From b2e6863d937b7e902746b554e5227f3a046cee04 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer <akohlmey@gmail.com> Date: Fri, 15 Jun 2018 17:01:26 -0400 Subject: [PATCH] add reference log file. --- .../USER/misc/pair_entropy/log.pairentropy | 316 ++++++++++++++++++ 1 file changed, 316 insertions(+) create mode 100644 examples/USER/misc/pair_entropy/log.pairentropy diff --git a/examples/USER/misc/pair_entropy/log.pairentropy b/examples/USER/misc/pair_entropy/log.pairentropy new file mode 100644 index 0000000000..21474639af --- /dev/null +++ b/examples/USER/misc/pair_entropy/log.pairentropy @@ -0,0 +1,316 @@ +LAMMPS (30 Mar 2018) + using 1 OpenMP thread(s) per MPI task +echo both + +units metal +atom_style full + +read_data data.interface + triclinic box = (0 0 0) to (138.4 34.57 34.57) with tilt (0 0 0) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 4096 atoms + reading velocities ... + 4096 velocities + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +mass 1 22.98977 + +neigh_modify delay 10 every 1 +pair_style eam/fs +pair_coeff * * Na_MendelevM_2014.eam.fs Na +timestep 0.002 +thermo 500 + +neighbor 4. bin + +# Define computes +# Global density, no average +compute 1 all pentropy/atom 0.25 7.75 +# Local density, no average +compute 2 all pentropy/atom 0.25 7.75 local yes +# Global density, average over neighbors +compute 3 all pentropy/atom 0.25 7.75 avg yes 5. +# Local density, average over neighbors +compute 4 all pentropy/atom 0.25 7.75 avg yes 5. local yes + +dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4 + + +fix 1 all nph x 1. 1. 10. +fix 2 all temp/csvr 350. 350. 0.1 64582 + +run 100000 +WARNING: More than one compute pentropy/atom (../compute_pentropy_atom.cpp:138) +WARNING: More than one compute pentropy/atom (../compute_pentropy_atom.cpp:138) +WARNING: More than one compute pentropy/atom (../compute_pentropy_atom.cpp:138) +WARNING: More than one compute pentropy/atom (../compute_pentropy_atom.cpp:138) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.2 + ghost atom cutoff = 13.2 + binsize = 6.6, bins = 21 6 6 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair eam/fs, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard + (2) compute pentropy/atom, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (3) compute pentropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none + (4) compute pentropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none + (5) compute pentropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 25.68 | 25.69 | 25.69 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75 + 500 359.33758 -4285.247 0 -4095.0423 471.98587 165847.18 + 1000 348.99659 -4276.2274 0 -4091.4964 149.27188 166966.18 + 1500 341.56622 -4278.7772 0 -4097.9793 -296.95842 168025.4 + 2000 342.09406 -4277.6906 0 -4096.6132 -438.11647 168413.94 + 2500 352.25274 -4275.2717 0 -4088.8172 -330.50608 168120.05 + 3000 350.51318 -4282.4462 0 -4096.9125 -120.66318 167436.33 + 3500 353.70665 -4282.2946 0 -4095.0705 203.76807 166696.51 + 4000 349.96779 -4287.1098 0 -4101.8647 256.9956 166337.2 + 4500 343.72356 -4285.8089 0 -4103.869 206.49403 166407.34 + 5000 352.6139 -4287.1902 0 -4100.5445 