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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -53.045097 0.0000000) to (37.508548 53.045097 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9783345 6.7848380 5.7200000 Created 683 atoms using lattice units in orthogonal box = (0.0000000 -53.045097 0.0000000) to (37.508548 53.045097 5.7200000) create_atoms CPU = 0.002 seconds 683 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9783345 6.7848380 5.7200000 Created 691 atoms using lattice units in orthogonal box = (0.0000000 -53.045097 0.0000000) to (37.508548 53.045097 5.7200000) create_atoms CPU = 0.002 seconds 691 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 1363 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_876687166519_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4523.1531 0 -4523.1531 4897.7075 83 0 -4567.1073 0 -4567.1073 -3756.7039 Loop time of 7.75089 on 1 procs for 83 steps with 1363 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4523.15305777816 -4567.10335079207 -4567.10734945506 Force two-norm initial, final = 53.972831 0.15890926 Force max component initial, final = 9.1114507 0.033742388 Final line search alpha, max atom move = 1.0000000 0.033742388 Iterations, force evaluations = 83 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7181 | 7.7181 | 7.7181 | 0.0 | 99.58 Neigh | 0.007061 | 0.007061 | 0.007061 | 0.0 | 0.09 Comm | 0.011966 | 0.011966 | 0.011966 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01374 | | | 0.18 Nlocal: 1363.00 ave 1363 max 1363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5332.00 ave 5332 max 5332 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: 103220.0 ave 103220 max 103220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103220 Ave neighs/atom = 75.730007 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4567.1073 0 -4567.1073 -3756.7039 22761.534 86 0 -4567.2472 0 -4567.2472 253.35742 22644.265 Loop time of 0.221468 on 1 procs for 3 steps with 1363 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 = -4567.10734945505 -4567.2428381457 -4567.24715096629 Force two-norm initial, final = 93.434293 6.5818130 Force max component initial, final = 64.420178 4.4990713 Final line search alpha, max atom move = 0.00010543112 0.00047434215 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22013 | 0.22013 | 0.22013 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021694 | 0.00021694 | 0.00021694 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001116 | | | 0.50 Nlocal: 1363.00 ave 1363 max 1363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5312.00 ave 5312 max 5312 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: 103892.0 ave 103892 max 103892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103892 Ave neighs/atom = 76.223037 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.181 | 5.181 | 5.181 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4567.2472 0 -4567.2472 253.35742 Loop time of 2.307e-06 on 1 procs for 0 steps with 1363 atoms 130.0% 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 | | 2.307e-06 | | |100.00 Nlocal: 1363.00 ave 1363 max 1363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5312.00 ave 5312 max 5312 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: 103958.0 ave 103958 max 103958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103958 Ave neighs/atom = 76.271460 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.181 | 5.181 | 5.181 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 -4567.2472 -4567.2472 37.467988 105.78956 5.7128794 253.35742 253.35742 317.98389 128.01226 314.0761 2.5934927 1132.088 Loop time of 2.079e-06 on 1 procs for 0 steps with 1363 atoms 240.5% 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 | | 2.079e-06 | | |100.00 Nlocal: 1363.00 ave 1363 max 1363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5312.00 ave 5312 max 5312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51979.0 ave 51979 max 51979 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103958.0 ave 103958 max 103958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103958 Ave neighs/atom = 76.271460 Neighbor list builds = 0 Dangerous builds = 0 1363 -4567.24715096629 eV 2.5934927284438 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08