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 = 3.6149390 3.6149390 3.6149390 Created orthogonal box = (0.0000000 -44.714326 0.0000000) to (21.078536 44.714326 5.1122958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1995693 6.1372605 5.1122958 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -44.714326 0.0000000) to (21.078536 44.714326 5.1122958) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1995693 6.1372605 5.1122958 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.714326 0.0000000) to (21.078536 44.714326 5.1122958) create_atoms CPU = 0.001 seconds 412 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 6 22 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 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 816 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_547744193826_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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.999 | 4.999 | 4.999 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2554.3941 0 -2554.3941 71795.1 39 0 -2880.6684 0 -2880.6684 9514.2079 Loop time of 0.524414 on 1 procs for 39 steps with 816 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 = -2554.39414083815 -2880.66572576361 -2880.66844414215 Force two-norm initial, final = 535.51859 0.16049924 Force max component initial, final = 111.93318 0.019544804 Final line search alpha, max atom move = 1.0000000 0.019544804 Iterations, force evaluations = 39 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50956 | 0.50956 | 0.50956 | 0.0 | 97.17 Neigh | 0.0091569 | 0.0091569 | 0.0091569 | 0.0 | 1.75 Comm | 0.0032406 | 0.0032406 | 0.0032406 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002453 | | | 0.47 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6562.00 ave 6562 max 6562 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: 164728.0 ave 164728 max 164728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164728 Ave neighs/atom = 201.87255 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.000 | 5.000 | 5.000 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -2880.6684 0 -2880.6684 9514.2079 9636.8056 47 0 -2881.0186 0 -2881.0186 -123.67338 9702.694 Loop time of 0.0824383 on 1 procs for 8 steps with 816 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 = -2880.66844414216 -2881.0183608057 -2881.01861379047 Force two-norm initial, final = 112.45614 1.6140800 Force max component initial, final = 100.38947 1.4534513 Final line search alpha, max atom move = 0.00044357674 0.00064471718 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.079903 | 0.079903 | 0.079903 | 0.0 | 96.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048206 | 0.00048206 | 0.00048206 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002053 | | | 2.49 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6546.00 ave 6546 max 6546 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: 163840.0 ave 163840 max 163840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163840 Ave neighs/atom = 200.78431 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 5.138 | 5.138 | 5.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2881.0186 0 -2881.0186 -123.67338 Loop time of 1.874e-06 on 1 procs for 0 steps with 816 atoms 160.1% 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 | | 1.874e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6546.00 ave 6546 max 6546 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: 163296.0 ave 163296 max 163296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163296 Ave neighs/atom = 200.11765 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 5.138 | 5.138 | 5.138 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 -2881.0186 -2881.0186 21.090797 90.069599 5.1076497 -123.67338 -123.67338 -102.76736 -28.466874 -239.78589 2.4487868 545.22283 Loop time of 1.974e-06 on 1 procs for 0 steps with 816 atoms 202.6% 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 | | 1.974e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6546.00 ave 6546 max 6546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81648.0 ave 81648 max 81648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163296.0 ave 163296 max 163296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163296 Ave neighs/atom = 200.11765 Neighbor list builds = 0 Dangerous builds = 0 816 -2881.01861379047 eV 2.44878683686641 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00