[born] ~/Analyzing>python Python 2.2.2 (#1, Feb 24 2003, 19:13:11) [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import pstats >>> p6=pstats.Stats('600.0profile') >>> p6.strip_dirs() >>> p6.pstats.sort('cumulative') Traceback (most recent call last): File "", line 1, in ? AttributeError: Stats instance has no attribute 'pstats' >>> p6.sort_stats('cumulative') >>> p6.print_stats() Wed Jan 21 09:05:01 2004 600.0profile 494177565 function calls (494176589 primitive calls) in -9070.652 CPU seconds Ordered by: cumulative time ncalls tottime percall cumtime percall filename:lineno(function) 7612160 91.590 0.000 6936.690 0.001 RandomArray.py:87(standard_normal) 7612160 6478.150 0.001 6845.100 0.001 RandomArray.py:37(_build_random_array) 1164/194 0.150 0.000 2266.040 11.681 TAD.py:300(WhenDidItHappen) 500 0.190 0.000 2059.300 4.119 TAD.py:281(Relaxation) 3256 3.590 0.001 2045.230 0.628 IonDynamics2.py:179(__call__) 194 0.220 0.001 1907.030 9.830 TransisionStateEnergy.py:41(FindTransisionStateEnergy) 162800 90.030 0.001 1906.170 0.012 IonDynamics2.py:191(_VerletUpdate_) 91430001 1751.360 0.000 1751.360 0.000 warnings.py:59(warn_explicit) 11187743 163.460 0.000 1538.450 0.000 __init__.py:388(GetCartesianPositions) 11187743 733.780 0.000 1374.990 0.000 asapparallel.py:55(GetCartesianPositions) 15227096 192.330 0.000 1235.550 0.000 __init__.py:370(__len__) 9617034 225.700 0.000 1117.110 0.000 __init__.py:400(SetCartesianMomenta) 57540 37.700 0.001 1078.380 0.019 NudgedElasticBand.py:458(GetGeneralizedForces) 287700 114.320 0.000 1034.020 0.004 NudgedElasticBand.py:471(GetOneGeneralizedForce) 1968739 78.040 0.000 1003.360 0.001 TAD.py:351(CopyAtoms) 14163907 788.340 0.000 788.350 0.000 Numeric.py:587(sum) 3324366 91.450 0.000 763.250 0.000 __init__.py:380(SetGeneralizedPositions) 9197943 323.450 0.000 740.540 0.000 asapparallel.py:52(SetCartesianPositions) 13425364 701.800 0.000 701.800 0.000 __init__.py:405(GetCartesianMomenta) 976 0.070 0.000 610.140 0.625 IsAnyAtomMoved.py:127(Relaxation) 3356849 39.390 0.000 578.370 0.000 __init__.py:392(GetGeneralizedPositions) 19180 1.710 0.000 535.430 0.028 TransisionStateEnergy.py:182(CalcAll) 876480 150.770 0.000 462.420 0.001 NudgedElasticBand.py:336(GetOneGeneralizedDisplacementVector) 194 0.070 0.000 342.510 1.766 TransisionStateEnergy.py:279(SetUpNEB) 1849830 20.720 0.000 330.210 0.000 Filters.py:29(GetGeneralizedPositions) 1849830 34.530 0.000 309.490 0.000 Filters.py:177(GetCartesianPositions) 287700 3.030 0.000 296.220 0.001 NudgedElasticBand.py:347(GetOneGeneralizedTangent) 287700 31.370 0.000 293.190 0.001 NudgedElasticBand.py:376(GetEnergyBiasedTangent) 5259000 53.920 0.000 195.300 0.000 NudgedElasticBand.py:315(GetOneEnergy) 110400 5.930 0.000 157.200 0.001 NudgedElasticBand.py:324(GetMaximumEnergyImage) 287700 3.390 0.000 142.270 0.000 Filters.py:26(GetGeneralizedForces) 5259000 52.610 0.000 141.380 0.000 Filters.py:207(GetTotalPotentialEnergy) 287700 5.240 0.000 138.880 0.000 Filters.py:174(GetCartesianForces) 441600 5.790 0.000 135.800 0.000 NudgedElasticBand.py:330(GetMaximumEnergy) 162800 32.400 0.000 135.470 0.001 IonDynamics2.py:201(_CorrectMomenta_) 9536418 135.310 0.000 135.310 0.000 IonDynamics.py:153(_setmomenta) 441600 25.240 0.000 130.010 0.000 