212 lines
9.9 KiB
Groff
212 lines
9.9 KiB
Groff
LAMMPS (17 Aug 2017)
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Processor partition = 4
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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 295 ${temper_T} 100.0 iso 1 1 1000
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fix myfix all npt temp 295 295 100.0 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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50 223.44965 -7675.7636 1223.6082 -5118.0353 -23854.901 0.99531214
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100 258.05368 -6964.3986 482.14839 -4941.5246 12745.624 1.010825
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150 279.95689 -6874.6176 472.25664 -4730.8609 7091.9355 1.0193879
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200 275.57578 -7193.9232 1079.6288 -4468.952 -17877.542 1.0195441
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250 279.43717 -6402.2754 479.97988 -4253.8984 23273.809 1.0116181
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300 292.20824 -6863.5426 998.78846 -4120.1066 -14524.477 0.99985013
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350 297.83477 -6520.8204 705.46814 -4037.1112 1640.5321 0.99100268
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400 300.71476 -6441.8834 652.50284 -3993.9443 7052.2304 0.98787311
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450 298.04546 -6757.2898 986.07239 -3991.7184 -11211.612 0.98470906
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500 290.54704 -6432.0836 676.82263 -4020.5317 9503.0303 0.98022653
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Loop time of 11.0411 on 2 procs for 500 steps with 2004 atoms
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Performance: 7.825 ns/day, 3.067 hours/ns, 45.286 timesteps/s
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99.2% 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 | 7.7513 | 7.8142 | 7.8771 | 2.3 | 70.77
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Bond | 0.087844 | 0.089858 | 0.091872 | 0.7 | 0.81
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Kspace | 1.1507 | 1.2078 | 1.2649 | 5.2 | 10.94
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Neigh | 1.2777 | 1.2798 | 1.282 | 0.2 | 11.59
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Comm | 0.21883 | 0.2369 | 0.25497 | 3.7 | 2.15
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Output | 0.00052476 | 0.00053084 | 0.00053692 | 0.0 | 0.00
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Modify | 0.35187 | 0.38007 | 0.40828 | 4.6 | 3.44
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Other | | 0.03188 | | | 0.29
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Nlocal: 1002 ave 1018 max 986 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8685.5 ave 8713 max 8658 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 352674 ave 363841 max 341507 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 705348
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Ave neighs/atom = 351.97
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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 100 295 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) = 0.268595
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0229274
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estimated relative force accuracy = 6.90452e-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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500 290.54704 -6432.0826 676.82263 -4020.5307 9503.0509 0.98022653
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550 299.80307 -6732.1631 858.08424 -4084.0858 -5804.5234 0.97922483
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600 282.09517 -6605.4814 819.96587 -4101.2486 -819.40251 0.98081741
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650 294.53657 -6522.7525 767.04478 -3997.1588 4596.0585 0.98382352
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700 305.841 -6619.4153 905.5064 -3887.8662 -5973.5686 0.98622017
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750 307.23206 -6438.653 789.70387 -3814.6009 6681.8219 0.98950206
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800 307.87505 -6564.5918 887.75178 -3838.6527 -1917.6181 0.98688326
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850 298.61627 -6528.5749 847.91654 -3897.7513 -3785.6609 0.9806677
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900 300.37107 -6492.7964 828.13288 -3871.2792 3123.0873 0.97992098
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950 313.50832 -6648.6955 936.69562 -3840.1788 -3465.5075 0.97832705
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1000 300.79594 -6452.6853 828.10459 -3828.6598 2639.7489 0.9724972
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1050 316.04685 -6570.6422 935.04399 -3748.6208 -2434.9525 0.96835974
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1100 311.0203 -6489.14 897.50532 -3734.6686 -1557.8625 0.97044387
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1150 311.75575 -6489.2845 888.02191 -3739.9054 1954.7864 0.97411485
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1200 304.34674 -6521.7138 905.22814 -3799.3644 -1699.1298 0.98025305
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1250 305.82 -6594.6645 927.05285 -3841.6942 1061.9124 0.98818343
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1300 300.78043 -6566.1931 942.90743 -3827.4574 -864.10057 0.99107957
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1350 314.72676 -6545.9508 912.22446 -3754.6305 606.75529 0.9929135
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1400 315.913 -6551.4197 960.628 -3704.6134 1064.6728 0.99029667
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1450 309.18966 -6497.0696 918.08358 -3732.9498 -1325.2759 0.98343775
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1500 312.58526 -6494.4875 891.16465 -3737.013 1380.3782 0.98291945
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1550 317.55684 -6590.3216 970.14576 -3724.1828 -1866.6608 0.9847875
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1600 307.38151 -6552.4153 940.826 -3776.3487 -390.22458 0.98596757
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1650 295.78641 -6508.499 880.69089 -3861.7969 -1368.3717 0.98931642
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1700 306.06415 -6655.9157 976.17248 -3852.3681 -1599.4137 0.99512042
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1750 303.02767 -6625.01 920.50823 -3895.2561 2274.9319 1.0015941
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1800 295.63701 -6674.2337 928.57382 -3980.5406 -290.52041 1.0049878
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1850 302.04323 -6768.1711 959.29198 -4005.5112 -688.59334 1.0096755
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1900 299.41653 -6746.3896 940.56717 -4018.1373 1011.075 1.0170047
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1950 298.83395 -6766.5655 950.11421 -4032.2445 -187.97792 1.0202189
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2000 299.45823 -6824.2159 958.18625 -4078.0956 -715.67202 1.0223031
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2050 290.49349 -6835.2073 950.68063 -4150.1172 -345.43177 1.0232367
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2100 283.23103 -6798.203 936.42547 -4170.729 300.36081 1.0201704
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2150 295.58133 -6797.5304 933.21906 -4099.5245 -293.26979 1.0191458
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2200 287.12783 -6693.6112 942.32795 -4036.9686 -1430.1972 1.0191149
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2250 301.19592 -6762.0204 998.15337 -3965.5579 -956.39215 1.0207659
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2300 303.62433 -6716.6297 960.83467 -3942.987 77.237938 1.0202529
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2350 292.95455 -6741.789 993.45295 -3999.2326 1009.5683 1.0189011
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2400 295.01475 -6781.545 966.72586 -4053.4151 109.26284 1.0174852
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2450 300.36482 -6827.3015 978.76759 -4055.187 -395.9959 1.0168907
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2500 303.77029 -6833.9094 987.05071 -4033.1791 259.58796 1.0139892
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Loop time of 46.7422 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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99.3% 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 | 31.75 | 32.061 | 32.372 | 5.5 | 68.59
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Bond | 0.36191 | 0.36261 | 0.36331 | 0.1 | 0.78
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Kspace | 4.6321 | 4.925 | 5.2179 | 13.2 | 10.54
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Neigh | 5.3267 | 5.3348 | 5.3429 | 0.3 | 11.41
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Comm | 0.88959 | 0.96174 | 1.0339 | 7.4 | 2.06
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Output | 0.0022326 | 0.0022967 | 0.0023608 | 0.1 | 0.00
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Modify | 1.4187 | 1.5349 | 1.6512 | 9.4 | 3.28
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Other | | 1.56 | | | 3.34
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Nlocal: 1002 ave 1009 max 995 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8864 ave 8880 max 8848 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 364886 ave 365536 max 364236 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 729772
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Ave neighs/atom = 364.158
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 206
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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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