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 4.031999975442886*${_u_distance} variable lattice_constant_converted equal 4.031999975442886*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 57.305486718099075*${_u_distance} variable xmax_converted equal 57.305486718099075*1 variable ymin_converted equal -57.30951871807452*${_u_distance} variable ymin_converted equal -57.30951871807452*1 variable ymax_converted equal 57.30951871807452*${_u_distance} variable ymax_converted equal 57.30951871807452*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031999975442886*${_u_distance} variable zmax_converted equal 4.031999975442886*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03199997544289 Lattice spacing in x,y,z = 4.032 4.032 4.032 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 57.3054867180991 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.3054867180991 -57.3095187180745 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.3054867180991 -57.3095187180745 57.3095187180745 ${zmin_converted} ${zmax_converted} units box region whole block 0 57.3054867180991 -57.3095187180745 57.3095187180745 0 ${zmax_converted} units box region whole block 0 57.3054867180991 -57.3095187180745 57.3095187180745 0 4.03199997544289 units box create_box 2 whole Created orthogonal box = (0 -57.3095 0) to (57.3055 57.3095 4.032) 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 57.3095187180745 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -9 0 orient y 9 11 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 11 -9 0 orient y 9 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67381 5.67381 4.032 create_atoms 1 region upper Created 810 atoms create_atoms CPU = 0.000249147 secs group upper type 1 810 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.395701681598353 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -57.3095187180745 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 9 0 orient y -9 11 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 11 9 0 orient y -9 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67381 5.67381 4.032 create_atoms 2 region lower Created 810 atoms create_atoms CPU = 0.000166893 secs group lower type 2 810 atoms in group lower displace_atoms lower move -6.395701681598353 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000 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*4.03199997544289 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01599998772144 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 13 26 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1596 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 13 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.562 | 5.562 | 5.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5328.9943 0 -5328.9943 -568.96299 302 0 -5348.48 0 -5348.48 -5464.8223 Loop time of 3.48522 on 1 procs for 302 steps with 1596 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5328.99433065 -5348.48001745 -5348.48001745 Force two-norm initial, final = 22.171 1.69498e-05 Force max component initial, final = 5.04795 3.84539e-06 Final line search alpha, max atom move = 1 3.84539e-06 Iterations, force evaluations = 302 599 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4195 | 3.4195 | 3.4195 | 0.0 | 98.12 Neigh | 0.0075281 | 0.0075281 | 0.0075281 | 0.0 | 0.22 Comm | 0.038098 | 0.038098 | 0.038098 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02006 | | | 0.58 Nlocal: 1596 ave 1596 max 1596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11503 ave 11503 max 11503 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: 279560 ave 279560 max 279560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279560 Ave neighs/atom = 175.163 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) = 5.562 | 5.562 | 5.562 Mbytes Step Temp E_pair E_mol TotEng Press Volume 302 0 -5348.48 0 -5348.48 -5464.8223 26483.384 1302 0 -5348.6816 0 -5348.6816 -1330.3822 26345.532 Loop time of 12.9414 on 1 procs for 1000 steps with 1596 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 = -5348.48001745 -5348.68158915 -5348.68158915 Force two-norm initial, final = 108.176 0.00333555 Force max component initial, final = 78.1187 0.00159898 Final line search alpha, max atom move = 0.209486 0.000334963 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.46 | 12.46 | 12.46 | 0.0 | 96.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1075 | 0.1075 | 0.1075 | 0.0 | 0.83 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3742 | | | 2.89 Nlocal: 1596 ave 1596 max 1596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10499 ave 10499 max 10499 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: 279360 ave 279360 max 279360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279360 Ave neighs/atom = 175.038 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 13 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.692 | 5.692 | 5.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5348.6816 0 -5348.6816 -1330.3822 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1596 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 | | 2.146e-06 | | |100.00 Nlocal: 1596 ave 1596 max 1596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10499 ave 10499 max 10499 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: 279584 ave 279584 max 279584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279584 Ave neighs/atom = 175.178 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) = 5.692 | 5.692 | 5.692 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 -5348.6816 -5348.6816 57.210979 114.61904 4.0176383 -1330.3822 -1330.3822 -0.097079787 -3990.96 -0.089690274 2.5076844 685.99283 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1596 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: 1596 ave 1596 max 1596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10499 ave 10499 max 10499 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 139792 ave 139792 max 139792 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 279584 ave 279584 max 279584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279584 Ave neighs/atom = 175.178 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_078.5788/numatoms.out 1596 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5348.68158915102-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5348.68158915102-1596*${isolated_atom_energy} variable adjusted_pe_metal equal -5348.68158915102-1596*0 print "${adjusted_pe_metal} eV" file output/dump_078.5788/energy.out -5348.68158915102 eV print "${mindist_metal} Angstroms" file output/dump_078.5788/mindistance.out 2.50768440073099 Angstroms write_dump all cfg output/dump_078.5788/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_078.5788/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:16