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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -72.401345 0.0000000) to (41.800936 72.401345 6.2545236) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6150511 5.7632912 6.2545236 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -72.401345 0.0000000) to (41.800936 72.401345 6.2545236) create_atoms CPU = 0.010 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6150511 5.7632912 6.2545236 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.401345 0.0000000) to (41.800936 72.401345 6.2545236) create_atoms CPU = 0.010 seconds 1610 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 29 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3214 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 13.78 | 13.78 | 13.78 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12656.31 0 -12656.31 34564.136 123 0 -13306.115 0 -13306.115 3777.5906 Loop time of 31.9131 on 1 procs for 123 steps with 3214 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 = -12656.3095700847 -13306.1034864395 -13306.1148773255 Force two-norm initial, final = 687.61666 0.46183145 Force max component initial, final = 153.53654 0.065709168 Final line search alpha, max atom move = 0.62696252 0.041197186 Iterations, force evaluations = 123 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.863 | 30.863 | 30.863 | 0.0 | 96.71 Neigh | 0.8535 | 0.8535 | 0.8535 | 0.0 | 2.67 Comm | 0.11231 | 0.11231 | 0.11231 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08449 | | | 0.26 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20539.0 ave 20539 max 20539 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: 1.22077e+06 ave 1.22077e+06 max 1.22077e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1220768 Ave neighs/atom = 379.82825 Neighbor list builds = 6 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 123 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.78 | 13.78 | 13.78 Mbytes Step Temp E_pair E_mol TotEng Press Volume 123 0 -13306.115 0 -13306.115 3777.5906 37857.931 126 0 -13306.288 0 -13306.288 20.955599 37940.504 Loop time of 0.84691 on 1 procs for 3 steps with 3214 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 = -13306.1148773255 -13306.285044955 -13306.2880179719 Force two-norm initial, final = 183.43591 4.1608475 Force max component initial, final = 159.74252 2.8039395 Final line search alpha, max atom move = 5.6304294e-05 0.00015787383 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83583 | 0.83583 | 0.83583 | 0.0 | 98.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029848 | 0.0029848 | 0.0029848 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008093 | | | 0.96 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20543.0 ave 20543 max 20543 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: 1.22070e+06 ave 1.2207e+06 max 1.2207e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1220696 Ave neighs/atom = 379.80585 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 13.29 | 13.29 | 13.29 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13306.288 0 -13306.288 20.955599 Loop time of 6.395e-06 on 1 procs for 0 steps with 3214 atoms 172.0% 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 | | 6.395e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20539.0 ave 20539 max 20539 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: 1.22016e+06 ave 1.22016e+06 max 1.22016e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1220160 Ave neighs/atom = 379.63908 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 13.29 | 13.29 | 13.29 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 -13306.288 -13306.288 41.825342 145.07596 6.2527081 20.955599 20.955599 -114.10217 58.596736 118.37223 2.2557747 1034.2386 Loop time of 7.126e-06 on 1 procs for 0 steps with 3214 atoms 266.6% 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 | | 7.126e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20539.0 ave 20539 max 20539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 610080.0 ave 610080 max 610080 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.22016e+06 ave 1.22016e+06 max 1.22016e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1220160 Ave neighs/atom = 379.63908 Neighbor list builds = 0 Dangerous builds = 0 3214 -13306.2880179719 eV 2.25577469210203 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34