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 -53.779377 0.0000000) to (26.889688 53.779377 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0518708 4.0518708 3.1472000 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -53.779377 0.0000000) to (26.889688 53.779377 3.1472000) create_atoms CPU = 0.002 seconds 292 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0518708 4.0518708 3.1472000 Created 293 atoms using lattice units in orthogonal box = (0.0000000 -53.779377 0.0000000) to (26.889688 53.779377 3.1472000) create_atoms CPU = 0.001 seconds 293 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 = 9 35 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 = 585 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 = 9 35 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3785.8684 0 -3785.8684 66967.241 35 0 -3967.9342 0 -3967.9342 14884.497 Loop time of 0.427639 on 1 procs for 35 steps with 585 atoms 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3785.86838751334 -3967.93058020275 -3967.93422594904 Force two-norm initial, final = 353.64003 0.25839243 Force max component initial, final = 157.10539 0.10141091 Final line search alpha, max atom move = 0.92319847 0.093622395 Iterations, force evaluations = 35 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41502 | 0.41502 | 0.41502 | 0.0 | 97.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0068248 | 0.0068248 | 0.0068248 | 0.0 | 1.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005792 | | | 1.35 Nlocal: 585.000 ave 585 max 585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4205.00 ave 4205 max 4205 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: 34224.0 ave 34224 max 34224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34224 Ave neighs/atom = 58.502564 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 = 9 35 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -3967.9342 0 -3967.9342 14884.497 9102.399 43 0 -3968.5374 0 -3968.5374 -212.61328 9148.4997 Loop time of 0.0660371 on 1 procs for 8 steps with 585 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 = -3967.93422594905 -3968.53699195272 -3968.53736397075 Force two-norm initial, final = 189.49090 2.3640768 Force max component initial, final = 181.27783 1.6418855 Final line search alpha, max atom move = 0.00027834851 0.00045701637 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062073 | 0.062073 | 0.062073 | 0.0 | 94.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085868 | 0.00085868 | 0.00085868 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003105 | | | 4.70 Nlocal: 585.000 ave 585 max 585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4200.00 ave 4200 max 4200 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: 34258.0 ave 34258 max 34258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34258 Ave neighs/atom = 58.560684 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 = 9 35 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3968.5374 0 -3968.5374 -212.61328 Loop time of 6.355e-06 on 1 procs for 0 steps with 585 atoms 188.8% 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 | | 6.355e-06 | | |100.00 Nlocal: 585.000 ave 585 max 585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4200.00 ave 4200 max 4200 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: 34110.0 ave 34110 max 34110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34110 Ave neighs/atom = 58.307692 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 = 9 35 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) = 4.619 | 4.619 | 4.619 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 -3968.5374 -3968.5374 26.877109 108.3309 3.1420638 -212.61328 -212.61328 -287.40884 -112.39133 -238.03967 2.4362908 322.80612 Loop time of 7.698e-06 on 1 procs for 0 steps with 585 atoms 259.8% 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 | | 7.698e-06 | | |100.00 Nlocal: 585.000 ave 585 max 585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4200.00 ave 4200 max 4200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17055.0 ave 17055 max 17055 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34110.0 ave 34110 max 34110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34110 Ave neighs/atom = 58.307692 Neighbor list builds = 0 Dangerous builds = 0 585 -3968.53736397075 eV 2.43629077773633 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42