NudgedElasticBand.py:308(GetListOfEnergies) 194 0.020 0.000 125.690 0.648 TransisionStateEnergy.py:188(Relaxation) 9234712 120.520 0.000 120.520 0.000 __init__.py:325(ClearMemory) 2137530 96.510 0.000 96.510 0.000 Filters.py:173(_Pick_) 5259000 48.290 0.000 88.770 0.000 __init__.py:524(GetTotalPotentialEnergy) 19180 1.620 0.000 62.900 0.003 NudgedElasticBand.py:449(SetGeneralizedPositions) 95900 2.470 0.000 61.280 0.001 Filters.py:32(SetGeneralizedPositions) 95900 2.750 0.000 58.810 0.001 Filters.py:180(SetCartesianPositions) 9536418 57.780 0.000 57.780 0.000 IonDynamics.py:150(_getmomenta) 5276065 27.300 0.000 57.690 0.000 __init__.py:517(GetEnergy) 29735 1.210 0.000 57.380 0.002 ParTAD.py:141(ExchangeInformations) 34999 2.300 0.000 57.000 0.002 __init__.py:307(GetScaledPositions) 36769 1.980 0.000 56.140 0.002 __init__.py:720(__init__) 30235 45.430 0.002 55.720 0.002 ParTAD.py:87(RecieveDataFromAllWaitingSlaves) 36769 4.660 0.000 49.790 0.001 __init__.py:739(_InitFromListOfAtoms) 3456686 -122.589 -0.000 43.581 0.000 asapparallel.py:102(CalculateStresses) 34999 8.600 0.000 38.990 0.001 LinearAlgebra.py:78(solve_linear_equations) 818940 20.240 0.000 31.550 0.000 NudgedElasticBand.py:149(_length) 142682 4.130 0.000 29.050 0.000 __init__.py:333(GetUnitCell) 34999 29.050 0.001 29.050 0.001 LinearAlgebra.py:53(_fastCopyAndTranspose) 19374 8.220 0.000 28.680 0.001 NudgedElasticBand.py:436(GetGeneralizedPositions) 582 0.380 0.001 28.650 0.049 NEBSpheres.py:55(GetBall) 95900 5.810 0.000 26.350 0.000 Filters.py:175(_Make_) 776 0.780 0.001 24.110 0.031 SelectAtoms.py:18(SelectAtoms) 1464789 23.530 0.000 23.530 0.000 Numeric.py:330(dot) 194 6.510 0.034 22.410 0.116 NEBSpheres.py:13(__init__) 95900 20.540 0.000 20.540 0.000 Numeric.py:162(put) 68746 1.460 0.000 19.370 0.000 __init__.py:348(GetCoordinateBasis) 265620 5.220 0.000 13.300 0.000 NudgedElasticBand.py:284(GetOneSpringConstant) 142682 4.250 0.000 13.020 0.000 asapparallel.py:45(GetSuperCell) 6984 0.070 0.000 12.450 0.002 :0(?) 142682 2.070 0.000 11.160 0.000 __init__.py:253(initFromCpp) 280803 10.290 0.000 10.290 0.000 CommSuite.py:87(CommRecieveDataFromSlave) 323456 3.870 0.000 9.730 0.000 IonDynamics2.py:15(_dotproduct_) 4074 2.470 0.001 9.230 0.002 Numeric.py:560(compress) 142682 2.860 0.000 9.090 0.000 asapparallel.py:13(GetPeriodic) 307656 8.560 0.000 8.560 0.000 Numeric.py:229(concatenate) 33341 2.790 0.000 8.480 0.000 IonDynamics.py:102(__init__) 268764 8.100 0.000 8.100 0.000 Numeric.py:697(shape) 105911 1.840 0.000 6.780 0.000 asapparallel.py:19(GetBasis) 4074 6.580 0.002 6.760 0.002 Numeric.py:542(nonzero) 36769 1.170 0.000 6.220 0.000 __init__.py:425(SetAtomicNumbers) 776 0.110 0.000 6.000 0.008 __init__.py:528(GetEnergies) 36769 4.360 0.000 5.880 0.000 asapparallel.py:73(__init__) 776 3.320 0.004 5.860 0.008 TypesFromAtomicNumbers.py:22(GetTypes) 36769 0.650 0.000 4.840 0.000 __init__.py:356(SetPotential) 36769 2.290 0.000 4.190 0.000 asapparallel.py:42(SetPotential) 38283 0.640 0.000 4.140 0.000 __init__.py:441(GetAtomicNumbers) 388 0.330 0.001 3.770 0.010 TransisionStateEnergy.py:155(SetInterpolatedPositions) 36769 0.880 0.000 3.590 0.000 __init__.py:244(__init__) 38283 1.420 0.000 3.500 0.000 asapparallel.py:61(GetAtomicNumbers) 29735 2.280 0.000 3.190 