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 = 3.6461252 3.6461252 3.6461252 Created orthogonal box = (0.0000000 -44.056299 0.0000000) to (53.957726 44.056299 8.9311464) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1740285 5.4315985 5.9540976 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -44.056299 0.0000000) to (53.957726 44.056299 8.9311464) create_atoms CPU = 0.003 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1740285 5.4315985 5.9540976 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -44.056299 0.0000000) to (53.957726 44.056299 8.9311464) create_atoms CPU = 0.002 seconds 1757 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 21 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3480 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_331285495617_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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12613.1 0 -12613.1 37495.229 59 0 -13520.219 0 -13520.219 -7143.9701 Loop time of 2.47454 on 1 procs for 59 steps with 3480 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 = -12613.1000933387 -13520.2069529292 -13520.2189608217 Force two-norm initial, final = 722.89712 0.45532448 Force max component initial, final = 108.56743 0.029896074 Final line search alpha, max atom move = 1.0000000 0.029896074 Iterations, force evaluations = 59 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3928 | 2.3928 | 2.3928 | 0.0 | 96.70 Neigh | 0.047086 | 0.047086 | 0.047086 | 0.0 | 1.90 Comm | 0.014936 | 0.014936 | 0.014936 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0197 | | | 0.80 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12925.0 ave 12925 max 12925 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: 772212.0 ave 772212 max 772212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 772212 Ave neighs/atom = 221.90000 Neighbor list builds = 1 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -13520.219 0 -13520.219 -7143.9701 42461.844 63 0 -13520.829 0 -13520.829 -32.465396 42275.309 Loop time of 0.172154 on 1 procs for 4 steps with 3480 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13520.2189608217 -13520.8246896115 -13520.8289358559 Force two-norm initial, final = 359.97641 5.4493561 Force max component initial, final = 264.22995 3.8557944 Final line search alpha, max atom move = 3.4942811e-05 0.00013473229 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16694 | 0.16694 | 0.16694 | 0.0 | 96.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007554 | 0.0007554 | 0.0007554 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004459 | | | 2.59 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12729.0 ave 12729 max 12729 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: 773936.0 ave 773936 max 773936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773936 Ave neighs/atom = 222.39540 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 11.30 | 11.30 | 11.30 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13520.829 0 -13520.829 -32.465396 Loop time of 2.259e-06 on 1 procs for 0 steps with 3480 atoms 221.3% 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 | | 2.259e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12724.0 ave 12724 max 12724 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: 774900.0 ave 774900 max 774900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774900 Ave neighs/atom = 222.67241 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 11.30 | 11.30 | 11.30 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 -13520.829 -13520.829 53.843907 87.859665 8.9363605 -32.465396 -32.465396 123.14204 -145.70987 -74.828357 2.3678941 1408.2146 Loop time of 2.759e-06 on 1 procs for 0 steps with 3480 atoms 253.7% 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 | | 2.759e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12724.0 ave 12724 max 12724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387450.0 ave 387450 max 387450 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 774900.0 ave 774900 max 774900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774900 Ave neighs/atom = 222.67241 Neighbor list builds = 0 Dangerous builds = 0 3480 -13520.8289358559 eV 2.36789413718832 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03