forked from lijiext/lammps
178 lines
13 KiB
Groff
178 lines
13 KiB
Groff
|
LAMMPS (18 Jul 2015)
|
||
|
|
# 250 butane 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
|
||
|
|
special_bonds lj/coul 0.0 0.0 0.5
|
||
|
|
|
||
|
|
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||
|
|
pair_modify mix geometric tail yes
|
||
|
|
kspace_style pppm 1.0e-4
|
||
|
|
|
||
|
|
read_data data.butane
|
||
|
|
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||
|
|
2 by 1 by 2 MPI processor grid
|
||
|
|
reading atoms ...
|
||
|
|
4500 atoms
|
||
|
|
scanning bonds ...
|
||
|
|
5 = max bonds/atom
|
||
|
|
scanning angles ...
|
||
|
|
6 = max angles/atom
|
||
|
|
scanning dihedrals ...
|
||
|
|
9 = max dihedrals/atom
|
||
|
|
reading bonds ...
|
||
|
|
4250 bonds
|
||
|
|
reading angles ...
|
||
|
|
6000 angles
|
||
|
|
reading dihedrals ...
|
||
|
|
6750 dihedrals
|
||
|
|
5 = max # of 1-2 neighbors
|
||
|
|
8 = max # of 1-3 neighbors
|
||
|
|
12 = max # of 1-4 neighbors
|
||
|
|
17 = max # of special neighbors
|
||
|
|
|
||
|
|
group gBUTANE molecule 1:250
|
||
|
|
4500 atoms in group gBUTANE
|
||
|
|
group gCORES type 1 2 3
|
||
|
|
3500 atoms in group gCORES
|
||
|
|
group gDRUDES type 4 5
|
||
|
|
1000 atoms in group gDRUDES
|
||
|
|
|
||
|
|
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||
|
|
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||
|
|
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||
|
|
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||
|
|
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||
|
|
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||
|
|
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||
|
|
pair_coeff 1 * thole 1.368000
|
||
|
|
pair_coeff 2 * thole 1.368000
|
||
|
|
pair_coeff 4 * thole 1.368000
|
||
|
|
pair_coeff 5 * thole 1.368000
|
||
|
|
|
||
|
|
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 N D D
|
||
|
|
|
||
|
|
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||
|
|
0 = # of size 2 clusters
|
||
|
|
500 = # of size 3 clusters
|
||
|
|
500 = # of size 4 clusters
|
||
|
|
0 = # of frozen angles
|
||
|
|
|
||
|
|
comm_modify vel yes
|
||
|
|
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 ...
|
||
|
|
G vector (1/distance) = 0.367867
|
||
|
|
grid = 36 36 36
|
||
|
|
stencil order = 5
|
||
|
|
estimated absolute RMS force accuracy = 0.031354
|
||
|
|
estimated relative force accuracy = 9.44215e-05
|
||
|
|
using double precision FFTs
|
||
|
|
3d grid and FFT values/proc = 26875 11664
|
||
|
|
Rebuild special list taking Drude particles into account
|
||
|
|
Old max number of 1-2 to 1-4 neighbors: 17
|
||
|
|
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||
|
|
Neighbor list info ...
