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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -66.255805 0.0000000) to (23.424965 66.255805 5.1737092) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2847466 5.6559834 5.1737092 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -66.255805 0.0000000) to (23.424965 66.255805 5.1737092) create_atoms CPU = 0.004 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2847466 5.6559834 5.1737092 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -66.255805 0.0000000) to (23.424965 66.255805 5.1737092) create_atoms CPU = 0.003 seconds 658 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 = 7 35 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1308 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_267721408934_005#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 = 7 35 2 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) = 5.111 | 5.111 | 5.111 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5052.1223 0 -5052.1223 33391.074 391 0 -5283.6759 0 -5283.6759 -67810.057 Loop time of 8.33435 on 1 procs for 391 steps with 1308 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5052.12234417961 -5283.67197842726 -5283.67591324407 Force two-norm initial, final = 506.70786 0.16879725 Force max component initial, final = 173.01725 0.018924432 Final line search alpha, max atom move = 1.0000000 0.018924432 Iterations, force evaluations = 391 755 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.1137 | 8.1137 | 8.1137 | 0.0 | 97.35 Neigh | 0.092473 | 0.092473 | 0.092473 | 0.0 | 1.11 Comm | 0.073093 | 0.073093 | 0.073093 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0551 | | | 0.66 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8280.00 ave 8280 max 8280 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: 198892.0 ave 198892 max 198892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198892 Ave neighs/atom = 152.05810 Neighbor list builds = 7 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 = 7 35 2 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 : 391 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.501 | 5.501 | 5.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 391 0 -5283.6759 0 -5283.6759 -67810.057 16059.606 437 0 -5311.0381 0 -5311.0381 -245.8676 15273.459 Loop time of 0.586922 on 1 procs for 46 steps with 1308 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 = -5283.67591324408 -5311.03698585456 -5311.03805774042 Force two-norm initial, final = 1276.2927 6.5520806 Force max component initial, final = 923.74400 4.5599943 Final line search alpha, max atom move = 0.00022987457 0.0010482267 Iterations, force evaluations = 46 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54948 | 0.54948 | 0.54948 | 0.0 | 93.62 Neigh | 0.013695 | 0.013695 | 0.013695 | 0.0 | 2.33 Comm | 0.0039733 | 0.0039733 | 0.0039733 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01978 | | | 3.37 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8643.00 ave 8643 max 8643 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: 209056.0 ave 209056 max 209056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209056 Ave neighs/atom = 159.82875 Neighbor list builds = 1 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 = 6 36 2 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) = 5.641 | 5.641 | 5.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5311.0381 0 -5311.0381 -245.8676 Loop time of 2.169e-06 on 1 procs for 0 steps with 1308 atoms 138.3% 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 | | 2.169e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8649.00 ave 8649 max 8649 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: 209152.0 ave 209152 max 209152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209152 Ave neighs/atom = 159.90214 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 = 6 36 2 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) = 5.641 | 5.641 | 5.641 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 -5311.0381 -5311.0381 22.785914 134.01908 5.0015466 -245.8676 -245.8676 -58.599935 -483.78228 -195.22058 2.2827054 3529.3064 Loop time of 2.687e-06 on 1 procs for 0 steps with 1308 atoms 260.5% 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 | | 2.687e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8649.00 ave 8649 max 8649 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104576.0 ave 104576 max 104576 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 209152.0 ave 209152 max 209152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209152 Ave neighs/atom = 159.90214 Neighbor list builds = 0 Dangerous builds = 0 1308 -5311.03805774043 eV 2.28270541985639 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09