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 = 3.5224675 3.5224675 3.5224675 Created orthogonal box = (0.0000000 -69.741298 0.0000000) to (42.707648 69.741298 8.6282479) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9389797 4.9815213 5.7521653 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -69.741298 0.0000000) to (42.707648 69.741298 8.6282479) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9389797 4.9815213 5.7521653 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.741298 0.0000000) to (42.707648 69.741298 8.6282479) create_atoms CPU = 0.003 seconds 2358 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 39 3 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 4704 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_763197941039_000#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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 11.47 | 11.47 | 11.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19237.076 0 -19237.076 91363.312 111 0 -20865.131 0 -20865.131 14164.044 Loop time of 6.32585 on 1 procs for 111 steps with 4704 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 = -19237.0756669551 -20865.1114637537 -20865.1310777563 Force two-norm initial, final = 1796.7459 0.67141815 Force max component initial, final = 281.60602 0.073116150 Final line search alpha, max atom move = 1.0000000 0.073116150 Iterations, force evaluations = 111 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.151 | 6.151 | 6.151 | 0.0 | 97.24 Neigh | 0.093363 | 0.093363 | 0.093363 | 0.0 | 1.48 Comm | 0.032635 | 0.032635 | 0.032635 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0489 | | | 0.77 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13690.0 ave 13690 max 13690 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: 654540.0 ave 654540 max 654540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654540 Ave neighs/atom = 139.14541 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -20865.131 0 -20865.131 14164.044 51398.245 119 0 -20867.679 0 -20867.679 -128.36074 51772.573 Loop time of 0.358063 on 1 procs for 8 steps with 4704 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 = -20865.1310777563 -20867.6771377914 -20867.6786859955 Force two-norm initial, final = 858.86121 10.534548 Force max component initial, final = 728.81281 10.126738 Final line search alpha, max atom move = 6.6563580e-05 0.00067407192 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30083 | 0.30083 | 0.30083 | 0.0 | 84.02 Neigh | 0.047205 | 0.047205 | 0.047205 | 0.0 | 13.18 Comm | 0.0015686 | 0.0015686 | 0.0015686 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008456 | | | 2.36 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13658.0 ave 13658 max 13658 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: 654240.0 ave 654240 max 654240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654240 Ave neighs/atom = 139.08163 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 10.98 | 10.98 | 10.98 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20867.679 0 -20867.679 -128.36074 Loop time of 2.451e-06 on 1 procs for 0 steps with 4704 atoms 571.2% 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 | | 2.451e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13658.0 ave 13658 max 13658 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: 654528.0 ave 654528 max 654528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654528 Ave neighs/atom = 139.14286 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 12 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 10.98 | 10.98 | 10.98 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 -20867.679 -20867.679 42.727293 140.47693 8.6256012 -128.36074 -128.36074 -313.53058 11.137427 -82.689071 2.2966821 1784.4037 Loop time of 2.471e-06 on 1 procs for 0 steps with 4704 atoms 323.8% 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 | | 2.471e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13658.0 ave 13658 max 13658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327264.0 ave 327264 max 327264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 654528.0 ave 654528 max 654528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654528 Ave neighs/atom = 139.14286 Neighbor list builds = 0 Dangerous builds = 0 4704 -20867.6786859955 eV 2.29668205455807 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07