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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0763986 5.2514766 5.0973115 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0763986 5.2514766 5.0973115 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) create_atoms CPU = 0.002 seconds 916 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 36 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1806 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.158 | 5.158 | 5.158 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7595.8844 0 -7595.8844 1107.9666 192 0 -7657.3753 0 -7657.3753 -15072.112 Loop time of 35.6605 on 1 procs for 192 steps with 1806 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7595.88437361145 -7657.3683252706 -7657.37533454596 Force two-norm initial, final = 41.105865 0.23947232 Force max component initial, final = 8.2178442 0.050967178 Final line search alpha, max atom move = 0.89034224 0.045378232 Iterations, force evaluations = 192 348 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 35.463 | 35.463 | 35.463 | 0.0 | 99.45 Neigh | 0.09582 | 0.09582 | 0.09582 | 0.0 | 0.27 Comm | 0.05189 | 0.05189 | 0.05189 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04959 | | | 0.14 Nlocal: 1806.00 ave 1806 max 1806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7418.00 ave 7418 max 7418 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: 138160.0 ave 138160 max 138160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138160 Ave neighs/atom = 76.500554 Neighbor list builds = 6 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 192 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.158 | 5.158 | 5.158 Mbytes Step Temp E_pair E_mol TotEng Press Volume 192 0 -7657.3753 0 -7657.3753 -15072.112 21353.65 201 0 -7658.6372 0 -7658.6372 -242.1777 21153.808 Loop time of 0.813269 on 1 procs for 9 steps with 1806 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 = -7657.37533454596 -7658.63661020016 -7658.63724574679 Force two-norm initial, final = 322.72681 0.39033082 Force max component initial, final = 288.13921 0.056224804 Final line search alpha, max atom move = 0.00013359350 7.5112682e-06 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80809 | 0.80809 | 0.80809 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075115 | 0.00075115 | 0.00075115 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004431 | | | 0.54 Nlocal: 1806.00 ave 1806 max 1806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7410.00 ave 7410 max 7410 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: 138156.0 ave 138156 max 138156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138156 Ave neighs/atom = 76.498339 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.296 | 5.296 | 5.296 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7658.6372 0 -7658.6372 -242.1777 Loop time of 3.788e-06 on 1 procs for 0 steps with 1806 atoms 184.8% 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 | | 3.788e-06 | | |100.00 Nlocal: 1806.00 ave 1806 max 1806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7440.00 ave 7440 max 7440 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: 138496.0 ave 138496 max 138496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138496 Ave neighs/atom = 76.686600 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.296 | 5.296 | 5.296 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 -7658.6372 -7658.6372 38.42937 108.856 5.0567668 -242.1777 -242.1777 -2.698393 -722.04983 -1.784893 2.3355013 1400.1167 Loop time of 2.231e-06 on 1 procs for 0 steps with 1806 atoms 224.1% 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 | | 2.231e-06 | | |100.00 Nlocal: 1806.00 ave 1806 max 1806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7440.00 ave 7440 max 7440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69248.0 ave 69248 max 69248 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138496.0 ave 138496 max 138496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138496 Ave neighs/atom = 76.686600 Neighbor list builds = 0 Dangerous builds = 0 1806 -7658.63724574679 eV 2.33550134868082 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:37