LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 4.073718130588532*${_u_distance} variable lattice_constant_converted equal 4.073718130588532*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 77.82827560554254*${_u_distance} variable xmax_converted equal 77.82827560554254*1 variable ymin_converted equal -77.83234932367313*${_u_distance} variable ymin_converted equal -77.83234932367313*1 variable ymax_converted equal 77.83234932367313*${_u_distance} variable ymax_converted equal 77.83234932367313*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.073718130588532*${_u_distance} variable zmax_converted equal 4.073718130588532*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.07371813058853 Lattice spacing in x,y,z = 4.07372 4.07372 4.07372 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.8282756055425 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.8282756055425 -77.8323493236731 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.8282756055425 -77.8323493236731 77.8323493236731 ${zmin_converted} ${zmax_converted} units box region whole block 0 77.8282756055425 -77.8323493236731 77.8323493236731 0 ${zmax_converted} units box region whole block 0 77.8282756055425 -77.8323493236731 77.8323493236731 0 4.07371813058853 units box create_box 2 whole Created orthogonal box = (0 -77.8323 0) to (77.8283 77.8323 4.07372) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 77.8323493236731 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.75716 5.75716 4.07372 create_atoms 1 region upper Created 1462 atoms create_atoms CPU = 0.000517845 secs group upper type 1 1462 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.59723792854426 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -77.8323493236731 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 13 0 orient y -13 14 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 14 13 0 orient y -13 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.75716 5.75716 4.07372 create_atoms 2 region lower Created 1462 atoms create_atoms CPU = 0.00041008 secs group lower type 2 1462 atoms in group lower displace_atoms lower move -8.59723792854426 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) pair_coeff * * Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*4.07371813058853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03685906529426 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 17 34 1 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2892 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 17 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.91 | 10.91 | 10.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8824.9769 0 -8824.9769 442.38954 289 0 -8862.8399 0 -8862.8399 -3944.2327 Loop time of 9.63033 on 1 procs for 289 steps with 2892 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 = -8824.97694843 -8862.83991416 -8862.83991416 Force two-norm initial, final = 28.5316 4.06439e-05 Force max component initial, final = 4.91349 3.61717e-06 Final line search alpha, max atom move = 1 3.61717e-06 Iterations, force evaluations = 289 552 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.4882 | 9.4882 | 9.4882 | 0.0 | 98.52 Neigh | 0.044073 | 0.044073 | 0.044073 | 0.0 | 0.46 Comm | 0.064722 | 0.064722 | 0.064722 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03333 | | | 0.35 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19511 ave 19511 max 19511 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 575320 ave 575320 max 575320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575320 Ave neighs/atom = 198.935 Neighbor list builds = 4 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 10.93 | 10.93 | 10.93 Mbytes Step Temp E_pair E_mol TotEng Press Volume 289 0 -8862.8399 0 -8862.8399 -3944.2327 49353.564 1289 0 -8863.0573 0 -8863.0573 -1544.7472 49105.927 Loop time of 33.7854 on 1 procs for 1000 steps with 2892 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -8862.83991416 -8863.05727228 -8863.05727228 Force two-norm initial, final = 122.001 0.00502039 Force max component initial, final = 88.7831 0.00320919 Final line search alpha, max atom move = 0.554157 0.0017784 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.859 | 32.859 | 32.859 | 0.0 | 97.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.21971 | 0.21971 | 0.21971 | 0.0 | 0.65 Output | 2.2888e-05 | 2.2888e-05 | 2.2888e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.7065 | | | 2.09 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21138 ave 21138 max 21138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 575632 ave 575632 max 575632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575632 Ave neighs/atom = 199.043 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal 0.143095413925774 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 17 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8863.0573 0 -8863.0573 -1544.7472 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2892 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21138 ave 21138 max 21138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 575872 ave 575872 max 575872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575872 Ave neighs/atom = 199.126 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom 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 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 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 -8863.0573 -8863.0573 77.640282 155.6647 4.0630922 -1544.7472 -1544.7472 -0.059309269 -4634.0779 -0.10443298 2.601105 187.83436 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2892 atoms 0.0% 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 | | 1.192e-06 | | |100.00 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21138 ave 21138 max 21138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287936 ave 287936 max 287936 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 575872 ave 575872 max 575872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575872 Ave neighs/atom = 199.126 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.7578/numatoms.out 2892 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8863.05727228476-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8863.05727228476-2892*${isolated_atom_energy} variable adjusted_pe_metal equal -8863.05727228476-2892*0.143095413925774 print "${adjusted_pe_metal} eV" file output/dump_085.7578/energy.out -9276.8892093581 eV print "${mindist_metal} Angstroms" file output/dump_085.7578/mindistance.out 2.60110503469771 Angstroms write_dump all cfg output/dump_085.7578/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_085.7578/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:43