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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -35.911291 0.0000000) to (17.955645 35.911291 3.5213918) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1436105 4.1436105 3.5213918 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -35.911291 0.0000000) to (17.955645 35.911291 3.5213918) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1436105 4.1436105 3.5213918 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -35.911291 0.0000000) to (17.955645 35.911291 3.5213918) create_atoms CPU = 0.000 seconds 210 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 24 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_700541006254_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1747.9971 0 -1747.9971 61523.337 47 0 -1822.8199 0 -1822.8199 -3075.5169 Loop time of 1.2605 on 1 procs for 47 steps with 412 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1747.99714789678 -1822.81837574197 -1822.81986985134 Force two-norm initial, final = 272.74519 0.13277870 Force max component initial, final = 96.064644 0.030829286 Final line search alpha, max atom move = 1.0000000 0.030829286 Iterations, force evaluations = 47 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2529 | 1.2529 | 1.2529 | 0.0 | 99.40 Neigh | 0.0026746 | 0.0026746 | 0.0026746 | 0.0 | 0.21 Comm | 0.0025515 | 0.0025515 | 0.0025515 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00239 | | | 0.19 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3166.00 ave 3166 max 3166 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: 31924.0 ave 31924 max 31924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31924 Ave neighs/atom = 77.485437 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1822.8199 0 -1822.8199 -3075.5169 4541.26 50 0 -1822.8343 0 -1822.8343 108.22564 4533.3926 Loop time of 0.072378 on 1 procs for 3 steps with 412 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 = -1822.81986985133 -1822.83427655602 -1822.83434861111 Force two-norm initial, final = 16.547680 0.56106944 Force max component initial, final = 13.795026 0.34532556 Final line search alpha, max atom move = 0.0015430706 0.00053286171 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071676 | 0.071676 | 0.071676 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013088 | 0.00013088 | 0.00013088 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000571 | | | 0.79 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 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: 32096.0 ave 32096 max 32096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32096 Ave neighs/atom = 77.902913 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.583 | 4.583 | 4.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1822.8343 0 -1822.8343 108.22564 Loop time of 1.793e-06 on 1 procs for 0 steps with 412 atoms 223.1% 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 | | 1.793e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 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: 32120.0 ave 32120 max 32120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32120 Ave neighs/atom = 77.961165 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.583 | 4.583 | 4.583 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 -1822.8343 -1822.8343 17.950461 71.875612 3.5137121 108.22564 108.22564 118.93931 122.13392 83.603679 2.3255892 187.21955 Loop time of 1.845e-06 on 1 procs for 0 steps with 412 atoms 216.8% 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 | | 1.845e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16060.0 ave 16060 max 16060 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32120.0 ave 32120 max 32120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32120 Ave neighs/atom = 77.961165 Neighbor list builds = 0 Dangerous builds = 0 412 -1822.83434861111 eV 2.32558917277367 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01