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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -77.378726 0.0000000) to (44.674628 77.378726 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5913386 5.9196840 7.0055407 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -77.378726 0.0000000) to (44.674628 77.378726 7.0055407) create_atoms CPU = 0.009 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5913386 5.9196840 7.0055407 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.378726 0.0000000) to (44.674628 77.378726 7.0055407) create_atoms CPU = 0.008 seconds 1465 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 47 3 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2928 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.778 | 5.778 | 5.778 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9494.0352 0 -9494.0352 17264.704 144 0 -9812.0308 0 -9812.0308 3366.6613 Loop time of 59.3261 on 1 procs for 144 steps with 2928 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 = -9494.03518000655 -9812.02144103822 -9812.03075961772 Force two-norm initial, final = 344.32964 0.26261056 Force max component initial, final = 88.439568 0.059972702 Final line search alpha, max atom move = 1.0000000 0.059972702 Iterations, force evaluations = 144 240 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 58.883 | 58.883 | 58.883 | 0.0 | 99.25 Neigh | 0.30289 | 0.30289 | 0.30289 | 0.0 | 0.51 Comm | 0.059268 | 0.059268 | 0.059268 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0808 | | | 0.14 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9463.00 ave 9463 max 9463 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: 226684.0 ave 226684 max 226684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226684 Ave neighs/atom = 77.419399 Neighbor list builds = 8 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 144 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.777 | 5.777 | 5.777 Mbytes Step Temp E_pair E_mol TotEng Press Volume 144 0 -9812.0308 0 -9812.0308 3366.6613 48434.429 150 0 -9812.4306 0 -9812.4306 -20.620869 48640.757 Loop time of 1.79714 on 1 procs for 6 steps with 2928 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 = -9812.03075961772 -9812.43049479967 -9812.43057754303 Force two-norm initial, final = 194.91716 1.6148953 Force max component initial, final = 169.67794 1.3279073 Final line search alpha, max atom move = 0.00038225643 0.00050760110 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7882 | 1.7882 | 1.7882 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016077 | 0.0016077 | 0.0016077 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007313 | | | 0.41 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9444.00 ave 9444 max 9444 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: 226728.0 ave 226728 max 226728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226728 Ave neighs/atom = 77.434426 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.915 | 5.915 | 5.915 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9812.4306 0 -9812.4306 -20.620869 Loop time of 7.006e-06 on 1 procs for 0 steps with 2928 atoms 185.6% 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 | | 7.006e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9444.00 ave 9444 max 9444 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: 226656.0 ave 226656 max 226656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226656 Ave neighs/atom = 77.409836 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 14 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 5.915 | 5.915 | 5.915 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 -9812.4306 -9812.4306 44.652177 155.53991 7.0035115 -20.620869 -20.620869 -43.717919 8.7481433 -26.89283 2.519811 1435.359 Loop time of 6.325e-06 on 1 procs for 0 steps with 2928 atoms 332.0% 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 | | 6.325e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9444.00 ave 9444 max 9444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113328.0 ave 113328 max 113328 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 226656.0 ave 226656 max 226656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226656 Ave neighs/atom = 77.409836 Neighbor list builds = 0 Dangerous builds = 0 2928 -9812.43057754303 eV 2.51981104883656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:02