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 66.94411827235*${_u_distance} variable xmax_converted equal 66.94411827235*1 variable ymin_converted equal -66.94819992727862*${_u_distance} variable ymin_converted equal -66.94819992727862*1 variable ymax_converted equal 66.94819992727862*${_u_distance} variable ymax_converted equal 66.94819992727862*1 variable zmin_converted equal 0.0*${_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 66.94411827235 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.94411827235 -66.9481999272786 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.94411827235 -66.9481999272786 66.9481999272786 ${zmin_converted} ${zmax_converted} units box region whole block 0 66.94411827235 -66.9481999272786 66.9481999272786 0 ${zmax_converted} units box region whole block 0 66.94411827235 -66.9481999272786 66.9481999272786 0 4.08165492862463 units box create_box 2 whole Created orthogonal box = (0 -66.9482 0) to (66.9441 66.9482 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 66.9481999272786 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -10 0 orient y 10 13 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 13 -10 0 orient y 10 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72385 5.72385 4.08165 create_atoms 1 region upper Created 1078 atoms create_atoms CPU = 0.000446081 secs group upper type 1 1078 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.380548760085527 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -66.9481999272786 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 10 0 orient y -10 13 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 13 10 0 orient y -10 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72385 5.72385 4.08165 create_atoms 2 region lower Created 1078 atoms create_atoms CPU = 0.000293016 secs group lower type 2 1078 atoms in group lower displace_atoms lower move -7.380548760085527 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 12 23 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 28 atoms, new total = 2128 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 = 12 23 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) = 12.38 | 12.38 | 12.38 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7584.8772 0 -7584.8772 -1477.3776 258 0 -7606.57 0 -7606.57 -7063.3905 Loop time of 13.2207 on 1 procs for 258 steps with 2128 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7584.87722983 -7606.57001011 -7606.57001011 Force two-norm initial, final = 14.9728 9.49995e-06 Force max component initial, final = 3.5077 1.16611e-06 Final line search alpha, max atom move = 1 1.16611e-06 Iterations, force evaluations = 258 489 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.056 | 13.056 | 13.056 | 0.0 | 98.75 Neigh | 0.070463 | 0.070463 | 0.070463 | 0.0 | 0.53 Comm | 0.06766 | 0.06766 | 0.06766 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02691 | | | 0.20 Nlocal: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21798 ave 21798 max 21798 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: 905656 ave 905656 max 905656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 905656 Ave neighs/atom = 425.59 Neighbor list builds = 4 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) = 12.38 | 12.38 | 12.38 Mbytes Step Temp E_pair E_mol TotEng Press Volume 258 0 -7606.57 0 -7606.57 -7063.3905 36586.226 1258 0 -7607.0033 0 -7607.0033 -1517.5088 36367.289 Loop time of 54.0726 on 1 procs for 1000 steps with 2128 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 = -7606.57001011 -7607.00334402 -7607.00334402 Force two-norm initial, final = 198.908 0.00268062 Force max component initial, final = 149.683 0.00267489 Final line search alpha, max atom move = 1 0.00267489 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53.08 | 53.08 | 53.08 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.23964 | 0.23964 | 0.23964 | 0.0 | 0.44 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.7525 | | | 1.39 Nlocal: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21805 ave 21805 max 21805 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: 906100 ave 906100 max 906100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 906100 Ave neighs/atom = 425.799 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 = 12 23 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) = 11.9 | 11.9 | 11.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7607.0033 0 -7607.0033 -1517.5088 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2128 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: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21819 ave 21819 max 21819 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: 906908 ave 906908 max 906908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 906908 Ave neighs/atom = 426.179 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) = 11.9 | 11.9 | 11.9 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 -7607.0033 -7607.0033 66.821018 133.8964 4.0647041 -1517.5088 -1517.5088 0.11762678 -4552.6375 -0.0066223967 2.5683428 589.14703 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2128 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: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21819 ave 21819 max 21819 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 453454 ave 453454 max 453454 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 906908 ave 906908 max 906908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 906908 Ave neighs/atom = 426.179 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_075.1372/numatoms.out 2128 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7607.00334401993-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7607.00334401993-2128*${isolated_atom_energy} variable adjusted_pe_metal equal -7607.00334401993-2128*2.2204e-16 print "${adjusted_pe_metal} eV" file output/dump_075.1372/energy.out -7607.00334401993 eV print "${mindist_metal} Angstroms" file output/dump_075.1372/mindistance.out 2.56834281129704 Angstroms write_dump all cfg output/dump_075.1372/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_075.1372/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:07