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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -28.889418 0.0000000) to (20.425881 28.889418 4.0449272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6045673 4.5312248 4.0449272 Created 205 atoms using lattice units in orthogonal box = (0.0000000 -28.889418 0.0000000) to (20.425881 28.889418 4.0449272) create_atoms CPU = 0.001 seconds 205 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6045673 4.5312248 4.0449272 Created 205 atoms using lattice units in orthogonal box = (0.0000000 -28.889418 0.0000000) to (20.425881 28.889418 4.0449272) create_atoms CPU = 0.000 seconds 205 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 3 atoms, new total = 407 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1663.4739 0 -1663.4739 35914.8 26 0 -1727.8883 0 -1727.8883 4828.2859 Loop time of 1.05892 on 1 procs for 26 steps with 407 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 = -1663.47388701293 -1727.88689970829 -1727.88829087879 Force two-norm initial, final = 111.67298 0.14628832 Force max component initial, final = 26.826033 0.028488817 Final line search alpha, max atom move = 1.0000000 0.028488817 Iterations, force evaluations = 26 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0568 | 1.0568 | 1.0568 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010245 | 0.0010245 | 0.0010245 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001047 | | | 0.10 Nlocal: 407.000 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2513.00 ave 2513 max 2513 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: 23352.0 ave 23352 max 23352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23352 Ave neighs/atom = 57.375921 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -1727.8883 0 -1727.8883 4828.2859 4773.7569 30 0 -1727.9244 0 -1727.9244 1197.7835 4783.3463 Loop time of 0.144654 on 1 procs for 4 steps with 407 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 = -1727.88829087879 -1727.92356195449 -1727.92443422841 Force two-norm initial, final = 21.014415 0.42291818 Force max component initial, final = 21.004800 0.24302407 Final line search alpha, max atom move = 0.00048730247 0.00011842623 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14406 | 0.14406 | 0.14406 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011262 | 0.00011262 | 0.00011262 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004819 | | | 0.33 Nlocal: 407.000 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2501.00 ave 2501 max 2501 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: 23478.0 ave 23478 max 23478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23478 Ave neighs/atom = 57.685504 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1727.9244 0 -1727.9244 1197.7835 Loop time of 1.629e-06 on 1 procs for 0 steps with 407 atoms 122.8% 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 | | 1.629e-06 | | |100.00 Nlocal: 407.000 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2501.00 ave 2501 max 2501 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: 23476.0 ave 23476 max 23476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23476 Ave neighs/atom = 57.680590 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.951 | 4.951 | 4.951 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 -1727.9244 -1727.9244 20.496604 57.778837 4.0390677 1197.7835 1197.7835 62.791449 3449.2763 81.282722 2.2203012 364.52746 Loop time of 1.455e-06 on 1 procs for 0 steps with 407 atoms 137.5% 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 | | 1.455e-06 | | |100.00 Nlocal: 407.000 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2501.00 ave 2501 max 2501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11738.0 ave 11738 max 11738 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23476.0 ave 23476 max 23476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23476 Ave neighs/atom = 57.680590 Neighbor list builds = 0 Dangerous builds = 0 407 -1727.92443422841 eV 2.2203011511019 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01