LAMMPS (5 Oct 2016) # This script reproduces stress trajectories from Fig. 1 in # Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004) # # Three thermostatting scenarios are visited: undamped (nodrag), # damped (drag) and Nose-Hoover chain (nhchains). # # The axial and shear stress trajectories are printed to the # file "stress_vs_t.dat". For the damped case, the original figure # seems to be a plot of 2*tau, rather than tau. # # The script also demonstrates how to # orient a crystal along <110>, # and how to use the lj/cubic pair style. units lj boundary p p p atom_style atomic # Set up FCC lattice with z axis along <110> lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0 Lattice spacing in x,y,z = 1.41421 2 2 region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice create_box 1 mycell Created orthogonal box = (0 0 0) to (7.07107 10 10) 1 by 2 by 2 MPI processor grid mass * 1.0 create_atoms 1 box Created 1000 atoms # Using units of Rmin, so sigma = 2^-1/6 = 0.8908987 pair_style lj/cubic pair_coeff * * 1.0 0.8908987 # Relax box dimensions fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100 thermo 100 thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz min_modify line quadratic minimize 0.0 1.0e-6 10000 100000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.84754 ghost atom cutoff = 1.84754 binsize = 0.923769 -> bins = 8 11 11 Memory usage per processor = 3.63062 Mbytes Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz 0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999 100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999 134 0 -6.3344257 -6.3344257 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199 Loop time of 0.0299768 on 4 procs for 134 steps with 1000 atoms 98.4% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -6.2937539309 -6.33442568056 -6.33442568056 Force two-norm initial, final = 3395.29 5.80609e-10 Force max component initial, final = 1960.27 3.41627e-10 Final line search alpha, max atom move = 1 3.41627e-10 Iterations, force evaluations = 134 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.01485 | 0.017638 | 0.020133 | 1.4 | 58.84 Neigh | 0.00022697 | 0.00027376 | 0.00033092 | 0.2 | 0.91 Comm | 0.0026414 | 0.0050641 | 0.0078235 | 2.6 | 16.89 Output | 1.502e-05 | 1.6749e-05 | 2.0027e-05 | 0.0 | 0.06 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006985 | | | 23.30 Nlocal: 250 ave 305 max 205 min Histogram: 1 0 0 0 2 0 0 0 0 1 Nghost: 829 ave 874 max 774 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 5250 ave 6445 max 4305 min Histogram: 1 0 0 2 0 0 0 0 0 1 Total # of neighbors = 21000 Ave neighs/atom = 21 Neighbor list builds = 1 Dangerous builds = 0 # Define initial velocity velocity all create 0.01 87287 mom yes rot yes dist gaussian write_restart restart.equil Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.84754 ghost atom cutoff = 1.84754 binsize = 0.923769 -> bins = 8 11 11 # Start Run #1 log log.nodrag