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 = 2.8510000 2.8510000 2.8510000 Created orthogonal box = (0.0000000 -31.875149 0.0000000) to (15.615570 31.875149 6.9834953) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1641521 3.8250179 4.6556635 Created 300 atoms using lattice units in orthogonal box = (0.0000000 -31.875149 0.0000000) to (15.615570 31.875149 6.9834953) create_atoms CPU = 0.001 seconds 300 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1641521 3.8250179 4.6556635 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -31.875149 0.0000000) to (15.615570 31.875149 6.9834953) create_atoms CPU = 0.000 seconds 306 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 = 6 22 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 6 atoms, new total = 600 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_549900287421_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 = 6 22 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) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2527.8749 0 -2527.8749 20068.719 17 0 -2558.6006 0 -2558.6006 10199.637 Loop time of 0.582214 on 1 procs for 17 steps with 600 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 = -2527.87490628655 -2558.59835787076 -2558.60056595674 Force two-norm initial, final = 35.919139 0.12492799 Force max component initial, final = 5.8785474 0.0098941662 Final line search alpha, max atom move = 1.0000000 0.0098941662 Iterations, force evaluations = 17 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5803 | 0.5803 | 0.5803 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084196 | 0.00084196 | 0.00084196 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001073 | | | 0.18 Nlocal: 600.000 ave 600 max 600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2757.00 ave 2757 max 2757 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: 39180.0 ave 39180 max 39180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39180 Ave neighs/atom = 65.300000 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 ghost atom cutoff = 6 binsize = 3, bins = 6 22 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -2558.6006 0 -2558.6006 10199.637 6952.0505 32 0 -2559.6636 0 -2559.6636 -9.4039595 6992.5058 Loop time of 0.310199 on 1 procs for 15 steps with 600 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 = -2558.60056595674 -2559.66132351555 -2559.66359580921 Force two-norm initial, final = 141.94729 0.57458776 Force max component initial, final = 140.87879 0.11927415 Final line search alpha, max atom move = 0.00022863846 2.7270657e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30711 | 0.30711 | 0.30711 | 0.0 | 99.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004185 | 0.0004185 | 0.0004185 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00267 | | | 0.86 Nlocal: 600.000 ave 600 max 600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2757.00 ave 2757 max 2757 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: 38460.0 ave 38460 max 38460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38460 Ave neighs/atom = 64.100000 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 = 6 22 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2559.6636 0 -2559.6636 -9.4039595 Loop time of 2.285e-06 on 1 procs for 0 steps with 600 atoms 175.1% 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 | | 2.285e-06 | | |100.00 Nlocal: 600.000 ave 600 max 600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2757.00 ave 2757 max 2757 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: 38448.0 ave 38448 max 38448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38448 Ave neighs/atom = 64.080000 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 = 6 22 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) = 4.612 | 4.612 | 4.612 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 -2559.6636 -2559.6636 15.509311 64.68158 6.9704324 -9.4039595 -9.4039595 -16.286347 -27.728235 15.802704 2.3631909 438.17641 Loop time of 2.298e-06 on 1 procs for 0 steps with 600 atoms 174.1% 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 | | 2.298e-06 | | |100.00 Nlocal: 600.000 ave 600 max 600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2757.00 ave 2757 max 2757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19224.0 ave 19224 max 19224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38448.0 ave 38448 max 38448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38448 Ave neighs/atom = 64.080000 Neighbor list builds = 0 Dangerous builds = 0 600 -2559.66359580921 eV 2.36319091298332 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01