LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -60.197347 0.0000000) to (30.096924 60.197347 3.4986963) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8805823 4.8805823 3.4986963 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.197347 0.0000000) to (30.096924 60.197347 3.4986963) create_atoms CPU = 0.001 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8805823 4.8805823 3.4986963 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.197347 0.0000000) to (30.096924 60.197347 3.4986963) create_atoms CPU = 0.001 seconds 594 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1180 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_715003088863_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.468 | 5.468 | 5.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4805.2754 0 -4805.2754 11051.982 63 0 -4845.8329 0 -4845.8329 -1995.4487 Loop time of 2.20619 on 1 procs for 63 steps with 1180 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4805.27540787281 -4845.8280818751 -4845.83285243675 Force two-norm initial, final = 33.054567 0.26386178 Force max component initial, final = 8.7629871 0.060212611 Final line search alpha, max atom move = 1.0000000 0.060212611 Iterations, force evaluations = 63 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1514 | 2.1514 | 2.1514 | 0.0 | 97.52 Neigh | 0.025449 | 0.025449 | 0.025449 | 0.0 | 1.15 Comm | 0.017009 | 0.017009 | 0.017009 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0123 | | | 0.56 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9823.00 ave 9823 max 9823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206320.0 ave 206320 max 206320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206320 Ave neighs/atom = 174.84746 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.467 | 5.467 | 5.467 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -4845.8329 0 -4845.8329 -1995.4487 12677.561 68 0 -4845.9646 0 -4845.9646 -3247.2601 12692.056 Loop time of 0.0758594 on 1 procs for 5 steps with 1180 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4845.83285243673 -4845.96061993474 -4845.96461662999 Force two-norm initial, final = 42.267829 0.47394793 Force max component initial, final = 30.067555 0.085788652 Final line search alpha, max atom move = 0.00015954983 1.3687565e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073391 | 0.073391 | 0.073391 | 0.0 | 96.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047372 | 0.00047372 | 0.00047372 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001994 | | | 2.63 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9800.00 ave 9800 max 9800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206660.0 ave 206660 max 206660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206660 Ave neighs/atom = 175.13559 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.605 | 5.605 | 5.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4845.9646 0 -4845.9646 -3247.2601 Loop time of 1.881e-06 on 1 procs for 0 steps with 1180 atoms 106.3% 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 | | 1.881e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9817.00 ave 9817 max 9817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206672.0 ave 206672 max 206672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206672 Ave neighs/atom = 175.14576 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.605 | 5.605 | 5.605 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 -4845.9646 -4845.9646 29.98607 120.39469 3.5156456 -3247.2601 -3247.2601 7.3716863 -9754.1131 4.9609527 2.2489444 256.11297 Loop time of 2.19e-06 on 1 procs for 0 steps with 1180 atoms 182.6% 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 | | 2.19e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9817.00 ave 9817 max 9817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103336.0 ave 103336 max 103336 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206672.0 ave 206672 max 206672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206672 Ave neighs/atom = 175.14576 Neighbor list builds = 0 Dangerous builds = 0 1180 -4845.96461662999 eV 2.2489443702884 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02