.011 0.011 network.py:775(applyModifiedStrongCollisionMethod)
2590 0.000 0.000 network.py:817(calculateRateCoefficients)
378 0.000 0.000 nodes.py:62(__new__)
72822 0.009 0.009 nodes.py:126(__init__)
7 0.000 0.000 nonlin.py:1429(_nonlin_wrapper)
132346 0.018 0.018 optimize.py:46(is_array_scalar)
18654 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)
10335 0.001 0.001 parser.py:468(parse_concat)
1272 0.000 0.000 parser.py:688(parse_subscript)
20543956 1.562 1.562 pdep.py:98(getLeakCoefficient)
763 0.000 0.000 pdep.py:128(getMaximumLeakSpecies)
425 0.000 0.000 pdep.py:231(merge)
31953985 2.283 2.283 pdep.py:293(updateConfigurations)
6505068 0.476 0.476 pdep.py:352(update)
2 0.000 0.000 posixpath.py:80(split)
187 0.000 0.000 posixpath.py:118(dirname)
38 0.000 0.000 re.py:226(_compile)
1231133 0.221 0.221 runtime.py:270(__init__)
264692 0.033 0.033 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)
5721 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)
98773 0.023 0.023 statesfit.py:383(evaluate)
184000 0.023 0.023 statesfit.py:424(evaluate)
3000 0.001 0.001 statesfit.py:474(evaluate)
2646202 0.329 0.329 thermo.py:775(__addThermoData)
1 0.000 0.000 utils.py:460(__setitem__)
model.py:68(generateThermoData) <- 16 0.001 0.178 main.py:212(initialize)
33018 1.465 1551.695 model.py:504(enlarge)
38 0.002 0.707 model.py:1086(addSeedMechanismToCore)
15 0.001 0.197 model.py:1127(addReactionLibraryToEdge)
main.py:446(saveEverything) <- 158 0.002 1407.628 main.py:309(execute)
pdep.py:352(update) <- 3289804 40.901 1361.483 model.py:1250(updateUnimolecularReactionNetworks)
thermo.py:534(getThermoData) <- 33087 0.312 1133.450 model.py:68(generateThermoData)
model.py:484(react) <- 10395 0.088 1057.795 model.py:504(enlarge)
700 0.006 53.539 pdep.py:185(exploreIsomer)
kinetics.py:3110(generateReactions) <- 15551 0.060 1111.206 model.py:484(react)
kinetics.py:3156(generateReactionsFromFamilies) <- 15551 0.634 1047.278 kinetics.py:3110(generateReactions)
kinetics.py:2365(generateReactions) <- 342122 7.535 1046.575 kinetics.py:3156(generateReactionsFromFamilies)
output.py:52(saveOutputHTML) <- 1 0.003 0.075 main.py:212(initialize)
158 1.488 962.130 main.py:600(saveOutputHTML)
main.py:600(saveOutputHTML) <- 158 0.017 962.161 main.py:446(saveEverything)
environment.py:879(render) <- 159 0.002 936.790 output.py:52(saveOutputHTML)
{method 'join' of 'unicode' objects} <- 9699 0.003 0.003 compiler.py:1212(visit_Output)
159 5.944 936.785 environment.py:879(render)
1 0.000 0.000 utils.py:10(<module>)
thermo.py:604(getThermoDataFromGroups) <- 32907 1.029 926.686 thermo.py:534(getThermoData)
thermo.py:635(estimateThermoViaGroupAdditivity) <- 54809 3.580 922.808 thermo.py:604(getThermoDataFromGroups)
51646 8.023 745.348 thermo.py:635(estimateThermoViaGroupAdditivity)
kinetics.py:2471(__generateReactions) <- 682203 17.467 652.823 kinetics.py:2365(generateReactions)
42553 4.264 253.842 kinetics.py:2445(calculateDegeneracy)
