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 4.024845376610756*${_u_distance} variable lattice_constant_converted equal 4.024845376610756*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 60.50669342371342*${_u_distance} variable xmax_converted equal 60.50669342371342*1 variable ymin_converted equal -60.510718269090034*${_u_distance} variable ymin_converted equal -60.510718269090034*1 variable ymax_converted equal 60.510718269090034*${_u_distance} variable ymax_converted equal 60.510718269090034*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.024845376610756*${_u_distance} variable zmax_converted equal 4.024845376610756*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.02484537661076 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 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 60.5066934237134 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.5066934237134 -60.51071826909 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.5066934237134 -60.51071826909 60.51071826909 ${zmin_converted} ${zmax_converted} units box region whole block 0 60.5066934237134 -60.51071826909 60.51071826909 0 ${zmax_converted} units box region whole block 0 60.5066934237134 -60.51071826909 60.51071826909 0 4.02484537661076 units box create_box 2 whole Created orthogonal box = (0 -60.5107 0) to (60.5067 60.5107 4.02485) 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 60.51071826909 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.28366 4.28366 4.02485 create_atoms 1 region upper Created 906 atoms create_atoms CPU = 0.000265837 secs group upper type 1 906 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.764983370267808 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -60.51071826909 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.28366 4.28366 4.02485 create_atoms 2 region lower Created 906 atoms create_atoms CPU = 0.000113964 secs group lower type 2 906 atoms in group lower displace_atoms lower move -6.764983370267808 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005 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*4.02484537661076 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01242268830538 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 15 29 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1784 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 15 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.589 | 5.589 | 5.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4695.9922 0 -4695.9922 -2107.2913 1158 0 -4710.358 0 -4710.358 -7356.0806 Loop time of 13.322 on 1 procs for 1158 steps with 1784 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4695.99216782 -4710.35798002 -4710.35798002 Force two-norm initial, final = 11.5353 2.63491e-05 Force max component initial, final = 2.60945 3.31193e-06 Final line search alpha, max atom move = 1 3.31193e-06 Iterations, force evaluations = 1158 2306 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.073 | 13.073 | 13.073 | 0.0 | 98.13 Neigh | 0.013448 | 0.013448 | 0.013448 | 0.0 | 0.10 Comm | 0.14773 | 0.14773 | 0.14773 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08787 | | | 0.66 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11272 ave 11272 max 11272 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: 250472 ave 250472 max 250472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250472 Ave neighs/atom = 140.399 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) = 5.591 | 5.591 | 5.591 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1158 0 -4710.358 0 -4710.358 -7356.0806 29472.361 2158 0 -4710.6562 0 -4710.6562 -2648.5925 29294.93 Loop time of 12.493 on 1 procs for 1000 steps with 1784 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 = -4710.35798002 -4710.65620133 -4710.65620132 Force two-norm initial, final = 137.868 6.79063e-05 Force max component initial, final = 102.475 3.19527e-05 Final line search alpha, max atom move = 1 3.19527e-05 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.965 | 11.965 | 11.965 | 0.0 | 95.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11735 | 0.11735 | 0.11735 | 0.0 | 0.94 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.411 | | | 3.29 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11301 ave 11301 max 11301 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: 250400 ave 250400 max 250400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250400 Ave neighs/atom = 140.359 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 -0.0307342631051472 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 15 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.729 | 5.729 | 5.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4710.6562 0 -4710.6562 -2648.5925 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11330 ave 11330 max 11330 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: 250880 ave 250880 max 250880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250880 Ave neighs/atom = 140.628 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) = 5.729 | 5.729 | 5.729 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 -4710.6562 -4710.6562 60.355625 121.02144 4.0106282 -2648.5925 -2648.5925 0.0017431716 -7945.7805 0.0011531656 2.6772672 318.05086 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11330 ave 11330 max 11330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125440 ave 125440 max 125440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 250880 ave 250880 max 250880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250880 Ave neighs/atom = 140.628 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_007.6281/numatoms.out 1784 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4710.65620132476-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4710.65620132476-1784*${isolated_atom_energy} variable adjusted_pe_metal equal -4710.65620132476-1784*-0.0307342631051472 print "${adjusted_pe_metal} eV" file output/dump_007.6281/energy.out -4655.82627594518 eV print "${mindist_metal} Angstroms" file output/dump_007.6281/mindistance.out 2.67726724720915 Angstroms write_dump all cfg output/dump_007.6281/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_007.6281/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:25