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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -53.261614 0.0000000) to (13.315404 53.261614 4.2107003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3261614 5.3261614 4.2107003 Created 160 atoms using lattice units in orthogonal box = (0.0000000 -53.261614 0.0000000) to (13.315404 53.261614 4.2107003) create_atoms CPU = 0.002 seconds 160 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3261614 5.3261614 4.2107003 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -53.261614 0.0000000) to (13.315404 53.261614 4.2107003) create_atoms CPU = 0.001 seconds 162 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 24 1 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 320 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1180.5198 0 -1180.5198 10250.461 20 0 -1191.1835 0 -1191.1835 2570.1346 Loop time of 0.343555 on 1 procs for 20 steps with 320 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 = -1180.51977119451 -1191.1826729467 -1191.18347471585 Force two-norm initial, final = 25.948514 0.041865910 Force max component initial, final = 6.7151935 0.011602820 Final line search alpha, max atom move = 1.0000000 0.011602820 Iterations, force evaluations = 20 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33807 | 0.33807 | 0.33807 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003061 | 0.003061 | 0.003061 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002426 | | | 0.71 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4070.00 ave 4070 max 4070 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: 55960.0 ave 55960 max 55960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55960 Ave neighs/atom = 174.87500 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -1191.1835 0 -1191.1835 2570.1346 5972.4563 32 0 -1191.2769 0 -1191.2769 -0.59038842 6010.689 Loop time of 0.152602 on 1 procs for 12 steps with 320 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 = -1191.18347471585 -1191.27647255659 -1191.27688206093 Force two-norm initial, final = 19.840383 0.13395518 Force max component initial, final = 18.435800 0.036384798 Final line search alpha, max atom move = 0.0014758362 5.3698001e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13946 | 0.13946 | 0.13946 | 0.0 | 91.39 Neigh | 0.0077403 | 0.0077403 | 0.0077403 | 0.0 | 5.07 Comm | 0.0014667 | 0.0014667 | 0.0014667 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003936 | | | 2.58 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4075.00 ave 4075 max 4075 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: 55408.0 ave 55408 max 55408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55408 Ave neighs/atom = 173.15000 Neighbor list builds = 1 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1191.2769 0 -1191.2769 -0.59038842 Loop time of 6.475e-06 on 1 procs for 0 steps with 320 atoms 185.3% 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 | | 6.475e-06 | | |100.00 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4075.00 ave 4075 max 4075 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: 55392.0 ave 55392 max 55392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55392 Ave neighs/atom = 173.10000 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.608 | 4.608 | 4.608 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 -1191.2769 -1191.2769 13.282333 107.77919 4.1987011 -0.59038842 -0.59038842 -5.8654954 -5.5765655 9.6708957 2.7691454 235.43569 Loop time of 6.896e-06 on 1 procs for 0 steps with 320 atoms 246.5% 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 | | 6.896e-06 | | |100.00 Nlocal: 320.000 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4075.00 ave 4075 max 4075 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27696.0 ave 27696 max 27696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55392.0 ave 55392 max 55392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55392 Ave neighs/atom = 173.10000 Neighbor list builds = 0 Dangerous builds = 0 320 -1191.27688206093 eV 2.76914542085155 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01