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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -55.875955 0.0000000) to (39.510267 55.875955 5.2332627) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2384632 5.3915396 5.2332627 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -55.875955 0.0000000) to (39.510267 55.875955 5.2332627) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2384632 5.3915396 5.2332627 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -55.875955 0.0000000) to (39.510267 55.875955 5.2332627) create_atoms CPU = 0.002 seconds 916 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 11 29 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.578 | 5.578 | 5.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6646.8764 0 -6646.8764 71844.61 535 0 -7363.1388 0 -7363.1388 -86436.464 Loop time of 17.3412 on 1 procs for 535 steps with 1824 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 = -6646.87637898943 -7363.1321395844 -7363.13883901086 Force two-norm initial, final = 869.22120 0.21612184 Force max component initial, final = 172.84214 0.043256975 Final line search alpha, max atom move = 1.0000000 0.043256975 Iterations, force evaluations = 535 1004 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.82 | 16.82 | 16.82 | 0.0 | 96.99 Neigh | 0.29447 | 0.29447 | 0.29447 | 0.0 | 1.70 Comm | 0.12491 | 0.12491 | 0.12491 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1019 | | | 0.59 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9718.00 ave 9718 max 9718 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: 288630.0 ave 288630 max 288630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288630 Ave neighs/atom = 158.24013 Neighbor list builds = 16 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 535 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.585 | 5.585 | 5.585 Mbytes Step Temp E_pair E_mol TotEng Press Volume 535 0 -7363.1388 0 -7363.1388 -86436.464 23106.675 587 0 -7416.2182 0 -7416.2182 -33.291754 21621.136 Loop time of 0.984158 on 1 procs for 52 steps with 1824 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 = -7363.13883901087 -7416.21213061866 -7416.21817604563 Force two-norm initial, final = 2236.0424 7.4143514 Force max component initial, final = 1708.6231 2.9789919 Final line search alpha, max atom move = 6.6516596e-05 0.00019815240 Iterations, force evaluations = 52 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93432 | 0.93432 | 0.93432 | 0.0 | 94.94 Neigh | 0.018581 | 0.018581 | 0.018581 | 0.0 | 1.89 Comm | 0.0050859 | 0.0050859 | 0.0050859 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02617 | | | 2.66 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10002.0 ave 10002 max 10002 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: 297632.0 ave 297632 max 297632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297632 Ave neighs/atom = 163.17544 Neighbor list builds = 1 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 6.114 | 6.114 | 6.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7416.2182 0 -7416.2182 -33.291754 Loop time of 2.581e-06 on 1 procs for 0 steps with 1824 atoms 155.0% 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 | | 2.581e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10275.0 ave 10275 max 10275 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: 300752.0 ave 300752 max 300752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300752 Ave neighs/atom = 164.88596 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 6.114 | 6.114 | 6.114 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 -7416.2182 -7416.2182 38.95046 111.34299 4.9854345 -33.291754 -33.291754 -217.62251 67.143786 50.603461 2.3071243 5554.4259 Loop time of 2.559e-06 on 1 procs for 0 steps with 1824 atoms 234.5% 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 | | 2.559e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10275.0 ave 10275 max 10275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 150376.0 ave 150376 max 150376 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 300752.0 ave 300752 max 300752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300752 Ave neighs/atom = 164.88596 Neighbor list builds = 0 Dangerous builds = 0 1824 -7416.21817604563 eV 2.30712425587108 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19