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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7941954 5.5194308 5.9005197 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7941954 5.5194308 5.9005197 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) create_atoms CPU = 0.001 seconds 507 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 30 3 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1007 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_694335101831_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3463.5836 0 -3463.5836 29093.998 44 0 -3551.3386 0 -3551.3386 5351.8996 Loop time of 2.79357 on 1 procs for 44 steps with 1007 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3463.5836293316 -3551.33661696872 -3551.3386322151 Force two-norm initial, final = 153.17907 0.14362365 Force max component initial, final = 36.016286 0.054445847 Final line search alpha, max atom move = 1.0000000 0.054445847 Iterations, force evaluations = 44 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7842 | 2.7842 | 2.7842 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0045343 | 0.0045343 | 0.0045343 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004889 | | | 0.18 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4921.00 ave 4921 max 4921 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: 133104.0 ave 133104 max 133104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133104 Ave neighs/atom = 132.17875 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3551.3386 0 -3551.3386 5351.8996 11888.259 49 0 -3551.5028 0 -3551.5028 -297.55424 11935.591 Loop time of 0.241689 on 1 procs for 5 steps with 1007 atoms 95.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3551.3386322151 -3551.50081371136 -3551.50278506165 Force two-norm initial, final = 80.046198 4.0563320 Force max component initial, final = 69.484912 2.8123091 Final line search alpha, max atom move = 0.00016227964 0.00045638052 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23983 | 0.23983 | 0.23983 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032303 | 0.00032303 | 0.00032303 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001533 | | | 0.63 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4991.00 ave 4991 max 4991 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: 131162.0 ave 131162 max 131162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131162 Ave neighs/atom = 130.25025 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3551.5028 0 -3551.5028 -297.55424 Loop time of 1.973e-06 on 1 procs for 0 steps with 1007 atoms 202.7% 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 | | 1.973e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4947.00 ave 4947 max 4947 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: 130604.0 ave 130604 max 130604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130604 Ave neighs/atom = 129.69613 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.125 | 5.125 | 5.125 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 -3551.5028 -3551.5028 13.53244 99.802786 8.8374133 -297.55424 -297.55424 -359.55444 -156.16752 -376.94077 2.2926268 425.84623 Loop time of 1.855e-06 on 1 procs for 0 steps with 1007 atoms 215.6% 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 | | 1.855e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4947.00 ave 4947 max 4947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65302.0 ave 65302 max 65302 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 130604.0 ave 130604 max 130604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130604 Ave neighs/atom = 129.69613 Neighbor list builds = 0 Dangerous builds = 0 1007 -3551.50278506165 eV 2.29262680447053 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03