212 lines
9.9 KiB
Groff
212 lines
9.9 KiB
Groff
LAMMPS (17 Aug 2017)
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Processor partition = 7
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using 1 OpenMP thread(s) per MPI task
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# Solvated 5-mer peptide
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# Demonstrating temper/npt
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 1 by 2 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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14 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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1365 bonds
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reading angles ...
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786 angles
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reading dihedrals ...
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207 dihedrals
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reading impropers ...
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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thermo_style custom step temp epair emol etotal press density
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thermo 50
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variable temper_T world 275 280 285 290 295 300 305 310
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variable rep world 0 1 2 3 4 5 6 7
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fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
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fix myfix all npt temp 310 ${temper_T} 100.0 iso 1 1 1000
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fix myfix all npt temp 310 310 100.0 iso 1 1 1000
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run 500
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 6776 1800
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmm/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
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Step Temp E_pair E_mol TotEng Press Density
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0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
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50 224.5362 -7670.5503 1225.9519 -5103.9909 -23918.514 0.99480995
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100 261.00419 -6946.2961 483.78483 -4904.1694 12827.309 1.0097087
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150 284.14624 -6832.0094 472.66187 -4662.8346 7354.8252 1.0180355
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200 284.05862 -7160.8537 1102.3553 -4362.5087 -18524.276 1.0178951
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250 290.82577 -6319.5357 471.77841 -4111.3638 22989.86 1.0099523
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300 306.50487 -6809.5465 1015.3715 -3964.1684 -13215.763 0.99625687
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350 319.20654 -6502.4307 761.98704 -3834.601 -965.94424 0.98284646
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400 316.81299 -6295.1539 646.79195 -3756.8102 8469.8917 0.97675631
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450 312.90373 -6639.6427 1048.7063 -3722.7251 -13014.646 0.97486033
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500 319.55848 -6335.5865 712.00927 -3715.6334 9980.2286 0.97468964
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Loop time of 10.7877 on 2 procs for 500 steps with 2004 atoms
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Performance: 8.009 ns/day, 2.997 hours/ns, 46.349 timesteps/s
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99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 7.6698 | 7.7211 | 7.7724 | 1.8 | 71.57
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Bond | 0.085352 | 0.086755 | 0.088159 | 0.5 | 0.80
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Kspace | 1.089 | 1.1417 | 1.1944 | 4.9 | 10.58
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Neigh | 1.2554 | 1.2554 | 1.2554 | 0.0 | 11.64
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Comm | 0.16438 | 0.17539 | 0.1864 | 2.6 | 1.63
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Output | 0.00045967 | 0.0004642 | 0.00046873 | 0.0 | 0.00
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Modify | 0.35006 | 0.37517 | 0.40028 | 4.1 | 3.48
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Other | | 0.0317 | | | 0.29
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Nlocal: 1002 ave 1004 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8709.5 ave 8714 max 8705 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 350398 ave 352725 max 348070 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 700795
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Ave neighs/atom = 349.698
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 51
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Dangerous builds = 0
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temper/npt 2000 100 ${temper_T} myfix 0 58728 1
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temper/npt 2000 100 310 myfix 0 58728 1
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.268436
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0230577
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estimated relative force accuracy = 6.94376e-05
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using double precision FFTs
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3d grid and FFT values/proc = 6776 1800
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Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
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Step Temp E_pair E_mol TotEng Press Density
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500 319.55848 -6335.5878 712.00927 -3715.6347 9980.2224 0.97468964
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550 312.3068 -6517.9692 882.51888 -3770.8031 -4737.1103 0.97368346
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600 306.74828 -6500.9408 860.97959 -3808.5014 -1687.6369 0.97333001
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650 309.25363 -6453.3615 753.23233 -3853.711 4484.0534 0.97330212
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700 305.22336 -6644.7434 922.38867 -3899.9996 -5823.8028 0.97262421
