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lammps/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1
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log.temper_npt-17Aug17.g++.8.1
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LAMMPS (17 Aug 2017)
Processor partition = 1
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 280 ${temper_T} 100.0 iso 1 1 1000
fix myfix all npt temp 280 280 100.0 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
50 222.19861 -7681.6246 1220.9355 -5134.0385 -23782.584 0.99586813
100 254.66243 -6984.8813 480.32613 -4984.0772 12653.925 1.0120499
150 275.28565 -6924.9875 473.42216 -4807.9551 6796.8759 1.0208676
200 266.52981 -7245.4283 1066.0809 -4588.0144 -17643.106 1.0213699
250 265.06051 -6458.7243 468.97999 -4407.1839 22476.585 1.0143215
300 276.91573 -6986.8723 1020.9402 -4312.5895 -14559.244 1.005554
350 284.26789 -6635.8191 681.27092 -4257.3089 2625.7849 0.99664411
400 284.48799 -6543.0099 637.61352 -4206.8431 7901.0269 0.99079237
450 271.30029 -6770.4441 1003.5624 -4147.0663 -13046.51 0.9856127
500 292.02418 -6514.8219 628.56367 -4142.7096 9871.7492 0.98625432
Loop time of 11.1841 on 2 procs for 500 steps with 2004 atoms
Performance: 7.725 ns/day, 3.107 hours/ns, 44.706 timesteps/s
98.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.8072 | 7.9267 | 8.0463 | 4.2 | 70.88
Bond | 0.08858 | 0.091102 | 0.093624 | 0.8 | 0.81
Kspace | 1.1403 | 1.2665 | 1.3927 | 11.2 | 11.32
Neigh | 1.2478 | 1.2496 | 1.2514 | 0.2 | 11.17
Comm | 0.21574 | 0.23191 | 0.24809 | 3.4 | 2.07
Output | 0.00054431 | 0.00054872 | 0.00055313 | 0.0 | 0.00
Modify | 0.36159 | 0.38512 | 0.40864 | 3.8 | 3.44
Other | | 0.03255 | | | 0.29
Nlocal: 1002 ave 1026 max 978 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8640.5 ave 8690 max 8591 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354518 ave 367457 max 341580 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 709037
Ave neighs/atom = 353.811
Ave special neighs/atom = 2.34032
Neighbor list builds = 49
Dangerous builds = 0
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
temper/npt 2000 100 280 myfix 0 58728 1
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268766
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0227872
estimated relative force accuracy = 6.8623e-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
500 292.02418 -6514.8215 628.56367 -4142.7092 9871.7534 0.98625432
550 282.55729 -6813.6685 882.47773 -4244.1648 -5377.4053 0.98629839
600 274.41644 -6737.0424 793.45027 -4305.1716 -306.54594 0.98725369
650 274.38967 -6664.1973 722.25014 -4303.6865 4628.1283 0.99175575
700 282.07693 -6819.1345 897.72476 -4237.2518 -7210.1942 0.99693402
750 281.80476 -6580.3192 776.69527 -4121.091 5466.9616 1.0060075
800 288.76507 -6726.7205 885.07773 -4117.5529 -2623.0756 1.0132495
850 289.21519 -6755.4289 847.00353 -4181.648 776.75991 1.0160602
900 280.679 -6694.3766 777.91069 -4240.6544 2272.2098 1.0170439
950 280.93616 -6813.8865 910.52053 -4226.0191 -3872.8603 1.0202606
1000 289.91762 -6710.0317 786.39268 -4192.6678 4456.0575 1.0222223
1050 292.7318 -6830.313 882.85834 -4199.6812 -2434.3412 1.0214856
1100 280.61029 -6789.3828 846.07872 -4267.9028 580.25027 1.0202095
1150 277.27283 -6806.9599 852.2013 -4299.2838 18.428929 1.0180062
1200 284.68488 -6849.8644 877.54803 -4272.5875 -1041.3591 1.0171686
1250 290.47153 -6864.5918 827.15634 -4303.1571 2658.2245 1.0175104
1300 279.84219 -6892.8497 884.4759 -4337.5586 -1800.8783 1.0176916
1350 275.59818 -6848.0359 848.53171 -4354.028 1599.2311 1.0197901
1400 276.67929 -6893.565 900.40614 -4341.2278 295.46659 1.0221449
1450 281.18148 -6902.3901 931.40362 -4292.1748 -1585.1315 1.0243322
1500 282.82339 -6846.4364 887.9988 -4269.8228 2142.9076 1.0291373
1550 291.40537 -6898.3742 920.23257 -4238.2876 -355.99408 1.0308242
1600 279.9548 -6863.2068 923.64788 -4268.0713 233.83555 1.0259922
1650 282.90611 -6848.3952 903.97971 -4255.3069 369.65523 1.0200083
1700 292.24099 -6884.346 965.54265 -4173.9603 -971.39092 1.0155909
1750 285.95609 -6805.2486 955.25719 -4142.6727 646.23287 1.012031
1800 293.50173 -6823.8152 919.24584 -4152.199 530.19678 1.0078324
1850 300.737 -6918.3747 942.10944 -4180.6963 -949.67639 1.0061029
1900 284.98969 -6913.5357 956.78373 -4255.2032 -163.02524 1.0095568
1950 282.78589 -6905.1978 951.94384 -4264.8631 -891.31043 1.0177223
2000 289.82463 -6977.0203 1022.9525 -4223.6518 -540.73403 1.0269481
2050 292.13474 -6900.8375 924.54552 -4232.0833 2656.3028 1.0310097
2100 284.54116 -6958.82 968.35681 -4291.5924 -286.70605 1.0264636
2150 268.14376 -6966.2184 973.69354 -4391.5558 -1446.0052 1.0190957
2200 275.09872 -6957.02 982.37472 -4332.1512 -1449.1984 1.0199163
2250 285.69237 -7002.4814 1014.3438 -4282.3934 -1530.0347 1.0264012
2300 282.59746 -6922.8242 980.57612 -4254.9822 381.8231 1.0332785
2350 290.98138 -6993.8628 1022.527 -4234.0132 -559.9386 1.0396092
2400 281.29903 -6963.5226 967.13898 -4316.8702 1438.7922 1.0452404
2450 278.44605 -6968.5134 945.32295 -4360.7108 1102.9302 1.0498791
2500 278.65789 -7034.3651 1032.8711 -4337.7496 -923.32414 1.0527955
Loop time of 46.7418 on 2 procs for 2000 steps with 2004 atoms
Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
98.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.141 | 33.146 | 33.152 | 0.1 | 70.91
Bond | 0.36441 | 0.36647 | 0.36853 | 0.3 | 0.78
Kspace | 4.9269 | 4.9539 | 4.9808 | 1.2 | 10.60
Neigh | 5.2154 | 5.223 | 5.2306 | 0.3 | 11.17
Comm | 0.90923 | 0.97305 | 1.0369 | 6.5 | 2.08
Output | 0.0021682 | 0.0027286 | 0.003289 | 1.1 | 0.01
Modify | 1.454 | 1.5534 | 1.6528 | 8.0 | 3.32
Other | | 0.5229 | | | 1.12
Nlocal: 1002 ave 1005 max 999 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 9059.5 ave 9084 max 9035 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 378277 ave 380641 max 375913 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 756554
Ave neighs/atom = 377.522
Ave special neighs/atom = 2.34032
Neighbor list builds = 197
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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