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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -43.676947 0.0000000) to (53.493117 43.676947 8.8542437) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1294770 5.3848291 5.9028292 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -43.676947 0.0000000) to (53.493117 43.676947 8.8542437) create_atoms CPU = 0.007 seconds 1752 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1294770 5.3848291 5.9028292 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -43.676947 0.0000000) to (53.493117 43.676947 8.8542437) create_atoms CPU = 0.006 seconds 1758 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3510 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_887933271505_003#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.213 | 5.213 | 5.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11235.55 0 -11235.55 70991.106 52 0 -12433.839 0 -12433.839 4656.0099 Loop time of 3.90461 on 1 procs for 52 steps with 3510 atoms 73.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -11235.5500608282 -12433.839194793 -12433.839194793 Force two-norm initial, final = 929.28459 0.48593579 Force max component initial, final = 157.39451 0.044162679 Final line search alpha, max atom move = 2.9802322e-08 1.3161504e-09 Iterations, force evaluations = 52 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.797 | 3.797 | 3.797 | 0.0 | 97.24 Neigh | 0.036525 | 0.036525 | 0.036525 | 0.0 | 0.94 Comm | 0.029881 | 0.029881 | 0.029881 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04123 | | | 1.06 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7180.00 ave 7180 max 7180 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: 192456.0 ave 192456 max 192456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192456 Ave neighs/atom = 54.830769 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.213 | 5.213 | 5.213 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -12433.839 0 -12433.839 4656.0099 41374.394 54 0 -12433.865 0 -12433.865 4354.4411 41383.318 Loop time of 0.363637 on 1 procs for 2 steps with 3510 atoms 77.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12433.839194793 -12433.8596539124 -12433.8645863265 Force two-norm initial, final = 209.45655 196.03432 Force max component initial, final = 130.58462 122.66081 Final line search alpha, max atom move = 1.2576279e-07 1.5426166e-05 Iterations, force evaluations = 2 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34952 | 0.34952 | 0.34952 | 0.0 | 96.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025769 | 0.0025769 | 0.0025769 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01154 | | | 3.17 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7194.00 ave 7194 max 7194 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: 192552.0 ave 192552 max 192552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192552 Ave neighs/atom = 54.858120 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.351 | 5.351 | 5.351 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12433.865 0 -12433.865 4354.4411 Loop time of 6.826e-06 on 1 procs for 0 steps with 3510 atoms 146.5% 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 | | 6.826e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7194.00 ave 7194 max 7194 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: 192540.0 ave 192540 max 192540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192540 Ave neighs/atom = 54.854701 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 20 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.351 | 5.351 | 5.351 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 -12433.865 -12433.865 53.496375 87.360719 8.8549223 4354.4411 4354.4411 3660.8475 4749.2477 4653.2282 2.3532945 1534.6444 Loop time of 6.916e-06 on 1 procs for 0 steps with 3510 atoms 231.3% 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 | | 6.916e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7194.00 ave 7194 max 7194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96270.0 ave 96270 max 96270 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192540.0 ave 192540 max 192540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192540 Ave neighs/atom = 54.854701 Neighbor list builds = 0 Dangerous builds = 0 3510 -12433.8645863265 eV 2.35329449054851 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04