forked from lijiext/lammps
212 lines
9.9 KiB
Groff
212 lines
9.9 KiB
Groff
LAMMPS (17 Aug 2017)
|
|
Processor partition = 3
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Solvated 5-mer peptide
|
|
# Demonstrating temper/npt
|
|
units real
|
|
atom_style full
|
|
|
|
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
|
bond_style harmonic
|
|
angle_style charmm
|
|
dihedral_style charmm
|
|
improper_style harmonic
|
|
kspace_style pppm 0.0001
|
|
|
|
read_data data.peptide
|
|
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
|
1 by 1 by 2 MPI processor grid
|
|
reading atoms ...
|
|
2004 atoms
|
|
reading velocities ...
|
|
2004 velocities
|
|
scanning bonds ...
|
|
3 = max bonds/atom
|
|
scanning angles ...
|
|
6 = max angles/atom
|
|
scanning dihedrals ...
|
|
14 = max dihedrals/atom
|
|
scanning impropers ...
|
|
1 = max impropers/atom
|
|
reading bonds ...
|
|
1365 bonds
|
|
reading angles ...
|
|
786 angles
|
|
reading dihedrals ...
|
|
207 dihedrals
|
|
reading impropers ...
|
|
12 impropers
|
|
4 = max # of 1-2 neighbors
|
|
7 = max # of 1-3 neighbors
|
|
14 = max # of 1-4 neighbors
|
|
18 = max # of special neighbors
|
|
|
|
neighbor 2.0 bin
|
|
neigh_modify delay 5
|
|
|
|
timestep 2.0
|
|
|
|
thermo_style custom step temp epair emol etotal press density
|
|
thermo 50
|
|
|
|
variable temper_T world 275 280 285 290 295 300 305 310
|
|
variable rep world 0 1 2 3 4 5 6 7
|
|
fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
|
|
fix myfix all npt temp 290 ${temper_T} 100.0 iso 1 1 1000
|
|
fix myfix all npt temp 290 290 100.0 iso 1 1 1000
|
|
run 500
|
|
PPPM initialization ...
|
|
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
|
G vector (1/distance) = 0.268725
|
|
grid = 15 15 15
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.0228209
|
|
estimated relative force accuracy = 6.87243e-05
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 6776 1800
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 5 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 12
|
|
ghost atom cutoff = 12
|
|
binsize = 6, bins = 5 5 5
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/charmm/coul/long, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press Density
|
|
0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122
|
|
50 223.053 -7677.6519 1222.7567 -5123.1433 -23832.135 0.99549097
|
|
100 256.97829 -6970.9352 481.56411 -4955.0662 12716.194 1.0112202
|
|
150 278.44824 -6890.5623 472.60764 -4755.4621 6994.6533 1.0198648
|
|
200 271.15638 -7198.8095 1073.0275 -4506.826 -17647.735 1.020128
|
|
250 271.19291 -6398.4699 477.07511 -4302.2206 23076.406 1.0123626
|
|
300 295.5039 -6953.4923 1007.5309 -4181.6369 -15039.211 1.0007168
|
|
350 297.29537 -6594.1646 707.50773 -4111.6362 1990.9893 0.99116796
|
|
400 294.93533 -6450.921 630.83559 -4059.1555 6431.7427 0.98805162
|
|
450 295.23265 -6781.3296 1002.9096 -4015.715 -12070.145 0.98722232
|
|
500 284.70036 -6389.6524 668.83647 -4020.9946 10958.208 0.98502274
|
|
Loop time of 11.0942 on 2 procs for 500 steps with 2004 atoms
|
|
|
|
Performance: 7.788 ns/day, 3.082 hours/ns, 45.069 timesteps/s
|
|
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 7.7626 | 7.8378 | 7.913 | 2.7 | 70.65
|
|
Bond | 0.086271 | 0.08859 | 0.090909 | 0.8 | 0.80
|
|
Kspace | 1.1309 | 1.2146 | 1.2982 | 7.6 | 10.95
|
|
Neigh | 1.2958 | 1.2978 | 1.2999 | 0.2 | 11.70
|
|
Comm | 0.24052 | 0.24249 | 0.24445 | 0.4 | 2.19
|
|
Output | 0.00055242 | 0.00056267 | 0.00057292 | 0.0 | 0.01
|
|
Modify | 0.35597 | 0.3786 | 0.40124 | 3.7 | 3.41
|
|
Other | | 0.03375 | | | 0.30
|
|
|
|
Nlocal: 1002 ave 1015 max 989 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Nghost: 8686.5 ave 8717 max 8656 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Neighs: 354166 ave 365049 max 343283 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 708332
|
|
Ave neighs/atom = 353.459
|
|
Ave special neighs/atom = 2.34032
|
|
Neighbor list builds = 52
|
|
Dangerous builds = 0
|
|
temper/npt 2000 100 ${temper_T} myfix 0 58728 1
|
|
temper/npt 2000 100 290 myfix 0 58728 1
|
|
PPPM initialization ...
