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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -64.134054 0.0000000) to (45.346855 64.134054 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7681873 6.2215805 5.5400000 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -64.134054 0.0000000) to (45.346855 64.134054 5.5400000) create_atoms CPU = 0.008 seconds 1079 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7681873 6.2215805 5.5400000 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -64.134054 0.0000000) to (45.346855 64.134054 5.5400000) create_atoms CPU = 0.007 seconds 1079 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 40 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 2143 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_070797404269_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.224 | 5.224 | 5.224 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12185.189 0 -12185.189 19808.844 26 0 -12333.699 0 -12333.699 4551.3844 Loop time of 3.50704 on 1 procs for 26 steps with 2143 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 = -12185.188827138 -12333.6895893021 -12333.6993834208 Force two-norm initial, final = 131.70205 0.39885162 Force max component initial, final = 19.988289 0.15334549 Final line search alpha, max atom move = 0.46641143 0.071522089 Iterations, force evaluations = 26 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4878 | 3.4878 | 3.4878 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0089422 | 0.0089422 | 0.0089422 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01025 | | | 0.29 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8493.00 ave 8493 max 8493 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: 166896.0 ave 166896 max 166896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166896 Ave neighs/atom = 77.879608 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.224 | 5.224 | 5.224 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -12333.699 0 -12333.699 4551.3844 32223.717 28 0 -12333.741 0 -12333.741 2019.2644 32268.671 Loop time of 0.401667 on 1 procs for 2 steps with 2143 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 = -12333.6993834208 -12333.7400115853 -12333.7405063736 Force two-norm initial, final = 82.152387 0.42593699 Force max component initial, final = 62.950237 0.15324826 Final line search alpha, max atom move = 0.00021915480 3.3585092e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39742 | 0.39742 | 0.39742 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010272 | 0.0010272 | 0.0010272 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003224 | | | 0.80 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8493.00 ave 8493 max 8493 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: 166074.0 ave 166074 max 166074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166074 Ave neighs/atom = 77.496034 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.362 | 5.362 | 5.362 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12333.741 0 -12333.741 2019.2644 Loop time of 6.565e-06 on 1 procs for 0 steps with 2143 atoms 167.6% 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 | | 6.565e-06 | | |100.00 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8493.00 ave 8493 max 8493 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: 166074.0 ave 166074 max 166074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166074 Ave neighs/atom = 77.496034 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.362 | 5.362 | 5.362 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 -12333.741 -12333.741 45.370694 128.26811 5.5448137 2019.2644 2019.2644 -1.3364043 6063.9215 -4.7918591 2.5464171 890.29106 Loop time of 7.217e-06 on 1 procs for 0 steps with 2143 atoms 291.0% 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 | | 7.217e-06 | | |100.00 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8493.00 ave 8493 max 8493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 83037.0 ave 83037 max 83037 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 166074.0 ave 166074 max 166074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166074 Ave neighs/atom = 77.496034 Neighbor list builds = 0 Dangerous builds = 0 2143 -12333.7405063736 eV 2.54641709349353 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04