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lammps/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4
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log.swm4-ndp.lang.8Jul15.linux.4
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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
comm_modify vel yes
read_data data.swm4-ndp
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 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 = 1500 300
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
fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
500 rigid bodies with 2000 atoms
0.832099 = max distance from body owner to body atom
fix NVE DRUDES nve
compute TEMP all temp/drude
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 = 1500 300
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 = 15.0906 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 0.47649789 2915.1578 4579.5774 -1664.4195 561.91893 0 600.76451 155095.13 -157922.23 27379.77 14058.574 1024.9188 1455.9194 160.86778
40 0.97488093 1320.1721 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914
60 1.4631288 284.06852 2671.4325 -2387.3639 575.54157 0 387.8792 154580.74 -157931.53 12104.741 15031.425 597.87207 886.98502 18.450413
80 1.937151 -462.53017 2214.284 -2676.8142 560.36347 0 254.65245 154447.22 -157939.05 6285.2465 15651.216 495.56131 739.13811 7.4024411
100 2.3922298 -965.19662 1839.831 -2805.0276 544.59528 0 115.80812 154469.59 -157935.02 2361.9397 16295.72 411.75795 615.12769 4.196977
120 2.832803 -1316.6351 1649.585 -2966.2202 554.6664 0 50.928925 154365.49 -157937.3 -493.85523 16925.293 369.18052 552.0345 2.7331855
140 3.2340388 -1590.9162 1440.6669 -3031.5831 526.07679 0 -24.44055 154404.35 -157937.57 -2586.2431 17517.285 322.42421 482.16117 2.297578
160 3.6521859 -1742.3401 1326.8812 -3069.2213 539.49044 0 -43.846659 154369.1 -157933.96 -3549.2196 18059.707 296.95874 444.11026 2.0644677
180 4.033325 -1895.1332 1224.1816 -3119.3148 555.27887 0 -18.261233 154275.94 -157932.27 -3762.2304 18545.518 273.97437 409.78413 1.806893
200 4.4333398 -2004.4682 1176.8828 -3181.351 565.0443 0 0.21425471 154190.38 -157936.99 -4346.6036 18973.342 263.38879 393.94856 1.7400558
220 4.8055639 -2094.1888 1098.3856 -3192.5744 592.45764 0 36.50238 154113.36 -157934.89 -4135.0794 19341.735 245.82095 367.67707 1.617053
240 5.1688328 -2178.9829 1086.8322 -3265.8151 617.63697 0 96.836936 153957.27 -157937.56 -4121.5262 19651.8 243.23528 363.77401 1.6722646
260 5.5313618 -2264.8265 1078.4348 -3343.2613 663.35817 0 167.76882 153763.13 -157937.52 -3799.3346 19907.052 241.35592 360.97385 1.6377289
280 5.8937738 -2325.7764 1097.4356 -3423.212 717.74089 0 235.0127 153562.96 -157938.92 -3696.0526 20111.414 245.60833 367.31076 1.7042318
300 6.254128 -2390.4932 1068.1054 -3458.5986 751.64681 0 295.31516 153435.34 -157940.9 -3512.2095 20268.754 239.04419 357.49427 1.665921
320 6.6138928 -2455.1776 1041.7419 -3496.9195 765.8972 0 331.14997 153345 -157938.97 -3020.0674 20383.474 233.14397 348.62385 1.7179273
