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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -41.198022 0.0000000) to (35.678534 41.198022 6.9971362) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4038394 6.3381573 6.9971362 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -41.198022 0.0000000) to (35.678534 41.198022 6.9971362) create_atoms CPU = 0.002 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4038394 6.3381573 6.9971362 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -41.198022 0.0000000) to (35.678534 41.198022 6.9971362) create_atoms CPU = 0.002 seconds 627 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 14 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1248 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.694 | 6.694 | 6.694 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3314.3709 0 -3314.3709 26762.377 89 0 -3575.4884 0 -3575.4884 3767.2681 Loop time of 3.20236 on 1 procs for 89 steps with 1248 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 = -3314.37088940011 -3575.48514811674 -3575.48843201849 Force two-norm initial, final = 251.27964 0.18038247 Force max component initial, final = 77.810263 0.045474732 Final line search alpha, max atom move = 0.92930097 0.042259713 Iterations, force evaluations = 89 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.066 | 3.066 | 3.066 | 0.0 | 95.74 Neigh | 0.10794 | 0.10794 | 0.10794 | 0.0 | 3.37 Comm | 0.016311 | 0.016311 | 0.016311 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01206 | | | 0.38 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10275.0 ave 10275 max 10275 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: 511368.0 ave 511368 max 511368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 511368 Ave neighs/atom = 409.75000 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.694 | 6.694 | 6.694 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -3575.4884 0 -3575.4884 3767.2681 20569.971 93 0 -3575.6266 0 -3575.6266 3.9637115 20672.149 Loop time of 0.151297 on 1 procs for 4 steps with 1248 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 = -3575.48843201849 -3575.62594395403 -3575.62660424558 Force two-norm initial, final = 87.141329 0.80156404 Force max component initial, final = 64.471332 0.56612750 Final line search alpha, max atom move = 0.00024581551 0.00013916292 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14822 | 0.14822 | 0.14822 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005534 | 0.0005534 | 0.0005534 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002523 | | | 1.67 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10286.0 ave 10286 max 10286 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: 511516.0 ave 511516 max 511516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 511516 Ave neighs/atom = 409.86859 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.832 | 6.832 | 6.832 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3575.6266 0 -3575.6266 3.9637115 Loop time of 2.308e-06 on 1 procs for 0 steps with 1248 atoms 173.3% 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 | | 2.308e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10272.0 ave 10272 max 10272 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: 501010.0 ave 501010 max 501010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 501010 Ave neighs/atom = 401.45032 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.832 | 6.832 | 6.832 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 -3575.6266 -3575.6266 35.736756 82.624632 7.0010144 3.9637115 3.9637115 -43.948808 19.859317 35.980626 2.5538059 1206.2214 Loop time of 2.704e-06 on 1 procs for 0 steps with 1248 atoms 221.9% 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 | | 2.704e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10272.0 ave 10272 max 10272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 250505.0 ave 250505 max 250505 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 501010.0 ave 501010 max 501010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 501010 Ave neighs/atom = 401.45032 Neighbor list builds = 0 Dangerous builds = 0 1248 -3575.62660424561 eV 2.55380588023236 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03