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 61.77476721892352*${_u_distance} variable xmax_converted equal 61.77476721892352*1 variable ymin_converted equal -61.77881421848233*${_u_distance} variable ymin_converted equal -61.77881421848233*1 variable ymax_converted equal 61.77881421848233*${_u_distance} variable ymax_converted equal 61.77881421848233*1 variable zmin_converted equal 0.0*${_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 61.7747672189235 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.7747672189235 -61.7788142184823 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.7747672189235 -61.7788142184823 61.7788142184823 ${zmin_converted} ${zmax_converted} units box region whole block 0 61.7747672189235 -61.7788142184823 61.7788142184823 0 ${zmax_converted} units box region whole block 0 61.7747672189235 -61.7788142184823 61.7788142184823 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -61.7788 0) to (61.7748 61.7788 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 61.7788142184823 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -8 0 orient y 8 13 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 13 -8 0 orient y 8 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.56768 5.56768 4.047 create_atoms 1 region upper Created 934 atoms create_atoms CPU = 0.000384092 secs group upper type 1 934 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.868951885113186 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.7788142184823 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 8 0 orient y -8 13 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 13 8 0 orient y -8 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.56768 5.56768 4.047 create_atoms 2 region lower Created 934 atoms create_atoms CPU = 0.000250101 secs group lower type 2 934 atoms in group lower displace_atoms lower move -6.868951885113186 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 18 35 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 28 atoms, new total = 1840 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 = 18 35 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) = 14.22 | 14.22 | 14.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6127.8798 0 -6127.8798 1443.493 349 0 -6161.8998 0 -6161.8998 -5238.6823 Loop time of 20.6996 on 1 procs for 349 steps with 1840 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 = -6127.87984711 -6161.89979938 -6161.89979938 Force two-norm initial, final = 29.8633 5.42482e-06 Force max component initial, final = 7.11477 9.82429e-07 Final line search alpha, max atom move = 1 9.82429e-07 Iterations, force evaluations = 349 688 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.623 | 20.623 | 20.623 | 0.0 | 99.63 Neigh | 0.0094898 | 0.0094898 | 0.0094898 | 0.0 | 0.05 Comm | 0.03953 | 0.03953 | 0.03953 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02788 | | | 0.13 Nlocal: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9510 ave 9510 max 9510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78384 ave 78384 max 78384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156768 ave 156768 max 156768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156768 Ave neighs/atom = 85.2 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) = 14.23 | 14.23 | 14.23 Mbytes Step Temp E_pair E_mol TotEng Press Volume 349 0 -6161.8998 0 -6161.8998 -5238.6823 30889.711 1349 0 -6162.1488 0 -6162.1488 -1051.6844 30720.779 Loop time of 60.2937 on 1 procs for 1000 steps with 1840 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 = -6161.89979938 -6162.14883168 -6162.14883168 Force two-norm initial, final = 127.885 0.00413243 Force max component initial, final = 92.6945 0.00224298 Final line search alpha, max atom move = 1 0.00224298 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 59.809 | 59.809 | 59.809 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10342 | 0.10342 | 0.10342 | 0.0 | 0.17 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3808 | | | 0.63 Nlocal: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9534 ave 9534 max 9534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78466 ave 78466 max 78466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156932 ave 156932 max 156932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156932 Ave neighs/atom = 85.2891 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 = 18 35 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) = 13.1 | 13.1 | 13.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6162.1488 0 -6162.1488 -1051.6844 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1840 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: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9558 ave 9558 max 9558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78506 ave 78506 max 78506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157012 ave 157012 max 157012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157012 Ave neighs/atom = 85.3326 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) = 13.1 | 13.1 | 13.1 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 -6162.1488 -6162.1488 61.61683 123.55763 4.0351837 -1051.6844 -1051.6844 -0.11667861 -3154.8269 -0.10969329 2.4521544 1267.0059 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1840 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: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9558 ave 9558 max 9558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78506 ave 78506 max 78506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157012 ave 157012 max 157012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157012 Ave neighs/atom = 85.3326 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_063.2150/numatoms.out 1840 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6162.14883167953-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6162.14883167953-1840*${isolated_atom_energy} variable adjusted_pe_metal equal -6162.14883167953-1840*0 print "${adjusted_pe_metal} eV" file output/dump_063.2150/energy.out -6162.14883167953 eV print "${mindist_metal} Angstroms" file output/dump_063.2150/mindistance.out 2.45215436335549 Angstroms write_dump all cfg output/dump_063.2150/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_063.2150/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:21