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lammps/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4
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log.toluene.nh.11Aug17.linux.4
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LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4
read_data data.toluene extra/special/per/atom 1
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
2 by 1 by 2 MPI processor grid
reading atoms ...
5500 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
8 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
5500 bonds
reading angles ...
6000 angles
reading dihedrals ...
6000 dihedrals
reading impropers ...
1500 impropers
5 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
comm_modify vel yes
group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
neighbor 2.0 bin
variable vTEMP equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gCORES create ${vTEMP} 12345
velocity gCORES create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C C C C N N D D D D D
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
1250 = # of size 2 clusters
0 = # of size 3 clusters
250 = # of size 4 clusters
0 = # of frozen angles
compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude
fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse
fix fMOMENTUM all momentum 100 linear 1 1 1
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.382011
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.0325934
estimated relative force accuracy = 9.8154e-05
using double precision FFTs
3d grid and FFT values/proc = 34263 16000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/thole/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
50 1.1419601 6863.6417 4633.9267 321.70512 2229.715 735.2547 604.69459 648.35773 49.039129 824.06033 1306091.3 -1306722.9 17914.827 48631.318 504.18525 0.0086839775
100 2.3001912 6628.0719 4376.1868 303.81182 2251.8851 598.11248 651.43051 919.41359 74.216825 589.6504 1306135.1 -1306716 17450.721 48631.318 476.14276 0.0075129701
150 3.473469 6336.1884 4726.0692 328.10201 1610.1192 560.01225 621.30109 640.32474 45.531174 288.99129 1306173.9 -1306720 18303.624 48631.318 514.21215 0.006192153
200 4.6296241 5997.6192 4565.6288 316.96362 1431.9903 524.27651 591.79844 718.11014 56.374557 88.66084 1306183 -1306730.3 17986.183 48631.318 496.75522 0.0068120542
250 5.7982912 5648.1756 4433.1557 307.76682 1215.0199 502.13686 578.8537 665.27326 49.096119 -19.019961 1306179.2 -1306740.5 11771.328 48631.318 482.34141 0.0071619522
300 6.9468622 5317.8583 4075.2077 282.91669 1242.6505 602.55113 637.40818 647.27073 44.769725 -123.22347 1306183.3 -1306749.5 3571.1872 48631.318 443.3952 0.0071733908
350 8.0925181 4996.7094 3935.7988 273.23838 1060.9106 455.75195 634.3655 638.77824 45.831051 -157.63039 1306198.1 -1306754.3 13525.265 48631.318 428.22739 0.0063722017
400 9.2309761 4695.9294 3742.6584 259.82983 953.27093 457.49585 620.73048 591.94413 42.495714 -183.91838 1306186.7 -1306762.2 10901.217 48631.318 407.21326 0.0057875
450 10.363872 4417.8018 3513.6374 243.9303 904.1644 519.61261 580.76003 624.06933 45.631272 -286.60025 1306184.3 -1306763.6 2956.9021 48631.318 382.29485 0.0057536673
500 11.493601 4165.0005 3333.7203 231.43976 831.28022 465.52341 579.36085 580.60004 42.345149 -254.82269 1306183.9 -1306765.6 5818.5549 48631.318 362.71904 0.0059224858
550 12.636785 3934.5207 3211.9362 222.98504 722.58446 431.14864 581.46511 517.20249 39.188194 -265.4704 1306182.7 -1306763.6 8537.9415 48631.318 349.46863 0.0055762027
600 13.759642 3714.8658 3121.0493 216.67532 593.81649 425.12998 539.89497 490.30506 34.564567 -305.82067 1306175.2 -1306765.5 7402.7688 48631.318 339.57967 0.005748668
650 14.880794 3516.2453 2930.7499 203.464 585.49542 511.91457 512.48857 521.40634 37.766798 -391.65394 1306163.5 -1306770 381.72898 48631.318 318.87448 0.0054629381
700 15.99791 3342.7693 2864.1576 198.8409 478.61174 451.54685 498.82406 489.17206 35.231269 -375.78888 1306153.8 -1306774.2 3691.2706 48631.318 311.62801 0.0071278792
750 17.111346 3181.7665 2786.7104 193.46422 395.05608 409.83191 508.19537 454.56183 32.890719 -379.80694 1306149 -1306779.6 7428.3698 48631.318 303.20196 0.0062331873
800 18.219225 3032.4162 2699.8707 187.43547 332.54543 453.40674 486.16573 441.12346 32.847783 -437.39291 1306144.4 -1306788 1701.7675 48631.318 293.75377 0.0056528077
850 19.320825 2898.4936 2563.6961 177.9817 334.79757 463.66634 486.19928 453.38802 34.062236 -455.86081 1306144.2 -1306790.9 -285.04073 48631.318 278.93762 0.0052778244
900 20.41979 2780.3551 2528.3241 175.52604 252.03099 396.92693 451.7645 435.59756 33.035261 -413.46181 1306142.9 -1306794.7 3836.4347 48631.318 275.08801 0.0070307677
