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Example simulations of polarizable systems using Drude oscillators
==================================================================
Each example comes in two versions for demonstrating the use of
Nosé-Hoover or Langevin thermostats.
* `butane` -- simulation in NVT ensemble with Thole damping
* `ethanol` -- simulation in NpT ensemble with Thole damping
* `swm4-ndp` -- 4-site rigid water model in NpT ensemble (no Thole
damping)

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# 250 butane system for drude polarizability example (Langevin)
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
comm_modify vel yes
group gBUTANE molecule 1:250
group gCORES type 1 2 3
group gDRUDES type 4 5
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 gDRUDES create ${vTEMP_D} 12345
fix fDRUDE all drude C C N D D
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 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

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# 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
group gBUTANE molecule 1:250
group gCORES type 1 2 3
group gDRUDES type 4 5
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 gDRUDES create ${vTEMP_D} 12345
fix fDRUDE all drude C C N D D
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
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 fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 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

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LAMMPS (18 Jul 2015)
# 250 butane system for drude polarizability example (Langevin)
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)
1 by 1 by 1 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
comm_modify vel yes
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
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 ...
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 = 79507 46656
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 = 20.1567 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 2.8944459 3475.1575 2067.5082 189.21692 1407.6493 846.00752 810.92425 115.58516 0 -764.28457 595242.38 -594842.96 3029.5187 55742.797 202.89871 152.54291
100 5.6009829 2975.2938 1988.4777 181.98411 986.81605 358.65377 931.63831 175.54125 0 -919.10691 595306.8 -594866.71 2010.6143 55742.797 231.36532 50.118891
150 8.2652578 2904.7202 1962.6821 179.62331 942.03808 234.91712 997.34884 195.22618 0 -909.31364 595293.23 -594869.37 4956.5664 55742.797 241.54715 14.313437
200 10.97319 2905.616 1909.813 174.78477 995.80302 228.33514 1082.3513 200.51771 0 -943.19777 595298.16 -594870.37 2973.6338 55742.797 238.34584 5.1137785
250 13.676164 2934.0626 1952.0155 178.6471 982.0471 212.76463 1131.5055 194.94566 0 -983.79846 595297.63 -594871 1591.8677 55742.797 244.66672 2.4161409
300 16.381759 2995.4781 2017.7772 184.66557 977.70088 213.25867 1133.9492 195.13329 0 -992.6543 595299.31 -594871.29 2817.7518 55742.797 253.21545 1.6812532
350 19.14905 3058.4882 1982.338 181.4222 1076.1502 228.54692 1197.9766 205.68279 0 -982.30502 595297.25 -594871 1408.2609 55742.797 248.83728 1.4672371
400 21.914272 3016.5895 1998.3531 182.8879 1018.2363 238.06518 1169.309 197.52924 0 -1014.8678 595298.98 -594870.78 1454.1926 55742.797 250.8778 1.3985907
450 24.629148 3014.232 1979.0496 181.12125 1035.1824 216.45567 1198.2831 197.81853 0 -1005.5029 595298.68 -594870.56 1296.2887 55742.797 248.44786 1.4025051
500 27.390589 3054.4694 2023.8824 185.22432 1030.587 220.97548 1197.2137 199.51957 0 -1014.3543 595298.28 -594871.05 2481.3102 55742.797 254.08894 1.4000969
550 30.147365 3088.0877 2020.1967 184.887 1067.8909 221.93439 1216.8427 213.27263 0 -1012.4867 595299.44 -594871.11 1697.8283 55742.797 253.63701 1.3687703
600 32.854639 3112.7966 2031.7038 185.94013 1081.0928 220.37419 1254.8806 208.09272 0 -1030.3329 595298.95 -594870.87 -75.358619 55742.797 255.05809 1.439614
650 35.725004 3155.4753 2025.6962 185.39031 1129.7792 221.82928 1284.1281 210.16702 0 -1015.1565 595299.63 -594870.82 1286.1601 55742.797 254.30974 1.4197689
700 38.70379 3134.5524 2054.9292 188.0657 1079.6232 225.36387 1243.5643 191.53984 0 -1010.9148 595301.25 -594871.18 700.78109 55742.797 257.97902 1.4421042
750 41.679769 3189.6098 2103.3042 192.49294 1086.3056 219.5641 1243.9772 203.81533 0 -1010.2161 595299.86 -594870.7 482.90086 55742.797 264.08828 1.3795515
800 44.637671 3173.7718 2053.4131 187.92694 1120.3587 219.52183 1256.8457 218.62858 0 -1003.175 595299.34 -594870.81 538.9293 55742.797 257.80398 1.4002525
850 47.531367 3221.5884 2084.0326 190.72922 1137.5559 224.32279 1277.7167 218.74781 0 -1011.3685 595298.54 -594870.4 145.40179 55742.797 261.66451 1.3777132
900 50.379314 3214.7916 2054.2398 188.00261 1160.5518 222.07439 1296.738 225.4151 0 -1013.6054 595300.61 -594870.68 490.09072 55742.797 257.90629 1.4047863
950 53.038527 3213.4974 2122.2134 194.2235 1091.284 221.85551 1252.3002 201.89089 0 -1014.1089 595300.04 -594870.69 1203.4321 55742.797 266.42418 1.4941572
1000 55.653448 3212.7244 2079.8287 190.34449 1132.8956 225.42816 1261.5078 204.71764 0 -986.95829 595298.68 -594870.48 790.47665 55742.797 261.10437 1.4611106
1050 58.290098 3216.1124 2106.2454 192.76212 1109.8669 213.54607 1261.1068 207.93437 0 -1001.5715 595299.05 -594870.2 69.145866 55742.797 264.43815 1.4332898
1100 60.921228 3218.0797 2082.4185 190.5815 1135.6611 236.95827 1266.8625 198.25038 0 -995.08857 595298.88 -594870.2 694.35787 55742.797 261.43907 1.4374087
1150 63.510285 3208.3968 2119.1968 193.94742 1089.2 210.20908 1236.1825 202.19163 0 -988.56762 595299.35 -594870.17 1528.4475 55742.797 266.08185 1.3950176
1200 66.140576 3219.1289 2078.071 190.18362 1141.0579 234.57015 1268.2146 206.93186 0 -997.01686 595298.32 -594869.97 939.70203 55742.797 260.89628 1.4263352
1250 68.774998 3268.5006 2115.3231 193.5929 1153.1775 241.50662 1262.3711 220.71001 0 -1000.1626 595298.37 -594869.62 -187.61926 55742.797 265.57695 1.4418423
1300 71.409732 3324.099 2138.7146 195.73368 1185.3844 242.3031 1279.7915 223.94399 0 -989.04901 595298.47 -594870.08 258.69655 55742.797 268.51674 1.4497832
1350 73.990336 3290.8471 2103.0993 192.47419 1187.7477 219.60844 1312.8653 221.57552 0 -993.69832 595297.61 -594870.21 1651.4259 55742.797 264.03877 1.4428477
1400 76.620059 3227.0141 2052.6998 187.86167 1174.3143 236.01325 1272.4804 217.65692 0 -979.6779 595297.5 -594869.66 595.11702 55742.797 257.67276 1.5108922
1450 79.249466 3253.5975 2107.984 192.92124 1145.6135 248.51645 1261.8304 208.79164 0 -1002.8333 595299.15 -594869.84 170.12671 55742.797 264.66781 1.4041436
1500 81.830899 3276.1976 2101.6206 192.33886 1174.577 242.38394 1288.61 204.9722 0 -989.7383 595298.02 -594869.67 619.26135 55742.797 263.84288 1.4691362
1550 84.449908 3271.9376 2117.6914 193.80965 1154.2463 234.62432 1268.5368 202.02117 0 -979.66071 595298.65 -594869.92 568.43047 55742.797 265.86458 1.4693675
1600 87.073373 3281.1387 2105.1447 192.66139 1175.994 219.69265 1288.3244 205.52796 0 -966.68015 595298.79 -594869.67 1351.6273 55742.797 264.27256 1.5056051
1650 89.695136 3287.675 2131.7955 195.10045 1155.8795 235.54527 1262.9178 220.26583 0 -991.68887 595298.56 -594869.72 -750.34342 55742.797 267.63101 1.4905169
1700 92.342235 3295.9626 2079.4982 190.31424 1216.4644 232.74928 1329.4691 218.51323 0 -992.04439 595297.16 -594869.38 589.94184 55742.797 261.06357 1.4590401
1750 94.911541 3315.2639 2097.2605 191.93983 1218.0035 241.24927 1312.3575 214.88139 0 -978.98823 595298.34 -594869.84 -92.971422 55742.797 263.26817 1.5389785
1800 97.525025 3241.5219 2086.8653 190.98847 1154.6566 221.03432 1282.1774 209.03793 0 -986.54668 595299 -594870.05 456.17335 55742.797 261.96332 1.5311996
1850 100.13804 3222.7069 2040.0335 186.70245 1182.6734 242.74754 1272.8794 221.80974 0 -982.51665 595296.99 -594869.24 279.00233 55742.797 256.09213 1.4766233
1900 102.70693 3190.3766 2032.3946 186.00335 1157.9819 213.06329 1268.187 220.21025 0 -971.50314 595297.54 -594869.51 499.15225 55742.797 255.16226 1.3935863
1950 105.30868 3208.3096 2053.9844 187.97923 1154.3252 212.46296 1277.2726 210.16078 0 -974.19087 595298.44 -594869.82 807.22906 55742.797 257.85261 1.4622515
2000 107.9105 3231.8811 2053.6913 187.9524 1178.1899 229.11239 1280.6492 220.1084 0 -979.25259 595297.02 -594869.45 474.05197 55742.797 257.80782 1.4833297
Loop time of 107.911 on 1 procs for 2000 steps with 4500 atoms
Pair time (%) = 65.8442 (61.0173)
Bond time (%) = 16.6061 (15.3887)
Kspce time (%) = 20.7451 (19.2244)
Neigh time (%) = 1.24307 (1.15195)
Comm time (%) = 0.386346 (0.358024)
Outpt time (%) = 0.00603366 (0.00559135)
Other time (%) = 3.07976 (2.854)
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8739 ave 8739 max 8739 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 860638 ave 860638 max 860638 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 860638
Ave neighs/atom = 191.253
Ave special neighs/atom = 13.3333
Neighbor list builds = 28
Dangerous builds = 0

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LAMMPS (18 Jul 2015)
# 250 butane system for drude polarizability example (Langevin)
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
comm_modify vel yes
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
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 ...
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 0.91017509 3449.6475 2040.7698 186.76984 1408.8777 836.85155 816.32124 115.24642 0 -758.7276 595242.44 -594843.26 3042.2937 55742.797 199.51659 152.7045
100 1.829694 2917.9137 1947.102 178.19743 970.81176 363.96553 932.94225 165.60761 0 -931.00296 595306.34 -594867.04 1697.0127 55742.797 226.24749 49.885738
150 2.6620312 2853.3142 1959.0731 179.29301 894.24108 244.19792 978.17893 187.28366 0 -941.03478 595295.44 -594869.82 4597.2005 55742.797 241.05848 14.405808
200 3.4969041 2885.6715 1928.6381 176.50762 957.03347 227.09245 1066.5297 186.6858 0 -949.52603 595296.49 -594870.24 2602.8275 55742.797 240.70211 5.1458056
250 4.621171 2905.8961 1939.7876 177.52802 966.10847 215.77945 1122.1238 195.98218 0 -993.52132 595296.54 -594870.79 1808.1681 55742.797 243.04306 2.643716
300 5.5216351 2968.5517 1974.9277 180.74402 993.624 210.11413 1158.7871 194.142 0 -996.53154 595297.91 -594870.79 3371.8618 55742.797 247.7682 1.8321312
350 6.3789251 2996.151 1992.9982 182.39782 1003.1527 217.80518 1150.726 205.32316 0 -996.14478 595296.05 -594870.61 3022.9945 55742.797 250.15947 1.5176819
400 7.208317 2991.7201 1975.3852 180.78589 1016.3349 221.46133 1169.8254 213.90874 0 -1016.9906 595298.44 -594870.31 753.59124 55742.797 247.99744 1.3743032
450 8.0359671 3061.6051 2009.1302 183.87421 1052.4749 212.54169 1234.7697 205.71762 0 -1028.2259 595297.95 -594870.28 996.71341 55742.797 252.23801 1.3870863
500 8.8456361 3127.3783 2009.8033 183.93581 1117.5749 222.16507 1246.5854 215.82607 0 -994.66665 595298.3 -594870.63 2537.6157 55742.797 252.32947 1.367397
550 9.6647151 3181.037 2069.9836 189.44346 1111.0534 218.00575 1246.961 212.55852 0 -992.83597 595296.16 -594869.79 1333.8768 55742.797 259.86467 1.4641506
600 10.484356 3194.2009 2007.5349 183.7282 1186.666 228.93838 1309.4718 215.93595 0 -995.70641 595297.81 -594869.79 1336.7994 55742.797 252.00698 1.4677515
650 11.30116 3145.4387 2028.2544 185.62444 1117.1843 209.73722 1277.9793 217.12799 0 -1015.2398 595297.88 -594870.3 1442.6875 55742.797 254.61499 1.4639962
700 12.106719 3163.3345 2053.2645 187.91335 1110.07 209.45249 1257.3108 216.7541 0 -1000.1505 595296.63 -594869.92 1093.9724 55742.797 257.76091 1.4652884
750 12.924665 3145.6215 2010.7195 184.01966 1134.902 224.53065 1248.3301 222.25374 0 -988.4479 595298.83 -594870.59 470.73988 55742.797 252.39115 1.5116555
800 13.736913 3191.2614 2043.4195 187.01234 1147.842 225.71717 1239.3564 234.89539 0 -980.97352 595299.07 -594870.22 1472.0305 55742.797 256.53524 1.4309304
850 14.550736 3157.6279 2004.8472 183.48223 1152.7806 217.72587 1269.3398 224.40554 0 -987.51794 595299.15 -594870.32 293.76575 55742.797 251.69397 1.4007963
900 15.344895 3188.5027 2077.065 190.09155 1111.4377 216.92608 1251.4141 213.7672 0 -1000.1269 595299.5 -594870.05 702.56821 55742.797 260.7853 1.3847905
950 16.157597 3205.6761 2090.9807 191.3651 1114.6954 223.7729 1252.7887 225.91029 0 -1016.3682 595299.15 -594870.56 -19.492925 55742.797 262.50762 1.4603579
1000 16.969809 3231.5931 2078.7058 190.24172 1152.8873 228.77504 1273.1611 219.28923 0 -995.58473 595296.82 -594869.57 1292.4071 55742.797 260.98775 1.3954023
1050 17.771785 3264.2837 2106.0113 192.7407 1158.2724 224.16481 1278.5557 212.91309 0 -985.93386 595298.71 -594870.14 1357.1588 55742.797 264.40381 1.4463397
1100 18.572331 3243.3355 2125.1664 194.49376 1118.1691 227.38559 1247.5134 210.61488 0 -996.85878 595299.68 -594870.17 650.53225 55742.797 266.82195 1.4240918
1150 19.40463 3255.4144 2096.5982 191.87922 1158.8162 234.11389 1267.4257 217.02225 0 -989.70892 595299.81 -594869.84 688.78475 55742.797 263.2133 1.4631154
1200 20.321045 3266.2609 2088.3727 191.12642 1177.8882 225.40174 1284.1097 225.77008 0 -985.63518 595297.81 -594869.57 182.80287 55742.797 262.21901 1.3550749
1250 21.233994 3277.4365 2093.1481 191.56346 1184.2884 250.33569 1267.9985 235.70102 0 -999.80819 595299.96 -594869.9 780.87528 55742.797 262.80001 1.4077597
1300 22.113268 3280.4141 2121.4996 194.15818 1158.9145 228.23585 1259.7304 230.65174 0 -989.06345 595298.99 -594869.63 932.19341 55742.797 266.34543 1.4646736
1350 23.007421 3272.2214 2088.047 191.09662 1184.1744 224.66504 1284.656 217.03214 0 -970.5252 595297.72 -594869.37 63.097535 55742.797 262.16781 1.3823451
1400 23.903494 3239.3096 2099.1837 192.11584 1140.1259 221.3215 1252.8691 215.64014 0 -978.70393 595298.89 -594869.89 1125.3057 55742.797 263.59141 1.3221979
1450 24.833224 3226.293 2042.7354 186.94973 1183.5576 241.40449 1273.025 233.66813 0 -994.70934 595299.55 -594869.38 -412.31857 55742.797 256.45155 1.4245996
1500 25.736203 3245.4596 2097.0431 191.91994 1148.4164 250.3854 1248.1507 212.36871 0 -990.48467 595297.36 -594869.36 245.49743 55742.797 263.28349 1.4252034
1550 26.633033 3308.5518 2113.8467 193.45778 1194.7051 234.5293 1286.7563 233.20552 0 -987.36764 595297.06 -594869.48 1324.7098 55742.797 265.37419 1.4864431
1600 27.530123 3319.786 2130.8949 195.01803 1188.8911 234.06508 1292.3987 225.94876 0 -992.81161 595299.1 -594869.81 343.14209 55742.797 267.51024 1.5104547
1650 28.41116 3239.0425 2066.8485 189.15654 1172.194 219.46922 1303.0071 210.00869 0 -989.28577 595298.63 -594869.64 -505.97551 55742.797 259.48305 1.4300292
1700 29.313339 3281.3023 2054.581 188.03383 1226.7213 224.72686 1339.1948 208.65914 0 -974.24634 595297.79 -594869.4 331.11846 55742.797 257.92342 1.4735531
1750 30.216241 3237.8348 2043.3835 187.00904 1194.4513 238.16066 1281.9383 221.74494 0 -976.72731 595299.4 -594870.06 612.69867 55742.797 256.53793 1.4116726
1800 31.113153 3242.1274 2087.94 191.08683 1154.1873 240.53142 1256.6966 210.49591 0 -983.16111 595299.34 -594869.72 -8.1277769 55742.797 262.14149 1.4166426
1850 31.993161 3249.8016 2079.8947 190.35052 1169.9069 233.21641 1269.4077 215.23716 0 -975.12835 595296.5 -594869.33 1156.1724 55742.797 261.13101 1.4122227
1900 32.891621 3251.9579 2097.6037 191.97124 1154.3541 243.13703 1228.3357 235.37914 0 -983.06313 595300.37 -594869.8 293.60486 55742.797 263.33664 1.4715416
1950 33.791255 3202.0703 2076.0894 190.00227 1125.9809 233.71337 1217.6976 227.58496 0 -981.8352 595298.07 -594869.25 -544.65606 55742.797 260.61868 1.5018224
2000 34.690323 3215.7987 2015.5993 184.46625 1200.1994 242.43605 1281.6846 227.48326 0 -980.70325 595298.82 -594869.52 248.82508 55742.797 253.04055 1.4169879
Loop time of 34.6904 on 4 procs for 2000 steps with 4500 atoms
Pair time (%) = 16.514 (47.6038)
Bond time (%) = 4.35555 (12.5555)
Kspce time (%) = 10.6198 (30.613)
Neigh time (%) = 0.393407 (1.13405)
Comm time (%) = 1.18699 (3.42165)
Outpt time (%) = 0.00467861 (0.0134867)
Other time (%) = 1.6161 (4.65863)
Nlocal: 1125 ave 1219 max 1009 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 5768 ave 5890 max 5664 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 215002 ave 223956 max 206872 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 860008
Ave neighs/atom = 191.113
Ave special neighs/atom = 13.3333
Neighbor list builds = 29
Dangerous builds = 0

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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)
1 by 1 by 1 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 = 79507 46656
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 = 20.1567 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 2.8816051 2130.0808 1490.8248 136.43926 639.25601 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137
100 5.569447 2172.0554 1656.5476 151.60609 515.50773 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117
150 8.2248161 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6234 55742.797 218.02975 0.12336382
200 10.911476 2271.1314 1750.9955 160.2499 520.13587 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.4949 55742.797 220.19714 0.23035017
250 13.588019 2333.7822 1793.0252 164.09642 540.75705 153.18169 833.95287 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339004
300 16.26521 2403.6147 1909.3441 174.74185 494.27059 144.27299 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3721 55742.797 239.06243 3.0455686
350 18.937858 2448.2389 1862.67 170.47027 585.56885 181.70523 821.7917 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806435
400 21.590191 2498.6994 1942.5496 177.7808 556.14976 168.5792 828.99117 182.0756 0 -1050.149 595296.43 -594869.77 485.86761 55742.797 244.23632 0.3882729
450 24.247025 2552.9641 1890.0917 172.97989 662.87241 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452669 55742.797 237.65323 0.34464588
500 26.850275 2608.55 1970.0729 180.29971 638.4771 187.01392 838.62129 176.10775 0 -985.23355 595290.89 -594868.93 3471.1633 55742.797 247.59402 0.66791252
550 29.482354 2667.002 1875.8227 171.67399 791.17931 178.48765 1003.6885 176.78989 0 -991.21705 595292.35 -594868.92 1767.0543 55742.797 235.34039 1.7252619
600 32.10773 2715.2399 1883.279 172.35639 831.96094 186.79504 1047.6877 183.04311 0 -1010.5423 595293.27 -594868.29 931.85523 55742.797 236.28437 1.7094253
650 34.715398 2754.4497 1970.794 180.3657 783.65568 166.02823 963.09399 184.8464 0 -952.45217 595290.25 -594868.11 2640.017 55742.797 247.67755 0.68709275
700 37.337317 2795.9461 1928.2674 176.4737 867.67874 176.09641 1002.4636 186.11483 0 -920.14356 595291.32 -594868.18 664.78904 55742.797 242.41897 0.44316381
750 39.927419 2838.2052 2043.2258 186.99461 794.97945 170.34991 941.73148 193.53082 0 -940.49604 595298.1 -594868.23 410.24758 55742.797 256.84035 0.55229077
800 42.469991 2881.9788 1945.9722 178.09402 936.00667 197.5203 1021.5571 202.83524 0 -915.18511 595297.49 -594868.21 -716.81442 55742.797 244.35112 1.2303511
850 45.05362 2923.3858 2106.5752 192.79231 816.81052 195.94987 886.41681 184.36064 0 -878.10485 595296.29 -594868.1 -1407.5711 55742.797 264.3276 1.8387296
900 47.651245 2950.6673 2039.6221 186.6648 911.04515 183.79618 1000.7954 184.49766 0 -890.38965 595299.97 -594867.63 -1085.794 55742.797 256.21167 1.0198208
950 50.451391 2976.6436 2006.5932 183.64202 970.05039 228.60059 985.21322 206.18529 0 -881.65815 595299.54 -594867.83 -1851.9703 55742.797 252.23637 0.54012241
1000 53.018937 3003.743 2056.8471 188.24122 946.89587 171.73287 976.85675 207.05097 0 -836.24563 595294.95 -594867.45 282.61914 55742.797 258.5658 0.52076804
1050 55.532595 3031.3535 2095.4846 191.7773 935.86887 203.54188 945.75569 204.8504 0 -846.10969 595294.45 -594866.62 -376.91112 55742.797 263.27093 0.93584407
1100 58.115412 3058.5347 2047.3098 187.36838 1011.2249 211.94076 1001.093 223.66214 0 -855.82424 595297.13 -594866.78 -1381.6531 55742.797 256.93409 1.6724456
1150 60.799698 3078.3996 2123.1811 194.31206 955.21855 189.50189 937.18685 224.21465 0 -823.63222 595294.38 -594866.43 524.70113 55742.797 266.5974 1.3568376
1200 63.295243 3093.556 2005.8939 183.57802 1087.6621 201.3428 1044.9909 219.39202 0 -805.37122 595293.83 -594866.52 -370.32492 55742.797 252.0829 0.71475597
1250 65.797931 3108.5155 2175.8972 199.13661 932.61826 156.6571 969.72254 225.30586 0 -850.00503 595297.25 -594866.31 -1015.3093 55742.797 273.53154 0.55100418
1300 68.300441 3122.9792 2090.3719 191.30939 1032.6073 209.92015 984.36624 236.75408 0 -825.27583 595292.92 -594866.08 -798.51816 55742.797 262.69421 0.75855207
1350 70.793202 3136.8213 2084.47 190.76925 1052.3513 186.49827 1004.7564 234.55362 0 -798.08335 595290.25 -594865.63 702.53782 55742.797 261.71553 1.3884089
1400 73.326733 3144.9028 2180.3659 199.54558 964.53687 170.02484 962.43948 235.07761 0 -829.27156 595291.77 -594865.51 1682.2488 55742.797 273.7286 1.5246324
1450 75.821906 3146.3365 2013.3816 184.26329 1132.9549 193.77936 1084.1403 252.3227 0 -821.23045 595288.54 -594864.6 -160.21484 55742.797 252.96375 0.87780357
1500 78.325264 3150.6861 2107.4863 192.87569 1043.1998 185.11752 988.72532 245.47682 0 -796.86739 595285.46 -594864.71 2242.3101 55742.797 264.90216 0.61222547
1550 80.779931 3156.3483 2074.5953 189.86552 1081.7531 166.52863 1062.4971 238.93518 0 -810.65247 595289.34 -594864.9 2224.9015 55742.797 260.73559 0.68881715
1600 83.275807 3163.8714 2000.6756 183.10045 1163.1958 210.70823 1110.4519 256.16493 0 -840.1463 595290.73 -594864.71 -830.17884 55742.797 251.26533 1.1443116
1650 85.768304 3169.3489 2056.4309 188.20313 1112.918 214.6419 1021.762 268.00157 0 -815.69477 595289 -594864.8 813.12089 55742.797 258.12835 1.5476743
1700 88.261463 3168.7666 2119.4079 193.96675 1049.3587 147.25006 1027.6415 246.49221 0 -797.55007 595290.74 -594865.22 412.59618 55742.797 266.23017 1.0703149
1750 90.746918 3168.2304 2066.7675 189.14913 1101.463 224.44009 1005.0052 243.56874 0 -797.83359 595291.25 -594864.96 -858.91314 55742.797 259.74684 0.69942293
1800 93.246077 3169.7579 2109.6017 193.06929 1060.1562 204.57678 981.05867 249.37843 0 -801.42006 595291.51 -594864.95 137.05559 55742.797 265.15197 0.65571606
1850 95.734661 3174.8532 2133.5052 195.25692 1041.348 175.87566 982.18775 244.55231 0 -786.49546 595290.43 -594865.21 882.03323 55742.797 268.02768 1.006296
1900 98.221874 3180.3842 2106.4808 192.78367 1073.9034 207.8879 977.47746 250.68948 0 -788.04039 595290.55 -594864.66 574.40162 55742.797 264.45175 1.4759897
1950 100.72148 3182.921 2084.8893 190.80763 1098.0317 207.26976 1007.5583 256.52302 0 -800.37789 595291.76 -594864.71 -981.75066 55742.797 261.81202 1.271779
2000 103.20588 3185.2881 2079.8136 190.3431 1105.4745 185.44441 1008.6997 251.0561 0 -766.97142 595292.22 -594864.97 661.65951 55742.797 261.35563 0.78600155
Loop time of 103.206 on 1 procs for 2000 steps with 4500 atoms
Pair time (%) = 60.3651 (58.49)
Bond time (%) = 16.8315 (16.3087)
Kspce time (%) = 20.1106 (19.4859)
Neigh time (%) = 1.52801 (1.48054)
Comm time (%) = 0.328804 (0.318591)
Outpt time (%) = 0.00495553 (0.00480159)
Other time (%) = 4.03695 (3.91155)
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10060 ave 10060 max 10060 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 774908 ave 774908 max 774908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 774908
Ave neighs/atom = 172.202
Ave special neighs/atom = 13.3333
Neighbor list builds = 35
Dangerous builds = 0

