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 = 2.8552583 2.8552583 2.8552583 Created orthogonal box = (0.0000000 -46.039657 0.0000000) to (23.019828 46.039657 2.8552583) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8956633 3.8956633 2.8552583 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -46.039657 0.0000000) to (23.019828 46.039657 2.8552583) create_atoms CPU = 0.001 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8956633 3.8956633 2.8552583 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.039657 0.0000000) to (23.019828 46.039657 2.8552583) create_atoms CPU = 0.000 seconds 261 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 24 1 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 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_942420706858_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1985.1091 0 -1985.1091 109435.39 35 0 -2143.2388 0 -2143.2388 10417.676 Loop time of 0.333472 on 1 procs for 35 steps with 521 atoms 95.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1985.10912516732 -2143.23733864964 -2143.23880686619 Force two-norm initial, final = 301.32108 0.10787440 Force max component initial, final = 146.40226 0.030209542 Final line search alpha, max atom move = 0.94939070 0.028680658 Iterations, force evaluations = 35 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32678 | 0.32678 | 0.32678 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0040952 | 0.0040952 | 0.0040952 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002599 | | | 0.78 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6724.00 ave 6724 max 6724 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: 88462.0 ave 88462 max 88462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88462 Ave neighs/atom = 169.79271 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -2143.2388 0 -2143.2388 10417.676 6052.1482 44 0 -2143.5704 0 -2143.5704 -127.33174 6089.746 Loop time of 0.0601252 on 1 procs for 9 steps with 521 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 = -2143.23880686619 -2143.56853305953 -2143.57044339885 Force two-norm initial, final = 86.551619 1.6530662 Force max component initial, final = 80.982561 1.1152145 Final line search alpha, max atom move = 0.00031154984 0.00034744490 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.056871 | 0.056871 | 0.056871 | 0.0 | 94.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059161 | 0.00059161 | 0.00059161 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002663 | | | 4.43 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6724.00 ave 6724 max 6724 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: 88120.0 ave 88120 max 88120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88120 Ave neighs/atom = 169.13628 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.665 | 4.665 | 4.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2143.5704 0 -2143.5704 -127.33174 Loop time of 2.045e-06 on 1 procs for 0 steps with 521 atoms 146.7% 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 | | 2.045e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6731.00 ave 6731 max 6731 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: 87842.0 ave 87842 max 87842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87842 Ave neighs/atom = 168.60269 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.665 | 4.665 | 4.665 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 -2143.5704 -2143.5704 22.976341 92.879286 2.8536417 -127.33174 -127.33174 173.13438 -261.88929 -293.24029 2.2288494 219.73226 Loop time of 1.981e-06 on 1 procs for 0 steps with 521 atoms 201.9% 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 | | 1.981e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6731.00 ave 6731 max 6731 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43921.0 ave 43921 max 43921 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87842.0 ave 87842 max 87842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87842 Ave neighs/atom = 168.60269 Neighbor list builds = 0 Dangerous builds = 0 521 -2143.57044339885 eV 2.2288493878472 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00