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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -65.039682 0.0000000) to (45.990000 65.039682 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2455556 6.0221928 5.1100000 Created 1295 atoms using lattice units in orthogonal box = (0.0000000 -65.039682 0.0000000) to (45.990000 65.039682 5.1100000) create_atoms CPU = 0.004 seconds 1295 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2455556 6.0221928 5.1100000 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -65.039682 0.0000000) to (45.990000 65.039682 5.1100000) create_atoms CPU = 0.004 seconds 1299 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2594 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.717 | 5.717 | 5.717 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8463.5975 0 -8463.5975 62723.593 81 0 -9160.427 0 -9160.427 4978.4192 Loop time of 18.1696 on 1 procs for 81 steps with 2594 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8463.59752000073 -9160.41790220677 -9160.42704558488 Force two-norm initial, final = 562.36206 0.30889597 Force max component initial, final = 91.740461 0.039215352 Final line search alpha, max atom move = 1.0000000 0.039215352 Iterations, force evaluations = 81 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.012 | 18.012 | 18.012 | 0.0 | 99.13 Neigh | 0.071957 | 0.071957 | 0.071957 | 0.0 | 0.40 Comm | 0.049962 | 0.049962 | 0.049962 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03543 | | | 0.19 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10202.0 ave 10202 max 10202 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: 224176.0 ave 224176 max 224176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224176 Ave neighs/atom = 86.420971 Neighbor list builds = 2 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.717 | 5.717 | 5.717 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -9160.427 0 -9160.427 4978.4192 30569.809 85 0 -9160.6276 0 -9160.6276 1.2788948 30676.814 Loop time of 1.21003 on 1 procs for 4 steps with 2594 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 = -9160.42704558488 -9160.627540575 -9160.62756069927 Force two-norm initial, final = 169.87752 0.33904984 Force max component initial, final = 125.46371 0.095553605 Final line search alpha, max atom move = 0.0012188130 0.00011646198 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2009 | 1.2009 | 1.2009 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013877 | 0.0013877 | 0.0013877 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007727 | | | 0.64 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10202.0 ave 10202 max 10202 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: 224836.0 ave 224836 max 224836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224836 Ave neighs/atom = 86.675405 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.855 | 5.855 | 5.855 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9160.6276 0 -9160.6276 1.2788948 Loop time of 4.298e-06 on 1 procs for 0 steps with 2594 atoms 162.9% 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 | | 4.298e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10174.0 ave 10174 max 10174 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: 224628.0 ave 224628 max 224628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224628 Ave neighs/atom = 86.595220 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.855 | 5.855 | 5.855 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 -9160.6276 -9160.6276 46.044561 130.38171 5.1099335 1.2788948 1.2788948 -2.8705695 5.0021353 1.7051185 2.3630779 1334.8534 Loop time of 4.641e-06 on 1 procs for 0 steps with 2594 atoms 215.5% 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 | | 4.641e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10174.0 ave 10174 max 10174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112314.0 ave 112314 max 112314 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224628.0 ave 224628 max 224628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224628 Ave neighs/atom = 86.595220 Neighbor list builds = 0 Dangerous builds = 0 2594 -9160.62756069927 eV 2.36307790048467 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20