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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -56.463886 0.0000000) to (28.231943 56.463886 3.6147299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0910061 5.0910061 3.6147299 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.463886 0.0000000) to (28.231943 56.463886 3.6147299) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0910061 5.0910061 3.6147299 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.463886 0.0000000) to (28.231943 56.463886 3.6147299) create_atoms CPU = 0.001 seconds 490 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 970 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3333.5173 0 -3333.5173 19929.978 21 0 -3423.2213 0 -3423.2213 1243.2173 Loop time of 0.584564 on 1 procs for 21 steps with 970 atoms 35.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3333.51725973837 -3423.2184731324 -3423.22131448957 Force two-norm initial, final = 202.72351 0.16310294 Force max component initial, final = 64.476374 0.044315333 Final line search alpha, max atom move = 1.0000000 0.044315333 Iterations, force evaluations = 21 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57664 | 0.57664 | 0.57664 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039951 | 0.0039951 | 0.0039951 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003928 | | | 0.67 Nlocal: 970.000 ave 970 max 970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5674.00 ave 5674 max 5674 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: 52252.0 ave 52252 max 52252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52252 Ave neighs/atom = 53.868041 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -3423.2213 0 -3423.2213 1243.2173 11524.375 25 0 -3423.262 0 -3423.262 11.645894 11534.875 Loop time of 0.108506 on 1 procs for 4 steps with 970 atoms 37.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3423.22131448956 -3423.25868883704 -3423.2619795515 Force two-norm initial, final = 25.210796 0.60372156 Force max component initial, final = 23.861482 0.53423079 Final line search alpha, max atom move = 0.00013080914 6.9882270e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10469 | 0.10469 | 0.10469 | 0.0 | 96.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062585 | 0.00062585 | 0.00062585 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003186 | | | 2.94 Nlocal: 970.000 ave 970 max 970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5676.00 ave 5676 max 5676 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: 52436.0 ave 52436 max 52436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52436 Ave neighs/atom = 54.057732 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.718 | 4.718 | 4.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 3426.6545 0 3426.6545 11.645894 Loop time of 3.737e-06 on 1 procs for 0 steps with 970 atoms 107.0% 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 | | 3.737e-06 | | |100.00 Nlocal: 970.000 ave 970 max 970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5676.00 ave 5676 max 5676 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: 52440.0 ave 52440 max 52440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52440 Ave neighs/atom = 54.061856 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.718 | 4.718 | 4.718 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 3426.6545 -3423.262 28.18096 112.86065 3.6267243 11.645894 11.645894 74.069843 -26.232027 -12.900135 2.2570702 188.48465 Loop time of 3.537e-06 on 1 procs for 0 steps with 970 atoms 113.1% 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 | | 3.537e-06 | | |100.00 Nlocal: 970.000 ave 970 max 970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5676.00 ave 5676 max 5676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26220.0 ave 26220 max 26220 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52440.0 ave 52440 max 52440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52440 Ave neighs/atom = 54.061856 Neighbor list builds = 0 Dangerous builds = 0 970 3426.65454421641 eV 2.25707020664107 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01