252 lines
17 KiB
Groff
252 lines
17 KiB
Groff
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)
|
|
1 by 1 by 1 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 = 103823 64000
|
|
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) = 42.06 | 42.06 | 42.06 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 4.311986 8083.3901 4729.9995 328.37487 3353.3906 1812.5186 685.40417 646.10358 50.083281 804.80656 1305984.8 -1306630.3 16960.287 48631.318 448.67988 116.22125
|
|
100 8.756623 6206.7865 3683.944 255.75365 2522.8425 977.52675 777.45439 838.58809 68.086914 471.97862 1306097.1 -1306707.9 15657.142 48631.318 380.53159 35.760643
|
|
150 13.134938 5386.0219 3582.482 248.70976 1803.5399 752.25928 803.04832 643.43249 49.76684 131.97853 1306139.2 -1306716.2 15140.102 48631.318 383.61303 10.880935
|
|
200 17.508189 4846.4097 3254.3932 225.93257 1592.0166 700.43329 812.26722 657.52279 51.044716 -64.045174 1306160.5 -1306725.7 13844.277 48631.318 351.90677 3.8489009
|
|
250 21.871676 4473.215 3091.5333 214.6262 1381.6817 688.24707 842.63267 590.45999 48.22798 -214.02425 1306156.6 -1306730.5 8808.7402 48631.318 335.32872 1.8372171
|
|
300 26.226064 4191.8834 2883.8468 200.2078 1308.0367 734.36657 856.15482 584.87904 47.590787 -343.44615 1306163.4 -1306734.9 3389.3777 48631.318 313.03581 1.3011826
|
|
350 30.568716 3972.0739 2756.8392 191.39044 1215.2347 664.4688 866.06348 580.13632 48.515297 -378.8729 1306173.3 -1306738.3 8458.1149 48631.318 299.31146 1.1345329
|
|
400 34.845648 3838.3528 2731.3975 189.62419 1106.9552 684.0318 870.67752 548.93014 44.038787 -460.1537 1306160.4 -1306741 6697.9188 48631.318 296.54405 1.1332149
|
|
450 39.17477 3731.18 2607.8585 181.04762 1123.3216 719.57572 894.99915 571.99504 47.625227 -537.60494 1306171.9 -1306745.2 2450.4224 48631.318 283.13713 1.0721818
|
|
500 43.497489 3607.0055 2565.9469 178.13796 1041.0586 717.36452 841.34375 551.39834 45.985413 -542.47313 1306170.9 -1306743.4 3077.1849 48631.318 278.59462 1.0410963
|
|
550 47.812038 3513.8132 2548.7259 176.94241 965.08736 673.81272 852.38161 522.99297 44.276434 -552.27379 1306171.2 -1306747.4 4659.7275 48631.318 276.70124 1.0757459
|
|
600 52.124423 3386.9627 2471.0692 171.55118 915.89348 689.99732 833.61298 517.49343 43.023588 -594.96363 1306170.6 -1306743.8 2159.7328 48631.318 268.27854 1.0287605
|
|
650 56.370068 3374.3191 2413.6719 167.56644 960.64717 703.32428 874.12028 535.41271 43.256032 -617.25815 1306168.6 -1306746.8 1262.4757 48631.318 261.99584 1.0950976
|
|
700 60.667476 3342.9467 2412.9563 167.51676 929.99042 683.70355 882.22521 527.03932 43.661355 -616.70117 1306161 -1306751 2950.9009 48631.318 261.92814 1.0771869
|
|
750 64.964696 3327.7938 2414.3547 167.61385 913.43902 695.12778 863.48248 542.99202 46.408369 -639.60076 1306160.7 -1306755.6 1583.0277 48631.318 262.09771 1.0464936
|
|
800 69.256916 3391.689 2452.2049 170.24155 939.48407 694.2176 892.61592 557.53726 45.495129 -654.56675 1306155.2 -1306751 1232.1671 48631.318 266.20601 1.0640309
|
|
850 73.527972 3386.8618 2486.6928 172.63584 900.16902 696.7684 880.27643 545.11446 46.474227 -665.90464 1306154.7 -1306757.3 1129.2062 48631.318 269.97945 1.027015
|
|
900 77.775993 3368.0724 2416.7145 167.77767 951.35789 718.66654 893.18396 537.79136 46.404626 -641.29596 1306152.9 -1306756.3 1673.0743 48631.318 262.34697 1.0597091
|
|
950 82.028341 3300.4793 2409.5613 167.28107 890.918 728.06888 890.51193 515.08456 44.36547 -671.13741 1306142.3 -1306758.2 1038.6579 48631.318 261.57036 1.0567234
|
|
1000 86.189789 3333.2955 2452.2486 170.24458 881.04692 699.8414 915.33862 506.83261 41.77374 -665.68264 1306141.6 -1306758.7 467.42142 48631.318 266.19104 1.0987814
|
|
1050 90.384168 3303.87 2376.9713 165.01854 926.89875 706.12941 930.65844 524.73304 42.644613 -657.19573 1306139.3 -1306759.4 1737.6624 48631.318 258.00246 1.0954432
|
|
1100 94.549452 3367.668 2454.9154 170.42973 912.75259 715.68494 935.8363 516.52205 43.261761 -671.86101 1306137.9 -1306764.6 961.79199 48631.318 266.492 1.0797548
|
|
