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 = 3.4919386 3.4919386 3.4919386 Created orthogonal box = (0.0000000 -40.119320 0.0000000) to (28.368643 40.119320 4.9383469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2982793 5.4708164 4.9383469 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -40.119320 0.0000000) to (28.368643 40.119320 4.9383469) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2982793 5.4708164 4.9383469 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.119320 0.0000000) to (28.368643 40.119320 4.9383469) create_atoms CPU = 0.001 seconds 532 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 9 24 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 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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_108408461881_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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4045.3931 0 -4045.3931 112353.49 86 0 -4668.3857 0 -4668.3857 12327.338 Loop time of 1.79522 on 1 procs for 86 steps with 1056 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4045.39309779976 -4668.38141981946 -4668.38569937765 Force two-norm initial, final = 995.44834 0.25735684 Force max component initial, final = 214.52446 0.029732456 Final line search alpha, max atom move = 1.0000000 0.029732456 Iterations, force evaluations = 86 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7709 | 1.7709 | 1.7709 | 0.0 | 98.64 Neigh | 0.0077141 | 0.0077141 | 0.0077141 | 0.0 | 0.43 Comm | 0.0089368 | 0.0089368 | 0.0089368 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007678 | | | 0.43 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5772.00 ave 5772 max 5772 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: 139984.0 ave 139984 max 139984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139984 Ave neighs/atom = 132.56061 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -4668.3857 0 -4668.3857 12327.338 11240.968 91 0 -4668.7518 0 -4668.7518 229.72776 11315.533 Loop time of 0.0785909 on 1 procs for 5 steps with 1056 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 = -4668.38569937765 -4668.74964006968 -4668.75178575179 Force two-norm initial, final = 159.95441 3.2507139 Force max component initial, final = 127.30009 2.9350416 Final line search alpha, max atom move = 0.00011745477 0.00034473463 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076911 | 0.076911 | 0.076911 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003024 | 0.0003024 | 0.0003024 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001378 | | | 1.75 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5807.00 ave 5807 max 5807 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: 140344.0 ave 140344 max 140344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140344 Ave neighs/atom = 132.90152 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.143 | 5.143 | 5.143 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4668.7518 0 -4668.7518 229.72776 Loop time of 1.671e-06 on 1 procs for 0 steps with 1056 atoms 179.5% 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 | | 1.671e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5807.00 ave 5807 max 5807 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: 140288.0 ave 140288 max 140288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140288 Ave neighs/atom = 132.84848 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.143 | 5.143 | 5.143 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 -4668.7518 -4668.7518 28.426686 80.572965 4.9403697 229.72776 229.72776 141.76117 417.30672 130.1154 2.3360274 700.51552 Loop time of 1.627e-06 on 1 procs for 0 steps with 1056 atoms 122.9% 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 | | 1.627e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5807.00 ave 5807 max 5807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70144.0 ave 70144 max 70144 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 140288.0 ave 140288 max 140288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140288 Ave neighs/atom = 132.84848 Neighbor list builds = 0 Dangerous builds = 0 1056 -4668.75178575179 eV 2.33602738842737 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02