1LAMMPS (11 May 2018) 2# simple sucrose model with LATTE 3 4units metal 5atom_style full 6atom_modify sort 0 0.0 # turn off sorting of the coordinates 7 8read_data data.sucrose 9 orthogonal box = (0 0 0) to (17.203 18.009 21.643) 10 1 by 1 by 1 MPI processor grid 11 reading atoms ... 12 45 atoms 13 0 = max # of 1-2 neighbors 14 0 = max # of 1-3 neighbors 15 0 = max # of 1-4 neighbors 16 1 = max # of special neighbors 17 18# replicate system if requested 19 20variable x index 1 21variable y index 1 22variable z index 1 23 24variable nrep equal v_x*v_y*v_z 25if "${nrep} > 1" then "replicate $x $y $z" 26 27# initialize system 28 29velocity all create 0.0 87287 loop geom 30 31pair_style zero 1.0 32pair_coeff * * 33 34neighbor 1.0 bin 35neigh_modify every 1 delay 0 check yes 36 37timestep 0.00025 38 39fix 1 all nve 40 41fix 2 all latte NULL 42fix_modify 2 energy yes 43 44thermo_style custom step temp pe etotal press 45 46# dynamics 47 48thermo 10 49run 100 50Neighbor list info ... 51 update every 1 steps, delay 0 steps, check yes 52 max neighbors/atom: 2000, page size: 100000 53 master list distance cutoff = 2 54 ghost atom cutoff = 2 55 binsize = 1, bins = 18 19 22 56 1 neighbor lists, perpetual/occasional/extra = 1 0 0 57 (1) pair zero, perpetual 58 attributes: half, newton on 59 pair build: half/bin/newton 60 stencil: half/bin/3d/newton 61 bin: standard 62Per MPI rank memory allocation (min/avg/max) = 0.5064 | 0.5064 | 0.5064 Mbytes 63Step Temp PotEng TotEng Press 64 0 0 -251.26617 -251.26617 16.617234 65 10 0.025263709 -251.26631 -251.26617 8.0576708 66 20 0.034232467 -251.26636 -251.26617 1.6673442 67 30 0.059079556 -251.2665 -251.26617 11.058458 68 40 0.055499766 -251.26648 -251.26617 14.837775 69 50 0.058499509 -251.2665 -251.26617 6.7183113 70 60 0.071094535 -251.26657 -251.26617 6.6133687 71 70 0.084309439 -251.26665 -251.26617 12.372721 72 80 0.1089929 -251.26679 -251.26617 8.8355516 73 90 0.11378257 -251.26681 -251.26617 5.1177922 74 100 0.13003966 -251.26691 -251.26617 8.2431185 75Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms 76 77Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s 781799.6% CPU use with 1 MPI tasks x no OpenMP threads 79 80MPI task timing breakdown: 81Section | min time | avg time | max time |%varavg| %total 82--------------------------------------------------------------- 83Pair | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.00 84Bond | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00 85Neigh | 0 | 0 | 0 | 0.0 | 0.00 86Comm | 0.00016689 | 0.00016689 | 0.00016689 | 0.0 | 0.00 87Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 88Modify | 27.837 | 27.837 | 27.837 | 0.0 |100.00 89Other | | 0.0005403 | | | 0.00 90 91Nlocal: 45 ave 45 max 45 min 92Histogram: 1 0 0 0 0 0 0 0 0 0 93Nghost: 0 ave 0 max 0 min 94Histogram: 1 0 0 0 0 0 0 0 0 0 95Neighs: 59 ave 59 max 59 min 96Histogram: 1 0 0 0 0 0 0 0 0 0 97 98Total # of neighbors = 59 99Ave neighs/atom = 1.31111 100Ave special neighs/atom = 0 101Neighbor list builds = 0 102Dangerous builds = 0 103Total wall time: 0:00:28 104