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@ -0,0 +1,177 @@
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

File diff suppressed because it is too large Load Diff

View File

@ -0,0 +1,80 @@
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 2.600 8.0
kspace_style pppm 1.0e-4
comm_modify vel yes
read_data data.ethanol
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 CTO
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff 1 1 thole 2.051000
pair_coeff 1 2 thole 1.580265
pair_coeff 1 4 thole 1.416087
pair_coeff 1 6 thole 2.051000
pair_coeff 1 7 thole 1.580265
pair_coeff 1 8 thole 1.416087
pair_coeff 2 2 thole 1.217570
pair_coeff 2 4 thole 1.091074
pair_coeff 2 6 thole 1.580265
pair_coeff 2 7 thole 1.217570
pair_coeff 2 8 thole 1.091074
pair_coeff 4 4 thole 0.977720
pair_coeff 4 6 thole 1.416087
pair_coeff 4 7 thole 1.091074
pair_coeff 4 8 thole 0.977720
pair_coeff 6 6 thole 2.051000
pair_coeff 6 7 thole 1.580265
pair_coeff 6 8 thole 1.416087
pair_coeff 7 7 thole 1.217570
pair_coeff 7 8 thole 1.091074
pair_coeff 8 8 thole 0.977720
group gETHANOL molecule 1:250
group gATOMS type 1 2 3 4 5
group gDRUDES type 6 7 8
neighbor 2.0 bin
variable vTEMP equal 300.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gATOMS create ${vTEMP} 12345
velocity gDRUDES create ${vTEMP_D} 12345
fix fDRUDE all drude C C N C N D D D
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0
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 20
timestep 0.5
run 2000

View File

@ -0,0 +1,86 @@
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 2.600 8.0
kspace_style pppm 1.0e-4
read_data data.ethanol
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 CTO
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff 1 1 thole 2.051000
pair_coeff 1 2 thole 1.580265
pair_coeff 1 4 thole 1.416087
pair_coeff 1 6 thole 2.051000
pair_coeff 1 7 thole 1.580265
pair_coeff 1 8 thole 1.416087
pair_coeff 2 2 thole 1.217570
pair_coeff 2 4 thole 1.091074
pair_coeff 2 6 thole 1.580265
pair_coeff 2 7 thole 1.217570
pair_coeff 2 8 thole 1.091074
pair_coeff 4 4 thole 0.977720
pair_coeff 4 6 thole 1.416087
pair_coeff 4 7 thole 1.091074
pair_coeff 4 8 thole 0.977720
pair_coeff 6 6 thole 2.051000
pair_coeff 6 7 thole 1.580265
pair_coeff 6 8 thole 1.416087
pair_coeff 7 7 thole 1.217570
pair_coeff 7 8 thole 1.091074
pair_coeff 8 8 thole 0.977720
group gETHANOL molecule 1:250
group gATOMS type 1 2 3 4 5
group gDRUDES type 6 7 8
neighbor 2.0 bin
variable vTEMP equal 300.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gATOMS create ${vTEMP} 12345
velocity gDRUDES create ${vTEMP_D} 12345
fix fDRUDE all drude C C N C N D D D
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
comm_modify vel yes
compute cTEMP_ATOM gATOMS temp
compute cTEMP all temp/drude
fix fDTDIR all drude/transform/direct
fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
fix_modify fNPT temp cTEMP_ATOM press thermo_press
fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0
fix fDTINV all drude/transform/inverse
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 20
timestep 0.5
run 2000

View File

@ -0,0 +1,254 @@
LAMMPS (8 Jul 2015)
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 2.600 8.0
kspace_style pppm 1.0e-4
comm_modify vel yes
read_data data.ethanol
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
1 by 1 by 1 MPI processor grid
reading atoms ...
3000 atoms
scanning bonds ...
5 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
9 = max dihedrals/atom
reading bonds ...
2750 bonds
reading angles ...
3250 angles
reading dihedrals ...
3000 dihedrals
5 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
10 = max # of 1-4 neighbors
11 = max # of special neighbors
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 CTO
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff 1 1 thole 2.051000
pair_coeff 1 2 thole 1.580265
pair_coeff 1 4 thole 1.416087
pair_coeff 1 6 thole 2.051000
pair_coeff 1 7 thole 1.580265
pair_coeff 1 8 thole 1.416087
pair_coeff 2 2 thole 1.217570
pair_coeff 2 4 thole 1.091074
pair_coeff 2 6 thole 1.580265
pair_coeff 2 7 thole 1.217570
pair_coeff 2 8 thole 1.091074
pair_coeff 4 4 thole 0.977720
pair_coeff 4 6 thole 1.416087
pair_coeff 4 7 thole 1.091074
pair_coeff 4 8 thole 0.977720
pair_coeff 6 6 thole 2.051000
pair_coeff 6 7 thole 1.580265
pair_coeff 6 8 thole 1.416087
pair_coeff 7 7 thole 1.217570
pair_coeff 7 8 thole 1.091074
pair_coeff 8 8 thole 0.977720
group gETHANOL molecule 1:250
3000 atoms in group gETHANOL
group gATOMS type 1 2 3 4 5
2250 atoms in group gATOMS
group gDRUDES type 6 7 8
750 atoms in group gDRUDES
neighbor 2.0 bin
variable vTEMP equal 300.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gATOMS create ${vTEMP} 12345
velocity gATOMS create 300 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C N C N D D D
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
250 = # of size 2 clusters
250 = # 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 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0
fix fNPH all nph iso 1 ${vPRESS} 500.0
fix fNPH all nph iso 1 1 500.0
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 20
timestep 0.5
run 2000
PPPM initialization ...
G vector (1/distance) = 0.379738
grid = 30 30 30
stencil order = 5
estimated absolute RMS force accuracy = 0.0289979
estimated relative force accuracy = 8.73262e-05
using double precision FFTs
3d grid and FFT values/proc = 50653 27000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 11
New max number of 1-2 to 1-4 neighbors: 11 (+0)
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 10
Memory usage per processor = 17.0416 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 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301
20 1.385576 10970.012 5646.6301 758.03417 5323.3819 2059.5936 2216.9884 125.92554 0 1728.6053 514096.92 -514904.65 75436.064 22442.45 899.51659 426.89782
40 2.8551838 8946.3004 5328.0205 715.26229 3618.2799 1462.1369 1696.2859 256.70292 0 1227.1291 513938.28 -514962.25 46638.926 23048.183 913.15135 252.56746
60 4.256644 7510.9138 4723.1153 634.05655 2787.7985 1200.8153 1745.4103 301.30777 0 557.91727 513950.17 -514967.82 37797.472 23517.111 840.69781 151.04819
80 5.6700039 6349.0396 4602.1226 617.81383 1746.917 881.77472 1380.8268 300.54011 0 204.13917 513929.54 -514949.9 33853.354 23924.249 841.20585 95.742025
100 7.1165569 5485.3222 4144.7402 556.41234 1340.582 784.84009 1301.8671 289.61557 0 -77.062714 514016.28 -514974.95 23857.465 24318.637 768.91722 59.825738
120 8.510273 4862.0053 3777.3363 507.09006 1084.669 621.87069 1297.2363 283.15963 0 -165.00092 514030.24 -514982.84 17467.301 24661.1 708.90876 35.503627
140 9.89271 4340.9652 3447.5936 462.82361 893.3716 643.1449 1248.6314 275.36087 0 -264.51028 513962.87 -514972.13 14982.178 24941.74 650.92753 23.297372
160 11.266981 3926.9368 3280.8104 440.43373 646.12637 590.77624 1125.7232 275.3221 0 -402.26335 514039.99 -514983.43 17555.529 25182.215 623.03896 13.767615
180 12.636709 3510.3411 3034.5182 407.37013 475.82289 580.88726 1065.7063 271.62555 0 -478.17514 514008.07 -514972.29 9901.7384 25408.806 577.95511 8.7953435
200 13.951961 3233.2057 2804.8754 376.54165 428.33026 560.57334 1096.7788 268.56938 0 -524.79217 514009.74 -514982.54 8543.4492 25602.16 535.31334 5.5723047
220 15.315 3020.0557 2679.3857 359.69523 340.66996 534.37676 1086.1078 252.72365 0 -554.44877 514000.87 -514978.96 7630.6161 25763.835 511.8744 4.1309201
240 16.66608 2817.6362 2557.8968 343.3859 259.73947 533.53125 1096.7513 235.23483 0 -594.78212 513968.14 -514979.14 6067.9397 25911.192 489.07601 2.9844639
260 18.020921 2631.1316 2460.4934 330.30994 170.63824 520.23801 1043.849 228.55335 0 -637.15729 514004.04 -514988.88 5635.1903 26047.493 470.67196 2.358136
280 19.327414 2462.7215 2379.403 319.42393 83.318543 525.36331 972.01762 226.26993 0 -624.36335 513966.76 -514982.73 4763.2439 26167.845 455.32938 1.8853017
300 20.664073 2314.007 2233.3945 299.82295 80.612529 521.07514 985.58156 216.6623 0 -622.92535 513969.51 -514989.29 3501.9257 26271.903 427.41388 1.7110326
320 21.998284 2171.6005 2216.0458 297.49398 -44.445373 513.1225 926.87268 206.39293 0 -647.39127 513946.45 -514989.89 3556.0249 26368.557 424.16134 1.5401544
340 23.295565 2048.7645 2103.0412 282.32362 -54.276671 517.24017 972.17593 198.86832 0 -648.49462 513890.61 -514984.68 3723.4258 26461.822 402.56097 1.3933654
360 24.639426 1940.255 2045.2119 274.5603 -104.95688 499.1817 932.32957 187.5616 0 -652.16846 513915.39 -514987.25 2301.433 26551.361 391.50737 1.3177372
380 25.919177 1826.4337 1933.9251 259.62057 -107.49138 518.5733 919.38362 182.08763 0 -651.72644 513909.35 -514985.16 2618.7931 26632.025 370.16974 1.3263382
400 27.23436 1760.0079 1974.3468 265.04699 -214.33884 494.88766 905.27809 184.94874 0 -673.15814 513861.2 -514987.5 2096.731 26707.742 377.93896 1.2790015
420 28.50932 1674.2459 1875.0429 251.7159 -200.79701 494.32791 919.1307 191.42967 0 -660.09631 513843.82 -514989.41 358.06627 26778.924 358.8831 1.3234648
440 29.823068 1636.3668 1886.8736 253.30412 -250.50682 501.37304 885.96911 179.94725 0 -646.55634 513813.44 -514984.68 465.97294 26842.197 361.1633 1.2949713
460 31.092765 1593.0934 1860.7484 249.79693 -267.65503 491.39115 906.9344 174.33035 0 -666.38274 513814.92 -514988.85 126.16052 26894.743 356.1632 1.2759204
480 32.406062 1505.0407 1837.1657 246.63106 -332.12503 509.85902 860.16645 173.43061 0 -651.2259 513765.85 -514990.2 1646.3283 26939.521 351.6473 1.2643358
500 33.677199 1442.2558 1798.394 241.42613 -356.13819 522.53768 861.77071 168.42903 0 -655.02572 513738.55 -514992.4 1526.9168 26984.71 344.22043 1.2508825
520 34.98888 1429.2148 1796.9298 241.22958 -367.71495 524.55666 871.69773 162.68814 0 -664.81406 513731.94 -514993.79 -680.86121 27027.519 343.9346 1.2628675
540 36.290854 1386.5466 1788.8853 240.14964 -402.33868 549.35219 874.93475 154.34652 0 -656.82759 513667.79 -514991.93 -112.10182 27063.585 342.37563 1.3021222
560 37.52542 1344.4167 1829.4102 245.58992 -484.99349 543.86102 827.43025 144.96524 0 -643.51447 513638.79 -514996.53 701.10406 27094.487 350.14354 1.3040182
580 38.796225 1286.7629 1718.567 230.70973 -431.80414 561.04865 874.04358 152.41827 0 -615.40981 513590.72 -514994.62 826.08615 27125.818 328.91939 1.2462575
600 40.032106 1275.3861 1701.9169 228.47454 -426.53082 558.07219 895.26591 163.23964 0 -608.79386 513561.43 -514995.74 284.53547 27152.441 325.68878 1.3366627
620 41.297358 1273.8918 1712.1906 229.85372 -438.29876 558.54787 859.08268 175.40704 0 -603.76978 513568.36 -514995.92 -799.98388 27171.09 327.70761 1.2215062
640 42.526453 1217.1518 1736.1072 233.06442 -518.95534 572.52862 823.16123 163.5653 0 -606.82177 513521.07 -514992.46 -528.59646 27187.499 332.28172 1.2466277
660 43.751388 1139.8934 1675.8281 224.97222 -535.93471 572.5104 829.99341 152.69698 0 -620.77477 513527.1 -514997.46 127.63393 27203.689 320.71564 1.270961
680 44.951294 1132.7801 1684.9691 226.19937 -552.18903 579.17897 824.9868 153.95243 0 -613.89121 513497.59 -514994 -375.69988 27217.538 322.46995 1.266406
700 46.114508 1123.7259 1689.7673 226.8435 -566.04141 579.34852 817.35591 160.76324 0 -604.95952 513473.67 -514992.22 539.9968 27228.562 323.38291 1.2824201
720 47.311101 1109.2452 1679.3944 225.45099 -570.14919 580.49864 815.37954 166.39557 0 -599.53737 513460.9 -514993.78 1379.628 27240.51 321.38269 1.3097525
740 48.482072 1103.9038 1664.1003 223.39782 -560.19651 598.28549 826.45607 162.40108 0 -577.67737 513419.55 -514989.21 -688.06905 27252.803 318.47888 1.2441535
760 49.66032 1069.6322 1656.8299 222.42181 -587.19776 602.32252 832.89566 153.82032 0 -575.90234 513395.07 -514995.41 40.843646 27264.248 317.07409 1.2699292
780 50.861186 1034.9853 1655.3151 222.21845 -620.3298 585.98097 809.14501 152.10567 0 -574.09092 513399.41 -514992.88 -542.13898 27275.872 316.80217 1.2268067
800 52.028532 1040.3169 1665.5678 223.59483 -625.25085 605.03042 803.57295 148.68705 0 -581.69335 513396.32 -514997.16 535.8591 27285.478 318.74392 1.2821524
820 53.219595 1058.9481 1736.3976 233.1034 -677.4495 598.69968 784.98413 145.24433 0 -598.32684 513390.35 -514998.4 661.30446 27295.669 332.34879 1.2200226
840 54.41621 1045.3784 1676.8277 225.10642 -631.4493 612.87881 813.63091 148.70121 0 -579.94856 513372.94 -514999.65 -709.36037 27305.36 320.91078 1.2627849
860 55.601647 1020.7309 1672.697 224.55189 -651.96607 601.90752 814.84165 150.80576 0 -580.50172 513365.58 -515004.6 -495.61008 27311.4 320.12878 1.239739
880 56.769503 989.87899 1623.5853 217.95888 -633.70636 614.6379 850.57766 146.023 0 -574.97001 513330.69 -515000.67 642.87966 27315.764 310.68993 1.2958041
900 57.983504 951.29928 1656.7713 222.41394 -705.47199 612.66694 803.70933 146.11306 0 -578.97014 513313.84 -515002.83 -24.66438 27323.702 317.06441 1.2662666
920 59.146542 990.23712 1682.9256 225.92504 -692.68849 625.49291 805.11902 145.39781 0 -566.50947 513298.1 -515000.28 -197.4677 27331.656 322.09842 1.2192545
940 60.311439 975.32007 1655.1496 222.19623 -679.82952 644.56888 830.44185 142.39994 0 -571.05582 513274.28 -515000.46 -57.36251 27336.591 316.75027 1.2738836
960 61.537265 970.70957 1646.9748 221.0988 -676.26523 621.55653 860.81553 137.50196 0 -570.35847 513277.66 -515003.44 356.66027 27339.657 315.18748 1.2637636
980 62.841358 922.60821 1622.7907 217.8522 -700.18247 618.71597 851.23286 133.07652 0 -567.79027 513264.96 -515000.37 5.1281321 27344.467 310.55109 1.2643077
1000 64.061049 903.52078 1692.943 227.26982 -789.4222 615.63909 786.17473 136.0751 0 -548.92889 513225.82 -515004.21 -1215.8274 27349.08 323.99743 1.2690479
1020 65.198298 880.82937 1611.9406 216.39562 -731.11119 641.95133 825.78985 138.47494 0 -548.19881 513212.76 -515001.89 -120.47994 27348.478 308.46852 1.2703282
1040 66.338573 859.35882 1637.2347 219.79124 -777.87584 642.91383 781.96671 129.07882 0 -535.68978 513205.22 -515001.36 -128.41699 27349.25 313.3121 1.2828435
1060 67.506762 843.6634 1588.9732 213.31236 -745.30982 645.93104 848.24527 128.71177 0 -531.00457 513167.02 -515004.21 111.3449 27352.063 304.04699 1.3138151
1080 68.625545 819.34273 1604.5527 215.40383 -785.20997 653.64454 797.74835 132.82208 0 -520.03981 513152.36 -515001.74 -705.09278 27353.042 307.03668 1.306641
1100 69.741567 799.10089 1574.7957 211.40909 -775.69478 654.13763 825.37479 142.68152 0 -514.52184 513120.3 -515003.67 1350.915 27353.287 301.3473 1.2713755
1120 70.887971 807.77511 1606.5291 215.66916 -798.75403 677.02 802.76738 138.71115 0 -519.19695 513103.61 -515001.67 551.01047 27358.309 307.4238 1.2874498
1140 72.009922 822.40019 1605.593 215.54349 -783.19283 664.08656 825.14971 139.5036 0 -525.0726 513119.2 -515006.06 -1500.6927 27365.732 307.25006 1.2741015
1160 73.11993 799.60355 1627.1824 218.44176 -827.57881 660.53797 810.61642 135.99659 0 -549.15929 513120.99 -515006.56 -463.83247 27365.87 311.39885 1.2506312
1180 74.237157 808.71869 1627.4862 218.48255 -818.76747 671.07453 814.08104 132.68184 0 -536.0374 513101.27 -515001.83 -1497.9686 27360.344 311.48219 1.1920705
1200 75.389495 800.76402 1602.0973 215.0742 -801.33325 661.27319 818.56681 137.56688 0 -528.29009 513116.11 -515006.56 727.09082 27352.249 306.62538 1.1680129
1220 76.512266 786.90424 1625.6159 218.23148 -838.7117 654.42667 808.06282 144.23638 0 -544.37793 513103.11 -515004.17 -1016.333 27347.251 311.10383 1.2383451
1240 77.618425 784.43915 1618.0202 217.21178 -833.58101 652.75565 810.84854 144.21786 0 -538.55907 513104.01 -515006.86 -1688.0609 27338.945 309.66351 1.2014646
1260 78.767789 792.64493 1616.6996 217.03449 -824.05464 659.33158 832.96211 136.95679 0 -535.25333 513087.8 -515005.85 -240.86746 27324.585 309.38787 1.2538953
1280 79.890153 772.02964 1579.0067 211.9744 -806.97707 680.62465 825.10068 128.65485 0 -522.39638 513085.1 -515004.06 1026.3484 27308.077 302.15133 1.2789362
1300 81.045542 794.71268 1640.9493 220.28991 -846.23661 653.48559 809.8286 126.57126 0 -529.35975 513101 -515007.77 -222.24259 27295.577 314.02093 1.2904787
1320 82.165808 784.00371 1619.7825 217.44836 -835.77876 666.10367 843.1839 129.04786 0 -537.48412 513064.75 -515001.38 -904.29245 27284.448 309.98624 1.2367093
1340 83.287128 768.52183 1621.7783 217.71629 -853.25649 658.65554 797.98287 135.92558 0 -517.31157 513072.35 -515000.86 556.43774 27269.699 310.3284 1.3310985
1360 84.450531 750.55548 1561.8653 209.67325 -811.30983 659.33682 849.22159 146.12076 0 -514.99584 513050.84 -515001.83 156.64838 27254.169 298.83628 1.3466087
1380 85.572197 744.55824 1600.9118 214.91506 -856.35357 669.28688 822.92318 135.57716 0 -509.75984 513027.33 -515001.71 395.88113 27246.862 306.32946 1.3282506
1400 86.727889 740.37698 1618.0191 217.21163 -877.6421 680.34192 804.16104 122.37614 0 -510.05578 513028.7 -515003.17 -1778.0909 27242.463 309.60983 1.3262175
1420 87.853329 707.95242 1606.2301 215.62901 -898.27766 681.75825 834.81666 117.56052 0 -511.14444 512980.84 -515002.11 132.87977 27231.78 307.36642 1.2875563
1440 88.999557 701.0459 1631.5857 219.03289 -930.53982 689.29026 778.55166 121.13791 0 -503.03703 512986.74 -515003.22 502.08629 27220.348 312.26072 1.2092436
1460 90.173845 691.9965 1611.7145 216.36527 -919.71797 691.89285 800.91685 123.97376 0 -504.76462 512970.72 -515002.46 530.64797 27214.26 308.41315 1.2983911
1480 91.318457 691.7249 1594.0369 213.99213 -902.31197 688.47809 838.61898 125.21502 0 -504.16566 512953.09 -515003.55 -1094.2326 27210.327 305.01536 1.3192889
1500 92.483926 665.64633 1571.5229 210.96973 -905.87653 681.91529 823.02708 127.30163 0 -506.25486 512973.62 -515005.48 -1022.5661 27200.233 300.72872 1.2507982
1520 93.612424 675.29951 1631.0635 218.96279 -955.76401 670.77264 825.29942 133.56984 0 -531.08736 512951.49 -515005.81 -389.61365 27187.165 312.13799 1.2620465
1540 94.741199 653.89323 1632.9694 219.21864 -979.07615 678.96106 792.69599 132.07987 0 -515.25022 512939.14 -515006.7 -1030.2457 27174.091 312.51532 1.234099
1560 95.9062 636.91726 1590.0999 213.46361 -953.18262 687.04134 809.44011 127.54619 0 -523.45302 512956.52 -515010.28 -951.93121 27155.942 304.27362 1.288966
1580 97.028125 627.56968 1601.8646 215.04297 -974.29496 686.96797 803.53231 128.08068 0 -517.28126 512935.11 -515010.71 -1043.2395 27131.362 306.54052 1.2619672
1600 98.159189 639.59673 1591.5973 213.66464 -952.00062 695.73225 820.03411 126.92265 0 -523.57295 512936.97 -515008.08 -516.36154 27101.901 304.53745 1.3431812
1620 99.322595 631.83759 1582.6681 212.46592 -950.83047 708.36138 817.50888 123.99588 0 -518.92537 512930.72 -515012.49 -2198.9765 27071.135 302.85679 1.2706043
1640 100.45901 621.88183 1569.4451 210.6908 -947.56326 703.57599 823.87187 132.80048 0 -497.70649 512900.32 -515010.43 -1335.78 27038.969 300.32548 1.2622751
1660 101.60839 642.07332 1595.5476 214.19493 -953.47423 705.46998 794.82235 141.09052 0 -484.29874 512898.11 -515008.66 -403.23344 27004.83 305.30235 1.3253687
1680 102.77636 620.05889 1604.721 215.42642 -984.66208 704.63874 808.2235 139.26176 0 -475.937 512849.25 -515010.1 -336.0674 26974.635 307.06907 1.3063348
1700 103.9216 625.14905 1627.936 218.54293 -1002.7869 700.41444 790.63143 141.47429 0 -472.95296 512847.83 -515010.18 432.43074 26948.842 311.5388 1.2611748
1720 105.07527 635.67026 1585.5068 212.84701 -949.83654 711.22133 826.38676 138.90157 0 -470.74615 512857.96 -515013.56 -927.08791 26927.403 303.39054 1.2949652
1740 106.19526 622.55036 1629.9419 218.81221 -1007.3915 701.72972 807.03841 133.88234 0 -462.62233 512821.73 -515009.15 60.724835 26906.734 311.91698 1.2759906
1760 107.3157 601.07861 1563.031 209.82973 -961.95237 721.05163 813.03641 135.83107 0 -472.1521 512852.13 -515011.85 1071.0762 26889.11 299.11764 1.211508
1780 108.47195 615.76689 1612.7311 216.50175 -996.96425 712.00335 812.2101 135.93651 0 -469.54632 512821.55 -515009.11 -1171.9908 26876.291 308.62781 1.2522701
1800 109.60652 590.39061 1576.6095 211.65259 -986.21891 706.7567 822.39219 137.15671 0 -470.15251 512825.84 -515008.21 -1051.5297 26860.1 301.6752 1.3176335
1820 110.78553 603.65994 1596.51 214.32414 -992.85007 711.49043 808.94991 132.38543 0 -461.89866 512827.37 -515011.15 180.50052 26844.34 305.50815 1.2756752
1840 111.93685 591.93917 1596.2013 214.2827 -1004.2621 720.41618 814.51338 137.96161 0 -460.4745 512793.12 -515009.8 605.10058 26833.73 305.47844 1.2069138
1860 113.12134 609.8248 1577.7772 211.80934 -967.95236 716.21723 808.30329 144.61624 0 -461.04538 512833.46 -515009.51 -1143.3982 26826.019 301.93343 1.2373879
1880 114.2602 614.25513 1599.756 214.7599 -985.50088 748.39555 792.89735 140.36606 0 -460.16996 512800.85 -515007.84 -261.10141 26816.306 306.15319 1.2225442
1900 115.40316 615.77501 1599.1853 214.68329 -983.41029 729.35936 798.81735 146.34452 0 -492.16069 512844.21 -515009.98 493.95161 26806.893 306.01603 1.2873103
1920 116.55442 628.99417 1652.3184 221.81616 -1023.3242 715.08536 813.8821 147.49091 0 -508.7856 512818.33 -515009.33 -2250.9701 26803.895 316.19125 1.3118467
1940 117.73809 613.28705 1595.717 214.21768 -982.42996 719.54904 821.80704 150.0739 0 -493.66309 512828.25 -515008.45 -2187.7221 26796.819 305.33907 1.3154875
1960 118.91834 594.22322 1584.9306 212.76966 -990.7074 717.75467 820.27772 151.35897 0 -491.90915 512819.49 -515007.68 -736.31063 26780.283 303.29276 1.2654066
1980 120.06148 614.4096 1572.4353 211.09222 -958.02568 732.31342 826.01815 154.79578 0 -487.35165 512824.93 -515008.73 39.731855 26764.092 300.89417 1.2728833
2000 121.20194 604.51985 1580.7247 212.20504 -976.20489 716.50209 820.59198 155.66948 0 -482.48478 512823.08 -515009.56 -465.82593 26752.509 302.47674 1.2881296
Loop time of 121.202 on 1 procs for 2000 steps with 3000 atoms
Pair time (%) = 58.9106 (48.6053)
Bond time (%) = 7.9266 (6.53999)
Kspce time (%) = 14.2366 (11.7462)
Neigh time (%) = 1.79608 (1.48189)
Comm time (%) = 0.562635 (0.464213)
Outpt time (%) = 0.0137095 (0.0113113)
Other time (%) = 37.7558 (31.1511)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10007 ave 10007 max 10007 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 720894 ave 720894 max 720894 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 720894
Ave neighs/atom = 240.298
Ave special neighs/atom = 10.5
Neighbor list builds = 49
Dangerous builds = 0

