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 4.045270472764969*${_u_distance} variable lattice_constant_converted equal 4.045270472764969*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 37.29555096543085*${_u_distance} variable xmax_converted equal 37.29555096543085*1 variable ymin_converted equal -74.59514720133446*${_u_distance} variable ymin_converted equal -74.59514720133446*1 variable ymax_converted equal 74.59514720133446*${_u_distance} variable ymax_converted equal 74.59514720133446*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045270472764969*${_u_distance} variable zmax_converted equal 4.045270472764969*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04527047276497 Lattice spacing in x,y,z = 4.04527 4.04527 4.04527 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 37.2955509654308 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.2955509654308 -74.5951472013345 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.2955509654308 -74.5951472013345 74.5951472013345 ${zmin_converted} ${zmax_converted} units box region whole block 0 37.2955509654308 -74.5951472013345 74.5951472013345 0 ${zmax_converted} units box region whole block 0 37.2955509654308 -74.5951472013345 74.5951472013345 0 4.04527047276497 units box create_box 2 whole Created orthogonal box = (0 -74.5951 0) to (37.2956 74.5951 4.04527) 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 74.5951472013345 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -6 0 orient y 6 7 0 orient z 0 0 1 lattice fcc 4.04527047276497 orient x 7 -6 0 orient y 6 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70403 5.70403 4.04527 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000334978 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.148795005781799 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.5951472013345 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 6 0 orient y -6 7 0 orient z 0 0 1 lattice fcc 4.04527047276497 orient x 7 6 0 orient y -6 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70403 5.70403 4.04527 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.000204086 secs group lower type 2 682 atoms in group lower displace_atoms lower move -4.148795005781799 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_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*4.04527047276497 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02263523638248 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 32 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1352 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.932 | 5.932 | 5.932 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4586.0587 0 -4586.0587 2400.0009 229 0 -4605.3649 0 -4605.3649 -2149.7379 Loop time of 3.03388 on 1 procs for 229 steps with 1352 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 = -4586.05870017 -4605.36488695 -4605.36488695 Force two-norm initial, final = 24.132 2.62668e-06 Force max component initial, final = 5.42025 4.07926e-07 Final line search alpha, max atom move = 1 4.07926e-07 Iterations, force evaluations = 229 449 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9866 | 2.9866 | 2.9866 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.032657 | 0.032657 | 0.032657 | 0.0 | 1.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01461 | | | 0.48 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12454 ave 12454 max 12454 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: 300436 ave 300436 max 300436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300436 Ave neighs/atom = 222.216 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) = 5.932 | 5.932 | 5.932 Mbytes Step Temp E_pair E_mol TotEng Press Volume 229 0 -4605.3649 0 -4605.3649 -2149.7379 22508.428 1229 0 -4605.412 0 -4605.412 -500.59703 22462 Loop time of 13.0956 on 1 procs for 1000 steps with 1352 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 = -4605.36488695 -4605.41196999 -4605.41196999 Force two-norm initial, final = 39.7416 0.00512658 Force max component initial, final = 37.5076 0.00332982 Final line search alpha, max atom move = 1 0.00332982 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.566 | 12.566 | 12.566 | 0.0 | 95.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12927 | 0.12927 | 0.12927 | 0.0 | 0.99 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4001 | | | 3.06 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12454 ave 12454 max 12454 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: 289400 ave 289400 max 289400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289400 Ave neighs/atom = 214.053 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.689 | 5.689 | 5.689 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4605.412 0 -4605.412 -500.59703 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12454 ave 12454 max 12454 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: 293192 ave 293192 max 293192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293192 Ave neighs/atom = 216.858 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) = 5.689 | 5.689 | 5.689 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 -4605.412 -4605.412 37.319458 149.19029 4.0343402 -500.59703 -500.59703 -0.23766267 -1501.3624 -0.19097696 2.5560097 177.20166 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12454 ave 12454 max 12454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146596 ave 146596 max 146596 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 293192 ave 293192 max 293192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293192 Ave neighs/atom = 216.858 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_081.2026/numatoms.out 1352 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4605.41196999133-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4605.41196999133-1352*${isolated_atom_energy} variable adjusted_pe_metal equal -4605.41196999133-1352*0 print "${adjusted_pe_metal} eV" file output/dump_081.2026/energy.out -4605.41196999133 eV print "${mindist_metal} Angstroms" file output/dump_081.2026/mindistance.out 2.5560096904346 Angstroms write_dump all cfg output/dump_081.2026/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_081.2026/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:16