81.796762 166694.74 + 5500 347.36366 -4287.0285 0 -4103.1618 -42.768886 167038.64 + 6000 350.3976 -4290.0332 0 -4104.5607 -133.74621 167194.61 + 6500 357.56345 -4286.2623 0 -4096.9967 -11.542553 167113.93 + 7000 355.32488 -4287.3852 0 -4099.3045 45.672669 166919.78 + 7500 347.11842 -4290.6564 0 -4106.9196 28.644843 166818.56 + 8000 352.57322 -4289.7964 0 -4103.1722 18.522414 166836.67 + 8500 354.8297 -4293.8761 0 -4106.0575 -42.234561 166867.25 + 9000 349.62065 -4298.6714 0 -4113.61 -92.546785 166824.11 + 9500 349.33305 -4300.1874 0 -4115.2784 -4.988033 166653.27 + 10000 351.2575 -4295.7452 0 -4109.8175 141.2923 166425.91 + 10500 352.35614 -4302.4997 0 -4115.9904 96.025177 166301.54 + 11000 345.79485 -4304.9271 0 -4121.8908 6.6400444 166310.83 + 11500 349.20236 -4307.0045 0 -4122.1646 25.603816 166291.49 + 12000 354.36642 -4304.3937 0 -4116.8204 43.401924 166335.86 + 12500 343.7124 -4302.9267 0 -4120.9928 -5.23105 166523.78 + 13000 363.53804 -4303.9652 0 -4111.5371 -17.241844 166690.48 + 13500 356.23025 -4304.3329 0 -4115.773 -121.76358 166814.59 + 14000 347.55 -4306.8848 0 -4122.9195 -174.52441 166791.16 + 14500 345.85547 -4309.3314 0 -4126.2631 -43.958619 166461.73 + 15000 350.84805 -4310.3616 0 -4124.6506 118.60917 165964.43 + 15500 349.59675 -4320.2537 0 -4135.2051 143.5776 165581.16 + 16000 349.05247 -4310.2702 0 -4125.5096 299.15489 165512.52 + 16500 357.63567 -4318.1626 0 -4128.8588 70.60951 165914.49 + 17000 352.29836 -4313.8988 0 -4127.4202 -116.44882 166435.75 + 17500 350.49924 -4315.0109 0 -4129.4846 -248.88877 166746.88 + 18000 352.05592 -4314.5162 0 -4128.1659 -164.78373 166635.14 + 18500 348.83853 -4316.1558 0 -4131.5085 -84.641318 166256.38 + 19000 352.52592 -4309.9888 0 -4123.3897 190.51243 165908.63 + 19500 346.13457 -4317.9779 0 -4134.7618 44.213931 165816.35 + 20000 340.17775 -4314.0744 0 -4134.0114 64.495233 165894.74 + 20500 354.06551 -4316.181 0 -4128.7669 -1.4490795 166094.86 + 21000 344.8874 -4316.8088 0 -4134.2529 -118.9424 166286.09 + 21500 354.15586 -4317.3745 0 -4129.9126 -104.15677 166331.42 + 22000 345.8013 -4317.8175 0 -4134.7778 -80.729172 166262.57 + 22500 349.11462 -4323.1371 0 -4138.3436 -107.29158 166095.83 + 23000 343.99139 -4319.5125 0 -4137.4309 71.487855 165825.41 + 23500 349.80225 -4324.909 0 -4139.7516 34.440631 165638.23 + 24000 348.65063 -4325.2073 0 -4140.6594 53.656181 165646.33 + 24500 356.4067 -4331.0609 0 -4142.4076 -53.238796 165745.71 + 25000 349.90889 -4325.3671 0 -4140.1532 7.5156313 165867.84 + 25500 348.55479 -4335.2096 0 -4150.7124 -154.7789 165856.27 + 26000 346.09492 -4332.421 0 -4149.2259 -50.232622 165660.79 + 26500 344.75355 -4334.4345 0 -4151.9494 54.441512 165388.22 + 27000 346.01888 -4340.9678 0 -4157.813 77.590267 165122.38 + 27500 350.13903 -4338.2832 0 -4152.9475 134.25294 165063.15 + 28000 349.4507 -4336.2772 0 -4151.3059 120.90268 165197.05 + 28500 349.89188 -4337.2205 0 -4152.0156 -7.4448137 165466.05 + 29000 352.06855 -4336.4999 0 -4150.1429 -72.487845 165711.12 + 29500 348.70134 -4335.081 0 -4150.5063 -122.13386 165799.73 + 30000 349.80677 -4341.2595 0 -4156.0997 -177.94864 165698.03 + 30500 347.84982 -4339.92 0 -4155.796 -11.150253 165358.49 + 31000 350.8215 -4337.9393 0 -4152.2423 169.74393 164968.86 + 31500 350.71421 -4340.8771 0 -4155.2369 221.49124 164741.67 + 32000 349.9693 -4342.8528 0 -4157.6069 171.42476 164849.23 + 32500 352.56459 -4340.4746 0 -4153.855 50.564424 165207.87 + 33000 348.20348 -4340.6347 0 -4156.3235 -142.44617 165619.29 + 33500 345.52103 -4341.0103 0 -4158.119 -239.73388 165867.73 + 34000 340.18612 -4339.2415 0 -4159.1741 -229.24652 165814.16 + 34500 346.29644 -4342.3771 0 -4159.0754 -66.184467 165447.7 + 35000 348.41012 -4339.9899 0 -4155.5693 116.11721 165057.16 + 35500 349.8102 -4342.6138 0 -4157.4521 162.46419 164869.8 + 36000 345.12148 -4342.1816 0 -4159.5018 93.299897 164971.27 + 36500 350.1662 -4340.7476 0 -4155.3975 17.1695 165283.86 + 37000 345.02071 -4333.5625 0 -4150.9361 -19.777882 165591.43 + 37500 351.61529 -4339.4316 0 -4153.3145 -163.6161 165720.09 + 38000 351.12679 -4334.814 0 -4148.9555 -41.24883 165586.63 + 38500 357.46153 -4338.5489 0 -4149.3373 48.449588 165358.68 + 39000 354.37011 -4343.9595 0 -4156.3842 24.197319 165158.97 + 39500 344.87813 -4340.2123 0 -4157.6613 45.305702 165085.33 + 40000 357.02868 -4344.263 0 -4155.2805 38.581773 165138.93 + 40500 356.49851 -4340.4739 0 -4151.772 43.25324 165302.5 + 41000 355.84229 -4342.0156 0 -4153.661 -84.423576 165491.7 + 41500 345.13117 -4338.685 0 -4156.0001 -103.00745 165528 + 42000 346.53963 -4336.6348 0 -4153.2044 -13.071264 165436.39 + 42500 351.00431 -4335.7733 0 -4149.9796 68.464006 165317.65 + 43000 355.65919 -4342.096 0 -4153.8384 -5.7513562 165240.95 + 43500 346.67881 -4340.4327 0 -4156.9286 27.104052 165178.78 + 44000 344.93607 -4341.5588 0 -4158.9771 29.983072 165226.93 + 44500 344.96898 -4344.4191 0 -4161.82 -63.544956 165331.7 + 45000 355.79519 -4340.2996 0 -4151.97 -5.5354943 165421.38 + 45500 354.21428 -4340.4899 0 -4152.9971 -45.808519 165514.22 + 46000 347.90456 -4337.7045 0 -4153.5516 -70.472446 165549.25 + 46500 342.30611 -4339.8561 0 -4158.6665 -89.138875 165515.54 + 47000 349.18619 -4339.6708 0 -4154.8395 -22.391799 165392.52 + 47500 355.54068 -4340.9861 0 -4152.7912 48.059812 165261.21 + 48000 349.85193 -4341.0492 0 -4155.8655 10.4874 165233.41 + 48500 350.48062 -4340.3555 0 -4154.839 34.514274 165241.37 + 49000 350.22062 -4337.3446 0 -4151.9657 66.516852 165234.86 + 49500 353.48854 -4342.606 0 -4155.4973 18.178574 165232.42 + 50000 355.4353 -4340.503 0 -4152.3639 82.642485 165242.94 + 50500 356.03755 -4337.8136 0 -4149.3557 79.237302 165308.35 + 51000 348.26583 -4338.9903 0 -4154.6461 23.965877 165360.09 + 51500 353.84885 -4342.682 0 -4155.3826 -65.297839 165421.25 + 52000 348.38906 -4335.7957 0 -4151.3863 -16.337804 165488.67 + 52500 348.33732 -4340.4442 0 -4156.0621 -71.786085 165459.21 + 53000 351.36882 -4340.8694 0 -4154.8828 -11.818052 165334.01 + 53500 349.66487 -4340.899 0 -4155.8143 64.774989 165157.06 + 54000 354.52673 -4341.5591 0 -4153.9009 103.84648 165043.7 + 54500 347.97543 -4341.7648 0 -4157.5743 60.697135 165103.56 + 55000 349.7801 -4341.6796 0 -4156.5339 3.186648 165284.19 + 55500 349.90814 -4337.5213 0 -4152.3079 -15.40375 165470.58 + 56000 350.89011 -4341.7859 0 -4156.0527 -101.06113 165536.95 + 56500 338.10783 -4336.0802 0 -4157.1129 0.46390075 165365.62 + 57000 355.8832 -4336.8791 0 -4148.5029 163.76227 165095.76 + 57500 343.20161 -4337.579 0 -4155.9154 173.89034 164877.3 + 58000 347.30883 -4338.8572 0 -4155.0196 196.75267 164858.65 + 58500 347.11195 -4338.1293 0 -4154.3959 107.96277 165100.21 + 59000 356.20588 -4336.869 0 -4148.322 32.98048 165438.3 + 59500 352.20196 -4340.4404 0 -4154.0127 -147.74801 165733.29 + 60000 348.50087 -4338.2613 0 -4153.7927 -201.37766 165872.68 + 60500 350.83512 -4338.2378 0 -4152.5337 -157.3473 165788.59 + 61000 358.06869 -4336.2653 0 -4146.7323 49.66101 165406.04 + 61500 351.59222 -4342.9905 0 -4156.8856 123.56829 164946.67 + 62000 357.85029 -4342.5571 0 -4153.1396 272.18018 164672.22 + 62500 353.07998 -4345.1721 0 -4158.2797 182.18366 164762.57 + 63000 350.29241 -4336.295 0 -4150.8781 96.838396 165199.84 + 63500 351.93686 -4344.5516 0 -4158.2643 -231.395 165711.73 + 64000 351.23761 -4338.6588 0 -4152.7416 -237.8481 165989.41 + 64500 347.96971 -4335.4865 0 -4151.299 -189.76455 165932.6 + 65000 354.37539 -4337.2906 0 -4149.7125 -43.526372 165522.64 + 65500 357.5777 -4346.4633 0 -4157.1902 81.72156 165007.06 + 66000 354.14242 -4345.6382 0 -4158.1834 195.69703 164658.89 + 66500 349.96045 -4338.6632 0 -4153.422 257.21076 164693.92 + 67000 347.83399 -4342.9995 0 -4158.8839 39.429532 165109.39 + 67500 349.19688 -4339.7486 0 -4154.9116 -70.657587 165534.67 + 68000 345.04999 -4335.0979 0 -4152.456 -178.5504 165788.23 + 68500 352.27772 -4337.4216 0 -4150.9539 -159.95859 165787.12 + 69000 352.83425 -4340.4687 0 -4153.7064 -93.500881 165526.1 + 69500 347.74369 -4339.3835 0 -4155.3157 84.591777 165119.47 + 70000 352.65319 -4339.132 0 -4152.4655 214.03749 164904.63 + 70500 349.83427 -4340.3861 0 -4155.2117 123.57829 165013.52 + 71000 348.51668 -4344.6661 0 -4160.1891 -33.962211 165235.42 + 71500 345.71481 -4339.4514 0 -4156.4576 -73.059935 165447.89 + 72000 354.93417 -4341.68 0 -4153.8061 -94.767012 165533.4 + 72500 342.42761 -4341.9235 0 -4160.6696 -129.2131 165509.21 + 73000 349.91799 -4336.9832 0 -4151.7645 14.219496 165403.37 + 73500 344.75733 -4339.5268 0 -4157.0398 18.088244 165274.21 + 74000 353.01313 -4335.8263 0 -4148.9693 165.34097 165149.7 + 74500 353.70264 -4340.5322 0 -4153.3102 55.785855 165128.92 + 75000 355.60934 -4337.9827 0 -4149.7514 103.87392 165190.99 + 75500 349.91446 -4339.5314 0 -4154.3146 -9.8601217 165344.74 + 76000 343.95016 -4344.3242 0 -4162.2644 -180.90986 165482.68 + 76500 348.77873 -4339.8225 0 -4155.2069 -82.808012 165511.02 + 77000 346.21282 -4336.4572 0 -4153.1998 7.4507551 165423.52 + 77500 355.35737 -4339.7581 0 -4151.6602 16.915858 165319.8 + 78000 351.13843 -4339.5992 0 -4153.7345 25.286516 165279.14 + 78500 349.57827 -4338.7768 0 -4153.738 13.676393 165287.51 + 79000 350.44899 -4341.8942 0 -4156.3945 -35.020193 165301.74 + 79500 345.50828 -4338.3401 0 -4155.4555 12.691593 165316.89 + 80000 349.19427 -4341.8139 0 -4156.9783 -60.176128 165350.63 + 80500 347.23088 -4340.8887 0 -4157.0923 -8.1510933 165352.41 + 81000 350.69564 -4338.1451 0 -4152.5148 63.352509 165336.37 + 81500 353.51603 -4341.4634 0 -4154.3402 18.963339 165273.49 + 82000 357.99109 -4339.5813 0 -4150.0894 111.83287 165142.45 + 82500 348.95721 -4339.3975 