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 -51.135947 0.0000000) to (18.079287 51.135947 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9307147 5.4235095 4.4508129 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -51.135947 0.0000000) to (18.079287 51.135947 4.4508129) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9307147 5.4235095 4.4508129 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -51.135947 0.0000000) to (18.079287 51.135947 4.4508129) create_atoms CPU = 0.001 seconds 266 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 = 6 33 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 2 atoms, new total = 528 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 = 6 33 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) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2886.4633 0 -2886.4633 108557.21 116 0 -3580.6041 0 -3580.6041 5332.91 Loop time of 0.646667 on 1 procs for 116 steps with 528 atoms 86.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2886.46326822851 -3580.60091699138 -3580.60409692972 Force two-norm initial, final = 875.82838 0.24749466 Force max component initial, final = 264.56445 0.042012298 Final line search alpha, max atom move = 1.0000000 0.042012298 Iterations, force evaluations = 116 220 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63057 | 0.63057 | 0.63057 | 0.0 | 97.51 Neigh | 0.0029908 | 0.0029908 | 0.0029908 | 0.0 | 0.46 Comm | 0.0069914 | 0.0069914 | 0.0069914 | 0.0 | 1.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006111 | | | 0.94 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3468.00 ave 3468 max 3468 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: 31136.0 ave 31136 max 31136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31136 Ave neighs/atom = 58.969697 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 = 6 33 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 : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -3580.6041 0 -3580.6041 5332.91 8229.5662 120 0 -3580.7292 0 -3580.7292 -624.71614 8246.0363 Loop time of 0.0157362 on 1 procs for 4 steps with 528 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 = -3580.60409692972 -3580.72622974055 -3580.72917360725 Force two-norm initial, final = 70.231442 5.9161812 Force max component initial, final = 64.217459 4.4897174 Final line search alpha, max atom move = 0.00011516245 0.00051704687 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.01475 | 0.01475 | 0.01475 | 0.0 | 93.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019727 | 0.00019727 | 0.00019727 | 0.0 | 1.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007885 | | | 5.01 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3488.00 ave 3488 max 3488 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: 30792.0 ave 30792 max 30792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30792 Ave neighs/atom = 58.318182 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 = 6 33 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) = 4.616 | 4.616 | 4.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3580.7292 0 -3580.7292 -624.71614 Loop time of 1.788e-06 on 1 procs for 0 steps with 528 atoms 111.9% 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 | | 1.788e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3476.00 ave 3476 max 3476 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: 30768.0 ave 30768 max 30768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30768 Ave neighs/atom = 58.272727 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 = 6 33 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) = 4.616 | 4.616 | 4.616 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 -3580.7292 -3580.7292 18.090035 102.61662 4.442098 -624.71614 -624.71614 -661.34808 -342.17179 -870.62856 2.45944 364.1228 Loop time of 2.165e-06 on 1 procs for 0 steps with 528 atoms 184.8% 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 | | 2.165e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3476.00 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15384.0 ave 15384 max 15384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30768.0 ave 30768 max 30768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30768 Ave neighs/atom = 58.272727 Neighbor list builds = 0 Dangerous builds = 0 528 -3580.72917360725 eV 2.459439990458 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