forked from lijiext/lammps
104 lines
3.2 KiB
Groff
104 lines
3.2 KiB
Groff
LAMMPS (11 May 2018)
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# simple sucrose model with LATTE
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units metal
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atom_style full
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atom_modify sort 0 0.0 # turn off sorting of the coordinates
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read_data data.sucrose
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orthogonal box = (0 0 0) to (17.203 18.009 21.643)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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45 atoms
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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# replicate system if requested
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variable x index 1
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variable y index 1
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variable z index 1
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variable nrep equal v_x*v_y*v_z
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if "${nrep} > 1" then "replicate $x $y $z"
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# initialize system
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velocity all create 0.0 87287 loop geom
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pair_style zero 1.0
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pair_coeff * *
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.00025
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fix 1 all nve
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fix 2 all latte NULL
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fix_modify 2 energy yes
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thermo_style custom step temp pe etotal press
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# dynamics
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thermo 10
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run 100
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2
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ghost atom cutoff = 2
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binsize = 1, bins = 18 19 22
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair zero, 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) = 0.5064 | 0.5064 | 0.5064 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -251.26617 -251.26617 16.617234
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10 0.025263709 -251.26631 -251.26617 8.0576708
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20 0.034232467 -251.26636 -251.26617 1.6673442
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30 0.059079556 -251.2665 -251.26617 11.058458
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40 0.055499766 -251.26648 -251.26617 14.837775
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50 0.058499509 -251.2665 -251.26617 6.7183113
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60 0.071094535 -251.26657 -251.26617 6.6133687
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70 0.084309439 -251.26665 -251.26617 12.372721
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80 0.1089929 -251.26679 -251.26617 8.8355516
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90 0.11378257 -251.26681 -251.26617 5.1177922
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100 0.13003966 -251.26691 -251.26617 8.2431185
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Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms
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Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s
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1799.6% CPU use with 1 MPI tasks x no 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 | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.00
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Bond | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00016689 | 0.00016689 | 0.00016689 | 0.0 | 0.00
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Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00
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Modify | 27.837 | 27.837 | 27.837 | 0.0 |100.00
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Other | | 0.0005403 | | | 0.00
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Nlocal: 45 ave 45 max 45 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 59 ave 59 max 59 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 59
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Ave neighs/atom = 1.31111
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:28
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