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lammps/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2
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log.temper_npt-17Aug17.g++.8.2
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LAMMPS (17 Aug 2017)
Processor partition = 2
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
# Demonstrating temper/npt
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style custom step temp epair emol etotal press density
thermo 50
variable temper_T world 275 280 285 290 295 300 305 310
variable rep world 0 1 2 3 4 5 6 7
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 285 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 285 285 100.0 iso 1 1 1000
run 500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
50 222.63643 -7679.59 1221.8685 -5128.4568 -23807.78 0.99567623
100 255.85049 -6977.7653 480.95894 -4969.235 12685.571 1.0116281
150 276.83083 -6906.8603 472.9485 -4781.076 6899.3786 1.0203576
200 267.19755 -7210.264 1068.2756 -4546.6687 -17521.505 1.0207097
250 263.8837 -6392.2545 463.0506 -4353.6698 22886.964 1.0130132
300 280.88953 -6919.81 1005.9833 -4236.7581 -14774.964 1.0024942
350 289.59472 -6621.8351 734.60058 -4158.1911 2409.0738 0.99451628
400 288.29076 -6495.283 634.61137 -4139.4136 6594.965 0.98796525
450 281.92055 -6838.8449 1025.3043 -4130.3164 -12795.112 0.98591519
500 298.25519 -6578.7232 652.75467 -4145.2172 10282.835 0.98902709
Loop time of 11.0965 on 2 procs for 500 steps with 2004 atoms
Performance: 7.786 ns/day, 3.082 hours/ns, 45.059 timesteps/s
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.9379 | 7.9449 | 7.952 | 0.2 | 71.60
Bond | 0.090588 | 0.090927 | 0.091265 | 0.1 | 0.82
Kspace | 1.1684 | 1.176 | 1.1837 | 0.7 | 10.60
Neigh | 1.2553 | 1.2556 | 1.256 | 0.0 | 11.32
Comm | 0.20599 | 0.21536 | 0.22474 | 2.0 | 1.94
Output | 0.00049877 | 0.00050557 | 0.00051236 | 0.0 | 0.00
Modify | 0.35224 | 0.37667 | 0.40111 | 4.0 | 3.39
Other | | 0.03635 | | | 0.33
Nlocal: 1002 ave 1007 max 997 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8699.5 ave 8735 max 8664 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 355600 ave 363554 max 347647 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 711201
Ave neighs/atom = 354.891
Ave special neighs/atom = 2.34032
Neighbor list builds = 50
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 285 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268844
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0227233
estimated relative force accuracy = 6.84305e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
Step Temp E_pair E_mol TotEng Press Density
500 298.25519 -6578.7239 652.75467 -4145.218 10282.81 0.98902709
550 280.55812 -6800.9339 904.37474 -4221.4693 -6284.3677 0.99138729
600 282.54117 -6736.9067 793.64464 -4256.3323 379.51956 0.99544144
650 289.246 -6695.3988 727.43292 -4241.0045 3741.9292 1.0004679
700 298.37935 -6898.8951 912.35329 -4205.0492 -5179.2622 1.0029455
750 276.21453 -6657.3814 738.83164 -4269.3936 6422.8684 1.003042
800 273.34049 -6770.7481 842.34057 -4296.411 -2699.1945 1.0011122
850 279.30106 -6766.7842 807.51048 -4291.6893 -583.46522 1.0039015
900 286.09076 -6808.4366 807.15205 -4293.1617 1405.0223 1.0062162
950 283.04021 -6838.8107 869.45604 -4279.4454 -2826.6403 1.008228
1000 278.36762 -6776.1595 827.04427 -4287.104 2510.6216 1.0123638
1050 276.46194 -6858.6173 893.69758 -4314.2864 -1818.0617 1.0153108
1100 270.91883 -6818.5634 864.2518 -4336.7738 1021.1432 1.0153455
1150 274.70844 -6747.0957 849.98378 -4256.948 1453.2165 1.0141005
1200 292.66211 -6864.4907 917.17522 -4199.958 -2889.5663 1.0130738
1250 288.1024 -6814.0744 887.46443 -4206.4766 2384.4467 1.0139599
1300 286.54446 -6864.9998 900.886 -4253.2821 -2397.0043 1.0140796
1350 274.86169 -6804.6738 866.75191 -4296.843 1112.3802 1.0143892
1400 275.30771 -6837.4182 904.04812 -4289.6282 136.99961 1.0170328
1450 296.09129 -6868.8691 910.61078 -4190.4268 -1076.0085 1.0204782
1500 292.50596 -6812.8248 889.10378 -4177.2959 1069.9919 1.0198406
1550 284.3886 -6876.901 909.58572 -4269.3554 -1153.6899 1.0177539
1600 276.41187 -6876.8574 907.69862 -4318.8244 114.8894 1.0158964
1650 275.68967 -6919.4356 902.04604 -4371.3672 -1493.2092 1.0141832
1700 271.20923 -6893.2373 912.27766 -4361.688 -563.23529 1.0157743
1750 279.40649 -6842.0743 892.63677 -4281.2237 944.83039 1.0207184
1800 282.84659 -6889.8537 934.73963 -4266.3608 -895.12942 1.0238833
1850 279.58052 -6900.6624 951.17313 -4280.2364 648.68857 1.024366
1900 276.44092 -6841.9805 881.15423 -4310.3185 1052.7352 1.0229576
1950 289.89625 -6960.295 949.2514 -4280.2 -2500.9996 1.0210089
2000 283.75058 -6908.6985 930.56698 -4283.9809 1529.221 1.0211902
2050 284.00141 -6837.2348 943.57188 -4198.0147 -710.45695 1.0190262
2100 294.53504 -6879.4583 983.431 -4137.4874 -496.16699 1.0172736
2150 296.46029 -6854.8307 926.58211 -4158.2139 757.20038 1.017548
2200 284.26196 -6896.5957 989.5222 -4209.8697 -1953.1733 1.0187998
2250 284.51713 -6852.3924 938.51853 -4215.1465 210.72971 1.0208918
2300 289.88921 -6867.2253 969.05163 -4167.372 -80.492209 1.0240397
2350 296.17997 -6836.2421 954.2497 -4113.6314 -389.76698 1.0272081
2400 309.56546 -6833.5714 970.44217 -4014.8493 610.57346 1.0294586
2450 300.61402 -6827.9964 1025.4417 -4007.7199 1121.4824 1.0284326
2500 298.82336 -6815.7862 945.53298 -4086.1097 -726.1131 1.0224541
Loop time of 46.7423 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 32.492 | 32.625 | 32.758 | 2.3 | 69.80
Bond | 0.3584 | 0.36552 | 0.37265 | 1.2 | 0.78
Kspace | 4.7476 | 4.8898 | 5.0319 | 6.4 | 10.46
Neigh | 5.1461 | 5.1463 | 5.1464 | 0.0 | 11.01
Comm | 0.86246 | 0.89403 | 0.92559 | 3.3 | 1.91
Output | 0.0020437 | 0.0020902 | 0.0021367 | 0.1 | 0.00
Modify | 1.4279 | 1.5187 | 1.6095 | 7.4 | 3.25
Other | | 1.301 | | | 2.78
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8922 ave 9009 max 8835 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 367689 ave 371637 max 363741 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 735378
Ave neighs/atom = 366.955
Ave special neighs/atom = 2.34032
Neighbor list builds = 200
Dangerous builds = 0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
Total wall time: 0:00:58
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