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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -57.962138 0.0000000) to (20.492710 57.962138 5.0449566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5889210 6.1474995 5.0449566 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.962138 0.0000000) to (20.492710 57.962138 5.0449566) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5889210 6.1474995 5.0449566 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.962138 0.0000000) to (20.492710 57.962138 5.0449566) create_atoms CPU = 0.002 seconds 530 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1050 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.614 | 4.614 | 4.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4302.2177 0 -4302.2177 26438.196 103 0 -4435.1041 0 -4435.1041 38413.684 Loop time of 5.94135 on 1 procs for 103 steps with 1050 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 = -4302.21767322779 -4435.0996677525 -4435.10405719031 Force two-norm initial, final = 246.08531 0.35219494 Force max component initial, final = 77.028812 0.079762062 Final line search alpha, max atom move = 0.91514596 0.072993929 Iterations, force evaluations = 103 189 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9158 | 5.9158 | 5.9158 | 0.0 | 99.57 Neigh | 0.005359 | 0.005359 | 0.005359 | 0.0 | 0.09 Comm | 0.0093962 | 0.0093962 | 0.0093962 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01083 | | | 0.18 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4702.00 ave 4702 max 4702 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: 60660.0 ave 60660 max 60660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60660 Ave neighs/atom = 57.771429 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -4435.1041 0 -4435.1041 38413.684 11984.812 114 0 -4437.1704 0 -4437.1704 -23.776696 12126.17 Loop time of 0.441748 on 1 procs for 11 steps with 1050 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4435.10405719031 -4437.1678143683 -4437.17044961366 Force two-norm initial, final = 509.32443 1.8913137 Force max component initial, final = 375.23454 0.31789332 Final line search alpha, max atom move = 4.9635174e-05 1.5778690e-05 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43228 | 0.43228 | 0.43228 | 0.0 | 97.86 Neigh | 0.0052475 | 0.0052475 | 0.0052475 | 0.0 | 1.19 Comm | 0.00077032 | 0.00077032 | 0.00077032 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003449 | | | 0.78 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4758.00 ave 4758 max 4758 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: 59892.0 ave 59892 max 59892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59892 Ave neighs/atom = 57.040000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.753 | 4.753 | 4.753 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4437.1704 0 -4437.1704 -23.776696 Loop time of 2.074e-06 on 1 procs for 0 steps with 1050 atoms 144.6% 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 | | 2.074e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4761.00 ave 4761 max 4761 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: 59884.0 ave 59884 max 59884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59884 Ave neighs/atom = 57.032381 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.753 | 4.753 | 4.753 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 -4437.1704 -4437.1704 20.558144 117.0626 5.0387358 -23.776696 -23.776696 -42.135931 -40.916162 11.722005 2.3709965 732.00618 Loop time of 1.955e-06 on 1 procs for 0 steps with 1050 atoms 153.5% 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 | | 1.955e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4761.00 ave 4761 max 4761 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29942.0 ave 29942 max 29942 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59884.0 ave 59884 max 59884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59884 Ave neighs/atom = 57.032381 Neighbor list builds = 0 Dangerous builds = 0 1050 -4437.17044961366 eV 2.37099646808889 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06