chemkin.py:893(writeKineticsEntry) <- 11060 0.257 1.109 chemkin.py:893(writeKineticsEntry)
615487 21.328 428.325 chemkin.py:1075(saveChemkinFile)
615487 20.441 436.111 {method 'toChemkin' of 'rmgpy.reaction.Reaction' objects}
network.py:817(calculateRateCoefficients) <- 518 5.415 844.083 pdep.py:352(update)
runtime.py:163(call) <- 9774438 13.182 822.427 <template>:5(root)
chemkin.py:763(getSpeciesIdentifier) <- 17889 0.069 1.845 chemkin.py:818(writeThermoEntry)
9761604 34.325 772.233 chemkin.py:893(writeKineticsEntry)
17889 0.072 1.835 chemkin.py:1065(saveSpeciesDictionary)
17889 0.072 1.864 chemkin.py:1075(saveChemkinFile)
{method 'getFormula' of 'rmgpy.molecule.Molecule' objects} <- 4229733 631.140 693.277 chemkin.py:763(getSpeciesIdentifier)
178138 33.886 37.921 model.py:222(checkForExistingSpecies)
33087 7.280 7.853 model.py:252(makeNewSpecies)
Ordered by: cumulative time
List reduced from 1953 to 25 due to restriction <25>
Function called...
ncalls tottime cumtime
main.py:309(execute) -> 157 0.001 0.002 __init__.py:98(__init__)
157 0.000 0.005 __init__.py:366(get_memory_info)
1734 0.004 0.176 __init__.py:1594(info)
157 0.001 0.002 genericpath.py:15(exists)
1 0.005 118.001 main.py:212(initialize)
158 0.002 1407.628 main.py:446(saveEverything)
157 0.084 4.144 main.py:643(saveExecutionStatistics)
158 422.833 46115.275 model.py:504(enlarge)
157 0.000 0.001 model.py:1031(getModelSize)
150 0.001 0.014 pdep.py:128(getMaximumLeakSpecies)
157 0.001 0.001 posixpath.py:60(join)
255 0.000 0.000 {isinstance}
1354 0.000 0.000 {method 'append' of 'list' objects}
474 13635.259 14360.285 {method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects}
157 0.000 0.000 {posix.getpid}
157 0.001 0.001 {time.gmtime}
157 0.002 0.002 {time.strftime}
157 0.000 0.000 {time.time}
model.py:504(enlarge) -> 749 0.002 0.101 __init__.py:1594(info)
110 0.000 0.000 display.py:36(do_nothing)
33018 1.465 1551.695 model.py:68(generateThermoData)
10395 0.088 1057.795 model.py:484(react)
812 34.667 708.131 model.py:649(processNewReactions)
93432 0.557 328.779 model.py:703(generateKinetics)
159 0.154 8.387 model.py:779(printEnlargeSummary)
111 19.679 26.814 model.py:824(addSpeciesToCore)
160 38084.212 41975.686 model.py:1250(updateUnimolecularReactionNetworks)
701 0.008 53.662 pdep.py:185(exploreIsomer)
3848437 21.837 26.811 pdep.py:293(updateConfigurations)
21467 0.391 0.391 {delattr}
21467 0.009 0.009 {hasattr}
187790 0.049 0.049 {isinstance}
972411704 55.998 55.998 {len}
94 0.000 0.000 {method 'append' of 'list' objects}
11025 0.007 0.007 {method 'extend' of 'list' objects}
93432 0.980 1.916 {method 'fixBarrierHeight' of 'rmgpy.reaction.Reaction' objects}
111 0.001 0.001 {method 'format' of 'str' objects}
model.py:1250(updateUnimolecularReactionNetworks) -> 11 0.000 0.002 __init__.py:1584(warning)
225 0.001 0.056 __init__.py:1594(info)
44 0.000 0.000 __init__.py:1602(debug)
65 0.004 0.004 pdep.py:231(merge)
