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 -38.928714 0.0000000) to (12.976238 38.928714 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8165406 3.8165406 3.1472000 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -38.928714 0.0000000) to (12.976238 38.928714 3.1472000) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8165406 3.8165406 3.1472000 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -38.928714 0.0000000) to (12.976238 38.928714 3.1472000) create_atoms CPU = 0.001 seconds 103 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 = 5 25 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 1 atoms, new total = 204 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 = 5 25 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) = 4.389 | 4.389 | 4.389 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1163.3461 0 -1163.3461 124932.17 83 0 -1381.6957 0 -1381.6957 13439.017 Loop time of 0.382837 on 1 procs for 83 steps with 204 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1163.34612805901 -1381.69444142369 -1381.69572594696 Force two-norm initial, final = 449.30092 0.16774220 Force max component initial, final = 154.46924 0.032700023 Final line search alpha, max atom move = 1.0000000 0.032700023 Iterations, force evaluations = 83 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36904 | 0.36904 | 0.36904 | 0.0 | 96.40 Neigh | 0.0020063 | 0.0020063 | 0.0020063 | 0.0 | 0.52 Comm | 0.0071338 | 0.0071338 | 0.0071338 | 0.0 | 1.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004658 | | | 1.22 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2121.00 ave 2121 max 2121 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: 11960.0 ave 11960 max 11960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11960 Ave neighs/atom = 58.627451 Neighbor list builds = 1 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 = 5 25 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.389 | 4.389 | 4.389 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -1381.6957 0 -1381.6957 13439.017 3179.6051 91 0 -1381.9113 0 -1381.9113 -205.52687 3193.7482 Loop time of 0.0255611 on 1 procs for 8 steps with 204 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1381.69572594696 -1381.91124145619 -1381.91132626695 Force two-norm initial, final = 65.206134 0.86018978 Force max component initial, final = 63.300611 0.44535574 Final line search alpha, max atom move = 0.0010942781 0.00048734303 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023722 | 0.023722 | 0.023722 | 0.0 | 92.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041755 | 0.00041755 | 0.00041755 | 0.0 | 1.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001421 | | | 5.56 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2121.00 ave 2121 max 2121 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: 11908.0 ave 11908 max 11908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11908 Ave neighs/atom = 58.372549 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 = 5 26 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) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1381.9113 0 -1381.9113 -205.52687 Loop time of 6.235e-06 on 1 procs for 0 steps with 204 atoms 192.5% 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 | | 6.235e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2111.00 ave 2111 max 2111 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: 11868.0 ave 11868 max 11868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11868 Ave neighs/atom = 58.176471 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 = 5 26 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) = 4.527 | 4.527 | 4.527 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 -1381.9113 -1381.9113 12.972049 78.4133 3.1398027 -205.52687 -205.52687 -223.34515 -170.48137 -222.7541 2.5967698 181.12771 Loop time of 6.666e-06 on 1 procs for 0 steps with 204 atoms 225.0% 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 | | 6.666e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2111.00 ave 2111 max 2111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5934.00 ave 5934 max 5934 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11868.0 ave 11868 max 11868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11868 Ave neighs/atom = 58.176471 Neighbor list builds = 0 Dangerous builds = 0 204 -1381.91132626695 eV 2.59676975558867 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