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lammps/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1
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log.swm4-ndp.nh.8Jul15.linux.1
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LAMMPS (8 Jul 2015)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3
read_data data.swm4-ndp
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
2500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
2000 bonds
reading angles ...
500 angles
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
pair_coeff * 2* 0.000000 0.0
group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES
variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
fix DRUDE all drude C N N D
velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345
delete_bonds ATOMS multi
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 14
2000 total bonds, 500 turned on, 1500 turned off
500 total angles, 0 turned on, 500 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
comm_modify vel yes
compute TATOM ATOMS temp/com
compute TEMP all temp/drude
fix DTDIR all drude/transform/direct
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
500 rigid bodies with 2000 atoms
0.832099 = max distance from body owner to body atom
fix_modify RIGID temp TATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395)
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
fix NVT DRUDES nvt temp 1 1 100.0
fix DTINV all drude/transform/inverse
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20
run 2000
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 24.8361 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
20 1.5779378 3742.6839 5338.7884 -1596.1045 567.30749 0 662.23765 155098.36 -157924.01 31679.424 13979.574 1194.8318 1690.2246 201.65659
40 3.2595179 2752.8331 4407.7651 -1654.932 793.00135 0 870.33079 154593.76 -157912.03 27394.571 14278.56 986.46688 1450.7477 55.932382
60 4.9160559 1995.591 3982.0372 -1986.4462 660.67737 0 750.60932 154536.67 -157934.4 22230.527 14691.401 891.1881 1315.7324 40.317107
80 6.5368109 1376.4607 3451.5429 -2075.0822 617.73899 0 606.3673 154625.69 -157924.88 17342.36 15201.343 772.46238 1147.1933 21.455584
100 8.1206679 885.61474 3037.6308 -2152.0161 536.23281 0 448.92334 154793.04 -157930.22 13263.15 15783.251 679.82802 1011.6854 14.7536
120 9.6622779 487.58833 2926.9844 -2439.396 534.45257 0 332.92672 154624.58 -157931.35 8680.1072 16409.225 655.06511 977.0118 9.8615914
140 11.151044 159.92993 2531.0941 -2371.1641 507.26614 0 248.61605 154802.7 -157929.75 6399.7614 17052.819 566.46405 845.55948 7.1402545
160 12.594065 -100.92554 2408.1685 -2509.0941 490.99513 0 134.36067 154800.59 -157935.04 3836.8939 17698.15 538.95306 805.19219 5.3968881
180 13.99897 -313.40437 2221.7416 -2535.1459 469.97779 0 75.805558 154853.24 -157934.17 1959.0151 18334.826 497.23032 743.14066 4.4151864
200 15.366489 -490.94535 2067.2605 -2558.2059 455.16264 0 77.545085 154841.14 -157932.06 1193.2843 18956.449 462.65715 691.7234 3.5993432
220 16.600555 -642.90899 1962.7268 -2605.6358 481.409 0 64.82886 154779.27 -157931.14 257.97318 19559.017 439.26229 657.06726 2.7738353
240 17.905356 -770.44499 1795.759 -2566.204 467.25833 0 68.82314 154829.98 -157932.26 19.366424 20139.417 401.89456 601.24562 2.3886434
