Skip to content

Instantly share code, notes, and snippets.

@rwest

rwest/Profiling_data.txt

Created June 11, 2012 14:51
Show Gist options
  • Save rwest/2910440 to your computer and use it in GitHub Desktop.
Save rwest/2910440 to your computer and use it in GitHub Desktop.
Download ZIP
Profiling data for RMG-Py/examples/rmg/methylformate
Raw
profile.dot
digraph {
graph [ranksep=0.25, fontname=Arial, nodesep=0.125];
node [fontname=Arial, style="filled,rounded", height=0, width=0, shape=box, fontcolor=white];
edge [fontname=Arial];
26 [color="#0d1375", fontcolor="#ffffff", fontsize="10.00", label="output:52:saveOutputHTML\n1.55%\n(0.00%)\n159"];
26 -> 886 [color="#0d1375", label="1.51%\n159", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1375", labeldistance="0.50", penwidth="0.50"];
28 [color="#0d1375", fontcolor="#ffffff", fontsize="10.00", label="main:600:saveOutputHTML\n1.55%\n(0.00%)\n158"];
28 -> 26 [color="#0d1375", label="1.55%\n158", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1375", labeldistance="0.50", penwidth="0.50"];
30 [color="#ff0000", fontcolor="#ffffff", fontsize="10.00", label="main:309:execute\n100.00%\n(0.00%)\n1"];
30 -> 613 [color="#0c8791", label="23.16%\n474", arrowsize="0.48", fontsize="10.00", fontcolor="#0c8791", labeldistance="0.93", penwidth="0.93"];
30 -> 1734 [color="#0d1676", label="2.27%\n158", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1676", labeldistance="0.50", penwidth="0.50"];
30 -> 239 [color="#d3d906", label="74.37%\n158", arrowsize="0.86", fontsize="10.00", fontcolor="#d3d906", labeldistance="2.97", penwidth="2.97"];
32 [color="#0d1676", fontcolor="#ffffff", fontsize="10.00", label="pdep:352:update\n2.20%\n(0.07%)\n3289804"];
32 -> 308 [color="#0d1274", label="1.36%\n518", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1274", labeldistance="0.50", penwidth="0.50"];
58 [color="#0d1274", fontcolor="#ffffff", fontsize="10.00", label="runtime:163:call\n1.33%\n(0.02%)\n9774438"];
138 [color="#0d1174", fontcolor="#ffffff", fontsize="10.00", label="model:649:processNewReactions\n1.14%\n(0.06%)\n812"];
174 [color="#0d1375", fontcolor="#ffffff", fontsize="10.00", label="kinetics:2471:__generateReactions\n1.46%\n(0.04%)\n724756"];
187 [color="#0d1776", fontcolor="#ffffff", fontsize="10.00", label="model:68:generateThermoData\n2.50%\n(0.00%)\n33087"];
187 -> 802 [color="#0d1475", label="1.83%\n33087", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1475", labeldistance="0.50", penwidth="0.50"];
239 [color="#d5d906", fontcolor="#ffffff", fontsize="10.00", label="model:504:enlarge\n74.54%\n(0.68%)\n160"];
239 -> 138 [color="#0d1174", label="1.14%\n812", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1174", labeldistance="0.50", penwidth="0.50"];
239 -> 244 [color="#0d1475", label="1.71%\n10395", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1475", labeldistance="0.50", penwidth="0.50"];
239 -> 375 [color="#94cf07", label="67.70%\n160", arrowsize="0.82", fontsize="10.00", fontcolor="#94cf07", labeldistance="2.71", penwidth="2.71"];
239 -> 187 [color="#0d1776", label="2.50%\n33018", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1776", labeldistance="0.50", penwidth="0.50"];
242 [color="#0d1375", fontcolor="#ffffff", fontsize="10.00", label="thermo:604:getThermoDataFromGroups\n1.49%\n(0.00%)\n32907"];
242 -> 762 [color="#0d1375", label="1.49%\n54809", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1375", labeldistance="0.50", penwidth="0.50"];
244 [color="#0d1475", fontcolor="#ffffff", fontsize="10.00", label="model:484:react\n1.79%\n(0.00%)\n11095"];
244 -> 621 [color="#0d1475", label="1.79%\n15551", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1475", labeldistance="0.50", penwidth="0.50"];
276 [color="#0d1174", fontcolor="#ffffff", fontsize="10.00", label="numeric:65:zeros_like\n1.01%\n(0.12%)\n60642609"];
290 [color="#0d1e78", fontcolor="#ffffff", fontsize="10.00", label="~:0:<len>\n4.13%\n(4.13%)\n44812899017"];
308 [color="#0d1274", fontcolor="#ffffff", fontsize="10.00", label="network:817:calculateRateCoefficients\n1.36%\n(0.01%)\n518"];
308 -> 749 [color="#0d1074", label="0.87%\n518", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1074", labeldistance="0.50", penwidth="0.50"];
312 [color="#0d1475", fontcolor="#ffffff", fontsize="10.00", label="kinetics:2365:generateReactions\n1.69%\n(0.01%)\n342122"];
312 -> 174 [color="#0d1174", label="1.05%\n682203", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1174", labeldistance="0.50", penwidth="0.50"];
