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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -45.251969 0.0000000) to (15.083990 45.251969 3.6584048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4364675 4.4364675 3.6584048 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -45.251969 0.0000000) to (15.083990 45.251969 3.6584048) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4364675 4.4364675 3.6584048 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -45.251969 0.0000000) to (15.083990 45.251969 3.6584048) create_atoms CPU = 0.000 seconds 206 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1124.2111 0 -1124.2111 213415.57 71 0 -1583.6855 0 -1583.6855 1490.5206 Loop time of 0.422478 on 1 procs for 71 steps with 408 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 = -1124.21112413721 -1583.68424847874 -1583.68546658848 Force two-norm initial, final = 1354.8531 0.11253061 Force max component initial, final = 427.87480 0.043150459 Final line search alpha, max atom move = 1.0000000 0.043150459 Iterations, force evaluations = 71 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41118 | 0.41118 | 0.41118 | 0.0 | 97.33 Neigh | 0.0035612 | 0.0035612 | 0.0035612 | 0.0 | 0.84 Comm | 0.0043965 | 0.0043965 | 0.0043965 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003337 | | | 0.79 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756.00 ave 3756 max 3756 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: 55124.0 ave 55124 max 55124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55124 Ave neighs/atom = 135.10784 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -1583.6855 0 -1583.6855 1490.5206 4994.3095 114 0 -1585.0899 0 -1585.0899 275.31112 4980.7913 Loop time of 0.173962 on 1 procs for 43 steps with 408 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 = -1583.68546658847 -1585.08869131796 -1585.08991380452 Force two-norm initial, final = 73.078397 2.3680396 Force max component initial, final = 63.066403 1.5018937 Final line search alpha, max atom move = 0.00046403113 0.00069692541 Iterations, force evaluations = 43 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16103 | 0.16103 | 0.16103 | 0.0 | 92.57 Neigh | 0.0033702 | 0.0033702 | 0.0033702 | 0.0 | 1.94 Comm | 0.0017131 | 0.0017131 | 0.0017131 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007848 | | | 4.51 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3856.00 ave 3856 max 3856 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: 55880.0 ave 55880 max 55880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55880 Ave neighs/atom = 136.96078 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.604 | 4.604 | 4.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1585.0899 0 -1585.0899 275.31112 Loop time of 1.808e-06 on 1 procs for 0 steps with 408 atoms 165.9% 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 | | 1.808e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3864.00 ave 3864 max 3864 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: 56392.0 ave 56392 max 56392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56392 Ave neighs/atom = 138.21569 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.604 | 4.604 | 4.604 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 -1585.0899 -1585.0899 14.935116 88.660037 3.7615067 275.31112 275.31112 478.34757 375.80345 -28.217649 2.2932367 223.42108 Loop time of 1.896e-06 on 1 procs for 0 steps with 408 atoms 211.0% 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 | | 1.896e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3864.00 ave 3864 max 3864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28196.0 ave 28196 max 28196 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56392.0 ave 56392 max 56392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56392 Ave neighs/atom = 138.21569 Neighbor list builds = 0 Dangerous builds = 0 408 -1585.08991380451 eV 2.29323673789755 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01