0.000 ParTAD.py:166(ProcessData) 36769 0.560 0.000 2.900 0.000 __init__.py:152(__init__) 500 0.160 0.000 2.750 0.006 ParTAD.py:127(SpecialSetUp) 36769 0.990 0.000 2.710 0.000 asapparallel.py:25(__init__) 615368 2.380 0.000 2.380 0.000 TypesFromAtomicNumbers.py:23() 36769 0.800 0.000 2.370 0.000 asapparallel.py:58(SetAtomicNumbers) 36769 0.830 0.000 2.340 0.000 asapparallel.py:268(__init__) 1002 0.150 0.000 2.190 0.002 RW.py:44(Write) 1002 1.520 0.002 2.040 0.002 __init__.py:693(_Write) 35547 2.010 0.000 2.010 0.000 asapparallel.py:249(__del__) 29541 1.310 0.000 1.310 0.000 CommSuite.py:71(CommDoNotSendNewStateCandidate) 1000 0.580 0.001 1.260 0.001 CommSuite.py:38(CommBroadcastStateFromMasterToSlaves) 500 0.040 0.000 1.160 0.002 ParTAD.py:213(NextStateStop) 500 0.010 0.000 1.140 0.002 TransisionStateEnergy.py:30(__init__) 104997 0.980 0.000 0.980 0.000 Numeric.py:241(transpose) 179451 0.930 0.000 0.930 0.000 __init__.py:262(SetAtoms) 500 0.010 0.000 0.850 0.002 IsAnyAtomMoved.py:23(__init__) 35547 0.820 0.000 0.820 0.000 asapparallel.py:36(__del__) 142682 0.800 0.000 0.800 0.000 asapparallel.py:4(__init__) 34999 0.620 0.000 0.620 0.000 LinearAlgebra.py:24(_commonType) 2716 0.070 0.000 0.610 0.000 NEBSpheres.py:79(ConstrainSphereFilter) 2716 0.530 0.000 0.540 0.000 Filters.py:165(__init__) 1276 0.030 0.000 0.420 0.000 __init__.py:445(GetMasses) 500 0.010 0.000 0.420 0.001 IonDynamics2.py:72(__init__) 36771 0.400 0.000 0.400 0.000 __init__.py:602(GetClasses) 36769 0.230 0.000 0.400 0.000 __init__.py:319(__init__) 500 0.380 0.001 0.390 0.001 IonDynamics2.py:96(_updatevars) 34999 0.390 0.000 0.390 0.000 LinearAlgebra.py:65(_assertRank2) 776 0.030 0.000 0.390 0.001 __init__.py:313(SetScaledPositions) 500 0.010 0.000 0.370 0.001 TAD.py:374(SaveNewStateCandidate) 37502 0.360 0.000 0.360 0.000 __init__.py:454(SetMasses) 34999 0.330 0.000 0.330 0.000 LinearAlgebra.py:70(_assertSquareness) 194 0.060 0.000 0.300 0.002 TransisionStateEnergy.py:227(PrintInfo) 36682 0.280 0.000 0.280 0.000 Warning.py:40(__call__) 33341 0.280 0.000 0.280 0.000 IonDynamics.py:128(SetTimestep) 733 0.250 0.000 0.250 0.000 Translator.py:19(__call__) 36771 0.250 0.000 0.250 0.000 __init__.py:300(GetPeriodic) 194 0.040 0.000 0.240 0.001 ArrayPrinter.py:11(array2string) 194 0.000 0.000 0.240 0.001 Numeric.py:350(array_str) 500 0.020 0.000 0.220 0.000 IonDynamics2.py:174(__init__) 776 0.030 0.000 0.210 0.000 __init__.py:352(GetPeriodicBoundaries) 1657 0.210 0.000 0.210 0.000 TAD.py:356(CalculateTimeLow) 765 0.180 0.000 0.200 0.000 TransisionStateEnergy.py:215(DetermindBarrier) 2328 0.070 0.000 0.180 0.000 AtomsInArrays.py:321(_getcartesiandata) 4074 0.180 0.000 0.180 0.000 Numeric.py:145(repeat) 33191 0.130 0.000 0.130 0.000 IonDynamics.py:114(__del__) 194 0.040 0.000 0.130 0.001 ArrayPrinter.py:96(_floatFormat) 500 0.110 0.000 0.110 0.000 CommSuite.py:127(CommBarrier) 776 0.010 0.000 0.090 0.000 AtomsInArrays.py:259(__init__) 1358 0.060 0.000 0.090 0.000 ArrayPrinter.py:119() 194 0.030 0.000 0.080 0.000 CommSuite.py:53(CommSendNewStateCandidate) 500 0.070 0.000 0.070 0.000 TAD.py:364(CalculateTimeHighLimit) 500 0.070 0.000 0.070 0.000 CommSuite.py:131(StopAllSlaves) 3880 0.050 0.000 0.060 0.000 AtomsInArrays.py:352(__getattr__) 500 0.020 0.000 0.060 