324 [color="#0d1274", fontcolor="#ffffff", fontsize="10.00", label="chemkin:763:getSpeciesIdentifier\n1.25%\n(0.06%)\n9815271"];
324 -> 918 [color="#0d1174", label="1.12%\n4229733", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1174", labeldistance="0.50", penwidth="0.50"];
340 [color="#0d1074", fontcolor="#ffffff", fontsize="10.00", label="network:372:calculateDensitiesOfStates\n0.87%\n(0.00%)\n518"];
340 -> 614 [color="#0d1074", label="0.87%\n6583", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1074", labeldistance="0.50", penwidth="0.50"];
375 [color="#94cf07", fontcolor="#ffffff", fontsize="10.00", label="model:1250:updateUnimolecularReactionNetworks\n67.70%\n(61.47%)\n160"];
375 -> 32 [color="#0d1676", label="2.20%\n3289804", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1676", labeldistance="0.50", penwidth="0.50"];
375 -> 290 [color="#0d1e78", label="4.01%\n43678774188", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1e78", labeldistance="0.50", penwidth="0.50"];
381 [color="#0d1375", fontcolor="#ffffff", fontsize="10.00", label="chemkin:893:writeKineticsEntry\n1.39%\n(0.07%)\n1242034"];
381 -> 324 [color="#0d1274", label="1.25%\n9761604", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1274", labeldistance="0.50", penwidth="0.50"];
590 [color="#0d1274", fontcolor="#ffffff", fontsize="10.00", label="thermo:793:__getGroupThermoData\n1.17%\n(0.03%)\n1956275"];
613 [color="#0c8791", fontcolor="#ffffff", fontsize="10.00", label="~:0:<method 'simulate' of\n'rmgpy.solver.base.ReactionSystem'\nobjects>\n23.16%\n(22.01%)\n474"];
613 -> 276 [color="#0d1174", label="1.01%\n60457854", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1174", labeldistance="0.50", penwidth="0.50"];
614 [color="#0d1074", fontcolor="#ffffff", fontsize="10.00", label="~:0:<method 'getDensityOfStates'\nof 'rmgpy.statmech.StatesModel'\nobjects>\n0.87%\n(0.82%)\n6583"];
620 [color="#0d1475", fontcolor="#ffffff", fontsize="10.00", label="kinetics:3156:generateReactionsFromFamilies\n1.69%\n(0.00%)\n15551"];
620 -> 312 [color="#0d1475", label="1.69%\n342122", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1475", labeldistance="0.50", penwidth="0.50"];
621 [color="#0d1475", fontcolor="#ffffff", fontsize="10.00", label="kinetics:3110:generateReactions\n1.79%\n(0.00%)\n15551"];
621 -> 620 [color="#0d1475", label="1.69%\n15551", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1475", labeldistance="0.50", penwidth="0.50"];
655 [color="#0d1375", fontcolor="#ffffff", fontsize="10.00", label="~:0:<method 'join' of 'unicode'\nobjects>\n1.51%\n(0.01%)\n9859"];
749 [color="#0d1074", fontcolor="#ffffff", fontsize="10.00", label="network:702:initialize\n0.87%\n(0.00%)\n518"];
749 -> 340 [color="#0d1074", label="0.87%\n518", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1074", labeldistance="0.50", penwidth="0.50"];
762 [color="#0d1375", fontcolor="#ffffff", fontsize="10.00", label="thermo:635:estimateThermoViaGroupAdditivity\n1.49%\n(0.02%)\n106455"];
762 -> 590 [color="#0d1274", label="1.17%\n1956275", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1274", labeldistance="0.50", penwidth="0.50"];
762 -> 762 [color="#0d1274", label="1.20%\n51646", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1274", labeldistance="0.50", penwidth="0.50"];
802 [color="#0d1475", fontcolor="#ffffff", fontsize="10.00", label="thermo:534:getThermoData\n1.83%\n(0.00%)\n33087"];
802 -> 242 [color="#0d1375", label="1.49%\n32907", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1375", labeldistance="0.50", penwidth="0.50"];
886 [color="#0d1375", fontcolor="#ffffff", fontsize="10.00", label="environment:879:render\n1.51%\n(0.00%)\n159"];
886 -> 655 [color="#0d1375", label="1.51%\n159", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1375", labeldistance="0.50", penwidth="0.50"];
918 [color="#0d1274", fontcolor="#ffffff", fontsize="10.00", label="~:0:<method 'getFormula' of\n'rmgpy.molecule.Molecule'\nobjects>\n1.19%\n(1.09%)\n4440958"];
1734 [color="#0d1676", fontcolor="#ffffff", fontsize="10.00", label="main:446:saveEverything\n2.27%\n(0.00%)\n158"];
1734 -> 28 [color="#0d1375", label="1.55%\n158", arrowsize="0.35", fontsize="10.00", fontcolor="#0d1375", labeldistance="0.50", penwidth="0.50"];
}
Display the source blob
Display the rendered blob
Raw
profile.svg
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
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}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment