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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -69.568480 0.0000000) to (34.782204 69.568480 4.0709491) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2411541 5.2411541 4.0709491 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.568480 0.0000000) to (34.782204 69.568480 4.0709491) create_atoms CPU = 0.001 seconds 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2411541 5.2411541 4.0709491 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.568480 0.0000000) to (34.782204 69.568480 4.0709491) create_atoms CPU = 0.001 seconds 586 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 46 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1156 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 46 2 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) = 4.613 | 4.613 | 4.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3877.6744 0 -3877.6744 -1279.3578 22 0 -3883.6414 0 -3883.6414 -5758.7837 Loop time of 1.54379 on 1 procs for 22 steps with 1156 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3877.67438957547 -3883.63895947161 -3883.64143184454 Force two-norm initial, final = 9.4029604 0.14949485 Force max component initial, final = 3.1624150 0.041984846 Final line search alpha, max atom move = 1.0000000 0.041984846 Iterations, force evaluations = 22 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5376 | 1.5376 | 1.5376 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025951 | 0.0025951 | 0.0025951 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003617 | | | 0.23 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4762.00 ave 4762 max 4762 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: 61896.0 ave 61896 max 61896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61896 Ave neighs/atom = 53.543253 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 46 2 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.613 | 4.613 | 4.613 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -3883.6414 0 -3883.6414 -5758.7837 19701.318 26 0 -3883.7522 0 -3883.7522 -2000.9252 19626.823 Loop time of 0.228822 on 1 procs for 4 steps with 1156 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 = -3883.64143184454 -3883.7519783672 -3883.75218170311 Force two-norm initial, final = 79.289577 0.25646412 Force max component initial, final = 67.042078 0.11145538 Final line search alpha, max atom move = 0.00033634042 3.7486949e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22705 | 0.22705 | 0.22705 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026617 | 0.00026617 | 0.00026617 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001511 | | | 0.66 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4769.00 ave 4769 max 4769 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: 62064.0 ave 62064 max 62064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62064 Ave neighs/atom = 53.688581 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 46 2 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) = 4.769 | 4.769 | 4.769 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3883.7522 0 -3883.7522 -2000.9252 Loop time of 1.735e-06 on 1 procs for 0 steps with 1156 atoms 172.9% 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 | | 1.735e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6460.00 ave 6460 max 6460 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: 62072.0 ave 62072 max 62072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62072 Ave neighs/atom = 53.695502 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 46 2 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) = 4.769 | 4.769 | 4.769 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 -3883.7522 -3883.7522 34.689122 139.13696 4.0664384 -2000.9252 -2000.9252 8.3793395 -6020.2433 9.0882423 2.5439753 644.17664 Loop time of 2.324e-06 on 1 procs for 0 steps with 1156 atoms 172.1% 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 | | 2.324e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6460.00 ave 6460 max 6460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31036.0 ave 31036 max 31036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62072.0 ave 62072 max 62072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62072 Ave neighs/atom = 53.695502 Neighbor list builds = 0 Dangerous builds = 0 1156 -3883.75218170311 eV 2.54397527434406 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02