View File

@ -0,0 +1,254 @@
LAMMPS (8 Jul 2015)
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 2.600 8.0
kspace_style pppm 1.0e-4
comm_modify vel yes
read_data data.ethanol
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
1 by 2 by 2 MPI processor grid
reading atoms ...
3000 atoms
scanning bonds ...
5 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
9 = max dihedrals/atom
reading bonds ...
2750 bonds
reading angles ...
3250 angles
reading dihedrals ...
3000 dihedrals
5 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
10 = max # of 1-4 neighbors
11 = max # of special neighbors
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 CTO
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff 1 1 thole 2.051000
pair_coeff 1 2 thole 1.580265
pair_coeff 1 4 thole 1.416087
pair_coeff 1 6 thole 2.051000
pair_coeff 1 7 thole 1.580265
pair_coeff 1 8 thole 1.416087
pair_coeff 2 2 thole 1.217570
pair_coeff 2 4 thole 1.091074
pair_coeff 2 6 thole 1.580265
pair_coeff 2 7 thole 1.217570
pair_coeff 2 8 thole 1.091074
pair_coeff 4 4 thole 0.977720
pair_coeff 4 6 thole 1.416087
pair_coeff 4 7 thole 1.091074
pair_coeff 4 8 thole 0.977720
pair_coeff 6 6 thole 2.051000
pair_coeff 6 7 thole 1.580265
pair_coeff 6 8 thole 1.416087
pair_coeff 7 7 thole 1.217570
pair_coeff 7 8 thole 1.091074
pair_coeff 8 8 thole 0.977720
group gETHANOL molecule 1:250
3000 atoms in group gETHANOL
group gATOMS type 1 2 3 4 5
2250 atoms in group gATOMS
group gDRUDES type 6 7 8
750 atoms in group gDRUDES
neighbor 2.0 bin
variable vTEMP equal 300.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gATOMS create ${vTEMP} 12345
velocity gATOMS create 300 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C N C N D D D
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
250 = # of size 2 clusters
250 = # 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 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0
fix fNPH all nph iso 1 ${vPRESS} 500.0
fix fNPH all nph iso 1 1 500.0
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 20
timestep 0.5
run 2000
PPPM initialization ...
G vector (1/distance) = 0.379738
grid = 30 30 30
stencil order = 5
estimated absolute RMS force accuracy = 0.0289979
estimated relative force accuracy = 8.73262e-05
using double precision FFTs
3d grid and FFT values/proc = 17908 7200
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 11
New max number of 1-2 to 1-4 neighbors: 11 (+0)
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 10
Memory usage per processor = 13.7041 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 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301
20 0.44569397 10977.424 5649.3945 758.40528 5328.0296 2062.3394 2228.2308 127.20754 0 1716.2152 514097.63 -514903.59 75539.256 22441.778 900.65907 425.71739
40 0.90527296 8971.2482 5307.0059 712.44118 3664.2423 1468.3059 1727.5451 263.87315 0 1220.4282 513944.02 -514959.93 46706.836 23047.009 909.55477 251.59684
60 1.361037 7598.4556 4774.303 640.92826 2824.1526 1194.6529 1771.6791 314.85714 0 553.82536 513952.92 -514963.78 37332.483 23513.741 850.78562 150.29304
80 1.7987111 6500.1249 4632.1069 621.83909 1868.0179 914.33309 1444.251 317.2453 0 213.21366 513930.08 -514951.11 33258.709 23919.334 847.28599 94.967207
100 2.243571 5591.6251 4319.2496 579.83942 1272.3755 772.49711 1235.8559 306.35507 0 -56.084846 513990.28 -514976.52 21846.137 24315.14 802.34652 59.892261
120 2.672169 4952.948 3881.7989 521.11369 1071.1491 630.90018 1260.1994 299.84546 0 -147.02839 514014.84 -514987.6 17197.209 24657.008 728.80233 35.812029
140 3.0969729 4374.1711 3440.8515 461.91852 933.31957 670.31509 1238.1527 300.45294 0 -260.41129 513963.49 -514978.68 17258.201 24938.237 649.62114 23.329848
160 3.522228 3923.495 3251.4038 436.48603 672.0912 632.18705 1144.4394 307.33026 0 -436.52375 514013.97 -514989.32 17850.515 25184.125 617.40474 13.751472
180 3.939676 3558.426 3060.6065 410.87237 497.81946 621.75343 1085.8467 297.16091 0 -495.18434 513968.41 -514980.17 9891.4148 25413.786 582.97006 8.7537197
200 4.3550711 3228.7597 2864.5929 384.55845 364.16674 591.37767 1077.5669 257.51603 0 -521.62174 513950.21 -514990.89 5932.7994 25603.593 546.64932 5.8336845
220 4.781127 2922.9928 2668.3732 358.21686 254.61956 552.45115 1045.2477 238.95571 0 -548.2597 513955.3 -514989.07 7141.8585 25759.687 509.85961 3.9098706
240 5.195529 2721.2831 2574.4897 345.61343 146.79339 548.06208 1035.0795 226.53387 0 -609.08183 513928.26 -514982.06 6976.8028 25904.957 492.22535 3.0535597
260 5.5978601 2525.9513 2461.0955 330.39077 64.855761 536.85769 1022.3488 211.33422 0 -633.79065 513919.59 -514991.49 4541.0707 26037.832 470.78293 2.3688827
280 6.0106721 2338.1989 2324.5678 312.06255 13.63115 519.14801 970.18634 197.76634 0 -621.14257 513937.12 -514989.44 2916.5572 26148.311 444.7787 1.975451
300 6.4294651 2194.9975 2189.2141 293.89194 5.7833943 530.82824 982.37216 190.98549 0 -652.12498 513946.6 -514992.88 4231.0047 26242.419 418.97109 1.6488796
320 6.825505 2045.5803 2132.2428 286.24381 -86.66256 531.61575 935.95137 188.46723 0 -683.29899 513935.09 -514994.49 1717.7425 26334.126 408.09021 1.554221
340 7.23614 1929.4862 2083.5954 279.71312 -154.10925 509.11673 906.18183 186.63991 0 -668.08147 513908.15 -514996.11 2743.5013 26418.758 398.8054 1.4581893
360 7.6401701 1853.7734 1992.7639 267.5194 -138.99054 525.44894 891.90785 178.2228 0 -654.5178 513920.68 -515000.73 3824.9512 26497.054 381.4442 1.3381947
380 8.035013 1760.9758 1947.1807 261.40007 -186.20493 517.02356 919.61194 172.55666 0 -676.58938 513879.08 -514997.89 2968.2379 26574.581 372.73009 1.2814975
400 8.439594 1687.9145 1906.019 255.8743 -218.10451 535.676 922.06535 176.24936 0 -683.92633 513833.49 -515001.66 1305.3348 26642.871 364.83666 1.2876267
420 8.849108 1605.8081 1889.1783 253.61351 -283.37015 517.23187 857.77943 180.22369 0 -663.03698 513825.85 -515001.41 2618.2332 26704.387 361.60626 1.2936035
440 9.2419581 1518.1322 1794.7348 240.93491 -276.60265 531.28729 893.06522 188.20612 0 -667.29018 513778.24 -515000.11 1458.8151 26764.917 343.52984 1.2323667
460 9.6461852 1455.546 1796.4 241.15845 -340.85398 527.34366 846.65226 188.77031 0 -650.31889 513748.59 -515001.89 169.77154 26818.027 343.8413 1.2433195
480 10.037471 1423.2564 1780.6643 239.04601 -357.40797 555.56132 861.65053 179.25353 0 -642.23744 513684.59 -514996.23 1737.2169 26861.945 340.81112 1.2754844
500 10.442603 1414.4159 1792.7736 240.67163 -378.35771 562.25347 865.25285 172.51254 0 -638.36916 513656.76 -514996.77 2862.5086 26905.68 343.13664 1.264128
520 10.840656 1359.8057 1801.5592 241.85105 -441.75349 573.49082 804.76936 169.51784 0 -635.89324 513643.32 -514996.96 927.77773 26956.407 344.82065 1.2649106
540 11.24422 1319.969 1763.9685 236.80467 -443.9995 564.76203 851.23442 169.85422 0 -632.66442 513600.38 -514997.57 402.68456 26999.135 337.63034 1.2312338
560 11.656965 1288.5175 1741.1847 233.74605 -452.66718 589.0843 843.68941 164.33111 0 -639.59483 513593.61 -515003.78 2031.8562 27036.616 333.27376 1.1999696
580 12.050085 1250.4981 1701.8135 228.46065 -451.3154 576.17535 877.82925 152.94556 0 -632.24298 513574.54 -515000.56 328.36451 27076.846 325.70282 1.2583556
600 12.463133 1212.0751 1699.8202 228.19306 -487.74513 586.11242 850.6289 146.9891 0 -635.87543 513564.76 -515000.36 -593.07635 27114.131 325.34702 1.1966401
620 12.857609 1202.6969 1724.5891 231.51816 -521.8922 586.546 815.3615 149.33058 0 -627.92161 513553.83 -514999.04 -16.881985 27141.295 330.08328 1.2224592
640 13.267988 1180.7392 1717.1928 230.52525 -536.45363 595.45079 837.47314 150.14341 0 -635.92342 513512.84 -514996.44 1253.4658 27161.366 328.61164 1.3535393
660 13.661833 1146.6245 1693.9969 227.4113 -547.37231 603.66965 823.99031 147.75109 0 -616.07296 513489.44 -514996.15 -632.85642 27186.187 324.23124 1.1905446
680 14.057714 1112.6845 1649.8772 221.48844 -537.19275 594.76928 869.75332 148.3474 0 -610.67856 513459.02 -514998.41 -656.86895 27208.556 315.75904 1.2280206
700 14.46045 1080.853 1662.6225 223.19944 -581.76952 607.13692 800.72097 155.37025 0 -590.53466 513444.43 -514998.9 1478.4986 27230.38 318.17518 1.2929123
720 14.858115 1074.1453 1681.4035 225.7207 -607.2582 602.55649 804.73664 155.69335 0 -578.62035 513406.54 -514998.16 -312.12065 27255.88 321.76305 1.3178416
740 15.262165 1057.2173 1626.1913 218.30872 -568.97405 614.54113 851.40449 158.65878 0 -585.61227 513391.12 -514999.09 -252.45558 27276.192 311.20516 1.2592718
760 15.664885 1062.4809 1661.9166 223.10468 -599.4357 613.01783 805.30824 157.10102 0 -572.92999 513401.46 -515003.4 8.2424603 27294.015 318.05423 1.2582564
780 16.067218 1054.4338 1611.1036 216.28327 -556.66986 619.88711 869.25572 154.03862 0 -563.00792 513365.76 -515002.61 -325.5131 27313.202 308.30577 1.2766112
800 16.469454 1045.3661 1667.4808 223.85165 -622.11476 607.72536 819.84304 154.6324 0 -551.0017 513351.46 -515004.78 -711.73517 27333.225 319.1255 1.2459692
820 16.874566 1025.6074 1655.4437 222.23572 -629.83638 617.12876 822.09062 147.69173 0 -566.57998 513354.87 -515005.04 399.28085 27347.385 316.79906 1.2953686
840 17.272044 995.37917 1669.6204 224.13888 -674.24128 600.79611 821.7655 140.46192 0 -568.05887 513337.46 -515006.66 583.69527 27361.364 319.5132 1.2991152
860 17.673279 971.05977 1639.0518 220.03518 -667.99202 608.93496 824.23202 133.94234 0 -564.33929 513334.29 -515005.05 -413.73876 27378.37 313.69629 1.2004828
880 18.080302 944.37506 1628.7217 218.64842 -684.34669 617.46083 825.05882 135.40531 0 -569.6048 513312.82 -515005.49 512.87669 27389.533 311.69643 1.2448601
900 18.477336 949.5982 1677.4393 225.18853 -727.84115 624.49844 772.75351 136.94704 0 -549.4139 513292.05 -515004.67 271.20937 27400.579 321.05001 1.211493
920 18.873705 932.25995 1610.381 216.18626 -678.12109 623.29028 843.94403 144.55915 0 -557.17786 513270.07 -515002.81 1097.4299 27412.447 308.17027 1.2686712
940 19.284093 916.57919 1640.5258 220.23305 -723.94658 619.65583 814.76133 144.02609 0 -552.83588 513253.39 -515002.95 -342.60513 27424.209 313.98093 1.1943711
960 19.678839 941.9627 1630.8148 218.9294 -688.85213 647.73279 836.44195 147.48183 0 -533.27218 513217.4 -515004.64 -291.64501 27431.009 312.08648 1.2709839
980 20.091488 888.07492 1615.6407 216.89235 -727.56578 644.39061 818.66717 151.18945 0 -530.05167 513198.49 -515010.26 835.04931 27433.771 309.19916 1.2205907
1000 20.484026 903.45687 1626.7477 218.38341 -723.29085 660.33039 814.13089 154.52432 0 -517.32081 513174.16 -515009.12 -597.08083 27441.855 311.29984 1.2872278
1020 20.884939 884.61313 1628.0576 218.55926 -743.44446 659.18164 792.2445 148.42138 0 -501.95147 513167.72 -515009.06 -227.27612 27447.478 311.54441 1.3024911
1040 21.279846 852.14085 1593.0292 213.85686 -740.88834 648.79571 822.31823 141.59479 0 -492.90372 513148.22 -515008.91 1544.7468 27454.311 304.83469 1.2878493
1060 21.655111 848.20594 1615.8134 216.91553 -767.60742 629.3671 795.01871 137.79728 0 -487.7332 513167.91 -515009.96 818.90975 27467.219 309.21127 1.2684583
1080 22.037992 831.86637 1618.7361 217.30789 -786.86971 636.48473 828.1039 138.80398 0 -531.02117 513152.33 -515011.57 -796.09024 27482.281 309.76171 1.2933978
1100 22.412974 796.80267 1592.7483 213.81915 -795.94567 625.90981 798.78644 146.80857 0 -536.96836 513184.36 -515014.85 -84.200922 27491.353 304.78282 1.2860228
1120 22.801171 772.10069 1567.5834 210.44088 -795.48274 658.82509 788.14264 148.88807 0 -539.176 513162.6 -515014.76 867.66407 27496.215 299.95125 1.3027473
1140 23.17888 770.63813 1565.9379 210.21998 -795.2998 640.7064 799.36864 147.80124 0 -535.9357 513166.65 -515013.89 -1183.537 27499.574 299.64709 1.2856405
1160 23.563832 764.75496 1564.5598 210.03497 -799.80482 647.22053 811.27899 146.29888 0 -543.29534 513150.92 -515012.23 -1228.125 27500.914 299.39235 1.2526237
1180 23.941609 764.17598 1617.4255 217.13195 -853.24954 659.94837 768.65464 144.94873 0 -529.07191 513110.91 -515008.64 107.09246 27498.487 309.51287 1.287252
1200 24.317012 762.98696 1589.6792 213.40714 -826.69227 651.88091 816.19739 145.19502 0 -517.91574 513088.48 -515010.53 -1052.4085 27492.624 304.22381 1.2172354
1220 24.706198 764.88104 1566.9504 210.3559 -802.06936 679.17803 822.8538 134.80594 0 -509.18914 513076.83 -515006.55 694.03102 27483.433 299.85098 1.253554
1240 25.083107 767.93518 1615.6009 216.887 -847.66571 671.38696 801.01511 123.2586 0 -498.24308 513061.33 -515006.42 -367.46541 27476.952 309.13859 1.3441052
1260 25.461219 769.84629 1597.441 214.44912 -827.59471 670.93506 820.00134 122.64096 0 -489.27375 513053.94 -515005.84 -58.54717 27470.667 305.70834 1.2250043
1280 25.850924 761.02257 1637.0908 219.77192 -876.06819 685.99978 801.7347 121.99508 0 -498.90642 513022.12 -515009.01 667.72097 27460.84 313.30874 1.2269128
1300 26.230407 725.15653 1614.5991 216.75252 -889.44257 676.06266 795.73111 129.44616 0 -500.04123 513019.86 -515010.51 346.28961 27453.003 309.01166 1.1958813
1320 26.616651 690.04147 1555.4057 208.80608 -865.36428 674.77824 814.17441 138.30234 0 -503.84683 513024.03 -515012.8 -953.72011 27450.174 297.64076 1.2471902
1340 26.997168 731.37012 1629.8044 218.79375 -898.43423 672.50861 814.71248 139.58285 0 -509.67436 512995.22 -515010.78 -1831.2948 27443.855 311.896 1.2621742
1360 27.377617 745.65434 1610.5181 216.20467 -864.8638 691.11602 810.45797 140.60405 0 -508.77522 513011.95 -515010.21 -479.36536 27427.931 308.19958 1.2616878
1380 27.768431 746.41678 1674.6182 224.8098 -928.2014 661.11056 795.29365 134.53957 0 -512.17435 513003.03 -515010 726.71849 27412.674 320.49072 1.2545772
1400 28.151466 706.81871 1607.416 215.78822 -900.5973 709.47611 804.4224 129.7539 0 -509.52634 512973.57 -515008.29 -712.21584 27401.879 307.61219 1.2445794
1420 28.544365 667.95202 1582.3831 212.42766 -914.43103 664.88892 801.83372 136.47795 0 -514.32654 513008.75 -515012.06 -674.60825 27385.407 302.81863 1.2330197
1440 28.92417 662.21363 1572.2132 211.0624 -909.99957 695.6883 812.01519 141.73013 0 -511.80853 512960.55 -515008.18 -73.453766 27362.02 300.86905 1.233181
1460 29.303746 673.3058 1590.356 213.49799 -917.05016 660.8122 809.16185 137.34151 0 -506.78651 512991.4 -515008.98 487.20204 27337.657 304.34864 1.2293292
1480 29.683979 690.74904 1599.4915 214.72439 -908.74246 688.89665 819.23241 129.49598 0 -495.16925 512954.44 -515005.64 487.60757 27316.061 306.12959 1.159563
1500 30.073856 696.13426 1627.5685 218.49359 -931.4342 677.25983 808.26514 125.60011 0 -489.59764 512955.4 -515008.36 519.17541 27293.341 311.4741 1.2480919
1520 30.451939 716.4485 1613.3483 216.5846 -896.89978 696.36687 820.98027 134.70464 0 -469.43851 512929.25 -515008.76 544.98379 27271.903 308.73614 1.2765559
1540 30.839949 711.84578 1602.4823 215.1259 -890.63656 708.76314 793.80104 146.48285 0 -451.73842 512918.02 -515005.96 454.52189 27257.543 306.63893 1.3081885
1560 31.255883 702.95447 1604.1384 215.34821 -901.1839 701.09472 795.80519 150.09855 0 -450.00841 512908.1 -515006.27 -175.16964 27248.208 306.99599 1.217717
1580 31.634972 666.16399 1593.9574 213.98146 -927.79341 709.48317 798.22341 141.85062 0 -483.91855 512915.54 -515008.98 -174.37068 27241.403 305.02798 1.2549165
1600 32.013681 688.42678 1613.6536 216.62559 -925.22683 708.7011 810.24587 137.18807 0 -474.54073 512902.73 -515009.55 175.74764 27236.695 308.81599 1.2269417
1620 32.377997 686.38631 1599.6555 214.7464 -913.26914 723.55612 796.07516 144.8931 0 -474.73319 512907.37 -515010.43 33.582792 27234.316 306.09396 1.3145429
1640 32.739099 705.79223 1615.3667 216.85556 -909.57442 705.06325 806.35123 150.08668 0 -479.53397 512919.18 -515010.72 -276.47112 27230.877 309.12408 1.2740414
1660 33.111364 701.27726 1607.2688 215.76845 -905.99149 721.97907 787.92231 144.01692 0 -463.68107 512916.64 -515012.87 929.51954 27224.725 307.57382 1.2682264
1680 33.474256 700.51394 1604.7821 215.43463 -904.2682 712.18636 816.32021 135.23856 0 -471.34583 512915.88 -515012.55 169.46579 27223.825 307.07661 1.316103
1700 33.847599 653.51775 1574.3177 211.34492 -920.79992 708.22805 829.01689 135.77013 0 -456.72703 512872.35 -515009.44 -1331.9277 27225.869 301.24451 1.2944188
1720 34.210801 646.19978 1583.018 212.5129 -936.81823 721.83771 788.24431 140.19453 0 -469.87575 512893.23 -515010.45 722.29697 27224.305 302.91185 1.3016769
1740 34.57351 650.08331 1600.9298 214.91747 -950.84647 709.99119 789.79721 138.23225 0 -460.97413 512880.98 -515008.87 1102.6045 27225.414 306.34618 1.3045986
1760 34.947762 647.44786 1591.6127 213.6667 -944.16484 703.25888 831.27698 133.1631 0 -463.47718 512860.59 -515008.98 1152.8885 27230.97 304.56068 1.2966664
1780 35.311829 634.92036 1581.508 212.31019 -946.58767 707.7771 807.97758 140.70709 0 -473.2579 512882.95 -515012.74 229.64632 27235.632 302.63254 1.2770484
1800 35.686407 609.58199 1563.2412 209.85795 -953.65919 706.83652 811.29431 136.56443 0 -482.58705 512887.2 -515012.97 -1428.3239 27239.537 299.14762 1.235579
1820 36.050632 615.78755 1553.6653 208.57243 -937.87771 721.32849 827.06658 126.75248 0 -476.19143 512873.72 -515010.55 -1558.7353 27240.307 297.30295 1.2564383
1840 36.425851 595.24691 1623.2931 217.91965 -1028.0462 715.62813 759.44377 125.14223 0 -486.38933 512873.86 -515015.73 -393.40048 27233.914 310.63049 1.3037899
1860 36.791862 584.14833 1580.8506 212.22194 -996.70229 725.49209 786.41557 129.34385 0 -497.01606 512871.73 -515012.67 -445.7964 27227.234 302.53512 1.2082224
1880 37.159068 571.94192 1587.3128 213.08945 -1015.3709 727.21492 776.53831 128.97058 0 -472.95741 512835.25 -515010.39 -2430.0222 27217.82 303.74009 1.2871788
1900 37.534434 588.18296 1575.532 211.50794 -987.34908 735.18962 822.01431 121.27343 0 -474.15326 512820.83 -515012.5 -1004.9937 27200.966 301.48221 1.2875721
1920 37.899018 595.6429 1593.2862 213.89136 -997.64331 728.16052 813.67464 116.25522 0 -474.41478 512829.4 -515010.72 56.20061 27185.033 304.87735 1.3063391
1940 38.263855 552.10655 1586.7384 213.01234 -1034.6318 727.69915 794.08444 116.66262 0 -474.42985 512811.77 -515010.42 229.42949 27173.976 303.61874 1.3140118
1960 38.637106 571.50083 1614.8554 216.78693 -1043.3546 729.51741 761.23804 128.23909 0 -464.44507 512811.41 -515009.31 -496.32744 27162.867 309.02606 1.2732453
1980 38.999486 554.31018 1603.5237 215.26569 -1049.2135 738.87358 785.7371 126.13553 0 -468.044 512779.36 -515011.27 467.45037 27149.813 306.82565 1.3387674
2000 39.362048 570.16479 1585.0529 212.78608 -1014.8882 754.53304 813.00379 125.06015 0 -448.86583 512751.21 -515009.83 -257.98779 27141.691 303.29539 1.313977
Loop time of 39.3621 on 4 procs for 2000 steps with 3000 atoms
Pair time (%) = 15.1636 (38.5233)
Bond time (%) = 2.04281 (5.18978)
Kspce time (%) = 8.76608 (22.2704)
Neigh time (%) = 0.513343 (1.30415)
Comm time (%) = 1.60174 (4.06924)
Outpt time (%) = 0.00888807 (0.0225803)
Other time (%) = 11.2657 (28.6206)
Nlocal: 750 ave 771 max 713 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 5881.75 ave 5954 max 5826 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 178004 ave 198102 max 168052 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 712018
Ave neighs/atom = 237.339
Ave special neighs/atom = 10.5
Neighbor list builds = 50
Dangerous builds = 0

