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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -43.703947 0.0000000) to (35.681180 43.703947 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0973115 5.0537811 5.8858683 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.703947 0.0000000) to (35.681180 43.703947 8.8288024) create_atoms CPU = 0.001 seconds 1184 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0973115 5.0537811 5.8858683 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.703947 0.0000000) to (35.681180 43.703947 8.8288024) create_atoms CPU = 0.001 seconds 1184 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 29 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 2320 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.148 | 5.148 | 5.148 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9751.5988 0 -9751.5988 -2694.653 108 0 -9814.8254 0 -9814.8254 -16640.858 Loop time of 14.9556 on 1 procs for 108 steps with 2320 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 = -9751.59881571771 -9814.81707695919 -9814.82544969554 Force two-norm initial, final = 36.190363 0.25516450 Force max component initial, final = 5.7048949 0.017109437 Final line search alpha, max atom move = 1.0000000 0.017109437 Iterations, force evaluations = 108 204 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.894 | 14.894 | 14.894 | 0.0 | 99.59 Neigh | 0.027339 | 0.027339 | 0.027339 | 0.0 | 0.18 Comm | 0.013152 | 0.013152 | 0.013152 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02075 | | | 0.14 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6198.00 ave 6198 max 6198 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: 179824.0 ave 179824 max 179824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179824 Ave neighs/atom = 77.510345 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.148 | 5.148 | 5.148 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -9814.8254 0 -9814.8254 -16640.858 27535.418 120 0 -9816.7756 0 -9816.7756 -2501.6449 27286.667 Loop time of 1.1144 on 1 procs for 12 steps with 2320 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 = -9814.8254496955 -9816.77556970506 -9816.77559803215 Force two-norm initial, final = 398.10047 1.0384401 Force max component initial, final = 375.57190 0.41895269 Final line search alpha, max atom move = 0.0010833510 0.00045387282 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1087 | 1.1087 | 1.1087 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075048 | 0.00075048 | 0.00075048 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004987 | | | 0.45 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6225.00 ave 6225 max 6225 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: 179840.0 ave 179840 max 179840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179840 Ave neighs/atom = 77.517241 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.286 | 5.286 | 5.286 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9816.7756 0 -9816.7756 -2501.6449 Loop time of 1.966e-06 on 1 procs for 0 steps with 2320 atoms 152.6% 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 | | 1.966e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6250.00 ave 6250 max 6250 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: 180240.0 ave 180240 max 180240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180240 Ave neighs/atom = 77.689655 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.286 | 5.286 | 5.286 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 -9816.7756 -9816.7756 35.290357 87.407894 8.8459358 -2501.6449 -2501.6449 24.329977 -7552.7423 23.477567 2.2088347 2214.3537 Loop time of 1.981e-06 on 1 procs for 0 steps with 2320 atoms 201.9% 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 | | 1.981e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6250.00 ave 6250 max 6250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90120.0 ave 90120 max 90120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180240.0 ave 180240 max 180240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180240 Ave neighs/atom = 77.689655 Neighbor list builds = 0 Dangerous builds = 0 2320 -9816.77559803215 eV 2.2088346583915 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16