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 = 4.0499992 4.0499992 4.0499992 Created orthogonal box = (0.0000000 -41.302050 0.0000000) to (20.651025 41.302050 4.0499992) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7656211 4.7656211 4.0499992 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -41.302050 0.0000000) to (20.651025 41.302050 4.0499992) create_atoms CPU = 0.000 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7656211 4.7656211 4.0499992 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -41.302050 0.0000000) to (20.651025 41.302050 4.0499992) create_atoms CPU = 0.000 seconds 210 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.447 | 4.447 | 4.447 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1296.7743 0 -1296.7743 24643.294 71 0 -1374.9619 0 -1374.9619 -3141.5933 Loop time of 2.93998 on 1 procs for 71 steps with 412 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1296.77434006494 -1374.9609086394 -1374.96188281129 Force two-norm initial, final = 185.23374 0.080728536 Force max component initial, final = 65.337080 0.011686449 Final line search alpha, max atom move = 1.0000000 0.011686449 Iterations, force evaluations = 71 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9282 | 2.9282 | 2.9282 | 0.0 | 99.60 Neigh | 0.0028524 | 0.0028524 | 0.0028524 | 0.0 | 0.10 Comm | 0.0046429 | 0.0046429 | 0.0046429 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004246 | | | 0.14 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3191.00 ave 3191 max 3191 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: 32852.0 ave 32852 max 32852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32852 Ave neighs/atom = 79.737864 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.447 | 4.447 | 4.447 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -1374.9619 0 -1374.9619 -3141.5933 6908.7288 75 0 -1374.998 0 -1374.998 -197.74886 6882.1138 Loop time of 0.129065 on 1 procs for 4 steps with 412 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 = -1374.96188281129 -1374.99746895954 -1374.99798310958 Force two-norm initial, final = 24.220479 1.6878993 Force max component initial, final = 18.325006 1.5050511 Final line search alpha, max atom move = 0.00064548970 0.00097149499 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12815 | 0.12815 | 0.12815 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016801 | 0.00016801 | 0.00016801 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007504 | | | 0.58 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3183.00 ave 3183 max 3183 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: 32552.0 ave 32552 max 32552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32552 Ave neighs/atom = 79.009709 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1374.998 0 -1374.998 -197.74886 Loop time of 1.703e-06 on 1 procs for 0 steps with 412 atoms 176.2% 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 | | 1.703e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3183.00 ave 3183 max 3183 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: 32680.0 ave 32680 max 32680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32680 Ave neighs/atom = 79.320388 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.585 | 4.585 | 4.585 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 -1374.998 -1374.998 20.652405 82.545313 4.0370004 -197.74886 -197.74886 -95.774945 -148.21584 -349.25579 2.5549401 230.22428 Loop time of 1.977e-06 on 1 procs for 0 steps with 412 atoms 202.3% 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 | | 1.977e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3183.00 ave 3183 max 3183 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16340.0 ave 16340 max 16340 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32680.0 ave 32680 max 32680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32680 Ave neighs/atom = 79.320388 Neighbor list builds = 0 Dangerous builds = 0 412 -1374.99798310958 eV 2.55494011623909 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03