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 = 3.5618363 3.5618363 3.5618363 Created orthogonal box = (0.0000000 -43.913268 0.0000000) to (15.525685 43.913268 5.0371973) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7199891 4.6224492 5.0371973 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -43.913268 0.0000000) to (15.525685 43.913268 5.0371973) create_atoms CPU = 0.003 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7199891 4.6224492 5.0371973 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.913268 0.0000000) to (15.525685 43.913268 5.0371973) create_atoms CPU = 0.002 seconds 306 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 4 21 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 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 608 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_322509103239_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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 4.950 | 4.950 | 4.950 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2279.5941 0 -2279.5941 37283.521 113 0 -2382.0265 0 -2382.0265 4071.0101 Loop time of 2.98166 on 1 procs for 113 steps with 608 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2279.59407794503 -2382.02417104573 -2382.02646778877 Force two-norm initial, final = 188.88342 0.21483518 Force max component initial, final = 55.430617 0.030469153 Final line search alpha, max atom move = 0.95061423 0.028964410 Iterations, force evaluations = 113 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8921 | 2.8921 | 2.8921 | 0.0 | 97.00 Neigh | 0.038509 | 0.038509 | 0.038509 | 0.0 | 1.29 Comm | 0.030139 | 0.030139 | 0.030139 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02088 | | | 0.70 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5920.00 ave 5920 max 5920 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: 136144.0 ave 136144 max 136144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136144 Ave neighs/atom = 223.92105 Neighbor list builds = 2 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -2382.0265 0 -2382.0265 4071.0101 6868.5565 117 0 -2382.0691 0 -2382.0691 37.770404 6883.8677 Loop time of 0.0955199 on 1 procs for 4 steps with 608 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2382.02646778876 -2382.06780791398 -2382.0690743104 Force two-norm initial, final = 34.873223 0.52818452 Force max component initial, final = 29.003072 0.45950287 Final line search alpha, max atom move = 0.00013419054 6.1660935e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.092042 | 0.092042 | 0.092042 | 0.0 | 96.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091035 | 0.00091035 | 0.00091035 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002567 | | | 2.69 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5886.00 ave 5886 max 5886 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: 136092.0 ave 136092 max 136092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136092 Ave neighs/atom = 223.83553 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.092 | 5.092 | 5.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2382.0691 0 -2382.0691 37.770404 Loop time of 8.119e-06 on 1 procs for 0 steps with 608 atoms 172.4% 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 | | 8.119e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5886.00 ave 5886 max 5886 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: 135908.0 ave 135908 max 135908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135908 Ave neighs/atom = 223.53289 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.092 | 5.092 | 5.092 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 -2382.0691 -2382.0691 15.511197 88.091194 5.0379599 37.770404 37.770404 106.84658 8.8227962 -2.3581616 2.325549 551.47809 Loop time of 7.247e-06 on 1 procs for 0 steps with 608 atoms 262.2% 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 | | 7.247e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5886.00 ave 5886 max 5886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67954.0 ave 67954 max 67954 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 135908.0 ave 135908 max 135908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135908 Ave neighs/atom = 223.53289 Neighbor list builds = 0 Dangerous builds = 0 608 -2382.0690743104 eV 2.32554896695272 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03