|
||
|
|
2 neighbor list requests
|
||
|
|
update every 1 steps, delay 10 steps, check yes
|
||
|
|
master list distance cutoff = 10
|
||
|
|
ghost atom cutoff = 10
|
||
|
|
Memory usage per processor = 14.7792 Mbytes
|
||
|
|
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||
|
|
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655
|
||
|
|
50 1.019057 2130.0808 1490.8248 136.43926 639.25599 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137
|
||
|
|
100 2.043848 2172.0553 1656.5476 151.60609 515.50769 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117
|
||
|
|
150 3.0405529 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6233 55742.797 218.02975 0.12336381
|
||
|
|
200 4.0440719 2271.1314 1750.9955 160.2499 520.13584 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.495 55742.797 220.19714 0.23035002
|
||
|
|
250 5.0482569 2333.7821 1793.0252 164.09642 540.75694 153.18169 833.95288 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339003
|
||
|
|
300 6.044857 2403.6147 1909.3441 174.74185 494.27053 144.273 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3723 55742.797 239.06243 3.0455683
|
||
|
|
350 7.0382209 2448.239 1862.67 170.47027 585.56896 181.70522 821.79171 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806438
|
||
|
|
400 8.025661 2498.6992 1942.5496 177.78079 556.14963 168.5792 828.99116 182.0756 0 -1050.149 595296.43 -594869.77 485.86784 55742.797 244.23632 0.38827289
|
||
|
|
450 9.010309 2552.9639 1890.0917 172.97988 662.87225 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452466 55742.797 237.65323 0.34464586
|
||
|
|
500 9.979717 2608.5501 1970.0729 180.29971 638.47718 187.01392 838.62128 176.10774 0 -985.23355 595290.89 -594868.93 3471.1636 55742.797 247.59402 0.66791289
|
||
|
|
550 10.965174 2667.002 1875.8227 171.674 791.17932 178.48766 1003.6885 176.78987 0 -991.21707 595292.35 -594868.92 1767.0547 55742.797 235.34039 1.7252612
|
||
|
|
600 11.944224 2715.2397 1883.279 172.35639 831.96067 186.79504 1047.6877 183.0431 0 -1010.5423 595293.27 -594868.29 931.85415 55742.797 236.28437 1.7094243
|
||
|
|
650 12.916431 2754.4495 1970.794 180.36571 783.65547 166.02823 963.09393 184.84638 0 -952.45216 595290.25 -594868.11 2640.0169 55742.797 247.67755 0.68709272
|
||
|
|
700 13.889729 2795.9463 1928.2674 176.47369 867.67893 176.09642 1002.4636 186.11482 0 -920.14357 595291.32 -594868.18 664.78857 55742.797 242.41896 0.44316458
|
||
|
|
750 14.849284 2838.2051 2043.2257 186.9946 794.97938 170.34989 941.73149 193.53082 0 -940.49605 595298.1 -594868.23 410.24692 55742.797 256.84034 0.55228895
|
||
|
|
800 15.765569 2881.9786 1945.9721 178.09402 936.00653 197.52035 1021.5571 202.83523 0 -915.18508 595297.49 -594868.21 -716.8133 55742.797 244.35111 1.2303486
|
||
|
|
850 16.62147 2923.386 2106.5752 192.79231 816.81079 195.9499 886.4168 184.36063 0 -878.10486 595296.29 -594868.1 -1407.5716 55742.797 264.3276 1.8387295
|
||
|
|
900 17.476931 2950.6672 2039.6221 186.6648 911.04508 183.7962 1000.7955 184.49765 0 -890.38971 595299.97 -594867.63 -1085.795 55742.797 256.21167 1.0198179
|
||
|
|
950 18.332394 2976.6435 2006.5931 183.64202 970.05037 228.60059 985.21322 206.18531 0 -881.65816 595299.54 -594867.83 -1851.9704 55742.797 252.23636 0.54012295
|
||
|
|
1000 19.192022 3003.7432 2056.8471 188.24122 946.89612 171.73291 976.85679 207.05089 0 -836.24565 595294.95 -594867.45 282.61893 55742.797 258.5658 0.52076763
|
||
|
|
1050 20.070536 3031.3535 2095.4845 191.77729 935.86893 203.54188 945.75571 204.85039 0 -846.10968 595294.45 -594866.62 -376.91144 55742.797 263.27092 0.93584075
|
||
|
|
1100 20.978902 3058.5346 2047.3099 187.36839 1011.2247 211.94079 1001.093 223.66207 0 -855.82432 595297.13 -594866.78 -1381.6546 55742.797 256.93411 1.6724371
|
||
|
|
