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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -69.024535 0.0000000) to (34.510438 69.024535 3.6580991) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0408505 5.0408505 3.6580991 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -69.024535 0.0000000) to (34.510438 69.024535 3.6580991) create_atoms CPU = 0.001 seconds 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0408505 5.0408505 3.6580991 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -69.024535 0.0000000) to (34.510438 69.024535 3.6580991) create_atoms CPU = 0.001 seconds 714 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 = 10 38 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 = 1422 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 38 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) = 5.111 | 5.111 | 5.111 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5472.7314 0 -5472.7314 13401.851 189 0 -5531.95 0 -5531.95 -3799.2213 Loop time of 3.45244 on 1 procs for 189 steps with 1422 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 = -5472.73135044603 -5531.94454702113 -5531.94996158032 Force two-norm initial, final = 47.601459 0.26335587 Force max component initial, final = 12.796600 0.081339853 Final line search alpha, max atom move = 1.0000000 0.081339853 Iterations, force evaluations = 189 355 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3699 | 3.3699 | 3.3699 | 0.0 | 97.61 Neigh | 0.033384 | 0.033384 | 0.033384 | 0.0 | 0.97 Comm | 0.026767 | 0.026767 | 0.026767 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0224 | | | 0.65 Nlocal: 1422.00 ave 1422 max 1422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9833.00 ave 9833 max 9833 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: 195808.0 ave 195808 max 195808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195808 Ave neighs/atom = 137.69902 Neighbor list builds = 3 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 = 10 38 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 : 189 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.493 | 5.493 | 5.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 189 0 -5531.95 0 -5531.95 -3799.2213 17427.674 222 0 -5539.5889 0 -5539.5889 -15093.192 17620.08 Loop time of 0.355363 on 1 procs for 33 steps with 1422 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 = -5531.94996158033 -5539.58451092415 -5539.58887006956 Force two-norm initial, final = 411.33790 1.6227705 Force max component initial, final = 389.07503 0.28346485 Final line search alpha, max atom move = 9.2911777e-05 2.6337223e-05 Iterations, force evaluations = 33 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34051 | 0.34051 | 0.34051 | 0.0 | 95.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024289 | 0.0024289 | 0.0024289 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01243 | | | 3.50 Nlocal: 1422.00 ave 1422 max 1422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9838.00 ave 9838 max 9838 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: 196548.0 ave 196548 max 196548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196548 Ave neighs/atom = 138.21941 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 = 10 38 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) = 5.631 | 5.631 | 5.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5539.5889 0 -5539.5889 -15093.192 Loop time of 2.12e-06 on 1 procs for 0 steps with 1422 atoms 188.7% 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 | | 2.12e-06 | | |100.00 Nlocal: 1422.00 ave 1422 max 1422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9898.00 ave 9898 max 9898 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: 197720.0 ave 197720 max 197720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197720 Ave neighs/atom = 139.04360 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 = 10 38 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) = 5.631 | 5.631 | 5.631 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 -5539.5889 -5539.5889 33.862529 138.04907 3.7692504 -15093.192 -15093.192 25.291269 -45297.649 -7.2171805 2.2760621 615.30928 Loop time of 2.177e-06 on 1 procs for 0 steps with 1422 atoms 275.6% 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 | | 2.177e-06 | | |100.00 Nlocal: 1422.00 ave 1422 max 1422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9898.00 ave 9898 max 9898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98860.0 ave 98860 max 98860 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 197720.0 ave 197720 max 197720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197720 Ave neighs/atom = 139.04360 Neighbor list builds = 0 Dangerous builds = 0 1422 -5338.48732086493 eV 2.27606208252992 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04