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 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 67.03941027148915*${_u_distance} variable xmax_converted equal 67.03941027148915*1 variable ymin_converted equal -67.04346027037603*${_u_distance} variable ymin_converted equal -67.04346027037603*1 variable ymax_converted equal 67.04346027037603*${_u_distance} variable ymax_converted equal 67.04346027037603*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 67.0394102714891 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.0394102714891 -67.043460270376 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.0394102714891 -67.043460270376 67.043460270376 ${zmin_converted} ${zmax_converted} units box region whole block 0 67.0394102714891 -67.043460270376 67.043460270376 0 ${zmax_converted} units box region whole block 0 67.0394102714891 -67.043460270376 67.043460270376 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -67.0435 0) to (67.0394 67.0435 4.05) 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 67.043460270376 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -7 0 orient y 7 15 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 15 -7 0 orient y 7 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.38273 5.38273 4.05 create_atoms 1 region upper Created 1098 atoms create_atoms CPU = 0.000401974 secs group upper type 1 1098 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.448825410761081 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -67.043460270376 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 7 0 orient y -7 15 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 15 7 0 orient y -7 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.38273 5.38273 4.05 create_atoms 2 region lower Created 1098 atoms create_atoms CPU = 0.000287056 secs group lower type 2 1098 atoms in group lower displace_atoms lower move -7.448825410761081 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_811588957187_000-files/b'library-Al.meam' Al ./SM_811588957187_000-files/b'Al.meam' 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*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 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 ghost atom cutoff = 7 binsize = 3.5, bins = 20 39 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 = 2168 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 ghost atom cutoff = 7 binsize = 3.5, bins = 20 39 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) = 14.69 | 14.69 | 14.69 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7221.6935 0 -7221.6935 3284.7433 404 0 -7260.472 0 -7260.472 -3115.6755 Loop time of 16.8126 on 1 procs for 404 steps with 2168 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 = -7221.69354355 -7260.47204277 -7260.47204277 Force two-norm initial, final = 50.9607 3.72512e-05 Force max component initial, final = 12.0876 8.42172e-06 Final line search alpha, max atom move = 1 8.42172e-06 Iterations, force evaluations = 404 799 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.72 | 16.72 | 16.72 | 0.0 | 99.45 Neigh | 0.0052321 | 0.0052321 | 0.0052321 | 0.0 | 0.03 Comm | 0.051167 | 0.051167 | 0.051167 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03615 | | | 0.22 Nlocal: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10800 ave 10800 max 10800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85112 ave 85112 max 85112 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170224 ave 170224 max 170224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170224 Ave neighs/atom = 78.5166 Neighbor list builds = 1 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) = 14.72 | 14.72 | 14.72 Mbytes Step Temp E_pair E_mol TotEng Press Volume 404 0 -7260.472 0 -7260.472 -3115.6755 36405.878 1404 0 -7260.6047 0 -7260.6047 -415.62198 36275.224 Loop time of 43.9348 on 1 procs for 1000 steps with 2168 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 = -7260.47204277 -7260.60473577 -7260.60473579 Force two-norm initial, final = 98.5598 0.0132826 Force max component initial, final = 78.0443 0.0064511 Final line search alpha, max atom move = 0.0736183 0.000474919 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.398 | 43.398 | 43.398 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11499 | 0.11499 | 0.11499 | 0.0 | 0.26 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4214 | | | 0.96 Nlocal: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10422 ave 10422 max 10422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85026 ave 85026 max 85026 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170052 ave 170052 max 170052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170052 Ave neighs/atom = 78.4373 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 ghost atom cutoff = 7 binsize = 3.5, bins = 20 39 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) = 13.6 | 13.6 | 13.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7260.6047 0 -7260.6047 -415.62198 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2168 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: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10537 ave 10537 max 10537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85536 ave 85536 max 85536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171072 ave 171072 max 171072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171072 Ave neighs/atom = 78.9077 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) = 13.6 | 13.6 | 13.6 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 -7260.6047 -7260.6047 66.980988 134.08692 4.038984 -415.62198 -415.62198 -0.26639565 -1246.3154 -0.28415226 2.4792253 1168.9514 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2168 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: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10537 ave 10537 max 10537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85536 ave 85536 max 85536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171072 ave 171072 max 171072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171072 Ave neighs/atom = 78.9077 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_050.0338/numatoms.out 2168 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7260.60473578692-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7260.60473578692-2168*${isolated_atom_energy} variable adjusted_pe_metal equal -7260.60473578692-2168*0 print "${adjusted_pe_metal} eV" file output/dump_050.0338/energy.out -7260.60473578692 eV print "${mindist_metal} Angstroms" file output/dump_050.0338/mindistance.out 2.47922528477744 Angstroms write_dump all cfg output/dump_050.0338/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_050.0338/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:00