260 lines
17 KiB
Groff
260 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 (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)
|
|
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
|
|
|
|
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 = 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 4.462481 6863.642 4633.9267 321.70512 2229.7153 735.2547 604.6946 648.35773 49.039129 824.06033 1306091.3 -1306722.9 17914.827 48631.318 504.18525 0.0086839843
|
|
100 8.8666639 6628.0722 4376.1868 303.81182 2251.8853 598.11249 651.43051 919.41359 74.216826 589.6504 1306135.1 -1306716 17450.721 48631.318 476.14276 0.0075129702
|
|
150 13.323556 6336.1884 4726.0692 328.10201 1610.1192 560.01225 621.30109 640.32475 45.531175 288.99128 1306173.9 -1306720 18303.624 48631.318 514.21215 0.0061921467
|
|
200 17.710109 5997.6194 4565.6288 316.96362 1431.9906 524.2765 591.79843 718.11015 56.374558 88.660843 1306183 -1306730.3 17986.182 48631.318 496.75522 0.00681205
|
|
250 22.154451 5648.1758 4433.1558 307.76682 1215.02 502.13687 578.85369 665.27326 49.096119 -19.019967 1306179.2 -1306740.5 11771.328 48631.318 482.34141 0.0071619539
|
|
300 26.524393 5317.8584 4075.2077 282.91669 1242.6506 602.55113 637.40817 647.27074 44.769726 -123.22347 1306183.3 -1306749.5 3571.1867 48631.318 443.3952 0.0071733829
|
|
350 30.881443 4996.709 3935.7988 273.23838 1060.9102 455.75196 634.36552 638.77826 45.831053 -157.6304 1306198.1 -1306754.3 13525.264 48631.318 428.22739 0.0063722044
|
|
400 35.218285 4695.9297 3742.6585 259.82983 953.27122 457.49584 620.73047 591.94411 42.495713 -183.91838 1306186.7 -1306762.2 10901.217 48631.318 407.21326 0.005787501
|
|
450 39.545502 4417.8027 3513.6374 243.9303 904.16528 519.61263 580.76003 624.06933 45.631271 -286.60025 1306184.3 -1306763.6 2956.9012 48631.318 382.29486 0.0057536613
|
|
500 43.868895 4165.0012 3333.7203 231.43976 831.28089 465.5234 579.36085 580.60005 42.34515 -254.82269 1306183.9 -1306765.6 5818.5565 48631.318 362.71904 0.0059224891
|
|
550 48.242395 3934.5209 3211.9362 222.98504 722.58462 431.14864 581.46511 517.2025 39.188196 -265.47041 1306182.7 -1306763.6 8537.9404 48631.318 349.46863 0.0055762504
|
|
600 52.542171 3714.8655 3121.0494 216.67532 593.81611 425.12998 539.89496 490.30508 34.564566 -305.82069 1306175.2 -1306765.5 7402.7677 48631.318 339.57967 0.0057486673
|
|
650 56.830079 3516.2452 2930.7498 203.46399 585.49537 511.91461 512.48859 521.40636 37.766801 -391.65392 1306163.5 -1306770 381.72879 48631.318 318.87447 0.0054629243
|
|
700 61.119511 3342.7694 2864.1576 198.8409 478.6118 451.54683 498.82407 489.17207 35.23127 -375.78886 1306153.8 -1306774.2 3691.2716 48631.318 311.62801 0.0071278731
|
|
750 65.401576 3181.7673 2786.7104 193.46422 395.05691 409.83192 508.19542 454.56182 32.890716 -379.80692 1306149 -1306779.6 7428.3698 48631.318 303.20195 0.006233194
|
|
800 69.680899 3032.4158 2699.8707 187.43547 332.54509 453.40673 486.16575 441.1235 32.847786 -437.39338 1306144.4 -1306788 1701.7652 48631.318 293.75377 0.0056528223
|
|
850 73.96463 2898.4928 2563.6959 177.98169 334.7969 463.66637 486.19929 453.38803 34.062233 -455.86062 1306144.2 -1306790.9 -285.03665 48631.318 278.9376 0.0052777781
|
|
900 78.229548 2780.3555 2528.3241 175.52604 252.03136 396.92692 451.76463 435.59744 33.035257 -413.46176 1306142.9 -1306794.7 3836.4341 48631.318 275.08801 0.0070306435
|
|
950 82.482848 2679.3417 2456.8817 170.56624 222.45998 385.66656 434.6516 418.37977 32.156722 -387.2201 1306136.9 -1306798.1 5510.2309 48631.318 267.31515 0.0064042654
|
|
1000 86.722726 2593.4365 2367.4477 164.35738 225.98882 427.8524 453.27435 415.48809 31.097577 -436.62051 1306131.8 -1306796.9 1166.3909 48631.318 257.58464 0.0059160543
|
|
1050 90.888482 2524.7788 2305.0253 160.02377 219.75349 432.90807 438.86657 412.79356 30.892593 -414.29436 1306119.4 -1306800.8 1698.2687 48631.318 250.79245 0.0065593259
|
|
1100 95.024656 2471.8176 2311.0953 160.44518 160.72227 378.43572 453.3435 392.48525 29.012472 -409.64374 1306119.6 -1306802.5 4190.91 48631.318 251.45323 0.0059713432
|
|
