400 lines
18 KiB
Groff
400 lines
18 KiB
Groff
LAMMPS (24 Dec 2020)
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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 = 1.4142135 2.0000000 2.0000000
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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 = (0.0000000 0.0000000 0.0000000) to (7.0710677 9.9999999 9.9999999)
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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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create_atoms CPU = 0.105 seconds
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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:188)
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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 = 1.8475372
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ghost atom cutoff = 1.8475372
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binsize = 0.92376862, 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 -6.2937536 -6.2937536 -2.7722424 -2.7722424 -2.7722424 7.0710677 9.9999999 9.9999999
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100 0 -6.3319014 -6.3319014 -0.75971257 -0.75971257 -0.75971257 7.0003571 9.8999999 9.8999999
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134 0 -6.3344253 -6.3344253 -4.303004e-13 -4.72443e-13 -4.7038971e-13 6.9780267 9.8684199 9.8684199
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Loop time of 0.38554 on 4 procs for 134 steps with 1000 atoms
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75.8% 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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-6.29375358358589 -6.33442531515435 -6.33442531515435
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Force two-norm initial, final = 3395.2895 5.5617370e-10
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Force max component initial, final = 1960.2713 3.2533415e-10
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Final line search alpha, max atom move = 1.0000000 3.2533415e-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 | 0.031873 | 0.042436 | 0.055233 | 4.3 | 11.01
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Neigh | 0.0004189 | 0.00049466 | 0.00058317 | 0.0 | 0.13
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Comm | 0.085755 | 0.095315 | 0.10484 | 2.7 | 24.72
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Output | 2.8372e-05 | 3.0637e-05 | 3.6955e-05 | 0.0 | 0.01
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.2473 | | | 64.13
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Nlocal: 250.000 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: 829.000 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: 5250.00 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 = 21.000000
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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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System init for write_restart ...
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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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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
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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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read_restart CPU = 0.006 seconds
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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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# 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 econserve 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 = 1.7475372
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ghost atom cutoff = 1.7475372
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binsize = 0.87376862, 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) = 3.086 | 3.086 | 3.086 Mbytes
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Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
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1000 0.010586669 0.015864123 -2.1721826 -4183.9265 129.03333 58.456619 8.3141284 -4.1817701 0.93542364 23.507245 3.7366151
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2000 0.33213628 0.49770621 -5.5847928 -972.65689 12.097176 1.2026574 9.4616027 -0.9675698 -0.35714344 13.85823 0.59422982
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3000 0.46981589 0.70401911 -3.9208694 -3177.4622 63.005615 22.559014 8.6828715 -3.1742453 -0.16959033 18.776506 2.284245
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4000 0.5486246 0.82211396 -4.170224 -2897.9717 38.4091 4.9062274 8.6573154 -2.8946236 -0.45434723 14.506949 1.8023381
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5000 0.30607733 0.45865688 -4.73528 -1914.3534 35.002193 6.2096608 8.6658138 -1.9100768 -0.19602135 13.896788 1.714585
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6000 0.13928238 0.20871465 -4.3038564 -1672.0118 50.372856 12.190245 8.3966652 -1.6679166 0.11455965 15.089171 2.2725288
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7000 0.055325106 0.082904671 -5.2030895 -1689.3101 30.859753 6.5561993 8.6850199 -1.6841899 0.020593532 13.15254 1.5972063
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8000 0.02793065 0.041854078 -4.5281755 -966.55101 48.144696 12.229149 8.4107035 -0.96206469 0.19920754 14.821718 2.2112004
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9000 0.018182543 0.02724654 -4.9847463 -1618.778 37.347471 8.7290944 8.5607031 -1.6138205 0.10912671 13.773572 1.8458347
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10000 0.0082850143 0.012415094 -5.0129769 -1686.404 36.462176 8.3390717 8.5689886 -1.6814034 0.10655037 13.652105 1.8181142
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Loop time of 22.212 on 4 procs for 10000 steps with 1000 atoms
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Performance: 38897.956 tau/day, 450.208 timesteps/s
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76.8% 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 | 3.4702 | 3.5904 | 3.684 | 4.4 | 16.16
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Neigh | 0.1001 | 0.10727 | 0.11784 | 2.0 | 0.48
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Comm | 5.1418 | 5.2862 | 5.3573 | 3.7 | 23.80
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Output | 0.083086 | 0.095493 | 0.11021 | 4.0 | 0.43
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Modify | 11.789 | 11.841 | 11.967 | 2.1 | 53.31
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Other | | 1.292 | | | 5.82
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Nlocal: 250.000 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: 927.500 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: 5049.00 ave 5203 max 4889 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 20196
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Ave neighs/atom = 20.196000
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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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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
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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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read_restart CPU = 0.001 seconds
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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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# 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 econserve 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 = 1.7475372
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ghost atom cutoff = 1.7475372
