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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -55.222817 0.0000000) to (39.048428 55.222817 5.9548295) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.2648239 7.0633835 5.9548295 Created 687 atoms using lattice units in orthogonal box = (0.0000000 -55.222817 0.0000000) to (39.048428 55.222817 5.9548295) create_atoms CPU = 0.004 seconds 687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.2648239 7.0633835 5.9548295 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -55.222817 0.0000000) to (39.048428 55.222817 5.9548295) create_atoms CPU = 0.003 seconds 695 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 25 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1376 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_878712978062_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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.489 | 5.489 | 5.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4051.311 0 -4051.311 174421.29 399 0 -5138.9158 0 -5138.9158 -1385.2274 Loop time of 16.6488 on 1 procs for 399 steps with 1376 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 = -4051.3110482622 -5138.91174338502 -5138.91578686631 Force two-norm initial, final = 2230.3541 0.11537259 Force max component initial, final = 382.85873 0.0096208138 Final line search alpha, max atom move = 1.0000000 0.0096208138 Iterations, force evaluations = 399 782 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.323 | 16.323 | 16.323 | 0.0 | 98.04 Neigh | 0.18024 | 0.18024 | 0.18024 | 0.0 | 1.08 Comm | 0.078742 | 0.078742 | 0.078742 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06727 | | | 0.40 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8016.00 ave 8016 max 8016 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: 212040.0 ave 212040 max 212040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212040 Ave neighs/atom = 154.09884 Neighbor list builds = 11 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 399 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.489 | 5.489 | 5.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 399 0 -5138.9158 0 -5138.9158 -1385.2274 25681.562 412 0 -5139.3831 0 -5139.3831 2.445835 25668.31 Loop time of 0.246594 on 1 procs for 13 steps with 1376 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 = -5138.9157868663 -5139.38123233001 -5139.38312534656 Force two-norm initial, final = 72.562180 0.31315924 Force max component initial, final = 48.757066 0.064426170 Final line search alpha, max atom move = 0.00032475557 2.0922758e-05 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24104 | 0.24104 | 0.24104 | 0.0 | 97.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094172 | 0.00094172 | 0.00094172 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004611 | | | 1.87 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7968.00 ave 7968 max 7968 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: 211568.0 ave 211568 max 211568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211568 Ave neighs/atom = 153.75581 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.627 | 5.627 | 5.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5139.3831 0 -5139.3831 2.445835 Loop time of 2.116e-06 on 1 procs for 0 steps with 1376 atoms 141.8% 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 | | 2.116e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7984.00 ave 7984 max 7984 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: 205148.0 ave 205148 max 205148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205148 Ave neighs/atom = 149.09012 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.627 | 5.627 | 5.627 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 -5139.3831 -5139.3831 38.832834 109.63201 6.0292158 2.445835 2.445835 3.9991798 2.7287679 0.60955732 2.7962785 12978.326 Loop time of 2.621e-06 on 1 procs for 0 steps with 1376 atoms 267.1% 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 | | 2.621e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7984.00 ave 7984 max 7984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102574.0 ave 102574 max 102574 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205148.0 ave 205148 max 205148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205148 Ave neighs/atom = 149.09012 Neighbor list builds = 0 Dangerous builds = 0 1376 -5139.38312534656 eV 2.7962784609915 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17