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 -32.095268 0.0000000) to (27.795318 32.095268 5.4511103) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9889032 4.9377336 5.4511103 Created 310 atoms using lattice units in orthogonal box = (0.0000000 -32.095268 0.0000000) to (27.795318 32.095268 5.4511103) create_atoms CPU = 0.001 seconds 310 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9889032 4.9377336 5.4511103 Created 315 atoms using lattice units in orthogonal box = (0.0000000 -32.095268 0.0000000) to (27.795318 32.095268 5.4511103) create_atoms CPU = 0.001 seconds 315 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 21 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 = 625 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 21 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3850.3869 0 -3850.3869 107911.7 89 0 -4224.3279 0 -4224.3279 14532.161 Loop time of 0.46723 on 1 procs for 89 steps with 625 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 = -3850.38690481546 -4224.32433746619 -4224.32788294154 Force two-norm initial, final = 533.49544 0.23190771 Force max component initial, final = 227.74000 0.052287339 Final line search alpha, max atom move = 1.0000000 0.052287339 Iterations, force evaluations = 89 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45163 | 0.45163 | 0.45163 | 0.0 | 96.66 Neigh | 0.0065371 | 0.0065371 | 0.0065371 | 0.0 | 1.40 Comm | 0.0043912 | 0.0043912 | 0.0043912 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004669 | | | 1.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2985.00 ave 2985 max 2985 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: 36880.0 ave 36880 max 36880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36880 Ave neighs/atom = 59.008000 Neighbor list builds = 2 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 21 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 : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -4224.3279 0 -4224.3279 14532.161 9725.851 95 0 -4224.7128 0 -4224.7128 -7.0679473 9771.7744 Loop time of 0.0268158 on 1 procs for 6 steps with 625 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 = -4224.32788294154 -4224.71184204085 -4224.71275471005 Force two-norm initial, final = 173.43205 0.77583177 Force max component initial, final = 146.80310 0.20840820 Final line search alpha, max atom move = 0.00011334291 2.3621592e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.025436 | 0.025436 | 0.025436 | 0.0 | 94.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001159 | | | 4.32 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2981.00 ave 2981 max 2981 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: 36872.0 ave 36872 max 36872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36872 Ave neighs/atom = 58.995200 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 21 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4224.7128 0 -4224.7128 -7.0679473 Loop time of 1.764e-06 on 1 procs for 0 steps with 625 atoms 170.1% 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 | | 1.764e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2981.00 ave 2981 max 2981 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: 36764.0 ave 36764 max 36764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36764 Ave neighs/atom = 58.822400 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 21 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) = 4.627 | 4.627 | 4.627 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 -4224.7128 -4224.7128 27.750387 64.484238 5.4607313 -7.0679473 -7.0679473 -17.412521 -34.326877 30.535556 2.4193937 657.50465 Loop time of 1.795e-06 on 1 procs for 0 steps with 625 atoms 222.8% 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 | | 1.795e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2981.00 ave 2981 max 2981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18382.0 ave 18382 max 18382 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36764.0 ave 36764 max 36764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36764 Ave neighs/atom = 58.822400 Neighbor list builds = 0 Dangerous builds = 0 625 -4224.71275471005 eV 2.41939371878631 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