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 = 3.5937292 3.5937292 3.5937292 Created orthogonal box = (0.0000000 -40.658404 0.0000000) to (6.2245215 40.658404 8.8028028) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2245215 5.0823006 5.8685352 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -40.658404 0.0000000) to (6.2245215 40.658404 8.8028028) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2245215 5.0823006 5.8685352 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -40.658404 0.0000000) to (6.2245215 40.658404 8.8028028) create_atoms CPU = 0.001 seconds 198 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 2 24 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 384 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 2 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1640.5676 0 -1640.5676 -0.0070866555 1 0 -1640.5676 0 -1640.5676 -0.0070866556 Loop time of 0.075426 on 1 procs for 1 steps with 384 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 = -1640.56760170598 -1640.56760170598 -1640.56760170598 Force two-norm initial, final = 1.1889700e-07 3.9151547e-08 Force max component initial, final = 2.9842595e-08 1.0721059e-08 Final line search alpha, max atom move = 1.0000000 1.0721059e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075094 | 0.075094 | 0.075094 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013602 | 0.00013602 | 0.00013602 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001956 | | | 0.26 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3518.00 ave 3518 max 3518 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: 51456.0 ave 51456 max 51456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51456 Ave neighs/atom = 134.00000 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 2 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -1640.5676 0 -1640.5676 -0.0070866556 4455.611 2 0 -1640.5676 0 -1640.5676 -3.0133768e-07 4455.611 Loop time of 0.0751387 on 1 procs for 1 steps with 384 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 = -1640.56760170598 -1640.56760170598 -1640.56760170603 Force two-norm initial, final = 3.4136251e-05 2.0984600e-07 Force max component initial, final = 1.9950939e-05 1.6897271e-07 Final line search alpha, max atom move = 1.0000000 1.6897271e-07 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.074595 | 0.074595 | 0.074595 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010573 | 0.00010573 | 0.00010573 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004375 | | | 0.58 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3518.00 ave 3518 max 3518 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: 51456.0 ave 51456 max 51456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51456 Ave neighs/atom = 134.00000 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 2 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.654 | 4.654 | 4.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1640.5676 0 -1640.5676 -3.0132992e-07 Loop time of 2.303e-06 on 1 procs for 0 steps with 384 atoms 173.7% 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 | | 2.303e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3518.00 ave 3518 max 3518 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: 51456.0 ave 51456 max 51456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51456 Ave neighs/atom = 134.00000 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 2 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.654 | 4.654 | 4.654 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 -1640.5676 -1640.5676 6.2245215 81.316809 8.8028028 -3.0132992e-07 -3.0132992e-07 3.2446288e-05 -6.076026e-05 2.7409982e-05 2.5411503 3.4812465e-16 Loop time of 3.047e-06 on 1 procs for 0 steps with 384 atoms 196.9% 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 | | 3.047e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3518.00 ave 3518 max 3518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25728.0 ave 25728 max 25728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51456.0 ave 51456 max 51456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51456 Ave neighs/atom = 134.00000 Neighbor list builds = 0 Dangerous builds = 0 384 -1640.56760170603 eV 2.54115027125954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00