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)
|
|
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
|
|
special bonds CPU = 0.00199628 secs
|
|
read_data CPU = 0.0169649 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 = 0.000807762 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 = 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 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 4782.1702 4728.7435 328.28767 53.426722 1812.2203 685.37824 683.70917 -3277.1645 797.34329 1305983.2 -1306631.2 16874.358 48631.318 448.52419 116.25477
|
|
100 2906.0879 3699.8031 256.85465 -793.7152 978.15364 778.36908 862.30899 -3270.1722 468.44888 1306096.8 -1306707.6 15631.384 48631.318 382.26408 35.748403
|
|
150 2089.0918 3593.0499 249.44342 -1503.9581 751.32283 803.47802 668.4757 -3277.5983 128.17444 1306138.5 -1306716.3 15193.04 48631.318 384.75632 10.892446
|
|
200 1547.3302 3248.639 225.53309 -1701.3089 699.65977 814.31164 692.83227 -3276.3957 -66.671816 1306160.9 -1306725.9 13787.676 48631.318 351.28242 3.8458668
|
|
250 1177.9323 3095.949 214.93276 -1918.0167 688.87262 842.44531 615.89218 -3278.4465 -210.06178 1306154.3 -1306731 8808.5835 48631.318 335.8115 1.8330994
|
|
300 895.90313 2870.3451 199.27046 -1974.442 734.95873 858.58147 624.00862 -3278.6022 -342.01951 1306163.6 -1306735 3388.4841 48631.318 311.56815 1.2987715
|
|
350 669.25785 2764.9587 191.95413 -2095.7009 662.44028 860.79714 602.69567 -3278.776 -376.37081 1306172.3 -1306738.8 8494.9184 48631.318 300.19414 1.1358594
|
|
400 531.21609 2722.6775 189.01881 -2191.4614 684.34049 868.77818 576.86096 -3280.1649 -459.66591 1306160 -1306741.6 6726.3087 48631.318 295.59622 1.1315427
|
|
450 427.05425 2611.7588 181.3184 -2184.7046 719.2042 891.88178 591.2282 -3279.339 -534.65069 1306172.2 -1306745.2 2398.5394 48631.318 283.56126 1.0726045
|
|
500 310.44891 2556.0967 177.45412 -2245.6477 720.86526 841.50195 586.3417 -3279.3029 -539.81715 1306169.5 -1306744.8 3028.595 48631.318 277.52314 1.0406334
|
|
550 207.83114 2531.3051 175.73299 -2323.4739 674.71188 855.2132 555.53227 -3280.0378 -553.93222 1306171.9 -1306746.9 4609.4408 48631.318 274.80629 1.0748601
|
|
600 88.81557 2459.9059 170.77619 -2371.0903 692.4485 834.47484 550.85905 -3280.9086 -595.31802 1306171.4 -1306744 2107.9995 48631.318 267.06312 1.0301965
|
|
650 75.616307 2416.9747 167.79573 -2341.3584 703.57186 869.98959 564.81201 -3280.7522 -619.8016 1306168 -1306747.2 1236.4829 48631.318 262.3542 1.0968447
|
|
700 49.832719 2415.7344 167.70963 -2365.9017 683.61663 882.67915 555.23571 -3280.7778 -615.06862 1306159.9 -1306751.4 2985.7048 48631.318 262.23095 1.0762424
|
|
750 41.513638 2427.218 168.50687 -2385.7044 698.87619 863.2938 564.58197 -3280.0156 -637.29964 1306160.1 -1306755.3 1653.117 48631.318 263.49803 1.0451977
|
|
800 109.53032 2481.9041 172.30339 -2372.3738 697.22709 897.36555 561.28745 -3280.6784 -651.29564 1306155 -1306751.3 1219.8761 48631.318 269.43698 1.0647792
|
|
850 98.142203 2502.3132 173.72026 -2404.171 696.5382 878.83293 566.44302 -3280.2837 -663.94587 1306155.6 -1306757.4 1122.7487 48631.318 271.67716 1.030267
|
|
900 62.992675 2409.7324 167.29295 -2346.7397 722.00541 896.64662 560.66083 -3279.4915 -644.05458 1306153.6 -1306756.1 1604.295 48631.318 261.58656 1.0609836
|
|
950 5.6677468 2403.5067 166.86073 -2397.839 725.07222 891.00249 556.81977 -3279.7848 -672.66389 1306141 -1306759.2 1019.1694 48631.318 260.91187 1.0562387
|
|
1000 38.526968 2444.97 169.73928 -2406.4431 704.72993 920.68493 534.59035 -3281.2673 -667.78091 1306141.1 -1306758.5 486.79846 48631.318 265.39928 1.098473
|
|
1050 21.698026 2388.6306 165.82798 -2366.9326 712.15539 934.39244 546.92027 -3281.1469 -654.7449 1306137.4 -1306761.9 1556.1256 48631.318 259.28203 1.0760765
|
|
1100 -26.971225 2433.8428 168.96678 -2460.814 710.11081 881.19212 524.51547 -3281.7925 -667.53202 1306137.1 -1306764.4 1203.8971 48631.318 264.20441 1.0706085
