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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -70.514978 0.0000000) to (28.785957 70.514978 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9086297 6.1109453 6.6478321 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -70.514978 0.0000000) to (28.785957 70.514978 9.9717481) create_atoms CPU = 0.002 seconds 1205 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9086297 6.1109453 6.6478321 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -70.514978 0.0000000) to (28.785957 70.514978 9.9717481) create_atoms CPU = 0.002 seconds 1205 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 47 4 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 29 atoms, new total = 2381 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 47 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7985.562 0 -7985.562 -160.78871 73 0 -8001.8438 0 -8001.8438 -4515.7537 Loop time of 7.93987 on 1 procs for 73 steps with 2381 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 = -7985.56197345038 -8001.8369182485 -8001.84381769761 Force two-norm initial, final = 15.741309 0.25901893 Force max component initial, final = 2.4605684 0.072670008 Final line search alpha, max atom move = 1.0000000 0.072670008 Iterations, force evaluations = 73 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.9173 | 7.9173 | 7.9173 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0080592 | 0.0080592 | 0.0080592 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01451 | | | 0.18 Nlocal: 2381.00 ave 2381 max 2381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5890.00 ave 5890 max 5890 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: 127636.0 ave 127636 max 127636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127636 Ave neighs/atom = 53.606048 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 47 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -8001.8438 0 -8001.8438 -4515.7537 40482.129 76 0 -8002.0279 0 -8002.0279 -918.30075 40336.804 Loop time of 0.361677 on 1 procs for 3 steps with 2381 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 = -8001.84381769757 -8002.02732645392 -8002.02787990177 Force two-norm initial, final = 146.57775 0.36068021 Force max component initial, final = 105.50647 0.15795929 Final line search alpha, max atom move = 0.00032687891 5.1633559e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35957 | 0.35957 | 0.35957 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028049 | 0.00028049 | 0.00028049 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00183 | | | 0.51 Nlocal: 2381.00 ave 2381 max 2381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5870.00 ave 5870 max 5870 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: 128198.0 ave 128198 max 128198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128198 Ave neighs/atom = 53.842083 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 47 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8002.0279 0 -8002.0279 -918.30075 Loop time of 2.227e-06 on 1 procs for 0 steps with 2381 atoms 179.6% 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 | | 2.227e-06 | | |100.00 Nlocal: 2381.00 ave 2381 max 2381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5870.00 ave 5870 max 5870 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: 128204.0 ave 128204 max 128204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128204 Ave neighs/atom = 53.844603 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 47 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.235 | 5.235 | 5.235 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 -8002.0279 -8002.0279 28.726965 141.02996 9.9563548 -918.30075 -918.30075 6.2612798 -2766.0439 4.8803852 2.5398072 959.96752 Loop time of 2.277e-06 on 1 procs for 0 steps with 2381 atoms 219.6% 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 | | 2.277e-06 | | |100.00 Nlocal: 2381.00 ave 2381 max 2381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5870.00 ave 5870 max 5870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64102.0 ave 64102 max 64102 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128204.0 ave 128204 max 128204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128204 Ave neighs/atom = 53.844603 Neighbor list builds = 0 Dangerous builds = 0 2381 -8002.02787990177 eV 2.53980721536619 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08