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lammps/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4
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log.toluene.lang.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 (Langevin)
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
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve
compute cTEMP all temp/drude
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 1.0658228 8014.6879 4671.7498 324.33095 3342.9381 1798.7991 670.22837 651.99307 50.352024 819.34616 1305984.9 -1306632.7 17255.952 48631.318 442.52888 116.12397
100 2.136163 6185.5007 3697.0414 256.66292 2488.4593 974.42931 774.88353 840.46625 66.896007 427.27085 1306105.5 -1306701 15044.739 48631.318 381.93582 35.802658
150 3.202647 5418.0644 3628.2714 251.88864 1789.7929 764.02696 804.61034 641.14915 47.995428 108.05084 1306138.9 -1306714.9 15258.194 48631.318 388.65363 10.777816
200 4.2728949 4838.4235 3303.8964 229.36927 1534.5271 702.10438 772.85348 625.99718 52.299187 -63.792745 1306166.5 -1306721.4 13487.722 48631.318 357.35337 3.7423617
250 5.3275268 4461.2438 3084.8973 214.16551 1376.3465 693.85145 823.23815 599.85313 48.280277 -230.56822 1306167.8 -1306726.1 8779.0061 48631.318 334.59262 1.8620294
300 6.3794398 4179.6462 2885.0738 200.29299 1294.5724 739.337 868.84011 555.04912 44.838819 -354.73738 1306171.3 -1306730 4410.8735 48631.318 313.17473 1.2892347
350 7.427706 3934.3968 2756.2421 191.34899 1178.1546 666.16877 877.32996 548.99846 45.087026 -404.32209 1306179 -1306734.1 8477.8828 48631.318 299.22663 1.1698531
400 8.4820418 3800.4769 2674.8317 185.69716 1125.6452 693.29433 841.29833 579.61438 48.325361 -470.18802 1306170.5 -1306737.2 6265.7532 48631.318 290.39105 1.1303952
450 9.528651 3685.28 2616.9074 181.67583 1068.3726 702.68328 886.66644 555.74511 46.160811 -557.70651 1306176.6 -1306741.7 2701.7737 48631.318 284.11064 1.091646
500 10.579133 3582.6591 2517.6443 174.78461 1065.0148 701.82101 894.9429 554.06012 46.074357 -570.49878 1306181.8 -1306743.2 3643.7426 48631.318 273.31525 1.0831346
550 11.629649 3542.0402 2527.0386 175.4368 1015.0016 688.73877 916.2381 521.69932 44.014375 -580.05437 1306171 -1306746.6 2928.6632 48631.318 274.34257 1.0740018
600 12.684143 3507.0443 2519.9749 174.94641 987.06936 711.58734 894.63276 525.57884 42.944226 -603.24423 1306161.2 -1306745.7 2082.9907 48631.318 273.57124 1.0784841
650 13.737965 3416.2001 2445.9361 169.80635 970.26394 706.95207 891.76446 540.90369 45.970985 -626.32832 1306160.2 -1306749.2 1912.8783 48631.318 265.5023 1.1021764
700 14.777375 3419.7572 2446.117 169.81891 973.64019 664.17579 936.51992 551.67148 45.696531 -634.70926 1306159.6 -1306749.4 2215.7085 48631.318 265.53614 1.0774684
750 15.795347 3418.6537 2449.343 170.04287 969.31069 706.12432 899.61553 553.21874 45.793213 -642.75298 1306158.1 -1306750.8 1022.2516 48631.318 265.89304 1.0681488
800 16.835794 3385.2449 2465.4963 171.16429 919.74864 692.34918 888.91243 530.24204 45.132243 -638.54787 1306154.6 -1306753 1601.1391 48631.318 267.64361 1.0797553
850 17.87536 3397.1124 2426.3129 168.44403 970.79951 717.48898 878.71057 580.26487 46.675101 -646.96926 1306150.9 -1306756.3 1048.7905 48631.318 263.38063 1.0785255
900 18.899639 3324.2064 2447.5004 169.91495 876.70599 683.62339 881.77789 531.98758 43.646731 -648.59248 1306144.4 -1306760.2 2221.5859 48631.318 265.69596 1.0608373
950 19.938468 3316.6329 2398.6988 166.52695 917.93405 702.84237 885.96473 540.35376 45.671318 -638.80334 1306144.4 -1306762.5 1955.2237 48631.318 260.38167 1.0687233
1000 20.973543 3287.4205 2384.191 165.51976 903.22949 705.56988 889.96387 535.23674 44.902139 -661.28175 1306150.4 -1306761.6 90.200683 48631.318 258.81506 1.0477545
1050 21.990961 3297.7806 2392.0372 166.06448 905.74339 697.33157 889.75086 537.2395 46.319713 -636.03286 1306135.9 -1306764.8 1893.8234 48631.318 259.67633 1.0344207
1100 23.006456 3240.651 2370.2217 164.54996 870.42931 693.87289 897.0846 526.89184 43.778979 -657.83716 1306132.1 -1306765.5 799.62979 48631.318 257.28711 1.0618941
