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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5125435 3.5125435 3.1465590 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) create_atoms CPU = 0.002 seconds 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5125435 3.5125435 3.1465590 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.739885 0.0000000) to (25.368369 50.739885 3.1465590) create_atoms CPU = 0.001 seconds 261 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 518 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_356501945107_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3413.6852 0 -3413.6852 61489.658 49 0 -3513.3331 0 -3513.3331 -3408.7123 Loop time of 3.49015 on 1 procs for 49 steps with 518 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 = -3413.6852229931 -3513.33022226294 -3513.33307343974 Force two-norm initial, final = 182.70404 0.27134996 Force max component initial, final = 72.801186 0.057836609 Final line search alpha, max atom move = 0.92189346 0.053319192 Iterations, force evaluations = 49 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4741 | 3.4741 | 3.4741 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0084641 | 0.0084641 | 0.0084641 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007541 | | | 0.22 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3902.00 ave 3902 max 3902 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: 33326.0 ave 33326 max 33326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33326 Ave neighs/atom = 64.335907 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -3513.3331 0 -3513.3331 -3408.7123 8100.4269 51 0 -3513.3614 0 -3513.3614 1573.8732 8085.0768 Loop time of 0.191447 on 1 procs for 2 steps with 518 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 = -3513.33307343974 -3513.36136190046 -3513.36142451921 Force two-norm initial, final = 42.061964 0.29022918 Force max component initial, final = 31.042912 0.075629874 Final line search alpha, max atom move = 0.0010709936 8.0999107e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18968 | 0.18968 | 0.18968 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041209 | 0.00041209 | 0.00041209 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001354 | | | 0.71 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3897.00 ave 3897 max 3897 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: 33084.0 ave 33084 max 33084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33084 Ave neighs/atom = 63.868726 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.618 | 4.618 | 4.618 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3513.3614 0 -3513.3614 1573.8732 Loop time of 6.515e-06 on 1 procs for 0 steps with 518 atoms 184.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3902.00 ave 3902 max 3902 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: 33090.0 ave 33090 max 33090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33090 Ave neighs/atom = 63.880309 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.618 | 4.618 | 4.618 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 -3513.3614 -3513.3614 25.341597 101.47977 3.1439143 1573.8732 1573.8732 8.2545598 4722.2604 -8.8952353 2.5239448 198.54002 Loop time of 1.0273e-05 on 1 procs for 0 steps with 518 atoms 204.4% 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 | | 1.027e-05 | | |100.00 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3902.00 ave 3902 max 3902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16545.0 ave 16545 max 16545 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33090.0 ave 33090 max 33090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33090 Ave neighs/atom = 63.880309 Neighbor list builds = 0 Dangerous builds = 0 518 -3513.36142451921 eV 2.52394475791914 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04