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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -71.524603 0.0000000) to (41.294749 71.524603 6.1787846) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5470558 5.6935007 6.1787846 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -71.524603 0.0000000) to (41.294749 71.524603 6.1787846) create_atoms CPU = 0.003 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5470558 5.6935007 6.1787846 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -71.524603 0.0000000) to (41.294749 71.524603 6.1787846) create_atoms CPU = 0.003 seconds 1610 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 52 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 52 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.333 | 5.333 | 5.333 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13076.391 0 -13076.391 35903.772 92 0 -13565.472 0 -13565.472 37868.032 Loop time of 13.7667 on 1 procs for 92 steps with 3216 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13076.3905048091 -13565.464455044 -13565.4718930004 Force two-norm initial, final = 566.54918 0.45059205 Force max component initial, final = 114.56402 0.067035475 Final line search alpha, max atom move = 1.0000000 0.067035475 Iterations, force evaluations = 92 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.677 | 13.677 | 13.677 | 0.0 | 99.35 Neigh | 0.047227 | 0.047227 | 0.047227 | 0.0 | 0.34 Comm | 0.016599 | 0.016599 | 0.016599 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02543 | | | 0.18 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8569.00 ave 8569 max 8569 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: 181820.0 ave 181820 max 181820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181820 Ave neighs/atom = 56.536070 Neighbor list builds = 3 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 52 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.334 | 5.334 | 5.334 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -13565.472 0 -13565.472 37868.032 36499.199 99 0 -13569.991 0 -13569.991 -76.661217 36868.853 Loop time of 1.00876 on 1 procs for 7 steps with 3216 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 = -13565.4718930005 -13569.9910045127 -13569.991075612 Force two-norm initial, final = 1504.8857 3.7379026 Force max component initial, final = 999.86361 2.1401337 Final line search alpha, max atom move = 0.00036487588 0.00078088318 Iterations, force evaluations = 7 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0023 | 1.0023 | 1.0023 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079031 | 0.00079031 | 0.00079031 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005628 | | | 0.56 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8595.00 ave 8595 max 8595 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: 182412.0 ave 182412 max 182412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182412 Ave neighs/atom = 56.720149 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 52 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.471 | 5.471 | 5.471 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13569.991 0 -13569.991 -76.661217 Loop time of 2.388e-06 on 1 procs for 0 steps with 3216 atoms 167.5% 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 | | 2.388e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8566.00 ave 8566 max 8566 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: 180192.0 ave 180192 max 180192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180192 Ave neighs/atom = 56.029851 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 52 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.471 | 5.471 | 5.471 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 -13569.991 -13569.991 41.363009 143.85408 6.1961985 -76.661217 -76.661217 -52.179124 -84.540554 -93.263974 2.2863346 1447.8161 Loop time of 2.484e-06 on 1 procs for 0 steps with 3216 atoms 201.3% 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 | | 2.484e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8566.00 ave 8566 max 8566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90096.0 ave 90096 max 90096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180192.0 ave 180192 max 180192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180192 Ave neighs/atom = 56.029851 Neighbor list builds = 0 Dangerous builds = 0 3216 -13569.991075612 eV 2.28633462813813 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15