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 -46.182620 0.0000000) to (32.656044 46.182620 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0755430 5.9070793 4.9800000 Created 687 atoms using lattice units in orthogonal box = (0.0000000 -46.182620 0.0000000) to (32.656044 46.182620 4.9800000) create_atoms CPU = 0.002 seconds 687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0755430 5.9070793 4.9800000 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -46.182620 0.0000000) to (32.656044 46.182620 4.9800000) create_atoms CPU = 0.002 seconds 695 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 = 11 31 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1376 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_000553624872_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 31 2 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) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5671.4644 0 -5671.4644 78942.509 59 0 -6099.8763 0 -6099.8763 8327.4919 Loop time of 5.31691 on 1 procs for 59 steps with 1376 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5671.46437192818 -6099.87116565933 -6099.87629176485 Force two-norm initial, final = 533.58943 0.24253083 Force max component initial, final = 82.974865 0.058118274 Final line search alpha, max atom move = 1.0000000 0.058118274 Iterations, force evaluations = 59 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2851 | 5.2851 | 5.2851 | 0.0 | 99.40 Neigh | 0.010199 | 0.010199 | 0.010199 | 0.0 | 0.19 Comm | 0.011067 | 0.011067 | 0.011067 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01055 | | | 0.20 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6100.00 ave 6100 max 6100 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: 107400.0 ave 107400 max 107400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107400 Ave neighs/atom = 78.052326 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 = 11 31 2 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -6099.8763 0 -6099.8763 8327.4919 15021.091 64 0 -6100.1401 0 -6100.1401 -49.848897 15088.24 Loop time of 0.401509 on 1 procs for 5 steps with 1376 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 = -6099.87629176485 -6100.14005765055 -6100.14013513201 Force two-norm initial, final = 150.08699 1.0485229 Force max component initial, final = 130.56255 0.86618531 Final line search alpha, max atom move = 0.00053522057 0.00046360019 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39836 | 0.39836 | 0.39836 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047106 | 0.00047106 | 0.00047106 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002679 | | | 0.67 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6079.00 ave 6079 max 6079 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: 107166.0 ave 107166 max 107166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107166 Ave neighs/atom = 77.882267 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 = 11 31 2 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) = 5.193 | 5.193 | 5.193 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6100.1401 0 -6100.1401 -49.848897 Loop time of 2.466e-06 on 1 procs for 0 steps with 1376 atoms 202.8% 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 | | 2.466e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6044.00 ave 6044 max 6044 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: 107078.0 ave 107078 max 107078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107078 Ave neighs/atom = 77.818314 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 = 11 31 2 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) = 5.193 | 5.193 | 5.193 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 -6100.1401 -6100.1401 32.661543 92.715603 4.9825201 -49.848897 -49.848897 -6.8424234 -50.680014 -92.024255 2.3516704 937.40117 Loop time of 3.141e-06 on 1 procs for 0 steps with 1376 atoms 254.7% 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 | | 3.141e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6044.00 ave 6044 max 6044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53539.0 ave 53539 max 53539 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107078.0 ave 107078 max 107078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107078 Ave neighs/atom = 77.818314 Neighbor list builds = 0 Dangerous builds = 0 1376 -6100.14013513201 eV 2.35167041602295 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06