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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -39.065419 0.0000000) to (18.415615 39.065419 4.4664427) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4163574 5.3619203 4.4664427 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -39.065419 0.0000000) to (18.415615 39.065419 4.4664427) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4163574 5.3619203 4.4664427 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -39.065419 0.0000000) to (18.415615 39.065419 4.4664427) create_atoms CPU = 0.001 seconds 206 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 406 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_228581001644_004#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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.469 | 4.469 | 4.469 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2144.8845 0 -2144.8845 160413.64 121 0 -2570.4994 0 -2570.4994 441.42616 Loop time of 0.520701 on 1 procs for 121 steps with 406 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2144.8845092991 -2570.49729259077 -2570.49936211492 Force two-norm initial, final = 874.04234 0.25834756 Force max component initial, final = 264.10702 0.031124676 Final line search alpha, max atom move = 1.0000000 0.031124676 Iterations, force evaluations = 121 216 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48975 | 0.48975 | 0.48975 | 0.0 | 94.06 Neigh | 0.019228 | 0.019228 | 0.019228 | 0.0 | 3.69 Comm | 0.0069592 | 0.0069592 | 0.0069592 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004767 | | | 0.92 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3883.00 ave 3883 max 3883 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: 67332.0 ave 67332 max 67332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67332 Ave neighs/atom = 165.84236 Neighbor list builds = 5 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 121 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.469 | 4.469 | 4.469 Mbytes Step Temp E_pair E_mol TotEng Press Volume 121 0 -2570.4994 0 -2570.4994 441.42616 6426.4404 127 0 -2570.824 0 -2570.824 -27.437924 6427.1816 Loop time of 0.0210359 on 1 procs for 6 steps with 406 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 = -2570.49936211492 -2570.82394824026 -2570.82400002764 Force two-norm initial, final = 106.34621 1.0627180 Force max component initial, final = 77.960813 0.66285049 Final line search alpha, max atom move = 0.0015120823 0.0010022845 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019778 | 0.019778 | 0.019778 | 0.0 | 94.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024632 | 0.00024632 | 0.00024632 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001011 | | | 4.81 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3867.00 ave 3867 max 3867 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: 67324.0 ave 67324 max 67324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67324 Ave neighs/atom = 165.82266 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.607 | 4.607 | 4.607 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2570.824 0 -2570.824 -27.437924 Loop time of 1.624e-06 on 1 procs for 0 steps with 406 atoms 123.2% 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 | | 1.624e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3862.00 ave 3862 max 3862 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: 67300.0 ave 67300 max 67300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67300 Ave neighs/atom = 165.76355 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.607 | 4.607 | 4.607 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 -2570.824 -2570.824 18.483878 78.225306 4.4450865 -27.437924 -27.437924 85.468948 -165.43605 -2.3466696 2.5619938 383.7432 Loop time of 1.399e-06 on 1 procs for 0 steps with 406 atoms 214.4% 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 | | 1.399e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3862.00 ave 3862 max 3862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33650.0 ave 33650 max 33650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67300.0 ave 67300 max 67300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67300 Ave neighs/atom = 165.76355 Neighbor list builds = 0 Dangerous builds = 0 406 -2570.82400002764 eV 2.56199384961652 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00