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 1 by 1 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 = 0.000465155 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) = 4.247 | 4.247 | 4.247 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 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13 6.9780266 9.8684199 9.8684199
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Loop time of 0.0724094 on 1 procs for 134 steps with 1000 atoms
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99.9% CPU use with 1 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 5.83329e-10
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Force max component initial, final = 1960.27 3.42093e-10
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Final line search alpha, max atom move = 1 3.42093e-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 | 0.054599 | 0.054599 | 0.054599 | 0.0 | 75.40
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Neigh | 0.0011106 | 0.0011106 | 0.0011106 | 0.0 | 1.53
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Comm | 0.002012 | 0.002012 | 0.002012 | 0.0 | 2.78
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Output | 1.955e-05 | 1.955e-05 | 1.955e-05 | 0.0 | 0.03
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.01467 | | | 20.26
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1724 ave 1724 max 1724 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 21000 ave 21000 max 21000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 1 by 1 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) = 2.771 | 2.771 | 2.771 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 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
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1000 0.0093381489 0.013993216 -2.170443 -6.3381216 129.15286 58.544417 8.3142516 -4.1816719 0.93744258 23.519053 3.7381989
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2000 0.24794909 0.37155171 -5.8915802 -6.0429087 8.3850692 1.3744507 9.5938765 -0.5228803 -0.2435043 13.910468 0.4103393
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3000 0.38920701 0.5832267 -3.768677 -6.6246124 72.742761 28.486747 8.623805 -3.439162 0.003825459 19.697379 2.5139668
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4000 0.67009971 1.0041444 -4.2080644 -6.1365367 35.596179 3.9344133 8.7508422 -2.9326167 -0.58039603 14.529822 1.6677129
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5000 0.41848975 0.62710689 -4.8393088 -6.1026724 30.626544 4.6387208 8.7827245 -1.8904705 -0.31996439 13.670884 1.5250343
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6000 0.22410139 0.33581594 -3.7652941 -6.0923259 50.807437 7.2229456 8.2549488 -2.6628477 -0.017396966 14.4806 2.3884652
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7000 0.095001485 0.14235972 -4.5436753 -6.7307217 35.8743 3.4938089 8.4476287 -2.3294061 -0.052272192 12.957528 1.8846881
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8000 0.043277437 0.064851239 -4.6264096 -6.2447456 39.658659 6.7266325 8.4327483 -1.6831873 0.070488482 13.553882 1.9918311
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9000 0.018271956 0.027380526 -4.4239627 -6.3085661 41.708324 5.9081923 8.3463321 -1.9119839 0.091057512 13.503882 2.1025305
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10000 0.0082840001 0.012413574 -4.622252 -6.3316699 39.830379 6.5596321 8.4109569 -1.7218314 0.099435465 13.482451 2.0110543
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Loop time of 6.20702 on 1 procs for 10000 steps with 1000 atoms
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Performance: 139197.321 tau/day, 1611.080 timesteps/s
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98.8% 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 | 5.0198 | 5.0198 | 5.0198 | 0.0 | 80.87
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Neigh | 0.21405 | 0.21405 | 0.21405 | 0.0 | 3.45
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Comm | 0.16164 | 0.16164 | 0.16164 | 0.0 | 2.60
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Output | 0.00053501 | 0.00053501 | 0.00053501 | 0.0 | 0.01
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Modify | 0.7419 | 0.7419 | 0.7419 | 0.0 | 11.95
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Other | | 0.06911 | | | 1.11
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1886 ave 1886 max 1886 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 20874 ave 20874 max 20874 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 20874
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Ave neighs/atom = 20.874
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Neighbor list builds = 188
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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 1 by 1 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) = 2.771 | 2.771 | 2.771 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 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
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1000 0.0062572991 0.0093765627 -5.9890874 -7.64465 18.918117 7.5844397 9.2338165 -1.6649392 0.02341947 13.976996 0.92138738
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2000 0.006845108 0.010257394 -5.4565813 -7.9786876 37.064254 15.537266 8.9496404 -2.5323637 0.1023062 16.325405 1.5455017
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3000 0.0073276109 0.010980425 -5.3663425 -7.9938818 39.907292 16.807488 8.9154852 -2.6385197 0.11818131 16.639049 1.6326833
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4000 0.0069296915 0.010384143 -5.3623404 -8.0023271 40.010741 16.851482 8.9144328 -2.6503708 0.11868152 16.651571 1.6356847
