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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -37.815598 0.0000000) to (13.368825 37.815598 4.0308524) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8613909 4.2969031 4.0308524 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.815598 0.0000000) to (13.368825 37.815598 4.0308524) create_atoms CPU = 0.001 seconds 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8613909 4.2969031 4.0308524 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.815598 0.0000000) to (13.368825 37.815598 4.0308524) create_atoms CPU = 0.001 seconds 178 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 348 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1476.6368 0 -1476.6368 -727.23357 40 0 -1485.6379 0 -1485.6379 -10852.024 Loop time of 1.76488 on 1 procs for 40 steps with 348 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1476.63679171501 -1485.63661251134 -1485.63785581348 Force two-norm initial, final = 18.611081 0.097114080 Force max component initial, final = 6.5921164 0.013863033 Final line search alpha, max atom move = 1.0000000 0.013863033 Iterations, force evaluations = 40 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7584 | 1.7584 | 1.7584 | 0.0 | 99.63 Neigh | 0.0018373 | 0.0018373 | 0.0018373 | 0.0 | 0.10 Comm | 0.0023731 | 0.0023731 | 0.0023731 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002275 | | | 0.13 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2776.00 ave 2776 max 2776 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: 22652.0 ave 22652 max 22652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22652 Ave neighs/atom = 65.091954 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1485.6379 0 -1485.6379 -10852.024 4075.5958 45 0 -1485.7343 0 -1485.7343 -555.18951 4049.9137 Loop time of 0.207079 on 1 procs for 5 steps with 348 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 = -1485.63785581348 -1485.73425147475 -1485.73431021201 Force two-norm initial, final = 42.701504 0.12268083 Force max component initial, final = 32.007221 0.032310099 Final line search alpha, max atom move = 0.0015410586 4.9791754e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20588 | 0.20588 | 0.20588 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021021 | 0.00021021 | 0.00021021 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009883 | | | 0.48 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2748.00 ave 2748 max 2748 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: 22552.0 ave 22552 max 22552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22552 Ave neighs/atom = 64.804598 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1485.7343 0 -1485.7343 -555.18951 Loop time of 2.59e-06 on 1 procs for 0 steps with 348 atoms 154.4% 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 | | 2.59e-06 | | |100.00 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2748.00 ave 2748 max 2748 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: 22564.0 ave 22564 max 22564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22564 Ave neighs/atom = 64.839080 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.580 | 4.580 | 4.580 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 -1485.7343 -1485.7343 13.332892 75.631195 4.0162473 -555.18951 -555.18951 -8.6143385 -1658.6516 1.6974071 2.2641179 271.24543 Loop time of 2.36e-06 on 1 procs for 0 steps with 348 atoms 169.5% 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 | | 2.36e-06 | | |100.00 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2748.00 ave 2748 max 2748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11282.0 ave 11282 max 11282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22564.0 ave 22564 max 22564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22564 Ave neighs/atom = 64.839080 Neighbor list builds = 0 Dangerous builds = 0 348 -1485.73431021201 eV 2.2641178809982 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02