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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -57.524922 0.0000000) to (28.760677 57.524922 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8671916 4.8671916 3.5673230 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -57.524922 0.0000000) to (28.760677 57.524922 3.5673230) create_atoms CPU = 0.003 seconds 521 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8671916 4.8671916 3.5673230 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -57.524922 0.0000000) to (28.760677 57.524922 3.5673230) create_atoms CPU = 0.002 seconds 521 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 17 atoms, new total = 1025 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4296.5528 0 -4296.5528 -7294.9109 100 0 -4319.5198 0 -4319.5198 8928.7987 Loop time of 13.9931 on 1 procs for 100 steps with 1025 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4296.55280484705 -4319.51559232772 -4319.51979860041 Force two-norm initial, final = 19.160915 0.30168961 Force max component initial, final = 5.7035522 0.068257440 Final line search alpha, max atom move = 0.99304366 0.067782618 Iterations, force evaluations = 100 196 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.931 | 13.931 | 13.931 | 0.0 | 99.56 Neigh | 0.010514 | 0.010514 | 0.010514 | 0.0 | 0.08 Comm | 0.025702 | 0.025702 | 0.025702 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02573 | | | 0.18 Nlocal: 1025.00 ave 1025 max 1025 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5302.00 ave 5302 max 5302 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: 57830.0 ave 57830 max 57830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57830 Ave neighs/atom = 56.419512 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -4319.5198 0 -4319.5198 8928.7987 11803.956 113 0 -4320.9877 0 -4320.9877 1535.7958 11888.684 Loop time of 1.18297 on 1 procs for 13 steps with 1025 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4319.51979860041 -4320.98502617287 -4320.98769432729 Force two-norm initial, final = 252.47874 10.257898 Force max component initial, final = 206.63670 9.5472161 Final line search alpha, max atom move = 0.00018071572 0.0017253320 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.172 | 1.172 | 1.172 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019639 | 0.0019639 | 0.0019639 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008954 | | | 0.76 Nlocal: 1025.00 ave 1025 max 1025 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5369.00 ave 5369 max 5369 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: 58360.0 ave 58360 max 58360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58360 Ave neighs/atom = 56.936585 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.734 | 4.734 | 4.734 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4320.9877 0 -4320.9877 1535.7958 Loop time of 6.254e-06 on 1 procs for 0 steps with 1025 atoms 0.0% 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 | | 6.254e-06 | | |100.00 Nlocal: 1025.00 ave 1025 max 1025 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378.00 ave 5378 max 5378 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: 58546.0 ave 58546 max 58546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58546 Ave neighs/atom = 57.118049 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.734 | 4.734 | 4.734 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 -4320.9877 -4320.9877 29.129731 115.04984 3.5474092 1535.7958 1535.7958 -335.44649 6222.2805 -1279.4466 2.2578756 400.23126 Loop time of 8.489e-06 on 1 procs for 0 steps with 1025 atoms 282.7% 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 | | 8.489e-06 | | |100.00 Nlocal: 1025.00 ave 1025 max 1025 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378.00 ave 5378 max 5378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29273.0 ave 29273 max 29273 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58546.0 ave 58546 max 58546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58546 Ave neighs/atom = 57.118049 Neighbor list builds = 0 Dangerous builds = 0 1025 -4320.98769432729 eV 2.25787560608596 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15