3289804 40.901 1361.483 pdep.py:352(update)
214354576 41.754 41.754 {isinstance}
43678774188 2486.316 2486.316 {len}
280 0.002 0.002 {method 'format' of 'str' objects}
1172 0.011 0.011 {method 'getEquilibriumConstant' of 'rmgpy.reaction.Reaction' objects}
2344 0.165 0.165 {method 'getRateCoefficient' of 'rmgpy.reaction.Reaction' objects}
282 0.000 0.000 {method 'insert' of 'list' objects}
933 1.681 1.681 {method 'remove' of 'list' objects}
160 0.000 0.000 {sum}
{method 'simulate' of 'rmgpy.solver.base.ReactionSystem' objects} -> 2037 0.006 0.595 __init__.py:1594(info)
2490014 2.351 38.704 fromnumeric.py:683(argmax)
1245007 2.935 13.264 fromnumeric.py:1379(sum)
60457854 77.131 624.981 numeric.py:65(zeros_like)
948 0.006 0.078 numeric.py:1791(ones)
9744177 19.197 47.403 pdep.py:98(getLeakCoefficient)
{len} -> 119 0.000 0.000 sre_parse.py:126(__len__)
model.py:68(generateThermoData) -> 33086 0.098 2.071 __init__.py:1610(log)
33086 0.049 0.184 fromnumeric.py:1379(sum)
33087 0.312 1133.450 thermo.py:534(getThermoData)
99260 0.065 0.065 {isinstance}
99257 0.015 0.015 {len}
33086 0.011 0.011 {math.sqrt}
33084 5.004 5.004 {method 'countInternalRotors' of 'rmgpy.molecule.Molecule' objects}
33086 0.265 0.265 {method 'format' of 'str' objects}
33087 0.030 0.030 {method 'getEnthalpy' of 'rmgpy.thermo.Wilhoit' objects}
66172 3.371 5.140 {method 'getHeatCapacities' of 'rmgpy.thermo.ThermoModel' objects}
33084 3.604 3.604 {method 'isLinear' of 'rmgpy.molecule.Molecule' objects}
55010 1.079 1.079 {method 'makeHydrogensExplicit' of 'rmgpy.molecule.Molecule' objects}
55008 0.803 0.803 {method 'makeHydrogensImplicit' of 'rmgpy.molecule.Molecule' objects}
33086 0.345 0.345 {numpy.core.multiarray.array}
66173 12.449 399.203 {rmgpy.thermo.convertThermoModel}
33087 0.041 0.041 {zip}
main.py:446(saveEverything) -> 158 0.017 962.161 main.py:600(saveOutputHTML)
158 0.017 445.465 main.py:608(saveChemkinFile)
pdep.py:352(update) -> 17 0.000 0.003 __init__.py:1584(warning)
17 0.000 0.002 __init__.py:1594(info)
3289804 19.019 25.606 main.py:109(copy)
518 0.005 6.914 main.py:183(saveInput)
3420 0.013 394.018 model.py:121(generateStatesData)
3999 0.013 0.082 model.py:455(makeNewPDepReaction)
1077 1.362 1.362 model.py:1008(addReactionToCore)
2922 3.767 3.768 model.py:1020(addReactionToEdge)
518 0.064 1.561 network.py:257(printSummary)
518 5.415 844.083 network.py:817(calculateRateCoefficients)
3999 0.014 0.014 pdep.py:57(__init__)
3289804 20.016 24.794 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}
6505068 0.476 0.476 {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 0.057 0.057 {method 'hasTemplate' of 'rmgpy.reaction.Reaction' objects}
517 0.001 0.001 {method 'index' of 'list' objects}
81491 0.012 0.012 {method 'isIsomerization' of 'rmgpy.reaction.Reaction' objects}
3682263 0.368 0.368 {method 'isPressureDependent' of 'rmgpy.kinetics.Arrhenius' objects}
517 0.000 0.000 {range}
5446 16.172 17.436 {rmgpy.measure.reaction.fitInterpolationModel}