1150 99.165724 2433.9279 2279.0766 158.22231 154.8513 395.30434 436.87933 414.39389 31.118973 -428.90902 1306110.2 -1306804.2 3274.8924 48631.318 247.96893 0.0069039065
|
|
1200 103.31062 2411.3777 2238.4638 155.40282 172.91381 453.61551 460.27693 408.59237 31.237062 -482.78549 1306110.2 -1306808.2 -523.10179 48631.318 243.55012 0.0068754631
|
|
1250 107.40149 2402.1932 2286.0576 158.70696 116.13565 416.44979 462.75875 391.75373 29.446705 -477.67214 1306102.2 -1306808.8 484.04837 48631.318 248.72579 0.011679749
|
|
1300 111.55448 2406.5029 2261.2729 156.98631 145.23005 408.68043 437.74725 400.4567 30.448106 -418.44274 1306096.8 -1306810.5 4490.4165 48631.318 245.99228 0.076574936
|
|
1350 115.71244 2459.1398 2317.5855 160.89575 141.55434 651.84862 447.40877 400.66793 29.060967 -461.45124 1305884.3 -1306810.3 693.59782 48631.318 250.14098 3.5622064
|
|
1400 119.88515 2479.5991 2285.6701 158.68006 193.929 582.54021 457.54475 430.29254 30.183876 -449.49979 1305955.6 -1306812.8 930.31169 48631.318 247.21826 2.5935077
|
|
1450 124.05689 2498.3537 2286.4924 158.73715 211.86128 434.79588 477.9598 402.79356 31.070492 -406.60813 1306086.4 -1306814.5 2933.4418 48631.318 248.74646 0.058608522
|
|
1500 128.29115 2546.66 2423.6257 168.25747 123.03432 392.07474 456.01536 385.97457 29.255586 -417.92459 1306089.9 -1306812.3 3333.3497 48631.318 263.694 0.011243575
|
|
1550 132.46344 2596.5481 2325.2227 161.42596 271.32542 462.52464 469.53612 461.20308 34.616094 -423.51186 1306080.4 -1306813.4 2155.0566 48631.318 252.98739 0.011191115
|
|
1600 136.64497 2646.7844 2387.8797 165.77585 258.90469 424.6071 484.95314 449.56642 33.318144 -395.67454 1306077 -1306814.8 1291.5449 48631.318 259.80403 0.012426122
|
|
1650 140.83234 2700.2847 2387.3033 165.73584 312.98138 431.00741 496.39504 455.52303 32.724808 -357.63815 1306070.3 -1306815.3 5007.2365 48631.318 259.70198 0.081729799
|
|
1700 145.02103 2777.9556 2386.7756 165.6992 391.18003 636.61544 523.12627 482.84847 35.186128 -391.10505 1305919.7 -1306815.2 2192.7076 48631.318 258.14043 2.7318649
|
|
1750 149.22218 2829.5998 2559.2796 177.67509 270.32019 684.587 479.93609 446.30457 31.888933 -385.84966 1305832.5 -1306819.1 1683.1471 48631.318 276.95798 2.6465587
|
|
1800 153.41978 2835.768 2465.6959 171.17815 370.07208 470.05934 508.38934 479.71489 37.826868 -369.0767 1306062.8 -1306819.6 3023.0762 48631.318 268.22249 0.097440318
|
|
1850 157.62632 2857.7601 2504.3893 173.86439 353.37083 436.06841 516.10132 487.71301 36.514956 -385.43181 1306078.9 -1306816.5 2950.5189 48631.318 272.47825 0.016816883
|
|
1900 161.8372 2867.791 2528.8957 175.56572 338.89527 446.38065 509.27013 485.03036 37.283587 -402.68445 1306076.6 -1306812.9 3161.5045 48631.318 275.1476 0.011615474
|
|
1950 166.10858 2861.34 2513.9103 174.52538 347.4297 470.9855 536.84666 467.9604 36.049051 -430.05716 1306079.3 -1306813.6 738.77866 48631.318 273.51233 0.020075246
|
|
2000 170.32286 2838.0367 2530.4481 175.6735 307.58858 423.18694 516.91384 454.72628 35.048394 -387.67176 1306074.6 -1306809.3 4321.7103 48631.318 275.24492 0.13775419
|
|
Loop time of 170.323 on 1 procs for 2000 steps with 5500 atoms
|
|
|
|
Performance: 0.507 ns/day, 47.312 hours/ns, 11.742 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 | 105.66 | 105.66 | 105.66 | 0.0 | 62.04
|
|
Bond | 19.802 | 19.802 | 19.802 | 0.0 | 11.63
|
|
Kspace | 35.029 | 35.029 | 35.029 | 0.0 | 20.57
|
|
Neigh | 2.7502 | 2.7502 | 2.7502 | 0.0 | 1.61
|
|
Comm | 0.62654 | 0.62654 | 0.62654 | 0.0 | 0.37
|
|
Output | 0.006705 | 0.006705 | 0.006705 | 0.0 | 0.00
|
|
Modify | 6.3072 | 6.3072 | 6.3072 | 0.0 | 3.70
|
|
Other | | 0.1366 | | | 0.08
|
|
|
|
Nlocal: 5500 ave 5500 max 5500 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 15407 ave 15407 max 15407 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 1.30509e+06 ave 1.30509e+06 max 1.30509e+06 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1305088
|
|
Ave neighs/atom = 237.289
|
|
Ave special neighs/atom = 15.6364
|
|
Neighbor list builds = 44
|
|
Dangerous builds = 0
|
|
Total wall time: 0:02:50
|