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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -51.703941 0.0000000) to (36.560208 51.703941 5.1194531) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7349345 4.5621125 5.1194531 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -51.703941 0.0000000) to (36.560208 51.703941 5.1194531) create_atoms CPU = 0.002 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7349345 4.5621125 5.1194531 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -51.703941 0.0000000) to (36.560208 51.703941 5.1194531) create_atoms CPU = 0.001 seconds 821 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1629 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_313717476091_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.109 | 5.109 | 5.109 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5623.3157 0 -5623.3157 26387.3 24 0 -5743.5978 0 -5743.5978 1486.0779 Loop time of 1.18616 on 1 procs for 24 steps with 1629 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5623.3157391604 -5743.59650882137 -5743.59784467312 Force two-norm initial, final = 155.21408 0.82336694 Force max component initial, final = 21.177252 0.22184348 Final line search alpha, max atom move = 0.52585226 0.11665689 Iterations, force evaluations = 24 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.179 | 1.179 | 1.179 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00316 | 0.00316 | 0.00316 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003987 | | | 0.34 Nlocal: 1629.00 ave 1629 max 1629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6200.00 ave 6200 max 6200 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: 126808.0 ave 126808 max 126808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126808 Ave neighs/atom = 77.844076 Neighbor list builds = 0 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.110 | 5.110 | 5.110 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -5743.5978 0 -5743.5978 1486.0779 19354.674 28 0 -5743.6961 0 -5743.6961 412.65923 19369.848 Loop time of 0.147719 on 1 procs for 4 steps with 1629 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 = -5743.59784467313 -5743.69181807084 -5743.696142446 Force two-norm initial, final = 51.198270 8.9783988 Force max component initial, final = 47.716081 6.8181113 Final line search alpha, max atom move = 0.00015915788 0.0010851561 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14597 | 0.14597 | 0.14597 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027929 | 0.00027929 | 0.00027929 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001473 | | | 1.00 Nlocal: 1629.00 ave 1629 max 1629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6243.00 ave 6243 max 6243 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: 126122.0 ave 126122 max 126122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126122 Ave neighs/atom = 77.422959 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.248 | 5.248 | 5.248 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5743.6961 0 -5743.6961 412.65923 Loop time of 1.584e-06 on 1 procs for 0 steps with 1629 atoms 189.4% 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 | | 1.584e-06 | | |100.00 Nlocal: 1629.00 ave 1629 max 1629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6251.00 ave 6251 max 6251 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: 126138.0 ave 126138 max 126138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126138 Ave neighs/atom = 77.432781 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.248 | 5.248 | 5.248 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 -5743.6961 -5743.6961 36.541437 103.77402 5.1080128 412.65923 412.65923 360.73709 565.95669 311.2839 2.3008554 855.70626 Loop time of 2e-06 on 1 procs for 0 steps with 1629 atoms 200.0% 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 | | 2e-06 | | |100.00 Nlocal: 1629.00 ave 1629 max 1629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6251.00 ave 6251 max 6251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63069.0 ave 63069 max 63069 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126138.0 ave 126138 max 126138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126138 Ave neighs/atom = 77.432781 Neighbor list builds = 0 Dangerous builds = 0 1629 -5743.696142446 eV 2.30085535479974 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01