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 = 3.8693370 3.8693370 3.8693370 Created orthogonal box = (0.0000000 -46.753377 0.0000000) to (57.260959 46.753377 9.4779013) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4907769 5.7641150 6.3186009 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -46.753377 0.0000000) to (57.260959 46.753377 9.4779013) create_atoms CPU = 0.003 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4907769 5.7641150 6.3186009 Created 1753 atoms using lattice units in orthogonal box = (0.0000000 -46.753377 0.0000000) to (57.260959 46.753377 9.4779013) create_atoms CPU = 0.002 seconds 1753 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 14 23 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 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 3476 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_042691367780_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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 6.612 | 6.612 | 6.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9174.373 0 -9174.373 66180.776 95 0 -11107.786 0 -11107.786 -5259.4306 Loop time of 4.51731 on 1 procs for 95 steps with 3476 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9174.37296726453 -11107.777366579 -11107.7859435027 Force two-norm initial, final = 1495.9814 0.30596570 Force max component initial, final = 265.60408 0.047418679 Final line search alpha, max atom move = 1.0000000 0.047418679 Iterations, force evaluations = 95 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3129 | 4.3129 | 4.3129 | 0.0 | 95.47 Neigh | 0.15213 | 0.15213 | 0.15213 | 0.0 | 3.37 Comm | 0.021431 | 0.021431 | 0.021431 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03089 | | | 0.68 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10870.0 ave 10870 max 10870 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: 519888.0 ave 519888 max 519888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519888 Ave neighs/atom = 149.56502 Neighbor list builds = 4 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.991 | 6.991 | 6.991 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -11107.786 0 -11107.786 -5259.4306 50747.398 99 0 -11108.221 0 -11108.221 444.67989 50545.782 Loop time of 0.174249 on 1 procs for 4 steps with 3476 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 = -11107.7859435027 -11108.2125227374 -11108.2212800123 Force two-norm initial, final = 299.57545 27.269264 Force max component initial, final = 232.25271 19.909797 Final line search alpha, max atom move = 3.4896004e-05 0.00069477236 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16997 | 0.16997 | 0.16997 | 0.0 | 97.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057508 | 0.00057508 | 0.00057508 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003705 | | | 2.13 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10608.0 ave 10608 max 10608 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: 509200.0 ave 509200 max 509200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509200 Ave neighs/atom = 146.49022 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 7.128 | 7.128 | 7.128 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11108.221 0 -11108.221 444.67989 Loop time of 2.152e-06 on 1 procs for 0 steps with 3476 atoms 185.9% 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 | | 2.152e-06 | | |100.00 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10608.0 ave 10608 max 10608 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: 517214.0 ave 517214 max 517214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517214 Ave neighs/atom = 148.79574 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 7.128 | 7.128 | 7.128 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 -11108.221 -11108.221 57.2462 93.17066 9.4767426 444.67989 444.67989 630.92876 126.48127 576.62965 2.5446851 1676.7605 Loop time of 2.985e-06 on 1 procs for 0 steps with 3476 atoms 301.5% 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 | | 2.985e-06 | | |100.00 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10608.0 ave 10608 max 10608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 258607.0 ave 258607 max 258607 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 517214.0 ave 517214 max 517214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517214 Ave neighs/atom = 148.79574 Neighbor list builds = 0 Dangerous builds = 0 3476 -11108.2212800123 eV 2.54468509093298 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05