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add new grid-based examples

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Steve Plimpton
2022-12-01 15:51:17 -07:00
parent 7ce4b2eb68
commit 1ba9ff7817
18 changed files with 32938 additions and 36 deletions
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examples/grid/log.1Dec22.grid.2d.g++.4 Normal file
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LAMMPS (3 Nov 2022)
WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
# 2d Lennard-Jones melt
units lj
atom_style atomic
dimension 2
lattice sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region box block 0 50 0 50 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 2500 atoms
using lattice units in orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678)
create_atoms CPU = 0.000 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
fix 2 all enforce2d
# load balancing
comm_style tiled
fix 100 all balance 100 0.9 rcb
# fix ave/grid
fix ave all ave/grid 10 10 100 10 10 1 vx vy
# dump grid
compute ave all property/grid 10 10 1 id ix iy
#dump ave all grid 100 tmp.dump.2d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
#dump_modify ave sort 1
#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count
#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2]
#dump 10 all image 100 tmp.image.*.2d.png type type # zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 # subbox yes 0.01
# run
thermo 100
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 20 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 51 51 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.555 | 2.556 | 2.557 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 -0.99804687 0 0.44137712 -0.58692863 5000
100 1.5598149 -1.1263538 0 0.43283708 1.5290994 5000
200 1.6032951 -1.1706712 0 0.43198254 1.3417115 5000
300 1.6027535 -1.1702899 0 0.43182248 1.3590294 5000
400 1.6099053 -1.1774853 0 0.43177606 1.3305193 5000
500 1.6163874 -1.184699 0 0.43104185 1.346977 5000
Loop time of 0.031365 on 4 procs for 500 steps with 2500 atoms
Performance: 6886659.462 tau/day, 15941.341 timesteps/s, 39.853 Matom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0098202 | 0.01197 | 0.018294 | 3.3 | 38.16
Neigh | 0.0023502 | 0.0025479 | 0.0030895 | 0.6 | 8.12
Comm | 0.0046956 | 0.012744 | 0.015481 | 4.1 | 40.63
Output | 5.6153e-05 | 6.3163e-05 | 7.3849e-05 | 0.0 | 0.20
Modify | 0.0032687 | 0.0036046 | 0.0046066 | 1.0 | 11.49
Other | | 0.0004358 | | | 1.39
Nlocal: 625 ave 627 max 623 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 212 ave 216 max 207 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 3621.75 ave 3673 max 3585 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 14487
Ave neighs/atom = 5.7948
Neighbor list builds = 25
Dangerous builds not checked
Total wall time: 0:00:00