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 = 4.0499994 4.0499994 4.0499994 Created orthogonal box = (0.0000000 -69.206421 0.0000000) to (34.603210 69.206421 4.0499994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2141824 5.2141824 4.0499994 Created 584 atoms using lattice units in orthogonal box = (0.0000000 -69.206421 0.0000000) to (34.603210 69.206421 4.0499994) create_atoms CPU = 0.002 seconds 584 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2141824 5.2141824 4.0499994 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -69.206421 0.0000000) to (34.603210 69.206421 4.0499994) create_atoms CPU = 0.002 seconds 586 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 = 8 32 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1168 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_117656786760_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 = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.454 | 5.454 | 5.454 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3895.1883 0 -3895.1883 3421.9876 22 0 -3915.4915 0 -3915.4915 3501.6858 Loop time of 0.931849 on 1 procs for 22 steps with 1168 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3895.18827926753 -3915.48922551909 -3915.49149852223 Force two-norm initial, final = 22.623425 0.091145299 Force max component initial, final = 6.8801699 0.0066149135 Final line search alpha, max atom move = 1.0000000 0.0066149135 Iterations, force evaluations = 22 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91847 | 0.91847 | 0.91847 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.007509 | 0.007509 | 0.007509 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00587 | | | 0.63 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8732.00 ave 8732 max 8732 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: 204904.0 ave 204904 max 204904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204904 Ave neighs/atom = 175.43151 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 = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.454 | 5.454 | 5.454 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -3915.4915 0 -3915.4915 3501.6858 19397.589 29 0 -3915.7292 0 -3915.7292 -14.544072 19483.28 Loop time of 0.227399 on 1 procs for 7 steps with 1168 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3915.49149852222 -3915.72666173995 -3915.72923669405 Force two-norm initial, final = 86.373224 0.39060562 Force max component initial, final = 79.341501 0.26947463 Final line search alpha, max atom move = 0.00020515432 5.5283885e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22018 | 0.22018 | 0.22018 | 0.0 | 96.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001794 | 0.001794 | 0.001794 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005421 | | | 2.38 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8732.00 ave 8732 max 8732 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: 203792.0 ave 203792 max 203792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203792 Ave neighs/atom = 174.47945 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 = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.592 | 5.592 | 5.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3915.7292 0 -3915.7292 -14.544072 Loop time of 6.896e-06 on 1 procs for 0 steps with 1168 atoms 203.0% 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 | | 6.896e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8717.00 ave 8717 max 8717 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: 203532.0 ave 203532 max 203532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203532 Ave neighs/atom = 174.25685 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 = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.592 | 5.592 | 5.592 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 -3915.7292 -3915.7292 34.583673 139.34148 4.0430633 -14.544072 -14.544072 -4.9884598 -16.52189 -22.121866 2.5237663 621.00469 Loop time of 7.347e-06 on 1 procs for 0 steps with 1168 atoms 217.8% 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 | | 7.347e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8717.00 ave 8717 max 8717 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101766.0 ave 101766 max 101766 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203532.0 ave 203532 max 203532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203532 Ave neighs/atom = 174.25685 Neighbor list builds = 0 Dangerous builds = 0 1168 -3844.20825393923 eV 2.52376627231117 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01