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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -41.247507 0.0000000) to (35.721389 41.247507 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4115313 6.3457703 7.0055407 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -41.247507 0.0000000) to (35.721389 41.247507 7.0055407) create_atoms CPU = 0.004 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4115313 6.3457703 7.0055407 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.247507 0.0000000) to (35.721389 41.247507 7.0055407) create_atoms CPU = 0.003 seconds 629 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 ghost atom cutoff = 8 binsize = 4, bins = 9 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1252 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_793141037706_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3652.2212 0 -3652.2212 54650.985 80 0 -4186.3557 0 -4186.3557 8272.8725 Loop time of 28.8094 on 1 procs for 80 steps with 1252 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 = -3652.22117955321 -4186.35189206242 -4186.35573178244 Force two-norm initial, final = 510.87251 0.15408025 Force max component initial, final = 112.25831 0.041330796 Final line search alpha, max atom move = 1.0000000 0.041330796 Iterations, force evaluations = 80 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.663 | 28.663 | 28.663 | 0.0 | 99.49 Neigh | 0.10209 | 0.10209 | 0.10209 | 0.0 | 0.35 Comm | 0.022533 | 0.022533 | 0.022533 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02204 | | | 0.08 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5949.00 ave 5949 max 5949 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: 166716.0 ave 166716 max 166716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166716 Ave neighs/atom = 133.15974 Neighbor list builds = 4 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 ghost atom cutoff = 8 binsize = 4, bins = 9 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -4186.3557 0 -4186.3557 8272.8725 20644.183 93 0 -4187.3789 0 -4187.3789 17.985337 20856.522 Loop time of 3.54754 on 1 procs for 13 steps with 1252 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4186.35573178244 -4187.37788568455 -4187.37889811575 Force two-norm initial, final = 205.19566 0.64947373 Force max component initial, final = 179.30127 0.32631650 Final line search alpha, max atom move = 0.00032079417 0.00010468043 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5108 | 3.5108 | 3.5108 | 0.0 | 98.96 Neigh | 0.025813 | 0.025813 | 0.025813 | 0.0 | 0.73 Comm | 0.0025549 | 0.0025549 | 0.0025549 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008386 | | | 0.24 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5918.00 ave 5918 max 5918 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: 166242.0 ave 166242 max 166242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166242 Ave neighs/atom = 132.78115 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.190 | 5.190 | 5.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4187.3789 0 -4187.3789 17.985337 Loop time of 6.324e-06 on 1 procs for 0 steps with 1252 atoms 221.4% 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 | | 6.324e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5914.00 ave 5914 max 5914 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: 166244.0 ave 166244 max 166244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166244 Ave neighs/atom = 132.78275 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 ghost atom cutoff = 8 binsize = 4, bins = 9 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.190 | 5.190 | 5.190 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 -4187.3789 -4187.3789 35.704262 83.519128 6.994165 17.985337 17.985337 14.701478 14.227941 25.026592 2.5329223 1043.0746 Loop time of 6.204e-06 on 1 procs for 0 steps with 1252 atoms 322.4% 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 | | 6.204e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5914.00 ave 5914 max 5914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 83122.0 ave 83122 max 83122 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 166244.0 ave 166244 max 166244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166244 Ave neighs/atom = 132.78275 Neighbor list builds = 0 Dangerous builds = 0 1252 -4187.37889811575 eV 2.53292232504805 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:33