|
|
1150 -49.171269 2375.9688 164.94895 -2425.14 729.78127 918.79575 518.21967 -3281.6542 -675.7239 1306130.4 -1306765 229.44016 48631.318 257.89845 1.086519
|
|
1200 -53.421342 2422.0091 168.14524 -2475.4304 710.67274 884.2589 523.32524 -3282.2275 -674.49333 1306130.9 -1306767.9 -131.09655 48631.318 262.91124 1.0804821
|
|
1250 -58.534776 2394.4031 166.22873 -2452.9378 680.27486 909.58096 532.81959 -3281.5551 -653.13731 1306127 -1306767.9 546.96357 48631.318 259.92916 1.0424914
|
|
1300 -24.151217 2431.9902 168.83817 -2456.1414 681.27127 919.39245 536.41899 -3281.3717 -661.90875 1306121.6 -1306771.5 1455.7512 48631.318 264.00712 1.0630558
|
|
1350 -38.973062 2438.6194 169.2984 -2477.5925 707.96118 912.62518 519.44533 -3281.6739 -687.67183 1306126.1 -1306774.4 -1470.4442 48631.318 264.70225 1.1091537
|
|
1400 11.896539 2384.5407 165.54404 -2372.6442 719.03374 950.93261 550.5639 -3280.4581 -663.4921 1306122 -1306771.3 465.12854 48631.318 258.83564 1.0785364
|
|
1450 -13.118691 2436.6246 169.15991 -2449.7433 661.04397 933.07103 561.29537 -3280.6997 -672.68495 1306123.9 -1306775.7 -108.46564 48631.318 264.50636 1.0718787
|
|
1500 -38.151755 2417.4849 167.83116 -2455.6367 688.81484 892.35701 565.29013 -3279.6716 -662.1817 1306116.9 -1306777.2 517.89634 48631.318 262.44549 1.0338083
|
|
1550 -71.663334 2405.7016 167.01311 -2477.3649 681.78925 876.31247 559.003 -3280.451 -649.16641 1306112.8 -1306777.7 925.49349 48631.318 261.148 1.0609731
|
|
1600 -13.900431 2419.481 167.96973 -2433.3814 718.46559 909.67964 559.06779 -3280.8163 -667.6092 1306108 -1306780.2 13.95808 48631.318 262.63632 1.080229
|
|
1650 -16.403222 2431.075 168.77464 -2447.4783 710.99509 907.65662 551.60307 -3279.8852 -661.52624 1306104.5 -1306780.8 726.89923 48631.318 263.91553 1.0489963
|
|
1700 -18.555086 2438.2062 169.26971 -2456.7613 665.90475 943.02217 542.86579 -3280.9017 -657.99229 1306108 -1306777.7 801.41078 48631.318 264.67663 1.0750708
|
|
1750 -6.9249446 2443.9707 169.6699 -2450.8956 733.23573 890.06857 560.83229 -3280.362 -670.93883 1306098.3 -1306782.1 47.037748 48631.318 265.30892 1.0661143
|
|
1800 -21.686222 2434.3375 169.00113 -2456.0237 729.35297 899.9733 561.59516 -3280.4727 -680.98901 1306096.5 -1306782 495.63617 48631.318 264.25723 1.0723683
|
|
1850 -72.916947 2408.8254 167.22998 -2481.7423 683.24984 904.13282 549.97726 -3279.6699 -652.63212 1306099.2 -1306786 -120.61674 48631.318 261.48504 1.0659808
|
|
1900 -55.4099 2415.455 167.69023 -2470.8649 700.4473 904.72264 565.5266 -3280.4533 -673.23082 1306099.6 -1306787.4 202.15936 48631.318 262.20353 1.0709756
|
|
1950 -79.877997 2409.2307 167.25812 -2489.1087 695.9536 894.4541 564.7034 -3279.3581 -680.33472 1306100.8 -1306785.3 213.72828 48631.318 261.52921 1.0658433
|
|
2000 -102.20457 2399.4263 166.57746 -2501.6309 689.67819 894.58596 565.53233 -3280.7595 -680.39032 1306096.4 -1306786.6 1113.7499 48631.318 260.46311 1.0647045
|
|
Loop time of 68.4185 on 1 procs for 2000 steps with 5500 atoms
|
|
|
|
Performance: 1.263 ns/day, 19.005 hours/ns, 29.232 timesteps/s
|
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 48.825 | 48.825 | 48.825 | 0.0 | 71.36
|
|
Bond | 2.8852 | 2.8852 | 2.8852 | 0.0 | 4.22
|
|
Kspace | 13.795 | 13.795 | 13.795 | 0.0 | 20.16
|
|
Neigh | 1.0731 | 1.0731 | 1.0731 | 0.0 | 1.57
|
|
Comm | 0.27067 | 0.27067 | 0.27067 | 0.0 | 0.40
|
|
Output | 0.0031168 | 0.0031168 | 0.0031168 | 0.0 | 0.00
|
|
Modify | 1.5207 | 1.5207 | 1.5207 | 0.0 | 2.22
|
|
Other | | 0.04541 | | | 0.07
|
|
|
|
Nlocal: 5500 ave 5500 max 5500 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 13157 ave 13157 max 13157 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 1.33822e+06 ave 1.33822e+06 max 1.33822e+06 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1338215
|
|
Ave neighs/atom = 243.312
|
|
Ave special neighs/atom = 15.6364
|
|
Neighbor list builds = 32
|
|
Dangerous builds = 0
|
|
Total wall time: 0:01:08
|