f07719e924
- move example folder to examples/USER/misc/ - comment out writing of trajectory files - reduce run length (for easier testing for regressions) - record example outputs for 1 and 4 MPI processes - rename readme.md to README.md for visibility
142 lines
5.8 KiB
Groff
142 lines
5.8 KiB
Groff
LAMMPS (22 Sep 2017)
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using 1 OpenMP thread(s) per MPI task
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units lj
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dimension 3
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boundary p p p
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atom_style atomic
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# truncated and shifted LJ potential
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pair_style lj/cut 2.5
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pair_modify shift yes
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# fcc lattice
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lattice fcc 0.9731
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Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
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region my_box block 0 8.0 0 8.0 0 20.0
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create_box 1 my_box
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Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
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1 by 1 by 4 MPI processor grid
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region particles block 0 8.0 0 8.0 0 20.0
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create_atoms 1 region particles
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Created 5120 atoms
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pair_coeff 1 1 1.0 1.0 2.5
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mass 1 1.0
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change_box all z final 0.0 34 remap units box
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orthogonal box = (0 0 0) to (12.8152 12.8152 34)
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# select particles in one side of the elongated box
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region left plane 0 0 10 0 0 1
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group left region left
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2688 atoms in group left
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velocity left create 6.0 1 mom yes rot yes
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# simulation parameters
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neighbor 0.6 bin
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timestep 0.004
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run_style verlet
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fix ensemble left nve # Note: only move particle in left-hand side
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fix langevin left langevin 3.0 0.8 100.0 2017
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# outout
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thermo_style custom step temp pzz pe lz
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thermo 100
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# dump dumpXYZ all xyz 100 traj.xyz
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# run reduced for demonstration purposes
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# run 10000
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run 5000
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.1
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ghost atom cutoff = 3.1
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binsize = 1.55, bins = 9 9 22
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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) = 3.23 | 3.23 | 3.23 Mbytes
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Step Temp Pzz PotEng Lz
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0 3.1494433 -3.4735106 -6.8707307 34
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100 1.7914373 6.4805818 -4.8420353 34
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200 1.740256 6.6108149 -4.7672571 34
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300 1.7663827 6.5188941 -4.8103672 34
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400 1.7440644 6.5156543 -4.7769467 34
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500 1.7471724 6.5208992 -4.7843928 34
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600 1.7320106 6.6557835 -4.7654637 34
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700 1.6839043 6.7689759 -4.7045352 34
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800 1.7216746 6.66436 -4.7601673 34
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900 1.7342542 6.3242367 -4.7790803 34
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1000 1.7338566 6.5803438 -4.7854529 34
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1100 1.7328856 6.3846366 -4.7902625 34
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1200 1.7546906 6.5048137 -4.8213443 34
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1300 1.7163891 6.3903221 -4.7665145 34
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1400 1.7011627 6.5782672 -4.7517875 34
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1500 1.7105234 6.5811813 -4.7677748 34
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1600 1.7334403 6.5032837 -4.8067749 34
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1700 1.7252102 6.5443871 -4.8058994 34
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1800 1.721958 6.3378188 -4.8150073 34
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1900 1.6797892 6.6780506 -4.7538618 34
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2000 1.7001774 6.3578192 -4.7894018 34
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2100 1.7127784 6.3219105 -4.8161059 34
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2200 1.696825 6.536793 -4.7946902 34
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2300 1.6704578 6.7186933 -4.7609628 34
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2400 1.6772498 6.3432817 -4.7778471 34
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2500 1.7073862 6.2153226 -4.8299181 34
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2600 1.6951557 6.4397257 -4.8156787 34
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2700 1.6845984 6.0123544 -4.8136864 34
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2800 1.6550565 6.2489392 -4.7829639 34
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2900 1.6892315 6.158499 -4.8423004 34
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3000 1.6814436 6.07976 -4.8400696 34
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3100 1.6387025 6.330166 -4.7878978 34
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3200 1.6747855 6.0767043 -4.8481995 34
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3300 1.6508768 6.2749233 -4.8181888 34
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3400 1.6426364 6.3934935 -4.8223824 34
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3500 1.6576512 6.0638185 -4.8559078 34
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3600 1.6444173 6.1376573 -4.8463113 34
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3700 1.6480039 5.9943705 -4.8601776 34
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3800 1.6467212 6.0556591 -4.8722719 34
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3900 1.6271804 6.116738 -4.8547278 34
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4000 1.6158134 5.9089534 -4.8477829 34
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4100 1.6388157 5.9890465 -4.8920284 34
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4200 1.6182368 6.0639887 -4.8724963 34
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4300 1.647633 5.6333906 -4.9267536 34
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4400 1.5856411 6.2675475 -4.8471239 34
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4500 1.5773417 6.1789163 -4.8469057 34
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4600 1.6181445 5.7988068 -4.922419 34
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4700 1.5876712 5.7398111 -4.8853849 34
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4800 1.5708353 6.2204997 -4.8718872 34
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4900 1.5514708 5.9782256 -4.8523812 34
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5000 1.553347 5.9286523 -4.86582 34
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Loop time of 8.10259 on 4 procs for 5000 steps with 5120 atoms
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Performance: 213265.164 tau/day, 617.087 timesteps/s
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99.2% 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 | 5.2964 | 5.6236 | 5.8982 | 9.0 | 69.40
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Neigh | 1.0562 | 1.1907 | 1.3257 | 8.7 | 14.70
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Comm | 0.43963 | 0.98786 | 1.5968 | 42.5 | 12.19
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Output | 0.0023124 | 0.004741 | 0.0090873 | 4.0 | 0.06
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Modify | 0.018652 | 0.22213 | 0.39884 | 36.4 | 2.74
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Other | | 0.07357 | | | 0.91
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Nlocal: 1280 ave 1337 max 1211 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 3416.25 ave 3549 max 3297 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Neighs: 74269.8 ave 77932 max 69612 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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Total # of neighbors = 297079
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Ave neighs/atom = 58.0232
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Neighbor list builds = 474
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Dangerous builds = 247
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write_data data.halfhalf
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Total wall time: 0:00:08
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