0.000 IonDynamics2.py:184(SetTimestep) 194 0.030 0.000 0.060 0.000 ArrayPrinter.py:135(_arrayToString) 776 0.040 0.000 0.040 0.000 AtomsInArrays.py:55(__init__) 6984 0.040 0.000 0.040 0.000 string.py:49(lower) 500 0.030 0.000 0.030 0.000 Numeric.py:129(asarray) 1358 0.030 0.000 0.030 0.000 ArrayPrinter.py:129(_digits) 1358 0.000 0.000 0.030 0.000 ArrayPrinter.py:51() 1000 0.030 0.000 0.030 0.000 IonDynamics2.py:33(__init__) 1358 0.030 0.000 0.030 0.000 ArrayPrinter.py:175(_formatFloat) 3880 0.020 0.000 0.020 0.000 AtomsInArrays.py:164(_getdata) 970 0.020 0.000 0.020 0.000 Numeric.py:536(ravel) 2716 0.010 0.000 0.010 0.000 Filters.py:162(__init__) 2 0.000 0.000 0.010 0.005 __init__.py:646(_InitializeWrite) 2 0.000 0.000 0.010 0.005 __init__.py:764(_InitializeWrite) 2 0.000 0.000 0.010 0.005 RW.py:20(__init__) 776 0.000 0.000 0.010 0.000 FakeUnitCell.py:28(GetUnitCell) 776 0.010 0.000 0.010 0.000 FakeUnitCell.py:10(__init__) 6984 0.010 0.000 0.010 0.000 SelectAtoms.py:94() 1006 0.010 0.000 0.010 0.000 RW.py:41(GetNetCDFFile) 2 0.000 0.000 0.000 0.000 posixpath.py:302(expanduser) 776 0.000 0.000 0.000 0.000 AtomsInArrays.py:149(SetPeriodicBoundaries) 1 0.000 0.000 0.000 0.000 TAD.py:449(_stoptimer) 776 0.000 0.000 0.000 0.000 AtomsInArrays.py:145(GetPeriodicBoundaries) 194 0.000 0.000 0.000 0.000 NudgedElasticBand.py:278(SetClimb) 2328 0.000 0.000 0.000 0.000 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__init__.py:462(CalculateForces) 1903040 59.870 0.000 -1442.797 -0.001 IonDynamics2.py:80(__call__) 7296858 -1840.029 -0.000 -1483.579 -0.000 asapparallel.py:99(CalculateForces) 3806080 831.463 0.000 -1502.667 -0.000 IonDynamics2.py:137(_LangevinUpdate_) 34078844 747.680 0.000 -1671.597 -0.000 asapparallel.py:39(GetNumberOfAtoms) 9197943 299.180 0.000 -2448.477 -0.000 __init__.py:374(SetCartesianPositions) 7264818 -3791.897 -0.001 -3126.887 -0.000 asapparallel.py:87(CalculateEnergy) 3456686 148.280 0.000 -3345.306 -0.001 __init__.py:472(CalculateStresses) 91430001 -5155.335 -0.000 -3403.975 -0.000 warnings.py:24(warn) 7263304 -3763.370 -0.001 -3419.390 -0.000 asapparallel.py:96(CalculateEnergies) 3456686 433.940 0.000 -3537.167 -0.001 asapparallel.py:105(CalculateStress) 3178806 1022.700 0.000 -4929.375 -0.002 IonDynamics.py:181(_CorrectMomenta) 3178806 1642.210 0.001 -6194.780 -0.002 IonDynamics.py:142(_VerletUpdate) 7262766 284.200 0.000 -6298.348 -0.001 __init__.py:466(CalculateEnergies) 7/1 0.000 0.000 -9070.652 -9070.652 :1(?) 1 0.000 0.000 -9070.652 -9070.652 profile:0(ParTAD.MakeParallelSimulation(500)) 1 0.160 0.160 -9070.652 -9070.652 TAD.py:83(MakeSimulation) 1 0.000 0.000 -9070.652 -9070.652 ParTAD.py:42(MakeParallelSimulation) 3806080 82.380 0.000 -10856.205 -0.003 __init__.py:485(CalculateEnergiesAndForces) 34107 62.580 0.002 -11061.575 -0.324 IonDynamics.py:123(__call__) 500 1.620 0.003 -11132.882 -22.266 TAD.py:162(NextState) 17867138 -13561.394 -0.001 -12727.364 -0.001 __init__.py:498(GetCartesianForces) 31001 12.840 0.000 -12728.615 -0.411 IsAnyAtomMoved.py:39(IsAnyAtomMoved) 31977 27.640 0.001 -13408.555 -0.419 IsAnyAtomMoved.py:108(MovedLength) 9967278 112.750 0.000 -14119.566 -0.001 __init__.py:509(GetGeneralizedForces) 29735 58.110 0.002 -15390.352 -0.518 TAD.py:258(EvolveSystem) >>>