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 = 2.8548760 2.8548760 2.8548760 Created orthogonal box = (0.0000000 -28.551615 0.0000000) to (2.8548760 28.551615 2.8548760) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 2.8548760 2.8548760 2.8548760 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -28.551615 0.0000000) to (2.8548760 28.551615 2.8548760) create_atoms CPU = 0.001 seconds 21 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 2.8548760 2.8548760 2.8548760 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -28.551615 0.0000000) to (2.8548760 28.551615 2.8548760) create_atoms CPU = 0.000 seconds 21 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 1 16 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 40 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 1 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.396 | 4.396 | 4.396 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -160.61583 0 -160.61583 -177.79155 1 0 -160.6159 0 -160.6159 -177.86935 Loop time of 0.00323474 on 1 procs for 1 steps with 40 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -160.615830532251 -160.615830532251 -160.615899574941 Force two-norm initial, final = 0.041392521 0.012870993 Force max component initial, final = 0.028510157 0.0075637650 Final line search alpha, max atom move = 1.0000000 0.0075637650 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0029194 | 0.0029194 | 0.0029194 | 0.0 | 90.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013799 | 0.00013799 | 0.00013799 | 0.0 | 4.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001774 | | | 5.48 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2134.00 ave 2134 max 2134 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: 5440.00 ave 5440 max 5440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5440 Ave neighs/atom = 136.00000 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 1 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.396 | 4.396 | 4.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -160.6159 0 -160.6159 -177.86935 465.40942 2 0 -160.6159 0 -160.6159 -39.2528 465.37314 Loop time of 0.00358036 on 1 procs for 1 steps with 40 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 = -160.615899574941 -160.615899574941 -160.615901293973 Force two-norm initial, final = 0.060883873 0.013061594 Force max component initial, final = 0.042078400 0.0075072378 Final line search alpha, max atom move = 0.023765162 0.00017841072 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0030885 | 0.0030885 | 0.0030885 | 0.0 | 86.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013223 | 0.00013223 | 0.00013223 | 0.0 | 3.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003596 | | | 10.04 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2134.00 ave 2134 max 2134 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: 5440.00 ave 5440 max 5440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5440 Ave neighs/atom = 136.00000 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 1 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -160.6159 0 -160.6159 -39.2528 Loop time of 6.395e-06 on 1 procs for 0 steps with 40 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2134.00 ave 2134 max 2134 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: 5440.00 ave 5440 max 5440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5440 Ave neighs/atom = 136.00000 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 1 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.534 | 4.534 | 4.534 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 -160.6159 -160.6159 2.8547647 57.10323 2.8547647 -39.2528 -39.2528 6.5432537 -130.84491 6.5432537 2.4723309 1.7899095e-05 Loop time of 6.325e-06 on 1 procs for 0 steps with 40 atoms 126.5% 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 | | 6.325e-06 | | |100.00 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2134.00 ave 2134 max 2134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2720.00 ave 2720 max 2720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5440.00 ave 5440 max 5440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5440 Ave neighs/atom = 136.00000 Neighbor list builds = 0 Dangerous builds = 0 40 -154.959036337443 eV 2.47233089115371 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00