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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -63.088311 0.0000000) to (36.424053 63.088311 5.4500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8927833 5.0219551 5.4500000 Created 804 atoms using lattice units in orthogonal box = (0.0000000 -63.088311 0.0000000) to (36.424053 63.088311 5.4500000) create_atoms CPU = 0.006 seconds 804 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8927833 5.0219551 5.4500000 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -63.088311 0.0000000) to (36.424053 63.088311 5.4500000) create_atoms CPU = 0.005 seconds 806 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 39 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1610 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_356501945107_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10157.644 0 -10157.644 126319.86 80 0 -10917.455 0 -10917.455 10162.437 Loop time of 17.8126 on 1 procs for 80 steps with 1610 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 = -10157.6437960852 -10917.4450319296 -10917.4550133834 Force two-norm initial, final = 714.52372 0.62824276 Force max component initial, final = 165.36938 0.15825163 Final line search alpha, max atom move = 0.31382125 0.049662723 Iterations, force evaluations = 80 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.759 | 17.759 | 17.759 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.026479 | 0.026479 | 0.026479 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02752 | | | 0.15 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6832.00 ave 6832 max 6832 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: 103912.0 ave 103912 max 103912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103912 Ave neighs/atom = 64.541615 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.111 | 5.111 | 5.111 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -10917.455 0 -10917.455 10162.437 25047.459 85 0 -10917.921 0 -10917.921 -7.3109893 25143.687 Loop time of 0.931116 on 1 procs for 5 steps with 1610 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 = -10917.4550133834 -10917.9176281606 -10917.9212735551 Force two-norm initial, final = 297.16326 1.2469018 Force max component initial, final = 249.89160 0.85748794 Final line search alpha, max atom move = 3.5168502e-05 3.0156567e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92541 | 0.92541 | 0.92541 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011367 | 0.0011367 | 0.0011367 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004567 | | | 0.49 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6434.00 ave 6434 max 6434 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: 103264.0 ave 103264 max 103264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103264 Ave neighs/atom = 64.139130 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.249 | 5.249 | 5.249 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10917.921 0 -10917.921 -7.3109893 Loop time of 6.405e-06 on 1 procs for 0 steps with 1610 atoms 203.0% 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 | | 6.405e-06 | | |100.00 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6434.00 ave 6434 max 6434 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: 103228.0 ave 103228 max 103228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103228 Ave neighs/atom = 64.116770 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.249 | 5.249 | 5.249 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 -10917.921 -10917.921 36.421435 126.63722 5.4514311 -7.3109893 -7.3109893 37.469615 -4.7483952 -54.654188 2.4953186 856.13831 Loop time of 6.936e-06 on 1 procs for 0 steps with 1610 atoms 230.7% 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 | | 6.936e-06 | | |100.00 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6434.00 ave 6434 max 6434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51614.0 ave 51614 max 51614 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103228.0 ave 103228 max 103228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103228 Ave neighs/atom = 64.116770 Neighbor list builds = 0 Dangerous builds = 0 1610 -10917.9212735551 eV 2.49531856909706 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19