950 21.517533 2679.3418 2456.8821 170.56626 222.45967 385.66649 434.6516 418.37957 32.156706 -387.22039 1306136.9 -1306798.1 5510.2277 48631.318 267.31518 0.0064041284
1000 22.614275 2593.435 2367.4471 164.35734 225.98798 427.85237 453.27432 415.48822 31.097611 -436.61808 1306131.8 -1306796.9 1166.3709 48631.318 257.58457 0.0059160188
1050 23.688642 2524.7784 2305.0257 160.0238 219.75264 432.90797 438.8666 412.79338 30.892595 -414.29467 1306119.4 -1306800.8 1698.2602 48631.318 250.7925 0.0065595368
1100 24.750163 2471.818 2311.095 160.44516 160.72297 378.43554 453.3434 392.485 29.012487 -409.64322 1306119.6 -1306802.5 4190.9174 48631.318 251.4532 0.0059713928
1150 25.813605 2433.9311 2279.0768 158.22233 154.85433 395.30409 436.87935 414.39367 31.118959 -428.90913 1306110.2 -1306804.2 3274.9237 48631.318 247.96895 0.0069037916
1200 26.876952 2411.3772 2238.4639 155.40283 172.91329 453.61525 460.27658 408.59192 31.237007 -482.78468 1306110.2 -1306808.2 -523.10237 48631.318 243.55013 0.0068752641
1250 27.929701 2402.1937 2286.0559 158.70685 116.13778 416.44884 462.75935 391.75448 29.446777 -477.6718 1306102.2 -1306808.8 484.0561 48631.318 248.72561 0.011679662
1300 29.000999 2406.5014 2261.274 156.98639 145.22737 408.678 437.74824 400.45662 30.448139 -418.44472 1306096.8 -1306810.5 4490.4105 48631.318 245.9924 0.076575975
1350 30.07322 2459.141 2317.5852 160.89573 141.55579 651.85736 447.40791 400.66662 29.060882 -461.45016 1305884.3 -1306810.3 693.5247 48631.318 250.14112 3.5619231
1400 31.14859 2479.6103 2285.6714 158.68015 193.93893 582.54135 457.54445 430.29301 30.184026 -449.49877 1305955.6 -1306812.8 930.44669 48631.318 247.21806 2.5941109
1450 32.226914 2498.357 2286.4857 158.73668 211.87137 434.79636 477.95951 402.79572 31.070593 -406.60139 1306086.4 -1306814.5 2933.5045 48631.318 248.74572 0.058613153
1500 33.410717 2546.6608 2423.6247 168.25741 123.03609 392.07322 456.01243 385.97344 29.255562 -417.91413 1306089.9 -1306812.3 3333.391 48631.318 263.6939 0.011242005
1550 34.466176 2596.5534 2325.2208 161.42583 271.33259 462.52172 469.54241 461.20405 34.616224 -423.51068 1306080.4 -1306813.4 2155.1194 48631.318 252.98718 0.011190963
1600 35.524206 2646.7837 2387.8846 165.77619 258.8991 424.60563 484.95051 449.57767 33.318683 -395.68293 1306077 -1306814.8 1291.42 48631.318 259.80456 0.01242131
1650 36.582854 2700.2921 2387.3119 165.73643 312.98026 431.01369 496.39909 455.52591 32.725057 -357.65832 1306070.3 -1306815.3 5006.9348 48631.318 259.70291 0.081728845
1700 37.641527 2777.9572 2386.7777 165.69934 391.1795 636.55763 523.11512 482.8483 35.185863 -391.0955 1305919.8 -1306815.2 2192.6733 48631.318 258.1403 2.7324891
1750 38.722299 2829.6167 2559.2488 177.67295 270.36793 684.60746 479.95058 446.29664 31.887359 -385.83616 1305832.5 -1306819 1683.6061 48631.318 276.955 2.6459088
1800 39.800548 2835.7772 2465.7031 171.17865 370.07414 470.05306 508.38361 479.70121 37.826988 -369.0694 1306062.8 -1306819.6 3022.9801 48631.318 268.22328 0.097437593
1850 40.878327 2857.76 2504.4099 173.86582 353.35016 436.05857 516.10495 487.70907 36.514477 -385.43957 1306078.9 -1306816.5 2950.6415 48631.318 272.48049 0.016822774
1900 41.9583 2867.7843 2528.8424 175.56202 338.94193 446.38058 509.30719 485.04661 37.284135 -402.67104 1306076.5 -1306812.9 3161.5835 48631.318 275.1418 0.011620333
1950 43.058281 2861.3388 2513.8846 174.5236 347.45414 470.99292 536.81741 467.97736 36.047648 -430.00695 1306079.3 -1306813.6 739.25154 48631.318 273.50953 0.020089235
2000 44.142059 2838.068 2530.3189 175.66453 307.74914 423.19157 516.85371 454.76945 35.048253 -387.49234 1306074.6 -1306809.3 4324.0966 48631.318 275.23081 0.13784772
Loop time of 44.1421 on 4 procs for 2000 steps with 5500 atoms
Performance: 1.957 ns/day, 12.262 hours/ns, 45.308 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.008 | 22.592 | 23.892 | 21.7 | 51.18
Bond | 4.8951 | 5.1338 | 5.2542 | 6.4 | 11.63
Kspace | 9.1158 | 10.514 | 12.296 | 35.3 | 23.82
Neigh | 0.63826 | 0.63849 | 0.63875 | 0.0 | 1.45
Comm | 0.78008 | 0.80146 | 0.84186 | 2.7 | 1.82
Output | 0.0036852 | 0.0040929 | 0.0052037 | 1.0 | 0.01
Modify | 4.3966 | 4.4074 | 4.4147 | 0.3 | 9.98
Other | | 0.05088 | | | 0.12
Nlocal: 1375 ave 1415 max 1340 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 8101 ave 8147 max 8056 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 326274 ave 342552 max 306832 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 1305095
Ave neighs/atom = 237.29
Ave special neighs/atom = 15.6364
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:44
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