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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -44.487701 0.0000000) to (15.728778 44.487701 5.1030893) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7948128 4.6829159 5.1030893 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -44.487701 0.0000000) to (15.728778 44.487701 5.1030893) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7948128 4.6829159 5.1030893 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -44.487701 0.0000000) to (15.728778 44.487701 5.1030893) create_atoms CPU = 0.001 seconds 306 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 ghost atom cutoff = 6 binsize = 3, bins = 6 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 608 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_549900287421_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 ghost atom cutoff = 6 binsize = 3, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2397.8433 0 -2397.8433 98747.821 102 0 -2581.1385 0 -2581.1385 3367.2222 Loop time of 4.64263 on 1 procs for 102 steps with 608 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 = -2397.84328006393 -2581.13652202794 -2581.1384733488 Force two-norm initial, final = 702.76642 0.11836932 Force max component initial, final = 239.51845 0.017170480 Final line search alpha, max atom move = 1.0000000 0.017170480 Iterations, force evaluations = 102 191 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6231 | 4.6231 | 4.6231 | 0.0 | 99.58 Neigh | 0.003642 | 0.003642 | 0.003642 | 0.0 | 0.08 Comm | 0.007908 | 0.007908 | 0.007908 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007974 | | | 0.17 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3410.00 ave 3410 max 3410 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: 46896.0 ave 46896 max 46896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46896 Ave neighs/atom = 77.131579 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.512 | 4.512 | 4.512 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -2581.1385 0 -2581.1385 3367.2222 7141.6423 108 0 -2581.2556 0 -2581.2556 -35.590423 7155.9735 Loop time of 0.209513 on 1 procs for 6 steps with 608 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 = -2581.1384733488 -2581.25503426259 -2581.2555940194 Force two-norm initial, final = 42.631654 1.0019616 Force max component initial, final = 29.481015 0.87031529 Final line search alpha, max atom move = 0.00017674443 0.00015382338 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20785 | 0.20785 | 0.20785 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027297 | 0.00027297 | 0.00027297 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001393 | | | 0.66 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3323.00 ave 3323 max 3323 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: 46624.0 ave 46624 max 46624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46624 Ave neighs/atom = 76.684211 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 ghost atom cutoff = 6 binsize = 3, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2581.2556 0 -2581.2556 -35.590423 Loop time of 2.46e-06 on 1 procs for 0 steps with 608 atoms 203.3% 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 | | 2.46e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3323.00 ave 3323 max 3323 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: 46616.0 ave 46616 max 46616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46616 Ave neighs/atom = 76.671053 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 ghost atom cutoff = 6 binsize = 3, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.650 | 4.650 | 4.650 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 -2581.2556 -2581.2556 15.661464 89.393752 5.1112746 -35.590423 -35.590423 95.838121 -7.4388368 -195.17055 2.3745114 652.52326 Loop time of 2.198e-06 on 1 procs for 0 steps with 608 atoms 227.5% 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 | | 2.198e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3323.00 ave 3323 max 3323 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23308.0 ave 23308 max 23308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46616.0 ave 46616 max 46616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46616 Ave neighs/atom = 76.671053 Neighbor list builds = 0 Dangerous builds = 0 608 -2581.2555940194 eV 2.37451140003577 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05