View File

@ -0,0 +1,263 @@
LAMMPS (8 Jul 2015)
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 2.600 8.0
kspace_style pppm 1.0e-4
read_data data.ethanol
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
1 by 1 by 1 MPI processor grid
reading atoms ...
3000 atoms
scanning bonds ...
5 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
9 = max dihedrals/atom
reading bonds ...
2750 bonds
reading angles ...
3250 angles
reading dihedrals ...
3000 dihedrals
5 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
10 = max # of 1-4 neighbors
11 = max # of special neighbors
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 CTO
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff 1 1 thole 2.051000
pair_coeff 1 2 thole 1.580265
pair_coeff 1 4 thole 1.416087
pair_coeff 1 6 thole 2.051000
pair_coeff 1 7 thole 1.580265
pair_coeff 1 8 thole 1.416087
pair_coeff 2 2 thole 1.217570
pair_coeff 2 4 thole 1.091074
pair_coeff 2 6 thole 1.580265
pair_coeff 2 7 thole 1.217570
pair_coeff 2 8 thole 1.091074
pair_coeff 4 4 thole 0.977720
pair_coeff 4 6 thole 1.416087
pair_coeff 4 7 thole 1.091074
pair_coeff 4 8 thole 0.977720
pair_coeff 6 6 thole 2.051000
pair_coeff 6 7 thole 1.580265
pair_coeff 6 8 thole 1.416087
pair_coeff 7 7 thole 1.217570
pair_coeff 7 8 thole 1.091074
pair_coeff 8 8 thole 0.977720
group gETHANOL molecule 1:250
3000 atoms in group gETHANOL
group gATOMS type 1 2 3 4 5
2250 atoms in group gATOMS
group gDRUDES type 6 7 8
750 atoms in group gDRUDES
neighbor 2.0 bin
variable vTEMP equal 300.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gATOMS create ${vTEMP} 12345
velocity gATOMS create 300 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C N C N D D D
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
250 = # of size 2 clusters
250 = # of size 3 clusters
250 = # of size 4 clusters
0 = # of frozen angles
comm_modify vel yes
compute cTEMP_ATOM gATOMS temp
compute cTEMP all temp/drude
fix fDTDIR all drude/transform/direct
fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500
fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500
fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500
fix_modify fNPT temp cTEMP_ATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349)
fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0
fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0
fix fNVT gDRUDES nvt temp 1 1 100.0
fix fDTINV all drude/transform/inverse
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 20
timestep 0.5
run 2000
PPPM initialization ...
G vector (1/distance) = 0.379738
grid = 30 30 30
stencil order = 5
estimated absolute RMS force accuracy = 0.0289979
estimated relative force accuracy = 8.73262e-05
using double precision FFTs
3d grid and FFT values/proc = 50653 27000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 11
New max number of 1-2 to 1-4 neighbors: 11 (+0)
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 10
Memory usage per processor = 17.0416 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 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301
20 1.485518 11385.192 5995.2334 804.83256 5389.9589 2039.7325 2312.5375 131.6961 0 1710.3266 514098.34 -514902.67 75867.639 22408.275 975.26848 406.07565
40 2.9579411 9812.3728 6009.1747 806.70411 3803.1981 1442.3489 1826.1439 275.19367 0 1288.2864 513934.98 -514963.76 48675.043 22980.115 1057.0176 221.56359
60 4.3728549 8857.9452 5779.5973 775.8844 3078.348 1190.8978 1938.6134 328.6837 0 619.31805 513970.98 -514970.15 39710.61 23440.966 1050.9011 133.14424
80 5.817939 8115.7843 5997.9225 805.19356 2117.8618 901.84106 1587.5472 325.40763 0 288.34562 513957.43 -514942.71 37588.951 23834.833 1111.65 89.054921
100 7.207612 7496.2553 5770.3833 774.64747 1725.872 829.63908 1420.6659 325.4016 0 62.343574 514051.62 -514963.79 27294.064 24225.918 1080.2687 60.498472
120 8.656971 6986.593 5396.9479 724.51547 1589.6452 678.24993 1535.5197 325.88462 0 -9.6649617 514027.05 -514967.4 21720.902 24578.195 1016.3014 42.715636
140 10.075453 6549.0006 5126.6341 688.22709 1422.3665 724.95472 1477.7714 315.11964 0 -99.456486 513960.58 -514956.6 19747.307 24877.008 969.51239 30.977085
160 11.492728 6131.3317 5000.4421 671.2864 1130.8896 703.24858 1302.1192 314.93994 0 -258.4539 514042.29 -514973.25 23050.008 25142.654 948.73049 23.021806
180 12.899685 5749.9765 4700.9451 631.0803 1049.0314 674.94525 1301.4114 310.04938 0 -326.73679 514044.26 -514954.9 14225.485 25400.048 893.75893 17.322076
200 14.301162 5429.601 4392.5738 589.68286 1037.0272 612.00108 1296.2432 303.16019 0 -300.38658 514093.7 -514967.69 10835.073 25622.866 836.16806 13.764486
220 15.696118 5133.8318 4290.7369 576.01173 843.09487 572.51989 1261.8055 289.99072 0 -383.71584 514078.3 -514975.81 12509.826 25814.229 817.78562 11.104636
240 17.080213 4850.3856 4120.3632 553.13985 730.0224 553.79224 1263.6533 278.92142 0 -487.76523 514091.35 -514969.93 10891.878 25996.167 785.87194 9.360776
260 18.465174 4583.9875 3911.0361 525.03865 672.95138 541.52251 1175.1552 273.43365 0 -475.23638 514139.68 -514981.61 8086.1512 26168.96 746.55574 7.4653786
280 19.852883 4349.224 3692.2792 495.67153 656.9448 598.81912 1148.0997 278.8781 0 -444.09603 514045.38 -514970.13 5124.6373 26323.056 705.04252 6.4783461
300 21.231065 4128.9017 3579.5067 480.53234 549.39506 584.06591 1089.5131 267.69425 0 -456.87099 514043.55 -514978.56 8350.7757 26456.831 683.9437 5.2650983
320 22.561911 3913.7712 3456.9151 464.07498 456.85609 556.31985 1103.3901 263.88855 0 -485.54294 514000.27 -514981.47 9117.6459 26592.844 660.74075 4.5694113
340 23.929412 3712.7166 3258.4133 437.42702 454.30336 533.72419 1069.0448 271.85689 0 -454.53939 514001.97 -514967.75 7187.6779 26736.819 622.98237 3.8812919
360 25.298241 3533.3834 3024.1004 405.9716 509.283 522.55431 1104.3208 276.30858 0 -456.06655 514036.53 -514974.36 4554.9866 26876.658 578.31181 3.3031408
380 26.653809 3367.1792 2971.2716 398.87957 395.9076 508.27241 1059.2248 257.85685 0 -499.68496 514032.55 -514962.31 5645.8914 27002.069 568.38695 2.8305175
400 27.984353 3204.91 2874.2403 385.85357 330.6697 543.88404 1018.8809 231.0702 0 -519.33317 514029.07 -514972.9 7250.7332 27123.905 549.89179 2.5832582
420 29.327209 3050.6948 2776.6044 372.74639 274.09045 517.42853 953.07587 226.06727 0 -505.60565 514057.02 -514973.9 4026.2599 27250.314 531.28066 2.3360848
440 30.659683 2916.2839 2640.2361 354.43958 276.04784 507.06292 983.97321 236.01275 0 -534.64355 514059.65 -514976.01 1708.709 27364.195 505.24974 2.0766005
460 31.992583 2787.525 2609.5902 350.32551 177.93474 485.64363 933.57925 234.95003 0 -560.61762 514069.83 -514985.45 3400.5279 27458.081 499.48923 1.8097259
480 33.31755 2662.4984 2514.178 337.51686 148.32032 464.67048 928.26208 239.37956 0 -570.38407 514070.86 -514984.47 5084.8141 27547.559 481.26944 1.6441427
500 34.613889 2540.5549 2433.5506 326.693 107.00428 473.2945 888.73268 239.40601 0 -565.68704 514057.33 -514986.07 3134.3501 27643.279 465.87942 1.4891047
520 35.938482 2432.2066 2375.3401 318.8785 56.866542 460.28751 838.60926 229.00792 0 -579.13212 514093.74 -514985.64 468.2133 27732.471 454.76753 1.3789356
540 37.265891 2328.8169 2275.0595 305.41629 53.757389 473.08203 875.54175 220.60944 0 -604.11384 514075.79 -514987.16 2632.7788 27804.408 435.55773 1.3457265
560 38.585909 2228.615 2278.3234 305.85446 -49.708475 455.58479 820.87878 215.10334 0 -604.72924 514052.45 -514989 3784.1482 27875.141 436.2741 1.1341618
580 39.864162 2134.4158 2127.9962 285.67372 6.4195621 480.68268 836.80009 219.13915 0 -563.30768 514019.28 -514986.18 1359.5813 27951.068 407.46382 1.1159366
600 41.132397 2048.4786 2102.9549 282.31205 -54.476369 486.301 796.4297 225.04029 0 -574.89865 514003.04 -514990.39 -91.415091 28017.963 402.69767 1.0358319
620 42.405012 1967.4398 2048.4364 274.99318 -80.996617 477.38045 786.20744 223.98682 0 -570.14553 513997.93 -514996.35 1828.8595 28070.312 392.2521 1.022392
640 43.643353 1888.1318 1981.566 266.01614 -93.434276 482.74658 801.17689 222.6863 0 -557.43781 513952.32 -514994.92 3812.5364 28123.574 379.47296 0.92888928
660 44.915581 1813.0614 1959.0105 262.98817 -145.94913 498.25019 750.64037 217.17325 0 -556.66234 513938.55 -514993.9 1151.2432 28187.531 375.17108 0.87739869
680 46.131009 1744.832 1911.6741 256.63347 -166.84215 497.042 725.1867 211.01897 0 -553.89849 513944.3 -514990.49 108.93436 28245.999 366.12859 0.80270448
700 47.378681 1678.1626 1915.3894 257.13223 -237.22675 490.51486 719.69339 202.0347 0 -569.53306 513909.13 -514989.07 2213.2126 28294.676 366.86703 0.7415387
720 48.690897 1612.159 1862.0857 249.97645 -249.92665 500.42275 728.44427 190.27551 0 -551.64449 513871.72 -514989.15 3052.5203 28347.921 356.64837 0.74199709
740 49.934569 1549.9154 1792.3586 240.61591 -242.44316 497.29161 738.6029 175.53735 0 -547.70029 513880.64 -514986.81 738.07583 28409.346 343.29748 0.7047584
760 51.094031 1493.142 1799.8956 241.62772 -306.75355 503.57846 709.28495 169.315 0 -559.17689 513862.16 -514991.92 -783.63021 28463.359 344.75885 0.66625263
780 52.252971 1437.0347 1824.9884 244.99631 -387.95371 510.42774 661.31982 170.22096 0 -556.6031 513818.26 -514991.58 1267.2418 28503.342 349.56302 0.68065177
800 53.379442 1382.5833 1736.7991 233.1573 -354.21576 514.27927 697.39594 172.11416 0 -554.93314 513805.74 -514988.82 1744.7887 28543.483 332.6636 0.66505935
820 54.535354 1332.0444 1690.9869 227.00722 -358.94246 509.37721 686.56084 172.95747 0 -552.9503 513815.42 -514990.31 -146.04973 28586.706 323.91193 0.59356881
840 55.662329 1285.5292 1685.7755 226.30763 -400.2463 507.19453 662.75433 170.55434 0 -559.51859 513807.26 -514988.49 -690.17907 28621.308 322.91069 0.59874377
860 56.818479 1239.7941 1704.701 228.84829 -464.90694 495.88426 658.89439 170.35 0 -574.82793 513772.87 -514988.08 747.19844 28645.708 326.53594 0.60530564
880 57.943864 1195.2063 1673.557 224.66734 -478.35068 498.99876 648.88199 170.51747 0 -557.50857 513743.81 -514983.05 1172.7738 28670.551 320.58027 0.57096305
900 59.0976 1153.211 1639.9315 220.15327 -486.72046 502.47627 643.51354 178.69816 0 -556.38628 513730.32 -514985.34 -511.45034 28697.8 314.13849 0.56088797
920 60.220959 1114.1597 1616.0109 216.94205 -501.85117 514.79499 630.19604 179.36393 0 -549.5453 513714.55 -514991.21 -1422.3991 28716.8 309.54311 0.58363424
940 61.375362 1076.2186 1627.0408 218.42275 -550.82218 512.57892 621.31041 171.65194 0 -553.00757 513686.04 -514989.39 298.61672 28723.941 311.6754 0.54200743
960 62.499341 1040.0389 1613.5611 216.61317 -573.52223 511.50602 601.98148 170.02159 0 -546.21393 513682.82 -514993.64 795.9161 28731.421 309.07527 0.57946382
980 63.655075 1005.556 1568.0264 210.50035 -562.47043 514.81982 629.32987 175.28567 0 -544.55487 513654.62 -514991.97 -1246.9263 28741.462 300.35589 0.55675479
1000 64.806202 973.43261 1565.2247 210.12423 -591.79208 505.29272 600.76239 165.17131 0 -554.93533 513685.36 -514993.44 -1299.5982 28742.028 299.81847 0.55749205
1020 65.904504 942.29451 1571.0425 210.90525 -628.74802 506.25414 614.54444 152.41332 0 -569.19989 513660.6 -514993.36 -197.56562 28733.474 300.93111 0.56370125
1040 67.002294 912.00673 1595.282 214.15928 -683.27525 489.63949 569.70488 159.39981 0 -590.61096 513680.38 -514991.79 467.80409 28724.916 305.58073 0.55701412
1060 68.131496 883.21094 1542.2424 207.03896 -659.03142 503.00762 589.40955 165.92561 0 -599.75208 513674.64 -514992.26 -2147.8302 28718.434 295.39729 0.59345978
1080 69.232333 856.19557 1533.4133 205.85369 -677.21769 507.87992 576.5184 168.18594 0 -578.48413 513634.34 -514985.66 -1762.0347 28699.147 293.70385 0.59551254
1100 70.364775 831.37376 1484.1452 199.23968 -652.77147 514.07523 608.66719 163.10107 0 -567.48676 513613.52 -514984.65 33.310994 28670.682 284.25195 0.61206838
1120 71.467535 808.52739 1521.0421 204.19292 -712.51473 513.69276 561.64386 163.23813 0 -559.45919 513591.61 -514983.24 -310.61111 28645.19 291.32265 0.61797603
1140 72.601129 786.87835 1489.4671 199.95412 -702.58878 523.98829 584.70722 162.29577 0 -549.08561 513559.92 -514984.41 -1685.4255 28620.437 285.26086 0.63846185
1160 73.705792 766.63847 1508.1762 202.46573 -741.53775 514.32182 584.88936 152.54558 0 -535.15913 513525.59 -514983.73 -1902.1776 28587.352 288.83351 0.67096701
1180 74.841457 749.02843 1510.9898 202.84344 -761.96133 536.04857 571.2202 147.21017 0 -519.34217 513485.23 -514982.33 867.83936 28547.617 289.35403 0.71492747
1200 75.948637 733.34578 1503.6833 201.86257 -770.33748 533.86604 589.40444 152.04389 0 -519.58392 513457.87 -514983.94 16.285861 28517.381 287.94489 0.73468233
1220 77.086539 718.25616 1498.0744 201.1096 -779.81819 559.89022 564.22113 156.14265 0 -507.10566 513432.51 -514985.47 -1279.2454 28491.203 286.86449 0.74672427
1240 78.196455 704.4456 1488.8421 199.87022 -784.3965 566.03391 579.8182 161.3278 0 -468.50406 513361.56 -514984.64 -54.414997 28461.145 285.0822 0.7757678
1260 79.336046 693.03071 1494.0932 200.57516 -801.06253 573.59408 573.29809 158.50778 0 -453.3769 513333.73 -514986.81 977.78497 28434.874 286.06644 0.82806578
1280 80.450187 683.34372 1478.8974 198.53519 -795.55372 580.51573 596.90975 153.51449 0 -437.44107 513297.84 -514986.89 809.72996 28418.785 283.14058 0.85789606
1300 81.562086 675.21003 1490.4096 200.08064 -815.19955 586.94949 575.877 144.63393 0 -412.94901 513274.99 -514984.7 -448.50658 28409.979 285.3107 0.94374006
1320 82.704837 668.21879 1489.4584 199.95295 -821.23962 576.22292 605.97557 140.59647 0 -423.93742 513262.85 -514982.94 -41.054413 28400.286 285.13719 0.9231239
1340 83.820401 662.582 1506.0415 202.17916 -843.45952 580.69502 578.24319 144.89986 0 -430.94868 513260.2 -514976.55 977.60126 28392.044 288.28069 1.0060194
1360 84.965785 658.24059 1527.9683 205.12273 -869.7277 577.91541 570.19843 152.39114 0 -451.12207 513259.47 -514978.58 371.63239 28390.774 292.47304 1.0318294
1380 86.080907 654.92452 1486.6437 199.57509 -831.71915 580.08964 585.152 157.63831 0 -437.00747 513263.59 -514981.18 -247.9673 28392.439 284.5256 1.0911219
1400 87.195704 652.93764 1510.6586 202.79899 -857.721 568.92903 573.37125 151.89337 0 -426.43036 513257.39 -514982.88 -51.617883 28392.618 289.11402 1.1268379
1420 88.34689 651.93794 1494.4977 200.62946 -842.55979 571.38046 600.63765 145.50987 0 -443.12588 513270.14 -514987.1 743.13616 28392.861 285.98783 1.1924311
1440 89.493044 651.84231 1520.3977 204.10641 -868.55537 569.30886 591.50444 144.87083 0 -452.53315 513268.23 -514989.93 461.56063 28397.854 290.94803 1.2038182
1460 90.608597 652.79726 1538.7134 206.56522 -885.91619 576.98896 569.0177 144.49629 0 -461.96923 513277.97 -514992.42 -706.12558 28404.942 294.4277 1.2773313
1480 91.757208 654.35279 1560.3813 209.47403 -906.02856 573.31257 551.02062 151.79154 0 -471.83285 513285.31 -514995.63 -636.13512 28406.735 298.57005 1.3040147
1500 92.886091 656.18474 1535.2238 206.09675 -879.03909 565.77757 581.30733 155.02848 0 -493.04533 513302.18 -514990.29 143.11549 28404.04 293.73748 1.3269254
1520 94.042872 658.68485 1540.4536 206.79882 -881.76871 562.4227 566.55678 153.51217 0 -481.25224 513306.12 -514989.13 320.11741 28402.365 294.71422 1.3871403
1540 95.163877 662.00561 1525.2953 204.7639 -863.28974 547.96338 591.50659 150.34534 0 -461.18073 513297.4 -514989.32 -131.34055 28402.834 291.79671 1.4143192
1560 96.312922 666.1124 1506.6675 202.2632 -840.55513 559.7266 593.99441 157.20165 0 -475.77029 513317.32 -514993.02 -361.762 28402.279 288.23662 1.3888658
1580 97.430754 670.56531 1535.7659 206.16953 -865.20063 562.32491 577.33497 164.90914 0 -495.18787 513321.56 -514996.14 281.32907 28399.686 293.815 1.3885206
1600 98.548553 676.03467 1559.0361 209.29344 -883.00142 570.63265 568.63747 171.76131 0 -497.53636 513299.62 -514996.12 -83.071675 28398.615 298.25471 1.4380743
1620 99.69614 681.61565 1551.6098 208.29649 -869.99417 572.80627 589.25676 175.66645 0 -486.29635 513275.79 -514997.22 -1208.1908 28396.28 296.81124 1.4843702
1640 100.81368 687.56466 1565.2232 210.12403 -877.65855 578.7743 586.81939 173.9181 0 -490.97778 513266.56 -514992.76 -587.86248 28386.365 299.44244 1.4342399
1660 101.96336 693.76095 1558.3222 209.1976 -864.56124 583.58497 605.24119 171.44101 0 -488.52963 513255.46 -514991.76 335.92415 28373.356 298.0981 1.4841753
1680 103.08285 699.76249 1608.1314 215.88426 -908.36892 585.35458 590.64567 171.79357 0 -478.93732 513211.41 -514988.64 91.212095 28363.527 307.67509 1.4177962
1700 104.23343 705.16423 1586.5697 212.9897 -881.40546 609.44211 582.01973 172.76356 0 -457.12517 513197.39 -514985.89 -662.76266 28354.912 303.56619 1.3605633
1720 105.38429 709.98606 1609.0843 216.01219 -899.09829 612.02708 597.82638 167.68834 0 -444.72348 513153.41 -514985.33 -92.038463 28343.124 307.84128 1.4562833
1740 106.50511 714.51622 1579.8945 212.09359 -865.37833 624.49924 619.60972 166.03466 0 -425.9731 513136.37 -514985.92 1173.1099 28332.574 302.27863 1.3790325
1760 107.65668 718.07347 1624.056 218.02206 -905.9825 608.96798 597.96224 154.72096 0 -409.37211 513132.37 -514990.63 786.32681 28330.712 310.74964 1.3669913
1780 108.77729 720.46707 1606.3817 215.64937 -885.91465 639.71765 615.06161 152.57928 0 -394.48439 513088.38 -514987.17 -271.86201 28334.236 307.3761 1.3327989
1800 109.92899 721.98649 1608.1038 215.88055 -886.11732 621.68949 602.68633 163.61329 0 -397.09967 513111.57 -514988.58 587.45646 28336.693 307.73281 1.2707867
1820 111.05093 722.92155 1567.2948 210.40212 -844.3732 657.9717 609.80843 174.58395 0 -387.74403 513087.19 -514986.18 1657.5204 28343.522 299.9292 1.2250789
1840 112.17289 723.61458 1561.6308 209.64177 -838.01626 621.38222 638.008 181.56394 0 -392.76804 513100.91 -514987.12 951.04423 28360.92 298.8574 1.192447
1860 113.32517 724.57888 1559.5079 209.35678 -834.92903 648.61916 621.88348 182.62731 0 -413.59874 513115.13 -514989.59 -474.05956 28382.975 298.4495 1.1946089
1880 114.44655 725.74322 1588.6378 213.26733 -862.89459 616.10137 598.6142 185.03327 0 -431.03949 513153.5 -514985.11 326.23753 28401.004 304.06324 1.1258592
1900 115.60092 726.63642 1552.6045 208.43002 -825.96805 615.20719 632.90186 175.31959 0 -439.29325 513177.07 -514987.17 1080.7061 28419.738 297.15171 1.1348451
1920 116.72882 727.57597 1579.3221 212.01674 -851.74611 606.50987 618.17792 169.75157 0 -442.63284 513179.83 -514983.38 -43.794187 28443.345 302.3028 1.0665772
1940 117.88137 728.52961 1573.1141 211.18335 -844.58454 624.72383 626.3057 166.98593 0 -453.41808 513175.12 -514984.3 -900.58801 28464.403 301.13166 1.0223996
1960 119.003 728.94698 1626.2629 218.31833 -897.31596 599.28223 602.89095 166.05528 0 -470.08979 513190.07 -514985.52 -260.33773 28477.732 311.33029 0.99933978
1980 120.15553 728.20483 1628.3695 218.60113 -900.16467 612.33461 601.10447 163.81406 0 -448.48915 513155.61 -514984.54 821.49207 28488.285 311.74795 0.96708127
2000 121.27853 726.32991 1617.7225 217.17182 -891.39259 608.69121 604.99032 169.22497 0 -445.16887 513154.27 -514983.4 -472.67394 28502.073 309.74198 0.88520672
Loop time of 121.279 on 1 procs for 2000 steps with 3000 atoms
Pair time (%) = 55.4018 (45.6815)
Bond time (%) = 7.86978 (6.48901)
Kspce time (%) = 13.9231 (11.4803)
Neigh time (%) = 2.17099 (1.79008)
Comm time (%) = 0.43024 (0.354754)
Outpt time (%) = 0.0126977 (0.0104699)
Other time (%) = 41.4699 (34.194)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10468 ave 10468 max 10468 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 662422 ave 662422 max 662422 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 662422
Ave neighs/atom = 220.807
Ave special neighs/atom = 10.5
Neighbor list builds = 63
Dangerous builds = 0