260 19.179106 -878.63388 1752.9497 -2631.5836 476.38325 0 71.933328 154747.16 -157927.06 -779.27927 20696.165 392.31375 587.06527 2.0260796
280 20.338816 -971.86313 1649.5511 -2621.4143 473.83718 0 58.460942 154779.6 -157933.32 -1008.6839 21226.44 369.17293 552.5314 1.7176302
300 21.569212 -1057.5245 1580.9766 -2638.5012 480.33124 0 92.042617 154721.84 -157932.72 -1273.0871 21728.981 353.82581 529.63244 1.5049172
320 22.749114 -1132.8131 1507.0527 -2639.8658 477.51281 0 107.39942 154707.48 -157932.26 -1098.1682 22203.702 337.28149 504.90539 1.3591193
340 23.866651 -1199.4814 1495.1233 -2694.6047 479.99745 0 106.51864 154656.08 -157937.2 -1429.2857 22652.428 334.61166 500.95977 1.2462004
360 25.082959 -1264.8469 1440.8985 -2705.7454 491.71868 0 107.29672 154624.8 -157929.57 -1584.3973 23073.056 322.47604 482.79111 1.2009575
380 26.115491 -1323.6479 1376.047 -2699.695 497.4857 0 130.64748 154603.75 -157931.58 -1822.0261 23465.375 307.96215 461.10877 1.0530068
400 27.098619 -1373.3921 1374.977 -2748.3691 504.29487 0 124.46131 154555.55 -157932.67 -2021.5919 23828.229 307.72267 460.78429 0.98399317
420 28.070089 -1426.0355 1375.3813 -2801.4168 515.478 0 142.00079 154473.71 -157932.61 -2208.8244 24160.02 307.81316 460.97813 0.86759754
440 29.088747 -1476.2448 1329.2669 -2805.5117 535.72651 0 196.6858 154393.5 -157931.42 -1618.3009 24460.675 297.49266 445.47247 0.93805929
460 30.039555 -1527.7744 1320.4118 -2848.1861 568.66085 0 263.35802 154252.43 -157932.64 -1494.5444 24734.828 295.51087 442.54962 0.84234766
480 30.98472 -1576.2009 1300.9323 -2877.1332 594.86236 0 314.31593 154144.87 -157931.19 -1089.6762 24985.934 291.15132 436.02273 0.82622001
500 31.921181 -1626.4788 1317.6697 -2944.1486 623.62396 0 334.61944 154026.32 -157928.71 -1168.0859 25218.234 294.89719 441.63818 0.82542904
520 32.850868 -1678.487 1262.6568 -2941.1438 633.47682 0 363.44379 153992.91 -157930.98 -1163.3304 25431.978 282.58518 423.21273 0.76490406
540 33.831238 -1726.1374 1271.5003 -2997.6376 640.74261 0 345.52688 153948.98 -157932.89 -1537.3705 25626.826 284.56437 426.19842 0.72713952
560 34.751061 -1771.2597 1269.233 -3040.4927 644.30805 0 317.8435 153929.28 -157931.92 -1722.5181 25799.253 284.05695 425.41542 0.77189915
580 35.665466 -1815.0265 1246.413 -3061.4395 683.24088 0 371.72686 153815.69 -157932.1 -1494.5382 25947.498 278.94979 417.73291 0.82565978
600 36.573731 -1858.3541 1196.3137 -3054.6678 696.06741 0 437.52527 153744.09 -157932.35 -954.95797 26075.526 267.73745 400.95599 0.76490653
620 37.479106 -1899.6548 1179.8195 -3079.4743 696.68256 0 400.17078 153755.86 -157932.18 -1545.546 26187.542 264.04602 395.42296 0.76404516
640 38.439799 -1936.5953 1175.0129 -3111.6082 690.67817 0 392.53009 153736.67 -157931.49 -1651.1722 26278.598 262.97029 393.82361 0.73771389
660 39.342719 -1974.4946 1176.582 -3151.0766 687.10898 0 368.78109 153725.56 -157932.53 -1642.1352 26346.954 263.32147 394.35652 0.72471807
680 40.233007 -2011.9427 1170.7634 -3182.7062 704.7553 0 376.83243 153670.03 -157934.32 -1891.1355 26391.697 262.01926 392.39338 0.74699214
700 41.124436 -2051.0351 1135.0688 -3186.1039 725.49013 0 408.02789 153612.64 -157932.26 -1554.558 26411.443 254.03072 380.39243 0.79925352