340 6.9748628 -2536.9935 1050.7304 -3587.7239 793.64536 0 352.69908 153205.74 -157939.81 -3447.9127 20457.612 235.15562 351.6381 1.7214573
360 7.3319299 -2603.5606 966.90943 -3570.47 819.14306 0 391.00909 153158.89 -157939.51 -3164.629 20490.764 216.39631 323.51872 1.7254892
380 7.691319 -2594.787 1024.7927 -3619.5797 836.44816 0 434.32118 153047.12 -157937.47 -2902.9345 20485.923 229.35071 342.91482 1.7641915
400 8.044276 -2647.3896 982.46478 -3629.8543 864.59805 0 479.08516 152963.5 -157937.04 -2535.9236 20447.668 219.87764 328.69587 1.8030508
420 8.3971269 -2687.5263 1023.0437 -3710.57 928.04551 0 538.49845 152760.83 -157937.94 -2383.6292 20380.427 228.95928 342.31215 1.8044964
440 8.753284 -2765.2192 999.28342 -3764.5026 966.26754 0 577.15359 152631.24 -157939.17 -2391.0923 20286.676 223.64168 334.34309 1.7947669
460 9.1102748 -2806.7385 1004.2311 -3810.9696 996.86893 0 599.41867 152532.79 -157940.05 -2476.5754 20168.782 224.74899 335.97767 1.8475589
480 9.471664 -2830.2582 1013.6925 -3843.9506 1009.5553 0 624.64584 152464.58 -157942.73 -2210.7254 20027.747 226.86645 339.14841 1.8588685
500 9.8365009 -2865.4993 1024.473 -3889.9723 1017.2606 0 658.56598 152375.13 -157940.93 -2047.5735 19865.992 229.27916 342.78576 1.8103481
520 10.207523 -2918.9299 973.10292 -3892.0328 1049.357 0 699.16951 152300.27 -157940.83 -1453.4121 19688.211 217.78243 325.51403 1.8799495
540 10.583098 -2970.1121 925.84385 -3895.956 1077.9578 0 758.25478 152208.67 -157940.84 -821.19447 19499.417 207.20575 309.67486 1.8442683
560 10.962813 -3008.9942 954.33133 -3963.3255 1114.7309 0 751.85274 152112.75 -157942.66 -1023.0801 19304.314 213.58131 319.23167 1.8463043
580 11.351938 -3069.9822 951.38041 -4021.3626 1127.8186 0 765.20411 152027.82 -157942.2 -954.30565 19101.694 212.92089 318.20155 1.9391088
600 11.74351 -3090.3867 973.25557 -4063.6423 1123.3487 0 744.86978 152009.46 -157941.32 -1226.2333 18891.444 217.81659 325.5949 1.8227604
620 12.138507 -3114.2347 1002.2136 -4116.4483 1159.4812 0 766.24573 151899.05 -157941.23 -1406.6638 18672.922 224.29746 335.32178 1.8002314
640 12.53874 -3160.3172 973.01388 -4133.3311 1181.5814 0 805.79135 151821.94 -157942.65 -1444.0821 18448.163 217.7625 325.51017 1.8464735
660 12.945363 -3185.1871 975.57462 -4160.7618 1177.1798 0 795.84414 151809.59 -157943.38 -962.08053 18220.064 218.3356 326.36793 1.8252243
680 13.358243 -3226.8034 977.21534 -4204.0187 1215.3088 0 862.3869 151662.05 -157943.76 -538.09214 17991.009 218.7028 326.90984 1.8513045
700 13.774714 -3267.0358 979.72611 -4246.7619 1229.2873 0 878.80049 151588.58 -157943.43 -526.4724 17765.058 219.26471 327.74412 1.86738
720 14.198356 -3275.0063 987.91851 -4262.9248 1260.2342 0 905.19546 151515.01 -157943.36 -285.51035 17544.004 221.09819 330.48021 1.8901628
740 14.624448 -3298.9204 992.679 -4291.5994 1283.7665 0 917.78414 151449.24 -157942.39 351.98558 17329.448 222.1636 332.09658 1.843264
760 15.05056 -3316.7113 1010.6458 -4327.3571 1296.6728 0 951.2091 151368.47 -157943.71 419.51796 17123.095 226.18459 338.07068 1.9518407
780 15.504961 -3294.5707 1053.9493 -4348.52 1300.722 0 975.60682 151317.15 -157942 1040.7668 16927.715 235.87602 352.49204 2.1793007