View File

@ -0,0 +1,263 @@
LAMMPS (8 Jul 2015)
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 2.600 8.0
kspace_style pppm 1.0e-4
read_data data.ethanol
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
1 by 2 by 2 MPI processor grid
reading atoms ...
3000 atoms
scanning bonds ...
5 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
9 = max dihedrals/atom
reading bonds ...
2750 bonds
reading angles ...
3250 angles
reading dihedrals ...
3000 dihedrals
5 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
10 = max # of 1-4 neighbors
11 = max # of special neighbors
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 CTO
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff 1 1 thole 2.051000
pair_coeff 1 2 thole 1.580265
pair_coeff 1 4 thole 1.416087
pair_coeff 1 6 thole 2.051000
pair_coeff 1 7 thole 1.580265
pair_coeff 1 8 thole 1.416087
pair_coeff 2 2 thole 1.217570
pair_coeff 2 4 thole 1.091074
pair_coeff 2 6 thole 1.580265
pair_coeff 2 7 thole 1.217570
pair_coeff 2 8 thole 1.091074
pair_coeff 4 4 thole 0.977720
pair_coeff 4 6 thole 1.416087
pair_coeff 4 7 thole 1.091074
pair_coeff 4 8 thole 0.977720
pair_coeff 6 6 thole 2.051000
pair_coeff 6 7 thole 1.580265
pair_coeff 6 8 thole 1.416087
pair_coeff 7 7 thole 1.217570
pair_coeff 7 8 thole 1.091074
pair_coeff 8 8 thole 0.977720
group gETHANOL molecule 1:250
3000 atoms in group gETHANOL
group gATOMS type 1 2 3 4 5
2250 atoms in group gATOMS
group gDRUDES type 6 7 8
750 atoms in group gDRUDES
neighbor 2.0 bin
variable vTEMP equal 300.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gATOMS create ${vTEMP} 12345
velocity gATOMS create 300 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C N C N D D D
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
250 = # of size 2 clusters
250 = # of size 3 clusters
250 = # of size 4 clusters
0 = # of frozen angles
comm_modify vel yes
compute cTEMP_ATOM gATOMS temp
compute cTEMP all temp/drude
fix fDTDIR all drude/transform/direct
fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500
fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500
fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500
fix_modify fNPT temp cTEMP_ATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349)
fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0
fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0
fix fNVT gDRUDES nvt temp 1 1 100.0
fix fDTINV all drude/transform/inverse
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 20
timestep 0.5
run 2000
PPPM initialization ...
G vector (1/distance) = 0.379738
grid = 30 30 30
stencil order = 5
estimated absolute RMS force accuracy = 0.0289979
estimated relative force accuracy = 8.73262e-05
using double precision FFTs
3d grid and FFT values/proc = 17908 7200
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 11
New max number of 1-2 to 1-4 neighbors: 11 (+0)
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 10
Memory usage per processor = 13.7041 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 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301
20 0.48582006 11385.192 5995.2334 804.83256 5389.9589 2039.7325 2312.5375 131.6961 0 1710.3266 514098.34 -514902.67 75867.639 22408.275 975.26848 406.07565
40 0.99611902 9812.3727 6009.1747 806.70411 3803.198 1442.3489 1826.1439 275.19367 0 1288.2864 513934.98 -514963.76 48675.043 22980.115 1057.0177 221.56359
60 1.4878449 8857.9452 5779.5973 775.8844 3078.348 1190.8978 1938.6134 328.6837 0 619.31805 513970.98 -514970.15 39710.611 23440.966 1050.9011 133.14424
80 1.9926319 8115.7842 5997.9225 805.19356 2117.8617 901.84105 1587.5472 325.40763 0 288.34562 513957.43 -514942.71 37588.95 23834.833 1111.65 89.05492
100 2.476769 7496.2555 5770.3833 774.64747 1725.8722 829.63908 1420.6659 325.4016 0 62.343573 514051.62 -514963.79 27294.064 24225.918 1080.2687 60.498473
120 2.9719281 6986.5933 5396.9479 724.51547 1589.6454 678.24993 1535.5197 325.88462 0 -9.6649715 514027.05 -514967.4 21720.902 24578.195 1016.3014 42.715633
140 3.4472849 6549.0004 5126.6341 688.22709 1422.3663 724.95473 1477.7714 315.11964 0 -99.456489 513960.58 -514956.6 19747.305 24877.008 969.51239 30.977084
160 3.8980451 6131.3313 5000.4421 671.2864 1130.8892 703.24856 1302.1192 314.93994 0 -258.4539 514042.28 -514973.25 23050.008 25142.654 948.73049 23.021804
180 4.3219371 5749.9765 4700.9451 631.0803 1049.0314 674.94524 1301.4114 310.04938 0 -326.73679 514044.26 -514954.9 14225.484 25400.048 893.75892 17.322075
200 4.740237 5429.6012 4392.5738 589.68286 1037.0274 612.00109 1296.2432 303.16019 0 -300.38659 514093.7 -514967.69 10835.073 25622.866 836.16806 13.764486
220 5.15255 5133.8314 4290.7369 576.01173 843.09448 572.5199 1261.8055 289.99074 0 -383.71584 514078.3 -514975.81 12509.825 25814.229 817.78562 11.104636
240 5.5619049 4850.3859 4120.3634 553.13987 730.0225 553.79223 1263.6533 278.92141 0 -487.76524 514091.35 -514969.93 10891.878 25996.167 785.87197 9.3607763
260 5.9694359 4583.988 3911.0361 525.03865 672.95183 541.52258 1175.1553 273.43363 0 -475.23639 514139.68 -514981.61 8086.1508 26168.96 746.55574 7.4653781
280 6.3831999 4349.2238 3692.2792 495.67153 656.94461 598.81909 1148.0997 278.87809 0 -444.09603 514045.38 -514970.13 5124.6371 26323.056 705.04252 6.4783461
300 6.8002019 4128.9011 3579.5067 480.53234 549.39444 584.0659 1089.513 267.69426 0 -456.87099 514043.55 -514978.56 8350.7748 26456.831 683.94371 5.2650989
320 7.2020841 3913.7715 3456.9151 464.07498 456.85644 556.31985 1103.3901 263.8886 0 -485.54294 514000.27 -514981.47 9117.645 26592.844 660.74075 4.5694128
340 7.614501 3712.7165 3258.4132 437.42702 454.30329 533.72422 1069.0449 271.85681 0 -454.53938 514001.97 -514967.75 7187.6789 26736.819 622.98237 3.8812925
360 8.0251679 3533.3831 3024.1004 405.97159 509.28269 522.55432 1104.3208 276.30864 0 -456.06652 514036.53 -514974.36 4554.9866 26876.658 578.3118 3.3031414
380 8.4368989 3367.1791 2971.2717 398.87959 395.90735 508.27248 1059.2247 257.85692 0 -499.68504 514032.55 -514962.31 5645.8885 27002.069 568.38697 2.8305185
400 8.841274 3204.9102 2874.2407 385.85361 330.66952 543.884 1018.8809 231.07032 0 -519.33317 514029.07 -514972.9 7250.7314 27123.905 549.89185 2.58326
420 9.2528131 3050.6946 2776.6047 372.74643 274.08991 517.42853 953.07588 226.06762 0 -505.60561 514057.02 -514973.9 4026.258 27250.314 531.28072 2.3360857
440 9.6643951 2916.2842 2640.2367 354.43965 276.04748 507.06285 983.97334 236.01271 0 -534.64347 514059.65 -514976.01 1708.7076 27364.195 505.24986 2.0765971
460 10.070477 2787.525 2609.5902 350.3255 177.93484 485.64382 933.57906 234.95019 0 -560.61753 514069.83 -514985.45 3400.5283 27458.081 499.48921 1.8097272
480 10.475857 2662.4983 2514.1778 337.51682 148.3205 464.67048 928.2622 239.37954 0 -570.38391 514070.86 -514984.47 5084.8137 27547.559 481.26939 1.6441432
500 10.904204 2540.5544 2433.5504 326.69297 107.00399 473.29419 888.73276 239.40578 0 -565.68691 514057.33 -514986.07 3134.3575 27643.279 465.87938 1.4891037
520 11.343421 2432.2068 2375.3395 318.87842 56.867315 460.28707 838.60936 229.00812 0 -579.13202 514093.74 -514985.64 468.2212 27732.471 454.76741 1.3789343
540 11.792302 2328.8171 2275.0598 305.41633 53.757301 473.0817 875.54202 220.60952 0 -604.11383 514075.79 -514987.16 2632.7729 27804.408 435.55777 1.3457292
560 12.22888 2228.6146 2278.324 305.85454 -49.709377 455.5848 820.87873 215.10398 0 -604.72916 514052.45 -514989 3784.1433 27875.141 436.27421 1.1341637
580 12.654423 2134.4153 2127.9966 285.67378 6.418699 480.68271 836.79983 219.13997 0 -563.30761 514019.28 -514986.18 1359.5795 27951.068 407.46389 1.1159357
600 13.083667 2048.478 2102.9555 282.31212 -54.477504 486.30135 796.43014 225.04094 0 -574.89912 514003.04 -514990.39 -91.420338 28017.963 402.69778 1.0358317
620 13.5203 1967.44 2048.4369 274.99325 -80.99691 477.38009 786.20772 223.98767 0 -570.14552 513997.92 -514996.35 1828.852 28070.312 392.2522 1.022388
640 13.946543 1888.1309 1981.5653 266.01604 -93.434406 482.74621 801.17707 222.68721 0 -557.43764 513952.32 -514994.92 3812.5405 28123.574 379.47281 0.92888841
660 14.383896 1813.0614 1959.0076 262.98777 -145.94621 498.24936 750.64093 217.17501 0 -556.66175 513938.55 -514993.9 1151.2704 28187.531 375.17051 0.8773937
680 14.80455 1744.8321 1911.6727 256.63328 -166.84059 497.04089 725.18698 211.02114 0 -553.89822 513944.3 -514990.49 108.9445 28245.999 366.1283 0.80270876
700 15.246875 1678.1628 1915.389 257.13218 -237.22624 490.51443 719.69473 202.03683 0 -569.53274 513909.13 -514989.07 2213.2168 28294.676 366.86695 0.74153849
720 15.683303 1612.159 1862.0857 249.97646 -249.9267 500.42186 728.44302 190.2785 0 -551.64436 513871.73 -514989.15 3052.5153 28347.921 356.64838 0.74199104
740 16.103407 1549.912 1792.3564 240.61562 -242.44438 497.29156 738.60345 175.54129 0 -547.7015 513880.63 -514986.81 737.97658 28409.346 343.29706 0.70477013
760 16.533572 1493.1418 1799.8951 241.62766 -306.75333 503.57865 709.28516 169.31508 0 -559.17797 513862.16 -514991.92 -783.64904 28463.359 344.75876 0.66625709
780 16.963103 1437.0356 1824.9946 244.99715 -387.959 510.43018 661.31998 170.2197 0 -556.60498 513818.25 -514991.58 1267.2099 28503.341 349.56422 0.68065257
800 17.384911 1382.5837 1736.8044 233.15801 -354.22065 514.28158 697.39733 172.11237 0 -554.93413 513805.74 -514988.82 1744.7575 28543.482 332.66462 0.66506284
820 17.818295 1332.0449 1690.9863 227.00714 -358.94137 509.37962 686.56323 172.95557 0 -552.94994 513815.42 -514990.31 -146.04099 28586.704 323.91181 0.59356692
840 18.239769 1285.5293 1685.7656 226.30629 -400.23625 507.19659 662.75791 170.55111 0 -559.5183 513807.26 -514988.49 -690.12588 28621.306 322.90879 0.59871543
860 18.672279 1239.7943 1704.6913 228.84697 -464.89697 495.88249 658.89516 170.34465 0 -574.82534 513772.88 -514988.07 747.30519 28645.706 326.53407 0.60529545
880 19.094243 1195.2074 1673.5516 224.66662 -478.34417 498.99767 648.88222 170.51909 0 -557.50585 513743.81 -514983.05 1172.8191 28670.55 320.57923 0.57095732
900 19.530344 1153.213 1639.9317 220.1533 -486.71872 502.48114 643.51414 178.70544 0 -556.38218 513730.3 -514985.34 -511.40662 28697.799 314.13852 0.56091919
920 19.954644 1114.1622 1615.9735 216.93702 -501.81127 514.7973 630.19712 179.3982 0 -549.54237 513714.55 -514991.21 -1422.316 28716.8 309.53594 0.58362776
940 20.390261 1076.2212 1626.9734 218.41371 -550.75226 512.58732 621.31396 171.70796 0 -553.00677 513686.03 -514989.39 298.59388 28723.942 311.66248 0.54203006
960 20.813949 1040.0451 1613.5266 216.60854 -573.48149 511.51922 601.98585 170.02867 0 -546.21382 513682.83 -514993.63 795.90454 28731.424 309.06864 0.57947773
980 21.252467 1005.5683 1568.0671 210.50581 -562.49882 514.83412 629.32638 175.23649 0 -544.55558 513654.63 -514991.97 -1246.8402 28741.467 300.36369 0.55676445
1000 21.687328 973.43654 1565.2947 210.13362 -591.85814 505.31069 600.76156 165.13032 0 -554.93709 513685.33 -514993.45 -1299.6769 28742.033 299.8319 0.55747244
1020 22.104826 942.30585 1571.1252 210.91634 -628.81931 506.25625 614.52982 152.39206 0 -569.20109 513660.58 -514993.37 -197.40138 28733.481 300.94692 0.5637722
1040 22.524452 912.01118 1595.3373 214.16671 -683.32616 489.65166 569.71087 159.37841 0 -590.61264 513680.34 -514991.8 467.8096 28724.925 305.59134 0.55703469
1060 22.949422 883.20635 1542.2363 207.03814 -659.02996 503.02658 589.43979 165.92415 0 -599.75711 513674.6 -514992.27 -2148.0784 28718.444 295.39616 0.59339691
1080 23.371693 856.19688 1533.476 205.86212 -677.27914 507.92146 576.49892 168.14482 0 -578.48635 513634.3 -514985.66 -1762.3643 28699.157 293.71591 0.59543987
1100 23.796874 831.36718 1484.0494 199.22681 -652.68218 514.09435 608.64804 163.13622 0 -567.49464 513613.56 -514984.63 33.441222 28670.69 284.23352 0.61219688
1120 24.215957 808.52756 1520.8457 204.16656 -712.31817 513.70662 561.61909 163.36198 0 -559.46566 513591.68 -514983.22 -310.69178 28645.197 291.28494 0.61812087
1140 24.641242 786.87445 1489.3947 199.9444 -702.52028 523.97711 584.65081 162.32286 0 -549.07998 513560 -514984.39 -1685.574 28620.442 285.24697 0.63849523
1160 25.055568 766.64827 1508.2693 202.47822 -741.62101 514.35266 584.91055 152.45332 0 -535.165 513525.54 -514983.72 -1901.0493 28587.357 288.85135 0.67096559
1180 25.482658 749.02928 1511.1172 202.86054 -762.08788 536.05747 571.22043 147.19144 0 -519.37083 513485.14 -514982.32 866.88063 28547.627 289.37844 0.71496578
1200 25.894749 733.35099 1503.6268 201.85499 -770.27581 533.87098 589.37041 152.16808 0 -519.57804 513457.84 -514983.94 14.805399 28517.39 287.93411 0.73458768
1220 26.325628 718.27504 1498.0867 201.11126 -779.81165 559.91487 564.18647 156.27378 0 -507.13199 513432.42 -514985.48 -1279.1075 28491.202 286.86673 0.74700594
1240 26.738918 704.4507 1488.7649 199.85985 -784.31417 566.05166 579.79847 161.35046 0 -468.44357 513361.55 -514984.62 -53.3159 28461.135 285.06732 0.77592838
1260 27.171522 693.03769 1494.1149 200.57807 -801.07721 573.62194 573.3094 158.43371 0 -453.27917 513333.62 -514986.78 977.9179 28434.863 286.07064 0.82794452
1280 27.586875 683.35215 1479.0049 198.54962 -795.65277 580.54264 596.95031 153.53994 0 -437.44286 513297.62 -514986.86 808.24663 28418.774 283.16101 0.85830865
1300 28.005456 675.21985 1490.3973 200.079 -815.1775 586.97926 575.85031 144.74048 0 -412.9591 513274.88 -514984.67 -448.16581 28409.96 285.30833 0.9437975
1320 28.436763 668.22782 1489.1302 199.90889 -820.90236 576.19343 605.89694 140.779 0 -423.95547 513263.1 -514982.91 -40.766531 28400.261 285.0744 0.92283057
1340 28.854671 662.60827 1506.0283 202.17738 -843.42002 580.70797 578.1842 144.8341 0 -430.96333 513260.37 -514976.56 977.60336 28392.015 288.27815 1.0060347
1360 29.284718 658.23752 1527.6526 205.08035 -869.41511 577.91716 570.16602 152.14574 0 -451.11548 513260.04 -514978.56 374.82603 28390.744 292.41271 1.031412
1380 29.707547 654.96847 1486.4979 199.55551 -831.52939 580.08595 585.05597 157.33942 0 -437.07207 513264.24 -514981.18 -245.84993 28392.431 284.49746 1.0915693
1400 30.132399 652.9829 1510.7519 202.81151 -857.76902 568.8718 573.40304 151.53282 0 -426.40132 513257.71 -514982.89 -48.059208 28392.645 289.13172 1.1272637
1420 30.56509 652.00089 1494.6519 200.65015 -842.65097 571.38637 600.46686 145.25854 0 -443.09809 513270.44 -514987.1 744.84418 28392.941 286.01743 1.1922923
1440 30.993519 651.93656 1520.3356 204.09807 -868.39904 569.20772 591.53184 144.73613 0 -452.45231 513268.58 -514990 462.47894 28397.996 290.93612 1.2038241
1460 31.413554 652.8797 1538.7905 206.57555 -885.91076 576.968 569.3361 144.29397 0 -461.95958 513278 -514992.55 -703.88926 28405.143 294.44272 1.2767432
1480 31.854234 654.43984 1560.998 209.55681 -906.55813 573.32119 550.83703 151.55603 0 -471.87704 513285.3 -514995.69 -634.5939 28407.003 298.6883 1.3039308
1500 32.258767 656.25668 1535.2085 206.0947 -878.95186 565.7821 581.34544 155.11099 0 -493.26681 513302.34 -514990.27 141.09795 28404.376 293.73526 1.3252685
1520 32.667376 658.76245 1540.1255 206.75478 -881.36305 562.28162 566.2439 153.62339 0 -481.21787 513306.74 -514989.04 320.45957 28402.754 294.65144 1.3869014
1540 33.067487 662.13708 1524.8473 204.70375 -862.71024 547.98628 591.76817 150.15973 0 -460.97843 513297.6 -514989.25 -130.86158 28403.27 291.71099 1.413931
1560 33.480413 666.19858 1506.8716 202.29059 -840.67298 559.57219 594.04584 156.75269 0 -475.69342 513317.61 -514992.96 -357.4244 28402.761 288.27566 1.3890257
1580 33.881172 670.71346 1535.3958 206.11984 -864.68236 562.04024 577.64202 164.82634 0 -495.24757 513322.21 -514996.15 278.58466 28400.233 293.74325 1.3903967
1600 34.282713 676.13061 1559.338 209.33397 -883.20743 570.25038 568.59163 172.20015 0 -497.5923 513299.59 -514996.24 -86.394917 28399.201 298.31271 1.4378209
1620 34.693053 681.80099 1552.6868 208.44108 -870.88582 572.69475 589.3952 176.11924 0 -485.89655 513274.18 -514997.38 -1204.2981 28396.883 297.01677 1.4865321
1640 35.094327 687.72244 1565.9114 210.21642 -878.189 578.48421 587.25138 174.28163 0 -490.691 513265.29 -514992.8 -581.44816 28387.006 299.57429 1.4344443
1660 35.50466 693.90688 1558.2867 209.19283 -864.37979 583.51938 605.39763 171.58103 0 -488.26355 513255.15 -514991.76 341.26177 28374.079 298.09208 1.4823162
1680 35.905614 699.81947 1608.5571 215.9414 -908.73759 585.45342 590.42357 171.65094 0 -478.75081 513211.28 -514988.8 77.131096 28364.346 307.75695 1.4172031
1700 36.320681 705.27021 1587.164 213.06948 -881.89376 609.44479 581.8672 172.3033 0 -457.17018 513197.71 -514986.05 -666.39751 28355.734 303.6806 1.3594258
1720 36.728727 710.00906 1608.1379 215.88513 -898.12885 612.49125 598.01777 167.03198 0 -445.09105 513154.85 -514985.42 -87.720392 28343.913 307.66062 1.454487
1740 37.130271 714.53567 1580.0753 212.11786 -865.53967 624.57295 619.34825 165.15138 0 -426.77348 513138.14 -514985.98 1176.8164 28333.357 302.31339 1.3787996
1760 37.542675 718.03805 1624.8218 218.12487 -906.78379 608.77029 596.31671 153.7484 0 -409.62158 513134.59 -514990.59 800.3654 28331.535 310.89569 1.3688034
1780 37.943518 720.37511 1609.0275 216.00455 -888.65236 640.15257 613.63079 151.83793 0 -394.53333 513087.34 -514987.08 -257.84624 28335.192 307.88341 1.3325434
1800 38.353172 721.7956 1606.901 215.71908 -885.1054 621.86791 602.54827 163.37359 0 -396.5738 513111.86 -514988.19 600.83028 28337.874 307.50221 1.2708112
1820 38.755103 722.6791 1563.6639 209.9147 -840.98481 658.28036 609.55302 175.97253 0 -386.62661 513087.76 -514985.92 1673.6509 28345.014 299.23272 1.2261086
1840 39.156883 723.36526 1560.0643 209.43147 -836.69905 621.56238 639.2919 183.25684 0 -391.12333 513097.3 -514986.98 948.98786 28362.795 298.55837 1.1894608
1860 39.568864 724.34062 1560.3485 209.46963 -836.00792 648.95076 621.00344 183.45409 0 -412.61997 513112.89 -514989.69 -494.41519 28385.176 298.60946 1.1973936
1880 39.96934 725.55016 1589.2514 213.34971 -863.70126 617.1181 598.13412 185.78351 0 -430.81566 513151.32 -514985.25 301.61577 28403.364 304.1812 1.1250834
1900 40.379241 726.4494 1555.4145 208.80726 -828.96513 616.25066 631.90687 175.77829 0 -439.44651 513173.5 -514986.96 1079.4893 28422.072 297.69125 1.1328664
1920 40.778163 727.328 1577.4105 211.76012 -850.08251 606.30559 616.55697 170.46944 0 -442.17245 513181.84 -514983.08 4.4471417 28445.679 301.93699 1.065083
1940 41.186491 728.19228 1574.1105 211.3171 -845.91818 625.03022 624.89302 167.86917 0 -451.74938 513172.29 -514984.25 -891.08022 28467.03 301.3211 1.026012
1960 41.58233 728.61768 1624.4163 218.07043 -895.79862 599.93561 599.92993 167.38843 0 -465.99755 513188.14 -514985.2 -216.32489 28480.762 310.97645 0.99894847
1980 41.996931 727.92162 1627.8345 218.52931 -899.91293 612.92861 601.82319 165.16403 0 -447.59836 513151.59 -514983.82 865.41931 28491.981 311.64212 0.97473559
2000 42.398021 726.10625 1615.3704 216.85607 -889.26418 609.59944 604.55036 169.50136 0 -443.24252 513152.61 -514982.28 -436.06261 28506.736 309.2898 0.88821892
Loop time of 42.3981 on 4 procs for 2000 steps with 3000 atoms
Pair time (%) = 14.495 (34.1878)
Bond time (%) = 2.06082 (4.86065)
Kspce time (%) = 7.76109 (18.3053)
Neigh time (%) = 0.634993 (1.49769)
Comm time (%) = 1.07386 (2.53281)
Outpt time (%) = 0.0100121 (0.0236145)
Other time (%) = 16.3623 (38.5921)
Nlocal: 750 ave 774 max 711 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 5796.5 ave 5864 max 5731 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 165579 ave 169096 max 157793 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 662315
Ave neighs/atom = 220.772
Ave special neighs/atom = 10.5
Neighbor list builds = 63
Dangerous builds = 0

File diff suppressed because it is too large Load Diff

View File

@ -0,0 +1,47 @@
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3
comm_modify vel yes
read_data data.swm4-ndp
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
pair_coeff * 2* 0.000000 0.0
group ATOMS type 1:3
group CORES type 1
group DRUDES type 4
variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
fix DRUDE all drude C N N D
velocity ATOMS create ${TK} 12345
velocity DRUDES create ${TDK} 12345
delete_bonds ATOMS multi
fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
fix NVE DRUDES nve
compute TEMP all temp/drude
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20
run 2000

View File

@ -0,0 +1,50 @@
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3
read_data data.swm4-ndp
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
pair_coeff * 2* 0.000000 0.0
group ATOMS type 1:3
group CORES type 1
group DRUDES type 4
variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
fix DRUDE all drude C N N D
velocity ATOMS create ${TK} 12345
velocity DRUDES create ${TDK} 12345
delete_bonds ATOMS multi
comm_modify vel yes
compute TATOM ATOMS temp/com
compute TEMP all temp/drude
fix DTDIR all drude/transform/direct
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix_modify RIGID temp TATOM press thermo_press
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
fix DTINV all drude/transform/inverse
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20
run 2000

