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 -41.752326 0.0000000) to (14.761676 41.752326 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3678823 4.7445825 4.4508129 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -41.752326 0.0000000) to (14.761676 41.752326 4.4508129) create_atoms CPU = 0.001 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3678823 4.7445825 4.4508129 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -41.752326 0.0000000) to (14.761676 41.752326 4.4508129) create_atoms CPU = 0.000 seconds 178 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 27 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 = 354 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 27 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) = 4.432 | 4.432 | 4.432 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2199.3225 0 -2199.3225 136790.66 40 0 -2395.9316 0 -2395.9316 16644.632 Loop time of 0.121835 on 1 procs for 40 steps with 354 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 = -2199.3225442754 -2395.92941695558 -2395.93156825647 Force two-norm initial, final = 319.03991 0.20769993 Force max component initial, final = 140.48054 0.035477461 Final line search alpha, max atom move = 1.0000000 0.035477461 Iterations, force evaluations = 40 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11713 | 0.11713 | 0.11713 | 0.0 | 96.14 Neigh | 0.0019201 | 0.0019201 | 0.0019201 | 0.0 | 1.58 Comm | 0.0014261 | 0.0014261 | 0.0014261 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001361 | | | 1.12 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2315.00 ave 2315 max 2315 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: 20912.0 ave 20912 max 20912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20912 Ave neighs/atom = 59.073446 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 27 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.432 | 4.432 | 4.432 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -2395.9316 0 -2395.9316 16644.632 5486.3775 50 0 -2396.5176 0 -2396.5176 -78.635159 5516.2409 Loop time of 0.0225209 on 1 procs for 10 steps with 354 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 = -2395.93156825647 -2396.51582465513 -2396.51759289461 Force two-norm initial, final = 137.98745 1.0084703 Force max component initial, final = 135.67035 0.36230418 Final line search alpha, max atom move = 0.00020792265 7.5331245e-05 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021089 | 0.021089 | 0.021089 | 0.0 | 93.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023891 | 0.00023891 | 0.00023891 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001193 | | | 5.30 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2315.00 ave 2315 max 2315 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: 20788.0 ave 20788 max 20788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20788 Ave neighs/atom = 58.723164 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 27 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) = 4.570 | 4.570 | 4.570 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2396.5176 0 -2396.5176 -78.635159 Loop time of 2.108e-06 on 1 procs for 0 steps with 354 atoms 142.3% 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 | | 2.108e-06 | | |100.00 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2315.00 ave 2315 max 2315 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: 20752.0 ave 20752 max 20752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20752 Ave neighs/atom = 58.621469 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 27 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) = 4.570 | 4.570 | 4.570 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 -2396.5176 -2396.5176 14.730312 84.299393 4.4422893 -78.635159 -78.635159 -86.816978 -106.23173 -42.856769 2.4324036 258.57665 Loop time of 1.958e-06 on 1 procs for 0 steps with 354 atoms 204.3% 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 | | 1.958e-06 | | |100.00 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2315.00 ave 2315 max 2315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10376.0 ave 10376 max 10376 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20752.0 ave 20752 max 20752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20752 Ave neighs/atom = 58.621469 Neighbor list builds = 0 Dangerous builds = 0 354 -2396.51759289461 eV 2.43240363647901 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