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 = 2.8553126 2.8553126 2.8553126 Created orthogonal box = (0.0000000 -41.573979 0.0000000) to (20.786989 41.573979 2.8553126) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5298661 3.5298661 2.8553126 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -41.573979 0.0000000) to (20.786989 41.573979 2.8553126) create_atoms CPU = 0.001 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5298661 3.5298661 2.8553126 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.573979 0.0000000) to (20.786989 41.573979 2.8553126) create_atoms CPU = 0.001 seconds 213 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 20 1 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 425 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1579.1281 0 -1579.1281 84764.602 39 0 -1696.938 0 -1696.938 13098.11 Loop time of 1.0329 on 1 procs for 39 steps with 425 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 = -1579.12814040828 -1696.93646974888 -1696.93801196067 Force two-norm initial, final = 428.13718 0.12548393 Force max component initial, final = 206.28041 0.035542818 Final line search alpha, max atom move = 1.0000000 0.035542818 Iterations, force evaluations = 39 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0165 | 1.0165 | 1.0165 | 0.0 | 98.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010152 | 0.010152 | 0.010152 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006249 | | | 0.60 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5608.00 ave 5608 max 5608 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: 96712.0 ave 96712 max 96712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96712 Ave neighs/atom = 227.55765 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.490 | 4.490 | 4.490 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -1696.938 0 -1696.938 13098.11 4935.11 49 0 -1697.2188 0 -1697.2188 179.26245 4972.0421 Loop time of 0.172527 on 1 procs for 10 steps with 425 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 = -1696.93801196066 -1697.21837771839 -1697.21877273716 Force two-norm initial, final = 76.430521 1.0354855 Force max component initial, final = 65.443606 0.72869203 Final line search alpha, max atom move = 0.00077608173 0.00056552457 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1666 | 0.1666 | 0.1666 | 0.0 | 96.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014218 | 0.0014218 | 0.0014218 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004507 | | | 2.61 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5624.00 ave 5624 max 5624 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: 96666.0 ave 96666 max 96666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96666 Ave neighs/atom = 227.44941 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1697.2188 0 -1697.2188 179.26245 Loop time of 6.184e-06 on 1 procs for 0 steps with 425 atoms 161.7% 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 | | 6.184e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5610.00 ave 5610 max 5610 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: 95386.0 ave 95386 max 95386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95386 Ave neighs/atom = 224.43765 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.627 | 4.627 | 4.627 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 -1697.2188 -1697.2188 20.769396 83.919951 2.8526317 179.26245 179.26245 234.61288 172.16302 131.01144 2.2840979 192.84865 Loop time of 7.617e-06 on 1 procs for 0 steps with 425 atoms 223.2% 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 | | 7.617e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5610.00 ave 5610 max 5610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47693.0 ave 47693 max 47693 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95386.0 ave 95386 max 95386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95386 Ave neighs/atom = 224.43765 Neighbor list builds = 0 Dangerous builds = 0 425 -1697.21877273716 eV 2.28409785469003 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01