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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -56.764863 0.0000000) to (34.759030 56.764863 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6062952 5.4930250 5.8858683 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -56.764863 0.0000000) to (34.759030 56.764863 8.8288024) create_atoms CPU = 0.004 seconds 1493 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6062952 5.4930250 5.8858683 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -56.764863 0.0000000) to (34.759030 56.764863 8.8288024) create_atoms CPU = 0.004 seconds 1493 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 38 3 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 34 atoms, new total = 2952 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 38 3 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) = 5.629 | 5.629 | 5.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12454.02 0 -12454.02 -480.42312 58 0 -12510.137 0 -12510.137 -11099.922 Loop time of 18.5354 on 1 procs for 58 steps with 2952 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12454.0203888324 -12510.1255868954 -12510.1370399853 Force two-norm initial, final = 37.849022 0.32313853 Force max component initial, final = 6.2295098 0.040199811 Final line search alpha, max atom move = 1.0000000 0.040199811 Iterations, force evaluations = 58 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.459 | 18.459 | 18.459 | 0.0 | 99.59 Neigh | 0.036674 | 0.036674 | 0.036674 | 0.0 | 0.20 Comm | 0.015276 | 0.015276 | 0.015276 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02463 | | | 0.13 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7707.00 ave 7707 max 7707 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: 229454.0 ave 229454 max 229454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229454 Ave neighs/atom = 77.728320 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -12510.137 0 -12510.137 -11099.922 34840.071 62 0 -12510.57 0 -12510.57 -3701.7223 34678.005 Loop time of 1.33991 on 1 procs for 4 steps with 2952 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 = -12510.1370399854 -12510.5682136971 -12510.5701520249 Force two-norm initial, final = 255.55713 0.36169887 Force max component initial, final = 200.08958 0.047456020 Final line search alpha, max atom move = 0.00011289556 5.3575741e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3338 | 1.3338 | 1.3338 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085751 | 0.00085751 | 0.00085751 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00523 | | | 0.39 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7683.00 ave 7683 max 7683 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: 230052.0 ave 230052 max 230052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230052 Ave neighs/atom = 77.930894 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 38 3 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) = 5.767 | 5.767 | 5.767 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12510.57 0 -12510.57 -3701.7223 Loop time of 2.996e-06 on 1 procs for 0 steps with 2952 atoms 166.9% 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 | | 2.996e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7699.00 ave 7699 max 7699 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: 230222.0 ave 230222 max 230222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230222 Ave neighs/atom = 77.988482 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 38 3 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) = 5.767 | 5.767 | 5.767 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 -12510.57 -12510.57 34.701118 113.52973 8.802399 -3701.7223 -3701.7223 -1.7363991 -11102.674 -0.75632553 2.3090645 1142.335 Loop time of 3.505e-06 on 1 procs for 0 steps with 2952 atoms 199.7% 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 | | 3.505e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7699.00 ave 7699 max 7699 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115111.0 ave 115111 max 115111 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 230222.0 ave 230222 max 230222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230222 Ave neighs/atom = 77.988482 Neighbor list builds = 0 Dangerous builds = 0 2952 -12510.5701520249 eV 2.30906448098732 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21