800 15.933704 -3363.0539 987.22337 -4350.2773 1325.1641 0 1013.664 151255.26 -157944.36 1462.6199 16747.7 220.94262 330.24432 1.8985721
820 16.364414 -3437.2117 980.5397 -4417.7514 1350.8684 0 1029.953 151144.46 -157943.03 817.95684 16584.026 219.4468 327.9943 1.9129039
840 16.799625 -3465.5868 981.23685 -4446.8236 1388.7125 0 1043.4314 151066.43 -157945.4 1366.0731 16434.707 219.60282 328.17006 2.0308095
860 17.241996 -3460.2301 1020.3681 -4480.5981 1418.4709 0 1090.9207 150954.21 -157944.2 1450.0443 16300.524 228.36046 341.31823 2.0218282
880 17.688347 -3499.5491 994.43799 -4493.9871 1444.4283 0 1113.276 150893.43 -157945.12 2227.6739 16183.439 222.55726 332.59403 2.0408296
900 18.136371 -3526.9176 952.87144 -4479.789 1443.8422 0 1118.5107 150902.72 -157944.87 2220.1643 16085.505 213.25458 318.69359 1.9574553
920 18.599828 -3545.2479 976.95271 -4522.2006 1443.4309 0 1118.3924 150859.69 -157943.71 2107.6215 16006.466 218.64402 326.75181 1.9926282
940 19.064528 -3560.4406 994.62379 -4555.0644 1431.3624 0 1098.4902 150860.38 -157945.3 1495.9356 15944.46 222.59885 332.62316 2.0953461
960 19.529192 -3590.569 964.78915 -4555.3582 1431.9284 0 1092.1793 150866.87 -157946.34 1559.1687 15897.003 215.92179 322.6406 2.0442546
980 19.991661 -3599.6592 986.56344 -4586.2227 1435.7543 0 1034.8682 150889.35 -157946.2 679.01087 15862.242 220.79492 330.01359 1.9307016
1000 20.427668 -3634.9266 939.78172 -4574.7083 1424.4834 0 1022.664 150924.73 -157946.59 733.04572 15834.345 210.32508 314.30018 1.9584145
1020 20.873712 -3669.298 934.76265 -4604.0606 1452.3 0 1016.3445 150873.46 -157946.16 143.60284 15811.749 209.2018 312.55492 2.0808526
1040 21.319204 -3682.4175 935.86127 -4618.2788 1447.0344 0 1035.4526 150844.58 -157945.34 515.93558 15792.261 209.44767 312.98247 1.9790896
1060 21.766855 -3704.0833 901.03929 -4605.1226 1476.4857 0 1067.779 150794.42 -157943.8 1092.0636 15777.267 201.65444 301.3325 1.8948719
1080 22.214459 -3699.4923 921.66268 -4621.155 1475.7351 0 1079.7576 150767.2 -157943.85 1003.4205 15769.569 206.27 308.27973 1.8458618
1100 22.662445 -3667.6761 957.47147 -4625.1476 1507.2355 0 1102.9252 150708.15 -157943.46 927.20789 15768.898 214.28408 320.17339 2.0742837
1120 23.085055 -3668.1399 935.38917 -4603.5291 1507.3367 0 1080.9826 150753.9 -157945.75 810.87137 15775.175 209.34202 312.79082 2.0279075
1140 23.534417 -3710.7149 937.22068 -4647.9356 1499.5413 0 1020.4759 150776.54 -157944.49 -138.27816 15786.277 209.75191 313.34734 2.1346658
1160 23.985544 -3711.7493 900.74897 -4612.4983 1430.3269 0 990.84122 150911.11 -157944.78 8.4592568 15798.538 201.58947 301.24561 1.8661211
1180 24.439474 -3729.7115 928.82825 -4658.5398 1435.7711 0 937.43508 150913.97 -157945.72 -905.33202 15809.125 207.87367 310.65722 1.8872897
1200 24.895124 -3738.2838 909.79315 -4648.077 1436.4199 0 938.10918 150922.8 -157945.41 -1112.9968 15812.511 203.61357 304.28121 1.8714711
1220 25.352201 -3757.8302 907.08742 -4664.9176 1424.1514 0 930.13653 150924.86 -157944.06 -1078.0621 15807.893 203.00803 303.40134 1.8521625
