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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -41.118883 0.0000000) to (35.609997 41.118883 6.9836950) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3915380 6.3259820 6.9836950 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -41.118883 0.0000000) to (35.609997 41.118883 6.9836950) create_atoms CPU = 0.002 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3915380 6.3259820 6.9836950 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.118883 0.0000000) to (35.609997 41.118883 6.9836950) create_atoms CPU = 0.001 seconds 629 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 19 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1247 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_019873715786_000#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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.446 | 5.446 | 5.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4067.6188 0 -4067.6188 11461.4 99 0 -4171.9283 0 -4171.9283 7373.0908 Loop time of 2.07895 on 1 procs for 99 steps with 1247 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4067.61883543408 -4171.92427239117 -4171.92831495191 Force two-norm initial, final = 52.119832 0.17982634 Force max component initial, final = 7.2068775 0.033664503 Final line search alpha, max atom move = 1.0000000 0.033664503 Iterations, force evaluations = 99 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0161 | 2.0161 | 2.0161 | 0.0 | 96.98 Neigh | 0.039735 | 0.039735 | 0.039735 | 0.0 | 1.91 Comm | 0.011726 | 0.011726 | 0.011726 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0114 | | | 0.55 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6202.00 ave 6202 max 6202 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: 215608.0 ave 215608 max 215608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215608 Ave neighs/atom = 172.90136 Neighbor list builds = 3 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.446 | 5.446 | 5.446 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -4171.9283 0 -4171.9283 7373.0908 20451.658 111 0 -4172.8622 0 -4172.8622 6.9845568 20622.293 Loop time of 0.155217 on 1 procs for 12 steps with 1247 atoms 94.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4171.9283149519 -4172.86079523382 -4172.86221216843 Force two-norm initial, final = 194.65464 0.65503786 Force max component initial, final = 177.92983 0.32787010 Final line search alpha, max atom move = 0.00024908604 8.1667863e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15115 | 0.15115 | 0.15115 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063717 | 0.00063717 | 0.00063717 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003431 | | | 2.21 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6205.00 ave 6205 max 6205 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: 215622.0 ave 215622 max 215622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215622 Ave neighs/atom = 172.91259 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.584 | 5.584 | 5.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4172.8622 0 -4172.8622 6.9845568 Loop time of 2.01e-06 on 1 procs for 0 steps with 1247 atoms 199.0% 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 | | 2.01e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6205.00 ave 6205 max 6205 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: 214946.0 ave 214946 max 214946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 214946 Ave neighs/atom = 172.37049 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.584 | 5.584 | 5.584 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 -4172.8622 -4172.8622 35.616499 83.181364 6.9608085 6.9845568 6.9845568 -7.5637019 3.1281364 25.389236 2.6012035 1206.7395 Loop time of 2.176e-06 on 1 procs for 0 steps with 1247 atoms 183.8% 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 | | 2.176e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6205.00 ave 6205 max 6205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107473.0 ave 107473 max 107473 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 214946.0 ave 214946 max 214946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 214946 Ave neighs/atom = 172.37049 Neighbor list builds = 0 Dangerous builds = 0 1247 -4172.86221216844 eV 2.60120350477822 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02