1150 98.65493 3350.0898 2485.3993 172.54604 864.69051 699.23072 933.76405 510.60424 42.381362 -684.53513 1306127.1 -1306763.8 -272.48178 48631.318 269.82496 1.0512421
|
|
1200 102.82045 3309.6871 2398.9577 166.54492 910.72944 705.58979 934.53183 531.90967 45.872142 -664.58495 1306126.9 -1306769.5 627.31931 48631.318 260.41866 1.0531639
|
|
1250 106.9899 3304.504 2491.6998 172.98344 812.80426 710.83366 881.33764 494.90045 41.71618 -672.49264 1306123.8 -1306767.3 136.11723 48631.318 270.51026 1.0516137
|
|
1300 111.16224 3318.9543 2462.0621 170.92588 856.89219 709.17314 932.87209 503.80373 43.426006 -680.2474 1306121.2 -1306773.3 1276.2503 48631.318 267.28591 1.0510113
|
|
1350 115.27184 3314.8515 2434.8483 169.03659 880.00316 710.91641 922.28347 540.40795 44.753548 -686.09335 1306124.5 -1306776.7 -438.87694 48631.318 264.31236 1.0731666
|
|
1400 119.44228 3349.0785 2457.7697 170.62788 891.30875 711.28064 936.58607 516.63511 42.396287 -653.09763 1306113.8 -1306776.3 350.79618 48631.318 266.80555 1.0745043
|
|
1450 123.61267 3364.1486 2459.8741 170.77397 904.27455 696.57265 946.32098 538.55368 44.69075 -652.75091 1306111 -1306780.1 502.47466 48631.318 267.03201 1.0789056
|
|
1500 127.72962 3341.9369 2454.3302 170.3891 887.60672 726.46979 903.40815 557.73064 47.536125 -667.65025 1306100.7 -1306780.6 -248.0975 48631.318 266.44821 1.044725
|
|
1550 131.91041 3270.4282 2437.7916 169.24093 832.63655 691.49462 910.83807 523.17366 44.83093 -654.48655 1306100.5 -1306783.7 490.32965 48631.318 264.63652 1.0662604
|
|
1600 136.0834 3252.0725 2429.6805 168.67782 822.39196 689.68155 898.22828 535.31963 43.84399 -660.93277 1306100.1 -1306783.9 1729.5956 48631.318 263.74523 1.0817172
|
|
1650 140.26444 3239.748 2442.6258 169.57653 797.12222 671.1832 907.1659 507.03947 43.048028 -648.14001 1306103.3 -1306786.5 970.43988 48631.318 265.15987 1.0708872
|
|
1700 144.3855 3202.9157 2410.267 167.33006 792.64869 686.40974 882.40791 527.02899 43.819792 -656.82001 1306096 -1306786.2 -107.50166 48631.318 261.64368 1.062837
|
|
1750 148.56592 3214.6107 2366.3264 164.27953 848.28434 696.38228 915.58636 538.2236 47.852688 -652.7697 1306093.6 -1306790.6 -164.14366 48631.318 256.84519 1.0937744
|
|
1800 152.74611 3209.5771 2421.4089 168.10357 788.16819 683.61816 869.45802 532.77927 45.708374 -658.39221 1306103.1 -1306788.1 277.61781 48631.318 262.83282 1.1036154
|
|
1850 156.86567 3146.3973 2362.3333 164.00232 784.064 697.87032 875.8451 523.54452 43.851379 -665.83106 1306101.5 -1306792.7 497.88657 48631.318 256.42683 1.0654271
|
|
1900 161.0419 3141.5496 2367.1077 164.33378 774.44186 693.39945 878.97447 515.65653 44.619392 -668.11692 1306103.8 -1306793.9 -1427.3998 48631.318 256.94212 1.0727903
|
|
1950 165.22235 3134.6473 2295.577 159.36784 839.07025 699.62719 905.76937 519.32307 46.109334 -645.08933 1306104.9 -1306791.6 1744.2846 48631.318 249.19694 1.0064565
|
|
2000 169.4 3146.866 2361.3821 163.93628 785.48386 682.24124 889.6864 534.94877 46.855983 -678.1614 1306104 -1306794.1 699.8735 48631.318 256.32873 1.0559143
|
|
Loop time of 169.4 on 1 procs for 2000 steps with 5500 atoms
|
|
|
|
Performance: 0.510 ns/day, 47.056 hours/ns, 11.806 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 107.93 | 107.93 | 107.93 | 0.0 | 63.71
|
|
Bond | 19.76 | 19.76 | 19.76 | 0.0 | 11.66
|
|
Kspace | 34.926 | 34.926 | 34.926 | 0.0 | 20.62
|
|
Neigh | 1.9932 | 1.9932 | 1.9932 | 0.0 | 1.18
|
|
Comm | 0.73555 | 0.73555 | 0.73555 | 0.0 | 0.43
|
|
Output | 0.0065863 | 0.0065863 | 0.0065863 | 0.0 | 0.00
|
|
Modify | 3.9135 | 3.9135 | 3.9135 | 0.0 | 2.31
|
|
Other | | 0.133 | | | 0.08
|
|
|
|
Nlocal: 5500 ave 5500 max 5500 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 13219 ave 13219 max 13219 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 1.33739e+06 ave 1.33739e+06 max 1.33739e+06 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1337388
|
|
Ave neighs/atom = 243.161
|
|
Ave special neighs/atom = 15.6364
|
|
Neighbor list builds = 32
|
|
Dangerous builds = 0
|
|
Total wall time: 0:02:49
|