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 4.050010219216347*${_u_distance} variable lattice_constant_converted equal 4.050010219216347*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 56.41011485980885*${_u_distance} variable xmax_converted equal 56.41011485980885*1 variable ymin_converted equal -56.41416487002807*${_u_distance} variable ymin_converted equal -56.41416487002807*1 variable ymax_converted equal 56.41416487002807*${_u_distance} variable ymax_converted equal 56.41416487002807*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050010219216347*${_u_distance} variable zmax_converted equal 4.050010219216347*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05001021921635 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 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 56.4101148598088 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.4101148598088 -56.4141648700281 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.4101148598088 -56.4141648700281 56.4141648700281 ${zmin_converted} ${zmax_converted} units box region whole block 0 56.4101148598088 -56.4141648700281 56.4141648700281 0 ${zmax_converted} units box region whole block 0 56.4101148598088 -56.4141648700281 56.4141648700281 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -56.4142 0) to (56.4101 56.4142 4.05001) 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 56.4141648700281 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -5 0 orient y 5 13 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 13 -5 0 orient y 5 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.23393 5.23393 4.05001 create_atoms 1 region upper Created 778 atoms create_atoms CPU = 0.000349998 secs group upper type 1 778 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.267774724732854 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -56.4141648700281 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 5 0 orient y -5 13 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 13 5 0 orient y -5 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.23393 5.23393 4.05001 create_atoms 2 region lower Created 778 atoms create_atoms CPU = 0.000207901 secs group lower type 2 778 atoms in group lower displace_atoms lower move -6.267774724732854 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_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*4.05001021921635 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500510960818 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 15 30 2 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1530 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 15 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.49 | 5.49 | 5.49 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5149.2806 0 -5149.2806 880.22792 244 0 -5167.2527 0 -5167.2527 -5616.9889 Loop time of 1.63212 on 1 procs for 244 steps with 1530 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 = -5149.28060798 -5167.25267012 -5167.25267012 Force two-norm initial, final = 24.7429 1.1839e-05 Force max component initial, final = 5.61792 2.45498e-06 Final line search alpha, max atom move = 1 2.45498e-06 Iterations, force evaluations = 244 474 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5862 | 1.5862 | 1.5862 | 0.0 | 97.19 Neigh | 0.007128 | 0.007128 | 0.007128 | 0.0 | 0.44 Comm | 0.023623 | 0.023623 | 0.023623 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01513 | | | 0.93 Nlocal: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9430 ave 9430 max 9430 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: 160332 ave 160332 max 160332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160332 Ave neighs/atom = 104.792 Neighbor list builds = 2 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) = 5.49 | 5.49 | 5.49 Mbytes Step Temp E_pair E_mol TotEng Press Volume 244 0 -5167.2527 0 -5167.2527 -5616.9889 25776.934 1244 0 -5167.518 0 -5167.518 -858.93558 25612.342 Loop time of 7.31912 on 1 procs for 1000 steps with 1530 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 = -5167.25267012 -5167.5179565 -5167.51795653 Force two-norm initial, final = 116.719 0.0109456 Force max component initial, final = 83.4686 0.00416337 Final line search alpha, max atom move = 0.0313162 0.000130381 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8843 | 6.8843 | 6.8843 | 0.0 | 94.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.094657 | 0.094657 | 0.094657 | 0.0 | 1.29 Output | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3402 | | | 4.65 Nlocal: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9425 ave 9425 max 9425 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: 157784 ave 157784 max 157784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157784 Ave neighs/atom = 103.127 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 15 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.246 | 5.246 | 5.246 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5167.518 0 -5167.518 -858.93558 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1530 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: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9435 ave 9435 max 9435 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: 175820 ave 175820 max 175820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175820 Ave neighs/atom = 114.915 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) = 5.246 | 5.246 | 5.246 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 -5167.518 -5167.518 56.263789 112.82833 4.0346155 -858.93558 -858.93558 0.16429913 -2577.2305 0.25944903 2.5619994 995.42313 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1530 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: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9435 ave 9435 max 9435 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87910 ave 87910 max 87910 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 175820 ave 175820 max 175820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175820 Ave neighs/atom = 114.915 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_042.0750/numatoms.out 1530 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5167.51795653127-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5167.51795653127-1530*${isolated_atom_energy} variable adjusted_pe_metal equal -5167.51795653127-1530*0 print "${adjusted_pe_metal} eV" file output/dump_042.0750/energy.out -5167.51795653127 eV print "${mindist_metal} Angstroms" file output/dump_042.0750/mindistance.out 2.56199942792777 Angstroms write_dump all cfg output/dump_042.0750/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_042.0750/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09