6044 0.002 0.002 {sum}
thermo.py:534(getThermoData) -> 99070 11.887 206.451 thermo.py:589(getThermoDataFromLibrary)
32907 1.029 926.686 thermo.py:604(getThermoDataFromGroups)
model.py:484(react) -> 15551 0.060 1111.206 kinetics.py:3110(generateReactions)
30118 0.016 0.016 {method 'clearLabeledAtoms' of 'rmgpy.molecule.Molecule' objects}
15551 0.005 0.005 {method 'extend' of 'list' objects}
30118 0.014 0.014 {method 'makeHydrogensImplicit' of 'rmgpy.molecule.Molecule' objects}
kinetics.py:3110(generateReactions) -> 15551 0.088 63.861 kinetics.py:3121(generateReactionsFromLibraries)
15551 0.634 1047.278 kinetics.py:3156(generateReactionsFromFamilies)
31102 0.008 0.008 {method 'extend' of 'list' objects}
kinetics.py:3156(generateReactionsFromFamilies) -> 342122 7.535 1046.575 kinetics.py:2365(generateReactions)
342122 0.062 0.062 {method 'extend' of 'list' objects}
15551 0.006 0.006 {method 'iteritems' of 'dict' objects}
kinetics.py:2365(generateReactions) -> 148271 0.482 0.482 kinetics.py:130(__init__)
42553 1.307 262.474 kinetics.py:2445(calculateDegeneracy)
682203 17.467 652.823 kinetics.py:2471(__generateReactions)
148271 0.681 0.950 kinetics.py:2630(getReactionPairs)
148271 0.222 104.819 kinetics.py:2695(getReactionTemplate)
29061 1.503 17.334 kinetics.py:2877(filterReactions)
119210 0.128 0.128 {hasattr}
29061 0.003 0.003 {len}
148271 0.027 0.027 {method 'append' of 'list' objects}
output.py:52(saveOutputHTML) -> 1 0.003 0.027 __init__.py:28(<module>)
159 0.002 0.007 environment.py:217(__init__)
159 0.001 7.305 environment.py:763(from_string)
159 0.002 936.790 environment.py:879(render)
17889 0.017 0.149 genericpath.py:15(exists)
159 0.000 0.004 genericpath.py:38(isdir)
73282 0.014 0.014 kinetics.py:114(getSource)
447513 0.084 0.084 kinetics.py:141(getSource)
1 0.000 0.000 molecule_draw.py:86(<module>)
148 0.015 0.633 molecule_draw.py:1111(drawMolecule)
18048 0.038 0.055 posixpath.py:60(join)
159 0.000 0.001 posixpath.py:118(dirname)
159 0.000 0.003 posixpath.py:341(abspath)
318 0.000 0.002 re.py:188(compile)
615487 0.143 0.143 {isinstance}
159 0.906 0.906 {method 'close' of 'file' objects}
17889 0.034 0.034 {method 'format' of 'str' objects}
159 0.000 0.000 {method 'keys' of 'dict' objects}
17889 0.012 0.012 {method 'search' of '_sre.SRE_Pattern' objects}
159 0.000 0.000 {method 'sort' of 'list' objects}
159 14.361 14.361 {method 'write' of 'file' objects}
159 0.187 0.187 {open}
main.py:600(saveOutputHTML) -> 158 0.000 0.013 __init__.py:1594(info)
158 1.488 962.130 output.py:52(saveOutputHTML)
158 0.001 0.001 posixpath.py:60(join)
environment.py:879(render) -> 159 0.000 0.004 environment.py:920(new_context)
159 5.944 936.785 {method 'join' of 'unicode' objects}
{method 'join' of 'unicode' objects} -> 67962 0.523 10.123 <template>:5(root)
1 0.000 0.000 utils.py:47(_test_gen_bug)
thermo.py:604(getThermoDataFromGroups) -> 54809 3.580 922.808 thermo.py:635(estimateThermoViaGroupAdditivity)