1240 25.780748 -3778.5355 905.88168 -4684.4171 1453.9568 0 959.37689 150846.21 -157943.96 -975.25032 15795.393 202.73818 303.00695 1.778808
1260 26.238145 -3773.7584 879.94641 -4653.7048 1473.5812 0 1002.67 150815.41 -157945.36 -360.58922 15776.466 196.93381 294.2433 1.9174557
1280 26.696751 -3755.4956 904.13603 -4659.6316 1493.7103 0 1017.8327 150773.94 -157945.12 -256.88128 15755.525 202.3475 302.35592 1.9294965
1300 27.158244 -3754.9246 903.51795 -4658.4425 1498.1329 0 1006.1786 150782.15 -157944.9 -455.2258 15732.436 202.20917 302.19365 1.8353806
1320 27.619539 -3758.1232 913.25769 -4671.3808 1500.2049 0 1032.0703 150739.71 -157943.37 -251.62277 15706.775 204.38895 305.38485 1.9968111
1340 28.079132 -3784.7481 937.61449 -4722.3626 1505.7439 0 993.46365 150723.27 -157944.84 -853.9871 15680.38 209.84005 313.60153 1.8911101
1360 28.514251 -3808.7787 864.89279 -4673.6715 1475.0618 0 1009.2569 150785.65 -157943.64 -331.64382 15650.208 193.56478 289.20988 1.8929896
1380 28.975972 -3798.7281 892.2622 -4690.9903 1465.561 0 993.58051 150793.83 -157943.96 -567.64508 15617.156 199.69011 298.39786 1.8757635
1400 29.439238 -3807.9228 893.51775 -4701.4406 1459.3875 0 1000.4434 150784.38 -157945.65 -456.80001 15580.856 199.97111 298.79789 1.925086
1420 29.904427 -3818.6783 890.66153 -4709.3398 1515.8208 0 1064.6851 150655.36 -157945.21 450.86768 15542.76 199.33188 297.83132 1.927452
1440 30.368352 -3822.016 910.79285 -4732.8089 1539.2325 0 1076.0339 150597.99 -157946.07 429.02044 15506.302 203.83731 304.53724 2.0216852
1460 30.835555 -3821.2117 931.47963 -4752.6914 1540.1582 0 1089.9477 150561.76 -157944.55 645.54716 15472.89 208.46705 311.56653 1.8487206
1480 31.306455 -3838.255 920.25737 -4758.5124 1546.6509 0 1107.4468 150533.86 -157946.47 556.76352 15443.298 205.95549 307.74395 1.9637305
1500 31.747528 -3839.4323 942.18813 -4781.6204 1557.1836 0 1105.7209 150502.68 -157947.21 535.34633 15417.723 210.86364 315.07463 2.0384198
1520 32.218974 -3827.551 925.42642 -4752.9774 1555.4578 0 1097.174 150540.89 -157946.5 680.16246 15396 207.11233 309.42351 2.0793499
1540 32.691924 -3836.1802 885.40721 -4721.5874 1558.3851 0 1144.6478 150521.13 -157945.75 1216.5367 15378.972 198.15595 296.02524 2.015983
1560 33.164075 -3830.4342 955.31807 -4785.7523 1574.0464 0 1105.7294 150481.06 -157946.59 169.17645 15369.126 213.80214 319.4694 2.0400237
1580 33.636497 -3808.4082 948.31996 -4756.7281 1556.8058 0 1079.1205 150552.4 -157945.06 603.87966 15363.124 212.23595 317.13706 2.0112224
1600 34.111529 -3835.9681 925.63461 -4761.6027 1575.0508 0 1091.3896 150517.16 -157945.2 356.94873 15359.871 207.15893 309.60148 1.8514712
1620 34.558112 -3865.8357 866.45292 -4732.2886 1577.3357 0 1137.1716 150497.63 -157944.43 945.81112 15359.844 193.91394 289.72922 1.8926829
1640 35.029171 -3849.5025 884.49282 -4733.9954 1547.0606 0 1101.4292 150561.92 -157944.41 703.96326 15365.598 197.95131 295.76038 1.913597
1660 35.495665 -3861.3162 906.62112 -4767.9373 1547.2773 0 1074.8986 150555.48 -157945.6 46.512723 15375.298 202.90367 303.1667 1.9573677
