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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -52.459156 0.0000000) to (30.284972 52.459156 7.0096089) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4896368 6.2446559 7.0096089 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.459156 0.0000000) to (30.284972 52.459156 7.0096089) create_atoms CPU = 0.002 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4896368 6.2446559 7.0096089 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.459156 0.0000000) to (30.284972 52.459156 7.0096089) create_atoms CPU = 0.001 seconds 676 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 9 30 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1332 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4436.3088 0 -4436.3088 2804.3375 41 0 -4463.5616 0 -4463.5616 -3322.3366 Loop time of 4.38597 on 1 procs for 41 steps with 1332 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 = -4436.30877812644 -4463.55777928634 -4463.56157669073 Force two-norm initial, final = 31.433697 0.18470650 Force max component initial, final = 6.5564268 0.028390740 Final line search alpha, max atom move = 1.0000000 0.028390740 Iterations, force evaluations = 41 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3667 | 4.3667 | 4.3667 | 0.0 | 99.56 Neigh | 0.0086981 | 0.0086981 | 0.0086981 | 0.0 | 0.20 Comm | 0.0045357 | 0.0045357 | 0.0045357 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006058 | | | 0.14 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5373.00 ave 5373 max 5373 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: 114016.0 ave 114016 max 114016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114016 Ave neighs/atom = 85.597598 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.067 | 5.067 | 5.067 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -4463.5616 0 -4463.5616 -3322.3366 22272.669 45 0 -4463.6543 0 -4463.6543 -474.76565 22191.069 Loop time of 0.418817 on 1 procs for 4 steps with 1332 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 = -4463.56157669073 -4463.65243122956 -4463.65430759973 Force two-norm initial, final = 63.872983 0.23179182 Force max component initial, final = 53.282731 0.035673686 Final line search alpha, max atom move = 0.00015083201 5.3807338e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41677 | 0.41677 | 0.41677 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029153 | 0.00029153 | 0.00029153 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001752 | | | 0.42 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5370.00 ave 5370 max 5370 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: 114032.0 ave 114032 max 114032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114032 Ave neighs/atom = 85.609610 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.204 | 5.204 | 5.204 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4463.6543 0 -4463.6543 -474.76565 Loop time of 2.087e-06 on 1 procs for 0 steps with 1332 atoms 191.7% 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 | | 2.087e-06 | | |100.00 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5370.00 ave 5370 max 5370 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: 114120.0 ave 114120 max 114120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114120 Ave neighs/atom = 85.675676 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.204 | 5.204 | 5.204 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 -4463.6543 -4463.6543 30.267222 104.91831 6.9880236 -474.76565 -474.76565 -2.007323 -1421.824 -0.46563159 2.5068567 1040.7749 Loop time of 2.261e-06 on 1 procs for 0 steps with 1332 atoms 221.1% 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 | | 2.261e-06 | | |100.00 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5370.00 ave 5370 max 5370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57060.0 ave 57060 max 57060 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114120.0 ave 114120 max 114120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114120 Ave neighs/atom = 85.675676 Neighbor list builds = 0 Dangerous builds = 0 1332 -4463.65430759973 eV 2.50685666222708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05