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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -49.649236 0.0000000) to (20.269216 49.649236 7.0214623) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8646117 4.3029338 4.6809748 Created 599 atoms using lattice units in orthogonal box = (0.0000000 -49.649236 0.0000000) to (20.269216 49.649236 7.0214623) create_atoms CPU = 0.001 seconds 599 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8646117 4.3029338 4.6809748 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -49.649236 0.0000000) to (20.269216 49.649236 7.0214623) create_atoms CPU = 0.001 seconds 601 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 8 35 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1200 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_142799717516_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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 8 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4981.6891 0 -4981.6891 28327.235 161 0 -5153.4429 0 -5153.4429 7945.0094 Loop time of 0.950519 on 1 procs for 161 steps with 1200 atoms 95.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4981.68905610328 -5153.43831219999 -5153.44294723909 Force two-norm initial, final = 108.49835 0.27966703 Force max component initial, final = 28.924305 0.063937085 Final line search alpha, max atom move = 1.0000000 0.063937085 Iterations, force evaluations = 161 305 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88982 | 0.88982 | 0.88982 | 0.0 | 93.61 Neigh | 0.034563 | 0.034563 | 0.034563 | 0.0 | 3.64 Comm | 0.011162 | 0.011162 | 0.011162 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01498 | | | 1.58 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4051.00 ave 4051 max 4051 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: 72774.0 ave 72774 max 72774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72774 Ave neighs/atom = 60.645000 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 8 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 161 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.593 | 4.593 | 4.593 Mbytes Step Temp E_pair E_mol TotEng Press Volume 161 0 -5153.4429 0 -5153.4429 7945.0094 14132.112 166 0 -5153.6903 0 -5153.6903 -6.8440756 14193.422 Loop time of 0.0204416 on 1 procs for 5 steps with 1200 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5153.44294723907 -5153.68983434761 -5153.69026178054 Force two-norm initial, final = 134.69005 0.38218057 Force max component initial, final = 117.73973 0.086294755 Final line search alpha, max atom move = 0.00036984129 3.1915364e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018785 | 0.018785 | 0.018785 | 0.0 | 91.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023767 | 0.00023767 | 0.00023767 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001419 | | | 6.94 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4352.00 ave 4352 max 4352 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: 73140.0 ave 73140 max 73140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73140 Ave neighs/atom = 60.950000 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 8 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.731 | 4.731 | 4.731 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5153.6903 0 -5153.6903 -6.8440756 Loop time of 1.714e-06 on 1 procs for 0 steps with 1200 atoms 116.7% 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 | | 1.714e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 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: 71760.0 ave 71760 max 71760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71760 Ave neighs/atom = 59.800000 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 8 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.731 | 4.731 | 4.731 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 -5153.6903 -5153.6903 20.27376 99.711997 7.0211038 -6.8440756 -6.8440756 -9.7432761 -7.1706512 -3.6182996 2.2702057 728.83052 Loop time of 1.745e-06 on 1 procs for 0 steps with 1200 atoms 171.9% 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 | | 1.745e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35880.0 ave 35880 max 35880 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71760.0 ave 71760 max 71760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71760 Ave neighs/atom = 59.800000 Neighbor list builds = 0 Dangerous builds = 0 1200 -5153.69026178054 eV 2.27020571945422 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01