1680 35.959871 -3857.7679 907.8657 -4765.6336 1547.7327 0 1089.3299 150543.52 -157946.22 383.48079 15386.165 203.18221 303.5736 2.0202069
1700 36.428885 -3869.0902 891.82145 -4760.9117 1512.1728 0 1012.6239 150658.31 -157944.02 -488.95961 15397.869 199.59147 298.24425 1.8990607
1720 36.903833 -3870.4685 893.82411 -4764.2926 1485.7646 0 989.27762 150706.25 -157945.59 -542.70653 15406.338 200.03967 298.80302 2.1113341
1740 37.380529 -3847.3408 893.93384 -4741.2746 1509.8117 0 1031.6641 150663.04 -157945.79 -307.1162 15410.521 200.06423 298.90093 2.0090208
1760 37.827319 -3840.438 868.84851 -4709.2865 1474.404 0 1018.599 150744.2 -157946.49 -276.44721 15412.838 194.45008 290.51398 1.9203414
1780 38.297568 -3842.0322 910.50606 -4752.5383 1494.2187 0 1002.3762 150696.05 -157945.18 -585.57252 15412.983 203.77313 304.47127 1.9624414
1800 38.76671 -3861.9431 881.98228 -4743.9254 1471.6721 0 978.01808 150752.55 -157946.17 -711.07254 15409.636 197.38944 294.90206 1.9749925
1820 39.233968 -3890.8613 856.10452 -4746.9658 1505.1405 0 991.9875 150701.72 -157945.82 -509.17282 15401.428 191.59795 286.24213 1.9311068
1840 39.704207 -3860.2881 907.57785 -4767.866 1492.5264 0 999.80677 150685.45 -157945.65 -697.50098 15387.414 203.11779 303.52338 1.9123566
1860 40.174673 -3879.0681 938.58496 -4817.653 1532.9628 0 1046.6919 150550.41 -157947.72 -311.83188 15369.15 210.05724 313.84514 2.0580305
1880 40.646746 -3871.1182 925.64972 -4796.7679 1531.6363 0 1064.5321 150553.96 -157946.9 136.0161 15350.638 207.16231 309.48972 2.0957912
1900 41.120691 -3868.9005 949.1652 -4818.0657 1593.1686 0 1150.4095 150384.01 -157945.65 753.94006 15333.301 212.42512 317.39691 2.0615952
1920 41.59464 -3868.6343 954.03473 -4822.669 1610.5603 0 1192.2159 150320.88 -157946.33 1209.5547 15321.106 213.51493 319.06152 2.011006
1940 42.037294 -3884.0548 926.13369 -4810.1885 1595.5448 0 1167.6153 150372.25 -157945.6 1289.8018 15318.433 207.27062 309.70304 1.9619634
1960 42.507917 -3889.403 953.52537 -4842.9284 1598.8799 0 1116.9498 150388.89 -157947.65 327.93587 15323.804 213.40093 318.9112 1.9579466
1980 42.973861 -3911.0951 911.40927 -4822.5043 1553.4244 0 1085.4519 150485.64 -157947.02 169.14591 15332.113 203.97527 304.77814 1.9637281
2000 43.43889 -3892.0279 902.31728 -4794.3452 1534.2125 0 1088.703 150530.25 -157947.51 473.37009 15341.654 201.94046 301.71557 1.9929295
Loop time of 43.4389 on 4 procs for 2000 steps with 2500 atoms
Pair time (%) = 30.8131 (70.9343)
Bond time (%) = 0.0167851 (0.0386406)
Kspce time (%) = 2.78529 (6.41196)
Neigh time (%) = 2.7229 (6.26835)
Comm time (%) = 2.36382 (5.4417)
Outpt time (%) = 0.00704503 (0.0162182)
Other time (%) = 4.72998 (10.8888)
Nlocal: 625 ave 641 max 600 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost: 13465.2 ave 13518 max 13362 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 585334 ave 608376 max 546210 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 2341334
Ave neighs/atom = 936.534
Ave special neighs/atom = 4
Neighbor list builds = 100
Dangerous builds = 7
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