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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -44.323917 0.0000000) to (19.191123 44.323917 6.7850866) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3970410 5.5400000 6.7850866 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -44.323917 0.0000000) to (19.191123 44.323917 6.7850866) create_atoms CPU = 0.003 seconds 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3970410 5.5400000 6.7850866 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -44.323917 0.0000000) to (19.191123 44.323917 6.7850866) create_atoms CPU = 0.002 seconds 396 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 28 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 752 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4302.2587 0 -4302.2587 -5408.5588 13 0 -4309.1935 0 -4309.1935 -17688.342 Loop time of 0.707224 on 1 procs for 13 steps with 752 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 = -4302.25873698545 -4309.19012990658 -4309.19354115797 Force two-norm initial, final = 6.3068722 0.16368888 Force max component initial, final = 0.87000425 0.020402635 Final line search alpha, max atom move = 1.0000000 0.020402635 Iterations, force evaluations = 13 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70257 | 0.70257 | 0.70257 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021936 | 0.0021936 | 0.0021936 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002463 | | | 0.35 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3613.00 ave 3613 max 3613 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: 57504.0 ave 57504 max 57504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57504 Ave neighs/atom = 76.468085 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -4309.1935 0 -4309.1935 -17688.342 11543.139 18 0 -4309.5192 0 -4309.5192 -6587.9991 11467.491 Loop time of 0.192652 on 1 procs for 5 steps with 752 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4309.19354115794 -4309.51706378026 -4309.51921049551 Force two-norm initial, final = 134.86559 2.0042621 Force max component initial, final = 110.27308 1.8363362 Final line search alpha, max atom move = 0.00012422736 0.00022812319 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18988 | 0.18988 | 0.18988 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052896 | 0.00052896 | 0.00052896 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002248 | | | 1.17 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3613.00 ave 3613 max 3613 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: 57632.0 ave 57632 max 57632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57632 Ave neighs/atom = 76.638298 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.697 | 4.697 | 4.697 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4309.5192 0 -4309.5192 -6587.9991 Loop time of 6.235e-06 on 1 procs for 0 steps with 752 atoms 160.4% 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 | | 6.235e-06 | | |100.00 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3613.00 ave 3613 max 3613 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: 57632.0 ave 57632 max 57632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57632 Ave neighs/atom = 76.638298 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.697 | 4.697 | 4.697 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 -4309.5192 -4309.5192 19.105658 88.647835 6.7707733 -6587.9991 -6587.9991 104.04784 -20124.067 256.02185 2.6565877 526.97728 Loop time of 6.455e-06 on 1 procs for 0 steps with 752 atoms 294.3% 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 | | 6.455e-06 | | |100.00 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3613.00 ave 3613 max 3613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28816.0 ave 28816 max 28816 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57632.0 ave 57632 max 57632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57632 Ave neighs/atom = 76.638298 Neighbor list builds = 0 Dangerous builds = 0 752 -4309.51921049551 eV 2.65658765728468 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01