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 -38.425106 0.0000000) to (38.425106 38.425106 3.6147299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1006777 5.1006777 3.6147299 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -38.425106 0.0000000) to (38.425106 38.425106 3.6147299) create_atoms CPU = 0.002 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1006777 5.1006777 3.6147299 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.425106 0.0000000) to (38.425106 38.425106 3.6147299) create_atoms CPU = 0.002 seconds 454 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 = 14 28 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 0 atoms, new total = 906 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 = 14 28 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2684.013 0 -2684.013 104537.77 35 0 -3213.482 0 -3213.482 3987.5015 Loop time of 1.4132 on 1 procs for 35 steps with 906 atoms 50.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -2684.01299332989 -3213.48201465225 -3213.48201465225 Force two-norm initial, final = 731.15357 1.2701970 Force max component initial, final = 204.79040 0.16185845 Final line search alpha, max atom move = 4.4003844e-09 7.1223940e-10 Iterations, force evaluations = 35 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.388 | 1.388 | 1.388 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014146 | 0.014146 | 0.014146 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01102 | | | 0.78 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4418.00 ave 4418 max 4418 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: 49412.0 ave 49412 max 49412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49412 Ave neighs/atom = 54.538631 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 28 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -3213.482 0 -3213.482 3987.5015 10674.216 48 0 -3214.7699 0 -3214.7699 9.6244037 10702.28 Loop time of 0.220407 on 1 procs for 13 steps with 906 atoms 53.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3213.48201465224 -3214.76937972668 -3214.7698701687 Force two-norm initial, final = 87.387724 1.6186010 Force max component initial, final = 76.496281 0.62230843 Final line search alpha, max atom move = 0.00016326768 0.00010160285 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21078 | 0.21078 | 0.21078 | 0.0 | 95.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020301 | 0.0020301 | 0.0020301 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007599 | | | 3.45 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4549.00 ave 4549 max 4549 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: 50280.0 ave 50280 max 50280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50280 Ave neighs/atom = 55.496689 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 = 14 28 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) = 4.680 | 4.680 | 4.680 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3214.7699 0 -3214.7699 9.6244037 Loop time of 6.435e-06 on 1 procs for 0 steps with 906 atoms 108.8% 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 | | 6.435e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4424.00 ave 4424 max 4424 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: 50456.0 ave 50456 max 50456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50456 Ave neighs/atom = 55.690949 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 = 14 28 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) = 4.680 | 4.680 | 4.680 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 -3214.7699 -3214.7699 38.124559 76.744887 3.6578173 9.6244037 9.6244037 48.200782 74.945121 -94.272692 2.3255133 160.27994 Loop time of 6.355e-06 on 1 procs for 0 steps with 906 atoms 188.8% 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 | | 6.355e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4424.00 ave 4424 max 4424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25228.0 ave 25228 max 25228 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50456.0 ave 50456 max 50456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50456 Ave neighs/atom = 55.690949 Neighbor list builds = 0 Dangerous builds = 0 906 -3214.7698701687 eV 2.32551333421859 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01