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 4.081654928624631*${_u_distance} variable lattice_constant_converted equal 4.081654928624631*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 60.26491281407226*${_u_distance} variable xmax_converted equal 60.26491281407226*1 variable ymin_converted equal -60.26899446900089*${_u_distance} variable ymin_converted equal -60.26899446900089*1 variable ymax_converted equal 60.26899446900089*${_u_distance} variable ymax_converted equal 60.26899446900089*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.081654928624631*${_u_distance} variable zmax_converted equal 4.081654928624631*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.08165492862463 Lattice spacing in x,y,z = 4.08165 4.08165 4.08165 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 60.2649128140723 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2649128140723 -60.2689944690009 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2649128140723 -60.2689944690009 60.2689944690009 ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2649128140723 -60.2689944690009 60.2689944690009 0 ${zmax_converted} units box region whole block 0 60.2649128140723 -60.2689944690009 60.2689944690009 0 4.08165492862463 units box create_box 2 whole Created orthogonal box = (0 -60.269 0) to (60.2649 60.269 4.08165) 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 60.2689944690009 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.52889 5.52889 4.08165 create_atoms 1 region upper Created 874 atoms create_atoms CPU = 0.000331163 secs group upper type 1 874 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.64417037710503 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -60.2689944690009 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.52889 5.52889 4.08165 create_atoms 2 region lower Created 874 atoms create_atoms CPU = 0.000230074 secs group lower type 2 874 atoms in group lower displace_atoms lower move -6.64417037710503 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_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*4.08165492862463 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.04082746431231 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 10 20 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 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1722 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 10 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.48 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6139.6418 0 -6139.6418 -2395.6824 363 0 -6151.9025 0 -6151.9025 -6945.2748 Loop time of 14.8329 on 1 procs for 363 steps with 1722 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 = -6139.64178259 -6151.90249655 -6151.90249655 Force two-norm initial, final = 10.79 1.40923e-08 Force max component initial, final = 2.35008 3.37944e-09 Final line search alpha, max atom move = 1 3.37944e-09 Iterations, force evaluations = 363 716 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.717 | 14.717 | 14.717 | 0.0 | 99.22 Neigh | 0.011581 | 0.011581 | 0.011581 | 0.0 | 0.08 Comm | 0.073354 | 0.073354 | 0.073354 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03071 | | | 0.21 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18522 ave 18522 max 18522 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: 731636 ave 731636 max 731636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 731636 Ave neighs/atom = 424.876 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) = 11.48 | 11.48 | 11.48 Mbytes Step Temp E_pair E_mol TotEng Press Volume 363 0 -6151.9025 0 -6151.9025 -6945.2748 29650.004 1363 0 -6152.2847 0 -6152.2847 -1117.2569 29463.127 Loop time of 41.0717 on 1 procs for 1000 steps with 1722 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 = -6151.90249655 -6152.28471851 -6152.28471853 Force two-norm initial, final = 168.521 0.0107763 Force max component initial, final = 124.686 0.00798598 Final line search alpha, max atom move = 0.0396292 0.000316478 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.314 | 40.314 | 40.314 | 0.0 | 98.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.18607 | 0.18607 | 0.18607 | 0.0 | 0.45 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.572 | | | 1.39 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18515 ave 18515 max 18515 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: 732312 ave 732312 max 732312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732312 Ave neighs/atom = 425.268 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 2.2204e-16 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 10 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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) = 10.99 | 10.99 | 10.99 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6152.2847 0 -6152.2847 -1117.2569 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1722 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: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18515 ave 18515 max 18515 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: 732912 ave 732912 max 732912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732912 Ave neighs/atom = 425.617 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) = 10.99 | 10.99 | 10.99 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 -6152.2847 -6152.2847 60.127849 120.53799 4.0651748 -1117.2569 -1117.2569 0.43328243 -3352.2457 0.041650763 2.5229808 979.16635 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1722 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: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18515 ave 18515 max 18515 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 366456 ave 366456 max 366456 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 732912 ave 732912 max 732912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732912 Ave neighs/atom = 425.617 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.6015/numatoms.out 1722 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6152.28471852723-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6152.28471852723-1722*${isolated_atom_energy} variable adjusted_pe_metal equal -6152.28471852723-1722*2.2204e-16 print "${adjusted_pe_metal} eV" file output/dump_056.6015/energy.out -6152.28471852723 eV print "${mindist_metal} Angstroms" file output/dump_056.6015/mindistance.out 2.52298075651944 Angstroms write_dump all cfg output/dump_056.6015/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_056.6015/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:56