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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -33.886114 0.0000000) to (41.498337 33.886114 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7426671 4.3564179 4.6763329 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -33.886114 0.0000000) to (41.498337 33.886114 7.0144993) create_atoms CPU = 0.004 seconds 841 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7426671 4.3564179 4.6763329 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -33.886114 0.0000000) to (41.498337 33.886114 7.0144993) create_atoms CPU = 0.004 seconds 841 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 25 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 25 atoms, new total = 1657 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 25 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) = 4.645 | 4.645 | 4.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6909.7239 0 -6909.7239 12572.457 47 0 -7063.7179 0 -7063.7179 -12565.643 Loop time of 6.64433 on 1 procs for 47 steps with 1657 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 = -6909.72394961744 -7063.7128982894 -7063.71793293419 Force two-norm initial, final = 157.96157 0.28308695 Force max component initial, final = 23.389900 0.061651467 Final line search alpha, max atom move = 1.0000000 0.061651467 Iterations, force evaluations = 47 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5839 | 6.5839 | 6.5839 | 0.0 | 99.09 Neigh | 0.037393 | 0.037393 | 0.037393 | 0.0 | 0.56 Comm | 0.0085848 | 0.0085848 | 0.0085848 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01445 | | | 0.22 Nlocal: 1657.00 ave 1657 max 1657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4498.00 ave 4498 max 4498 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: 96536.0 ave 96536 max 96536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96536 Ave neighs/atom = 58.259505 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 25 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.645 | 4.645 | 4.645 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -7063.7179 0 -7063.7179 -12565.643 19727.822 52 0 -7064.0994 0 -7064.0994 -3904.6848 19626.125 Loop time of 0.738248 on 1 procs for 5 steps with 1657 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 = -7063.71793293417 -7064.09759112612 -7064.09936427257 Force two-norm initial, final = 185.63220 0.35988734 Force max component initial, final = 163.09254 0.062715229 Final line search alpha, max atom move = 9.4674775e-05 5.9375503e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73329 | 0.73329 | 0.73329 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086004 | 0.00086004 | 0.00086004 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004102 | | | 0.56 Nlocal: 1657.00 ave 1657 max 1657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4500.00 ave 4500 max 4500 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: 96630.0 ave 96630 max 96630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96630 Ave neighs/atom = 58.316234 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 25 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) = 4.783 | 4.783 | 4.783 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7064.0994 0 -7064.0994 -3904.6848 Loop time of 6.886e-06 on 1 procs for 0 steps with 1657 atoms 188.8% 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 | | 6.886e-06 | | |100.00 Nlocal: 1657.00 ave 1657 max 1657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4501.00 ave 4501 max 4501 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: 96666.0 ave 96666 max 96666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96666 Ave neighs/atom = 58.337960 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 25 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) = 4.783 | 4.783 | 4.783 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 -7064.0994 -7064.0994 41.452251 67.772229 6.986098 -3904.6848 -3904.6848 -3.3214925 -11711.072 0.33897306 2.2884056 1998.7027 Loop time of 7.016e-06 on 1 procs for 0 steps with 1657 atoms 256.6% 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 | | 7.016e-06 | | |100.00 Nlocal: 1657.00 ave 1657 max 1657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4501.00 ave 4501 max 4501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48333.0 ave 48333 max 48333 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96666.0 ave 96666 max 96666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96666 Ave neighs/atom = 58.337960 Neighbor list builds = 0 Dangerous builds = 0 1657 -7064.09936427257 eV 2.28840564618541 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08