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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -62.063243 0.0000000) to (31.031621 62.063243 3.6073527) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0321548 5.0321548 3.6073527 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.063243 0.0000000) to (31.031621 62.063243 3.6073527) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0321548 5.0321548 3.6073527 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.063243 0.0000000) to (31.031621 62.063243 3.6073527) 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 21 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1184 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_151002396060_004#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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 11.42 | 11.42 | 11.42 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3855.5562 0 -3855.5562 40619.518 71 0 -4168.4816 0 -4168.4816 3702.5694 Loop time of 4.37156 on 1 procs for 71 steps with 1184 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3855.55619076907 -4168.47775586937 -4168.48159164609 Force two-norm initial, final = 441.63545 0.24543962 Force max component initial, final = 123.65794 0.044599390 Final line search alpha, max atom move = 1.0000000 0.044599390 Iterations, force evaluations = 71 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3058 | 4.3058 | 4.3058 | 0.0 | 98.50 Neigh | 0.030453 | 0.030453 | 0.030453 | 0.0 | 0.70 Comm | 0.02453 | 0.02453 | 0.02453 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01078 | | | 0.25 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18374.0 ave 18374 max 18374 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: 745592.0 ave 745592 max 745592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 745592 Ave neighs/atom = 629.72297 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.43 | 11.43 | 11.43 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4168.4816 0 -4168.4816 3702.5694 13894.967 78 0 -4168.6472 0 -4168.6472 -35.512069 13931.949 Loop time of 0.334795 on 1 procs for 7 steps with 1184 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 = -4168.4815916461 -4168.64709435049 -4168.64718952353 Force two-norm initial, final = 74.525398 1.0774421 Force max component initial, final = 53.936668 0.74817120 Final line search alpha, max atom move = 0.00050472774 0.00037762275 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32837 | 0.32837 | 0.32837 | 0.0 | 98.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013599 | 0.0013599 | 0.0013599 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005066 | | | 1.51 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18992.0 ave 18992 max 18992 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: 743296.0 ave 743296 max 743296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 743296 Ave neighs/atom = 627.78378 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4168.6472 0 -4168.6472 -35.512069 Loop time of 2.019e-06 on 1 procs for 0 steps with 1184 atoms 148.6% 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 | | 2.019e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19024.0 ave 19024 max 19024 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: 743744.0 ave 743744 max 743744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 743744 Ave neighs/atom = 628.16216 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 10.95 | 10.95 | 10.95 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 -4168.6472 -4168.6472 30.9408 124.1478 3.6269476 -35.512069 -35.512069 -63.692356 -86.054594 43.210742 2.2713671 269.39126 Loop time of 2.568e-06 on 1 procs for 0 steps with 1184 atoms 233.6% 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 | | 2.568e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19024.0 ave 19024 max 19024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 371872.0 ave 371872 max 371872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 743744.0 ave 743744 max 743744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 743744 Ave neighs/atom = 628.16216 Neighbor list builds = 0 Dangerous builds = 0 1184 -4168.64718952353 eV 2.27136706831723 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05