720 42.014817 -2087.2728 1127.2712 -3214.544 747.73788 0 483.80639 153486.98 -157933.07 -1246.9189 26409.313 252.28561 377.77086 0.81053421
740 42.908141 -2122.8783 1145.0602 -3267.9385 791.69089 0 545.96341 153327.46 -157933.05 -1064.8488 26390.224 256.26683 383.71741 0.85313379
760 43.799068 -2155.8658 1189.0654 -3344.9312 789.63603 0 492.27945 153309.89 -157936.74 -1502.4138 26356.52 266.11528 398.4847 0.84422302
780 44.690825 -2197.1759 1166.0016 -3363.1774 813.89866 0 521.14986 153239.56 -157937.79 -1316.1431 26304.488 260.95354 390.75511 0.82849551
800 45.65434 -2236.6034 1147.1342 -3383.7376 858.77647 0 581.50775 153111.46 -157935.49 -1059.9568 26235.547 256.73099 384.3699 0.93971538
820 46.655089 -2273.5686 1128.3309 -3401.8996 876.66305 0 635.8842 153020.42 -157934.87 -522.03009 26154.47 252.52277 378.09253 0.87820184
840 47.581215 -2310.5392 1107.1453 -3417.6845 906.73 0 663.59923 152946.29 -157934.31 -660.73299 26066.561 247.78139 370.96848 0.9116362
860 48.461532 -2342.7319 1130.0857 -3472.8176 942.10066 0 680.8635 152839.09 -157934.87 -541.95751 25971.767 252.91551 378.61448 1.0117334
880 49.348792 -2377.0856 1100.1359 -3477.2215 941.37588 0 700.77054 152814.73 -157934.1 -443.18233 25871.504 246.21267 368.56741 1.0107473
900 50.240716 -2408.6694 1120.4615 -3529.131 953.77939 0 683.49952 152768.93 -157935.34 -805.27426 25765.603 250.76159 375.35036 1.0825367
920 51.130132 -2442.8312 1111.7289 -3554.56 950.77289 0 674.01395 152754.6 -157933.95 -905.29746 25651.192 248.80721 372.46424 0.9955159
940 52.02236 -2475.7651 1083.1001 -3558.8652 929.08218 0 652.94438 152792.16 -157933.05 -788.57962 25527.175 242.40003 362.8243 1.0666862
960 52.924057 -2508.9913 1065.8755 -3574.8668 958.92048 0 698.81111 152699.64 -157932.24 -628.47136 25394.225 238.54512 356.97396 1.2103698
980 53.828788 -2536.4577 1080.5323 -3616.99 965.47688 0 709.51639 152642.64 -157934.62 -711.96055 25254.689 241.82535 361.89287 1.2066617
1000 54.736123 -2567.3495 1049.6524 -3617.0019 961.00327 0 711.26219 152645.74 -157935.01 -767.44539 25108.887 234.91437 351.52221 1.2288643
1020 55.707224 -2595.1206 1073.4918 -3668.6124 974.79134 0 682.20149 152609.52 -157935.12 -1086.5823 24955.503 240.24966 359.53972 1.1890491
1040 56.677394 -2626.5258 1072.5969 -3699.1227 1013.3934 0 711.73335 152511.92 -157936.17 -993.59976 24792.452 240.04939 359.23966 1.1887504
1060 57.582305 -2655.4118 1059.0687 -3714.4806 1011.7018 0 747.43846 152460.24 -157933.86 -555.51961 24621.133 237.02176 354.6316 1.3280226
1080 58.451085 -2684.3286 1093.9034 -3778.232 1041.5624 0 765.98574 152348.29 -157934.07 -993.29607 24444.559 244.81782 366.39031 1.183205
1100 59.320593 -2716.1558 1073.5935 -3789.7493 1046.6309 0 741.4524 152358.32 -157936.15 -1031.9439 24260.537 240.27243 359.559 1.2187426
1120 60.197434 -2748.4358 1043.9493 -3792.3851 1050.7685 0 732.61894 152361.65 -157937.42 -1173.2273 24068.431 233.638 349.62448 1.1977845
1140 61.088693 -2777.1545 1036.6106 -3813.7651 1060.884 0 757.21086 152307.36 -157939.22 -1043.4335 23867.228 231.99557 347.17994 1.1628589
1160 62.010573 -2805.5456 1027.0164 -3832.5621 1057.9262 0 777.84714 152269.56 -157937.89 -729.25379 23659.194 229.84839 343.97766 1.1301417
1180 62.973114 -2832.7144 1030.8608 -3863.5752 1084.2376 0 767.80175 152221.94 -157937.56 -1365.8515 23446.354 230.70875 345.24169 1.1814637
