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 4.0469995588064185*${_u_distance} variable lattice_constant_converted equal 4.0469995588064185*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 53.99370858126272*${_u_distance} variable xmax_converted equal 53.99370858126272*1 variable ymin_converted equal -53.99775558082153*${_u_distance} variable ymin_converted equal -53.99775558082153*1 variable ymax_converted equal 53.99775558082153*${_u_distance} variable ymax_converted equal 53.99775558082153*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.0469995588064185*${_u_distance} variable zmax_converted equal 4.0469995588064185*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04699955880642 Lattice spacing in x,y,z = 4.047 4.047 4.047 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 53.9937085812627 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.9937085812627 -53.9977555808215 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.9937085812627 -53.9977555808215 53.9977555808215 ${zmin_converted} ${zmax_converted} units box region whole block 0 53.9937085812627 -53.9977555808215 53.9977555808215 0 ${zmax_converted} units box region whole block 0 53.9937085812627 -53.9977555808215 53.9977555808215 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -53.9978 0) to (53.9937 53.9978 4.047) 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 53.9977555808215 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -3 0 orient y 3 13 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 13 -3 0 orient y 3 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.85337 4.85337 4.047 create_atoms 1 region upper Created 714 atoms create_atoms CPU = 0.000244856 secs group upper type 1 714 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.003748828856851 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -53.9977555808215 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 3 0 orient y -3 13 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 13 3 0 orient y -3 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.85337 4.85337 4.047 create_atoms 2 region lower Created 714 atoms create_atoms CPU = 0.000108957 secs group lower type 2 714 atoms in group lower displace_atoms lower move -6.003748828856851 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_871795249052_000-files/b'library.NAlTi' N Al Ti ./SM_871795249052_000-files/b'meam.NAlTi' 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*4.04699955880642 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02349977940321 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 16 31 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 20 atoms, new total = 1408 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 16 31 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4691.27 0 -4691.27 1458.0591 234 0 -4715.7243 0 -4715.7243 -4613.575 Loop time of 10.6167 on 1 procs for 234 steps with 1408 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 = -4691.27000297 -4715.72434011 -4715.72434011 Force two-norm initial, final = 25.9752 1.63398e-05 Force max component initial, final = 5.1745 3.35522e-06 Final line search alpha, max atom move = 1 3.35522e-06 Iterations, force evaluations = 234 456 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.573 | 10.573 | 10.573 | 0.0 | 99.59 Neigh | 0.0085378 | 0.0085378 | 0.0085378 | 0.0 | 0.08 Comm | 0.020925 | 0.020925 | 0.020925 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01454 | | | 0.14 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7650 ave 7650 max 7650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59996 ave 59996 max 59996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119992 ave 119992 max 119992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119992 Ave neighs/atom = 85.2216 Neighbor list builds = 2 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) = 13.32 | 13.32 | 13.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 234 0 -4715.7243 0 -4715.7243 -4613.575 23598.371 1234 0 -4715.8684 0 -4715.8684 -1029.6745 23488.071 Loop time of 45.5779 on 1 procs for 1000 steps with 1408 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4715.72434011 -4715.86843663 -4715.86843663 Force two-norm initial, final = 84.3287 0.00655355 Force max component initial, final = 65.9032 0.00554764 Final line search alpha, max atom move = 0.337563 0.00187268 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 45.194 | 45.194 | 45.194 | 0.0 | 99.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.084129 | 0.084129 | 0.084129 | 0.0 | 0.18 Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2997 | | | 0.66 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7654 ave 7654 max 7654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60032 ave 60032 max 60032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120064 ave 120064 max 120064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120064 Ave neighs/atom = 85.2727 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 0.0 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 16 31 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 12.19 | 12.19 | 12.19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4715.8684 0 -4715.8684 -1029.6745 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1408 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: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7666 ave 7666 max 7666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60078 ave 60078 max 60078 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120156 ave 120156 max 120156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120156 Ave neighs/atom = 85.3381 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) = 12.19 | 12.19 | 12.19 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 -4715.8684 -4715.8684 53.907083 107.99551 4.0345565 -1029.6745 -1029.6745 -0.13278036 -3088.5134 -0.37725396 2.4148207 839.59022 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1408 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: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7666 ave 7666 max 7666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60078 ave 60078 max 60078 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120156 ave 120156 max 120156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120156 Ave neighs/atom = 85.3381 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.9892/numatoms.out 1408 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4715.86843662894-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4715.86843662894-1408*${isolated_atom_energy} variable adjusted_pe_metal equal -4715.86843662894-1408*0 print "${adjusted_pe_metal} eV" file output/dump_025.9892/energy.out -4715.86843662894 eV print "${mindist_metal} Angstroms" file output/dump_025.9892/mindistance.out 2.41482067967231 Angstroms write_dump all cfg output/dump_025.9892/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_025.9892/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:56