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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -39.373878 0.0000000) to (7.8740713 39.373878 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7244428 4.7244428 3.5213917 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.373878 0.0000000) to (7.8740713 39.373878 3.5213917) create_atoms CPU = 0.002 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7244428 4.7244428 3.5213917 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.373878 0.0000000) to (7.8740713 39.373878 3.5213917) create_atoms CPU = 0.001 seconds 102 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 25 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 198 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_008996216289_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.415 | 4.415 | 4.415 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -865.14442 0 -865.14442 18963.748 86 0 -876.12078 0 -876.12078 -2267.7496 Loop time of 4.6048 on 1 procs for 86 steps with 198 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 = -865.144416942235 -876.119948177258 -876.120778877063 Force two-norm initial, final = 33.684377 0.096417698 Force max component initial, final = 10.186494 0.019602341 Final line search alpha, max atom move = 1.0000000 0.019602341 Iterations, force evaluations = 86 166 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5851 | 4.5851 | 4.5851 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011184 | 0.011184 | 0.011184 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008465 | | | 0.18 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2587.00 ave 2587 max 2587 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: 17148.0 ave 17148 max 17148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17148 Ave neighs/atom = 86.606061 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.414 | 4.414 | 4.414 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -876.12078 0 -876.12078 -2267.7496 2183.4934 88 0 -876.12876 0 -876.12876 2069.6348 2178.35 Loop time of 0.116195 on 1 procs for 2 steps with 198 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 = -876.120778877063 -876.128545845141 -876.128760336506 Force two-norm initial, final = 9.6406187 0.36550691 Force max component initial, final = 6.9055362 0.30572599 Final line search alpha, max atom move = 0.00076194654 0.00023294686 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11505 | 0.11505 | 0.11505 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028681 | 0.00028681 | 0.00028681 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008538 | | | 0.73 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2535.00 ave 2535 max 2535 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: 17188.0 ave 17188 max 17188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17188 Ave neighs/atom = 86.808081 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -876.12876 0 -876.12876 2069.6348 Loop time of 6.305e-06 on 1 procs for 0 steps with 198 atoms 174.5% 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 | | 6.305e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2535.00 ave 2535 max 2535 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: 17216.0 ave 17216 max 17216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17216 Ave neighs/atom = 86.949495 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.552 | 4.552 | 4.552 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 -876.12876 -876.12876 7.8650755 78.747756 3.5171151 2069.6348 2069.6348 224.60458 6116.6818 -132.38195 2.265254 120.47521 Loop time of 7.207e-06 on 1 procs for 0 steps with 198 atoms 291.4% 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 | | 7.207e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2535.00 ave 2535 max 2535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8608.00 ave 8608 max 8608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17216.0 ave 17216 max 17216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17216 Ave neighs/atom = 86.949495 Neighbor list builds = 0 Dangerous builds = 0 198 -876.128760336506 eV 2.26525399518296 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05