View File

@ -0,0 +1,230 @@
LAMMPS (8 Jul 2015)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3
comm_modify vel yes
read_data data.swm4-ndp
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
2500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
2000 bonds
reading angles ...
500 angles
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
pair_coeff * 2* 0.000000 0.0
group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES
variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
fix DRUDE all drude C N N D
velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345
delete_bonds ATOMS multi
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 14
2000 total bonds, 500 turned on, 1500 turned off
500 total angles, 0 turned on, 500 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
500 rigid bodies with 2000 atoms
0.832099 = max distance from body owner to body atom
fix NVE DRUDES nve
compute TEMP all temp/drude
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20
run 2000
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 24.8361 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
20 1.529202 2882.459 4527.8074 -1645.3484 561.72857 0 600.34616 155114.77 -157922.19 27167.702 14058.741 1013.3326 1438.6699 160.63128
40 3.073256 1331.3826 3348.9313 -2017.5487 681.52309 0 553.09465 154668.62 -157920.79 17925.93 14484.215 749.4977 1105.2032 36.587791
60 4.584862 297.35979 2604.4137 -2307.0539 583.99971 0 409.0399 154634.74 -157934.83 13017.752 15026.564 582.87312 864.55899 18.335649
80 6.053256 -374.31023 2263.3247 -2637.635 534.80338 0 212.27981 154543.18 -157927.9 6155.9261 15645.855 506.53672 755.45209 7.6929084
100 7.4787509 -905.58889 1911.7191 -2817.308 532.30405 0 87.570168 154497.48 -157934.66 2149.3099 16288.797 427.84666 639.27768 4.1289101
120 8.8570309 -1233.6894 1675.0881 -2908.7775 544.7643 0 59.500519 154422.72 -157935.76 233.4994 16915.818 374.88816 560.54169 2.8313123
140 10.102229 -1463.4927 1468.7443 -2932.237 539.69692 0 41.083584 154424.91 -157937.93 -1492.9865 17509.345 328.70799 491.66353 2.1394958
160 11.319324 -1695.7535 1385.9603 -3081.7137 552.91518 0 30.022893 154274.72 -157939.37 -3010.4983 18061.925 310.18075 463.968 1.9858941
180 12.62008 -1818.1958 1253.169 -3071.3648 559.57456 0 20.01719 154289.67 -157940.63 -3354.4536 18564.877 280.4618 419.57594 1.6725953
200 13.836408 -1949.6497 1210.0669 -3159.7167 570.055 0 16.319449 154195.04 -157941.13 -4118.0013 19014.456 270.81546 405.06925 1.766255
220 15.032024 -2031.6125 1148.1454 -3179.7579 598.02981 0 30.833041 154127.13 -157935.75 -4514.7299 19406.767 256.9573 384.33701 1.6839691
240 16.302775 -2118.6259 1120.0048 -3238.6307 613.2903 0 59.888138 154030.6 -157942.41 -4415.1944 19738.97 250.65937 374.93983 1.5971234
260 17.465169 -2203.4348 1065.8476 -3269.2823 614.19171 0 77.619746 153980.69 -157941.79 -4564.2677 20011.077 238.53887 356.80737 1.5247856
280 18.614435 -2317.9282 1033.2676 -3351.1958 650.51218 0 126.14976 153811.64 -157939.49 -4722.7543 20224.149 231.24742 345.8479 1.5839508
300 19.757547 -2377.6306 992.4842 -3370.1148 688.02217 0 179.77994 153701.18 -157939.1 -4126.4983 20378.439 222.12 332.08757 1.7406267
320 20.888309 -2419.6547 1023.0345 -3442.6892 720.31567 0 227.70007 153549.33 -157940.04 -4083.8776 20479.241 228.95722 342.33844 1.7368676
340 22.018005 -2456.7661 1048.83 -3505.5961 754.13021 0 264.44865 153415.74 -157939.91 -3894.7125 20529.721 234.73031 351.04714 1.6271854
360 23.241519 -2504.7475 1041.9912 -3546.7386 785.42547 0 335.38743 153271.47 -157939.03 -3464.4465 20531.323 233.19976 348.66924 1.7943874
380 24.370763 -2596.2223 1000.109 -3596.3313 825.31479 0 390.18238 153129.56 -157941.39 -3355.5804 20490.646 223.82645 334.61119 1.8093168
400 25.499192 -2666.6702 1006.474 -3673.1442 865.9858 0 422.51674 152978.57 -157940.21 -3329.4637 20411.001 225.25095 336.79016 1.7220267
420 26.635042 -2675.8885 1036.9567 -3712.8452 909.14044 0 490.71452 152826.18 -157938.88 -2907.7096 20294.317 232.07303 346.92895 1.8970394
440 27.774963 -2731.5399 1054.4488 -3785.9886 935.99349 0 530.9675 152684.75 -157937.7 -2566.587 20147.094 235.9878 352.84462 1.8021906
460 28.922784 -2808.5929 996.20283 -3804.7957 986.6991 0 582.25374 152565.95 -157939.7 -2489.2912 19973.682 222.95224 333.32237 1.7660757
480 30.07189 -2862.64 1012.7035 -3875.3436 1005.1596 0 610.07691 152450.62 -157941.2 -2031.6453 19777.635 226.64513 338.80268 1.8767218
500 31.210731 -2935.4679 989.23412 -3924.702 1019.9115 0 633.87354 152362.4 -157940.89 -2214.2821 19561.863 221.39263 330.98935 1.7563884
520 32.363073 -2989.4684 968.83888 -3958.3072 1057.5825 0 655.88302 152269.68 -157941.45 -2298.887 19328.548 216.82813 324.17678 1.6971802
540 33.631173 -3036.6833 1016.2589 -4052.9421 1091.2498 0 658.37327 152140.1 -157942.67 -2240.561 19080.875 227.44082 340.06628 1.7350202
560 34.815099 -3093.7794 947.7515 -4041.5309 1141.2318 0 764.1603 151995.79 -157942.71 -1157.5191 18819.961 212.10873 317.02152 1.858938
580 36.012327 -3166.4133 987.9563 -4154.3696 1199.2171 0 796.34125 151794.12 -157944.05 -1304.4967 18555.635 221.10665 330.55449 1.7687509
600 37.228579 -3194.8572 979.66264 -4174.5199 1206.8265 0 842.68836 151717.96 -157941.99 -843.16439 18290.222 219.25051 327.76152 1.7899831
620 38.457464 -3255.2052 965.87596 -4221.0812 1218.8406 0 849.13897 151653.64 -157942.7 -628.0114 18027.862 216.16502 323.08905 1.8846337
640 39.700987 -3269.6729 1003.1309 -4272.8038 1273.0417 0 928.68865 151468.54 -157943.07 117.71698 17770.578 224.50275 335.54575 1.9677468
660 40.961165 -3293.6967 1002.4504 -4296.1471 1299.7531 0 955.60765 151392.37 -157943.87 207.76414 17523.763 224.35045 335.3089 1.9848634
680 42.237597 -3310.539 1011.7934 -4322.3324 1358.9202 0 986.69345 151275.62 -157943.56 677.05046 17289.864 226.44145 338.46824 1.9349743
700 43.530486 -3380.6882 976.5597 -4357.2479 1378.7945 0 1003.8845 151205.15 -157945.07 605.30766 17069.732 218.55607 326.63938 1.9523301
720 44.837568 -3385.7377 1005.1302 -4390.8679 1389.9512 0 1012.3035 151151.06 -157944.19 817.35931 16863.381 224.95021 336.31657 1.7675955
740 46.162222 -3378.6942 1023.8252 -4402.5194 1400.0688 0 1063.4211 151077.64 -157943.65 1513.5741 16671.518 229.13418 342.45655 2.0311926
760 47.500172 -3425.4378 1036.4011 -4461.8389 1408.8321 0 1068.7339 151003.75 -157943.15 1350.0894 16496.502 231.9487 346.7108 1.9605952
780 48.851472 -3453.9533 1021.8895 -4475.8428 1425.2091 0 1104.5857 150938.44 -157944.08 1801.2205 16339.019 228.70097 341.83264 1.9802343
800 50.2129 -3497.6136 979.31494 -4476.9285 1441.1399 0 1119.8292 150908.27 -157946.17 1649.8638 16200.982 219.17269 327.47284 2.1340593
820 51.586885 -3545.7792 969.50276 -4515.282 1479.3831 0 1103.1191 150847.98 -157945.76 1410.2174 16081.771 216.97671 324.23659 2.0229826
840 52.968935 -3562.4777 972.83071 -4535.3084 1470.5582 0 1079.9217 150857.46 -157943.25 1608.0813 15977.891 217.72151 325.33963 2.0498221
860 54.3603 -3569.1307 987.8631 -4556.9938 1446.8392 0 1055.8137 150885.62 -157945.27 1110.2002 15887.947 221.08579 330.4231 1.9689916
880 55.752677 -3612.6783 957.13055 -4569.8088 1435.3619 0 1056.264 150883.35 -157944.78 914.27883 15809.361 214.20778 320.06673 2.0614732
900 57.105164 -3660.821 939.51428 -4600.3353 1463.6114 0 1070.121 150812.25 -157946.31 1261.3306 15740.285 210.26522 314.20385 1.967446
920 58.464501 -3685.0371 941.21956 -4626.2567 1483.8487 0 1096.8187 150737.38 -157944.31 1236.4144 15680.989 210.64687 314.81024 1.89883
940 59.82202 -3719.0907 915.61639 -4634.7071 1515.6474 0 1104.1119 150691.39 -157945.86 1066.5855 15632.292 204.91683 306.20627 1.9280979
960 61.189826 -3752.7758 893.54303 -4646.3189 1517.1996 0 1125.6182 150656.81 -157945.94 1449.4275 15593.029 199.97676 298.74917 2.0320058
980 62.459059 -3752.1139 925.61635 -4677.7302 1528.3468 0 1137.3575 150600.83 -157944.27 1493.1803 15564.263 207.15484 309.5242 2.0018169
1000 63.8395 -3737.7642 905.82477 -4643.589 1505.254 0 1110.1192 150686.75 -157945.72 1296.1084 15546.258 202.72544 302.92529 1.9202879
1020 65.169118 -3767.2178 892.14155 -4659.3593 1493.2162 0 1085.8721 150707.12 -157945.57 922.80521 15537.177 199.66311 298.24598 2.0980372
1040 66.474103 -3783.5702 891.57404 -4675.1442 1484.1631 0 1076.2171 150710.25 -157945.77 707.15481 15535.102 199.5361 298.15469 1.8998396
1060 67.68596 -3816.1219 868.55884 -4684.6807 1478.7568 0 1060.3026 150723.2 -157946.94 638.16846 15538.641 194.38525 290.46937 1.8282435
1080 69.003517 -3807.3485 875.34276 -4682.6913 1482.2148 0 1055.6143 150725.66 -157946.19 416.14661 15546.427 195.90351 292.75831 1.802085
1100 70.315532 -3814.5517 894.42504 -4708.9768 1492.6318 0 1053.4891 150692.22 -157947.31 341.55654 15557.253 200.17416 299.12904 1.8640462
1120 71.62724 -3837.42 886.31149 -4723.7315 1497.9422 0 1047.1133 150677.33 -157946.12 4.9308474 15569.465 198.35833 296.42678 1.8247148
1140 72.956868 -3802.3965 899.40687 -4701.8034 1479.6329 0 1020.1254 150744.44 -157946 -142.99064 15582.446 201.2891 300.81318 1.8383791
1160 74.274932 -3810.7658 902.84695 -4713.6127 1472.5916 0 1018.8174 150740.5 -157945.52 12.783208 15594.928 202.059 301.90406 1.9647721
1180 75.595463 -3786.4338 929.44447 -4715.8783 1477.4053 0 1016.2942 150735.81 -157945.39 -53.70556 15606.416 208.01158 310.85718 1.9043666
1200 76.915409 -3800.0338 897.43664 -4697.4705 1483.1401 0 1059.31 150706.14 -157946.06 534.37576 15617.028 200.84816 300.11638 1.9100302
1220 78.119883 -3799.6824 882.65153 -4682.3339 1488.5302 0 1036.1696 150739.15 -157946.19 155.57627 15628.242 197.53922 295.16257 1.8974641
1240 79.419663 -3800.7533 911.18613 -4711.9394 1475.5968 0 1005.3229 150752.61 -157945.47 -457.64009 15638.953 203.92533 304.69739 1.9733514
1260 80.721954 -3763.5149 950.12041 -4713.6353 1441.6787 0 964.69517 150825.9 -157945.91 -604.24646 15647.017 212.6389 317.74138 2.0086447
1280 82.018768 -3770.742 937.09634 -4707.8384 1445.4659 0 949.37244 150842.61 -157945.28 -993.94783 15650.702 209.72409 313.39122 1.9703726
1300 83.314893 -3777.4899 904.34062 -4681.8306 1435.5873 0 967.49755 150860.85 -157945.76 -640.04936 15648.293 202.39329 302.46077 1.8535337
1320 84.617907 -3766.6204 885.81908 -4652.4395 1416.0678 0 971.89494 150906.86 -157947.27 -366.46049 15641.654 198.24813 296.26647 1.8149522
1340 85.931152 -3774.8032 919.58694 -4694.3901 1425.1776 0 939.16654 150887.07 -157945.81 -950.33698 15631.589 205.80544 307.5014 2.0019282
1360 87.242691 -3787.4243 922.65238 -4710.0767 1430.1028 0 964.01827 150842.71 -157946.91 -767.13405 15614.998 206.4915 308.53756 1.9863831
1380 88.556261 -3792.754 900.77391 -4693.5279 1420.8035 0 953.09514 150878.52 -157945.95 -1072.9667 15593.378 201.59505 301.19366 1.9946415
1400 89.868914 -3772.1032 910.85489 -4682.9581 1401.9732 0 959.20659 150901.09 -157945.23 -640.48972 15566.828 203.85119 304.58411 1.9776581
1420 91.085535 -3782.5246 898.64718 -4681.1718 1436.1885 0 1010.9254 150817.16 -157945.45 -21.80524 15536.721 201.11908 300.5555 1.8440133
1440 92.406331 -3775.4206 919.73488 -4695.1554 1446.1057 0 1018.1835 150785.23 -157944.68 46.810177 15507.157 205.83855 307.4904 2.123189
1460 93.732761 -3757.7457 938.91361 -4696.6593 1451.5945 0 1008.6517 150787.38 -157944.28 -175.88589 15478.297 210.13079 313.97065 2.030827
1480 95.057074 -3776.8625 933.4271 -4710.2896 1469.7064 0 1033.8521 150731.34 -157945.19 171.44717 15450.004 208.9029 312.19981 1.8912834
1500 96.391192 -3764.5196 945.12068 -4709.6403 1483.0898 0 1052.3029 150699.59 -157944.62 431.18844 15423.716 211.51995 316.14058 1.85565
1520 97.721669 -3760.514 960.29952 -4720.8136 1507.6965 0 1068.2902 150648.96 -157945.76 714.27148 15402.108 214.917 321.14587 2.0294443
1540 99.056402 -3787.9932 950.73472 -4738.728 1514.4781 0 1058.2368 150635.29 -157946.73 547.92963 15384.955 212.77638 318.01984 1.8639142
1560 100.30064 -3822.5612 921.12091 -4743.6821 1519.8628 0 1084.8337 150596.5 -157944.88 479.4088 15370.571 206.14875 308.02344 1.987069
1580 101.63827 -3832.4207 936.50822 -4768.9289 1562.5808 0 1124.0034 150490.87 -157946.38 833.06708 15360.019 209.59246 313.15266 2.0528778
1600 102.98354 -3862.3688 922.42346 -4784.7923 1571.2038 0 1110.9988 150479.2 -157946.19 674.29885 15354.399 206.44026 308.48417 1.9395764
1620 104.32562 -3863.8731 946.37539 -4810.2485 1562.9498 0 1094.323 150478.98 -157946.5 -224.35579 15352.811 211.80075 316.51174 1.9551706
1640 105.66368 -3834.5163 952.04367 -4786.5599 1536.5144 0 1078.6783 150544.66 -157946.41 -30.565669 15352.152 213.06933 318.41145 1.9589345
1660 107.00124 -3859.131 892.31028 -4751.4413 1515.0462 0 1076.4059 150603.91 -157946.81 227.01045 15352.058 199.70087 298.41871 1.8658052
1680 108.2363 -3858.2995 918.6578 -4776.9573 1533.9319 0 1064.9106 150570.69 -157946.49 335.15388 15352.595 205.5975 307.20976 1.9617869
1700 109.5659 -3850.0817 929.25672 -4779.3384 1552.5519 0 1094.2161 150519.21 -157945.31 393.76719 15353.331 207.96956 310.72982 2.0330981
1720 110.90017 -3890.603 917.87519 -4808.4781 1566.3302 0 1075.6092 150495.91 -157946.33 -76.371955 15355.997 205.42235 306.92393 2.0083539
1740 112.13829 -3891.5259 936.37478 -4827.9007 1568.2195 0 1085.8514 150464.14 -157946.11 0.9297943 15358.36 209.5626 313.09836 2.0719603
1760 113.46951 -3881.0244 903.38798 -4784.4124 1524.2547 0 1079.0557 150557.47 -157945.19 192.41461 15360.098 202.18008 302.05776 2.0203699
1780 114.81068 -3885.7248 910.74799 -4796.4728 1532.8732 0 1055.4583 150560.36 -157945.17 -530.84683 15362.305 203.82727 304.58876 1.8966227
1800 116.14689 -3907.0506 885.50025 -4792.5508 1533.7624 0 1068.2841 150550.77 -157945.37 240.13827 15362.751 198.17677 296.0834 1.9671724
1820 117.48197 -3898.1244 894.18625 -4792.3107 1521.378 0 1059.1428 150574.05 -157946.88 34.574046 15361.495 200.12072 298.96924 2.0234207
1840 118.82815 -3874.3766 895.94028 -4770.3169 1523.7865 0 1077.7882 150573.72 -157945.61 324.16201 15359.092 200.51327 299.59285 1.9530985
1860 120.06522 -3892.2617 891.17198 -4783.4337 1526.1544 0 1091.1167 150543.11 -157943.82 574.32363 15357.261 199.44612 297.92332 2.0928308
1880 121.40834 -3906.8943 911.93286 -4818.8271 1552.4086 0 1113.1993 150462.35 -157946.79 279.12422 15356.96 204.09245 304.90059 2.0679776
1900 122.76151 -3922.7591 879.82965 -4802.5888 1550.6607 0 1108.3657 150485.77 -157947.38 356.47291 15359.386 196.90768 294.18644 1.9563556
1920 124.11267 -3960.2437 869.21003 -4829.4537 1521.5339 0 1036.9974 150558.9 -157946.89 -839.29936 15362.76 194.53099 290.66184 1.8802157
1940 125.45713 -3954.661 876.75754 -4831.4186 1506.7448 0 1007.0383 150601.14 -157946.34 -1316.6937 15361.338 196.22014 293.17781 1.9123591
1960 126.70769 -3938.7558 876.41976 -4815.1756 1481.7627 0 996.84388 150652.15 -157945.93 -887.63902 15352.095 196.14454 293.08662 1.8680915
1980 128.05176 -3911.4383 894.43818 -4805.8765 1516.4382 0 1037.517 150585.32 -157945.15 -176.75144 15336.185 200.1771 299.12472 1.8815139
2000 129.4091 -3920.2641 888.06919 -4808.3333 1495.9942 0 1040.703 150601.72 -157946.75 -243.72475 15316.676 198.75171 296.94612 1.9653682
Loop time of 129.409 on 1 procs for 2000 steps with 2500 atoms
Pair time (%) = 109.108 (84.3128)
Bond time (%) = 0.0499372 (0.0385887)
Kspce time (%) = 3.30969 (2.55754)
Neigh time (%) = 9.70209 (7.49723)
Comm time (%) = 0.829103 (0.640684)
Outpt time (%) = 0.00999022 (0.00771987)
Other time (%) = 6.39989 (4.94547)
Nlocal: 2500 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21780 ave 21780 max 21780 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.34087e+06 ave 2.34087e+06 max 2.34087e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2340869
Ave neighs/atom = 936.348
Ave special neighs/atom = 4
Neighbor list builds = 100
Dangerous builds = 6