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5000 0.0076142476 0.01140995 -5.3631447 -8.0108329 39.997648 16.846756 8.9145416 -2.6590981 0.11841154 16.649778 1.6353255
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6000 0.0077053839 0.011546518 -5.3628542 -8.0192007 39.991597 16.840313 8.9145803 -2.6678931 0.11818376 16.648851 1.6351691
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7000 0.0077405662 0.011599239 -5.3623534 -8.0275624 40.000448 16.844008 8.9145774 -2.6768081 0.11809914 16.650669 1.6353525
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8000 0.008067359 0.012088937 -5.3623759 -8.0359471 39.995327 16.840134 8.9146099 -2.6856601 0.11787118 16.649881 1.6352204
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9000 0.0083223114 0.012470984 -5.3622992 -8.0443714 40.00571 16.847763 8.9146503 -2.6945431 0.11781538 16.652389 1.6353987
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10000 0.0091249143 0.013673684 -5.3630142 -8.0529573 39.987196 16.837314 8.9146848 -2.7036168 0.11743028 16.648831 1.6349911
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Loop time of 5.48047 on 1 procs for 10000 steps with 1000 atoms
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Performance: 157650.687 tau/day, 1824.661 timesteps/s
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98.8% 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 | 4.5166 | 4.5166 | 4.5166 | 0.0 | 82.41
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Neigh | 0.012162 | 0.012162 | 0.012162 | 0.0 | 0.22
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Comm | 0.14168 | 0.14168 | 0.14168 | 0.0 | 2.59
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Output | 0.00053787 | 0.00053787 | 0.00053787 | 0.0 | 0.01
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Modify | 0.74394 | 0.74394 | 0.74394 | 0.0 | 13.57
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Other | | 0.06553 | | | 1.20
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1724 ave 1724 max 1724 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 21000 ave 21000 max 21000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 21000
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Ave neighs/atom = 21
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Neighbor list builds = 11
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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 1 by 1 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) = 2.771 | 2.771 | 2.771 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 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654
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1000 0.0083300394 0.012482564 -5.5023188 -6.3233387 35.610076 14.886667 8.9677982 -0.83350251 0.093761848 16.159481 1.500112
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2000 0.020386462 0.030549113 -5.2949349 -6.2805556 41.760388 17.563305 8.896033 -1.0161699 0.11780863 16.85284 1.6868235
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3000 0.049693152 0.074465188 -5.3469434 -6.2493961 39.030372 16.123483 8.9325594 -0.9769179 0.073097387 16.601986 1.6003716
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4000 0.11859514 0.17771482 -5.207077 -6.3242752 40.941558 16.507785 8.9213147 -1.2949131 0.018189678 16.904156 1.6487282
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5000 0.13014573 0.19502337 -5.2610248 -6.269279 39.059628 15.609345 8.9431685 -1.2032776 -0.00023747376 16.701437 1.5920344
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6000 0.1381307 0.20698886 -5.171005 -6.2931942 40.904837 16.242165 8.9222854 -1.3291781 -0.0044770368 16.905086 1.6471589
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7000 0.12107326 0.18142828 -5.2602554 -6.2438099 39.060928 15.57765 8.9397525 -1.1649827 0.0055890257 16.671524 1.594944
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8000 0.14333636 0.21478954 -5.1717123 -6.304602 40.876188 16.205815 8.9218142 -1.3476793 -0.0069396327 16.895033 1.6469846
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9000 0.12159663 0.18221255 -5.2591911 -6.2587685 39.228648 15.677869 8.9376641 -1.18179 0.0077357066 16.688862 1.6001283
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10000 0.15321883 0.22959841 -5.1881787 -6.3448453 40.666451 16.146177 8.922851 -1.386265 -0.0091929687 16.860705 1.6418699
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Loop time of 5.6426 on 1 procs for 10000 steps with 1000 atoms
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Performance: 153120.907 tau/day, 1772.233 timesteps/s
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98.7% 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 | 4.5653 | 4.5653 | 4.5653 | 0.0 | 80.91
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Neigh | 0.10885 | 0.10885 | 0.10885 | 0.0 | 1.93
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Comm | 0.14695 | 0.14695 | 0.14695 | 0.0 | 2.60
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Output | 0.00055218 | 0.00055218 | 0.00055218 | 0.0 | 0.01
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Modify | 0.75364 | 0.75364 | 0.75364 | 0.0 | 13.36
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|
Other | | 0.0673 | | | 1.19
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1724 ave 1724 max 1724 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 20654 ave 20654 max 20654 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 20654
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Ave neighs/atom = 20.654
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Neighbor list builds = 94
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Dangerous builds = 0
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Total wall time: 0:00:17
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