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 = 2.8553128 2.8553128 2.8553128 Created orthogonal box = (0.0000000 -36.342199 0.0000000) to (25.697815 36.342199 4.0380221) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7588546 4.9353603 4.0380221 Created 324 atoms using lattice units in orthogonal box = (0.0000000 -36.342199 0.0000000) to (25.697815 36.342199 4.0380221) create_atoms CPU = 0.003 seconds 324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7588546 4.9353603 4.0380221 Created 326 atoms using lattice units in orthogonal box = (0.0000000 -36.342199 0.0000000) to (25.697815 36.342199 4.0380221) create_atoms CPU = 0.003 seconds 326 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 644 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_884343146310_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.529 | 4.529 | 4.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2288.5621 0 -2288.5621 105013.63 90 0 -2567.3396 0 -2567.3396 1837.8146 Loop time of 1.86327 on 1 procs for 90 steps with 644 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 = -2288.56208259156 -2567.33750028758 -2567.33959819815 Force two-norm initial, final = 796.04325 0.21974051 Force max component initial, final = 276.70752 0.071430718 Final line search alpha, max atom move = 1.0000000 0.071430718 Iterations, force evaluations = 90 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7987 | 1.7987 | 1.7987 | 0.0 | 96.53 Neigh | 0.026486 | 0.026486 | 0.026486 | 0.0 | 1.42 Comm | 0.021524 | 0.021524 | 0.021524 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01657 | | | 0.89 Nlocal: 644.000 ave 644 max 644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5313.00 ave 5313 max 5313 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: 87968.0 ave 87968 max 87968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87968 Ave neighs/atom = 136.59627 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.529 | 4.529 | 4.529 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -2567.3396 0 -2567.3396 1837.8146 7542.3395 93 0 -2567.3759 0 -2567.3759 223.16555 7549.6906 Loop time of 0.0550502 on 1 procs for 3 steps with 644 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2567.33959819815 -2567.37452048863 -2567.37588698095 Force two-norm initial, final = 29.473920 1.9219867 Force max component initial, final = 29.224393 1.3740285 Final line search alpha, max atom move = 0.00025819592 0.00035476856 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052721 | 0.052721 | 0.052721 | 0.0 | 95.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000631 | 0.000631 | 0.000631 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001698 | | | 3.08 Nlocal: 644.000 ave 644 max 644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5411.00 ave 5411 max 5411 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: 87660.0 ave 87660 max 87660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87660 Ave neighs/atom = 136.11801 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.667 | 4.667 | 4.667 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2567.3759 0 -2567.3759 223.16555 Loop time of 7.107e-06 on 1 procs for 0 steps with 644 atoms 168.8% 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 | | 7.107e-06 | | |100.00 Nlocal: 644.000 ave 644 max 644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5411.00 ave 5411 max 5411 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: 87636.0 ave 87636 max 87636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87636 Ave neighs/atom = 136.08075 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.667 | 4.667 | 4.667 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 -2567.3759 -2567.3759 25.687802 72.851791 4.0342422 223.16555 223.16555 248.87587 292.26445 128.35634 2.2468622 497.54619 Loop time of 7.277e-06 on 1 procs for 0 steps with 644 atoms 247.4% 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 | | 7.277e-06 | | |100.00 Nlocal: 644.000 ave 644 max 644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5411.00 ave 5411 max 5411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43818.0 ave 43818 max 43818 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87636.0 ave 87636 max 87636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87636 Ave neighs/atom = 136.08075 Neighbor list builds = 0 Dangerous builds = 0 644 -2567.37588698095 eV 2.2468622062349 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02