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 4.061213478446007*${_u_distance} variable lattice_constant_converted equal 4.061213478446007*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 42.4003135130951*${_u_distance} variable xmax_converted equal 42.4003135130951*1 variable ymin_converted equal -42.40437472657354*${_u_distance} variable ymin_converted equal -42.40437472657354*1 variable ymax_converted equal 42.40437472657354*${_u_distance} variable ymax_converted equal 42.40437472657354*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.061213478446007*${_u_distance} variable zmax_converted equal 4.061213478446007*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.06121347844601 Lattice spacing in x,y,z = 4.06121 4.06121 4.06121 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 42.4003135130951 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.4003135130951 -42.4043747265735 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.4003135130951 -42.4043747265735 42.4043747265735 ${zmin_converted} ${zmax_converted} units box region whole block 0 42.4003135130951 -42.4043747265735 42.4043747265735 0 ${zmax_converted} units box region whole block 0 42.4003135130951 -42.4043747265735 42.4043747265735 0 4.06121347844601 units box create_box 2 whole Created orthogonal box = (0 -42.4044 0) to (42.4003 42.4044 4.06121) 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 42.4043747265735 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.05692 5.05692 4.06121 create_atoms 1 region upper Created 438 atoms create_atoms CPU = 0.000241995 secs group upper type 1 438 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.698137929009748 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.4043747265735 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.05692 5.05692 4.06121 create_atoms 2 region lower Created 438 atoms create_atoms CPU = 0.000106096 secs group lower type 2 438 atoms in group lower displace_atoms lower move -4.698137929009748 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Al__MO_411898953661_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.06121347844601 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03060673922301 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 18 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 856 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.005 | 5.005 | 5.005 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2260.3712 0 -2260.3712 1239.7951 316 0 -2288.7929 0 -2288.7929 -7483.0081 Loop time of 2.97754 on 1 procs for 316 steps with 856 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2260.37119041 -2288.79294871 -2288.79294871 Force two-norm initial, final = 22.6527 7.57744e-07 Force max component initial, final = 5.30018 5.00195e-08 Final line search alpha, max atom move = 1 5.00195e-08 Iterations, force evaluations = 316 617 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9245 | 2.9245 | 2.9245 | 0.0 | 98.22 Neigh | 0.0098009 | 0.0098009 | 0.0098009 | 0.0 | 0.33 Comm | 0.030084 | 0.030084 | 0.030084 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0132 | | | 0.44 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8210 ave 8210 max 8210 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: 190444 ave 190444 max 190444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190444 Ave neighs/atom = 222.481 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) = 5.005 | 5.005 | 5.005 Mbytes Step Temp E_pair E_mol TotEng Press Volume 316 0 -2288.7929 0 -2288.7929 -7483.0081 14603.789 1316 0 -2289.1146 0 -2289.1146 -1134.6061 14474.962 Loop time of 9.78416 on 1 procs for 1000 steps with 856 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2288.79294871 -2289.11456664 -2289.11456678 Force two-norm initial, final = 92.3277 0.0310374 Force max component initial, final = 73.6372 0.0152826 Final line search alpha, max atom move = 0.0382542 0.000584622 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.4248 | 9.4248 | 9.4248 | 0.0 | 96.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.087586 | 0.087586 | 0.087586 | 0.0 | 0.90 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2718 | | | 2.78 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8185 ave 8185 max 8185 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: 190480 ave 190480 max 190480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190480 Ave neighs/atom = 222.523 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.142 | 5.142 | 5.142 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2289.1146 0 -2289.1146 -1134.6061 Loop time of 1.90735e-06 on 1 procs for 0 steps with 856 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 | | 1.907e-06 | | |100.00 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8222 ave 8222 max 8222 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: 190884 ave 190884 max 190884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190884 Ave neighs/atom = 222.995 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) = 5.142 | 5.142 | 5.142 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 -2289.1146 -2289.1146 42.057338 84.808749 4.0582145 -1134.6061 -1134.6061 -0.89663285 -3401.2313 -1.6903165 2.583162 672.50208 Loop time of 9.53674e-07 on 1 procs for 0 steps with 856 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: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8222 ave 8222 max 8222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95442 ave 95442 max 95442 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 190884 ave 190884 max 190884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190884 Ave neighs/atom = 222.995 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_033.3985/numatoms.out 856 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2289.11456677805-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2289.11456677805-856*${isolated_atom_energy} variable adjusted_pe_metal equal -2289.11456677805-856*0 print "${adjusted_pe_metal} eV" file output/dump_033.3985/energy.out -2289.11456677805 eV print "${mindist_metal} Angstroms" file output/dump_033.3985/mindistance.out 2.58316204958461 Angstroms write_dump all cfg output/dump_033.3985/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_033.3985/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12