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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -51.395843 0.0000000) to (36.342349 51.395843 4.0380388) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9353808 4.7588744 4.0380388 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.395843 0.0000000) to (36.342349 51.395843 4.0380388) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9353808 4.7588744 4.0380388 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.395843 0.0000000) to (36.342349 51.395843 4.0380388) create_atoms CPU = 0.002 seconds 650 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.457 | 5.457 | 5.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5099.3898 0 -5099.3898 63450.167 59 0 -5335.6052 0 -5335.6052 4153.0624 Loop time of 1.12003 on 1 procs for 59 steps with 1298 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 = -5099.38975039872 -5335.59995452043 -5335.60515158164 Force two-norm initial, final = 364.45355 0.27039740 Force max component initial, final = 93.441879 0.062689209 Final line search alpha, max atom move = 1.0000000 0.062689209 Iterations, force evaluations = 59 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1047 | 1.1047 | 1.1047 | 0.0 | 98.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0080465 | 0.0080465 | 0.0080465 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007317 | | | 0.65 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8206.00 ave 8206 max 8206 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: 217276.0 ave 217276 max 217276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217276 Ave neighs/atom = 167.39291 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.457 | 5.457 | 5.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -5335.6052 0 -5335.6052 4153.0624 15084.867 62 0 -5335.6775 0 -5335.6775 3.2157716 15121.042 Loop time of 0.0644538 on 1 procs for 3 steps with 1298 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 = -5335.60515158166 -5335.6745518542 -5335.67746723006 Force two-norm initial, final = 74.221412 0.93443755 Force max component initial, final = 63.295212 0.72773452 Final line search alpha, max atom move = 8.0817996e-05 5.8814046e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062226 | 0.062226 | 0.062226 | 0.0 | 96.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039428 | 0.00039428 | 0.00039428 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001833 | | | 2.84 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8220.00 ave 8220 max 8220 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: 216544.0 ave 216544 max 216544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216544 Ave neighs/atom = 166.82897 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.595 | 5.595 | 5.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5335.6775 0 -5335.6775 3.2157716 Loop time of 1.709e-06 on 1 procs for 0 steps with 1298 atoms 175.5% 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 | | 1.709e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8206.00 ave 8206 max 8206 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: 216444.0 ave 216444 max 216444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216444 Ave neighs/atom = 166.75193 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.595 | 5.595 | 5.595 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 -5335.6775 -5335.6775 36.358243 103.01026 4.0373682 3.2157716 3.2157716 77.142109 -18.481847 -49.012947 2.2496978 526.88653 Loop time of 2.75e-06 on 1 procs for 0 steps with 1298 atoms 254.5% 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 | | 2.75e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8206.00 ave 8206 max 8206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108222.0 ave 108222 max 108222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 216444.0 ave 216444 max 216444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216444 Ave neighs/atom = 166.75193 Neighbor list builds = 0 Dangerous builds = 0 1298 -5335.67746723006 eV 2.24969775638517 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01