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 = 2.6534432 2.6534432 2.6534432 Created orthogonal box = (0.0000000 -35.201902 0.0000000) to (12.445752 35.201902 3.7525354) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5257279 4.0002161 3.7525354 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -35.201902 0.0000000) to (12.445752 35.201902 3.7525354) create_atoms CPU = 0.001 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5257279 4.0002161 3.7525354 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -35.201902 0.0000000) to (12.445752 35.201902 3.7525354) create_atoms CPU = 0.000 seconds 178 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 19 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 350 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_201919462778_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.485 | 4.485 | 4.485 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2669.5906 0 -2669.5906 222181.19 54 0 -2908.8322 0 -2908.8322 28540.975 Loop time of 1.37088 on 1 procs for 54 steps with 350 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 = -2669.59063095212 -2908.8294839197 -2908.83220597498 Force two-norm initial, final = 737.92314 0.32453485 Force max component initial, final = 256.04068 0.045344057 Final line search alpha, max atom move = 1.0000000 0.045344057 Iterations, force evaluations = 54 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3527 | 1.3527 | 1.3527 | 0.0 | 98.68 Neigh | 0.0094172 | 0.0094172 | 0.0094172 | 0.0 | 0.69 Comm | 0.005477 | 0.005477 | 0.005477 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003268 | | | 0.24 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4790.00 ave 4790 max 4790 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: 62328.0 ave 62328 max 62328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62328 Ave neighs/atom = 178.08000 Neighbor list builds = 2 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -2908.8322 0 -2908.8322 28540.975 3288.0776 59 0 -2909.0146 0 -2909.0146 -27.640962 3302.0556 Loop time of 0.0972955 on 1 procs for 5 steps with 350 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 = -2908.83220597499 -2909.01376005525 -2909.0145753322 Force two-norm initial, final = 109.59257 0.61473369 Force max component initial, final = 92.374861 0.26948345 Final line search alpha, max atom move = 0.00012424961 3.3483213e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095856 | 0.095856 | 0.095856 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028953 | 0.00028953 | 0.00028953 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00115 | | | 1.18 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4739.00 ave 4739 max 4739 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: 62532.0 ave 62532 max 62532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62532 Ave neighs/atom = 178.66286 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2909.0146 0 -2909.0146 -27.640962 Loop time of 1.912e-06 on 1 procs for 0 steps with 350 atoms 156.9% 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 | | 1.912e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4739.00 ave 4739 max 4739 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: 62444.0 ave 62444 max 62444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62444 Ave neighs/atom = 178.41143 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.622 | 4.622 | 4.622 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 -2909.0146 -2909.0146 12.449535 70.667738 3.753272 -27.640962 -27.640962 92.579929 -44.722216 -130.7806 2.1414853 193.20383 Loop time of 2.712e-06 on 1 procs for 0 steps with 350 atoms 184.4% 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 | | 2.712e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4739.00 ave 4739 max 4739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31222.0 ave 31222 max 31222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62444.0 ave 62444 max 62444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62444 Ave neighs/atom = 178.41143 Neighbor list builds = 0 Dangerous builds = 0 350 -2909.0145753322 eV 2.14148532507164 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01