1200 63.943778 -2860.0062 1032.0824 -3892.0886 1078.2587 0 781.38106 152185.86 -157937.59 -1050.1069 23225.033 230.98216 345.65138 1.1817665
1220 64.923382 -2887.3006 1026.4756 -3913.7762 1073.1543 0 809.51178 152141.13 -157937.57 -956.1976 22997.996 229.72734 343.81693 1.0887098
1240 65.912183 -2912.0696 1020.0729 -3932.1425 1095.3889 0 826.297 152085.57 -157939.4 -534.84968 22767.897 228.2944 341.63565 1.15531
1260 66.908861 -2938.0025 1009.7902 -3947.7927 1120.1948 0 846.76965 152025.28 -157940.04 -581.84084 22538.229 225.99312 338.22714 1.0731061
1280 67.970707 -2960.3724 1046.6347 -4007.0071 1144.3297 0 866.43256 151921.62 -157939.39 -368.35961 22310.088 234.239 350.59018 1.0681573
1300 68.984941 -2983.8905 1039.0599 -4022.9504 1162.4788 0 878.40157 151876.66 -157940.49 -408.4644 22085.613 232.54373 348.07145 1.0232144
1320 70.043952 -3009.5808 969.8918 -3979.4726 1186.5907 0 935.08613 151836.22 -157937.36 431.8242 21865.457 217.06378 324.88371 0.98977725
1340 71.117119 -3028.1057 1016.1027 -4044.2084 1215.7197 0 933.65661 151744.63 -157938.22 -118.90908 21653.612 227.40587 340.39676 0.96927182
1360 72.19871 -3048.8293 986.21586 -4035.0452 1231.0917 0 974.10814 151697.47 -157937.72 485.3122 21448.458 220.71713 330.39668 0.91660237
1380 73.289545 -3067.6975 1046.3647 -4114.0622 1252.358 0 948.20869 151626.66 -157941.29 -131.77945 21251.912 234.17856 350.55699 0.95332826
1400 74.389534 -3091.6437 1003.804 -4095.4478 1223.2343 0 914.21639 151708.69 -157941.59 -228.59592 21060.319 224.6534 336.27611 0.95868112
1420 75.496459 -3117.9845 1017.2871 -4135.2716 1252.8701 0 934.95412 151617.13 -157940.22 -328.62774 20872.161 227.67095 340.80959 0.93833238
1440 76.611495 -3137.2342 990.73612 -4127.9703 1224.5861 0 925.81135 151661.05 -157939.42 -23.294916 20687.614 221.72878 331.93708 0.86871384
1460 77.73649 -3159.4947 1040.535 -4200.0297 1218.936 0 881.92261 151636.87 -157937.75 -581.29505 20507.346 232.87387 348.59778 0.96029886
1480 78.872562 -3183.8273 1037.9432 -4221.7705 1246.5207 0 908.21966 151561.59 -157938.1 -884.42345 20328.04 232.29381 347.7323 0.95226246
1500 80.110645 -3206.5826 1008.5663 -4215.1489 1236.8936 0 929.15034 151558.28 -157939.47 -91.502556 20149.349 225.7192 337.88949 0.92718943
1520 81.168804 -3228.1152 994.3422 -4222.4574 1276.2214 0 948.25706 151492.45 -157939.39 -262.49453 19974.554 222.53583 333.16141 0.83959152
1540 82.328931 -3248.9878 997.70762 -4246.6954 1273.2453 0 944.04689 151475.31 -157939.3 -310.12487 19802.717 223.28901 334.28865 0.84316615
1560 83.500822 -3268.9264 1001.6639 -4270.5903 1283.2174 0 972.25539 151413.47 -157939.53 -368.92162 19633.499 224.17444 335.57814 0.91870789
1580 84.681217 -3289.8506 972.05937 -4261.9099 1290.892 0 995.40503 151394.08 -157942.29 309.3174 19467.313 217.54888 325.64947 0.91261747
1600 85.872982 -3306.0485 999.0593 -4305.1078 1336.2852 0 1018.2817 151281.27 -157940.94 78.176324 19307.332 223.59152 334.68976 0.94786237
1620 87.166941 -3323.911 1023.7518 -4347.6628 1346.5659 0 1012.0297 151235.76 -157942.02 401.58054 19152.885 229.11774 342.98696 0.92107142
1640 88.373719 -3346.3201 1013.0953 -4359.4153 1368.3551 0 1038.3633 151174.74 -157940.87 115.49888 19004.339 226.7328 339.39185 0.96123977
