forked from lijiext/lammps
402 lines
18 KiB
Groff
402 lines
18 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# This script reproduces stress trajectories from Fig. 1 in
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# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
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#
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# Three thermostatting scenarios are visited: undamped (nodrag),
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# damped (drag) and Nose-Hoover chain (nhchains).
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#
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# The axial and shear stress trajectories are printed to the
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# file "stress_vs_t.dat". For the damped case, the original figure
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# seems to be a plot of 2*tau, rather than tau.
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#
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# The script also demonstrates how to
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# orient a crystal along <110>,
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# and how to use the lj/cubic pair style.
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units lj
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boundary p p p
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atom_style atomic
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# Set up FCC lattice with z axis along <110>
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lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
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Lattice spacing in x,y,z = 1.41421 2 2
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region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
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create_box 1 mycell
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Created orthogonal box = (0 0 0) to (7.07107 10 10)
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1 by 2 by 2 MPI processor grid
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mass * 1.0
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create_atoms 1 box
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Created 1000 atoms
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Time spent = 0.0003438 secs
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# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
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pair_style lj/cubic
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pair_coeff * * 1.0 0.8908987
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# Relax box dimensions
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fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
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thermo 100
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thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
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min_modify line quadratic
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minimize 0.0 1.0e-6 10000 100000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.84754
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ghost atom cutoff = 1.84754
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binsize = 0.923769, bins = 8 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, 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) = 4.211 | 4.211 | 4.211 Mbytes
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Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
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0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
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100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
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134 0 -6.3344257 -6.3344257 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199
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Loop time of 0.0269771 on 4 procs for 134 steps with 1000 atoms
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94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = force tolerance
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Energy initial, next-to-last, final =
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-6.2937539309 -6.33442568056 -6.33442568056
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Force two-norm initial, final = 3395.29 5.80609e-10
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Force max component initial, final = 1960.27 3.41627e-10
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Final line search alpha, max atom move = 1 3.41627e-10
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Iterations, force evaluations = 134 137
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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 | 0.011534 | 0.013897 | 0.016008 | 1.3 | 51.51
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Neigh | 0.00024176 | 0.00029498 | 0.00035191 | 0.0 | 1.09
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Comm | 0.0029764 | 0.0050126 | 0.0073018 | 2.2 | 18.58
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Output | 1.8835e-05 | 1.9968e-05 | 2.2888e-05 | 0.0 | 0.07
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.007753 | | | 28.74
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Nlocal: 250 ave 305 max 205 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Nghost: 829 ave 874 max 774 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 5250 ave 6445 max 4305 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 21000
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Ave neighs/atom = 21
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Neighbor list builds = 1
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Dangerous builds = 0
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# Define initial velocity
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velocity all create 0.01 87287 mom yes rot yes dist gaussian
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write_restart restart.equil
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# Start Run #1
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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restoring atom style atomic from restart
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orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
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1 by 2 by 2 MPI processor grid
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restoring pair style lj/cubic from restart
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1000 atoms
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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reset_timestep 0
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# Pzz = 40.0, drag/damping term off
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fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
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# Specify reference state from paper, times 1000 atoms
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Add fix energy to output etotal
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fix_modify myhug energy yes
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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variable us equal f_myhug[2] # shock velocity [distance/time]
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variable up equal f_myhug[3] # particle velocity [distance/time]
