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 -36.405689 0.0000000) to (25.740161 36.405689 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5423814 5.7101310 5.0973115 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.405689 0.0000000) to (25.740161 36.405689 5.0973115) create_atoms CPU = 0.001 seconds 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5423814 5.7101310 5.0973115 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.405689 0.0000000) to (25.740161 36.405689 5.0973115) create_atoms CPU = 0.001 seconds 410 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 = 9 25 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 806 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_492310898779_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 = 9 25 2 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) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3380.7592 0 -3380.7592 838.36661 59 0 -3406.1999 0 -3406.1999 -13575.298 Loop time of 2.82148 on 1 procs for 59 steps with 806 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 = -3380.75916096887 -3406.1972575238 -3406.19994026434 Force two-norm initial, final = 27.428301 0.14433074 Force max component initial, final = 7.8343313 0.032508370 Final line search alpha, max atom move = 1.0000000 0.032508370 Iterations, force evaluations = 59 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8049 | 2.8049 | 2.8049 | 0.0 | 99.41 Neigh | 0.0082526 | 0.0082526 | 0.0082526 | 0.0 | 0.29 Comm | 0.0039469 | 0.0039469 | 0.0039469 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004392 | | | 0.16 Nlocal: 806.000 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3626.00 ave 3626 max 3626 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: 61696.0 ave 61696 max 61696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61696 Ave neighs/atom = 76.545906 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 25 2 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -3406.1999 0 -3406.1999 -13575.298 9553.262 74 0 -3406.9434 0 -3406.9434 1210.1473 9463.375 Loop time of 0.463572 on 1 procs for 15 steps with 806 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 = -3406.19994026434 -3406.94266394467 -3406.94339602777 Force two-norm initial, final = 130.67451 0.55301948 Force max component initial, final = 120.71291 0.099345268 Final line search alpha, max atom move = 0.00057166175 5.6791889e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46053 | 0.46053 | 0.46053 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049266 | 0.00049266 | 0.00049266 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002552 | | | 0.55 Nlocal: 806.000 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3620.00 ave 3620 max 3620 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: 61668.0 ave 61668 max 61668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61668 Ave neighs/atom = 76.511166 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 = 9 25 2 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) = 4.676 | 4.676 | 4.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3406.9434 0 -3406.9434 1210.1473 Loop time of 1.515e-06 on 1 procs for 0 steps with 806 atoms 198.0% 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 | | 1.515e-06 | | |100.00 Nlocal: 806.000 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3680.00 ave 3680 max 3680 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: 61840.0 ave 61840 max 61840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61840 Ave neighs/atom = 76.724566 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 = 9 25 2 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) = 4.676 | 4.676 | 4.676 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 -3406.9434 -3406.9434 25.367913 72.811379 5.1234447 1210.1473 1210.1473 16.5762 3628.2328 -14.367103 2.2655919 867.5592 Loop time of 1.782e-06 on 1 procs for 0 steps with 806 atoms 224.5% 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 | | 1.782e-06 | | |100.00 Nlocal: 806.000 ave 806 max 806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3680.00 ave 3680 max 3680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30920.0 ave 30920 max 30920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61840.0 ave 61840 max 61840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61840 Ave neighs/atom = 76.724566 Neighbor list builds = 0 Dangerous builds = 0 806 -3406.94339602777 eV 2.26559194102056 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03