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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -52.717246 0.0000000) to (26.356813 52.717246 3.6203867) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4756852 4.4756852 3.6203867 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -52.717246 0.0000000) to (26.356813 52.717246 3.6203867) create_atoms CPU = 0.001 seconds 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4756852 4.4756852 3.6203867 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -52.717246 0.0000000) to (26.356813 52.717246 3.6203867) create_atoms CPU = 0.000 seconds 426 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 36 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 12 atoms, new total = 840 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_390178379548_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 36 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) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2948.9901 0 -2948.9901 2182.8006 52 0 -2962.9716 0 -2962.9716 -6196.619 Loop time of 1.35629 on 1 procs for 52 steps with 840 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 = -2948.99012887154 -2962.9693179604 -2962.97161992334 Force two-norm initial, final = 29.015402 0.13278674 Force max component initial, final = 7.4718283 0.030034420 Final line search alpha, max atom move = 1.0000000 0.030034420 Iterations, force evaluations = 52 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3468 | 1.3468 | 1.3468 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046631 | 0.0046631 | 0.0046631 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004844 | | | 0.36 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4584.00 ave 4584 max 4584 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: 64860.0 ave 64860 max 64860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64860 Ave neighs/atom = 77.214286 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 36 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -2962.9716 0 -2962.9716 -6196.619 10060.755 55 0 -2963.0521 0 -2963.0521 -218.47808 10018.038 Loop time of 0.0789299 on 1 procs for 3 steps with 840 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 = -2962.97161992333 -2963.04938694859 -2963.05207862819 Force two-norm initial, final = 54.521302 5.0052104 Force max component initial, final = 41.910522 4.9652560 Final line search alpha, max atom move = 0.00012111629 0.00060137338 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.077743 | 0.077743 | 0.077743 | 0.0 | 98.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019995 | 0.00019995 | 0.00019995 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009867 | | | 1.25 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4584.00 ave 4584 max 4584 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: 65000.0 ave 65000 max 65000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65000 Ave neighs/atom = 77.380952 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 36 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) = 4.687 | 4.687 | 4.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2963.0521 0 -2963.0521 -218.47808 Loop time of 2.261e-06 on 1 procs for 0 steps with 840 atoms 176.9% 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 | | 2.261e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4588.00 ave 4588 max 4588 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: 65000.0 ave 65000 max 65000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65000 Ave neighs/atom = 77.380952 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 36 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) = 4.687 | 4.687 | 4.687 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 -2963.0521 -2963.0521 26.314413 105.43449 3.6108238 -218.47808 -218.47808 792.81179 -1351.2573 -96.988753 2.3372956 378.12732 Loop time of 2.157e-06 on 1 procs for 0 steps with 840 atoms 278.2% 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 | | 2.157e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4588.00 ave 4588 max 4588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32500.0 ave 32500 max 32500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65000.0 ave 65000 max 65000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65000 Ave neighs/atom = 77.380952 Neighbor list builds = 0 Dangerous builds = 0 840 -2963.05207862819 eV 2.33729555854379 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01