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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -43.539996 0.0000000) to (20.524951 43.539996 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0367502 5.9760778 4.9780318 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -43.539996 0.0000000) to (20.524951 43.539996 4.9780318) create_atoms CPU = 0.001 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0367502 5.9760778 4.9780318 Created 411 atoms using lattice units in orthogonal box = (0.0000000 -43.539996 0.0000000) to (20.524951 43.539996 4.9780318) create_atoms CPU = 0.001 seconds 411 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 ghost atom cutoff = 6 binsize = 3, bins = 7 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 816 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_937008984446_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 ghost atom cutoff = 6 binsize = 3, bins = 7 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2141.5636 0 -2141.5636 358538.23 35 0 -3618.6597 0 -3618.6597 8674.3425 Loop time of 1.77096 on 1 procs for 35 steps with 816 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 = -2141.56363398395 -3618.65617672586 -3618.65972404579 Force two-norm initial, final = 2938.4818 0.18668314 Force max component initial, final = 609.09305 0.031477895 Final line search alpha, max atom move = 1.0000000 0.031477895 Iterations, force evaluations = 35 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7591 | 1.7591 | 1.7591 | 0.0 | 99.33 Neigh | 0.0051155 | 0.0051155 | 0.0051155 | 0.0 | 0.29 Comm | 0.0030494 | 0.0030494 | 0.0030494 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003649 | | | 0.21 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3947.00 ave 3947 max 3947 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: 63752.0 ave 63752 max 63752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63752 Ave neighs/atom = 78.127451 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -3618.6597 0 -3618.6597 8674.3425 8897.2986 40 0 -3618.8473 0 -3618.8473 281.1519 8936.7351 Loop time of 0.225612 on 1 procs for 5 steps with 816 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 = -3618.65972404579 -3618.84588870748 -3618.84732087601 Force two-norm initial, final = 95.214050 3.0801877 Force max component initial, final = 85.510222 2.6573390 Final line search alpha, max atom move = 0.00020320387 0.00053998155 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22387 | 0.22387 | 0.22387 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002617 | 0.0002617 | 0.0002617 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001476 | | | 0.65 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940.00 ave 3940 max 3940 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: 63648.0 ave 63648 max 63648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63648 Ave neighs/atom = 78.000000 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 ghost atom cutoff = 6 binsize = 3, bins = 7 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.690 | 4.690 | 4.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3618.8473 0 -3618.8473 281.1519 Loop time of 2.136e-06 on 1 procs for 0 steps with 816 atoms 187.3% 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 | | 2.136e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940.00 ave 3940 max 3940 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: 63552.0 ave 63552 max 63552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63552 Ave neighs/atom = 77.882353 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 ghost atom cutoff = 6 binsize = 3, bins = 7 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.690 | 4.690 | 4.690 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 -3618.8473 -3618.8473 20.526248 87.444757 4.9789245 281.1519 281.1519 249.47545 478.40293 115.57732 2.3703274 493.47353 Loop time of 2.232e-06 on 1 procs for 0 steps with 816 atoms 268.8% 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 | | 2.232e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940.00 ave 3940 max 3940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31776.0 ave 31776 max 31776 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63552.0 ave 63552 max 63552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63552 Ave neighs/atom = 77.882353 Neighbor list builds = 0 Dangerous builds = 0 816 -3618.84732087601 eV 2.37032744558424 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02