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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -46.785632 0.0000000) to (33.082437 46.785632 5.1666087) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6482210 6.2761213 5.1666087 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -46.785632 0.0000000) to (33.082437 46.785632 5.1666087) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6482210 6.2761213 5.1666087 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -46.785632 0.0000000) to (33.082437 46.785632 5.1666087) create_atoms CPU = 0.005 seconds 660 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_673777079812_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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.499 | 5.499 | 5.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3991.0608 0 -3991.0608 28004.542 71 0 -4250.4612 0 -4250.4612 -9744.3997 Loop time of 3.83875 on 1 procs for 71 steps with 1304 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 = -3991.06078070503 -4250.45730441548 -4250.46115741026 Force two-norm initial, final = 346.19983 0.24608337 Force max component initial, final = 84.157591 0.019875998 Final line search alpha, max atom move = 1.0000000 0.019875998 Iterations, force evaluations = 71 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7521 | 3.7521 | 3.7521 | 0.0 | 97.74 Neigh | 0.038203 | 0.038203 | 0.038203 | 0.0 | 1.00 Comm | 0.026423 | 0.026423 | 0.026423 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02199 | | | 0.57 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8734.00 ave 8734 max 8734 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: 291304.0 ave 291304 max 291304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291304 Ave neighs/atom = 223.39264 Neighbor list builds = 1 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.502 | 5.502 | 5.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4250.4612 0 -4250.4612 -9744.3997 15993.575 86 0 -4252.1816 0 -4252.1816 50.922722 15850.385 Loop time of 0.500662 on 1 procs for 15 steps with 1304 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 = -4250.46115741026 -4252.18104160775 -4252.1815729344 Force two-norm initial, final = 253.67171 1.9336372 Force max component initial, final = 239.29552 1.6434364 Final line search alpha, max atom move = 0.00037992044 0.00062437510 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48641 | 0.48641 | 0.48641 | 0.0 | 97.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0031068 | 0.0031068 | 0.0031068 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01114 | | | 2.23 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8704.00 ave 8704 max 8704 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: 292192.0 ave 292192 max 292192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292192 Ave neighs/atom = 224.07362 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.640 | 5.640 | 5.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4252.1816 0 -4252.1816 50.922722 Loop time of 6.575e-06 on 1 procs for 0 steps with 1304 atoms 182.5% 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 | | 6.575e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8756.00 ave 8756 max 8756 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: 293312.0 ave 293312 max 293312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293312 Ave neighs/atom = 224.93252 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.640 | 5.640 | 5.640 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 -4252.1816 -4252.1816 32.609935 94.020339 5.1697326 50.922722 50.922722 37.559259 166.91784 -51.708938 2.3668482 1088.2592 Loop time of 7.187e-06 on 1 procs for 0 steps with 1304 atoms 292.2% 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 | | 7.187e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8756.00 ave 8756 max 8756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146656.0 ave 146656 max 146656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 293312.0 ave 293312 max 293312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293312 Ave neighs/atom = 224.93252 Neighbor list builds = 0 Dangerous builds = 0 1304 -4252.1815729344 eV 2.36684816635458 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05