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 = 2.5709721 2.5709721 2.5709721 Created orthogonal box = (0.0000000 -27.809316 0.0000000) to (9.2697719 27.809316 2.5709721) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5652969 3.5652969 2.5709721 Created 155 atoms using lattice units in orthogonal box = (0.0000000 -27.809316 0.0000000) to (9.2697719 27.809316 2.5709721) create_atoms CPU = 0.001 seconds 155 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5652969 3.5652969 2.5709721 Created 157 atoms using lattice units in orthogonal box = (0.0000000 -27.809316 0.0000000) to (9.2697719 27.809316 2.5709721) create_atoms CPU = 0.000 seconds 157 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 3 13 1 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 309 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_122703700223_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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 3 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.346 | 5.346 | 5.346 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 995.77195 0 995.77195 19353054 3 0 921.19358 0 921.19358 19163189 Loop time of 0.664188 on 1 procs for 3 steps with 309 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 995.771950846854 921.193582157239 921.193582157239 Force two-norm initial, final = 361.77204 62.396669 Force max component initial, final = 129.12300 15.743754 Final line search alpha, max atom move = 2.5046605e-12 3.9432759e-11 Iterations, force evaluations = 3 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65942 | 0.65942 | 0.65942 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033518 | 0.0033518 | 0.0033518 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001416 | | | 0.21 Nlocal: 309.000 ave 309 max 309 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9983.00 ave 9983 max 9983 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: 234472.0 ave 234472 max 234472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234472 Ave neighs/atom = 758.80906 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 3 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 3 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.346 | 5.346 | 5.346 Mbytes Step Temp E_pair E_mol TotEng Press Volume 3 0 921.19358 0 921.19358 19163189 1325.5213 4 0 921.19358 0 921.19358 19163189 1325.5213 Loop time of 0.664311 on 1 procs for 1 steps with 309 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 921.19358215724 921.19358215724 921.19358215724 Force two-norm initial, final = 27460.425 27460.425 Force max component initial, final = 15908.490 15908.490 Final line search alpha, max atom move = 1.4635622e-17 2.3283064e-13 Iterations, force evaluations = 1 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65189 | 0.65189 | 0.65189 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025343 | 0.0025343 | 0.0025343 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009891 | | | 1.49 Nlocal: 309.000 ave 309 max 309 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 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: 234588.0 ave 234588 max 234588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234588 Ave neighs/atom = 759.18447 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 3 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.484 | 5.484 | 5.484 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 921.19358 0 921.19358 19163189 Loop time of 1.996e-06 on 1 procs for 0 steps with 309 atoms 150.3% 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 | | 1.996e-06 | | |100.00 Nlocal: 309.000 ave 309 max 309 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 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: 234588.0 ave 234588 max 234588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234588 Ave neighs/atom = 759.18447 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 3 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.484 | 5.484 | 5.484 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 0 921.19358 921.19358 9.2697719 55.618631 2.5709721 19163189 19163189 19228819 19115192 19145556 1.4662401 106.98568 Loop time of 2.162e-06 on 1 procs for 0 steps with 309 atoms 231.3% 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 | | 2.162e-06 | | |100.00 Nlocal: 309.000 ave 309 max 309 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117294.0 ave 117294 max 117294 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 234588.0 ave 234588 max 234588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234588 Ave neighs/atom = 759.18447 Neighbor list builds = 0 Dangerous builds = 0 309 921.19358215724 eV 1.46624008616434 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02