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 4.03203821182251*${_u_distance} variable lattice_constant_converted equal 4.03203821182251*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 80.0336733118577*${_u_distance} variable xmax_converted equal 80.0336733118577*1 variable ymin_converted equal -80.03770535006952*${_u_distance} variable ymin_converted equal -80.03770535006952*1 variable ymax_converted equal 80.03770535006952*${_u_distance} variable ymax_converted equal 80.03770535006952*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.03203821182251*${_u_distance} variable zmax_converted equal 4.03203821182251*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03203821182251 Lattice spacing in x,y,z = 4.03204 4.03204 4.03204 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 80.0336733118577 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 80.0336733118577 -80.0377053500695 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 80.0336733118577 -80.0377053500695 80.0377053500695 ${zmin_converted} ${zmax_converted} units box region whole block 0 80.0336733118577 -80.0377053500695 80.0377053500695 0 ${zmax_converted} units box region whole block 0 80.0336733118577 -80.0377053500695 80.0377053500695 0 4.03203821182251 units box create_box 2 whole Created orthogonal box = (0 -80.0377 0) to (80.0337 80.0377 4.03204) 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 80.0377053500695 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 lattice fcc 4.03203821182251 orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68767 5.68767 4.03204 create_atoms 1 region upper Created 1578 atoms create_atoms CPU = 0.000532866 secs group upper type 1 1578 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.932244958575643 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -80.0377053500695 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 lattice fcc 4.03203821182251 orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68767 5.68767 4.03204 create_atoms 2 region lower Created 1578 atoms create_atoms CPU = 0.000466108 secs group lower type 2 1578 atoms in group lower displace_atoms lower move -8.932244958575643 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_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*4.03203821182251 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01601910591125 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 19 37 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 3120 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 19 37 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.93 | 10.93 | 10.93 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10437.631 0 -10437.631 -386.72683 361 0 -10463.566 0 -10463.566 -5075.7544 Loop time of 8.39933 on 1 procs for 361 steps with 3120 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 = -10437.6312871 -10463.5661699 -10463.5661699 Force two-norm initial, final = 24.0999 6.79247e-06 Force max component initial, final = 6.01995 1.56721e-06 Final line search alpha, max atom move = 1 1.56721e-06 Iterations, force evaluations = 361 716 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2703 | 8.2703 | 8.2703 | 0.0 | 98.46 Neigh | 0.01285 | 0.01285 | 0.01285 | 0.0 | 0.15 Comm | 0.071042 | 0.071042 | 0.071042 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04517 | | | 0.54 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17885 ave 17885 max 17885 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: 540872 ave 540872 max 540872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 540872 Ave neighs/atom = 173.356 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) = 10.93 | 10.93 | 10.93 Mbytes Step Temp E_pair E_mol TotEng Press Volume 361 0 -10463.566 0 -10463.566 -5075.7544 51656.148 1361 0 -10463.897 0 -10463.897 -1331.8944 51419.824 Loop time of 24.2241 on 1 procs for 1000 steps with 3120 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 = -10463.5661699 -10463.8967555 -10463.8967556 Force two-norm initial, final = 195.972 0.0215642 Force max component initial, final = 155.02 0.0133729 Final line search alpha, max atom move = 0.0554041 0.000740916 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.363 | 23.363 | 23.363 | 0.0 | 96.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.18491 | 0.18491 | 0.18491 | 0.0 | 0.76 Output | 2.2888e-05 | 2.2888e-05 | 2.2888e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.6764 | | | 2.79 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17885 ave 17885 max 17885 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: 541728 ave 541728 max 541728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 541728 Ave neighs/atom = 173.631 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 19 37 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 10.44 | 10.44 | 10.44 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10463.897 0 -10463.897 -1331.8944 Loop time of 1.62125e-05 on 1 procs for 0 steps with 3120 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 | | 1.621e-05 | | |100.00 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17905 ave 17905 max 17905 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: 542328 ave 542328 max 542328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 542328 Ave neighs/atom = 173.823 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) = 10.44 | 10.44 | 10.44 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 -10463.897 -10463.897 79.795579 160.07541 4.0255676 -1331.8944 -1331.8944 0.17506919 -3996.2742 0.41601531 2.5152245 985.0916 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3120 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 | | 1.192e-06 | | |100.00 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17905 ave 17905 max 17905 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271164 ave 271164 max 271164 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 542328 ave 542328 max 542328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 542328 Ave neighs/atom = 173.823 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_081.8288/numatoms.out 3120 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -10463.8967555568-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -10463.8967555568-3120*${isolated_atom_energy} variable adjusted_pe_metal equal -10463.8967555568-3120*0 print "${adjusted_pe_metal} eV" file output/dump_081.8288/energy.out -10463.8967555568 eV print "${mindist_metal} Angstroms" file output/dump_081.8288/mindistance.out 2.51522451346361 Angstroms write_dump all cfg output/dump_081.8288/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_081.8288/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:32