forked from lijiext/lammps
111 lines
3.9 KiB
Groff
111 lines
3.9 KiB
Groff
LAMMPS (5 Oct 2016)
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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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# 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: Resetting reneighboring criteria during minimization (../min.cpp:168)
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Neighbor list info ...
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1 neighbor list requests
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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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Memory usage per processor = 3.65406 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 0.0817621 on 1 procs for 134 steps with 1000 atoms
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100.3% CPU use with 1 MPI tasks x no 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 | 0.066955 | 0.066955 | 0.066955 | 0.0 | 81.89
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Neigh | 0.001004 | 0.001004 | 0.001004 | 0.0 | 1.23
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Comm | 0.0014298 | 0.0014298 | 0.0014298 | 0.0 | 1.75
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Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.02
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.01236 | | | 15.11
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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: 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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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 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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# Start Run #1
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log log.nodrag
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