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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -41.118642 0.0000000) to (29.072392 41.118642 5.7571914) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1304221 6.4493444 5.7571914 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -41.118642 0.0000000) to (29.072392 41.118642 5.7571914) create_atoms CPU = 0.003 seconds 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1304221 6.4493444 5.7571914 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -41.118642 0.0000000) to (29.072392 41.118642 5.7571914) create_atoms CPU = 0.002 seconds 410 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 27 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 804 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_304347095149_000#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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2690.8455 0 -2690.8455 -1589.381 26 0 -2697.3773 0 -2697.3773 -8560.2117 Loop time of 2.78077 on 1 procs for 26 steps with 804 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 = -2690.84552871906 -2697.37506295508 -2697.37732378651 Force two-norm initial, final = 9.3424148 0.18770414 Force max component initial, final = 2.2729986 0.039608764 Final line search alpha, max atom move = 1.0000000 0.039608764 Iterations, force evaluations = 26 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7723 | 2.7723 | 2.7723 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035453 | 0.0035453 | 0.0035453 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004929 | | | 0.18 Nlocal: 804.000 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3090.00 ave 3090 max 3090 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: 42888.0 ave 42888 max 42888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42888 Ave neighs/atom = 53.343284 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -2697.3773 0 -2697.3773 -8560.2117 13764.492 33 0 -2697.6417 0 -2697.6417 -1389.5204 13667.188 Loop time of 0.631588 on 1 procs for 7 steps with 804 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 = -2697.37732378651 -2697.64167277195 -2697.64170648001 Force two-norm initial, final = 95.213914 0.26922629 Force max component initial, final = 83.549591 0.055376489 Final line search alpha, max atom move = 0.00099736042 5.5230318e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62722 | 0.62722 | 0.62722 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007334 | 0.0007334 | 0.0007334 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003637 | | | 0.58 Nlocal: 804.000 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3090.00 ave 3090 max 3090 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: 43136.0 ave 43136 max 43136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43136 Ave neighs/atom = 53.651741 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.666 | 4.666 | 4.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2697.6417 0 -2697.6417 -1389.5204 Loop time of 6.415e-06 on 1 procs for 0 steps with 804 atoms 171.5% 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 | | 6.415e-06 | | |100.00 Nlocal: 804.000 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3090.00 ave 3090 max 3090 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: 43136.0 ave 43136 max 43136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43136 Ave neighs/atom = 53.651741 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.666 | 4.666 | 4.666 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 -2697.6417 -2697.6417 29.031378 82.237283 5.7245685 -1389.5204 -1389.5204 -6.4825145 -4162.5813 0.50269594 2.5843157 709.31158 Loop time of 6.826e-06 on 1 procs for 0 steps with 804 atoms 249.0% 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 | | 6.826e-06 | | |100.00 Nlocal: 804.000 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3090.00 ave 3090 max 3090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21568.0 ave 21568 max 21568 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43136.0 ave 43136 max 43136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43136 Ave neighs/atom = 53.651741 Neighbor list builds = 0 Dangerous builds = 0 804 -2697.64170648001 eV 2.5843156880478 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04