View File

@ -0,0 +1,230 @@
LAMMPS (8 Jul 2015)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3
comm_modify vel yes
read_data data.swm4-ndp
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
2500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
2000 bonds
reading angles ...
500 angles
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
pair_coeff * 2* 0.000000 0.0
group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES
variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
fix DRUDE all drude C N N D
velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345
delete_bonds ATOMS multi
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 1500 300
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 14
2000 total bonds, 500 turned on, 1500 turned off
500 total angles, 0 turned on, 500 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
500 rigid bodies with 2000 atoms
0.832099 = max distance from body owner to body atom
fix NVE DRUDES nve
compute TEMP all temp/drude
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20
run 2000
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 1500 300
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 15.0906 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
20 0.47649789 2915.1578 4579.5774 -1664.4195 561.91893 0 600.76451 155095.13 -157922.23 27379.77 14058.574 1024.9188 1455.9194 160.86778
40 0.97488093 1320.1721 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914
60 1.4631288 284.06852 2671.4325 -2387.3639 575.54157 0 387.8792 154580.74 -157931.53 12104.741 15031.425 597.87207 886.98502 18.450413
80 1.937151 -462.53017 2214.284 -2676.8142 560.36347 0 254.65245 154447.22 -157939.05 6285.2465 15651.216 495.56131 739.13811 7.4024411
100 2.3922298 -965.19662 1839.831 -2805.0276 544.59528 0 115.80812 154469.59 -157935.02 2361.9397 16295.72 411.75795 615.12769 4.196977
120 2.832803 -1316.6351 1649.585 -2966.2202 554.6664 0 50.928925 154365.49 -157937.3 -493.85523 16925.293 369.18052 552.0345 2.7331855
140 3.2340388 -1590.9162 1440.6669 -3031.5831 526.07679 0 -24.44055 154404.35 -157937.57 -2586.2431 17517.285 322.42421 482.16117 2.297578
160 3.6521859 -1742.3401 1326.8812 -3069.2213 539.49044 0 -43.846659 154369.1 -157933.96 -3549.2196 18059.707 296.95874 444.11026 2.0644677
180 4.033325 -1895.1332 1224.1816 -3119.3148 555.27887 0 -18.261233 154275.94 -157932.27 -3762.2304 18545.518 273.97437 409.78413 1.806893
200 4.4333398 -2004.4682 1176.8828 -3181.351 565.0443 0 0.21425471 154190.38 -157936.99 -4346.6036 18973.342 263.38879 393.94856 1.7400558
220 4.8055639 -2094.1888 1098.3856 -3192.5744 592.45764 0 36.50238 154113.36 -157934.89 -4135.0794 19341.735 245.82095 367.67707 1.617053
240 5.1688328 -2178.9829 1086.8322 -3265.8151 617.63697 0 96.836936 153957.27 -157937.56 -4121.5262 19651.8 243.23528 363.77401 1.6722646
260 5.5313618 -2264.8265 1078.4348 -3343.2613 663.35817 0 167.76882 153763.13 -157937.52 -3799.3346 19907.052 241.35592 360.97385 1.6377289
280 5.8937738 -2325.7764 1097.4356 -3423.212 717.74089 0 235.0127 153562.96 -157938.92 -3696.0526 20111.414 245.60833 367.31076 1.7042318
300 6.254128 -2390.4932 1068.1054 -3458.5986 751.64681 0 295.31516 153435.34 -157940.9 -3512.2095 20268.754 239.04419 357.49427 1.665921
320 6.6138928 -2455.1776 1041.7419 -3496.9195 765.8972 0 331.14997 153345 -157938.97 -3020.0674 20383.474 233.14397 348.62385 1.7179273
340 6.9748628 -2536.9935 1050.7304 -3587.7239 793.64536 0 352.69908 153205.74 -157939.81 -3447.9127 20457.612 235.15562 351.6381 1.7214573
360 7.3319299 -2603.5606 966.90943 -3570.47 819.14306 0 391.00909 153158.89 -157939.51 -3164.629 20490.764 216.39631 323.51872 1.7254892
380 7.691319 -2594.787 1024.7927 -3619.5797 836.44816 0 434.32118 153047.12 -157937.47 -2902.9345 20485.923 229.35071 342.91482 1.7641915
400 8.044276 -2647.3896 982.46478 -3629.8543 864.59805 0 479.08516 152963.5 -157937.04 -2535.9236 20447.668 219.87764 328.69587 1.8030508
420 8.3971269 -2687.5263 1023.0437 -3710.57 928.04551 0 538.49845 152760.83 -157937.94 -2383.6292 20380.427 228.95928 342.31215 1.8044964
440 8.753284 -2765.2192 999.28342 -3764.5026 966.26754 0 577.15359 152631.24 -157939.17 -2391.0923 20286.676 223.64168 334.34309 1.7947669
460 9.1102748 -2806.7385 1004.2311 -3810.9696 996.86893 0 599.41867 152532.79 -157940.05 -2476.5754 20168.782 224.74899 335.97767 1.8475589
480 9.471664 -2830.2582 1013.6925 -3843.9506 1009.5553 0 624.64584 152464.58 -157942.73 -2210.7254 20027.747 226.86645 339.14841 1.8588685
500 9.8365009 -2865.4993 1024.473 -3889.9723 1017.2606 0 658.56598 152375.13 -157940.93 -2047.5735 19865.992 229.27916 342.78576 1.8103481
520 10.207523 -2918.9299 973.10292 -3892.0328 1049.357 0 699.16951 152300.27 -157940.83 -1453.4121 19688.211 217.78243 325.51403 1.8799495
540 10.583098 -2970.1121 925.84385 -3895.956 1077.9578 0 758.25478 152208.67 -157940.84 -821.19447 19499.417 207.20575 309.67486 1.8442683
560 10.962813 -3008.9942 954.33133 -3963.3255 1114.7309 0 751.85274 152112.75 -157942.66 -1023.0801 19304.314 213.58131 319.23167 1.8463043
580 11.351938 -3069.9822 951.38041 -4021.3626 1127.8186 0 765.20411 152027.82 -157942.2 -954.30565 19101.694 212.92089 318.20155 1.9391088
600 11.74351 -3090.3867 973.25557 -4063.6423 1123.3487 0 744.86978 152009.46 -157941.32 -1226.2333 18891.444 217.81659 325.5949 1.8227604
620 12.138507 -3114.2347 1002.2136 -4116.4483 1159.4812 0 766.24573 151899.05 -157941.23 -1406.6638 18672.922 224.29746 335.32178 1.8002314
640 12.53874 -3160.3172 973.01388 -4133.3311 1181.5814 0 805.79135 151821.94 -157942.65 -1444.0821 18448.163 217.7625 325.51017 1.8464735
660 12.945363 -3185.1871 975.57462 -4160.7618 1177.1798 0 795.84414 151809.59 -157943.38 -962.08053 18220.064 218.3356 326.36793 1.8252243
680 13.358243 -3226.8034 977.21534 -4204.0187 1215.3088 0 862.3869 151662.05 -157943.76 -538.09214 17991.009 218.7028 326.90984 1.8513045
700 13.774714 -3267.0358 979.72611 -4246.7619 1229.2873 0 878.80049 151588.58 -157943.43 -526.4724 17765.058 219.26471 327.74412 1.86738
720 14.198356 -3275.0063 987.91851 -4262.9248 1260.2342 0 905.19546 151515.01 -157943.36 -285.51035 17544.004 221.09819 330.48021 1.8901628
740 14.624448 -3298.9204 992.679 -4291.5994 1283.7665 0 917.78414 151449.24 -157942.39 351.98558 17329.448 222.1636 332.09658 1.843264
760 15.05056 -3316.7113 1010.6458 -4327.3571 1296.6728 0 951.2091 151368.47 -157943.71 419.51796 17123.095 226.18459 338.07068 1.9518407
780 15.504961 -3294.5707 1053.9493 -4348.52 1300.722 0 975.60682 151317.15 -157942 1040.7668 16927.715 235.87602 352.49204 2.1793007
800 15.933704 -3363.0539 987.22337 -4350.2773 1325.1641 0 1013.664 151255.26 -157944.36 1462.6199 16747.7 220.94262 330.24432 1.8985721
820 16.364414 -3437.2117 980.5397 -4417.7514 1350.8684 0 1029.953 151144.46 -157943.03 817.95684 16584.026 219.4468 327.9943 1.9129039
840 16.799625 -3465.5868 981.23685 -4446.8236 1388.7125 0 1043.4314 151066.43 -157945.4 1366.0731 16434.707 219.60282 328.17006 2.0308095
860 17.241996 -3460.2301 1020.3681 -4480.5981 1418.4709 0 1090.9207 150954.21 -157944.2 1450.0443 16300.524 228.36046 341.31823 2.0218282
880 17.688347 -3499.5491 994.43799 -4493.9871 1444.4283 0 1113.276 150893.43 -157945.12 2227.6739 16183.439 222.55726 332.59403 2.0408296
900 18.136371 -3526.9176 952.87144 -4479.789 1443.8422 0 1118.5107 150902.72 -157944.87 2220.1643 16085.505 213.25458 318.69359 1.9574553
920 18.599828 -3545.2479 976.95271 -4522.2006 1443.4309 0 1118.3924 150859.69 -157943.71 2107.6215 16006.466 218.64402 326.75181 1.9926282
940 19.064528 -3560.4406 994.62379 -4555.0644 1431.3624 0 1098.4902 150860.38 -157945.3 1495.9356 15944.46 222.59885 332.62316 2.0953461
960 19.529192 -3590.569 964.78915 -4555.3582 1431.9284 0 1092.1793 150866.87 -157946.34 1559.1687 15897.003 215.92179 322.6406 2.0442546
980 19.991661 -3599.6592 986.56344 -4586.2227 1435.7543 0 1034.8682 150889.35 -157946.2 679.01087 15862.242 220.79492 330.01359 1.9307016
1000 20.427668 -3634.9266 939.78172 -4574.7083 1424.4834 0 1022.664 150924.73 -157946.59 733.04572 15834.345 210.32508 314.30018 1.9584145
1020 20.873712 -3669.298 934.76265 -4604.0606 1452.3 0 1016.3445 150873.46 -157946.16 143.60284 15811.749 209.2018 312.55492 2.0808526
1040 21.319204 -3682.4175 935.86127 -4618.2788 1447.0344 0 1035.4526 150844.58 -157945.34 515.93558 15792.261 209.44767 312.98247 1.9790896
1060 21.766855 -3704.0833 901.03929 -4605.1226 1476.4857 0 1067.779 150794.42 -157943.8 1092.0636 15777.267 201.65444 301.3325 1.8948719
1080 22.214459 -3699.4923 921.66268 -4621.155 1475.7351 0 1079.7576 150767.2 -157943.85 1003.4205 15769.569 206.27 308.27973 1.8458618
1100 22.662445 -3667.6761 957.47147 -4625.1476 1507.2355 0 1102.9252 150708.15 -157943.46 927.20789 15768.898 214.28408 320.17339 2.0742837
1120 23.085055 -3668.1399 935.38917 -4603.5291 1507.3367 0 1080.9826 150753.9 -157945.75 810.87137 15775.175 209.34202 312.79082 2.0279075
1140 23.534417 -3710.7149 937.22068 -4647.9356 1499.5413 0 1020.4759 150776.54 -157944.49 -138.27816 15786.277 209.75191 313.34734 2.1346658
1160 23.985544 -3711.7493 900.74897 -4612.4983 1430.3269 0 990.84122 150911.11 -157944.78 8.4592568 15798.538 201.58947 301.24561 1.8661211
1180 24.439474 -3729.7115 928.82825 -4658.5398 1435.7711 0 937.43508 150913.97 -157945.72 -905.33202 15809.125 207.87367 310.65722 1.8872897
1200 24.895124 -3738.2838 909.79315 -4648.077 1436.4199 0 938.10918 150922.8 -157945.41 -1112.9968 15812.511 203.61357 304.28121 1.8714711
1220 25.352201 -3757.8302 907.08742 -4664.9176 1424.1514 0 930.13653 150924.86 -157944.06 -1078.0621 15807.893 203.00803 303.40134 1.8521625
1240 25.780748 -3778.5355 905.88168 -4684.4171 1453.9568 0 959.37689 150846.21 -157943.96 -975.25032 15795.393 202.73818 303.00695 1.778808
1260 26.238145 -3773.7584 879.94641 -4653.7048 1473.5812 0 1002.67 150815.41 -157945.36 -360.58922 15776.466 196.93381 294.2433 1.9174557
1280 26.696751 -3755.4956 904.13603 -4659.6316 1493.7103 0 1017.8327 150773.94 -157945.12 -256.88128 15755.525 202.3475 302.35592 1.9294965
1300 27.158244 -3754.9246 903.51795 -4658.4425 1498.1329 0 1006.1786 150782.15 -157944.9 -455.2258 15732.436 202.20917 302.19365 1.8353806
1320 27.619539 -3758.1232 913.25769 -4671.3808 1500.2049 0 1032.0703 150739.71 -157943.37 -251.62277 15706.775 204.38895 305.38485 1.9968111
1340 28.079132 -3784.7481 937.61449 -4722.3626 1505.7439 0 993.46365 150723.27 -157944.84 -853.9871 15680.38 209.84005 313.60153 1.8911101
1360 28.514251 -3808.7787 864.89279 -4673.6715 1475.0618 0 1009.2569 150785.65 -157943.64 -331.64382 15650.208 193.56478 289.20988 1.8929896
1380 28.975972 -3798.7281 892.2622 -4690.9903 1465.561 0 993.58051 150793.83 -157943.96 -567.64508 15617.156 199.69011 298.39786 1.8757635
1400 29.439238 -3807.9228 893.51775 -4701.4406 1459.3875 0 1000.4434 150784.38 -157945.65 -456.80001 15580.856 199.97111 298.79789 1.925086
1420 29.904427 -3818.6783 890.66153 -4709.3398 1515.8208 0 1064.6851 150655.36 -157945.21 450.86768 15542.76 199.33188 297.83132 1.927452
1440 30.368352 -3822.016 910.79285 -4732.8089 1539.2325 0 1076.0339 150597.99 -157946.07 429.02044 15506.302 203.83731 304.53724 2.0216852
1460 30.835555 -3821.2117 931.47963 -4752.6914 1540.1582 0 1089.9477 150561.76 -157944.55 645.54716 15472.89 208.46705 311.56653 1.8487206
1480 31.306455 -3838.255 920.25737 -4758.5124 1546.6509 0 1107.4468 150533.86 -157946.47 556.76352 15443.298 205.95549 307.74395 1.9637305
1500 31.747528 -3839.4323 942.18813 -4781.6204 1557.1836 0 1105.7209 150502.68 -157947.21 535.34633 15417.723 210.86364 315.07463 2.0384198
1520 32.218974 -3827.551 925.42642 -4752.9774 1555.4578 0 1097.174 150540.89 -157946.5 680.16246 15396 207.11233 309.42351 2.0793499
1540 32.691924 -3836.1802 885.40721 -4721.5874 1558.3851 0 1144.6478 150521.13 -157945.75 1216.5367 15378.972 198.15595 296.02524 2.015983
1560 33.164075 -3830.4342 955.31807 -4785.7523 1574.0464 0 1105.7294 150481.06 -157946.59 169.17645 15369.126 213.80214 319.4694 2.0400237
1580 33.636497 -3808.4082 948.31996 -4756.7281 1556.8058 0 1079.1205 150552.4 -157945.06 603.87966 15363.124 212.23595 317.13706 2.0112224
1600 34.111529 -3835.9681 925.63461 -4761.6027 1575.0508 0 1091.3896 150517.16 -157945.2 356.94873 15359.871 207.15893 309.60148 1.8514712
1620 34.558112 -3865.8357 866.45292 -4732.2886 1577.3357 0 1137.1716 150497.63 -157944.43 945.81112 15359.844 193.91394 289.72922 1.8926829
1640 35.029171 -3849.5025 884.49282 -4733.9954 1547.0606 0 1101.4292 150561.92 -157944.41 703.96326 15365.598 197.95131 295.76038 1.913597
1660 35.495665 -3861.3162 906.62112 -4767.9373 1547.2773 0 1074.8986 150555.48 -157945.6 46.512723 15375.298 202.90367 303.1667 1.9573677
1680 35.959871 -3857.7679 907.8657 -4765.6336 1547.7327 0 1089.3299 150543.52 -157946.22 383.48079 15386.165 203.18221 303.5736 2.0202069
1700 36.428885 -3869.0902 891.82145 -4760.9117 1512.1728 0 1012.6239 150658.31 -157944.02 -488.95961 15397.869 199.59147 298.24425 1.8990607
1720 36.903833 -3870.4685 893.82411 -4764.2926 1485.7646 0 989.27762 150706.25 -157945.59 -542.70653 15406.338 200.03967 298.80302 2.1113341
1740 37.380529 -3847.3408 893.93384 -4741.2746 1509.8117 0 1031.6641 150663.04 -157945.79 -307.1162 15410.521 200.06423 298.90093 2.0090208
1760 37.827319 -3840.438 868.84851 -4709.2865 1474.404 0 1018.599 150744.2 -157946.49 -276.44721 15412.838 194.45008 290.51398 1.9203414
1780 38.297568 -3842.0322 910.50606 -4752.5383 1494.2187 0 1002.3762 150696.05 -157945.18 -585.57252 15412.983 203.77313 304.47127 1.9624414
1800 38.76671 -3861.9431 881.98228 -4743.9254 1471.6721 0 978.01808 150752.55 -157946.17 -711.07254 15409.636 197.38944 294.90206 1.9749925
1820 39.233968 -3890.8613 856.10452 -4746.9658 1505.1405 0 991.9875 150701.72 -157945.82 -509.17282 15401.428 191.59795 286.24213 1.9311068
1840 39.704207 -3860.2881 907.57785 -4767.866 1492.5264 0 999.80677 150685.45 -157945.65 -697.50098 15387.414 203.11779 303.52338 1.9123566
1860 40.174673 -3879.0681 938.58496 -4817.653 1532.9628 0 1046.6919 150550.41 -157947.72 -311.83188 15369.15 210.05724 313.84514 2.0580305
1880 40.646746 -3871.1182 925.64972 -4796.7679 1531.6363 0 1064.5321 150553.96 -157946.9 136.0161 15350.638 207.16231 309.48972 2.0957912
1900 41.120691 -3868.9005 949.1652 -4818.0657 1593.1686 0 1150.4095 150384.01 -157945.65 753.94006 15333.301 212.42512 317.39691 2.0615952
1920 41.59464 -3868.6343 954.03473 -4822.669 1610.5603 0 1192.2159 150320.88 -157946.33 1209.5547 15321.106 213.51493 319.06152 2.011006
1940 42.037294 -3884.0548 926.13369 -4810.1885 1595.5448 0 1167.6153 150372.25 -157945.6 1289.8018 15318.433 207.27062 309.70304 1.9619634
1960 42.507917 -3889.403 953.52537 -4842.9284 1598.8799 0 1116.9498 150388.89 -157947.65 327.93587 15323.804 213.40093 318.9112 1.9579466
1980 42.973861 -3911.0951 911.40927 -4822.5043 1553.4244 0 1085.4519 150485.64 -157947.02 169.14591 15332.113 203.97527 304.77814 1.9637281
2000 43.43889 -3892.0279 902.31728 -4794.3452 1534.2125 0 1088.703 150530.25 -157947.51 473.37009 15341.654 201.94046 301.71557 1.9929295
Loop time of 43.4389 on 4 procs for 2000 steps with 2500 atoms
Pair time (%) = 30.8131 (70.9343)
Bond time (%) = 0.0167851 (0.0386406)
Kspce time (%) = 2.78529 (6.41196)
Neigh time (%) = 2.7229 (6.26835)
Comm time (%) = 2.36382 (5.4417)
Outpt time (%) = 0.00704503 (0.0162182)
Other time (%) = 4.72998 (10.8888)
Nlocal: 625 ave 641 max 600 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost: 13465.2 ave 13518 max 13362 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 585334 ave 608376 max 546210 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 2341334
Ave neighs/atom = 936.534
Ave special neighs/atom = 4
Neighbor list builds = 100
Dangerous builds = 7

View File

@ -0,0 +1,236 @@
LAMMPS (8 Jul 2015)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3
read_data data.swm4-ndp
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
2500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
2000 bonds
reading angles ...
500 angles
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
pair_coeff * 2* 0.000000 0.0
group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES
variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
fix DRUDE all drude C N N D
velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345
delete_bonds ATOMS multi
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 14
2000 total bonds, 500 turned on, 1500 turned off
500 total angles, 0 turned on, 500 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
comm_modify vel yes
compute TATOM ATOMS temp/com
compute TEMP all temp/drude
fix DTDIR all drude/transform/direct
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
500 rigid bodies with 2000 atoms
0.832099 = max distance from body owner to body atom
fix_modify RIGID temp TATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395)
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
fix NVT DRUDES nvt temp 1 1 100.0
fix DTINV all drude/transform/inverse
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20
run 2000
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 24.8361 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
20 1.5779378 3742.6839 5338.7884 -1596.1045 567.30749 0 662.23765 155098.36 -157924.01 31679.424 13979.574 1194.8318 1690.2246 201.65659
40 3.2595179 2752.8331 4407.7651 -1654.932 793.00135 0 870.33079 154593.76 -157912.03 27394.571 14278.56 986.46688 1450.7477 55.932382
60 4.9160559 1995.591 3982.0372 -1986.4462 660.67737 0 750.60932 154536.67 -157934.4 22230.527 14691.401 891.1881 1315.7324 40.317107
80 6.5368109 1376.4607 3451.5429 -2075.0822 617.73899 0 606.3673 154625.69 -157924.88 17342.36 15201.343 772.46238 1147.1933 21.455584
100 8.1206679 885.61474 3037.6308 -2152.0161 536.23281 0 448.92334 154793.04 -157930.22 13263.15 15783.251 679.82802 1011.6854 14.7536
120 9.6622779 487.58833 2926.9844 -2439.396 534.45257 0 332.92672 154624.58 -157931.35 8680.1072 16409.225 655.06511 977.0118 9.8615914
140 11.151044 159.92993 2531.0941 -2371.1641 507.26614 0 248.61605 154802.7 -157929.75 6399.7614 17052.819 566.46405 845.55948 7.1402545
160 12.594065 -100.92554 2408.1685 -2509.0941 490.99513 0 134.36067 154800.59 -157935.04 3836.8939 17698.15 538.95306 805.19219 5.3968881
180 13.99897 -313.40437 2221.7416 -2535.1459 469.97779 0 75.805558 154853.24 -157934.17 1959.0151 18334.826 497.23032 743.14066 4.4151864
200 15.366489 -490.94535 2067.2605 -2558.2059 455.16264 0 77.545085 154841.14 -157932.06 1193.2843 18956.449 462.65715 691.7234 3.5993432
220 16.600555 -642.90899 1962.7268 -2605.6358 481.409 0 64.82886 154779.27 -157931.14 257.97318 19559.017 439.26229 657.06726 2.7738353
240 17.905356 -770.44499 1795.759 -2566.204 467.25833 0 68.82314 154829.98 -157932.26 19.366424 20139.417 401.89456 601.24562 2.3886434
260 19.179106 -878.63388 1752.9497 -2631.5836 476.38325 0 71.933328 154747.16 -157927.06 -779.27927 20696.165 392.31375 587.06527 2.0260796
280 20.338816 -971.86313 1649.5511 -2621.4143 473.83718 0 58.460942 154779.6 -157933.32 -1008.6839 21226.44 369.17293 552.5314 1.7176302
300 21.569212 -1057.5245 1580.9766 -2638.5012 480.33124 0 92.042617 154721.84 -157932.72 -1273.0871 21728.981 353.82581 529.63244 1.5049172
320 22.749114 -1132.8131 1507.0527 -2639.8658 477.51281 0 107.39942 154707.48 -157932.26 -1098.1682 22203.702 337.28149 504.90539 1.3591193
340 23.866651 -1199.4814 1495.1233 -2694.6047 479.99745 0 106.51864 154656.08 -157937.2 -1429.2857 22652.428 334.61166 500.95977 1.2462004
360 25.082959 -1264.8469 1440.8985 -2705.7454 491.71868 0 107.29672 154624.8 -157929.57 -1584.3973 23073.056 322.47604 482.79111 1.2009575
380 26.115491 -1323.6479 1376.047 -2699.695 497.4857 0 130.64748 154603.75 -157931.58 -1822.0261 23465.375 307.96215 461.10877 1.0530068
400 27.098619 -1373.3921 1374.977 -2748.3691 504.29487 0 124.46131 154555.55 -157932.67 -2021.5919 23828.229 307.72267 460.78429 0.98399317
420 28.070089 -1426.0355 1375.3813 -2801.4168 515.478 0 142.00079 154473.71 -157932.61 -2208.8244 24160.02 307.81316 460.97813 0.86759754
440 29.088747 -1476.2448 1329.2669 -2805.5117 535.72651 0 196.6858 154393.5 -157931.42 -1618.3009 24460.675 297.49266 445.47247 0.93805929
460 30.039555 -1527.7744 1320.4118 -2848.1861 568.66085 0 263.35802 154252.43 -157932.64 -1494.5444 24734.828 295.51087 442.54962 0.84234766
480 30.98472 -1576.2009 1300.9323 -2877.1332 594.86236 0 314.31593 154144.87 -157931.19 -1089.6762 24985.934 291.15132 436.02273 0.82622001
500 31.921181 -1626.4788 1317.6697 -2944.1486 623.62396 0 334.61944 154026.32 -157928.71 -1168.0859 25218.234 294.89719 441.63818 0.82542904
520 32.850868 -1678.487 1262.6568 -2941.1438 633.47682 0 363.44379 153992.91 -157930.98 -1163.3304 25431.978 282.58518 423.21273 0.76490406
540 33.831238 -1726.1374 1271.5003 -2997.6376 640.74261 0 345.52688 153948.98 -157932.89 -1537.3705 25626.826 284.56437 426.19842 0.72713952
560 34.751061 -1771.2597 1269.233 -3040.4927 644.30805 0 317.8435 153929.28 -157931.92 -1722.5181 25799.253 284.05695 425.41542 0.77189915
580 35.665466 -1815.0265 1246.413 -3061.4395 683.24088 0 371.72686 153815.69 -157932.1 -1494.5382 25947.498 278.94979 417.73291 0.82565978
600 36.573731 -1858.3541 1196.3137 -3054.6678 696.06741 0 437.52527 153744.09 -157932.35 -954.95797 26075.526 267.73745 400.95599 0.76490653
620 37.479106 -1899.6548 1179.8195 -3079.4743 696.68256 0 400.17078 153755.86 -157932.18 -1545.546 26187.542 264.04602 395.42296 0.76404516
640 38.439799 -1936.5953 1175.0129 -3111.6082 690.67817 0 392.53009 153736.67 -157931.49 -1651.1722 26278.598 262.97029 393.82361 0.73771389
660 39.342719 -1974.4946 1176.582 -3151.0766 687.10898 0 368.78109 153725.56 -157932.53 -1642.1352 26346.954 263.32147 394.35652 0.72471807
680 40.233007 -2011.9427 1170.7634 -3182.7062 704.7553 0 376.83243 153670.03 -157934.32 -1891.1355 26391.697 262.01926 392.39338 0.74699214
700 41.124436 -2051.0351 1135.0688 -3186.1039 725.49013 0 408.02789 153612.64 -157932.26 -1554.558 26411.443 254.03072 380.39243 0.79925352
720 42.014817 -2087.2728 1127.2712 -3214.544 747.73788 0 483.80639 153486.98 -157933.07 -1246.9189 26409.313 252.28561 377.77086 0.81053421
740 42.908141 -2122.8783 1145.0602 -3267.9385 791.69089 0 545.96341 153327.46 -157933.05 -1064.8488 26390.224 256.26683 383.71741 0.85313379
760 43.799068 -2155.8658 1189.0654 -3344.9312 789.63603 0 492.27945 153309.89 -157936.74 -1502.4138 26356.52 266.11528 398.4847 0.84422302
780 44.690825 -2197.1759 1166.0016 -3363.1774 813.89866 0 521.14986 153239.56 -157937.79 -1316.1431 26304.488 260.95354 390.75511 0.82849551
800 45.65434 -2236.6034 1147.1342 -3383.7376 858.77647 0 581.50775 153111.46 -157935.49 -1059.9568 26235.547 256.73099 384.3699 0.93971538
820 46.655089 -2273.5686 1128.3309 -3401.8996 876.66305 0 635.8842 153020.42 -157934.87 -522.03009 26154.47 252.52277 378.09253 0.87820184
840 47.581215 -2310.5392 1107.1453 -3417.6845 906.73 0 663.59923 152946.29 -157934.31 -660.73299 26066.561 247.78139 370.96848 0.9116362
860 48.461532 -2342.7319 1130.0857 -3472.8176 942.10066 0 680.8635 152839.09 -157934.87 -541.95751 25971.767 252.91551 378.61448 1.0117334
880 49.348792 -2377.0856 1100.1359 -3477.2215 941.37588 0 700.77054 152814.73 -157934.1 -443.18233 25871.504 246.21267 368.56741 1.0107473
900 50.240716 -2408.6694 1120.4615 -3529.131 953.77939 0 683.49952 152768.93 -157935.34 -805.27426 25765.603 250.76159 375.35036 1.0825367
920 51.130132 -2442.8312 1111.7289 -3554.56 950.77289 0 674.01395 152754.6 -157933.95 -905.29746 25651.192 248.80721 372.46424 0.9955159
940 52.02236 -2475.7651 1083.1001 -3558.8652 929.08218 0 652.94438 152792.16 -157933.05 -788.57962 25527.175 242.40003 362.8243 1.0666862
960 52.924057 -2508.9913 1065.8755 -3574.8668 958.92048 0 698.81111 152699.64 -157932.24 -628.47136 25394.225 238.54512 356.97396 1.2103698
980 53.828788 -2536.4577 1080.5323 -3616.99 965.47688 0 709.51639 152642.64 -157934.62 -711.96055 25254.689 241.82535 361.89287 1.2066617
1000 54.736123 -2567.3495 1049.6524 -3617.0019 961.00327 0 711.26219 152645.74 -157935.01 -767.44539 25108.887 234.91437 351.52221 1.2288643
1020 55.707224 -2595.1206 1073.4918 -3668.6124 974.79134 0 682.20149 152609.52 -157935.12 -1086.5823 24955.503 240.24966 359.53972 1.1890491
1040 56.677394 -2626.5258 1072.5969 -3699.1227 1013.3934 0 711.73335 152511.92 -157936.17 -993.59976 24792.452 240.04939 359.23966 1.1887504
1060 57.582305 -2655.4118 1059.0687 -3714.4806 1011.7018 0 747.43846 152460.24 -157933.86 -555.51961 24621.133 237.02176 354.6316 1.3280226
1080 58.451085 -2684.3286 1093.9034 -3778.232 1041.5624 0 765.98574 152348.29 -157934.07 -993.29607 24444.559 244.81782 366.39031 1.183205
1100 59.320593 -2716.1558 1073.5935 -3789.7493 1046.6309 0 741.4524 152358.32 -157936.15 -1031.9439 24260.537 240.27243 359.559 1.2187426
1120 60.197434 -2748.4358 1043.9493 -3792.3851 1050.7685 0 732.61894 152361.65 -157937.42 -1173.2273 24068.431 233.638 349.62448 1.1977845
1140 61.088693 -2777.1545 1036.6106 -3813.7651 1060.884 0 757.21086 152307.36 -157939.22 -1043.4335 23867.228 231.99557 347.17994 1.1628589
1160 62.010573 -2805.5456 1027.0164 -3832.5621 1057.9262 0 777.84714 152269.56 -157937.89 -729.25379 23659.194 229.84839 343.97766 1.1301417
1180 62.973114 -2832.7144 1030.8608 -3863.5752 1084.2376 0 767.80175 152221.94 -157937.56 -1365.8515 23446.354 230.70875 345.24169 1.1814637
1200 63.943778 -2860.0062 1032.0824 -3892.0886 1078.2587 0 781.38106 152185.86 -157937.59 -1050.1069 23225.033 230.98216 345.65138 1.1817665
1220 64.923382 -2887.3006 1026.4756 -3913.7762 1073.1543 0 809.51178 152141.13 -157937.57 -956.1976 22997.996 229.72734 343.81693 1.0887098
1240 65.912183 -2912.0696 1020.0729 -3932.1425 1095.3889 0 826.297 152085.57 -157939.4 -534.84968 22767.897 228.2944 341.63565 1.15531
1260 66.908861 -2938.0025 1009.7902 -3947.7927 1120.1948 0 846.76965 152025.28 -157940.04 -581.84084 22538.229 225.99312 338.22714 1.0731061
1280 67.970707 -2960.3724 1046.6347 -4007.0071 1144.3297 0 866.43256 151921.62 -157939.39 -368.35961 22310.088 234.239 350.59018 1.0681573
1300 68.984941 -2983.8905 1039.0599 -4022.9504 1162.4788 0 878.40157 151876.66 -157940.49 -408.4644 22085.613 232.54373 348.07145 1.0232144
1320 70.043952 -3009.5808 969.8918 -3979.4726 1186.5907 0 935.08613 151836.22 -157937.36 431.8242 21865.457 217.06378 324.88371 0.98977725
1340 71.117119 -3028.1057 1016.1027 -4044.2084 1215.7197 0 933.65661 151744.63 -157938.22 -118.90908 21653.612 227.40587 340.39676 0.96927182
1360 72.19871 -3048.8293 986.21586 -4035.0452 1231.0917 0 974.10814 151697.47 -157937.72 485.3122 21448.458 220.71713 330.39668 0.91660237
1380 73.289545 -3067.6975 1046.3647 -4114.0622 1252.358 0 948.20869 151626.66 -157941.29 -131.77945 21251.912 234.17856 350.55699 0.95332826
1400 74.389534 -3091.6437 1003.804 -4095.4478 1223.2343 0 914.21639 151708.69 -157941.59 -228.59592 21060.319 224.6534 336.27611 0.95868112
1420 75.496459 -3117.9845 1017.2871 -4135.2716 1252.8701 0 934.95412 151617.13 -157940.22 -328.62774 20872.161 227.67095 340.80959 0.93833238
1440 76.611495 -3137.2342 990.73612 -4127.9703 1224.5861 0 925.81135 151661.05 -157939.42 -23.294916 20687.614 221.72878 331.93708 0.86871384
1460 77.73649 -3159.4947 1040.535 -4200.0297 1218.936 0 881.92261 151636.87 -157937.75 -581.29505 20507.346 232.87387 348.59778 0.96029886
1480 78.872562 -3183.8273 1037.9432 -4221.7705 1246.5207 0 908.21966 151561.59 -157938.1 -884.42345 20328.04 232.29381 347.7323 0.95226246
1500 80.110645 -3206.5826 1008.5663 -4215.1489 1236.8936 0 929.15034 151558.28 -157939.47 -91.502556 20149.349 225.7192 337.88949 0.92718943
1520 81.168804 -3228.1152 994.3422 -4222.4574 1276.2214 0 948.25706 151492.45 -157939.39 -262.49453 19974.554 222.53583 333.16141 0.83959152
1540 82.328931 -3248.9878 997.70762 -4246.6954 1273.2453 0 944.04689 151475.31 -157939.3 -310.12487 19802.717 223.28901 334.28865 0.84316615
1560 83.500822 -3268.9264 1001.6639 -4270.5903 1283.2174 0 972.25539 151413.47 -157939.53 -368.92162 19633.499 224.17444 335.57814 0.91870789
1580 84.681217 -3289.8506 972.05937 -4261.9099 1290.892 0 995.40503 151394.08 -157942.29 309.3174 19467.313 217.54888 325.64947 0.91261747
1600 85.872982 -3306.0485 999.0593 -4305.1078 1336.2852 0 1018.2817 151281.27 -157940.94 78.176324 19307.332 223.59152 334.68976 0.94786237
1620 87.166941 -3323.911 1023.7518 -4347.6628 1346.5659 0 1012.0297 151235.76 -157942.02 401.58054 19152.885 229.11774 342.98696 0.92107142
1640 88.373719 -3346.3201 1013.0953 -4359.4153 1368.3551 0 1038.3633 151174.74 -157940.87 115.49888 19004.339 226.7328 339.39185 0.96123977
1660 89.588199 -3366.6764 980.18808 -4346.8645 1385.5623 0 1066.3348 151143.21 -157941.97 785.51107 18860.969 219.3681 328.38652 0.89253119
1680 90.812635 -3382.4343 999.75094 -4382.1852 1367.9173 0 1045.8848 151142.33 -157938.32 549.73441 18726.008 223.74631 334.953 0.88544944
1700 92.044767 -3400.8462 996.00209 -4396.8483 1351.6629 0 1019.0394 151174.27 -157941.83 32.327852 18598.28 222.90731 333.67893 0.91827006
1720 93.284649 -3418.3313 989.38116 -4407.7125 1347.9882 0 1026.3475 151161.41 -157943.46 700.69172 18474.978 221.42553 331.45637 0.92100955
1740 94.538928 -3435.1347 964.16624 -4399.301 1357.6456 0 1051.1466 151135.74 -157943.84 477.68306 18358.2 215.78238 322.997 0.92157841
1760 95.90276 -3452.4681 996.08241 -4448.5506 1365.9896 0 1001.3994 151128.36 -157944.3 -77.655143 18246.618 222.92529 333.72093 0.88815023
1780 97.200704 -3470.0186 947.16368 -4417.1823 1357.1769 0 1006.9477 151162.27 -157943.57 100.19368 18137.3 211.97718 317.3159 0.87577473
1800 98.461648 -3484.6818 988.75293 -4473.4348 1367.5971 0 995.1924 151106.14 -157942.36 -208.37477 18030.204 221.28494 331.23294 0.94635825
1820 99.729642 -3503.5324 959.4974 -4463.0298 1386.9033 0 1035.1867 151057.26 -157942.38 196.09637 17924.392 214.73749 321.44422 0.89454363
1840 101.00392 -3518.4137 985.10207 -4503.5157 1425.227 0 1062.1927 150951.14 -157942.08 189.40933 17821.795 220.46787 330.02248 0.91769756
1860 102.28783 -3531.6076 978.71334 -4510.3209 1447.6145 0 1081.8026 150905.2 -157944.94 369.13672 17723.495 219.03805 327.84302 0.99005655
1880 103.57975 -3546.6803 982.10151 -4528.7818 1416.6032 0 1040.8725 150959.42 -157945.68 206.83653 17629.384 219.79633 328.97668 0.9960403
1900 104.81168 -3563.7438 961.75306 -4525.4969 1426.2883 0 1055.2567 150936.42 -157943.46 223.06115 17537.856 215.24231 322.15829 0.97986655
1920 106.04042 -3579.7815 953.8957 -4533.6772 1420.242 0 1053.3469 150938.67 -157945.93 264.48404 17448.909 213.48382 319.52979 0.96489929
1940 107.27692 -3592.4628 995.11883 -4587.5816 1434.5738 0 1036.2736 150885.59 -157944.02 -203.71783 17362.885 222.70964 333.32982 1.0238542
1960 108.52049 -3607.1225 959.8186 -4566.9411 1454.811 0 1091.6157 150830.59 -157943.96 412.09226 17278.194 214.80937 321.46995 1.0586113
1980 109.76987 -3621.5836 950.82575 -4572.4094 1481.3655 0 1148.5036 150742.3 -157944.58 1156.6083 17197.362 212.79675 318.42806 1.1085537
2000 111.02457 -3632.4321 939.77229 -4572.2044 1484.3457 0 1154.0077 150733.65 -157944.21 1008.3019 17124.028 210.32297 314.7467 1.0548599
Loop time of 111.025 on 1 procs for 2000 steps with 2500 atoms
Pair time (%) = 87.5509 (78.8572)
Bond time (%) = 0.0493031 (0.0444073)
Kspce time (%) = 3.35179 (3.01896)
Neigh time (%) = 9.36055 (8.43106)
Comm time (%) = 0.69479 (0.625798)
Outpt time (%) = 0.0108259 (0.00975088)
Other time (%) = 10.0064 (9.01281)
Nlocal: 2500 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 20348 ave 20348 max 20348 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.09326e+06 ave 2.09326e+06 max 2.09326e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2093261
Ave neighs/atom = 837.304
Ave special neighs/atom = 4
Neighbor list builds = 120
Dangerous builds = 16

