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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -49.189465 0.0000000) to (60.244545 49.189465 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7768742 6.0644546 6.6478321 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -49.189465 0.0000000) to (60.244545 49.189465 9.9717481) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7768742 6.0644546 6.6478321 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -49.189465 0.0000000) to (60.244545 49.189465 9.9717481) create_atoms CPU = 0.002 seconds 1757 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 = 20 33 4 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 5 atoms, new total = 3503 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 = 20 33 4 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) = 5.236 | 5.236 | 5.236 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11457.38 0 -11457.38 16912.619 21 0 -11762.295 0 -11762.295 2071.3424 Loop time of 3.27491 on 1 procs for 21 steps with 3503 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 = -11457.3797984342 -11762.2868964506 -11762.2951474693 Force two-norm initial, final = 370.27129 0.21466401 Force max component initial, final = 73.648611 0.036653257 Final line search alpha, max atom move = 1.0000000 0.036653257 Iterations, force evaluations = 21 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2658 | 3.2658 | 3.2658 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029557 | 0.0029557 | 0.0029557 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006158 | | | 0.19 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7144.00 ave 7144 max 7144 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: 189490.0 ave 189490 max 189490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189490 Ave neighs/atom = 54.093634 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 20 33 4 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 : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.236 | 5.236 | 5.236 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -11762.295 0 -11762.295 2071.3424 59100.496 27 0 -11762.901 0 -11762.901 -55.448238 59250.288 Loop time of 0.727078 on 1 procs for 6 steps with 3503 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 = -11762.2951474692 -11762.9002283532 -11762.9007101285 Force two-norm initial, final = 236.90256 3.8744739 Force max component initial, final = 236.02326 3.1639844 Final line search alpha, max atom move = 0.00018513607 0.00058576764 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72294 | 0.72294 | 0.72294 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047344 | 0.00047344 | 0.00047344 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003662 | | | 0.50 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7126.00 ave 7126 max 7126 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: 188596.0 ave 188596 max 188596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188596 Ave neighs/atom = 53.838424 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 = 20 33 4 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) = 5.374 | 5.374 | 5.374 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11762.901 0 -11762.901 -55.448238 Loop time of 2.06e-06 on 1 procs for 0 steps with 3503 atoms 194.2% 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 | | 2.06e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7126.00 ave 7126 max 7126 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: 188564.0 ave 188564 max 188564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188564 Ave neighs/atom = 53.829289 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 = 20 33 4 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) = 5.374 | 5.374 | 5.374 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 -11762.901 -11762.901 60.168216 98.874861 9.9594979 -55.448238 -55.448238 -29.630466 -51.262615 -85.451633 2.4698241 1931.3159 Loop time of 2.337e-06 on 1 procs for 0 steps with 3503 atoms 256.7% 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 | | 2.337e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7126.00 ave 7126 max 7126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94282.0 ave 94282 max 94282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188564.0 ave 188564 max 188564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188564 Ave neighs/atom = 53.829289 Neighbor list builds = 0 Dangerous builds = 0 3503 -11762.9007101285 eV 2.46982406477591 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04