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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -67.048263 0.0000000) to (23.705141 67.048263 5.1123821) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0641058 6.2370477 5.1123821 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -67.048263 0.0000000) to (23.705141 67.048263 5.1123821) create_atoms CPU = 0.007 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0641058 6.2370477 5.1123821 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -67.048263 0.0000000) to (23.705141 67.048263 5.1123821) create_atoms CPU = 0.006 seconds 690 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 31 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1376 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.943 | 5.943 | 5.943 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4654.6997 0 -4654.6997 42767.43 93 0 -4863.585 0 -4863.585 1542.8591 Loop time of 6.38336 on 1 procs for 93 steps with 1376 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 = -4654.69967218656 -4863.58017987272 -4863.58496717089 Force two-norm initial, final = 539.54279 0.21271501 Force max component initial, final = 182.85023 0.033726126 Final line search alpha, max atom move = 1.0000000 0.033726126 Iterations, force evaluations = 93 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2692 | 6.2692 | 6.2692 | 0.0 | 98.21 Neigh | 0.041205 | 0.041205 | 0.041205 | 0.0 | 0.65 Comm | 0.042669 | 0.042669 | 0.042669 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03026 | | | 0.47 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10508.0 ave 10508 max 10508 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: 310736.0 ave 310736 max 310736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310736 Ave neighs/atom = 225.82558 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.947 | 5.947 | 5.947 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -4863.585 0 -4863.585 1542.8591 16251.123 96 0 -4863.6353 0 -4863.6353 -60.894288 16269.787 Loop time of 0.180131 on 1 procs for 3 steps with 1376 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 = -4863.58496717089 -4863.63505656651 -4863.63526447387 Force two-norm initial, final = 44.898176 1.6255883 Force max component initial, final = 39.809784 1.2502206 Final line search alpha, max atom move = 0.00029645216 0.00037063061 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17553 | 0.17553 | 0.17553 | 0.0 | 97.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012074 | 0.0012074 | 0.0012074 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003398 | | | 1.89 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10784.0 ave 10784 max 10784 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: 310600.0 ave 310600 max 310600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310600 Ave neighs/atom = 225.72674 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.085 | 6.085 | 6.085 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4863.6353 0 -4863.6353 -60.894288 Loop time of 7.146e-06 on 1 procs for 0 steps with 1376 atoms 195.9% 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 | | 7.146e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10757.0 ave 10757 max 10757 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: 310548.0 ave 310548 max 310548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310548 Ave neighs/atom = 225.68895 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.085 | 6.085 | 6.085 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 -4863.6353 -4863.6353 23.751023 133.92741 5.1148169 -60.894288 -60.894288 34.23477 -122.96091 -93.956722 2.3947636 569.1126 Loop time of 6.465e-06 on 1 procs for 0 steps with 1376 atoms 293.9% 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 | | 6.465e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10757.0 ave 10757 max 10757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155274.0 ave 155274 max 155274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 310548.0 ave 310548 max 310548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310548 Ave neighs/atom = 225.68895 Neighbor list builds = 0 Dangerous builds = 0 1376 -4863.63526447387 eV 2.39476364606107 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07