113 lines
3.9 KiB
Groff
113 lines
3.9 KiB
Groff
LAMMPS (3 Aug 2022)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# simple water model with LATTE
|
|
|
|
units metal
|
|
atom_style full
|
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
|
|
|
read_data data.water
|
|
Reading data file ...
|
|
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
24 atoms
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
0 = max # of 1-2 neighbors
|
|
0 = max # of 1-3 neighbors
|
|
0 = max # of 1-4 neighbors
|
|
1 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
read_data CPU = 0.001 seconds
|
|
|
|
# replicate system if requested
|
|
|
|
variable x index 1
|
|
variable y index 1
|
|
variable z index 1
|
|
|
|
variable nrep equal v_x*v_y*v_z
|
|
if "${nrep} > 1" then "replicate $x $y $z"
|
|
|
|
# initialize system
|
|
|
|
velocity all create 0.0 87287 loop geom
|
|
|
|
pair_style zero 1.0
|
|
pair_coeff * *
|
|
|
|
neighbor 1.0 bin
|
|
neigh_modify every 1 delay 0 check yes
|
|
|
|
timestep 0.00025
|
|
|
|
fix 1 all nve
|
|
|
|
fix 2 all latte
|
|
fix_modify 2 energy yes
|
|
|
|
thermo_style custom step temp pe etotal press
|
|
|
|
# dynamics
|
|
|
|
thermo 10
|
|
run 100
|
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 2
|
|
ghost atom cutoff = 2
|
|
binsize = 1, bins = 7 7 7
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair zero, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes
|
|
Step Temp PotEng TotEng Press
|
|
0 0 -104.95596 -104.95596 48235.442
|
|
10 336.53107 -105.96027 -104.95977 97996.851
|
|
20 529.06408 -106.53023 -104.95733 131519.85
|
|
30 753.62603 -107.19952 -104.959 49296.66
|
|
40 716.65648 -107.08803 -104.95742 28307.121
|
|
50 824.04392 -107.40823 -104.95836 102167.59
|
|
60 933.56146 -107.73479 -104.95933 92508.517
|
|
70 851.18489 -107.48767 -104.95711 13993.262
|
|
80 999.8028 -107.93147 -104.95907 36700.736
|
|
90 998.77488 -107.9257 -104.95636 107233.54
|
|
100 1281.4438 -108.76963 -104.95992 49702.386
|
|
Loop time of 3.14578 on 1 procs for 100 steps with 24 atoms
|
|
|
|
Performance: 0.687 ns/day, 34.953 hours/ns, 31.789 timesteps/s
|
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 3.0818e-05 | 3.0818e-05 | 3.0818e-05 | 0.0 | 0.00
|
|
Bond | 4.704e-06 | 4.704e-06 | 4.704e-06 | 0.0 | 0.00
|
|
Neigh | 1.8668e-05 | 1.8668e-05 | 1.8668e-05 | 0.0 | 0.00
|
|
Comm | 0.00010831 | 0.00010831 | 0.00010831 | 0.0 | 0.00
|
|
Output | 0.00021087 | 0.00021087 | 0.00021087 | 0.0 | 0.01
|
|
Modify | 3.1452 | 3.1452 | 3.1452 | 0.0 | 99.98
|
|
Other | | 0.0002339 | | | 0.01
|
|
|
|
Nlocal: 24 ave 24 max 24 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 77 ave 77 max 77 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 31 ave 31 max 31 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 31
|
|
Ave neighs/atom = 1.2916667
|
|
Ave special neighs/atom = 0
|
|
Neighbor list builds = 2
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:03
|