212 lines
9.9 KiB
Plaintext
212 lines
9.9 KiB
Plaintext
LAMMPS (17 Aug 2017)
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Processor partition = 0
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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 275 ${temper_T} 100.0 iso 1 1 1000
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fix myfix all npt temp 275 275 100.0 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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50 221.73889 -7683.7524 1219.961 -5139.8856 -23756.591 0.996067
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100 253.40719 -6992.3405 479.6715 -4999.6856 12620.614 1.0124851
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150 273.60252 -6943.8714 474.24744 -4836.0631 6691.4146 1.0213937
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200 265.37126 -7274.7854 1059.7586 -4630.6111 -17765.088 1.0221471
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250 263.1769 -6503.9902 470.29014 -4462.3859 21936.742 1.0159924
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300 274.03852 -7026.6057 1021.3683 -4369.0734 -14847.42 1.0095778
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350 283.20032 -6715.3608 688.9769 -4335.5187 3430.7111 1.0045615
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400 282.2987 -6645.6692 598.6786 -4361.5086 6318.9525 1.0001513
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450 265.89091 -6977.5705 985.58718 -4404.465 -13261.32 0.99833097
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500 270.30038 -6683.7902 650.5748 -4419.37 10014.277 1.000501
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Loop time of 11.0158 on 2 procs for 500 steps with 2004 atoms
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Performance: 7.843 ns/day, 3.060 hours/ns, 45.389 timesteps/s
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99.4% 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 | 7.6893 | 7.8012 | 7.9131 | 4.0 | 70.82
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Bond | 0.085948 | 0.089635 | 0.093322 | 1.2 | 0.81
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Kspace | 1.1113 | 1.2333 | 1.3552 | 11.0 | 11.20
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Neigh | 1.2316 | 1.2336 | 1.2356 | 0.2 | 11.20
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Comm | 0.24281 | 0.24305 | 0.2433 | 0.0 | 2.21
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Output | 0.00052857 | 0.00053537 | 0.00054216 | 0.0 | 0.00
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Modify | 0.35968 | 0.38071 | 0.40175 | 3.4 | 3.46
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Other | | 0.03378 | | | 0.31
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Nlocal: 1002 ave 1012 max 992 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8737.5 ave 8747 max 8728 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 359463 ave 359931 max 358995 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 718926
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Ave neighs/atom = 358.746
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 50
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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 100 275 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) = 0.269166
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0224625
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estimated relative force accuracy = 6.76451e-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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500 270.30038 -6683.7883 650.5748 -4419.3682 10014.295 1.000501
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550 270.02511 -6875.5939 861.97452 -4401.4176 -7136.4285 1.005266
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600 278.94444 -6786.546 772.05516 -4349.0356 1262.4902 1.0110761
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650 283.8929 -6763.9691 734.90211 -4334.0667 3664.1311 1.0138933
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700 276.67406 -6889.5452 847.87041 -4389.775 -4754.9929 1.0145005
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750 266.09032 -6720.4921 700.27463 -4431.5085 5654.8094 1.013756
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800 277.69948 -6917.9358 860.12186 -4399.7918 -4729.7009 1.0124281
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850 278.00722 -6808.1267 798.69768 -4349.5695 1468.5155 1.0139727
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900 276.49266 -6784.5965 818.01248 -4315.7673 2510.6047 1.0158115
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950 270.36225 -6847.6403 901.97122 -4331.4544 -3448.3968 1.0175668
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1000 276.75533 -6809.4075 781.83481 -4375.1877 3379.8584 1.0173101
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1050 271.67172 -6913.3268 847.97269 -4443.3211 -2045.5605 1.016761
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1100 265.73149 -6867.7958 840.08439 -4441.1449 -323.23893 1.0170333
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1150 274.51451 -6834.9841 792.48751 -4403.4906 2604.0644 1.0175885
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1200 274.22914 -6919.9496 890.14423 -4392.5032 -3454.4418 1.0167016
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1250 274.13019 -6817.7256 825.11317 -4355.901 2067.3849 1.0181714
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1300 287.36094 -6906.5403 854.11016 -4336.7237 -438.01206 1.0180794
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1350 275.51763 -6911.8172 855.25923 -4411.5627 -742.96412 1.0180086
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1400 269.90457 -6919.4028 855.55485 -4452.3659 311.08918 1.0213368
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1450 276.99478 -6980.8317 913.69108 -4413.326 -1810.1051 1.0265437
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1500 282.20313 -6926.698 863.56525 -4378.2213 932.7594 1.0301769
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1550 276.82056 -6917.141 910.22058 -4354.146 -899.64097 1.0361201
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1600 278.2946 -6903.7351 893.14524 -4349.0145 1399.9679 1.0421849
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1650 270.12097 -6863.0844 879.81355 -4370.4967 1132.9864 1.0410741
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1700 274.02565 -6912.4818 893.37432 -4383.0202 -1359.393 1.0366624
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1750 276.77322 -6866.3214 899.18224 -4314.6474 887.47588 1.0332821
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1800 287.02945 -6961.9217 950.89476 -4297.2996 -1298.0904 1.0313542
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1850 279.37232 -6930.51 898.78906 -4363.711 397.74804 1.0309206
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1900 277.14727 -6978.8634 915.53145 -4408.6069 636.36898 1.0285813
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1950 275.14272 -7010.256 927.28727 -4440.212 -2352.6961 1.0241747
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2000 270.84972 -6967.52 913.42253 -4436.9722 1669.9637 1.0251906
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2050 276.70108 -6992.4582 993.37473 -4347.0223 -500.38379 1.0325714
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2100 278.49569 -6922.9266 939.43518 -4320.7155 700.24515 1.0385166
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2150 279.69822 -6896.5008 923.58805 -4302.9571 702.22759 1.0415681
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2200 284.136 -6951.6694 974.70903 -4280.5086 352.95043 1.0452009
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2250 292.01941 -6960.5848 964.01635 -4253.0483 2680.7007 1.0430517
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2300 277.58812 -6995.5006 1010.8176 -4327.3258 -1508.9961 1.0328658
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2350 270.61616 -6978.93 966.12478 -4397.0745 -1636.7434 1.0267664
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2400 279.36012 -6991.4739 957.43125 -4366.1056 432.00482 1.0260429
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2450 286.38546 -7074.807 1004.3206 -4360.6042 160.9109 1.0251585
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2500 269.98622 -6932.0456 957.35208 -4362.724 1748.1568 1.0186556
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Loop time of 46.7361 on 2 procs for 2000 steps with 2004 atoms
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Performance: 7.395 ns/day, 3.246 hours/ns, 42.793 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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Pair | 32.381 | 32.617 | 32.854 | 4.1 | 69.79
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Bond | 0.3601 | 0.36578 | 0.37147 | 0.9 | 0.78
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Kspace | 4.6658 | 4.933 | 5.2002 | 12.0 | 10.56
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Neigh | 4.9833 | 4.9921 | 5.0009 | 0.4 | 10.68
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Comm | 0.96477 | 0.96532 | 0.96587 | 0.1 | 2.07
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Output | 0.0021896 | 0.0022331 | 0.0022767 | 0.1 | 0.00
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Modify | 1.4424 | 1.5379 | 1.6334 | 7.7 | 3.29
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Other | | 1.322 | | | 2.83
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Nlocal: 1002 ave 1011 max 993 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8835 ave 8847 max 8823 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 366395 ave 367166 max 365624 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 732790
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Ave neighs/atom = 365.664
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 195
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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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