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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -35.420139 0.0000000) to (25.045820 35.420139 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3127498 4.8300189 4.3599177 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -35.420139 0.0000000) to (25.045820 35.420139 4.3599177) create_atoms CPU = 0.002 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3127498 4.8300189 4.3599177 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -35.420139 0.0000000) to (25.045820 35.420139 4.3599177) create_atoms CPU = 0.001 seconds 266 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 528 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.236 | 5.236 | 5.236 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -713.67856 0 -713.67856 735665.68 225 0 -3423.855 0 -3423.855 5306.6064 Loop time of 66.7077 on 1 procs for 225 steps with 528 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 = -713.678559305925 -3423.85193825928 -3423.85504506298 Force two-norm initial, final = 7194.7017 0.25700090 Force max component initial, final = 2325.8968 0.096816962 Final line search alpha, max atom move = 1.0000000 0.096816962 Iterations, force evaluations = 225 423 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 66.508 | 66.508 | 66.508 | 0.0 | 99.70 Neigh | 0.16958 | 0.16958 | 0.16958 | 0.0 | 0.25 Comm | 0.016171 | 0.016171 | 0.016171 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01367 | | | 0.02 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3809.00 ave 3809 max 3809 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: 40456.0 ave 40456 max 40456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40456 Ave neighs/atom = 76.621212 Neighbor list builds = 7 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 225 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.236 | 5.236 | 5.236 Mbytes Step Temp E_pair E_mol TotEng Press Volume 225 0 -3423.855 0 -3423.855 5306.6064 7735.5965 231 0 -3424.1127 0 -3424.1127 24.080077 7753.8022 Loop time of 1.25641 on 1 procs for 6 steps with 528 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 = -3423.85504506297 -3424.11257362341 -3424.11272057636 Force two-norm initial, final = 95.319148 0.96924887 Force max component initial, final = 91.866635 0.51318873 Final line search alpha, max atom move = 0.0011579810 0.00059426280 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.255 | 1.255 | 1.255 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024637 | 0.00024637 | 0.00024637 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001211 | | | 0.10 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3820.00 ave 3820 max 3820 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: 40208.0 ave 40208 max 40208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40208 Ave neighs/atom = 76.151515 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.374 | 5.374 | 5.374 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3424.1127 0 -3424.1127 24.080077 Loop time of 2.039e-06 on 1 procs for 0 steps with 528 atoms 147.1% 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 | | 2.039e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3810.00 ave 3810 max 3810 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: 40022.0 ave 40022 max 40022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40022 Ave neighs/atom = 75.799242 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.374 | 5.374 | 5.374 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 -3424.1127 -3424.1127 25.170724 70.840882 4.3484557 24.080077 24.080077 13.949999 -47.471733 105.76196 2.4966448 1240.5779 Loop time of 1.815e-06 on 1 procs for 0 steps with 528 atoms 165.3% 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 | | 1.815e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3810.00 ave 3810 max 3810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20011.0 ave 20011 max 20011 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40022.0 ave 40022 max 40022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40022 Ave neighs/atom = 75.799242 Neighbor list builds = 0 Dangerous builds = 0 528 -3424.11272057636 eV 2.49664481701363 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:09