54809 0.013 0.013 {method 'append' of 'list' objects}
32907 0.077 0.077 {method 'argsort' of 'numpy.ndarray' objects}
54809 0.081 0.081 {method 'clearLabeledAtoms' of 'rmgpy.molecule.Molecule' objects}
54809 1.090 1.090 {method 'getEnthalpy' of 'rmgpy.thermo.ThermoData' objects}
54809 0.015 0.015 {method 'makeHydrogensExplicit' of 'rmgpy.molecule.Molecule' objects}
54809 1.159 1.159 {method 'updateAtomTypes' of 'rmgpy.molecule.Molecule' objects}
32907 0.390 0.390 {numpy.core.multiarray.array}
32907 0.024 0.024 {zip}
thermo.py:635(estimateThermoViaGroupAdditivity) -> 51646 8.023 745.348 thermo.py:635(estimateThermoViaGroupAdditivity)
1323101 34.463 39.723 thermo.py:775(__addThermoData)
1956275 20.629 723.196 thermo.py:793(__getGroupThermoData)
158101 0.130 0.130 {math.log}
284830 0.164 0.164 {method 'addAtom' of 'rmgpy.molecule.Molecule' objects}
340568 0.165 0.165 {method 'addBond' of 'rmgpy.molecule.Molecule' objects}
114546 0.022 0.022 {method 'append' of 'list' objects}
106455 139.558 139.558 {method 'calculateSymmetryNumber' of 'rmgpy.molecule.Molecule' objects}
51646 2.434 2.434 {method 'copy' of 'rmgpy.molecule.Molecule' objects}
229092 0.045 0.045 {method 'decrementRadical' of 'rmgpy.molecule.Atom' objects}
111476 0.028 0.028 {method 'getBond' of 'rmgpy.molecule.Molecule' objects}
54809 2.542 2.542 {method 'getSmallestSetOfSmallestRings' of 'rmgpy.graph.Graph' objects}
200980 0.049 0.049 {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 0.039 0.039 {method 'makeHydrogensExplicit' of 'rmgpy.molecule.Molecule' objects}
114546 0.268 0.268 {method 'removeAtom' of 'rmgpy.molecule.Molecule' objects}
114546 0.061 0.061 {method 'removeBond' of 'rmgpy.molecule.Molecule' objects}
158101 0.696 0.696 {method 'sortVertices' of 'rmgpy.graph.Graph' objects}
51646 0.960 0.960 {method 'updateAtomTypes' of 'rmgpy.molecule.Molecule' objects}
161848 0.712 0.712 {method 'updateConnectivityValues' of 'rmgpy.graph.Graph' objects}
818284 0.181 0.181 {range}
106455 0.058 0.058 {sum}
kinetics.py:2471(__generateReactions) -> 698369 12.923 495.598 kinetics.py:2236(__generateProductStructures)
628925 11.511 237.191 kinetics.py:2304(__createReaction)
1297151 4.074 36.830 kinetics.py:2346(__matchReactantToTemplate)
1406697 0.587 0.587 {isinstance}
11671821 0.982 0.982 {len}
628361 0.151 0.151 {method 'append' of 'list' objects}
1406697 16.680 16.680 {method 'copy' of 'rmgpy.molecule.Molecule' objects}
570137 53.750 53.750 {method 'generateResonanceIsomers' of 'rmgpy.molecule.Molecule' objects}
4619836 31.520 31.520 {method 'isIsomorphic' of 'rmgpy.molecule.Molecule' objects}
730384 0.435 0.435 {method 'lower' of 'str' objects}
1406697 9.812 9.812 {method 'makeHydrogensExplicit' of 'rmgpy.molecule.Molecule' objects}
316908 0.113 0.113 {method 'remove' of 'list' objects}
730384 0.408 0.408 {method 'startswith' of 'str' objects}
2131453 0.876 0.876 {range}
