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 = 3.6284291 3.6284291 3.6284291 Created orthogonal box = (0.0000000 -37.002861 0.0000000) to (32.045418 37.002861 6.2846235) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7517416 5.6927479 6.2846235 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -37.002861 0.0000000) to (32.045418 37.002861 6.2846235) create_atoms CPU = 0.002 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7517416 5.6927479 6.2846235 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -37.002861 0.0000000) to (32.045418 37.002861 6.2846235) create_atoms CPU = 0.001 seconds 629 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 9 20 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1247 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_650279905230_005#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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4711.5473 0 -4711.5473 106915.75 588 0 -5263.6546 0 -5263.6546 -8766.6482 Loop time of 11.393 on 1 procs for 588 steps with 1247 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4711.54732857138 -5263.64997668901 -5263.65460247364 Force two-norm initial, final = 827.16369 0.22792671 Force max component initial, final = 282.69115 0.060323911 Final line search alpha, max atom move = 0.88467849 0.053367266 Iterations, force evaluations = 588 1124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.011 | 11.011 | 11.011 | 0.0 | 96.65 Neigh | 0.2217 | 0.2217 | 0.2217 | 0.0 | 1.95 Comm | 0.083151 | 0.083151 | 0.083151 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07696 | | | 0.68 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6283.00 ave 6283 max 6283 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: 192958.0 ave 192958 max 192958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192958 Ave neighs/atom = 154.73777 Neighbor list builds = 16 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 588 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.061 | 5.061 | 5.061 Mbytes Step Temp E_pair E_mol TotEng Press Volume 588 0 -5263.6546 0 -5263.6546 -8766.6482 14904.263 602 0 -5266.1448 0 -5266.1448 -1.7523724 14818.747 Loop time of 0.161145 on 1 procs for 14 steps with 1247 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 = -5263.65460247364 -5266.14114572198 -5266.14476751588 Force two-norm initial, final = 292.76531 1.7079117 Force max component initial, final = 230.44594 0.30203014 Final line search alpha, max atom move = 0.00011913427 3.5982138e-05 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15487 | 0.15487 | 0.15487 | 0.0 | 96.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091821 | 0.00091821 | 0.00091821 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00536 | | | 3.33 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6299.00 ave 6299 max 6299 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: 192912.0 ave 192912 max 192912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192912 Ave neighs/atom = 154.70088 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.198 | 5.198 | 5.198 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5266.1448 0 -5266.1448 -1.7523724 Loop time of 2.179e-06 on 1 procs for 0 steps with 1247 atoms 137.7% 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 | | 2.179e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6218.00 ave 6218 max 6218 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: 194202.0 ave 194202 max 194202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194202 Ave neighs/atom = 155.73536 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.198 | 5.198 | 5.198 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 -5266.1448 -5266.1448 31.668097 73.582448 6.3593875 -1.7523724 -1.7523724 32.270461 -17.20999 -20.317589 2.2706122 2657.995 Loop time of 2.98e-06 on 1 procs for 0 steps with 1247 atoms 268.5% 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 | | 2.98e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6218.00 ave 6218 max 6218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97101.0 ave 97101 max 97101 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 194202.0 ave 194202 max 194202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194202 Ave neighs/atom = 155.73536 Neighbor list builds = 0 Dangerous builds = 0 1247 -5266.14447020791 eV 2.27061215515292 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11