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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -43.807448 0.0000000) to (14.602483 43.807448 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6163395 5.6163395 4.0500000 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -43.807448 0.0000000) to (14.602483 43.807448 4.0500000) create_atoms CPU = 0.001 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6163395 5.6163395 4.0500000 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -43.807448 0.0000000) to (14.602483 43.807448 4.0500000) create_atoms CPU = 0.001 seconds 158 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 4 21 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_664470114311_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1037.2417 0 -1037.2417 5509.4441 15 0 -1045.2222 0 -1045.2222 4889.6611 Loop time of 0.19236 on 1 procs for 15 steps with 312 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 = -1037.24172804407 -1045.22136444704 -1045.22222770138 Force two-norm initial, final = 12.977655 0.052138705 Force max component initial, final = 4.3388197 0.0083827526 Final line search alpha, max atom move = 1.0000000 0.0083827526 Iterations, force evaluations = 15 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18814 | 0.18814 | 0.18814 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023441 | 0.0023441 | 0.0023441 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001873 | | | 0.97 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3788.00 ave 3788 max 3788 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: 54628.0 ave 54628 max 54628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54628 Ave neighs/atom = 175.08974 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -1045.2222 0 -1045.2222 4889.6611 5181.5498 26 0 -1045.3625 0 -1045.3625 18.792832 5212.9766 Loop time of 0.0940583 on 1 procs for 11 steps with 312 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1045.22222770138 -1045.36250092372 -1045.36252171774 Force two-norm initial, final = 33.485524 0.20567828 Force max component initial, final = 31.537303 0.15056281 Final line search alpha, max atom move = 0.0073156309 0.0011014619 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089657 | 0.089657 | 0.089657 | 0.0 | 95.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001009 | 0.001009 | 0.001009 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003393 | | | 3.61 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3788.00 ave 3788 max 3788 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: 54216.0 ave 54216 max 54216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54216 Ave neighs/atom = 173.76923 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1045.3625 0 -1045.3625 18.792832 Loop time of 7.257e-06 on 1 procs for 0 steps with 312 atoms 165.4% 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 | | 7.257e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3788.00 ave 3788 max 3788 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: 54152.0 ave 54152 max 54152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54152 Ave neighs/atom = 173.56410 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.598 | 4.598 | 4.598 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 -1045.3625 -1045.3625 14.582108 88.496516 4.0396086 18.792832 18.792832 6.4061953 3.8164715 46.155829 2.5601504 206.05852 Loop time of 6.796e-06 on 1 procs for 0 steps with 312 atoms 250.1% 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 | | 6.796e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3788.00 ave 3788 max 3788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27076.0 ave 27076 max 27076 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54152.0 ave 54152 max 54152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54152 Ave neighs/atom = 173.56410 Neighbor list builds = 0 Dangerous builds = 0 312 -1043.46574436405 eV 2.56015036242586 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00