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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -41.746968 0.0000000) to (14.758670 41.746968 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3667890 4.7436161 4.4499063 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -41.746968 0.0000000) to (14.758670 41.746968 4.4499063) create_atoms CPU = 0.002 seconds 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3667890 4.7436161 4.4499063 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -41.746968 0.0000000) to (14.758670 41.746968 4.4499063) create_atoms CPU = 0.001 seconds 178 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 29 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 348 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2345.3981 0 -2345.3981 -3886.1857 16 0 -2357.2581 0 -2357.2581 -18074.541 Loop time of 0.523083 on 1 procs for 16 steps with 348 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 = -2345.39810502793 -2357.25663945675 -2357.25813513501 Force two-norm initial, final = 10.989414 0.10899437 Force max component initial, final = 2.9143559 0.016650299 Final line search alpha, max atom move = 1.0000000 0.016650299 Iterations, force evaluations = 16 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52022 | 0.52022 | 0.52022 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013261 | 0.0013261 | 0.0013261 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001534 | | | 0.29 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2092.00 ave 2092 max 2092 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: 19816.0 ave 19816 max 19816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19816 Ave neighs/atom = 56.942529 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 16 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press Volume 16 0 -2357.2581 0 -2357.2581 -18074.541 5483.4391 20 0 -2357.4258 0 -2357.4258 -3254.9752 5451.9592 Loop time of 0.122048 on 1 procs for 4 steps with 348 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 = -2357.25813513501 -2357.42557407491 -2357.42578795219 Force two-norm initial, final = 82.481641 1.1610819 Force max component initial, final = 61.516154 1.1530223 Final line search alpha, max atom move = 0.00040369470 0.00046546901 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12066 | 0.12066 | 0.12066 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028966 | 0.00028966 | 0.00028966 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001101 | | | 0.90 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2104.00 ave 2104 max 2104 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: 19896.0 ave 19896 max 19896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19896 Ave neighs/atom = 57.172414 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2357.4258 0 -2357.4258 -3254.9752 Loop time of 6.195e-06 on 1 procs for 0 steps with 348 atoms 193.7% 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 | | 6.195e-06 | | |100.00 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2104.00 ave 2104 max 2104 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: 19896.0 ave 19896 max 19896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19896 Ave neighs/atom = 57.172414 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.564 | 4.564 | 4.564 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 -2357.4258 -2357.4258 14.72063 83.493937 4.4357929 -3254.9752 -3254.9752 337.96729 -10096.323 -6.5699002 2.4048202 288.4805 Loop time of 6.385e-06 on 1 procs for 0 steps with 348 atoms 266.2% 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 | | 6.385e-06 | | |100.00 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2104.00 ave 2104 max 2104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9948.00 ave 9948 max 9948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 19896.0 ave 19896 max 19896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19896 Ave neighs/atom = 57.172414 Neighbor list builds = 0 Dangerous builds = 0 348 -2357.42578795219 eV 2.40482018178684 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00