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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -46.698077 0.0000000) to (16.510263 46.698077 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0037322 5.3065997 4.9780317 Created 352 atoms using lattice units in orthogonal box = (0.0000000 -46.698077 0.0000000) to (16.510263 46.698077 4.9780317) create_atoms CPU = 0.003 seconds 352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0037322 5.3065997 4.9780317 Created 360 atoms using lattice units in orthogonal box = (0.0000000 -46.698077 0.0000000) to (16.510263 46.698077 4.9780317) create_atoms CPU = 0.002 seconds 360 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 32 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 8 atoms, new total = 704 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_444394830472_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 32 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) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3124.9749 0 -3124.9749 4334.4774 12 0 -3128.6984 0 -3128.6984 3651.9376 Loop time of 0.67423 on 1 procs for 12 steps with 704 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3124.97486831427 -3128.69555276585 -3128.69838713542 Force two-norm initial, final = 12.986239 0.10726528 Force max component initial, final = 2.2673555 0.011190683 Final line search alpha, max atom move = 1.0000000 0.011190683 Iterations, force evaluations = 12 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66956 | 0.66956 | 0.66956 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022555 | 0.0022555 | 0.0022555 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002417 | | | 0.36 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3679.00 ave 3679 max 3679 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: 54944.0 ave 54944 max 54944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54944 Ave neighs/atom = 78.045455 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 32 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -3128.6984 0 -3128.6984 3651.9376 7676.1006 17 0 -3128.7932 0 -3128.7932 -112.59512 7691.9564 Loop time of 0.186279 on 1 procs for 5 steps with 704 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 = -3128.69838713542 -3128.79298440491 -3128.7931501149 Force two-norm initial, final = 46.936070 1.2741449 Force max component initial, final = 46.750053 1.0157593 Final line search alpha, max atom move = 0.00045015751 0.00045725168 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18349 | 0.18349 | 0.18349 | 0.0 | 98.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055794 | 0.00055794 | 0.00055794 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002233 | | | 1.20 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3707.00 ave 3707 max 3707 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: 54816.0 ave 54816 max 54816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54816 Ave neighs/atom = 77.863636 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 32 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) = 4.672 | 4.672 | 4.672 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3128.7932 0 -3128.7932 -112.59512 Loop time of 6.115e-06 on 1 procs for 0 steps with 704 atoms 163.5% 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 | | 6.115e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3735.00 ave 3735 max 3735 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: 54816.0 ave 54816 max 54816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54816 Ave neighs/atom = 77.863636 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 32 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) = 4.672 | 4.672 | 4.672 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 -3128.7932 -3128.7932 16.497001 93.782566 4.9717547 -112.59512 -112.59512 -152.27823 25.801089 -211.30822 2.360752 212.91441 Loop time of 6.836e-06 on 1 procs for 0 steps with 704 atoms 219.4% 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 | | 6.836e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3735.00 ave 3735 max 3735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27408.0 ave 27408 max 27408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54816.0 ave 54816 max 54816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54816 Ave neighs/atom = 77.863636 Neighbor list builds = 0 Dangerous builds = 0 704 -3128.7931501149 eV 2.36075199023586 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01