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 12.797736295524823*${_u_distance} variable xmax_converted equal 12.797736295524823*1 variable ymin_converted equal -51.1949921816581*${_u_distance} variable ymin_converted equal -51.1949921816581*1 variable ymax_converted equal 51.1949921816581*${_u_distance} variable ymax_converted equal 51.1949921816581*1 variable zmin_converted equal 0.0*${_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 12.7977362955248 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7977362955248 -51.1949921816581 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7977362955248 -51.1949921816581 51.1949921816581 ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7977362955248 -51.1949921816581 51.1949921816581 0 ${zmax_converted} units box region whole block 0 12.7977362955248 -51.1949921816581 51.1949921816581 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -51.195 0) to (12.7977 51.195 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 51.1949921816581 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.11909 5.11909 4.047 create_atoms 1 region upper Created 162 atoms create_atoms CPU = 0.000151873 secs group upper type 1 162 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.4230249470757705 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -51.1949921816581 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.11909 5.11909 4.047 create_atoms 2 region lower Created 162 atoms create_atoms CPU = 6.41346e-05 secs group lower type 2 162 atoms in group lower displace_atoms lower move -1.4230249470757705 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 4 29 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 6 atoms, new total = 318 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 = 4 29 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) = 10.7 | 10.7 | 10.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1052.648 0 -1052.648 8498.914 278 0 -1064.3443 0 -1064.3443 2254.0195 Loop time of 3.05446 on 1 procs for 278 steps with 318 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1052.64799085 -1064.34428405 -1064.34428405 Force two-norm initial, final = 24.8384 4.59775e-06 Force max component initial, final = 6.75818 1.29797e-06 Final line search alpha, max atom move = 1 1.29797e-06 Iterations, force evaluations = 278 553 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0376 | 3.0376 | 3.0376 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010785 | 0.010785 | 0.010785 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006101 | | | 0.20 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3124 ave 3124 max 3124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13644 ave 13644 max 13644 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27288 ave 27288 max 27288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27288 Ave neighs/atom = 85.8113 Neighbor list builds = 0 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) = 10.71 | 10.71 | 10.71 Mbytes Step Temp E_pair E_mol TotEng Press Volume 278 0 -1064.3443 0 -1064.3443 2254.0195 5303.0264 1063 0 -1064.347 0 -1064.347 1271.0461 5309.7824 Loop time of 8.66397 on 1 procs for 785 steps with 318 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1064.34428405 -1064.34696186 -1064.34696186 Force two-norm initial, final = 5.29904 0.000101957 Force max component initial, final = 4.46448 6.84565e-05 Final line search alpha, max atom move = 1 6.84565e-05 Iterations, force evaluations = 785 1570 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5366 | 8.5366 | 8.5366 | 0.0 | 98.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.030123 | 0.030123 | 0.030123 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0972 | | | 1.12 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3462 ave 3462 max 3462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13544 ave 13544 max 13544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27088 ave 27088 max 27088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27088 Ave neighs/atom = 85.1824 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 = 4 29 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) = 9.582 | 9.582 | 9.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1064.347 0 -1064.347 1271.0461 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3462 ave 3462 max 3462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13544 ave 13544 max 13544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27088 ave 27088 max 27088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27088 Ave neighs/atom = 85.1824 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) = 9.582 | 9.582 | 9.582 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 -1064.347 -1064.347 12.800302 102.38998 4.051343 1271.0461 1271.0461 0.02066024 3813.1063 0.011166536 2.4444259 320.32111 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3462 ave 3462 max 3462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13544 ave 13544 max 13544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27088 ave 27088 max 27088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27088 Ave neighs/atom = 85.1824 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_036.8699/numatoms.out 318 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1064.34696185715-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1064.34696185715-318*${isolated_atom_energy} variable adjusted_pe_metal equal -1064.34696185715-318*0 print "${adjusted_pe_metal} eV" file output/dump_036.8699/energy.out -1064.34696185715 eV print "${mindist_metal} Angstroms" file output/dump_036.8699/mindistance.out 2.44442592333428 Angstroms write_dump all cfg output/dump_036.8699/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_036.8699/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11