View File

@ -0,0 +1,236 @@
LAMMPS (8 Jul 2015)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3
read_data data.swm4-ndp
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
2500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
2000 bonds
reading angles ...
500 angles
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
pair_coeff * 2* 0.000000 0.0
group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES
variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
fix DRUDE all drude C N N D
velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345
delete_bonds ATOMS multi
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 1500 300
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 14
2000 total bonds, 500 turned on, 1500 turned off
500 total angles, 0 turned on, 500 turned off
0 total dihedrals, 0 turned on, 0 turned off
0 total impropers, 0 turned on, 0 turned off
comm_modify vel yes
compute TATOM ATOMS temp/com
compute TEMP all temp/drude
fix DTDIR all drude/transform/direct
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
500 rigid bodies with 2000 atoms
0.832099 = max distance from body owner to body atom
fix_modify RIGID temp TATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395)
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
fix NVT DRUDES nvt temp 1 1 100.0
fix DTINV all drude/transform/inverse
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20
run 2000
PPPM initialization ...
G vector (1/distance) = 0.217457
grid = 10 10 10
stencil order = 5
estimated absolute RMS force accuracy = 0.197288
estimated relative force accuracy = 0.000594128
using double precision FFTs
3d grid and FFT values/proc = 1500 300
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 15.0906 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
20 0.60629702 3742.7991 5338.7966 -1595.9975 567.29055 0 662.23349 155098.48 -157924 31679.046 13979.575 1194.8336 1690.2267 201.65776
40 1.2431891 2752.9388 4407.9332 -1654.9944 792.86725 0 870.27523 154593.92 -157912.06 27392.302 14278.564 986.5045 1450.7624 56.079837
60 1.875339 1995.9775 3980.851 -1984.8735 660.64216 0 750.43214 154538.47 -157934.42 22242.676 14691.413 890.92262 1315.3403 40.305321
80 2.471236 1377.1261 3449.7879 -2072.6618 617.64243 0 605.75693 154628.63 -157924.69 17345.214 15201.397 772.06962 1146.6088 21.44718
100 3.0357449 886.38995 3038.4108 -2152.0208 537.89929 0 450.99962 154789.13 -157930.05 13299.227 15783.335 680.00257 1011.6773 15.016231
120 3.585844 488.055 2928.1336 -2440.0786 536.23164 0 334.88597 154620.05 -157931.25 8694.3472 16409.509 655.3223 977.40122 9.8538294
140 4.117424 160.14918 2538.5116 -2378.3624 509.19396 0 249.89205 154793.34 -157930.79 6363.1137 17053.486 568.1241 847.92526 7.2744139
160 4.6321139 -103.57595 2403.1613 -2506.7372 494.69822 0 144.07174 154790.83 -157936.34 4017.2005 17699.095 537.83243 803.44775 5.3901399
180 5.126441 -315.61252 2216.7944 -2532.4069 477.29447 0 80.852363 154842.41 -157932.96 1958.1627 18336.716 496.12314 741.4685 4.440167
200 5.6090059 -490.61276 2058.9074 -2549.5202 470.23217 0 80.799455 154831.63 -157932.18 1260.1943 18960.132 460.78771 688.92684 3.5878733
220 6.0495639 -644.09355 2001.1189 -2645.2125 494.11524 0 53.071997 154741.65 -157934.05 -16.373549 19564.819 447.85452 669.94663 2.7746068
240 6.5042329 -773.76581 1911.0759 -2684.8417 491.56501 0 36.579309 154722.88 -157935.86 -773.18555 20144.755 427.70271 639.97688 2.2989541
260 6.9512041 -886.818 1719.7038 -2606.5218 462.97731 0 47.595907 154814.45 -157931.55 -696.23419 20696.487 384.87324 575.96351 1.9229602
280 7.3921249 -983.57561 1659.2167 -2642.7923 476.06924 0 65.542713 154749.27 -157933.68 -1099.4208 21220.613 371.3361 555.78067 1.7042918
300 7.8054619 -1069.4015 1531.598 -2600.9995 487.38132 0 130.06616 154709.03 -157927.47 -548.86446 21717.521 342.77477 513.11788 1.4030219
320 8.2272029 -1144.9139 1562.933 -2707.8469 509.00464 0 127.16899 154591.31 -157935.33 -1516.7077 22190.692 349.78761 523.61225 1.4145866
340 8.6145689 -1216.4369 1511.7737 -2728.2106 518.42214 0 144.71934 154541.92 -157933.27 -1345.493 22636.556 338.33806 506.55234 1.2328234
360 9.0159991 -1279.8637 1435.4044 -2715.2681 525.01973 0 153.83119 154536.21 -157930.33 -1447.797 23056.471 321.24646 480.9789 1.1390786
380 9.4004741 -1340.2241 1391.5909 -2731.815 536.93555 0 180.52081 154483.31 -157932.58 -1315.0222 23450.141 311.4409 466.34776 1.004293
400 9.7971771 -1398.7544 1401.1636 -2799.918 547.12264 0 190.99461 154394.23 -157932.27 -1686.7786 23818.238 313.5833 469.59825 0.92621346
420 10.175245 -1450.5676 1355.0166 -2805.5842 555.43355 0 178.57277 154392.99 -157932.58 -1948.3006 24158.665 303.2555 454.12588 0.90821389
440 10.550016 -1501.2755 1336.6037 -2837.8792 573.29095 0 195.76657 154324.78 -157931.72 -1845.698 24470.004 299.13465 447.99648 0.8127319
460 10.93798 -1551.1246 1327.3311 -2878.4557 580.57019 0 206.92238 154267.88 -157933.83 -2059.7154 24752.911 297.05944 444.88976 0.80466605
480 11.304226 -1597.9166 1280.274 -2878.1906 596.27629 0 247.5201 154210.94 -157932.93 -1714.1239 25006.108 286.52794 429.10945 0.79188456
500 11.66949 -1645.4221 1303.9947 -2949.4168 620.22431 0 275.42964 154086.38 -157931.45 -1833.6239 25232.592 291.83668 437.06941 0.78754301
520 12.030775 -1692.7733 1261.2365 -2954.0098 639.32812 0 295.13753 154045.85 -157934.32 -1715.0443 25432.412 282.26732 422.73896 0.75950535
540 12.389967 -1739.3602 1247.1301 -2986.4903 666.88476 0 341.37591 153937.16 -157931.91 -1556.9492 25607.225 279.11027 418.00746 0.75767537
560 12.765452 -1783.4916 1212.3647 -2995.8563 669.09681 0 366.501 153899.16 -157930.62 -1543.0147 25758.368 271.3297 406.37068 0.70509124
580 13.122579 -1824.6061 1200.7205 -3025.3267 699.41498 0 409.47507 153794.95 -157929.16 -1053.8519 25887.592 268.72372 402.43012 0.77346975
600 13.47702 -1864.0982 1206.4231 -3070.5213 726.9912 0 439.25863 153695.5 -157932.27 -1130.6737 26000.4 269.99996 404.33899 0.78190692
620 13.82937 -1902.6883 1167.061 -3069.7493 741.54351 0 453.21801 153667.95 -157932.46 -921.61026 26097.341 261.19065 391.14672 0.7561126
640 14.180362 -1941.2814 1168.4808 -3109.7622 758.6291 0 484.81029 153578.39 -157931.59 -1084.6877 26180.233 261.50841 391.64626 0.70968727
660 14.527615 -1977.9114 1159.1979 -3137.1094 746.51288 0 452.2958 153598.59 -157934.51 -1424.6628 26247.07 259.43088 388.52145 0.73088365
680 14.875155 -2015.8231 1149.125 -3164.9481 730.41157 0 417.95266 153620.83 -157934.15 -1485.3138 26293.983 257.17653 385.144 0.72723522
700 15.22063 -2052.4439 1175.9011 -3228.345 735.43016 0 393.72125 153577.95 -157935.44 -1936.2883 26318.916 263.16908 394.10321 0.77446426
720 15.565813 -2092.4868 1137.4051 -3229.892 739.27374 0 431.22089 153537.92 -157938.3 -1669.6367 26318.64 254.5536 381.18868 0.77432854
740 15.926298 -2128.2671 1117.2535 -3245.5206 763.39303 0 451.2336 153475.75 -157935.89 -1554.5185 26294.984 250.04362 374.42691 0.77695221
760 16.273413 -2164.5578 1132.9117 -3297.4695 791.93983 0 493.17297 153351.43 -157934.01 -1464.3621 26250.086 253.54797 379.63211 0.87260304
780 16.620524 -2201.7367 1138.2941 -3340.0308 832.89022 0 542.69718 153217.14 -157932.76 -1185.0268 26186.538 254.75255 381.43046 0.88724559
800 16.968419 -2236.9734 1127.0464 -3364.0197 849.94855 0 579.03844 153137.36 -157930.36 -957.1991 26107.922 252.23529 377.65702 0.8873688
820 17.320858 -2274.0191 1152.6791 -3426.6982 878.53555 0 605.98285 153020.89 -157932.1 -1004.5494 26016.264 257.97196 386.24526 0.90940959
840 17.671788 -2312.5555 1157.6702 -3470.2257 915.53242 0 653.69994 152892.11 -157931.56 -793.45868 25912.528 259.08897 387.88866 0.97141875
860 18.021136 -2351.0088 1136.5124 -3487.5212 921.37408 0 665.09396 152857.19 -157931.18 -528.38134 25800.163 254.35382 380.78143 0.98986969
880 18.370286 -2387.3364 1155.2826 -3542.619 934.02359 0 660.06761 152795.05 -157931.76 -775.58796 25681.702 258.55463 386.99987 1.1470186
900 18.737898 -2425.9324 1151.5543 -3577.4867 936.00838 0 670.95003 152749.78 -157934.22 -883.49007 25555.357 257.72021 385.72656 1.1920669
920 19.09607 -2461.264 1119.906 -3581.17 931.8496 0 682.4928 152739.5 -157935.01 -890.93067 25420.635 250.63726 375.12148 1.1675653
940 19.45002 -2496.7293 1081.4763 -3578.2056 971.61744 0 731.21429 152653.33 -157934.36 -483.6151 25277.795 242.03662 362.20568 1.2144341
960 19.805087 -2527.097 1111.841 -3638.938 964.7058 0 704.68407 152623.89 -157932.22 -841.64397 25129.524 248.8323 372.33505 1.3291216
980 20.160533 -2560.1354 1096.9132 -3657.0486 954.19645 0 693.42648 152627.51 -157932.19 -949.1276 24974.275 245.49142 367.3853 1.2126954
1000 20.518917 -2592.9079 1053.7186 -3646.6266 959.23242 0 684.31399 152644.74 -157934.91 -869.15319 24811.035 235.8244 352.90011 1.2013298
1020 20.849072 -2623.091 1066.4493 -3689.5404 998.09604 0 709.32917 152535.4 -157932.37 -881.38225 24640.265 238.67355 357.17132 1.2006706
1040 21.194962 -2652.822 1083.618 -3736.44 1011.32 0 727.70427 152458.99 -157934.45 -815.2175 24461.841 242.51594 362.90994 1.2429114
1060 21.530151 -2683.6347 1074.3994 -3758.0341 1029.3659 0 763.93884 152381.4 -157932.73 -616.78933 24277.069 240.45279 359.82116 1.235143
1080 21.868091 -2715.2991 1094.3032 -3809.6022 1068.1764 0 785.28284 152272.57 -157935.63 -541.23611 24088.232 244.9073 366.48583 1.2604348
1100 22.209137 -2747.0371 1066.1644 -3813.2016 1080.2369 0 833.94072 152208.13 -157935.51 -217.98411 23897.246 238.60979 357.0619 1.2283546
1120 22.551618 -2774.9066 1084.3361 -3859.2427 1113.055 0 847.43384 152114.69 -157934.42 -77.787494 23707.475 242.67665 363.13214 1.2803322
1140 22.899431 -2803.21 1072.4113 -3875.6213 1090.9217 0 807.02034 152161.17 -157934.73 -668.47773 23520.606 240.00786 359.14316 1.2572349
1160 23.252016 -2834.8697 1052.5943 -3887.464 1096.5034 0 789.77107 152162.88 -157936.62 -589.78074 23331.777 235.57277 352.55512 1.1369148
1180 23.609597 -2863.7817 1031.8109 -3895.5926 1087.1932 0 789.79657 152165.44 -157938.03 -586.94333 23140.391 230.92139 345.60929 1.0837566
1200 23.970129 -2891.3631 1042.111 -3933.4741 1093.7082 0 775.83298 152136.1 -157939.12 -1109.7168 22947.229 233.22659 349.07035 1.0726257
1220 24.3333 -2919.3393 1043.3795 -3962.7187 1095.6802 0 760.56643 152121.29 -157940.25 -1189.6331 22748.747 233.51046 349.50414 1.0560945
1240 24.699158 -2942.4201 1015.5889 -3958.009 1114.7861 0 821.20595 152042.69 -157936.69 -581.49954 22545.116 227.29088 340.1868 1.0444581
1260 25.06694 -2965.9906 1011.5209 -3977.5115 1137.3984 0 850.69736 151972.34 -157937.95 -557.09399 22340.759 226.38045 338.85243 0.98374803
1280 25.506043 -2989.5484 1016.7798 -4006.3282 1160.9102 0 882.24024 151890.5 -157939.98 -93.844073 22136.859 227.55742 340.60408 1.0089629
1300 25.885481 -3011.5964 1043.7628 -4055.3592 1184.2311 0 891.6381 151808.85 -157940.08 -307.32007 21936.757 233.59626 349.6133 1.0504806
1320 26.286564 -3035.1132 1037.5333 -4072.6466 1179.597 0 903.59052 151784.33 -157940.16 -91.53774 21739.794 232.20209 347.62923 0.8833997
1340 26.707803 -3061.1043 1034.7198 -4095.8241 1231.5568 0 955.77666 151655.57 -157938.72 53.261099 21546.978 231.57242 346.58931 1.0307605
1360 27.133179 -3085.252 983.77833 -4069.0303 1230.971 0 968.86383 151669.63 -157938.5 197.66951 21360.266 220.17161 329.49241 1.002352
1380 27.554558 -3101.9696 1037.9918 -4139.9614 1216.6215 0 897.01691 151685.79 -157939.39 -392.64446 21180.32 232.3047 347.61632 1.0380526
1400 27.956349 -3124.8379 1003.328 -4128.1659 1199.4883 0 863.54306 151748.07 -157939.27 -548.32584 21003.378 224.54686 336.16828 0.85494391
1420 28.361482 -3146.8927 1020.9417 -4167.8344 1210.319 0 850.57584 151710.13 -157938.86 -1093.8532 20825.938 228.48885 342.04449 0.9178739
1440 28.768238 -3170.6554 993.33274 -4163.9882 1239.5959 0 893.87046 151642.2 -157939.65 -436.10089 20645.122 222.30991 332.79717 0.88336557
1460 29.177687 -3191.0873 980.2106 -4171.2979 1257.3639 0 955.42122 151554.27 -157938.35 -139.1763 20465.429 219.37314 328.30589 0.99602014
1480 29.586943 -3208.4185 993.92387 -4202.3424 1243.9183 0 936.28667 151555.9 -157938.45 -261.1948 20289.512 222.4422 333.01034 0.85071989
1500 29.995233 -3229.0775 1028.0284 -4257.1059 1272.6443 0 960.80911 151449.75 -157940.31 -307.25416 20116.744 230.07487 344.43881 0.88683413
1520 30.435761 -3250.8294 998.11977 -4248.9491 1282.1976 0 990.08774 151419.81 -157941.05 64.772936 19947.298 223.38125 334.38841 0.90320757
1540 30.853458 -3268.3168 1004.1599 -4272.4768 1299.4164 0 987.20608 151381.91 -157941.01 -80.22578 19782.738 224.73305 336.30685 1.007422
1560 31.279241 -3289.0826 966.08591 -4255.1685 1287.1272 0 982.95309 151416.22 -157941.47 198.4371 19622.918 216.21201 323.54353 0.99939162
1580 31.708028 -3306.2125 979.26815 -4285.4807 1288.5111 0 952.23769 151415.68 -157941.91 -206.26434 19467.717 219.16222 328.0518 0.90689318
1600 32.140092 -3325.1219 984.21128 -4309.3331 1308.258 0 963.95207 151360.81 -157942.35 -284.04656 19314.766 220.2685 329.66568 0.9610293
1620 32.5727 -3340.9024 1013.5306 -4354.433 1318.1025 0 944.3489 151325.17 -157942.05 -653.005 19163.698 226.83023 339.47468 1.0097397
1640 32.982791 -3360.2312 974.13546 -4334.3667 1312.594 0 986.63361 151308.68 -157942.28 343.78235 19013.496 218.01352 326.28924 0.99083786
1660 33.419277 -3375.6484 982.60503 -4358.2535 1345.3148 0 970.47388 151266.28 -157940.32 -374.81541 18867.836 219.90902 329.06869 1.0301828
1680 33.858902 -3394.428 981.74052 -4376.1685 1319.3919 0 955.09161 151289.81 -157940.47 -162.3498 18724.14 219.71554 328.81202 0.99514477
1700 34.30191 -3412.8462 973.87976 -4386.7259 1341.294 0 965.41854 151248.54 -157941.98 -351.70824 18582.062 217.95629 326.03525 1.1973975
1720 34.776698 -3429.9352 986.76909 -4416.7043 1362.6752 0 1013.2358 151149.58 -157942.2 37.299904 18441.349 220.84095 330.4706 1.0534043
1740 35.222457 -3446.5561 971.25044 -4417.8065 1381.6012 0 1046.8608 151096.61 -157942.88 336.29665 18304.289 217.36784 325.28479 1.0839935
1760 35.644247 -3463.1798 999.75562 -4462.9354 1395.5442 0 1012.1296 151070.28 -157940.88 -252.71902 18172.322 223.74736 334.82695 1.1205298
1780 36.095301 -3481.5453 991.5153 -4473.0606 1403.686 0 1029.7008 151037.13 -157943.57 -108.73918 18043.082 221.90316 332.00846 1.1669904
1800 36.548801 -3496.9886 965.33662 -4462.3252 1390.3088 0 1050.6761 151040.12 -157943.43 539.62368 17917.488 216.04432 323.23991 1.1447201
1820 37.00671 -3510.113 991.32596 -4501.439 1392.0482 0 1034.7898 151015.68 -157943.96 152.36115 17797.781 221.86078 332.04409 1.050451
1840 37.465953 -3528.9352 974.95032 -4503.8855 1387.6457 0 1012.5199 151036.63 -157940.68 -250.11127 17681.765 218.19588 326.4633 1.104675
1860 37.926741 -3545.3967 970.46573 -4515.8624 1391.3683 0 1035.1551 151000.11 -157942.49 -218.15781 17567.52 217.19222 325.05524 1.0190724
1880 38.391252 -3561.7398 933.83134 -4495.5711 1404.458 0 1032.7156 151010.9 -157943.64 -1.9885562 17454.833 208.99337 312.70412 1.1301542
1900 38.856336 -3574.6165 984.6503 -4559.2668 1422.0814 0 1060.3245 150900.79 -157942.46 190.15103 17344.24 220.36676 329.66505 1.2027369
1920 39.32352 -3589.0687 963.85062 -4552.9193 1427.8662 0 1075.6986 150887.22 -157943.7 506.81653 17237.394 215.71175 322.81523 1.0733524
1940 39.79544 -3604.8214 970.89136 -4575.7128 1416.926 0 1037.9197 150913.56 -157944.12 -60.261935 17135.412 217.28748 325.12481 1.144127
1960 40.270815 -3620.548 963.48434 -4584.0323 1401.1546 0 1016.5609 150941.43 -157943.17 -388.03612 17035.264 215.62977 322.67138 1.1152888
1980 40.749353 -3638.3971 977.90456 -4616.3017 1415.5473 0 1009.486 150904.71 -157946.04 -640.67547 16934.97 218.85705 327.48198 1.1614525
2000 41.229238 -3654.2588 957.08437 -4611.3432 1418.1059 0 1031.2688 150883.23 -157943.95 -595.60403 16834.098 214.19745 320.55039 1.0631632
Loop time of 41.2293 on 4 procs for 2000 steps with 2500 atoms
Pair time (%) = 23.5391 (57.0932)
Bond time (%) = 0.0153775 (0.0372976)
Kspce time (%) = 3.17798 (7.70806)
Neigh time (%) = 2.51543 (6.10108)
Comm time (%) = 1.6585 (4.02262)
Outpt time (%) = 0.00876421 (0.0212572)
Other time (%) = 10.3141 (25.0165)
Nlocal: 625 ave 632 max 619 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 12577 ave 12644 max 12511 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 532752 ave 581561 max 492708 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 2131009
Ave neighs/atom = 852.404
Ave special neighs/atom = 4
Neighbor list builds = 120
Dangerous builds = 16