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 -59.381250 0.0000000) to (29.690625 59.381250 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3368329 4.3368329 3.1472000 Created 356 atoms using lattice units in orthogonal box = (0.0000000 -59.381250 0.0000000) to (29.690625 59.381250 3.1472000) create_atoms CPU = 0.002 seconds 356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3368329 4.3368329 3.1472000 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -59.381250 0.0000000) to (29.690625 59.381250 3.1472000) create_atoms CPU = 0.001 seconds 357 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 = 10 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 = 713 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 = 10 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) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4716.8859 0 -4716.8859 56341.003 26 0 -4839.3025 0 -4839.3025 11100.597 Loop time of 0.38158 on 1 procs for 26 steps with 713 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 = -4716.88587218006 -4839.29768264398 -4839.30251794033 Force two-norm initial, final = 235.83558 0.30957227 Force max component initial, final = 87.303179 0.061820053 Final line search alpha, max atom move = 1.0000000 0.061820053 Iterations, force evaluations = 26 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37068 | 0.37068 | 0.37068 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058071 | 0.0058071 | 0.0058071 | 0.0 | 1.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00509 | | | 1.33 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4887.00 ave 4887 max 4887 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: 41670.0 ave 41670 max 41670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41670 Ave neighs/atom = 58.443198 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 = 10 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -4839.3025 0 -4839.3025 11100.597 11097.445 33 0 -4839.7265 0 -4839.7265 42.184486 11138.939 Loop time of 0.0807536 on 1 procs for 7 steps with 713 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 = -4839.30251794033 -4839.72642278402 -4839.72648832798 Force two-norm initial, final = 169.80150 1.0464232 Force max component initial, final = 162.70706 0.78564470 Final line search alpha, max atom move = 0.00046688936 0.00036680916 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076117 | 0.076117 | 0.076117 | 0.0 | 94.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00099177 | 0.00099177 | 0.00099177 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003645 | | | 4.51 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4867.00 ave 4867 max 4867 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: 41556.0 ave 41556 max 41556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41556 Ave neighs/atom = 58.283310 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 = 10 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) = 4.658 | 4.658 | 4.658 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4839.7265 0 -4839.7265 42.184486 Loop time of 6.435e-06 on 1 procs for 0 steps with 713 atoms 139.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4867.00 ave 4867 max 4867 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: 41488.0 ave 41488 max 41488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41488 Ave neighs/atom = 58.187938 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 = 10 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) = 4.658 | 4.658 | 4.658 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 -4839.7265 -4839.7265 29.659529 119.43858 3.1443794 42.184486 42.184486 -10.765866 24.416887 112.90244 2.4144863 356.28521 Loop time of 8.119e-06 on 1 procs for 0 steps with 713 atoms 160.1% 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 | | 8.119e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4867.00 ave 4867 max 4867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20744.0 ave 20744 max 20744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41488.0 ave 41488 max 41488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41488 Ave neighs/atom = 58.187938 Neighbor list builds = 0 Dangerous builds = 0 713 -4839.72648832798 eV 2.41448627169749 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