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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -66.937504 0.0000000) to (38.644366 66.937504 6.0599201) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7016278 5.1206343 6.0599201 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -66.937504 0.0000000) to (38.644366 66.937504 6.0599201) create_atoms CPU = 0.003 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7016278 5.1206343 6.0599201 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -66.937504 0.0000000) to (38.644366 66.937504 6.0599201) create_atoms CPU = 0.002 seconds 1465 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2906 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.992 | 6.992 | 6.992 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11848.418 0 -11848.418 12196.701 68 0 -11927.883 0 -11927.883 -6042.5227 Loop time of 3.05526 on 1 procs for 68 steps with 2906 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 = -11848.4176120548 -11927.8727311194 -11927.8834344471 Force two-norm initial, final = 119.19982 0.42061687 Force max component initial, final = 21.962694 0.15167293 Final line search alpha, max atom move = 0.44287364 0.067171944 Iterations, force evaluations = 68 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9997 | 2.9997 | 2.9997 | 0.0 | 98.18 Neigh | 0.026497 | 0.026497 | 0.026497 | 0.0 | 0.87 Comm | 0.014142 | 0.014142 | 0.014142 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01495 | | | 0.49 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12059.0 ave 12059 max 12059 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: 507084.0 ave 507084 max 507084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507084 Ave neighs/atom = 174.49553 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.993 | 6.993 | 6.993 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -11927.883 0 -11927.883 -6042.5227 31351.087 71 0 -11927.977 0 -11927.977 -3301.801 31277.662 Loop time of 0.143549 on 1 procs for 3 steps with 2906 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 = -11927.8834344471 -11927.9761214773 -11927.9767396379 Force two-norm initial, final = 98.031255 0.48682742 Force max component initial, final = 89.239780 0.14407496 Final line search alpha, max atom move = 0.00014179622 2.0429285e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14057 | 0.14057 | 0.14057 | 0.0 | 97.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050799 | 0.00050799 | 0.00050799 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00247 | | | 1.72 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12128.0 ave 12128 max 12128 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: 508092.0 ave 508092 max 508092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508092 Ave neighs/atom = 174.84240 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.131 | 7.131 | 7.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11927.977 0 -11927.977 -3301.801 Loop time of 1.764e-06 on 1 procs for 0 steps with 2906 atoms 113.4% 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 | | 1.764e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12151.0 ave 12151 max 12151 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: 508218.0 ave 508218 max 508218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508218 Ave neighs/atom = 174.88575 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.131 | 7.131 | 7.131 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 -11927.977 -11927.977 38.572169 133.87501 6.0570439 -3301.801 -3301.801 -0.71260281 -9901.4839 -3.2063968 2.2412229 1082.4315 Loop time of 2.211e-06 on 1 procs for 0 steps with 2906 atoms 226.1% 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 | | 2.211e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12151.0 ave 12151 max 12151 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 254109.0 ave 254109 max 254109 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 508218.0 ave 508218 max 508218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508218 Ave neighs/atom = 174.88575 Neighbor list builds = 0 Dangerous builds = 0 2906 -11927.9767396379 eV 2.24122292618891 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03