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binsize = 0.87376862, 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) = 3.086 | 3.086 | 3.086 Mbytes
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Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
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1000 0.0063089135 0.0094539069 -5.9892322 -1671.0142 18.914957 7.5823225 9.2337797 -1.6650344 0.02342632 13.975435 0.92133641
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2000 0.006881368 0.01031173 -5.4566762 -2537.9852 37.064191 15.537213 8.9495783 -2.5325389 0.1023455 16.32485 1.5455517
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3000 0.0072427308 0.010853232 -5.3662814 -2644.0227 39.906002 16.80569 8.9154322 -2.6386673 0.1182133 16.638326 1.6327015
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4000 0.0070936511 0.010629836 -5.362616 -2655.9513 40.007995 16.850321 8.9143648 -2.6505993 0.11869211 16.650416 1.6356858
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5000 0.0074091959 0.01110268 -5.3628939 -2664.5927 39.998199 16.845204 8.9144816 -2.6592409 0.11846407 16.649379 1.6353872
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6000 0.0077388568 0.011596677 -5.362926 -2673.502 39.995216 16.842807 8.9145056 -2.6681507 0.11826568 16.648964 1.635306
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7000 0.0076023299 0.011392091 -5.3621079 -2682.3942 39.998343 16.839762 8.9144789 -2.6770435 0.1181081 16.649386 1.6353924
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8000 0.0076916892 0.011525996 -5.3617056 -2691.2334 40.000701 16.839078 8.9144843 -2.6858832 0.11795298 16.649924 1.635436
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9000 0.0082153298 0.012310672 -5.3620895 -2700.1796 40.006134 16.845865 8.914544 -2.6948298 0.11785245 16.651566 1.6354968
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10000 0.0088368733 0.013242055 -5.3625353 -2709.138 39.989575 16.835079 8.914577 -2.7037887 0.11749055 16.648403 1.6351305
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Loop time of 19.325 on 4 procs for 10000 steps with 1000 atoms
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Performance: 44708.822 tau/day, 517.463 timesteps/s
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77.5% 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 | 3.3012 | 3.4003 | 3.584 | 5.9 | 17.60
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Neigh | 0.0047636 | 0.0054044 | 0.0072584 | 1.5 | 0.03
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Comm | 4.5282 | 4.5961 | 4.651 | 2.1 | 23.78
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Output | 0.00071692 | 0.0062424 | 0.0086811 | 4.1 | 0.03
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Modify | 10.133 | 10.215 | 10.287 | 1.7 | 52.86
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Other | | 1.102 | | | 5.70
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Nlocal: 250.000 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: 829.000 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: 5250.00 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 = 21.000000
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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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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.046520549 0.065789991 0.065789991) to (7.0245472 9.9342099 9.9342099)
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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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read_restart CPU = 0.001 seconds
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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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# 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 econserve 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 = 1.7475372
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ghost atom cutoff = 1.7475372
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binsize = 0.87376862, 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) = 3.086 | 3.086 | 3.086 Mbytes
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Step Temp KinEng E_pair Econserve Pzz v_tau Lz f_myhug v_dele v_us v_up
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0 0.01 0.014985 -6.3344253 -6.3194403 0.014347835 -0.00026463907 9.8684199 0 -0.0048552735 2.378672 0.0041061045
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1000 0.0078345757 0.011740112 -5.5017136 -838.78091 35.616593 14.888102 8.9677603 -0.83329094 0.093891841 16.160627 1.5002802
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2000 0.019260442 0.028861773 -5.2936038 -1018.9574 41.771461 17.563025 8.8958988 -1.0136927 0.11811776 16.853931 1.6871615
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3000 0.04811126 0.072094723 -5.3454068 -976.69826 39.061528 16.137201 8.9322605 -0.97142494 0.073850795 16.606008 1.6012612
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4000 0.11854637 0.17764173 -5.2071392 -1296.5766 40.843143 16.426195 8.9202981 -1.2915471 0.017621672 16.874934 1.6476132
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5000 0.13634185 0.20430827 -5.2645154 -1258.4101 39.098283 15.627986 8.9407719 -1.2533499 -0.00067591716 16.688492 1.5948462
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|
6000 0.14222512 0.21312434 -5.1774698 -1369.5986 40.888661 16.260803 8.9214848 -1.3646342 -0.0041700902 16.894723 1.6475174
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|
7000 0.12683772 0.19006633 -5.2679854 -1210.973 39.084165 15.633846 8.9393379 -1.2058951 0.00572464 16.672829 1.595768
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|
8000 0.14531337 0.21775209 -5.1737911 -1372.667 40.861256 16.19118 8.9199953 -1.367711 -0.0065459838 16.876028 1.648237
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|
9000 0.12123505 0.18167072 -5.2546764 -1189.0875 39.276006 15.677923 8.9363537 -1.1840145 0.0075170176 16.687402 1.6022003
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|
10000 0.1477113 0.22134539 -5.1833959 -1353.4057 40.578404 16.080238 8.9245614 -1.3484436 -0.0098061873 16.857426 1.6386338
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|
Loop time of 18.9651 on 4 procs for 10000 steps with 1000 atoms
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|
|
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Performance: 45557.373 tau/day, 527.284 timesteps/s
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77.1% 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 | 3.1152 | 3.3473 | 3.5591 | 10.0 | 17.65
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Neigh | 0.045731 | 0.056706 | 0.066921 | 3.7 | 0.30
|
|
Comm | 3.9563 | 4.1638 | 4.4413 | 9.7 | 21.96
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Output | 0.00067329 | 0.0033167 | 0.011241 | 7.9 | 0.02
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|
Modify | 10.321 | 10.425 | 10.482 | 2.0 | 54.97
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|
Other | | 0.9693 | | | 5.11
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Nlocal: 250.000 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: 832.250 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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|
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Total # of neighbors = 20577
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Ave neighs/atom = 20.577000
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|
Neighbor list builds = 95
|
|
Dangerous builds = 0
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|
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Total wall time: 0:01:01
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