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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -43.374310 0.0000000) to (15.335134 43.374310 4.9753746) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6497864 4.5657169 4.9753746 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -43.374310 0.0000000) to (15.335134 43.374310 4.9753746) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6497864 4.5657169 4.9753746 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.374310 0.0000000) to (15.335134 43.374310 4.9753746) 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 19 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 604 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_149104665840_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 4.992 | 4.992 | 4.992 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2395.9322 0 -2395.9322 92851.904 54 0 -2638.0525 0 -2638.0525 -2508.5757 Loop time of 1.20336 on 1 procs for 54 steps with 604 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2395.93221644313 -2638.05010802084 -2638.05251208515 Force two-norm initial, final = 592.22410 0.15699968 Force max component initial, final = 195.40710 0.018676381 Final line search alpha, max atom move = 1.0000000 0.018676381 Iterations, force evaluations = 54 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1814 | 1.1814 | 1.1814 | 0.0 | 98.18 Neigh | 0.010857 | 0.010857 | 0.010857 | 0.0 | 0.90 Comm | 0.006739 | 0.006739 | 0.006739 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004353 | | | 0.36 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7606.00 ave 7606 max 7606 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: 196444.0 ave 196444 max 196444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196444 Ave neighs/atom = 325.23841 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.000 | 5.000 | 5.000 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -2638.0525 0 -2638.0525 -2508.5757 6618.7496 57 0 -2638.0676 0 -2638.0676 -10.229274 6609.2757 Loop time of 0.0728808 on 1 procs for 3 steps with 604 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 = -2638.05251208515 -2638.0674118791 -2638.06757613559 Force two-norm initial, final = 20.086443 0.20643536 Force max component initial, final = 16.058837 0.11803326 Final line search alpha, max atom move = 0.00070981496 8.3781771e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071181 | 0.071181 | 0.071181 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033612 | 0.00033612 | 0.00033612 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001364 | | | 1.87 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7606.00 ave 7606 max 7606 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: 195604.0 ave 195604 max 195604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195604 Ave neighs/atom = 323.84768 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.138 | 5.138 | 5.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2638.0676 0 -2638.0676 -10.229274 Loop time of 1.696e-06 on 1 procs for 0 steps with 604 atoms 117.9% 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 | | 1.696e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7606.00 ave 7606 max 7606 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: 195948.0 ave 195948 max 195948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195948 Ave neighs/atom = 324.41722 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 4 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.138 | 5.138 | 5.138 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 -2638.0676 -2638.0676 15.314251 86.825495 4.9706231 -10.229274 -10.229274 -28.573869 6.8336228 -8.9475768 2.3286353 276.75742 Loop time of 1.91e-06 on 1 procs for 0 steps with 604 atoms 209.4% 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 | | 1.91e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7606.00 ave 7606 max 7606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97974.0 ave 97974 max 97974 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 195948.0 ave 195948 max 195948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195948 Ave neighs/atom = 324.41722 Neighbor list builds = 0 Dangerous builds = 0 604 -2638.06757613559 eV 2.32863528929272 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01