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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -45.723118 0.0000000) to (11.430780 45.723118 3.6147299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5723118 4.5723118 3.6147299 Created 160 atoms using lattice units in orthogonal box = (0.0000000 -45.723118 0.0000000) to (11.430780 45.723118 3.6147299) create_atoms CPU = 0.002 seconds 160 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5723118 4.5723118 3.6147299 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -45.723118 0.0000000) to (11.430780 45.723118 3.6147299) create_atoms CPU = 0.001 seconds 162 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 5 34 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 322 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_887933271505_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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 5 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.429 | 4.429 | 4.429 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -957.88232 0 -957.88232 101318.68 17 0 -1138.0294 0 -1138.0294 15202.543 Loop time of 0.755548 on 1 procs for 17 steps with 322 atoms 30.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -957.882320889455 -1138.02942839407 -1138.02942839407 Force two-norm initial, final = 476.81105 1.2551095 Force max component initial, final = 235.36320 0.41010845 Final line search alpha, max atom move = 7.2152689e-09 2.9590428e-09 Iterations, force evaluations = 17 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74229 | 0.74229 | 0.74229 | 0.0 | 98.24 Neigh | 0.0034466 | 0.0034466 | 0.0034466 | 0.0 | 0.46 Comm | 0.0059366 | 0.0059366 | 0.0059366 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003878 | | | 0.51 Nlocal: 322.000 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2828.00 ave 2828 max 2828 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: 17604.0 ave 17604 max 17604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17604 Ave neighs/atom = 54.670807 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 5 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -1138.0294 0 -1138.0294 15202.543 3778.4835 20 0 -1138.0632 0 -1138.0632 13829.303 3782.1003 Loop time of 0.176676 on 1 procs for 3 steps with 322 atoms 29.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1138.02942839407 -1138.0625153798 -1138.06316775881 Force two-norm initial, final = 62.966172 57.439127 Force max component initial, final = 42.903095 39.557326 Final line search alpha, max atom move = 1.9716100e-07 7.7991619e-06 Iterations, force evaluations = 3 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1718 | 0.1718 | 0.1718 | 0.0 | 97.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012079 | 0.0012079 | 0.0012079 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003668 | | | 2.08 Nlocal: 322.000 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2828.00 ave 2828 max 2828 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: 17604.0 ave 17604 max 17604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17604 Ave neighs/atom = 54.670807 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 5 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.567 | 4.567 | 4.567 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1138.0632 0 -1138.0632 13829.303 Loop time of 6.245e-06 on 1 procs for 0 steps with 322 atoms 96.1% 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 | | 6.245e-06 | | |100.00 Nlocal: 322.000 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2828.00 ave 2828 max 2828 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: 17600.0 ave 17600 max 17600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17600 Ave neighs/atom = 54.658385 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 5 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.567 | 4.567 | 4.567 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 -1138.0632 -1138.0632 11.433645 91.475809 3.6161136 13829.303 13829.303 10700.632 14023.554 16763.723 2.2849357 165.57597 Loop time of 6.595e-06 on 1 procs for 0 steps with 322 atoms 257.8% 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 | | 6.595e-06 | | |100.00 Nlocal: 322.000 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2828.00 ave 2828 max 2828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8800.00 ave 8800 max 8800 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17600.0 ave 17600 max 17600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17600 Ave neighs/atom = 54.658385 Neighbor list builds = 0 Dangerous builds = 0 322 -1138.06316775881 eV 2.28493570814743 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01