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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -41.843523 0.0000000) to (29.587839 41.843523 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7409240 6.2453020 5.1120000 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.843523 0.0000000) to (29.587839 41.843523 5.1120000) create_atoms CPU = 0.005 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7409240 6.2453020 5.1120000 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.843523 0.0000000) to (29.587839 41.843523 5.1120000) create_atoms CPU = 0.004 seconds 538 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 31 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1072 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_887933271505_003#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3341.8278 0 -3341.8278 78514.709 37 0 -3798.6993 0 -3798.6993 1545.5905 Loop time of 1.88404 on 1 procs for 37 steps with 1072 atoms 51.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3341.82776103088 -3798.69926645766 -3798.69926645765 Force two-norm initial, final = 655.88084 0.92975486 Force max component initial, final = 136.54674 0.13827527 Final line search alpha, max atom move = 1.0218699e-08 1.4129934e-09 Iterations, force evaluations = 37 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8405 | 1.8405 | 1.8405 | 0.0 | 97.69 Neigh | 0.011744 | 0.011744 | 0.011744 | 0.0 | 0.62 Comm | 0.016907 | 0.016907 | 0.016907 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01486 | | | 0.79 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4382.00 ave 4382 max 4382 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: 58956.0 ave 58956 max 58956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58956 Ave neighs/atom = 54.996269 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -3798.6993 0 -3798.6993 1545.5905 12657.92 44 0 -3799.1601 0 -3799.1601 -100.0766 12671.962 Loop time of 0.163067 on 1 procs for 7 steps with 1072 atoms 49.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3798.69926645766 -3799.1578685018 -3799.16013757066 Force two-norm initial, final = 84.580608 1.8217210 Force max component initial, final = 75.643705 1.1745232 Final line search alpha, max atom move = 0.00021547764 0.00025308349 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15613 | 0.15613 | 0.15613 | 0.0 | 95.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013882 | 0.0013882 | 0.0013882 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005552 | | | 3.40 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4382.00 ave 4382 max 4382 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: 59016.0 ave 59016 max 59016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59016 Ave neighs/atom = 55.052239 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.733 | 4.733 | 4.733 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3799.1601 0 -3799.1601 -100.0766 Loop time of 8.109e-06 on 1 procs for 0 steps with 1072 atoms 111.0% 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 | | 8.109e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4396.00 ave 4396 max 4396 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: 59008.0 ave 59008 max 59008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59008 Ave neighs/atom = 55.044776 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.733 | 4.733 | 4.733 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 -3799.1601 -3799.1601 29.439857 84.226883 5.1104299 -100.0766 -100.0766 -119.86297 -149.45849 -30.908358 2.3440314 541.79722 Loop time of 6.565e-06 on 1 procs for 0 steps with 1072 atoms 213.3% 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 | | 6.565e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4396.00 ave 4396 max 4396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29504.0 ave 29504 max 29504 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59008.0 ave 59008 max 59008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59008 Ave neighs/atom = 55.044776 Neighbor list builds = 0 Dangerous builds = 0 1072 -3799.16013757066 eV 2.34403136675116 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02