LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.60566 3.60566 3.60566 Created orthogonal box = (0 -47.8381 0) to (16.9121 47.8381 5.09918) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.14984 5.43574 5.09918 Created 358 atoms create_atoms CPU = 0.000242949 secs 358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.14984 5.43574 5.09918 Created 358 atoms create_atoms CPU = 0.000174046 secs 358 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 5 25 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.67337 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 686 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.67337 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2839.1809 0 -2839.1809 -7564.0639 477 0 -2907.6505 0 -2907.6505 -38094.843 Loop time of 1.645 on 1 procs for 477 steps with 686 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2839.18093223 -2907.64807918 -2907.65048086 Force two-norm initial, final = 6.92074 0.16509 Force max component initial, final = 1.3444 0.0376771 Final line search alpha, max atom move = 0.771901 0.029083 Iterations, force evaluations = 477 755 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5448 | 1.5448 | 1.5448 | 0.0 | 93.91 Neigh | 0.061249 | 0.061249 | 0.061249 | 0.0 | 3.72 Comm | 0.025074 | 0.025074 | 0.025074 | 0.0 | 1.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01391 | | | 0.85 Nlocal: 686 ave 686 max 686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5718 ave 5718 max 5718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108332 ave 108332 max 108332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108332 Ave neighs/atom = 157.918 Neighbor list builds = 24 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 477 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press Volume 477 0 -2907.6505 0 -2907.6505 -38094.843 8250.894 500 0 -2916.3059 0 -2916.3059 32161.053 7923.6632 Loop time of 0.0641749 on 1 procs for 23 steps with 686 atoms 93.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2907.65048086 -2916.3055826 -2916.30590294 Force two-norm initial, final = 597.391 0.674745 Force max component initial, final = 462.343 0.135164 Final line search alpha, max atom move = 0.000452371 6.11443e-05 Iterations, force evaluations = 23 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060506 | 0.060506 | 0.060506 | 0.0 | 94.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084639 | 0.00084639 | 0.00084639 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002823 | | | 4.40 Nlocal: 686 ave 686 max 686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5712 ave 5712 max 5712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108318 ave 108318 max 108318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108318 Ave neighs/atom = 157.898 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.67337 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.105 | 5.105 | 5.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2916.3059 0 -2916.3059 32161.053 Loop time of 1.19209e-06 on 1 procs for 0 steps with 686 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.192e-06 | | |100.00 Nlocal: 686 ave 686 max 686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5806 ave 5806 max 5806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114578 ave 114578 max 114578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114578 Ave neighs/atom = 167.023 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.105 | 5.105 | 5.105 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2916.3059 -2916.3059 16.558456 95.676277 5.0015186 32161.053 32161.053 -26.758957 96492.696 17.220462 2.3744209 1604.7148 Loop time of 9.53674e-07 on 1 procs for 0 steps with 686 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 686 ave 686 max 686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5806 ave 5806 max 5806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57289 ave 57289 max 57289 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114578 ave 114578 max 114578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114578 Ave neighs/atom = 167.023 Neighbor list builds = 0 Dangerous builds = 0 686 -2916.30590293706 eV 2.37442092695666 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01