1660 89.588199 -3366.6764 980.18808 -4346.8645 1385.5623 0 1066.3348 151143.21 -157941.97 785.51107 18860.969 219.3681 328.38652 0.89253119
1680 90.812635 -3382.4343 999.75094 -4382.1852 1367.9173 0 1045.8848 151142.33 -157938.32 549.73441 18726.008 223.74631 334.953 0.88544944
1700 92.044767 -3400.8462 996.00209 -4396.8483 1351.6629 0 1019.0394 151174.27 -157941.83 32.327852 18598.28 222.90731 333.67893 0.91827006
1720 93.284649 -3418.3313 989.38116 -4407.7125 1347.9882 0 1026.3475 151161.41 -157943.46 700.69172 18474.978 221.42553 331.45637 0.92100955
1740 94.538928 -3435.1347 964.16624 -4399.301 1357.6456 0 1051.1466 151135.74 -157943.84 477.68306 18358.2 215.78238 322.997 0.92157841
1760 95.90276 -3452.4681 996.08241 -4448.5506 1365.9896 0 1001.3994 151128.36 -157944.3 -77.655143 18246.618 222.92529 333.72093 0.88815023
1780 97.200704 -3470.0186 947.16368 -4417.1823 1357.1769 0 1006.9477 151162.27 -157943.57 100.19368 18137.3 211.97718 317.3159 0.87577473
1800 98.461648 -3484.6818 988.75293 -4473.4348 1367.5971 0 995.1924 151106.14 -157942.36 -208.37477 18030.204 221.28494 331.23294 0.94635825
1820 99.729642 -3503.5324 959.4974 -4463.0298 1386.9033 0 1035.1867 151057.26 -157942.38 196.09637 17924.392 214.73749 321.44422 0.89454363
1840 101.00392 -3518.4137 985.10207 -4503.5157 1425.227 0 1062.1927 150951.14 -157942.08 189.40933 17821.795 220.46787 330.02248 0.91769756
1860 102.28783 -3531.6076 978.71334 -4510.3209 1447.6145 0 1081.8026 150905.2 -157944.94 369.13672 17723.495 219.03805 327.84302 0.99005655
1880 103.57975 -3546.6803 982.10151 -4528.7818 1416.6032 0 1040.8725 150959.42 -157945.68 206.83653 17629.384 219.79633 328.97668 0.9960403
1900 104.81168 -3563.7438 961.75306 -4525.4969 1426.2883 0 1055.2567 150936.42 -157943.46 223.06115 17537.856 215.24231 322.15829 0.97986655
1920 106.04042 -3579.7815 953.8957 -4533.6772 1420.242 0 1053.3469 150938.67 -157945.93 264.48404 17448.909 213.48382 319.52979 0.96489929
1940 107.27692 -3592.4628 995.11883 -4587.5816 1434.5738 0 1036.2736 150885.59 -157944.02 -203.71783 17362.885 222.70964 333.32982 1.0238542
1960 108.52049 -3607.1225 959.8186 -4566.9411 1454.811 0 1091.6157 150830.59 -157943.96 412.09226 17278.194 214.80937 321.46995 1.0586113
1980 109.76987 -3621.5836 950.82575 -4572.4094 1481.3655 0 1148.5036 150742.3 -157944.58 1156.6083 17197.362 212.79675 318.42806 1.1085537
2000 111.02457 -3632.4321 939.77229 -4572.2044 1484.3457 0 1154.0077 150733.65 -157944.21 1008.3019 17124.028 210.32297 314.7467 1.0548599
Loop time of 111.025 on 1 procs for 2000 steps with 2500 atoms
Pair time (%) = 87.5509 (78.8572)
Bond time (%) = 0.0493031 (0.0444073)
Kspce time (%) = 3.35179 (3.01896)
Neigh time (%) = 9.36055 (8.43106)
Comm time (%) = 0.69479 (0.625798)
Outpt time (%) = 0.0108259 (0.00975088)
Other time (%) = 10.0064 (9.01281)
Nlocal: 2500 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 20348 ave 20348 max 20348 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.09326e+06 ave 2.09326e+06 max 2.09326e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2093261
Ave neighs/atom = 837.304
Ave special neighs/atom = 4
Neighbor list builds = 120
Dangerous builds = 16
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