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 = 3.5192937 3.5192937 3.5192937 Created orthogonal box = (0.0000000 -67.331571 0.0000000) to (38.871869 67.331571 6.0955954) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7351938 5.1507799 6.0955954 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -67.331571 0.0000000) to (38.871869 67.331571 6.0955954) create_atoms CPU = 0.009 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7351938 5.1507799 6.0955954 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -67.331571 0.0000000) to (38.871869 67.331571 6.0955954) create_atoms CPU = 0.009 seconds 1465 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2906 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12845.91 0 -12845.91 4779.1577 38 0 -12889.087 0 -12889.087 -4824.6598 Loop time of 3.87889 on 1 procs for 38 steps with 2906 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 = -12845.910465411 -12889.0755782214 -12889.0873762813 Force two-norm initial, final = 59.627093 0.36637866 Force max component initial, final = 9.2578159 0.023789006 Final line search alpha, max atom move = 0.96232283 0.022892704 Iterations, force evaluations = 38 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7664 | 3.7664 | 3.7664 | 0.0 | 97.10 Neigh | 0.067614 | 0.067614 | 0.067614 | 0.0 | 1.74 Comm | 0.023944 | 0.023944 | 0.023944 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02092 | | | 0.54 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13552.0 ave 13552 max 13552 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: 506788.0 ave 506788 max 506788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506788 Ave neighs/atom = 174.39367 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -12889.087 0 -12889.087 -4824.6598 31908.053 40 0 -12889.149 0 -12889.149 -1858.5356 31854.681 Loop time of 0.274476 on 1 procs for 2 steps with 2906 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12889.0873762812 -12889.1480813175 -12889.1491728313 Force two-norm initial, final = 100.08220 0.37820086 Force max component initial, final = 81.376564 0.021974086 Final line search alpha, max atom move = 0.00013130168 2.8852345e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26826 | 0.26826 | 0.26826 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014678 | 0.0014678 | 0.0014678 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004748 | | | 1.73 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13552.0 ave 13552 max 13552 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: 506902.0 ave 506902 max 506902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506902 Ave neighs/atom = 174.43290 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 10.39 | 10.39 | 10.39 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12889.149 0 -12889.149 -1858.5356 Loop time of 6.706e-06 on 1 procs for 0 steps with 2906 atoms 193.9% 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 | | 6.706e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13552.0 ave 13552 max 13552 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: 506988.0 ave 506988 max 506988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506988 Ave neighs/atom = 174.46249 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 10.39 | 10.39 | 10.39 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 -12889.149 -12889.149 38.827955 134.66314 6.0922821 -1858.5356 -1858.5356 0.0016794963 -5575.443 -0.16532189 2.2493528 1011.5569 Loop time of 6.986e-06 on 1 procs for 0 steps with 2906 atoms 300.6% 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 | | 6.986e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13552.0 ave 13552 max 13552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 253494.0 ave 253494 max 253494 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 506988.0 ave 506988 max 506988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506988 Ave neighs/atom = 174.46249 Neighbor list builds = 0 Dangerous builds = 0 2906 -12889.1491728313 eV 2.24935282836069 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05