forked from lijiext/lammps
255 lines
17 KiB
Groff
255 lines
17 KiB
Groff
LAMMPS (7 Aug 2019)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
|
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 fourier
|
|
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
|
|
special bonds CPU = 0.000747919 secs
|
|
read_data CPU = 0.0168228 secs
|
|
|
|
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
|
|
find clusters CPU = 0.000355244 secs
|
|
|
|
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 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 ...
|
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
|
|
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 FFTW3
|
|
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 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 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
|
|
50 4712.9507 4669.1606 324.15119 43.790082 1798.561 670.61319 690.16967 -3276.9493 811.643 1305983.2 -1306633.5 17164.771 48631.318 442.24313 116.13094
|
|
100 2865.9139 3726.4166 258.70226 -860.50272 968.87546 749.70761 860.70151 -3270.7784 427.14745 1306104.7 -1306700.9 15017.273 48631.318 385.10628 35.845353
|
|
150 1982.6673 3535.974 245.481 -1553.3068 764.86116 768.15837 658.70182 -3278.7906 108.49859 1306136.5 -1306711.2 16495.352 48631.318 378.64023 10.723986
|
|
200 1440.0277 3240.5932 224.97452 -1800.5656 687.71813 791.29356 643.82915 -3276.9293 -99.549986 1306172.9 -1306719.8 13234.476 48631.318 350.46321 3.7468464
|
|
250 1103.2915 3018.496 209.55567 -1915.2045 677.97905 825.32748 642.78891 -3278.0801 -226.1853 1306168.5 -1306725.5 8774.9103 48631.318 327.36313 1.8722119
|
|
300 789.07159 2827.1716 196.27319 -2038.1 735.96101 852.72545 589.14167 -3280.0357 -374.66018 1306169 -1306730.2 2259.1028 48631.318 306.85585 1.3262598
|
|
350 599.10023 2732.3739 189.69197 -2133.2737 677.67006 863.22888 565.41674 -3280.5231 -403.28794 1306177.4 -1306733.2 7989.222 48631.318 296.64126 1.1534418
|
|
400 428.26436 2591.2884 179.89727 -2163.0241 676.18745 849.24505 612.34065 -3277.4703 -457.85799 1306173.6 -1306739.1 7282.1438 48631.318 281.34719 1.0502762
|
|
450 307.26859 2534.2468 175.93722 -2226.9782 712.17636 853.98862 578.01327 -3279.7731 -533.87422 1306179.7 -1306737.2 1897.9643 48631.318 275.11317 1.0980929
|
|
500 234.60959 2495.1082 173.22007 -2260.4987 707.43541 878.25753 547.08402 -3281.2756 -549.04991 1306176.5 -1306739.5 2683.0639 48631.318 270.85452 1.0984718
|
|
550 203.34751 2445.6535 169.78673 -2242.306 669.03724 892.85034 599.20664 -3279.0757 -559.81157 1306175.9 -1306740.4 4512.9992 48631.318 265.49465 1.0628812
|
|
600 205.63573 2526.5892 175.4056 -2320.9535 685.64073 887.97693 557.42296 -3280.0332 -597.34755 1306167.8 -1306742.5 2999.5823 48631.318 274.29935 1.064682
|
|
650 176.23031 2526.3124 175.38638 -2350.0821 714.15285 895.42115 540.39191 -3280.8567 -636.27783 1306165.7 -1306748.6 871.68316 48631.318 274.2807 1.0442089
|
|
700 106.97524 2441.1059 169.47101 -2334.1306 697.16018 905.51407 564.71847 -3279.6208 -631.62324 1306159.4 -1306749.6 1953.8241 48631.318 264.98935 1.0771037
|
|
750 76.695104 2435.6635 169.09318 -2358.9684 672.01039 934.63351 545.64024 -3281.1075 -629.89722 1306152.4 -1306752.6 3044.0155 48631.318 264.39002 1.0932471
|
|
800 57.614075 2456.928 170.56945 -2399.3139 720.76364 898.68013 534.10051 -3281.5897 -659.64354 1306145.5 -1306757.1 1691.9503 48631.318 266.72089 1.0622697
|
|
850 -44.931126 2390.0608 165.92727 -2434.9919 708.70192 888.26851 537.13087 -3281.355 -665.17283 1306137.8 -1306760.3 123.07165 48631.318 259.45151 1.0516426
|
|
900 -96.878205 2358.862 163.76133 -2455.7403 672.98976 868.41571 546.69492 -3280.6939 -636.80102 1306134.5 -1306760.9 1955.7005 48631.318 256.05598 1.05337
|
|
950 -80.012575 2374.4497 164.84349 -2454.4623 679.59722 880.35157 548.35372 -3280.6061 -643.44517 1306125.8 -1306764.5 1510.9809 48631.318 257.72442 1.1017392
|
|
1000 -21.440874 2440.6729 169.44096 -2462.1138 718.56593 868.65109 555.54643 -3279.8516 -686.71673 1306126.6 -1306765 -1148.6212 48631.318 264.92977 1.1019339
|
|
1050 16.46903 2382.6961 165.41598 -2366.2271 712.51245 913.35848 579.81678 -3280.0559 -657.12122 1306129.3 -1306764 1004.5778 48631.318 258.64076 1.0684155