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variable pzz equal pzz # axial stress
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variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
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#dump id all atom 500 dump.hugoniostat
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#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.74754
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ghost atom cutoff = 1.74754
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binsize = 0.873769, bins = 8 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, 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) = 2.717 | 2.809 | 3.086 Mbytes
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Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
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1000 0.010586668 0.015864122 -2.1721826 -6.3380886 129.03334 58.456626 8.3141284 -4.1817701 0.93542408 23.507246 3.7366154
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2000 0.3321368 0.49770699 -5.584787 -6.0546694 12.097343 1.2026972 9.4615963 -0.96758935 -0.3571439 13.858218 0.5942385
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3000 0.46981685 0.70402055 -3.9208474 -6.3911005 63.005989 22.559106 8.6828663 -3.1742737 -0.16958917 18.776521 2.2842567
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4000 0.54866493 0.82217439 -4.1703408 -6.2427645 38.408608 4.9066022 8.6573289 -2.894598 -0.45434132 14.506935 1.8023166
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5000 0.30625495 0.45892304 -4.7355785 -6.186448 35.000599 6.2097986 8.6658098 -1.9097925 -0.19603125 13.896448 1.7145489
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6000 0.13938196 0.20886386 -4.303964 -5.7629121 50.370681 12.189231 8.3966581 -1.6678119 0.11451271 15.088809 2.2724852
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7000 0.055349516 0.082941249 -5.2031342 -6.8043199 30.859256 6.5562297 8.6850282 -1.684127 0.020586458 13.152479 1.5971879
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8000 0.027926794 0.0418483 -4.5281656 -5.4484008 48.145681 12.229919 8.4107051 -0.96208352 0.19922201 14.821877 2.2112219
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9000 0.018195086 0.027265336 -4.9847444 -6.5712684 37.347655 8.7291385 8.5606968 -1.6137894 0.10912534 13.773573 1.8458438
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10000 0.0082893467 0.012421586 -5.0130076 -6.6821423 36.46118 8.3386716 8.5689995 -1.6815563 0.1065388 13.651975 1.8180818
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Loop time of 2.01177 on 4 procs for 10000 steps with 1000 atoms
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Performance: 429472.539 tau/day, 4970.747 timesteps/s
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98.1% 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 | 1.2437 | 1.2651 | 1.2843 | 1.7 | 62.89
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Neigh | 0.051696 | 0.052503 | 0.053247 | 0.3 | 2.61
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Comm | 0.24826 | 0.26724 | 0.28867 | 3.5 | 13.28
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Output | 0.00058603 | 0.00085759 | 0.0016623 | 0.0 | 0.04
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Modify | 0.37363 | 0.37671 | 0.38189 | 0.5 | 18.73
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Other | | 0.04935 | | | 2.45
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Nlocal: 250 ave 260 max 240 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 927.5 ave 934 max 921 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 5048.5 ave 5203 max 4889 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Total # of neighbors = 20194
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Ave neighs/atom = 20.194
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Neighbor list builds = 175
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Dangerous builds = 0
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# Start Run #2
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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restoring atom style atomic from restart
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orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
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1 by 2 by 2 MPI processor grid
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restoring pair style lj/cubic from restart
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1000 atoms
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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reset_timestep 0
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# Pzz = 40.0, drag/damping term on
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fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
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# Specify reference state from paper, times 1000 atoms
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Add fix energy to output etotal
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fix_modify myhug energy yes
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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variable us equal f_myhug[2] # shock velocity [distance/time]
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variable up equal f_myhug[3] # particle velocity [distance/time]
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variable pzz equal pzz # axial stress
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variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.74754
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ghost atom cutoff = 1.74754
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binsize = 0.873769, bins = 8 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, 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) = 2.717 | 2.809 | 3.086 Mbytes
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Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
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1000 0.0063089138 0.0094539073 -5.9892326 -7.6448129 18.914956 7.5823222 9.2337797 -1.6650342 0.023426454 13.975434 0.92133642
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2000 0.0068813683 0.01031173 -5.4566765 -7.9789037 37.064192 15.537213 8.9495783 -2.5325388 0.10234565 16.32485 1.5455517
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3000 0.0072427316 0.010853233 -5.3662818 -7.9940958 39.906002 16.80569 8.9154322 -2.6386672 0.11821344 16.638326 1.6327015
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4000 0.0070936522 0.010629838 -5.3626164 -8.0025859 40.007994 16.850321 8.9143648 -2.6505993 0.11869226 16.650416 1.6356859
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5000 0.0074091958 0.01110268 -5.3628943 -8.0110325 39.998199 16.845204 8.9144816 -2.6592409 0.11846422 16.649379 1.6353872
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6000 0.0077388573 0.011596678 -5.3629264 -8.0194804 39.995216 16.842807 8.9145056 -2.6681507 0.11826582 16.648964 1.635306
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7000 0.0076023298 0.011392091 -5.3621083 -8.0277598 39.998343 16.839762 8.9144789 -2.6770435 0.11810824 16.649386 1.6353924
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8000 0.007691692 0.011526001 -5.361706 -8.0360632 40.000701 16.839078 8.9144843 -2.6858833 0.11795313 16.649923 1.6354361
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9000 0.0082153298 0.012310672 -5.3620899 -8.0446091 40.006134 16.845865 8.914544 -2.6948299 0.11785259 16.651566 1.6354969