1150 21.886788 3078.3992 2123.1811 194.31206 955.21814 189.50191 937.18689 224.21463 0 -823.63239 595294.38 -594866.43 524.69914 55742.797 266.59741 1.3568273
|
||
|
|
1200 22.731807 3093.5558 2005.8937 183.57801 1087.6621 201.34278 1044.991 219.39206 0 -805.37129 595293.83 -594866.52 -370.32731 55742.797 252.08289 0.71475598
|
||
|
|
1250 23.577332 3108.5154 2175.8971 199.1366 932.61825 156.65715 969.72264 225.30585 0 -850.00508 595297.25 -594866.31 -1015.3099 55742.797 273.53152 0.55101046
|
||
|
|
1300 24.41954 3122.979 2090.3725 191.30944 1032.6065 209.92008 984.36627 236.75348 0 -825.27575 595292.92 -594866.08 -798.51517 55742.797 262.69428 0.75855174
|
||
|
|
1350 25.260247 3136.8213 2084.4701 190.76926 1052.3512 186.49846 1004.7564 234.55382 0 -798.08358 595290.25 -594865.63 702.53502 55742.797 261.71554 1.3884097
|
||
|
|
1400 26.111855 3144.9027 2180.3656 199.54555 964.53705 170.02479 962.43949 235.07796 0 -829.2718 595291.77 -594865.51 1682.2458 55742.797 273.72857 1.5246347
|
||
|
|
1450 26.950639 3146.3362 2013.3813 184.26326 1132.955 193.77936 1084.1402 252.32287 0 -821.23025 595288.54 -594864.6 -160.21134 55742.797 252.96371 0.87779957
|
||
|
|
1500 27.790502 3150.6919 2107.4861 192.87567 1043.2058 185.11758 988.72513 245.47693 0 -796.86696 595285.47 -594864.71 2242.3607 55742.797 264.90213 0.61222945
|
||
|
|
1550 28.619789 3156.3482 2074.5978 189.86575 1081.7504 166.52858 1062.4966 238.93331 0 -810.65249 595289.34 -594864.9 2224.9023 55742.797 260.7359 0.68881915
|
||
|
|
1600 29.460929 3163.8714 2000.6737 183.10027 1163.1978 210.70797 1110.4522 256.16659 0 -840.14623 595290.73 -594864.71 -830.17835 55742.797 251.26509 1.1443132
|
||
|
|
1650 30.299437 3169.3484 2056.4317 188.20321 1112.9167 214.64223 1021.7623 268.00145 0 -815.6963 595289 -594864.8 813.10459 55742.797 258.12846 1.5476742
|
||
|
|
1700 31.139599 3168.7665 2119.4084 193.96679 1049.3581 147.25025 1027.6419 246.49323 0 -797.55219 595290.74 -594865.22 412.56019 55742.797 266.23023 1.0703144
|
||
|
|
1750 31.982883 3168.2311 2066.7649 189.14889 1101.4662 224.43981 1005.0038 243.56888 0 -797.82899 595291.25 -594864.96 -858.8853 55742.797 259.74652 0.69941609
|
||
|
|
1800 32.826623 3169.7582 2109.6043 193.06952 1060.154 204.57671 981.05578 249.38028 0 -801.42264 595291.51 -594864.95 137.07377 55742.797 265.1523 0.65571522
|
||
|
|
1850 33.670608 3174.8602 2133.4946 195.25594 1041.3657 175.87741 982.18471 244.56078 0 -786.49062 595290.44 -594865.21 882.07943 55742.797 268.02634 1.0063027
|
||
|
|
1900 34.515605 3180.392 2106.493 192.78478 1073.8991 207.88481 977.47602 250.68433 0 -788.04013 595290.55 -594864.66 574.47687 55742.797 264.45328 1.4759962
|
||
|
|
1950 35.361549 3182.9198 2084.8984 190.80846 1098.0214 207.26715 1007.5534 256.52264 0 -800.37486 595291.76 -594864.71 -981.72234 55742.797 261.81317 1.2717649
|
||
|
|
2000 36.208456 3185.292 2079.8093 190.34271 1105.4827 185.44479 1008.7001 251.06381 0 -766.97114 595292.22 -594864.97 661.65731 55742.797 261.3551 0.78598984
|
||
|
|
Loop time of 36.2086 on 4 procs for 2000 steps with 4500 atoms
|
||
|
|
|
||
|
|
Pair time (%) = 15.6569 (43.2408)
|
||
|
|
Bond time (%) = 4.33273 (11.966)
|
||
|
|
Kspce time (%) = 10.271 (28.3662)
|
||
|
|
Neigh time (%) = 0.435532 (1.20284)
|
||
|
|
Comm time (%) = 0.83936 (2.31813)
|
||
|
|
Outpt time (%) = 0.00456434 (0.0126057)
|
||
|
|
Other time (%) = 4.66849 (12.8933)
|
||
|
|
|
||
|
|
Nlocal: 1125 ave 1165 max 1096 min
|
||
|
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||
|
|
Nghost: 5854.5 ave 5931 max 5788 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||
|
|
Neighs: 193727 ave 200966 max 187020 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
|
||
|
|
Total # of neighbors = 774908
|
||
|
|
Ave neighs/atom = 172.202
|
||
|
|
Ave special neighs/atom = 13.3333
|
||
|
|
Neighbor list builds = 35
|
||
|
|
Dangerous builds = 0
|