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 = 2.8553249 2.8553249 2.8553249 Created orthogonal box = (0.0000000 -29.946900 0.0000000) to (36.677312 29.946900 6.9940890) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6680216 4.3559127 4.6627260 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -29.946900 0.0000000) to (36.677312 29.946900 6.9940890) create_atoms CPU = 0.001 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6680216 4.3559127 4.6627260 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -29.946900 0.0000000) to (36.677312 29.946900 6.9940890) create_atoms CPU = 0.001 seconds 662 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1318 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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 -3175.9269 0 -3175.9269 337126.46 72 0 -5392.3805 0 -5392.3805 5313.7549 Loop time of 1.11532 on 1 procs for 72 steps with 1318 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3175.92689978094 -5392.37595322058 -5392.38049728857 Force two-norm initial, final = 3380.6790 0.24555561 Force max component initial, final = 432.44702 0.061173579 Final line search alpha, max atom move = 1.0000000 0.061173579 Iterations, force evaluations = 72 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0717 | 1.0717 | 1.0717 | 0.0 | 96.09 Neigh | 0.026794 | 0.026794 | 0.026794 | 0.0 | 2.40 Comm | 0.0074497 | 0.0074497 | 0.0074497 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009339 | | | 0.84 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5916.00 ave 5916 max 5916 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: 180556.0 ave 180556 max 180556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180556 Ave neighs/atom = 136.99241 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -5392.3805 0 -5392.3805 5313.7549 15364.22 77 0 -5392.6434 0 -5392.6434 -108.85201 15413.766 Loop time of 0.066833 on 1 procs for 5 steps with 1318 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 = -5392.38049728862 -5392.64275288806 -5392.64342425382 Force two-norm initial, final = 118.81195 3.0103278 Force max component initial, final = 96.985458 2.3888554 Final line search alpha, max atom move = 0.00015277559 0.00036495880 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064533 | 0.064533 | 0.064533 | 0.0 | 96.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033344 | 0.00033344 | 0.00033344 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001967 | | | 2.94 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5906.00 ave 5906 max 5906 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: 180328.0 ave 180328 max 180328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180328 Ave neighs/atom = 136.81942 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.206 | 5.206 | 5.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5392.6434 0 -5392.6434 -108.85201 Loop time of 1.972e-06 on 1 procs for 0 steps with 1318 atoms 202.8% 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 | | 1.972e-06 | | |100.00 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5906.00 ave 5906 max 5906 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: 180096.0 ave 180096 max 180096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180096 Ave neighs/atom = 136.64340 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.206 | 5.206 | 5.206 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 -5392.6434 -5392.6434 36.742519 60.123582 6.977422 -108.85201 -108.85201 -165.48473 86.645425 -247.71671 2.2649099 1446.74 Loop time of 2.717e-06 on 1 procs for 0 steps with 1318 atoms 184.0% 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 | | 2.717e-06 | | |100.00 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5906.00 ave 5906 max 5906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90048.0 ave 90048 max 90048 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180096.0 ave 180096 max 180096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180096 Ave neighs/atom = 136.64340 Neighbor list builds = 0 Dangerous builds = 0 1318 -5392.64342425382 eV 2.26490990753542 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01