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10000 0.0088368792 0.013242063 -5.3625357 -8.0530825 39.989575 16.835079 8.914577 -2.7037888 0.1174907 16.648402 1.6351306
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Loop time of 1.80214 on 4 procs for 10000 steps with 1000 atoms
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Performance: 479429.980 tau/day, 5548.958 timesteps/s
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98.4% 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 | 1.1353 | 1.1591 | 1.1787 | 1.5 | 64.32
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Neigh | 0.0028975 | 0.0029137 | 0.0029218 | 0.0 | 0.16
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Comm | 0.20882 | 0.22752 | 0.25213 | 3.4 | 12.62
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Output | 0.00058103 | 0.0007953 | 0.0014329 | 0.0 | 0.04
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Modify | 0.36598 | 0.36908 | 0.37078 | 0.3 | 20.48
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Other | | 0.04277 | | | 2.37
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Nlocal: 250 ave 258 max 239 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Nghost: 829 ave 840 max 821 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Neighs: 5250 ave 5360 max 5090 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Total # of neighbors = 21000
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Ave neighs/atom = 21
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Neighbor list builds = 10
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Dangerous builds = 0
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# Start Run #3
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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restoring atom style atomic from restart
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orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421)
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1 by 2 by 2 MPI processor grid
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restoring pair style lj/cubic from restart
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1000 atoms
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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reset_timestep 0
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# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
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fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
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# Specify reference state from paper, times 1000 atoms
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fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
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# Add fix energy to output etotal
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fix_modify myhug energy yes
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# Define output
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variable dele equal f_myhug[1] # energy delta [temperature]
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variable us equal f_myhug[2] # shock velocity [distance/time]
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variable up equal f_myhug[3] # particle velocity [distance/time]
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variable pzz equal pzz # axial stress
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variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
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variable time equal dt*step
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thermo 1000
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thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
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fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.74754
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ghost atom cutoff = 1.74754
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binsize = 0.873769, bins = 8 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, 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) = 2.717 | 2.809 | 3.086 Mbytes
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Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135
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1000 0.0078345827 0.011740122 -5.501714 -6.3232649 35.616592 14.888101 8.9677603 -0.833291 0.093891974 16.160626 1.5002802
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2000 0.019260469 0.028861813 -5.2936047 -6.2784351 41.771445 17.563018 8.895899 -1.0136922 0.11811779 16.853929 1.687161
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3000 0.048111305 0.072094791 -5.3454082 -6.2447367 39.061491 16.137184 8.932261 -0.97142325 0.073850675 16.606004 1.6012602
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4000 0.11854629 0.17764161 -5.2071426 -6.3210422 40.843054 16.426156 8.9202992 -1.2915412 0.017621345 16.874925 1.6476105
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5000 0.13634167 0.204308 -5.2645153 -6.3135608 39.098316 15.628006 8.9407716 -1.2533534 -0.00067532215 16.688495 1.5948471
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6000 0.14222646 0.21312635 -5.1774703 -6.3289809 40.888616 16.260775 8.9214855 -1.3646369 -0.0041713956 16.89472 1.6475159
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|
7000 0.12683662 0.19006468 -5.2679846 -6.2838171 39.084233 15.633883 8.939337 -1.2058972 0.0057260888 16.672835 1.5957701
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8000 0.14531516 0.21775476 -5.1737923 -6.3237483 40.861161 16.191124 8.9199968 -1.3677107 -0.0065481979 16.876021 1.6482339
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9000 0.12123357 0.18166851 -5.2546748 -6.2570254 39.276123 15.677988 8.9363522 -1.1840191 0.0075191856 16.687414 1.6022039
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10000 0.14771416 0.22134967 -5.1833988 -6.3104954 40.578265 16.080163 8.9245634 -1.3484463 -0.0098090911 16.857414 1.6386293
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Loop time of 1.8702 on 4 procs for 10000 steps with 1000 atoms
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Performance: 461983.152 tau/day, 5347.027 timesteps/s
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98.4% 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 | 1.1723 | 1.1812 | 1.1956 | 0.9 | 63.16
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Neigh | 0.028221 | 0.030409 | 0.035555 | 1.7 | 1.63
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Comm | 0.22963 | 0.24139 | 0.25155 | 1.6 | 12.91
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Output | 0.00055218 | 0.00077897 | 0.0014515 | 0.0 | 0.04
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Modify | 0.37165 | 0.37241 | 0.3732 | 0.1 | 19.91
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|
Other | | 0.04404 | | | 2.35
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Nlocal: 250 ave 257 max 244 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Nghost: 832.25 ave 840 max 822 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 5144.25 ave 5282 max 4949 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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Total # of neighbors = 20577
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Ave neighs/atom = 20.577
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Neighbor list builds = 95
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Dangerous builds = 0
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Total wall time: 0:00:05
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