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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -46.930651 0.0000000) to (33.184981 46.930651 4.0541907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9529823 4.5529736 4.0541907 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -46.930651 0.0000000) to (33.184981 46.930651 4.0541907) create_atoms CPU = 0.005 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9529823 4.5529736 4.0541907 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.930651 0.0000000) to (33.184981 46.930651 4.0541907) create_atoms CPU = 0.004 seconds 538 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 9 25 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1068 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.031 | 5.031 | 5.031 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3845.2836 0 -3845.2836 111126.43 174 0 -4553.0643 0 -4553.0643 -481.8325 Loop time of 6.28644 on 1 procs for 174 steps with 1068 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 = -3845.28355375407 -4553.0598058584 -4553.0643084992 Force two-norm initial, final = 1205.6816 0.29592145 Force max component initial, final = 299.16411 0.046446532 Final line search alpha, max atom move = 1.0000000 0.046446532 Iterations, force evaluations = 174 333 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1103 | 6.1103 | 6.1103 | 0.0 | 97.20 Neigh | 0.070921 | 0.070921 | 0.070921 | 0.0 | 1.13 Comm | 0.05949 | 0.05949 | 0.05949 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04571 | | | 0.73 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7143.00 ave 7143 max 7143 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: 177940.0 ave 177940 max 177940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177940 Ave neighs/atom = 166.61049 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 174 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.025 | 5.025 | 5.025 Mbytes Step Temp E_pair E_mol TotEng Press Volume 174 0 -4553.0643 0 -4553.0643 -481.8325 12627.935 177 0 -4553.1135 0 -4553.1135 7.6738103 12626.307 Loop time of 0.11119 on 1 procs for 3 steps with 1068 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 = -4553.06430849918 -4553.11306245348 -4553.11353045337 Force two-norm initial, final = 45.814585 0.66203686 Force max component initial, final = 33.209115 0.49811763 Final line search alpha, max atom move = 0.00016604313 8.2709009e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10732 | 0.10732 | 0.10732 | 0.0 | 96.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090341 | 0.00090341 | 0.00090341 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002963 | | | 2.66 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7150.00 ave 7150 max 7150 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: 177904.0 ave 177904 max 177904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177904 Ave neighs/atom = 166.57678 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.163 | 5.163 | 5.163 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4553.1135 0 -4553.1135 7.6738103 Loop time of 6.966e-06 on 1 procs for 0 steps with 1068 atoms 172.3% 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 | | 6.966e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7150.00 ave 7150 max 7150 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: 177868.0 ave 177868 max 177868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177868 Ave neighs/atom = 166.54307 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.163 | 5.163 | 5.163 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 -4553.1135 -4553.1135 33.156692 94.02364 4.0501218 7.6738103 7.6738103 63.153228 -5.3189612 -34.812836 2.3041539 464.37176 Loop time of 7.217e-06 on 1 procs for 0 steps with 1068 atoms 304.8% 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 | | 7.217e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7150.00 ave 7150 max 7150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88934.0 ave 88934 max 88934 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 177868.0 ave 177868 max 177868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177868 Ave neighs/atom = 166.54307 Neighbor list builds = 0 Dangerous builds = 0 1068 -4553.11353045337 eV 2.30415394971938 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06