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 25.932718596514913*${_u_distance} variable xmax_converted equal 25.932718596514913*1 variable ymin_converted equal -51.869487203249044*${_u_distance} variable ymin_converted equal -51.869487203249044*1 variable ymax_converted equal 51.869487203249044*${_u_distance} variable ymax_converted equal 51.869487203249044*1 variable zmin_converted equal 0.0*${_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 25.9327185965149 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.9327185965149 -51.869487203249 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.9327185965149 -51.869487203249 51.869487203249 ${zmin_converted} ${zmax_converted} units box region whole block 0 25.9327185965149 -51.869487203249 51.869487203249 0 ${zmax_converted} units box region whole block 0 25.9327185965149 -51.869487203249 51.869487203249 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -51.8695 0) to (25.9327 51.8695 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 51.869487203249 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -4 0 orient y 4 5 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 5 -4 0 orient y 4 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69255 5.69255 4.05001 create_atoms 1 region upper Created 330 atoms create_atoms CPU = 0.000211 secs group upper type 1 330 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.881405906844782 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -51.869487203249 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 4 0 orient y -4 5 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 5 4 0 orient y -4 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69255 5.69255 4.05001 create_atoms 2 region lower Created 330 atoms create_atoms CPU = 7.29561e-05 secs group lower type 2 330 atoms in group lower displace_atoms lower move -2.881405906844782 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 28 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 12 atoms, new total = 648 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 28 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) = 4.525 | 4.525 | 4.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2179.6481 0 -2179.6481 2043.6814 301 0 -2190.3198 0 -2190.3198 -5308.1369 Loop time of 0.772573 on 1 procs for 301 steps with 648 atoms 101.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2179.64809931 -2190.31980446 -2190.31980446 Force two-norm initial, final = 19.5101 8.17449e-06 Force max component initial, final = 6.02564 1.46116e-06 Final line search alpha, max atom move = 1 1.46116e-06 Iterations, force evaluations = 301 596 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75028 | 0.75028 | 0.75028 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014438 | 0.014438 | 0.014438 | 0.0 | 1.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007855 | | | 1.02 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5207 ave 5207 max 5207 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: 84764 ave 84764 max 84764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84764 Ave neighs/atom = 130.809 Neighbor list builds = 0 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) = 4.525 | 4.525 | 4.525 Mbytes Step Temp E_pair E_mol TotEng Press Volume 301 0 -2190.3198 0 -2190.3198 -5308.1369 10895.474 1301 0 -2190.3934 0 -2190.3934 -1479.0391 10840.411 Loop time of 3.45865 on 1 procs for 1000 steps with 648 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 = -2190.31980446 -2190.39339427 -2190.39339428 Force two-norm initial, final = 40.3251 0.00612933 Force max component initial, final = 29.5312 0.00372003 Final line search alpha, max atom move = 0.139068 0.000517339 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2188 | 3.2188 | 3.2188 | 0.0 | 93.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.054738 | 0.054738 | 0.054738 | 0.0 | 1.58 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1851 | | | 5.35 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5242 ave 5242 max 5242 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: 68944 ave 68944 max 68944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68944 Ave neighs/atom = 106.395 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 28 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) = 4.663 | 4.663 | 4.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2190.3934 0 -2190.3934 -1479.0391 Loop time of 9.53674e-07 on 1 procs for 0 steps with 648 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: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5242 ave 5242 max 5242 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: 74280 ave 74280 max 74280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74280 Ave neighs/atom = 114.63 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) = 4.663 | 4.663 | 4.663 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 -2190.3934 -2190.3934 25.902115 103.73897 4.0343035 -1479.0391 -1479.0391 0.32825116 -4437.9933 0.54767627 2.5336803 282.72345 Loop time of 9.53674e-07 on 1 procs for 0 steps with 648 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: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5242 ave 5242 max 5242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37140 ave 37140 max 37140 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74280 ave 74280 max 74280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74280 Ave neighs/atom = 114.63 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_077.3196/numatoms.out 648 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2190.39339428002-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2190.39339428002-648*${isolated_atom_energy} variable adjusted_pe_metal equal -2190.39339428002-648*0 print "${adjusted_pe_metal} eV" file output/dump_077.3196/energy.out -2190.39339428002 eV print "${mindist_metal} Angstroms" file output/dump_077.3196/mindistance.out 2.5336803064307 Angstroms write_dump all cfg output/dump_077.3196/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_077.3196/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:04