|
|
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
|
G vector (1/distance) = 0.268731
|
|
grid = 15 15 15
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.0228157
|
|
estimated relative force accuracy = 6.87089e-05
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 6776 1800
|
|
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press Density
|
|
500 284.70036 -6389.6523 668.83647 -4020.9946 10958.208 0.98502274
|
|
550 290.90514 -6715.0579 911.30009 -4066.8904 -6474.803 0.98383517
|
|
600 283.07652 -6555.4875 766.62589 -4098.7355 261.44315 0.98334866
|
|
650 293.39943 -6543.5525 727.38701 -4064.4058 5298.0746 0.98688936
|
|
700 295.77284 -6702.0803 912.68434 -4023.4658 -6806.6079 0.98957885
|
|
750 302.19503 -6545.9025 745.53299 -3996.0952 4624.9549 0.9931176
|
|
800 292.89947 -6664.6734 861.73293 -4054.1658 -1569.2753 0.99667377
|
|
850 288.96376 -6637.9753 841.33585 -4071.3632 -864.6336 1.0003373
|
|
900 291.22538 -6602.7272 806.80566 -4057.1422 2231.0477 1.0028411
|
|
950 290.78982 -6720.7893 893.26995 -4091.3406 -3898.6743 1.0021058
|
|
1000 285.74827 -6640.6252 810.15614 -4124.3911 558.53066 1.0051325
|
|
1050 288.3183 -6717.0357 867.9383 -4127.675 355.99916 1.0122228
|
|
1100 291.39421 -6746.7014 879.64717 -4127.2669 -736.99584 1.011619
|
|
1150 290.47863 -6710.1637 836.85441 -4138.9885 1105.9666 1.0069336
|
|
1200 288.94451 -6726.3595 867.56238 -4133.6359 -901.95525 1.0026837
|
|
1250 290.75557 -6716.8398 867.19843 -4113.6671 1376.8368 1.0000807
|
|
1300 289.52654 -6715.6758 904.46364 -4082.5758 -1400.2433 0.99935875
|
|
1350 292.30663 -6661.0526 904.32661 -4011.491 196.73374 0.99704618
|
|
1400 301.41479 -6661.807 880.88881 -3981.3023 1079.6673 0.99635503
|
|
1450 301.10415 -6704.7089 950.31941 -3956.6283 -1083.4574 0.99740883
|
|
1500 303.52341 -6687.1744 886.70817 -3988.2608 901.20455 0.99756877
|
|
1550 290.70908 -6738.4941 931.37971 -4071.4177 -56.269366 0.99843015
|
|
1600 289.8778 -6709.348 888.89193 -4089.7225 506.51952 1.0003118
|
|
1650 288.12183 -6724.4008 896.24971 -4107.9017 -1229.6117 1.004563
|
|
1700 297.81604 -6743.9356 906.62851 -4059.1778 1032.1913 1.0116813
|
|
1750 304.22415 -6761.8681 932.14203 -4013.3368 1825.359 1.015764
|
|
1800 286.62853 -6698.3527 911.17615 -4075.843 -1160.6136 1.0169905
|
|
1850 292.7719 -6787.8009 918.61838 -4121.1696 1455.4151 1.0203418
|
|
1900 290.87293 -6806.1448 960.43892 -4109.0309 -829.39096 1.022593
|
|
1950 304.5232 -6848.8518 954.93165 -4075.7453 915.93096 1.0221703
|
|
2000 286.15289 -6721.328 941.83273 -4071.0015 194.2717 1.0167052
|
|
2050 305.2696 -6720.8244 968.69939 -3929.4938 -1154.2389 1.0114409
|
|
2100 298.14935 -6678.8136 975.17824 -3923.516 794.1643 1.0070072
|
|
2150 301.51333 -6734.6863 950.33572 -3984.1464 -537.44292 1.0048337
|
|
2200 298.25074 -6736.277 945.4083 -4010.144 211.60185 1.0060101
|
|
2250 297.20864 -6820.7924 941.75394 -4104.5356 772.05119 1.0087884
|
|
2300 286.08552 -6853.0967 990.41746 -4154.5877 -760.47968 1.0110651
|
|
2350 295.49972 -6888.1433 937.27703 -4186.5667 966.37988 1.0150101
|
|
2400 289.60528 -6888.0768 967.74071 -4191.2297 1140.8847 1.0176507
|
|
2450 290.7003 -6906.443 998.89141 -4171.9073 -363.47638 1.0151765
|
|
2500 291.05855 -6817.2894 972.06896 -4107.4372 415.89846 1.0117849
|
|
Loop time of 46.7412 on 2 procs for 2000 steps with 2004 atoms
|
|
|
|
Performance: 7.394 ns/day, 3.246 hours/ns, 42.789 timesteps/s
|
|
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 31.884 | 32.272 | 32.659 | 6.8 | 69.04
|
|
Bond | 0.34239 | 0.35991 | 0.37742 | 2.9 | 0.77
|
|
Kspace | 4.6486 | 5.0781 | 5.5076 | 19.1 | 10.86
|
|
Neigh | 5.1657 | 5.1742 | 5.1828 | 0.4 | 11.07
|
|
Comm | 0.96743 | 0.96831 | 0.96918 | 0.1 | 2.07
|
|
Output | 0.0021966 | 0.0022568 | 0.002317 | 0.1 | 0.00
|
|
Modify | 1.4428 | 1.5251 | 1.6074 | 6.7 | 3.26
|
|
Other | | 1.362 | | | 2.91
|
|
|
|
Nlocal: 1002 ave 1004 max 1000 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Nghost: 8824 ave 8848 max 8800 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Neighs: 363564 ave 364653 max 362474 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 727127
|
|
Ave neighs/atom = 362.838
|
|
Ave special neighs/atom = 2.34032
|
|
Neighbor list builds = 201
|
|
Dangerous builds = 0
|
|
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
|
19 = # of size 2 clusters
|
|
6 = # of size 3 clusters
|
|
3 = # of size 4 clusters
|
|
640 = # of frozen angles
|
|
group peptide type <= 12
|
|
84 atoms in group peptide
|
|
Total wall time: 0:00:58
|