forked from lijiext/lammps
161 lines
5.8 KiB
Groff
161 lines
5.8 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 2d LJ crack simulation
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dimension 2
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boundary s s p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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# create geometry
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lattice hex 0.93
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Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
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region box block 0 100 0 40 -0.25 0.25
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create_box 5 box
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Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 8141 atoms
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Time spent = 0.00064826 secs
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mass 1 1.0
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mass 2 1.0
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mass 3 1.0
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mass 4 1.0
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mass 5 1.0
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# LJ potentials
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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# define groups
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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302 atoms in group lower
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region 2 block INF INF 38.75 INF INF INF
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group upper region 2
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302 atoms in group upper
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group boundary union lower upper
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604 atoms in group boundary
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group mobile subtract all boundary
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7537 atoms in group mobile
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region leftupper block INF 20 20 INF INF INF
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region leftlower block INF 20 INF 20 INF INF
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group leftupper region leftupper
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841 atoms in group leftupper
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group leftlower region leftlower
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841 atoms in group leftlower
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set group leftupper type 2
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841 settings made for type
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set group leftlower type 3
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841 settings made for type
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set group lower type 4
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302 settings made for type
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set group upper type 5
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302 settings made for type
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# initial velocities
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compute new mobile temp
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velocity mobile create 0.01 887723 temp new
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velocity upper set 0.0 0.3 0.0
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velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
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# fixes
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fix 1 all nve
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fix 2 boundary setforce NULL 0.0 0.0
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# run
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timestep 0.003
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thermo 200
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thermo_modify temp new
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
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neigh_modify exclude type 2 3
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#dump 1 all atom 500 dump.crack
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#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
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#dump_modify 2 pad 4
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#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
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#dump_modify 3 pad 4
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run 5000
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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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 = 80 56 1
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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/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.069 | 3.069 | 3.069 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917
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200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331
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400 0.06054278 -3.2510706 0 -3.1950271 -0.42811733 8677.8288
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600 0.060576995 -3.246816 0 -3.1907408 -0.60017647 8717.6131
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800 0.060802753 -3.2413477 0 -3.1850635 -0.74499308 8756.4512
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1000 0.061812114 -3.2349942 0 -3.1777756 -0.87130079 8796.9575
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1200 0.06317147 -3.2277552 0 -3.1692783 -0.98010628 8823.1488
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1400 0.065125405 -3.2198031 0 -3.1595175 -1.0690179 8858.8358
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1600 0.06725411 -3.2111272 0 -3.148871 -1.1440993 8892.6607
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1800 0.069389572 -3.2019689 0 -3.137736 -1.199078 8933.7591
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2000 0.071276448 -3.1921621 0 -3.1261826 -1.239553 8969.0463
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2200 0.073243486 -3.1818809 0 -3.1140805 -1.264839 8997.6559
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2400 0.075063494 -3.1711703 0 -3.1016851 -1.2772278 9038.4932
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2600 0.076789207 -3.1600658 0 -3.0889832 -1.2754953 9073.4997
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2800 0.07875979 -3.1487143 0 -3.0758075 -1.2637926 9106.2245
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3000 0.080591853 -3.1372361 0 -3.0626334 -1.2388824 9142.7862
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3200 0.08227693 -3.125423 0 -3.0492605 -1.2055283 9169.4322
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3400 0.084289444 -3.1136554 0 -3.03563 -1.1672422 9204.8205
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3600 0.086720297 -3.1021183 0 -3.0218427 -1.126381 9233.2656
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3800 0.089264018 -3.0909262 0 -3.0082959 -1.0899774 9265.4143
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4000 0.091377688 -3.0795096 0 -2.9949227 -1.0580229 9297.6799
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4200 0.092665135 -3.0678736 0 -2.9820949 -1.0390124 9331.6135
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4400 0.09055434 -3.0560482 0 -2.9722234 -1.0323741 9362.2075
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4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949
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4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155
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5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031
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Loop time of 2.06204 on 4 procs for 5000 steps with 8141 atoms
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Performance: 628504.111 tau/day, 2424.784 timesteps/s
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97.8% 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 | 1.4844 | 1.5266 | 1.5909 | 3.6 | 74.03
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Neigh | 0.081047 | 0.085878 | 0.093027 | 1.5 | 4.16
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Comm | 0.12993 | 0.19571 | 0.25179 | 11.6 | 9.49
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Output | 0.00072265 | 0.00096798 | 0.0016601 | 0.0 | 0.05
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Modify | 0.16787 | 0.17024 | 0.17234 | 0.4 | 8.26
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Other | | 0.0826 | | | 4.01
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Nlocal: 2035.25 ave 2064 max 2015 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Nghost: 198 ave 248 max 150 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 17850 ave 18247 max 17601 min
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Histogram: 1 1 0 0 1 0 0 0 0 1
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Total # of neighbors = 71400
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Ave neighs/atom = 8.77042
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Neighbor list builds = 106
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Dangerous builds = 0
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Total wall time: 0:00:02
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