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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -28.837365 0.0000000) to (20.391096 28.837365 4.0380388) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5984288 4.5235083 4.0380388 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -28.837365 0.0000000) to (20.391096 28.837365 4.0380388) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5984288 4.5235083 4.0380388 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -28.837365 0.0000000) to (20.391096 28.837365 4.0380388) create_atoms CPU = 0.000 seconds 206 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 = 6 16 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 2 atoms, new total = 408 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 16 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) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1409.9858 0 -1409.9858 157787.94 56 0 -1668.9771 0 -1668.9771 8686.1366 Loop time of 0.335921 on 1 procs for 56 steps with 408 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 = -1409.9858289392 -1668.97593639648 -1668.97709646055 Force two-norm initial, final = 797.22878 0.10145054 Force max component initial, final = 280.92672 0.019222100 Final line search alpha, max atom move = 1.0000000 0.019222100 Iterations, force evaluations = 56 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32706 | 0.32706 | 0.32706 | 0.0 | 97.36 Neigh | 0.0039944 | 0.0039944 | 0.0039944 | 0.0 | 1.19 Comm | 0.0028514 | 0.0028514 | 0.0028514 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002011 | | | 0.60 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3626.00 ave 3626 max 3626 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: 67460.0 ave 67460 max 67460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67460 Ave neighs/atom = 165.34314 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 = 6 16 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -1668.9771 0 -1668.9771 8686.1366 4748.9395 64 0 -1669.1715 0 -1669.1715 -245.45548 4774.3198 Loop time of 0.0350358 on 1 procs for 8 steps with 408 atoms 93.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1668.97709646055 -1669.17106829954 -1669.17148868461 Force two-norm initial, final = 59.635231 1.3499716 Force max component initial, final = 56.712252 0.97768249 Final line search alpha, max atom move = 0.00067031691 0.00065535711 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033588 | 0.033588 | 0.033588 | 0.0 | 95.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026583 | 0.00026583 | 0.00026583 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001182 | | | 3.37 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3626.00 ave 3626 max 3626 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: 67440.0 ave 67440 max 67440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67440 Ave neighs/atom = 165.29412 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 = 6 16 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1669.1715 0 -1669.1715 -245.45548 Loop time of 1.564e-06 on 1 procs for 0 steps with 408 atoms 127.9% 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 | | 1.564e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3626.00 ave 3626 max 3626 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: 67312.0 ave 67312 max 67312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67312 Ave neighs/atom = 164.98039 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 = 6 16 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) = 4.597 | 4.597 | 4.597 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 -1669.1715 -1669.1715 20.381823 58.086499 4.0326754 -245.45548 -245.45548 -327.94359 -218.96878 -189.45407 2.2356998 388.89332 Loop time of 1.45e-06 on 1 procs for 0 steps with 408 atoms 137.9% 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 | | 1.45e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3626.00 ave 3626 max 3626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33656.0 ave 33656 max 33656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67312.0 ave 67312 max 67312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67312 Ave neighs/atom = 164.98039 Neighbor list builds = 0 Dangerous builds = 0 408 -1669.17148868461 eV 2.23569984229879 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00