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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -41.698344 0.0000000) to (20.847740 41.698344 2.8636573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5401823 3.5401823 2.8636573 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.698344 0.0000000) to (20.847740 41.698344 2.8636573) create_atoms CPU = 0.002 seconds 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5401823 3.5401823 2.8636573 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.698344 0.0000000) to (20.847740 41.698344 2.8636573) create_atoms CPU = 0.001 seconds 213 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 ghost atom cutoff = 6 binsize = 3, bins = 7 28 1 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 420 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_321233176498_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 ghost atom cutoff = 6 binsize = 3, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1770.7776 0 -1770.7776 9393.6638 53 0 -1793.1204 0 -1793.1204 -8431.0072 Loop time of 2.90326 on 1 procs for 53 steps with 420 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 = -1770.77755417581 -1793.11910004197 -1793.12043717089 Force two-norm initial, final = 56.187840 0.10623454 Force max component initial, final = 23.643739 0.019528772 Final line search alpha, max atom move = 1.0000000 0.019528772 Iterations, force evaluations = 53 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8828 | 2.8828 | 2.8828 | 0.0 | 99.30 Neigh | 0.0052523 | 0.0052523 | 0.0052523 | 0.0 | 0.18 Comm | 0.0082621 | 0.0082621 | 0.0082621 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006914 | | | 0.24 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3375.00 ave 3375 max 3375 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: 26958.0 ave 26958 max 26958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26958 Ave neighs/atom = 64.185714 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.455 | 4.455 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1793.1204 0 -1793.1204 -8431.0072 4978.8476 59 0 -1793.245 0 -1793.245 1075.0799 4951.0453 Loop time of 0.243178 on 1 procs for 6 steps with 420 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1793.12043717089 -1793.24327780951 -1793.24498753625 Force two-norm initial, final = 49.843914 2.5591223 Force max component initial, final = 42.811071 2.3209291 Final line search alpha, max atom move = 0.00027425849 0.00063653451 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24058 | 0.24058 | 0.24058 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057365 | 0.00057365 | 0.00057365 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00202 | | | 0.83 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3350.00 ave 3350 max 3350 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: 26896.0 ave 26896 max 26896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26896 Ave neighs/atom = 64.038095 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 ghost atom cutoff = 6 binsize = 3, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.593 | 4.593 | 4.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1793.245 0 -1793.245 1075.0799 Loop time of 6.726e-06 on 1 procs for 0 steps with 420 atoms 178.4% 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 | | 6.726e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3350.00 ave 3350 max 3350 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: 26908.0 ave 26908 max 26908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26908 Ave neighs/atom = 64.066667 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 ghost atom cutoff = 6 binsize = 3, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.593 | 4.593 | 4.593 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 -1793.245 -1793.245 20.842899 83.396687 2.8483279 1075.0799 1075.0799 -344.63663 4316.9171 -747.04069 2.307675 249.49344 Loop time of 7.427e-06 on 1 procs for 0 steps with 420 atoms 242.4% 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 | | 7.427e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13454.0 ave 13454 max 13454 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26908.0 ave 26908 max 26908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26908 Ave neighs/atom = 64.066667 Neighbor list builds = 0 Dangerous builds = 0 420 -1793.24498753625 eV 2.30767497332327 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03