chemkin.py:893(writeKineticsEntry) -> 9761604 34.325 772.233 chemkin.py:763(getSpeciesIdentifier)
11060 0.257 1.109 chemkin.py:893(writeKineticsEntry)
11060 0.039 0.039 kinetics.py:102(__init__)
1251182 0.213 0.213 {any}
198548 0.245 0.245 {hasattr}
8773940 2.944 2.944 {isinstance}
1236662 0.160 0.160 {len}
189384 0.445 0.445 {method 'copy' of 'numpy.ndarray' objects}
17215535 28.200 28.472 {method 'format' of 'str' objects}
1360198 13.542 13.542 {method 'isIsomorphic' of 'rmgpy.molecule.Molecule' objects}
1032742 0.235 0.235 {method 'isPressureDependent' of 'rmgpy.kinetics.Arrhenius' objects}
189384 0.049 0.049 {method 'isPressureDependent' of 'rmgpy.kinetics.Chebyshev' objects}
9164 0.002 0.002 {method 'isPressureDependent' of 'rmgpy.kinetics.PDepArrhenius' objects}
5372 0.002 0.002 {method 'isPressureDependent' of 'rmgpy.kinetics.ThirdBody' objects}
5372 0.002 0.002 {method 'iteritems' of 'dict' objects}
4593952 1.504 1.504 {method 'join' of 'str' objects}
1041590 1.670 1.670 {method 'split' of 'str' objects}
1325688 0.631 0.631 {range}
9164 0.024 0.024 {zip}
network.py:817(calculateRateCoefficients) -> 518 0.001 0.080 __init__.py:1594(info)
7079 0.008 0.019 __init__.py:1602(debug)
20680 0.055 0.109 __init__.py:1610(log)
1036 0.001 0.005 fromnumeric.py:1774(amax)
1036 0.001 0.011 fromnumeric.py:1836(amin)
518 0.007 540.522 network.py:702(initialize)
20681 0.743 85.752 network.py:725(setConditions)
20680 0.393 211.950 network.py:775(applyModifiedStrongCollisionMethod)
2590 0.000 0.000 {len}
6562 0.039 0.040 {method 'format' of 'str' objects}
20680 0.023 0.023 {method 'lower' of 'str' objects}
518 0.006 0.006 {numpy.core.multiarray.zeros}
370360 0.151 0.151 {range}
runtime.py:163(call) -> 366410 0.122 0.122 kinetics.py:114(getSource)
2237565 0.761 0.761 kinetics.py:141(getSource)
473460 0.200 0.200 pdep.py:61(getSource)
9232305 6.812 6.812 {getattr}
9774438 5.110 5.110 {isinstance}
2425271 5.461 5.461 {method 'getMolecularWeight' of 'rmgpy.molecule.Molecule' objects}
2425271 100.699 123.501 {method 'getURL' of 'rmgpy.molecule.Molecule' objects}
615487 102.656 125.205 {method 'getURL' of 'rmgpy.reaction.Reaction' objects}
615487 2.960 439.071 {method 'toChemkin' of 'rmgpy.reaction.Reaction' objects}
615487 83.319 103.001 {method 'toHTML' of 'rmgpy.kinetics.KineticsModel' objects}
chemkin.py:763(getSpeciesIdentifier) -> 9813217 8.085 34.517 re.py:139(search)
26119620 3.075 3.075 {len}
12074616 12.371 12.371 {method 'format' of 'str' objects}
4229733 631.140 693.277 {method 'getFormula' of 'rmgpy.molecule.Molecule' objects}
{method 'getFormula' of 'rmgpy.molecule.Molecule' objects} -> 4440958 5.179 11.805 openbabel.py:2246(__init__)
4440958 5.733 12.295 pybel.py:195(__init__)
4440958 3.979 42.645 pybel.py:222(formula)
Raw
Profiling_data2.txt
================================================================================
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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