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750 297.24363 -6480.4086 771.41874 -3934.2782 5025.8889 0.97337406
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800 300.89643 -6587.4079 835.06282 -3955.8242 -1517.9426 0.97460241
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850 305.43206 -6685.1173 846.71999 -4014.7961 -1788.398 0.97836973
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900 289.95008 -6574.8681 806.12799 -4037.575 2604.847 0.98232784
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950 299.22424 -6671.7556 898.72395 -3986.4946 -2702.719 0.98919804
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1000 305.3932 -6576.089 826.21317 -3926.5066 2254.7456 0.99471125
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1050 304.62574 -6619.698 893.18161 -3907.7293 -1010.7916 0.99551385
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1100 304.13778 -6603.0961 846.91376 -3940.3087 -211.63132 0.99359493
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1150 285.80722 -6557.1116 859.12907 -3991.5526 1777.6534 0.99165538
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1200 295.20871 -6612.8101 855.05738 -3995.1906 -389.55216 0.98957199
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1250 301.4547 -6623.3355 907.78288 -3915.6984 1193.6428 0.98887879
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1300 302.29836 -6545.5769 862.86619 -3877.8194 443.76145 0.9853829
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1350 309.29624 -6539.3158 878.22476 -3814.4185 -769.46378 0.98002173
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1400 311.28962 -6582.4295 939.53596 -3784.3195 -239.11773 0.97952655
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1450 307.46833 -6597.7591 922.88062 -3839.1196 453.60414 0.98288752
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1500 308.8234 -6660.3138 910.39719 -3906.0672 356.0472 0.98507945
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1550 297.42322 -6596.3955 938.61921 -3881.9924 -883.10576 0.98730686
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1600 309.492 -6649.4174 963.57197 -3838.0041 470.91335 0.99194955
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1650 309.46921 -6602.6445 958.19972 -3796.7395 1417.6814 0.99437216
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1700 308.27043 -6575.0156 941.02926 -3793.4384 -445.78985 0.99171728
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1750 306.31262 -6515.703 929.60371 -3757.2406 944.20045 0.98661702
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1800 308.63008 -6484.7465 959.53268 -3682.5186 333.02755 0.98504191
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1850 316.69569 -6520.4677 975.02618 -3654.5901 -835.64735 0.98329409
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1900 316.03266 -6531.6456 948.03331 -3696.7196 -745.03047 0.98236945
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1950 308.97313 -6562.2733 955.48033 -3762.0496 -1147.5825 0.983921
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2000 305.67836 -6611.4675 991.3364 -3795.0594 -2361.1127 0.98852677
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2050 312.66709 -6687.3067 980.96042 -3839.5479 -244.80211 0.99714887
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2100 307.23751 -6664.4853 963.74125 -3866.3633 268.84485 1.0050595
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2150 296.36081 -6633.5455 966.74219 -3897.3626 -741.15958 1.0135557
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2200 306.79331 -6709.7668 989.09713 -3888.9411 -108.31295 1.0211476
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2250 310.62715 -6713.5021 973.14019 -3885.7431 1576.0539 1.0235204
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2300 304.34901 -6675.1811 1001.4509 -3856.5955 -481.96378 1.0180933
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2350 300.55584 -6592.7909 993.96783 -3804.3356 114.74351 1.0116595
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2400 307.16641 -6626.7049 984.70783 -3808.0408 620.2875 1.0087872
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2450 301.62279 -6643.7063 978.76012 -3864.0884 72.614095 1.0085247
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2500 307.17634 -6691.4794 975.63125 -3881.8326 495.45555 1.0099428
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Loop time of 46.7465 on 2 procs for 2000 steps with 2004 atoms
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Performance: 7.393 ns/day, 3.246 hours/ns, 42.784 timesteps/s
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99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 31.19 | 31.703 | 32.216 | 9.1 | 67.82
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Bond | 0.35397 | 0.35463 | 0.35528 | 0.1 | 0.76
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Kspace | 4.3783 | 4.8922 | 5.4062 | 23.2 | 10.47
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Neigh | 5.2885 | 5.2889 | 5.2893 | 0.0 | 11.31
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Comm | 0.67571 | 0.71687 | 0.75803 | 4.9 | 1.53
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Output | 0.0019109 | 0.0019529 | 0.0019948 | 0.1 | 0.00
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Modify | 1.4216 | 1.5185 | 1.6154 | 7.9 | 3.25
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Other | | 2.271 | | | 4.86
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Nlocal: 1002 ave 1010 max 994 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8811.5 ave 8832 max 8791 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 363080 ave 367967 max 358193 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 726160
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Ave neighs/atom = 362.355
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 207
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Dangerous builds = 0
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fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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group peptide type <= 12
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84 atoms in group peptide
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Total wall time: 0:00:58
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