1150 24.014558 3232.457 2377.9797 165.08855 854.47728 692.51558 897.77048 520.3269 43.903959 -657.38369 1306126.9 -1306769.6 178.21408 48631.318 258.13876 1.0479172
1200 25.010178 3238.4266 2392.0623 166.06622 846.36427 695.98996 887.237 522.01974 42.355716 -660.92843 1306124.7 -1306765 1006.1877 48631.318 259.66037 1.0698925
1250 26.01949 3198.3364 2332.7551 161.94888 865.58134 690.81786 897.35028 524.47996 44.421121 -640.92419 1306116.3 -1306766.8 2073.9672 48631.318 253.227 1.0326937
1300 27.026911 3237.6809 2386.3739 165.67131 851.30706 672.11785 901.04813 530.2964 44.020263 -655.33033 1306125.7 -1306766.5 579.46013 48631.318 259.05838 1.0374113
1350 28.033721 3285.9536 2371.155 164.61476 914.79862 718.12968 928.41764 524.02349 43.89896 -657.10221 1306127.3 -1306769.9 518.88041 48631.318 257.36737 1.0993197
1400 29.026742 3272.2173 2391.4158 166.02134 880.80147 712.59883 896.13616 532.95785 45.989768 -658.37495 1306125.6 -1306774.1 961.2067 48631.318 259.5968 1.0557033
1450 30.032566 3244.2627 2356.0955 163.56926 888.16727 714.72692 901.18382 534.59787 45.517573 -655.58258 1306124.5 -1306776.8 596.10558 48631.318 255.75173 1.058657
1500 31.03878 3244.8598 2408.5382 167.21004 836.32161 695.63105 867.27743 527.37333 44.496971 -648.96393 1306125.2 -1306774.7 443.71088 48631.318 261.45495 1.0648973
1550 32.041435 3239.3658 2367.1336 164.33557 872.23223 704.16965 884.5938 544.41685 46.110791 -654.61963 1306124.1 -1306776.5 -446.5562 48631.318 256.96289 1.0409003
1600 33.058977 3221.4258 2334.2656 162.05375 887.1602 713.8296 885.80472 533.86753 45.413663 -633.58824 1306119.6 -1306777.8 1527.9489 48631.318 253.36367 1.0817678
1650 34.080875 3224.4472 2385.9055 165.63879 838.54168 681.01628 879.88017 536.75983 43.884394 -643.24788 1306114 -1306773.8 1314.2208 48631.318 258.97106 1.1033457
1700 35.095047 3178.6575 2352.4294 163.31475 826.2281 700.79494 854.06687 549.39826 46.155483 -662.57181 1306115.2 -1306776.9 -187.36898 48631.318 255.35015 1.0638209
1750 36.093828 3219.473 2371.9421 164.6694 847.53093 699.44953 891.26068 541.91687 45.714235 -679.13432 1306120.3 -1306771.9 -618.32924 48631.318 257.48034 1.0512601
1800 37.110101 3202.0094 2371.8909 164.66585 830.11842 698.44522 858.38216 550.82008 46.315893 -667.77838 1306119.2 -1306775.3 -9.4963278 48631.318 257.46873 1.0619052
1850 38.121337 3202.0111 2366.6984 164.30536 835.31277 714.69988 849.6778 553.24258 46.502994 -667.44162 1306114.9 -1306776.3 131.11108 48631.318 256.90165 1.0656162
1900 39.132607 3228.7805 2365.934 164.25229 862.84648 720.68418 890.65533 554.75943 45.736726 -685.52803 1306115.1 -1306778.5 -82.525994 48631.318 256.81451 1.0726218
1950 40.127507 3218.4068 2443.0023 169.60267 775.40452 673.40001 874.63022 529.69964 43.166847 -680.57322 1306115.4 -1306780.3 622.76654 48631.318 265.20173 1.0693092
2000 41.138176 3257.463 2375.6246 164.92505 881.83842 677.60747 933.47776 547.01076 46.507189 -665.56273 1306123.7 -1306780.9 1829.3477 48631.318 257.88171 1.0500311
Loop time of 41.1383 on 4 procs for 2000 steps with 5500 atoms
Performance: 2.100 ns/day, 11.427 hours/ns, 48.617 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.082 | 22.483 | 24.145 | 26.6 | 54.65
Bond | 4.9992 | 5.0781 | 5.1544 | 2.7 | 12.34
Kspace | 9.1202 | 10.806 | 12.272 | 39.7 | 26.27
Neigh | 0.45045 | 0.45076 | 0.45094 | 0.0 | 1.10
Comm | 0.85982 | 0.87287 | 0.88725 | 1.2 | 2.12
Output | 0.0036495 | 0.004005 | 0.0049655 | 0.9 | 0.01
Modify | 1.4009 | 1.401 | 1.4013 | 0.0 | 3.41
Other | | 0.04245 | | | 0.10
Nlocal: 1375 ave 1398 max 1361 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 7745.75 ave 7788 max 7697 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 334374 ave 348629 max 319495 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1337494
Ave neighs/atom = 243.181
Ave special neighs/atom = 15.6364
Neighbor list builds = 31
Dangerous builds = 0
Total wall time: 0:00:41
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