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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897098 62.179117 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226304 5.5798613 6.0968189 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897098 62.179117 6.0968189) create_atoms CPU = 0.008 seconds 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226304 5.5798613 6.0968189 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897098 62.179117 6.0968189) create_atoms CPU = 0.007 seconds 1250 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 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 2484 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_937008984446_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 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.263 | 5.263 | 5.263 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10950.012 0 -10950.012 11138.69 27 0 -11018.444 0 -11018.444 -916.12638 Loop time of 11.0221 on 1 procs for 27 steps with 2484 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 = -10950.0118002045 -11018.4340929844 -11018.4439097949 Force two-norm initial, final = 95.555241 0.35468781 Force max component initial, final = 14.210213 0.073065646 Final line search alpha, max atom move = 1.0000000 0.073065646 Iterations, force evaluations = 27 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.965 | 10.965 | 10.965 | 0.0 | 99.48 Neigh | 0.03378 | 0.03378 | 0.03378 | 0.0 | 0.31 Comm | 0.0094113 | 0.0094113 | 0.0094113 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01389 | | | 0.13 Nlocal: 2484.00 ave 2484 max 2484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7219.00 ave 7219 max 7219 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: 193274.0 ave 193274 max 193274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193274 Ave neighs/atom = 77.807568 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.263 | 5.263 | 5.263 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -11018.444 0 -11018.444 -916.12638 27216.807 29 0 -11018.465 0 -11018.465 602.90938 27194.781 Loop time of 1.01959 on 1 procs for 2 steps with 2484 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 = -11018.4439097948 -11018.4633368533 -11018.4645418707 Force two-norm initial, final = 51.941662 0.37184318 Force max component initial, final = 50.149702 0.078066082 Final line search alpha, max atom move = 0.00010485828 8.1858754e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.015 | 1.015 | 1.015 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083627 | 0.00083627 | 0.00083627 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003715 | | | 0.36 Nlocal: 2484.00 ave 2484 max 2484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7236.00 ave 7236 max 7236 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: 193248.0 ave 193248 max 193248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193248 Ave neighs/atom = 77.797101 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 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.401 | 5.401 | 5.401 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11018.465 0 -11018.465 602.90938 Loop time of 6.485e-06 on 1 procs for 0 steps with 2484 atoms 185.0% 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 | | 6.485e-06 | | |100.00 Nlocal: 2484.00 ave 2484 max 2484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7239.00 ave 7239 max 7239 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: 193252.0 ave 193252 max 193252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193252 Ave neighs/atom = 77.798712 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 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.401 | 5.401 | 5.401 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 -11018.465 -11018.465 35.897705 124.35823 6.0917818 602.90938 602.90938 -4.5993294 1814.8768 -1.549278 2.2470375 968.80551 Loop time of 6.896e-06 on 1 procs for 0 steps with 2484 atoms 275.5% 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 | | 6.896e-06 | | |100.00 Nlocal: 2484.00 ave 2484 max 2484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7239.00 ave 7239 max 7239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96626.0 ave 96626 max 96626 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193252.0 ave 193252 max 193252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193252 Ave neighs/atom = 77.798712 Neighbor list builds = 0 Dangerous builds = 0 2484 -11018.4645418707 eV 2.2470375398947 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13