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 -56.700386 0.0000000) to (34.720000 56.700386 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0152381 4.0498230 4.6763329 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.700386 0.0000000) to (34.720000 56.700386 7.0144993) create_atoms CPU = 0.006 seconds 1182 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0152381 4.0498230 4.6763329 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.700386 0.0000000) to (34.720000 56.700386 7.0144993) create_atoms CPU = 0.005 seconds 1182 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 = 13 41 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 24 atoms, new total = 2340 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 = 13 41 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) = 5.161 | 5.161 | 5.161 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9946.8868 0 -9946.8868 5565.1509 18 0 -9998.1988 0 -9998.1988 -2362.6254 Loop time of 3.81261 on 1 procs for 18 steps with 2340 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 = -9946.88683874969 -9998.18940404437 -9998.1988174175 Force two-norm initial, final = 70.103757 0.45945350 Force max component initial, final = 13.501279 0.080619194 Final line search alpha, max atom move = 1.0000000 0.080619194 Iterations, force evaluations = 18 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8006 | 3.8006 | 3.8006 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0045063 | 0.0045063 | 0.0045063 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00747 | | | 0.20 Nlocal: 2340.00 ave 2340 max 2340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6157.00 ave 6157 max 6157 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: 135408.0 ave 135408 max 135408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135408 Ave neighs/atom = 57.866667 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 41 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.161 | 5.161 | 5.161 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -9998.1988 0 -9998.1988 -2362.6254 27618.012 20 0 -9998.2896 0 -9998.2896 1603.7486 27554.592 Loop time of 0.461732 on 1 procs for 2 steps with 2340 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 = -9998.19881741747 -9998.28713128062 -9998.28960303683 Force two-norm initial, final = 111.51840 1.0270535 Force max component initial, final = 82.087255 0.66620801 Final line search alpha, max atom move = 7.4857981e-05 4.9870987e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45898 | 0.45898 | 0.45898 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059841 | 0.00059841 | 0.00059841 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002156 | | | 0.47 Nlocal: 2340.00 ave 2340 max 2340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6157.00 ave 6157 max 6157 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: 135732.0 ave 135732 max 135732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135732 Ave neighs/atom = 58.005128 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 = 13 41 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) = 5.299 | 5.299 | 5.299 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9998.2896 0 -9998.2896 1603.7486 Loop time of 6.104e-06 on 1 procs for 0 steps with 2340 atoms 213.0% 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 | | 6.104e-06 | | |100.00 Nlocal: 2340.00 ave 2340 max 2340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6157.00 ave 6157 max 6157 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: 135744.0 ave 135744 max 135744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135744 Ave neighs/atom = 58.010256 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 = 13 41 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) = 5.299 | 5.299 | 5.299 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 -9998.2896 -9998.2896 34.681333 113.40077 7.0061944 1603.7486 1603.7486 -38.693881 4813.4769 36.462763 2.2287512 933.44127 Loop time of 6.675e-06 on 1 procs for 0 steps with 2340 atoms 314.6% 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 | | 6.675e-06 | | |100.00 Nlocal: 2340.00 ave 2340 max 2340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6157.00 ave 6157 max 6157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67872.0 ave 67872 max 67872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 135744.0 ave 135744 max 135744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135744 Ave neighs/atom = 58.010256 Neighbor list builds = 0 Dangerous builds = 0 2340 -9998.28960303683 eV 2.22875119527972 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05