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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -43.252122 0.0000000) to (15.291934 43.252122 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0973115 6.0072392 5.0973115 Created 288 atoms using lattice units in orthogonal box = (0.0000000 -43.252122 0.0000000) to (15.291934 43.252122 5.0973115) create_atoms CPU = 0.001 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0973115 6.0072392 5.0973115 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -43.252122 0.0000000) to (15.291934 43.252122 5.0973115) create_atoms CPU = 0.001 seconds 292 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 = 6 29 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 8 atoms, new total = 572 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 = 6 29 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) = 4.508 | 4.508 | 4.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2400.7841 0 -2400.7841 5989.4666 47 0 -2419.8473 0 -2419.8473 -6922.5953 Loop time of 2.00468 on 1 procs for 47 steps with 572 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2400.78411657691 -2419.84519163993 -2419.84731494551 Force two-norm initial, final = 29.010795 0.13324054 Force max component initial, final = 6.4699743 0.016566013 Final line search alpha, max atom move = 1.0000000 0.016566013 Iterations, force evaluations = 47 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9939 | 1.9939 | 1.9939 | 0.0 | 99.46 Neigh | 0.0036749 | 0.0036749 | 0.0036749 | 0.0 | 0.18 Comm | 0.0037827 | 0.0037827 | 0.0037827 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003338 | | | 0.17 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3483.00 ave 3483 max 3483 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: 44464.0 ave 44464 max 44464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44464 Ave neighs/atom = 77.734266 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 6 29 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.508 | 4.508 | 4.508 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -2419.8473 0 -2419.8473 -6922.5953 6742.8114 57 0 -2420.0375 0 -2420.0375 36.547433 6713.1882 Loop time of 0.27047 on 1 procs for 10 steps with 572 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 = -2419.84731494551 -2420.03748917071 -2420.03750787121 Force two-norm initial, final = 57.248490 0.47371220 Force max component initial, final = 51.202152 0.22540738 Final line search alpha, max atom move = 0.0020180575 0.00045488505 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26823 | 0.26823 | 0.26823 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000363 | 0.000363 | 0.000363 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001872 | | | 0.69 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3491.00 ave 3491 max 3491 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: 44472.0 ave 44472 max 44472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44472 Ave neighs/atom = 77.748252 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 = 5 29 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) = 4.645 | 4.645 | 4.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2420.0375 0 -2420.0375 36.547433 Loop time of 2.112e-06 on 1 procs for 0 steps with 572 atoms 142.0% 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 | | 2.112e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3476.00 ave 3476 max 3476 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: 44480.0 ave 44480 max 44480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44480 Ave neighs/atom = 77.762238 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 = 5 29 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) = 4.645 | 4.645 | 4.645 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 -2420.0375 -2420.0375 15.153769 86.670075 5.1113897 36.547433 36.547433 8.4728833 47.224878 53.944539 2.3369974 418.64755 Loop time of 2.018e-06 on 1 procs for 0 steps with 572 atoms 148.7% 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 | | 2.018e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22240.0 ave 22240 max 22240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44480.0 ave 44480 max 44480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44480 Ave neighs/atom = 77.762238 Neighbor list builds = 0 Dangerous builds = 0 572 -2420.03750787121 eV 2.33699742165963 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02