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 = 2.5709721 2.5709721 2.5709721 Created orthogonal box = (0.0000000 -31.277226 0.0000000) to (15.638613 31.277226 2.5709721) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 2.9586565 2.9586565 2.5709721 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -31.277226 0.0000000) to (15.638613 31.277226 2.5709721) create_atoms CPU = 0.001 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 2.9586565 2.9586565 2.5709721 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -31.277226 0.0000000) to (15.638613 31.277226 2.5709721) create_atoms CPU = 0.000 seconds 298 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 4 14 1 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 586 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_122703700223_003#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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 4 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 6.220 | 6.220 | 6.220 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 1805.2759 0 1805.2759 19258211 3 0 1739.9978 0 1739.9978 19171542 Loop time of 1.34658 on 1 procs for 3 steps with 586 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 1805.27588718856 1739.99780718143 1739.99780718143 Force two-norm initial, final = 361.83197 103.75380 Force max component initial, final = 123.35546 21.692574 Final line search alpha, max atom move = 1.0733196e-12 2.3283064e-11 Iterations, force evaluations = 3 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3392 | 1.3392 | 1.3392 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0052781 | 0.0052781 | 0.0052781 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002068 | | | 0.15 Nlocal: 586.000 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13405.0 ave 13405 max 13405 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: 444304.0 ave 444304 max 444304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444304 Ave neighs/atom = 758.19795 Neighbor list builds = 0 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 4 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 3 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.220 | 6.220 | 6.220 Mbytes Step Temp E_pair E_mol TotEng Press Volume 3 0 1739.9978 0 1739.9978 19171542 2515.0917 4 0 1739.9978 0 1739.9978 19171542 2515.0917 Loop time of 1.2891 on 1 procs for 1 steps with 586 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 1739.99780718143 1739.99780718143 1739.99780718143 Force two-norm initial, final = 52126.961 52126.961 Force max component initial, final = 30149.171 30149.171 Final line search alpha, max atom move = 3.8613109e-18 1.1641532e-13 Iterations, force evaluations = 1 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2708 | 1.2708 | 1.2708 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036252 | 0.0036252 | 0.0036252 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01469 | | | 1.14 Nlocal: 586.000 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13405.0 ave 13405 max 13405 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: 444316.0 ave 444316 max 444316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444316 Ave neighs/atom = 758.21843 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 4 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 6.358 | 6.358 | 6.358 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 1739.9978 0 1739.9978 19171542 Loop time of 2.569e-06 on 1 procs for 0 steps with 586 atoms 155.7% 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 | | 2.569e-06 | | |100.00 Nlocal: 586.000 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13405.0 ave 13405 max 13405 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: 444316.0 ave 444316 max 444316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444316 Ave neighs/atom = 758.21843 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 4 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 6.358 | 6.358 | 6.358 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 1739.9978 1739.9978 15.638613 62.554452 2.5709721 19171542 19171542 19165517 19205778 19143332 1.3551495 212.69971 Loop time of 2.742e-06 on 1 procs for 0 steps with 586 atoms 255.3% 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 | | 2.742e-06 | | |100.00 Nlocal: 586.000 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13405.0 ave 13405 max 13405 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 222158.0 ave 222158 max 222158 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 444316.0 ave 444316 max 444316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444316 Ave neighs/atom = 758.21843 Neighbor list builds = 0 Dangerous builds = 0 586 1739.99780718143 eV 1.35514946129651 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03