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 -56.649600 0.0000000) to (40.057316 56.649600 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4398824 5.2453333 4.4508129 Created 647 atoms using lattice units in orthogonal box = (0.0000000 -56.649600 0.0000000) to (40.057316 56.649600 4.4508129) create_atoms CPU = 0.002 seconds 647 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4398824 5.2453333 4.4508129 Created 649 atoms using lattice units in orthogonal box = (0.0000000 -56.649600 0.0000000) to (40.057316 56.649600 4.4508129) create_atoms CPU = 0.002 seconds 649 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 = 13 37 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 = 1296 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 = 13 37 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8530.1172 0 -8530.1172 63510.28 65 0 -8806.6949 0 -8806.6949 2600.086 Loop time of 0.659728 on 1 procs for 65 steps with 1296 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8530.11715252344 -8806.68824101453 -8806.69485932071 Force two-norm initial, final = 342.87936 0.35725681 Force max component initial, final = 87.884452 0.048243707 Final line search alpha, max atom move = 1.0000000 0.048243707 Iterations, force evaluations = 65 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64765 | 0.64765 | 0.64765 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0059498 | 0.0059498 | 0.0059498 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006129 | | | 0.93 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6268.00 ave 6268 max 6268 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: 75694.0 ave 75694 max 75694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75694 Ave neighs/atom = 58.405864 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 = 13 37 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -8806.6949 0 -8806.6949 2600.086 20199.844 67 0 -8806.7253 0 -8806.7253 -7.8958825 20217.645 Loop time of 0.0278353 on 1 procs for 2 steps with 1296 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 = -8806.69485932071 -8806.71795339784 -8806.72528485516 Force two-norm initial, final = 65.316766 0.43000942 Force max component initial, final = 49.678487 0.19945098 Final line search alpha, max atom move = 4.4148151e-05 8.8053921e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02658 | 0.02658 | 0.02658 | 0.0 | 95.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002327 | 0.0002327 | 0.0002327 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001022 | | | 3.67 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6280.00 ave 6280 max 6280 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: 75934.0 ave 75934 max 75934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75934 Ave neighs/atom = 58.591049 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 = 13 37 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) = 4.784 | 4.784 | 4.784 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8806.7253 0 -8806.7253 -7.8958825 Loop time of 1.534e-06 on 1 procs for 0 steps with 1296 atoms 195.6% 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 | | 1.534e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6280.00 ave 6280 max 6280 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: 75882.0 ave 75882 max 75882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75882 Ave neighs/atom = 58.550926 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 = 13 37 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) = 4.784 | 4.784 | 4.784 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 -8806.7253 -8806.7253 40.037164 113.36306 4.4544665 -7.8958825 -7.8958825 -6.8578329 -1.0110585 -15.818756 2.4521562 545.57175 Loop time of 1.823e-06 on 1 procs for 0 steps with 1296 atoms 219.4% 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 | | 1.823e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6280.00 ave 6280 max 6280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37941.0 ave 37941 max 37941 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75882.0 ave 75882 max 75882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75882 Ave neighs/atom = 58.550926 Neighbor list builds = 0 Dangerous builds = 0 1296 -8806.72528485516 eV 2.45215618114594 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