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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -43.111020 0.0000000) to (6.0968189 43.111020 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0968189 5.7481360 4.9780318 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -43.111020 0.0000000) to (6.0968189 43.111020 4.9780318) create_atoms CPU = 0.004 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0968189 5.7481360 4.9780318 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.111020 0.0000000) to (6.0968189 43.111020 4.9780318) create_atoms CPU = 0.002 seconds 122 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 2 20 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_101214310689_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 2 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.499 | 4.499 | 4.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1056.5648 0 -1056.5648 11497.815 46 0 -1064.2908 0 -1064.2908 6704.0771 Loop time of 0.807376 on 1 procs for 46 steps with 240 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 = -1056.56479043767 -1064.28994415322 -1064.29081043847 Force two-norm initial, final = 14.238088 0.099598439 Force max component initial, final = 4.5579480 0.013235048 Final line search alpha, max atom move = 1.0000000 0.013235048 Iterations, force evaluations = 46 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7926 | 0.7926 | 0.7926 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0092752 | 0.0092752 | 0.0092752 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005503 | | | 0.68 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4548.00 ave 4548 max 4548 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: 59756.0 ave 59756 max 59756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59756 Ave neighs/atom = 248.98333 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 2 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.499 | 4.499 | 4.499 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -1064.2908 0 -1064.2908 6704.0771 2616.8525 49 0 -1064.3115 0 -1064.3115 -4.0657177 2626.7068 Loop time of 0.0560354 on 1 procs for 3 steps with 240 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 = -1064.29081043847 -1064.3114488631 -1064.31146604707 Force two-norm initial, final = 18.991081 0.11804026 Force max component initial, final = 11.740902 0.038250358 Final line search alpha, max atom move = 0.0040781260 0.00015598978 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053884 | 0.053884 | 0.053884 | 0.0 | 96.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055504 | 0.00055504 | 0.00055504 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001596 | | | 2.85 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4548.00 ave 4548 max 4548 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: 59612.0 ave 59612 max 59612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59612 Ave neighs/atom = 248.38333 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 2 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.636 | 4.636 | 4.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1064.3115 0 -1064.3115 -4.0657177 Loop time of 6.435e-06 on 1 procs for 0 steps with 240 atoms 170.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4548.00 ave 4548 max 4548 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: 59544.0 ave 59544 max 59544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59544 Ave neighs/atom = 248.10000 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 2 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.636 | 4.636 | 4.636 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 -1064.3115 -1064.3115 6.103662 86.324163 4.9852707 -4.0657177 -4.0657177 23.357236 -18.433236 -17.121153 2.3623495 120.66991 Loop time of 7.096e-06 on 1 procs for 0 steps with 240 atoms 197.3% 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 | | 7.096e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4548.00 ave 4548 max 4548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29772.0 ave 29772 max 29772 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59544.0 ave 59544 max 59544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59544 Ave neighs/atom = 248.10000 Neighbor list builds = 0 Dangerous builds = 0 240 -1058.89955001009 eV 2.36234947201078 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01