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 = 3.6150007 3.6150007 3.6150007 Created orthogonal box = (0.0000000 -43.680220 0.0000000) to (53.497125 43.680220 8.8549071) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1298613 5.3852326 5.9032714 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -43.680220 0.0000000) to (53.497125 43.680220 8.8549071) create_atoms CPU = 0.002 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1298613 5.3852326 5.9032714 Created 1753 atoms using lattice units in orthogonal box = (0.0000000 -43.680220 0.0000000) to (53.497125 43.680220 8.8549071) create_atoms CPU = 0.002 seconds 1753 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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 17 28 3 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 6.428375000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 3476 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_642748370624_000#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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 17 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.428375000000001 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) = 6.065 | 6.065 | 6.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9954.407 0 -9954.407 134581.92 89 0 -12179.347 0 -12179.347 -3739.0744 Loop time of 1.66512 on 1 procs for 89 steps with 3476 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9954.40700689645 -12179.33464482 -12179.3467697006 Force two-norm initial, final = 3476.4665 0.27421057 Force max component initial, final = 658.36222 0.017479253 Final line search alpha, max atom move = 1.0000000 0.017479253 Iterations, force evaluations = 89 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.544 | 1.544 | 1.544 | 0.0 | 92.73 Neigh | 0.092185 | 0.092185 | 0.092185 | 0.0 | 5.54 Comm | 0.010201 | 0.010201 | 0.010201 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01871 | | | 1.12 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8614.00 ave 8614 max 8614 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: 299072.0 ave 299072 max 299072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299072 Ave neighs/atom = 86.039125 Neighbor list builds = 4 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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 17 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.428375000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.067 | 6.067 | 6.067 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -12179.347 0 -12179.347 -3739.0744 41383.695 93 0 -12179.634 0 -12179.634 282.34581 41271.31 Loop time of 0.0744217 on 1 procs for 4 steps with 3476 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12179.3467697006 -12179.6290434082 -12179.63408816 Force two-norm initial, final = 192.81154 16.983527 Force max component initial, final = 173.25481 12.967601 Final line search alpha, max atom move = 3.8805904e-05 0.00050321948 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071397 | 0.071397 | 0.071397 | 0.0 | 95.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041593 | 0.00041593 | 0.00041593 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002609 | | | 3.51 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8803.00 ave 8803 max 8803 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: 299024.0 ave 299024 max 299024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299024 Ave neighs/atom = 86.025316 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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 17 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.428375000000001 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) = 6.205 | 6.205 | 6.205 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12179.634 0 -12179.634 282.34581 Loop time of 1.2594e-05 on 1 procs for 0 steps with 3476 atoms 111.2% 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 | | 1.259e-05 | | |100.00 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8818.00 ave 8818 max 8818 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: 299100.0 ave 299100 max 299100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299100 Ave neighs/atom = 86.047181 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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 17 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.428375000000001 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) = 6.205 | 6.205 | 6.205 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 -12179.634 -12179.634 53.500794 87.064959 8.8602225 282.34581 282.34581 503.44442 -75.354345 418.94735 2.3155706 1380.7038 Loop time of 1.906e-06 on 1 procs for 0 steps with 3476 atoms 209.9% 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 | | 1.906e-06 | | |100.00 Nlocal: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8818.00 ave 8818 max 8818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149550.0 ave 149550 max 149550 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 299100.0 ave 299100 max 299100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299100 Ave neighs/atom = 86.047181 Neighbor list builds = 0 Dangerous builds = 0 3476 -12179.63408816 eV 2.3155705552304 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03