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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -60.209481 0.0000000) to (34.761960 60.209481 5.4511103) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1288138 4.6061898 5.4511103 Created 732 atoms using lattice units in orthogonal box = (0.0000000 -60.209481 0.0000000) to (34.761960 60.209481 5.4511103) create_atoms CPU = 0.002 seconds 732 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1288138 4.6061898 5.4511103 Created 734 atoms using lattice units in orthogonal box = (0.0000000 -60.209481 0.0000000) to (34.761960 60.209481 5.4511103) create_atoms CPU = 0.001 seconds 734 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1466 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_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.683 | 4.683 | 4.683 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9673.9638 0 -9673.9638 60791.156 92 0 -9961.9595 0 -9961.9595 6074.2168 Loop time of 1.13092 on 1 procs for 92 steps with 1466 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 = -9673.96380950207 -9961.95047173728 -9961.95947260016 Force two-norm initial, final = 354.55834 0.43515512 Force max component initial, final = 83.704585 0.058653708 Final line search alpha, max atom move = 1.0000000 0.058653708 Iterations, force evaluations = 92 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1099 | 1.1099 | 1.1099 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.009026 | 0.009026 | 0.009026 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01204 | | | 1.06 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5494.00 ave 5494 max 5494 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: 85688.0 ave 85688 max 85688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85688 Ave neighs/atom = 58.450205 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.683 | 4.683 | 4.683 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -9961.9595 0 -9961.9595 6074.2168 22818.343 94 0 -9962.0678 0 -9962.0678 2.2369437 22865.473 Loop time of 0.0308032 on 1 procs for 2 steps with 1466 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 = -9961.95947260017 -9962.05937936127 -9962.06778064209 Force two-norm initial, final = 155.02564 1.4022369 Force max component initial, final = 113.69348 1.0803257 Final line search alpha, max atom move = 4.4965306e-05 4.8577177e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.029604 | 0.029604 | 0.029604 | 0.0 | 96.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020929 | 0.00020929 | 0.00020929 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009901 | | | 3.21 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5540.00 ave 5540 max 5540 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: 85972.0 ave 85972 max 85972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85972 Ave neighs/atom = 58.643929 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.821 | 4.821 | 4.821 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9962.0678 0 -9962.0678 2.2369437 Loop time of 1.669e-06 on 1 procs for 0 steps with 1466 atoms 179.7% 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 | | 1.669e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5536.00 ave 5536 max 5536 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: 85864.0 ave 85864 max 85864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85864 Ave neighs/atom = 58.570259 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.821 | 4.821 | 4.821 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 -9962.0678 -9962.0678 34.759885 120.57443 5.4556518 2.2369437 2.2369437 -18.772457 -50.277862 75.76115 2.4926923 630.32385 Loop time of 1.751e-06 on 1 procs for 0 steps with 1466 atoms 171.3% 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 | | 1.751e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5536.00 ave 5536 max 5536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42932.0 ave 42932 max 42932 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85864.0 ave 85864 max 85864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85864 Ave neighs/atom = 58.570259 Neighbor list builds = 0 Dangerous builds = 0 1466 -9962.06778064209 eV 2.4926923240478 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42