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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -35.893422 0.0000000) to (31.081567 35.893422 6.0955968) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5787428 5.5215234 6.0955968 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -35.893422 0.0000000) to (31.081567 35.893422 6.0955968) create_atoms CPU = 0.004 seconds 630 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5787428 5.5215234 6.0955968 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -35.893422 0.0000000) to (31.081567 35.893422 6.0955968) create_atoms CPU = 0.004 seconds 630 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 = 9 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1234 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_677715648236_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 = 9 19 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) = 5.456 | 5.456 | 5.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5419.9959 0 -5419.9959 14403.301 62 0 -5456.6409 0 -5456.6409 -4729.5856 Loop time of 2.75689 on 1 procs for 62 steps with 1234 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 = -5419.99586921578 -5456.63581105898 -5456.64085807678 Force two-norm initial, final = 76.816588 0.25382067 Force max component initial, final = 18.500512 0.023531434 Final line search alpha, max atom move = 1.0000000 0.023531434 Iterations, force evaluations = 62 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7201 | 2.7201 | 2.7201 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019548 | 0.019548 | 0.019548 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01727 | | | 0.63 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6923.00 ave 6923 max 6923 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: 213716.0 ave 213716 max 213716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213716 Ave neighs/atom = 173.18963 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.456 | 5.456 | 5.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -5456.6409 0 -5456.6409 -4729.5856 13600.786 64 0 -5456.6795 0 -5456.6795 -1111.7839 13572.635 Loop time of 0.0942263 on 1 procs for 2 steps with 1234 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5456.6408580768 -5456.67854550675 -5456.67953429438 Force two-norm initial, final = 52.258118 1.0634249 Force max component initial, final = 41.811478 0.93464782 Final line search alpha, max atom move = 0.00013498288 0.00012616145 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091755 | 0.091755 | 0.091755 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061183 | 0.00061183 | 0.00061183 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00186 | | | 1.97 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6938.00 ave 6938 max 6938 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: 213492.0 ave 213492 max 213492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213492 Ave neighs/atom = 173.00810 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 = 9 19 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) = 5.594 | 5.594 | 5.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5456.6795 0 -5456.6795 -1111.7839 Loop time of 6.535e-06 on 1 procs for 0 steps with 1234 atoms 168.3% 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 | | 6.535e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6938.00 ave 6938 max 6938 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: 213576.0 ave 213576 max 213576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213576 Ave neighs/atom = 173.07618 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 = 9 19 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) = 5.594 | 5.594 | 5.594 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 -5456.6795 -5456.6795 31.055028 71.786843 6.0881787 -1111.7839 -1111.7839 110.23594 -3394.8795 -50.708236 2.1906552 827.06 Loop time of 6.886e-06 on 1 procs for 0 steps with 1234 atoms 275.9% 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 | | 6.886e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6938.00 ave 6938 max 6938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106788.0 ave 106788 max 106788 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 213576.0 ave 213576 max 213576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213576 Ave neighs/atom = 173.07618 Neighbor list builds = 0 Dangerous builds = 0 1234 -5456.67953429438 eV 2.19065523122433 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03