|
|
1100 35.847247 2483.1985 172.39325 -2447.3513 685.05704 889.42278 553.73166 -3280.0177 -663.67201 1306134.3 -1306766.2 699.1824 48631.318 269.56773 1.0838094
|
|
1150 -4.9817843 2431.4725 168.80223 -2436.4543 720.51056 868.17547 569.09902 -3280.5829 -677.99865 1306133.1 -1306768.7 435.19118 48631.318 263.96966 1.0303202
|
|
1200 -23.907197 2443.6035 169.64441 -2467.5107 684.96437 887.58483 549.43666 -3280.3144 -679.46182 1306137.2 -1306766.9 367.11148 48631.318 265.28645 1.0344036
|
|
1250 -16.904671 2389.9447 165.91921 -2406.8494 722.06959 902.90076 568.35616 -3280.6829 -683.32029 1306132.9 -1306769.1 76.759445 48631.318 259.41697 1.0908431
|
|
1300 -1.7822102 2410.2768 167.33074 -2412.0591 706.98675 904.31941 551.23506 -3280.7552 -651.51211 1306127.3 -1306769.6 1659.1113 48631.318 261.64093 1.0701648
|
|
1350 -3.569473 2446.3901 169.83786 -2449.9595 686.13971 894.85839 558.36242 -3279.9941 -664.59508 1306129 -1306773.7 783.32881 48631.318 265.5696 1.0709072
|
|
1400 -33.385576 2400.262 166.63547 -2433.6476 709.5808 890.68408 571.13105 -3280.1428 -674.51247 1306123.4 -1306773.8 -751.38571 48631.318 260.54522 1.080234
|
|
1450 -11.215152 2405.5409 167.00196 -2416.756 703.72038 913.21131 552.64196 -3280.9831 -649.19774 1306120.3 -1306776.4 1817.2174 48631.318 261.14741 1.031193
|
|
1500 -25.974102 2435.8375 169.10527 -2461.8116 689.93174 900.70619 552.63711 -3280.1497 -671.17989 1306124 -1306777.8 -98.941796 48631.318 264.45069 1.0190784
|
|
1550 -76.496407 2394.8126 166.25716 -2471.309 706.96953 886.06919 549.9101 -3280.8434 -659.57745 1306105.9 -1306779.7 -7.0989994 48631.318 259.95403 1.0772144
|
|
1600 -79.549932 2395.1114 166.2779 -2474.6614 684.11692 888.93332 562.94522 -3280.1665 -665.21744 1306114.4 -1306779.6 320.58515 48631.318 260.00641 1.0425978
|
|
1650 -99.702003 2360.5652 163.87957 -2460.2672 706.21244 900.9253 540.36599 -3280.2308 -655.96077 1306109.7 -1306781.3 307.35487 48631.318 256.23383 1.0666637
|
|
1700 -69.422658 2372.1727 164.68541 -2441.5954 676.79347 913.90473 581.60658 -3279.997 -670.33218 1306115.7 -1306779.3 -204.22848 48631.318 257.50963 1.0434075
|
|
1750 -80.889897 2425.3592 168.37782 -2506.2491 672.88937 911.52373 523.74733 -3280.4796 -673.90027 1306122 -1306782 965.12568 48631.318 263.26491 1.1001595
|
|
1800 -82.419368 2361.798 163.96515 -2444.2173 716.51571 882.9729 577.92505 -3278.9279 -671.67438 1306111.6 -1306782.6 -44.954517 48631.318 256.36957 1.0636692
|
|
1850 -93.715705 2373.3359 164.76616 -2467.0516 713.02466 907.03621 563.38626 -3280.2576 -693.30963 1306104.6 -1306781.5 -979.95945 48631.318 257.62543 1.0628288
|
|
1900 -73.60945 2449.5873 170.05983 -2523.1967 683.65116 893.94251 539.90847 -3281.4318 -680.16358 1306108 -1306787.1 598.18213 48631.318 265.91405 1.0766352
|
|
1950 -66.068291 2437.3691 169.21159 -2503.4374 672.5168 877.42934 573.56499 -3279.885 -668.54185 1306109.2 -1306787.7 733.05074 48631.318 264.61409 1.0224258
|
|
2000 -91.043979 2374.4077 164.84057 -2465.4516 692.13299 909.46192 574.60109 -3279.837 -672.33599 1306102.4 -1306791.8 -665.61581 48631.318 257.76275 1.0263294
|
|
Loop time of 23.7656 on 4 procs for 2000 steps with 5500 atoms
|
|
|
|
Performance: 3.636 ns/day, 6.602 hours/ns, 84.155 timesteps/s
|
|
94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 11.918 | 13.096 | 14.137 | 27.0 | 55.10
|
|
Bond | 0.74012 | 0.76511 | 0.79225 | 2.9 | 3.22
|
|
Kspace | 6.7821 | 7.8285 | 9.0172 | 35.4 | 32.94
|
|
Neigh | 0.37249 | 0.37262 | 0.37278 | 0.0 | 1.57
|
|
Comm | 0.70503 | 0.7188 | 0.72807 | 1.1 | 3.02
|
|
Output | 0.0018752 | 0.0047592 | 0.013386 | 7.2 | 0.02
|
|
Modify | 0.91164 | 0.91644 | 0.92123 | 0.5 | 3.86
|
|
Other | | 0.06335 | | | 0.27
|
|
|
|
Nlocal: 1375 ave 1381 max 1368 min
|
|
Histogram: 1 0 0 0 0 1 1 0 0 1
|
|
Nghost: 7803.75 ave 7856 max 7755 min
|
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
|
Neighs: 334465 ave 349504 max 315867 min
|
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
|
|
|
Total # of neighbors = 1337859
|
|
Ave neighs/atom = 243.247
|
|
Ave special neighs/atom = 15.6364
|
|
Neighbor list builds = 32
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:23
|