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 = 2.8552583 2.8552583 2.8552583 Created orthogonal box = (0.0000000 -34.500217 0.0000000) to (42.253964 34.500217 6.9939259) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0517500 4.2534514 4.6626173 Created 875 atoms using lattice units in orthogonal box = (0.0000000 -34.500217 0.0000000) to (42.253964 34.500217 6.9939259) create_atoms CPU = 0.004 seconds 875 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0517500 4.2534514 4.6626173 Created 881 atoms using lattice units in orthogonal box = (0.0000000 -34.500217 0.0000000) to (42.253964 34.500217 6.9939259) create_atoms CPU = 0.004 seconds 881 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 ghost atom cutoff = 8 binsize = 4, bins = 11 18 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1740 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_942420706858_005#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 ghost atom cutoff = 8 binsize = 4, bins = 11 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5523.9227 0 -5523.9227 168442.36 115 0 -7146.7459 0 -7146.7459 -1889.4334 Loop time of 6.78481 on 1 procs for 115 steps with 1740 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 = -5523.92270390899 -7146.73916146074 -7146.74588962722 Force two-norm initial, final = 1863.4409 0.26663669 Force max component initial, final = 342.74132 0.039865237 Final line search alpha, max atom move = 1.0000000 0.039865237 Iterations, force evaluations = 115 213 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5668 | 6.5668 | 6.5668 | 0.0 | 96.79 Neigh | 0.12822 | 0.12822 | 0.12822 | 0.0 | 1.89 Comm | 0.047283 | 0.047283 | 0.047283 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04246 | | | 0.63 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8084.00 ave 8084 max 8084 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: 293482.0 ave 293482 max 293482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293482 Ave neighs/atom = 168.66782 Neighbor list builds = 3 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 ghost atom cutoff = 8 binsize = 4, bins = 11 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 115 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press Volume 115 0 -7146.7459 0 -7146.7459 -1889.4334 20391.084 119 0 -7146.9381 0 -7146.9381 42.187574 20369.3 Loop time of 0.184481 on 1 procs for 4 steps with 1740 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 = -7146.74588962726 -7146.93406015363 -7146.9381074944 Force two-norm initial, final = 92.238261 1.0467372 Force max component initial, final = 66.712242 0.73024866 Final line search alpha, max atom move = 0.00010662865 7.7865427e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17951 | 0.17951 | 0.17951 | 0.0 | 97.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011103 | 0.0011103 | 0.0011103 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003863 | | | 2.09 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8084.00 ave 8084 max 8084 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: 293492.0 ave 293492 max 293492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293492 Ave neighs/atom = 168.67356 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 ghost atom cutoff = 8 binsize = 4, bins = 11 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.711 | 5.711 | 5.711 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7146.9381 0 -7146.9381 42.187574 Loop time of 6.234e-06 on 1 procs for 0 steps with 1740 atoms 192.5% 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 | | 6.234e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8088.00 ave 8088 max 8088 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: 293490.0 ave 293490 max 293490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293490 Ave neighs/atom = 168.67241 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 ghost atom cutoff = 8 binsize = 4, bins = 11 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.711 | 5.711 | 5.711 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 -7146.9381 -7146.9381 42.137653 69.216915 6.9838278 42.187574 42.187574 31.483695 37.723202 57.355824 2.2204156 1521.2321 Loop time of 7.327e-06 on 1 procs for 0 steps with 1740 atoms 259.3% 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 | | 7.327e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8088.00 ave 8088 max 8088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146745.0 ave 146745 max 146745 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 293490.0 ave 293490 max 293490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293490 Ave neighs/atom = 168.67241 Neighbor list builds = 0 Dangerous builds = 0 1740 -7146.9381074944 eV 2.22041557426834 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07