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 4.050010219216347*${_u_distance} variable lattice_constant_converted equal 4.050010219216347*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 24.63525040877407*${_u_distance} variable xmax_converted equal 24.63525040877407*1 variable ymin_converted equal -49.27455082776736*${_u_distance} variable ymin_converted equal -49.27455082776736*1 variable ymax_converted equal 49.27455082776736*${_u_distance} variable ymax_converted equal 49.27455082776736*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050010219216347*${_u_distance} variable zmax_converted equal 4.050010219216347*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05001021921635 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 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 24.6352504087741 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 24.6352504087741 -49.2745508277674 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 24.6352504087741 -49.2745508277674 49.2745508277674 ${zmin_converted} ${zmax_converted} units box region whole block 0 24.6352504087741 -49.2745508277674 49.2745508277674 0 ${zmax_converted} units box region whole block 0 24.6352504087741 -49.2745508277674 49.2745508277674 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -49.2746 0) to (24.6353 49.2746 4.05001) 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 49.2745508277674 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 -1 0 orient y 1 6 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 6 -1 0 orient y 1 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.66072 4.66072 4.05001 create_atoms 1 region upper Created 298 atoms create_atoms CPU = 0.000175953 secs group upper type 1 298 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.7372431386341987 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -49.2745508277674 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 1 0 orient y -1 6 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 6 1 0 orient y -1 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.66072 4.66072 4.05001 create_atoms 2 region lower Created 298 atoms create_atoms CPU = 6.29425e-05 secs group lower type 2 298 atoms in group lower displace_atoms lower move -2.7372431386341987 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_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*4.05001021921635 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500510960818 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 7 26 2 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 586 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.51 | 4.51 | 4.51 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1968.9521 0 -1968.9521 3412.5447 257 0 -1979.5391 0 -1979.5391 -3111.1475 Loop time of 0.772829 on 1 procs for 257 steps with 586 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1968.95209848 -1979.53907575 -1979.53907575 Force two-norm initial, final = 21.8919 4.14872e-06 Force max component initial, final = 8.10563 9.58862e-07 Final line search alpha, max atom move = 1 9.58862e-07 Iterations, force evaluations = 257 507 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7502 | 0.7502 | 0.7502 | 0.0 | 97.07 Neigh | 0.0016189 | 0.0016189 | 0.0016189 | 0.0 | 0.21 Comm | 0.01362 | 0.01362 | 0.01362 | 0.0 | 1.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007388 | | | 0.96 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4869 ave 4869 max 4869 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: 63592 ave 63592 max 63592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63592 Ave neighs/atom = 108.519 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) = 4.51 | 4.51 | 4.51 Mbytes Step Temp E_pair E_mol TotEng Press Volume 257 0 -1979.5391 0 -1979.5391 -3111.1475 9832.5411 1257 0 -1979.5773 0 -1979.5773 -243.918 9795.0441 Loop time of 2.94948 on 1 procs for 1000 steps with 586 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 = -1979.53907575 -1979.57726479 -1979.57726479 Force two-norm initial, final = 26.7136 0.00266659 Force max component initial, final = 20.6223 0.0026387 Final line search alpha, max atom move = 1 0.0026387 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7386 | 2.7386 | 2.7386 | 0.0 | 92.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.048853 | 0.048853 | 0.048853 | 0.0 | 1.66 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.162 | | | 5.49 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4879 ave 4879 max 4879 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: 64868 ave 64868 max 64868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64868 Ave neighs/atom = 110.696 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1979.5773 0 -1979.5773 -243.918 Loop time of 9.53674e-07 on 1 procs for 0 steps with 586 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: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4884 ave 4884 max 4884 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: 68748 ave 68748 max 68748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68748 Ave neighs/atom = 117.317 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) = 4.648 | 4.648 | 4.648 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 -1979.5773 -1979.5773 24.558221 98.549102 4.0472202 -243.918 -243.918 0.023692402 -732.20902 0.43131509 2.5554684 342.49052 Loop time of 1.19209e-06 on 1 procs for 0 steps with 586 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 | | 1.192e-06 | | |100.00 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4884 ave 4884 max 4884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34374 ave 34374 max 34374 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68748 ave 68748 max 68748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68748 Ave neighs/atom = 117.317 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_018.9246/numatoms.out 586 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1979.57726479162-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1979.57726479162-586*${isolated_atom_energy} variable adjusted_pe_metal equal -1979.57726479162-586*0 print "${adjusted_pe_metal} eV" file output/dump_018.9246/energy.out -1979.57726479162 eV print "${mindist_metal} Angstroms" file output/dump_018.9246/mindistance.out 2.5554683695758 Angstroms write_dump all cfg output/dump_018.9246/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_018.9246/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03