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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -45.642454 0.0000000) to (26.351683 45.642454 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6467892 5.4336254 6.0992294 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -45.642454 0.0000000) to (26.351683 45.642454 6.0992294) create_atoms CPU = 0.001 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6467892 5.4336254 6.0992294 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -45.642454 0.0000000) to (26.351683 45.642454 6.0992294) create_atoms CPU = 0.001 seconds 676 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 = 8 27 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_050461957184_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 = 8 27 2 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5754.4184 0 -5754.4184 45097.835 68 0 -5955.3285 0 -5955.3285 8996.7765 Loop time of 10.915 on 1 procs for 68 steps with 1344 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5754.41844207663 -5955.32407339785 -5955.32846761647 Force two-norm initial, final = 259.76233 0.20932686 Force max component initial, final = 61.400707 0.039166230 Final line search alpha, max atom move = 1.0000000 0.039166230 Iterations, force evaluations = 68 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.884 | 10.884 | 10.884 | 0.0 | 99.72 Neigh | 0.011164 | 0.011164 | 0.011164 | 0.0 | 0.10 Comm | 0.010128 | 0.010128 | 0.010128 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009618 | | | 0.09 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6551.00 ave 6551 max 6551 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: 179528.0 ave 179528 max 179528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179528 Ave neighs/atom = 133.57738 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 8 27 2 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -5955.3285 0 -5955.3285 8996.7765 14671.763 74 0 -5955.7484 0 -5955.7484 41.689647 14742.281 Loop time of 0.705325 on 1 procs for 6 steps with 1344 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 = -5955.32846761647 -5955.74583654701 -5955.74838696987 Force two-norm initial, final = 170.28084 1.1142245 Force max component initial, final = 153.66832 0.95529687 Final line search alpha, max atom move = 0.00013119921 0.00012533420 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70233 | 0.70233 | 0.70233 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044384 | 0.00044384 | 0.00044384 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002547 | | | 0.36 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6575.00 ave 6575 max 6575 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: 179544.0 ave 179544 max 179544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179544 Ave neighs/atom = 133.58929 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 = 8 27 2 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) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5955.7484 0 -5955.7484 41.689647 Loop time of 2.284e-06 on 1 procs for 0 steps with 1344 atoms 175.1% 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 | | 2.284e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6551.00 ave 6551 max 6551 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: 179264.0 ave 179264 max 179264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179264 Ave neighs/atom = 133.38095 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 = 8 27 2 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) = 5.235 | 5.235 | 5.235 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 -5955.7484 -5955.7484 26.367733 91.780267 6.0917571 41.689647 41.689647 -21.266057 42.641474 103.69352 2.2538677 711.69376 Loop time of 2.39e-06 on 1 procs for 0 steps with 1344 atoms 209.2% 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 | | 2.39e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6551.00 ave 6551 max 6551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89632.0 ave 89632 max 89632 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179264.0 ave 179264 max 179264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179264 Ave neighs/atom = 133.38095 Neighbor list builds = 0 Dangerous builds = 0 1344 -5955.74838696987 eV 2.2538676853997 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12