forked from lijiext/lammps
update melt example to use velocity with loop geom for consistent velocities
This commit is contained in:
Axel Kohlmeyer
parent
97977e3e68
commit
b6b101f29a
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@ -9,7 +9,7 @@ create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 3.0 87287
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velocity all create 3.0 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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@ -1,85 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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Time spent = 0.00041604 secs
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mass 1 1.0
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velocity all create 3.0 87287
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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#dump id all atom 50 dump.melt
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#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 3
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#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3
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thermo 50
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run 250
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/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) = 2.705 | 2.705 | 2.705 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 -6.7733681 0 -2.2744931 -3.7033504
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50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
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100 1.6503357 -4.756014 0 -2.2811293 5.8050524
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150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
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200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
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250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
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Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms
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Performance: 483592.231 tau/day, 1119.426 timesteps/s
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97.3% CPU use with 4 MPI tasks x 1 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 | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05
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Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29
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Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47
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Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09
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Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72
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Other | | 0.00085 | | | 0.38
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Nlocal: 1000 ave 1010 max 982 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 2703.75 ave 2713 max 2689 min
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Histogram: 1 0 0 0 0 0 0 2 0 1
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Neighs: 37915.5 ave 39239 max 36193 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Total # of neighbors = 151662
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Ave neighs/atom = 37.9155
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Neighbor list builds = 12
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Dangerous builds not checked
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Total wall time: 0:00:00
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@ -1,4 +1,4 @@
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LAMMPS (27 Nov 2018)
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LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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@ -6,17 +6,17 @@ units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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Time spent = 0.000645638 secs
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create_atoms CPU = 0.002 seconds
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mass 1 1.0
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velocity all create 3.0 87287
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velocity all create 3.0 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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@ -48,38 +48,38 @@ Neighbor list info ...
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pair build: half/bin/atomonly/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) = 3.221 | 3.221 | 3.221 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 3.222 | 3.222 | 3.222 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 -6.7733681 0 -2.2744931 -3.7033504
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50 1.6758903 -4.7955425 0 -2.2823355 5.670064
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100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
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150 1.6324555 -4.7286791 0 -2.280608 5.9589514
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200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
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250 1.6275257 -4.7224992 0 -2.281821 5.9567365
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Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms
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50 1.6842865 -4.8082494 0 -2.2824513 5.5666131
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100 1.6712577 -4.7875609 0 -2.281301 5.6613913
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150 1.6444751 -4.7471034 0 -2.2810074 5.8614211
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200 1.6471542 -4.7509053 0 -2.2807916 5.8805431
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250 1.6645597 -4.7774327 0 -2.2812174 5.7526089
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Loop time of 1.61045 on 1 procs for 250 steps with 4000 atoms
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Performance: 147983.915 tau/day, 342.555 timesteps/s
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Performance: 67062.020 tau/day, 155.236 timesteps/s
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99.9% CPU use with 1 MPI tasks x 1 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 | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12
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Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63
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Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86
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Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02
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Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97
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Other | | 0.002878 | | | 0.39
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Pair | 1.3961 | 1.3961 | 1.3961 | 0.0 | 86.69
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Neigh | 0.13555 | 0.13555 | 0.13555 | 0.0 | 8.42
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Comm | 0.037732 | 0.037732 | 0.037732 | 0.0 | 2.34
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Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02
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Modify | 0.038016 | 0.038016 | 0.038016 | 0.0 | 2.36
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Other | | 0.002731 | | | 0.17
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Nlocal: 4000 ave 4000 max 4000 min
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Nlocal: 4000.00 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5499 ave 5499 max 5499 min
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Nghost: 5506.00 ave 5506 max 5506 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 151513 ave 151513 max 151513 min
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Neighs: 151788.0 ave 151788 max 151788 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 151513
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Ave neighs/atom = 37.8783
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Total # of neighbors = 151788
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Ave neighs/atom = 37.947000
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Neighbor list builds = 12
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Dangerous builds not checked
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Total wall time: 0:00:00
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Total wall time: 0:00:01
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@ -0,0 +1,85 @@
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LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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create_atoms CPU = 0.001 seconds
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mass 1 1.0
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velocity all create 3.0 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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#dump id all atom 50 dump.melt
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#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 3
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#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3
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thermo 50
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run 250
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/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) = 2.706 | 2.706 | 2.706 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 -6.7733681 0 -2.2744931 -3.7033504
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50 1.6842865 -4.8082494 0 -2.2824513 5.5666131
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100 1.6712577 -4.7875609 0 -2.281301 5.6613913
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150 1.6444751 -4.7471034 0 -2.2810074 5.8614211
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200 1.6471542 -4.7509053 0 -2.2807916 5.8805431
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250 1.6645597 -4.7774327 0 -2.2812174 5.7526089
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Loop time of 0.490832 on 4 procs for 250 steps with 4000 atoms
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Performance: 220034.754 tau/day, 509.340 timesteps/s
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96.7% CPU use with 4 MPI tasks x 1 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 | 0.35932 | 0.37256 | 0.38746 | 1.9 | 75.90
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Neigh | 0.035928 | 0.038449 | 0.042344 | 1.3 | 7.83
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Comm | 0.053452 | 0.068917 | 0.08485 | 5.3 | 14.04
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Output | 0.00015545 | 0.00023746 | 0.00047684 | 0.0 | 0.05
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Modify | 0.0096958 | 0.0097951 | 0.0098989 | 0.1 | 2.00
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Other | | 0.0008721 | | | 0.18
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Nlocal: 1000.00 ave 1008 max 987 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 2711.25 ave 2728 max 2693 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 37947.0 ave 38966 max 37338 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Total # of neighbors = 151788
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Ave neighs/atom = 37.947000
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Neighbor list builds = 12
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Dangerous builds not checked
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Total wall time: 0:00:00
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