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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -62.608958 0.0000000) to (25.560000 62.608958 8.8542437) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1344000 5.4261097 5.9028292 Created 1196 atoms using lattice units in orthogonal box = (0.0000000 -62.608958 0.0000000) to (25.560000 62.608958 8.8542437) create_atoms CPU = 0.002 seconds 1196 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1344000 5.4261097 5.9028292 Created 1204 atoms using lattice units in orthogonal box = (0.0000000 -62.608958 0.0000000) to (25.560000 62.608958 8.8542437) create_atoms CPU = 0.002 seconds 1204 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 46 4 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 2380 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 46 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8339.0989 0 -8339.0989 4839.0025 19 0 -8397.1714 0 -8397.1714 -2570.3547 Loop time of 0.502188 on 1 procs for 19 steps with 2380 atoms 38.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8339.09888464355 -8397.16568784303 -8397.17138470074 Force two-norm initial, final = 89.374847 0.21100685 Force max component initial, final = 15.837935 0.046686870 Final line search alpha, max atom move = 1.0000000 0.046686870 Iterations, force evaluations = 19 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49654 | 0.49654 | 0.49654 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019948 | 0.0019948 | 0.0019948 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00365 | | | 0.73 Nlocal: 2380.00 ave 2380 max 2380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5947.00 ave 5947 max 5947 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: 127948.0 ave 127948 max 127948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127948 Ave neighs/atom = 53.759664 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 46 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -8397.1714 0 -8397.1714 -2570.3547 28338.626 21 0 -8397.2792 0 -8397.2792 -3.1159412 28285.191 Loop time of 0.0796927 on 1 procs for 2 steps with 2380 atoms 33.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8397.17138470076 -8397.27791031909 -8397.27921569081 Force two-norm initial, final = 79.539660 0.52944847 Force max component initial, final = 54.115646 0.41530467 Final line search alpha, max atom move = 0.00017363824 7.2112773e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.077725 | 0.077725 | 0.077725 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026968 | 0.00026968 | 0.00026968 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001698 | | | 2.13 Nlocal: 2380.00 ave 2380 max 2380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5947.00 ave 5947 max 5947 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: 128326.0 ave 128326 max 128326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128326 Ave neighs/atom = 53.918487 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 46 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.252 | 5.252 | 5.252 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 8399.927 0 8399.927 -3.1159412 Loop time of 2.126e-06 on 1 procs for 0 steps with 2380 atoms 188.1% 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 | | 2.126e-06 | | |100.00 Nlocal: 2380.00 ave 2380 max 2380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5947.00 ave 5947 max 5947 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: 128376.0 ave 128376 max 128376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128376 Ave neighs/atom = 53.939496 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 10 46 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.252 | 5.252 | 5.252 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 8399.927 -8397.2792 25.534177 125.17774 8.849325 -3.1159412 -3.1159412 4.3188953 9.8445853 -23.511304 2.2657939 560.26565 Loop time of 2.442e-06 on 1 procs for 0 steps with 2380 atoms 245.7% 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 | | 2.442e-06 | | |100.00 Nlocal: 2380.00 ave 2380 max 2380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5947.00 ave 5947 max 5947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64188.0 ave 64188 max 64188 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128376.0 ave 128376 max 128376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128376 Ave neighs/atom = 53.939496 Neighbor list builds = 0 Dangerous builds = 0 2380 8399.9269938421 eV 2.26579388289236 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00