212 lines
9.9 KiB
Groff
212 lines
9.9 KiB
Groff
LAMMPS (17 Aug 2017)
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Processor partition = 6
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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 305 ${temper_T} 100.0 iso 1 1 1000
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fix myfix all npt temp 305 305 100.0 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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50 224.19041 -7672.2342 1225.2069 -5108.4844 -23898.427 0.9949719
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100 260.06304 -6952.1103 483.25334 -4916.1343 12800.907 1.01007
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150 282.69922 -6844.8106 472.2939 -4684.6433 7274.1665 1.0184736
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200 283.07925 -7183.2915 1096.3999 -4396.7493 -18428.465 1.0184431
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250 283.61722 -6327.2943 475.82271 -4158.1172 23020.286 1.0107938
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300 301.71789 -6811.4188 1004.2807 -4005.7126 -14017.258 0.99889097
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350 311.03337 -6506.7477 765.85039 -3883.8531 763.04925 0.98860598
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400 317.775 -6392.1118 666.55754 -3828.2587 7828.8386 0.98148763
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450 303.51186 -6657.5211 1017.7742 -3827.6103 -12704.511 0.97662555
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500 296.45297 -6312.4144 719.53961 -3822.8838 8469.2935 0.97646495
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Loop time of 10.8893 on 2 procs for 500 steps with 2004 atoms
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Performance: 7.934 ns/day, 3.025 hours/ns, 45.917 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 | 7.7295 | 7.7574 | 7.7852 | 1.0 | 71.24
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Bond | 0.088436 | 0.089395 | 0.090353 | 0.3 | 0.82
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Kspace | 1.1269 | 1.16 | 1.1931 | 3.1 | 10.65
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Neigh | 1.2353 | 1.2377 | 1.2402 | 0.2 | 11.37
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Comm | 0.21436 | 0.23339 | 0.25242 | 3.9 | 2.14
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Output | 0.00055766 | 0.00056684 | 0.00057602 | 0.0 | 0.01
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Modify | 0.34907 | 0.37832 | 0.40758 | 4.8 | 3.47
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Other | | 0.03245 | | | 0.30
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Nlocal: 1002 ave 1007 max 997 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8685.5 ave 8750 max 8621 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 350698 ave 351936 max 349459 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 701395
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Ave neighs/atom = 349.998
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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 100 305 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) = 0.268487
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0230158
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estimated relative force accuracy = 6.93113e-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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500 296.45297 -6312.4159 719.53961 -3822.8853 8469.2763 0.97646495
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550 303.89646 -6501.1353 863.14038 -3823.5621 -2928.2904 0.98030197
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600 309.76597 -6524.1714 843.08835 -3831.606 -871.10399 0.98376234
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650 299.00298 -6442.6354 805.96883 -3851.4506 3266.5866 0.98567102
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700 309.92953 -6599.5125 902.18135 -3846.8775 -4895.7743 0.9877618
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750 310.03453 -6432.9154 800.77648 -3781.0583 4312.9432 0.98939465
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800 313.79353 -6482.8645 876.10518 -3733.2354 459.73904 0.9883653
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850 308.0727 -6473.4666 891.51665 -3742.5826 -1645.1499 0.9829221
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900 312.68166 -6456.773 820.7786 -3769.109 2194.8957 0.97822936
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950 305.94065 -6546.0017 902.97469 -3816.3892 -2693.7918 0.97584317
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1000 298.40902 -6464.4155 886.05639 -3796.6893 592.46618 0.9764313
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1050 308.71394 -6480.6485 854.83864 -3782.6139 843.67793 0.97834087
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1100 309.34645 -6526.4283 897.66923 -3781.7868 -297.6956 0.98046791
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1150 303.65216 -6540.534 858.53216 -3869.0276 623.45838 0.98196819
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1200 298.33689 -6610.5403 897.10898 -3932.1923 -1107.1097 0.98263413
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1250 302.10596 -6587.4254 875.62056 -3908.0623 1244.7382 0.98273784
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1300 316.19456 -6618.7414 894.33747 -3836.5445 -1399.1921 0.98252654
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1350 302.28789 -6625.1555 938.19878 -3882.1279 -57.818071 0.98275084
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1400 301.42717 -6602.0706 858.72022 -3943.6606 1462.1175 0.97898596
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1450 299.43442 -6655.6584 893.68574 -3974.1807 383.13882 0.97462948
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1500 301.76848 -6653.4568 896.33172 -3955.3975 -756.22375 0.96978565
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1550 310.10887 -6664.8547 953.35222 -3859.9781 -1305.0786 0.96689812
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1600 297.16621 -6510.7805 907.3012 -3829.2299 992.41943 0.96413868
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1650 295.71413 -6598.1621 990.18935 -3842.3931 -2049.7934 0.96131396
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1700 303.88264 -6629.5417 931.13321 -3884.0582 -630.7683 0.96321179
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1750 300.85941 -6666.8007 941.42895 -3929.0719 357.85887 0.96822524
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1800 299.34518 -6674.9694 932.15075 -3955.5595 -914.97614 0.97074982
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1850 298.12166 -6610.2338 910.63353 -3919.6462 1390.5062 0.97402953
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1900 307.86527 -6647.8711 931.49082 -3878.2514 -1629.6931 0.97542316
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1950 305.04604 -6616.6069 937.35845 -3857.952 858.37861 0.97770539
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2000 305.41215 -6597.2293 916.75863 -3856.9883 763.6265 0.98001111
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2050 294.66502 -6632.9068 1035.729 -3837.8618 -2248.1496 0.98430681
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2100 300.5948 -6569.1213 956.22884 -3818.1724 291.3677 0.99188971
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2150 305.73836 -6623.7387 1021.1569 -3777.1519 -603.41468 1.0003649
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2200 316.63308 -6681.0402 972.23429 -3818.3283 948.97143 1.0073383
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2250 306.36381 -6653.5361 947.42424 -3876.9476 900.19264 1.010245
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2300 301.9961 -6699.2583 1022.4799 -3873.6918 -499.39887 1.0119712
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2350 307.25098 -6642.8345 970.32723 -3838.0461 366.40507 1.0118686
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2400 311.79941 -6675.2645 1030.8811 -3782.7656 -1083.5459 1.0113601
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2450 309.31064 -6630.1585 958.35981 -3825.0401 471.39091 1.0099697
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2500 301.87691 -6689.2603 967.59935 -3919.2859 -854.45149 1.0097679
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Loop time of 46.7431 on 2 procs for 2000 steps with 2004 atoms
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Performance: 7.394 ns/day, 3.246 hours/ns, 42.787 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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Pair | 31.029 | 31.472 | 31.916 | 7.9 | 67.33
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Bond | 0.36154 | 0.36249 | 0.36343 | 0.2 | 0.78
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Kspace | 4.7001 | 5.1269 | 5.5536 | 18.8 | 10.97
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Neigh | 5.311 | 5.3205 | 5.33 | 0.4 | 11.38
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Comm | 0.86766 | 0.94238 | 1.0171 | 7.7 | 2.02
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Output | 0.0022194 | 0.0022837 | 0.0023479 | 0.1 | 0.00
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Modify | 1.4059 | 1.5219 | 1.638 | 9.4 | 3.26
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Other | | 1.994 | | | 4.27
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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: 8807.5 ave 8818 max 8797 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 363096 ave 369482 max 356711 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 726193
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Ave neighs/atom = 362.372
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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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