forked from lijiext/lammps
212 lines
9.9 KiB
Groff
212 lines
9.9 KiB
Groff
LAMMPS (17 Aug 2017)
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Processor partition = 5
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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 300 ${temper_T} 100.0 iso 1 1 1000
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fix myfix all npt temp 300 300 100.0 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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50 223.82864 -7673.9648 1224.4256 -5113.1564 -23877.062 0.99513919
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100 259.08234 -6958.1555 482.71038 -4928.5779 12773.331 1.010442
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150 281.33296 -6859.1832 472.14676 -4707.3204 7185.467 1.0189247
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200 278.97145 -7183.3765 1085.5768 -4432.1832 -18068.845 1.0189951
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250 279.03591 -6351.7829 479.41881 -4206.3627 23082.567 1.0112758
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300 300.6326 -6884.9027 1026.5309 -4063.426 -13809.886 0.99975981
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350 305.9627 -6542.2739 749.87415 -3965.6303 1365.919 0.98893682
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400 300.95813 -6356.16 664.78738 -3894.4833 7945.2634 0.98104761
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450 305.74067 -6698.3004 1016.1128 -3856.7437 -11928.509 0.97692928
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500 295.19123 -6343.4664 707.06763 -3873.9411 9895.6164 0.97622451
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Loop time of 11.1232 on 2 procs for 500 steps with 2004 atoms
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Performance: 7.768 ns/day, 3.090 hours/ns, 44.951 timesteps/s
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99.0% 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 | 7.8133 | 7.8368 | 7.8603 | 0.8 | 70.45
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Bond | 0.088746 | 0.089125 | 0.089505 | 0.1 | 0.80
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Kspace | 1.2047 | 1.2319 | 1.2591 | 2.5 | 11.07
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Neigh | 1.3081 | 1.31 | 1.3119 | 0.2 | 11.78
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Comm | 0.21978 | 0.23832 | 0.25687 | 3.8 | 2.14
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Output | 0.00053644 | 0.00054514 | 0.00055385 | 0.0 | 0.00
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Modify | 0.35216 | 0.38209 | 0.41202 | 4.8 | 3.44
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Other | | 0.03448 | | | 0.31
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Nlocal: 1002 ave 1003 max 1001 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8664.5 ave 8679 max 8650 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 350634 ave 352508 max 348761 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 701269
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Ave neighs/atom = 349.935
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 52
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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 100 300 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) = 0.26848
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0230214
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estimated relative force accuracy = 6.93284e-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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500 295.19123 -6343.4702 707.06763 -3873.9449 9895.5638 0.97622451
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550 302.94979 -6642.4394 911.36179 -3922.2969 -5410.8109 0.97461641
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600 297.33068 -6551.2919 805.26047 -3970.8 -646.78096 0.97348192
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650 294.80947 -6578.9544 780.59748 -4038.1786 3293.0695 0.97423526
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700 286.5511 -6718.4475 944.64841 -4062.9279 -5230.2518 0.97771554
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750 294.49463 -6602.2482 777.88337 -4066.0662 4142.887 0.9831379
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800 291.06018 -6664.3537 858.09465 -4068.466 -2624.3753 0.98991103
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850 293.82285 -6689.8325 860.75951 -4074.7853 -435.3378 0.99623629
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900 287.38111 -6671.9376 837.28605 -4118.8247 2185.0063 0.99906496
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950 288.54911 -6783.7293 916.92837 -4144.0005 -2644.9104 0.99578685
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1000 293.00277 -6687.2173 803.00518 -4134.8207 2220.968 0.98936787
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1050 301.16902 -6760.9066 892.18697 -4070.5711 -2974.6886 0.98583275
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1100 309.08554 -6738.1202 875.08899 -4017.6166 921.61791 0.98892607
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1150 298.58252 -6674.1083 871.86516 -4019.5376 944.64401 0.98978942
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1200 298.47184 -6760.3869 925.22004 -4053.1221 -798.3384 0.98947798
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1250 291.12935 -6703.3237 856.27457 -4108.8431 544.44438 0.98937896
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1300 293.02206 -6830.1194 917.90705 -4162.7058 432.93648 0.98837688
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1350 282.12152 -6775.1505 898.35169 -4192.3746 -968.85129 0.98738197
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1400 284.13008 -6684.782 848.15892 -4140.2066 -909.72792 0.98855422
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1450 283.07781 -6640.5698 889.19504 -4061.241 120.67624 0.99460963
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1500 299.32129 -6744.9956 896.07755 -4061.8016 -500.39827 1.002166
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1550 290.06547 -6763.7114 921.50981 -4110.3475 1970.1344 1.0045278
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1600 294.31127 -6824.5224 885.60385 -4181.7147 -1450.5522 1.0021664
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1650 289.14351 -6837.8321 902.7679 -4208.7148 -36.719886 1.0010127
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1700 284.10327 -6855.1076 903.75736 -4255.0939 984.04625 1.0006878
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1750 280.04385 -6904.9119 918.67229 -4314.2203 -1431.4015 1.0004286
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1800 281.68654 -6818.1122 846.72598 -4289.5591 520.17793 1.0021784
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1850 286.93593 -6902.5226 934.50057 -4254.8531 -793.77873 1.0057534
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1900 292.37295 -6876.9829 886.20947 -4245.1425 1563.8149 1.0119959
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1950 278.61219 -6897.2099 935.36125 -4298.3772 -498.09374 1.0139668
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2000 278.03754 -6936.4809 912.07762 -4364.3628 -475.0812 1.0140553
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2050 280.17142 -6999.6889 907.21584 -4419.692 -483.15119 1.0159549
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2100 275.01317 -7045.1909 966.49463 -4436.7129 516.29126 1.0192102
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2150 275.36286 -6985.3989 879.47784 -4461.8499 -33.602001 1.0183533
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2200 276.11062 -7026.4293 936.6898 -4441.2038 -1270.9384 1.0213402
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2250 283.79417 -7011.4884 977.04948 -4340.0281 -178.52826 1.0266779
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2300 276.26548 -6911.7259 909.12359 -4353.142 1380.5761 1.0284968
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2350 279.5692 -7056.2521 960.48747 -4426.5792 202.29669 1.0282733
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2400 270.18994 -6995.9308 932.57134 -4450.1735 -1921.755 1.0261097
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2450 273.41894 -6999.2367 955.71826 -4411.0536 -376.50236 1.0265598
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2500 279.53567 -6995.6096 941.2382 -4385.3862 300.84721 1.0300527
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Loop time of 46.7426 on 2 procs for 2000 steps with 2004 atoms
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Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
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98.6% 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 | 32.111 | 32.533 | 32.954 | 7.4 | 69.60
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Bond | 0.36551 | 0.36836 | 0.3712 | 0.5 | 0.79
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Kspace | 4.9203 | 5.3226 | 5.7249 | 17.4 | 11.39
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Neigh | 5.2618 | 5.2695 | 5.2772 | 0.3 | 11.27
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Comm | 0.89292 | 0.96319 | 1.0335 | 7.2 | 2.06
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Output | 0.0021534 | 0.0022 | 0.0022466 | 0.1 | 0.00
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Modify | 1.4108 | 1.5304 | 1.65 | 9.7 | 3.27
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Other | | 0.7537 | | | 1.61
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Nlocal: 1002 ave 1023 max 981 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8955 ave 9060 max 8850 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 370398 ave 378514 max 362281 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 740795
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Ave neighs/atom = 369.658
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 200
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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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