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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -48.392004 0.0000000) to (13.170635 48.392004 8.6222048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6445580 5.3768894 5.7481365 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -48.392004 0.0000000) to (13.170635 48.392004 8.6222048) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6445580 5.3768894 5.7481365 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -48.392004 0.0000000) to (13.170635 48.392004 8.6222048) create_atoms CPU = 0.001 seconds 507 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 3 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1000 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4405.8897 0 -4405.8897 4435.9851 75 0 -4435.836 0 -4435.836 -2399.9145 Loop time of 1.34081 on 1 procs for 75 steps with 1000 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4405.88969768944 -4435.83173975323 -4435.83600971523 Force two-norm initial, final = 37.524319 0.22966820 Force max component initial, final = 9.1732498 0.036586848 Final line search alpha, max atom move = 1.0000000 0.036586848 Iterations, force evaluations = 75 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.314 | 1.314 | 1.314 | 0.0 | 98.00 Neigh | 0.011865 | 0.011865 | 0.011865 | 0.0 | 0.88 Comm | 0.0074247 | 0.0074247 | 0.0074247 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007533 | | | 0.56 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5837.00 ave 5837 max 5837 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: 173970.0 ave 173970 max 173970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173970 Ave neighs/atom = 173.97000 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.054 | 5.054 | 5.054 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4435.836 0 -4435.836 -2399.9145 10990.784 77 0 -4435.8529 0 -4435.8529 -0.7884391 10975.995 Loop time of 0.0474415 on 1 procs for 2 steps with 1000 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 = -4435.83600971523 -4435.85095640314 -4435.85291286728 Force two-norm initial, final = 31.297099 0.67752065 Force max component initial, final = 26.976100 0.45380022 Final line search alpha, max atom move = 0.00017672075 8.0195916e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.046048 | 0.046048 | 0.046048 | 0.0 | 97.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024571 | 0.00024571 | 0.00024571 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001148 | | | 2.42 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6002.00 ave 6002 max 6002 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: 174432.0 ave 174432 max 174432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174432 Ave neighs/atom = 174.43200 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.192 | 5.192 | 5.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4435.8529 0 -4435.8529 -0.7884391 Loop time of 2.178e-06 on 1 procs for 0 steps with 1000 atoms 183.7% 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 | | 2.178e-06 | | |100.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6002.00 ave 6002 max 6002 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: 174440.0 ave 174440 max 174440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174440 Ave neighs/atom = 174.44000 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.192 | 5.192 | 5.192 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 -4435.8529 -4435.8529 13.169896 96.773585 8.6120135 -0.7884391 -0.7884391 -66.237938 65.085064 -1.2124432 2.2761926 365.33751 Loop time of 2.696e-06 on 1 procs for 0 steps with 1000 atoms 259.6% 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 | | 2.696e-06 | | |100.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6002.00 ave 6002 max 6002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87220.0 ave 87220 max 87220 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174440.0 ave 174440 max 174440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174440 Ave neighs/atom = 174.44000 Neighbor list builds = 0 Dangerous builds = 0 1000 -4435.85291286728 eV 2.27619260926872 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01