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 39.71059441498238*${_u_distance} variable xmax_converted equal 39.71059441498238*1 variable ymin_converted equal -79.4252208299402*${_u_distance} variable ymin_converted equal -79.4252208299402*1 variable ymax_converted equal 79.4252208299402*${_u_distance} variable ymax_converted equal 79.4252208299402*1 variable zmin_converted equal 0.0*${_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 39.7105944149824 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.7105944149824 -79.4252208299402 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.7105944149824 -79.4252208299402 79.4252208299402 ${zmin_converted} ${zmax_converted} units box region whole block 0 39.7105944149824 -79.4252208299402 79.4252208299402 0 ${zmax_converted} units box region whole block 0 39.7105944149824 -79.4252208299402 79.4252208299402 0 4.03199997544289 units box create_box 2 whole Created orthogonal box = (0 -79.4252 0) to (39.7106 79.4252 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 79.4252208299402 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -4 0 orient y 4 9 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 9 -4 0 orient y 4 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.32204 5.32204 4.032 create_atoms 1 region upper Created 777 atoms create_atoms CPU = 0.000363111 secs group upper type 1 777 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.431986010808247 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -79.4252208299402 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 4 0 orient y -4 9 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 9 4 0 orient y -4 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.32204 5.32204 4.032 create_atoms 2 region lower Created 777 atoms create_atoms CPU = 0.000218153 secs group lower type 2 777 atoms in group lower displace_atoms lower move -4.431986010808247 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 9 36 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 12 atoms, new total = 1542 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 = 9 36 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) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5150.627 0 -5150.627 1708.2365 730 0 -5169.7804 0 -5169.7804 -1676.318 Loop time of 9.019 on 1 procs for 730 steps with 1542 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5150.62698478 -5169.78035151 -5169.78035151 Force two-norm initial, final = 25.9924 2.11081e-06 Force max component initial, final = 6.66909 6.09337e-07 Final line search alpha, max atom move = 1 6.09337e-07 Iterations, force evaluations = 730 1453 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.8617 | 8.8617 | 8.8617 | 0.0 | 98.26 Neigh | 0.007133 | 0.007133 | 0.007133 | 0.0 | 0.08 Comm | 0.10104 | 0.10104 | 0.10104 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04912 | | | 0.54 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11725 ave 11725 max 11725 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: 270474 ave 270474 max 270474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270474 Ave neighs/atom = 175.405 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) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press Volume 730 0 -5169.7804 0 -5169.7804 -1676.318 25434.039 1730 0 -5169.8105 0 -5169.8105 -61.146926 25382.807 Loop time of 12.7741 on 1 procs for 1000 steps with 1542 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5169.78035151 -5169.81046354 -5169.81046367 Force two-norm initial, final = 40.4794 0.0567708 Force max component initial, final = 32.325 0.0488571 Final line search alpha, max atom move = 0.0477739 0.00233409 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.282 | 12.282 | 12.282 | 0.0 | 96.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11346 | 0.11346 | 0.11346 | 0.0 | 0.89 Output | 1.6212e-05 | 1.6212e-05 | 1.6212e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3789 | | | 2.97 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10833 ave 10833 max 10833 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: 270356 ave 270356 max 270356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270356 Ave neighs/atom = 175.328 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 = 9 36 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) = 5.701 | 5.701 | 5.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5169.8105 0 -5169.8105 -61.146926 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1542 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: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10823 ave 10823 max 10823 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: 270412 ave 270412 max 270412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270412 Ave neighs/atom = 175.364 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) = 5.701 | 5.701 | 5.701 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 -5169.8105 -5169.8105 39.646316 158.85044 4.0304021 -61.146926 -61.146926 -0.57353769 -179.78457 -3.0826671 2.4994411 682.74598 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1542 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: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10823 ave 10823 max 10823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135206 ave 135206 max 135206 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270412 ave 270412 max 270412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270412 Ave neighs/atom = 175.364 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_047.9250/numatoms.out 1542 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5169.81046367054-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5169.81046367054-1542*${isolated_atom_energy} variable adjusted_pe_metal equal -5169.81046367054-1542*0 print "${adjusted_pe_metal} eV" file output/dump_047.9250/energy.out -5169.81046367054 eV print "${mindist_metal} Angstroms" file output/dump_047.9250/mindistance.out 2.49944107465387 Angstroms write_dump all cfg output/dump_047.9250/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_047.9250/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:21