0 -4154.6873 133.99884 165049.94 + 83000 348.40851 -4341.4694 0 -4157.0497 99.552375 165079.83 + 83500 351.56311 -4340.478 0 -4154.3885 43.625398 165236.42 + 84000 350.94582 -4342.5887 0 -4156.826 -61.009621 165425.36 + 84500 348.85285 -4340.2908 0 -4155.6359 -121.20155 165518.82 + 85000 350.93338 -4338.5274 0 -4152.7712 -24.578168 165453.02 + 85500 350.05705 -4341.015 0 -4155.7227 44.257207 165274.03 + 86000 354.23801 -4340.9418 0 -4153.4364 95.178264 165077.53 + 86500 361.17307 -4345.1753 0 -4153.9991 161.19621 164939.38 + 87000 350.69942 -4342.2517 0 -4156.6193 132.57345 164951.93 + 87500 351.46682 -4338.9653 0 -4152.9268 83.174091 165203.95 + 88000 345.03368 -4341.8378 0 -4159.2045 -169.97976 165616.84 + 88500 351.70033 -4339.5377 0 -4153.3755 -203.97263 165858.93 + 89000 355.54446 -4339.2207 0 -4151.0238 -123.1241 165752.79 + 89500 350.31818 -4334.7628 0 -4149.3323 77.462164 165324.49 + 90000 351.20604 -4343.5238 0 -4157.6233 133.64807 164890.85 + 90500 348.0003 -4348.9685 0 -4164.7649 118.91427 164657.96 + 91000 347.21483 -4342.3391 0 -4158.5512 226.41338 164732.47 + 91500 347.27277 -4342.6341 0 -4158.8156 10.500178 165159.97 + 92000 344.50771 -4340.5474 0 -4158.1925 -199.65031 165723.91 + 92500 349.4828 -4342.4558 0 -4157.4674 -334.92794 166050.96 + 93000 349.90926 -4338.4776 0 -4153.2635 -265.95682 165968.52 + 93500 343.01305 -4340.5317 0 -4158.968 -100.92764 165495.12 + 94000 347.78156 -4341.2655 0 -4157.1777 146.28391 164933.04 + 94500 353.69177 -4341.067 0 -4153.8507 304.79658 164618.69 + 95000 346.04459 -4345.6353 0 -4162.4669 171.92493 164732.34 + 95500 347.79068 -4338.9943 0 -4154.9017 76.774034 165167.7 + 96000 344.56458 -4340.0235 0 -4157.6384 -160.40807 165608.59 + 96500 340.37553 -4342.8492 0 -4162.6815 -276.60876 165807.48 + 97000 347.18941 -4341.2676 0 -4157.4932 -178.69421 165633 + 97500 349.64071 -4340.366 0 -4155.2941 41.608903 165242.92 + 98000 349.52995 -4342.5772 0 -4157.5639 173.81028 164884.94 + 98500 350.04404 -4338.4153 0 -4153.1299 265.77826 164754.57 + 99000 345.61445 -4341.8018 0 -4158.861 130.70276 164941.11 + 99500 353.39327 -4337.2886 0 -4150.2304 79.630342 165241.58 + 100000 349.21591 -4340.4937 0 -4155.6466 -98.981878 165526.52 +Loop time of 333.54 on 4 procs for 100000 steps with 4096 atoms + +Performance: 51.808 ns/day, 0.463 hours/ns, 299.814 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 262.06 | 266.81 | 271.72 | 26.0 | 79.99 +Bond | 0.0072134 | 0.010317 | 0.013051 | 2.4 | 0.00 +Neigh | 33.331 | 33.927 | 34.4 | 7.3 | 10.17 +Comm | 7.4881 | 11.613 | 16.368 | 106.5 | 3.48 +Output | 12.849 | 12.854 | 12.867 | 0.2 | 3.85 +Modify | 6.3196 | 7.428 | 9.0238 | 42.1 | 2.23 +Other | | 0.8935 | | | 0.27 + +Nlocal: 1024 ave 1029 max 1016 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 4741.75 ave 4759 max 4706 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 124070 ave 125011 max 122645 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +FullNghs: 248139 ave 250140 max 245351 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 992556 +Ave neighs/atom = 242.323 +Ave special neighs/atom = 0 +Neighbor list builds = 1222 +Dangerous builds = 0 + +Total wall time: 0:05:33 -- GitLab