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 52.571346416764584*${_u_distance} variable xmax_converted equal 52.571346416764584*1 variable ymin_converted equal -52.57537845497641*${_u_distance} variable ymin_converted equal -52.57537845497641*1 variable ymax_converted equal 52.57537845497641*${_u_distance} variable ymax_converted equal 52.57537845497641*1 variable zmin_converted equal 0.0*${_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 52.5713464167646 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.5713464167646 -52.5753784549764 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.5713464167646 -52.5753784549764 52.5753784549764 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.5713464167646 -52.5753784549764 52.5753784549764 0 ${zmax_converted} units box region whole block 0 52.5713464167646 -52.5753784549764 52.5753784549764 0 4.03203821182251 units box create_box 2 whole Created orthogonal box = (0 -52.5754 0) to (52.5713 52.5754 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 52.5753784549764 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 lattice fcc 4.03203821182251 orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.3294 4.3294 4.03204 create_atoms 1 region upper Created 681 atoms create_atoms CPU = 0.00029397 secs group upper type 1 681 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.867282164682384 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -52.5753784549764 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 lattice fcc 4.03203821182251 orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.3294 4.3294 4.03204 create_atoms 2 region lower Created 681 atoms create_atoms CPU = 0.000139952 secs group lower type 2 681 atoms in group lower displace_atoms lower move -5.867282164682384 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 13 25 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 23 atoms, new total = 1339 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 = 13 25 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) = 5.476 | 5.476 | 5.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4470.9858 0 -4470.9858 204.59257 193 0 -4486.4881 0 -4486.4881 -8012.7682 Loop time of 1.75561 on 1 procs for 193 steps with 1339 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 = -4470.98581303 -4486.48808409 -4486.48808409 Force two-norm initial, final = 18.138 1.24335e-05 Force max component initial, final = 4.706 2.38897e-06 Final line search alpha, max atom move = 1 2.38897e-06 Iterations, force evaluations = 193 380 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7283 | 1.7283 | 1.7283 | 0.0 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017073 | 0.017073 | 0.017073 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0102 | | | 0.58 Nlocal: 1339 ave 1339 max 1339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9001 ave 9001 max 9001 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: 231376 ave 231376 max 231376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231376 Ave neighs/atom = 172.798 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) = 5.483 | 5.483 | 5.483 Mbytes Step Temp E_pair E_mol TotEng Press Volume 193 0 -4486.4881 0 -4486.4881 -8012.7682 22288.772 1193 0 -4486.6816 0 -4486.6816 -3764.4265 22168.538 Loop time of 10.0901 on 1 procs for 1000 steps with 1339 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 = -4486.48808409 -4486.6816489 -4486.6816489 Force two-norm initial, final = 95.8324 0.00554615 Force max component initial, final = 75.7632 0.00469079 Final line search alpha, max atom move = 0.398383 0.00186873 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6653 | 9.6653 | 9.6653 | 0.0 | 95.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.099552 | 0.099552 | 0.099552 | 0.0 | 0.99 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3252 | | | 3.22 Nlocal: 1339 ave 1339 max 1339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9926 ave 9926 max 9926 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: 230442 ave 230442 max 230442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230442 Ave neighs/atom = 172.1 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 = 13 25 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) = 5.621 | 5.621 | 5.621 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4486.6816 0 -4486.6816 -3764.4265 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1339 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: 1339 ave 1339 max 1339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9938 ave 9938 max 9938 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: 230916 ave 230916 max 230916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230916 Ave neighs/atom = 172.454 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) = 5.621 | 5.621 | 5.621 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 -4486.6816 -4486.6816 52.356322 105.15076 4.0267579 -3764.4265 -3764.4265 0.33762839 -11293.591 -0.026426047 2.6337447 338.78952 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1339 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: 1339 ave 1339 max 1339 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9938 ave 9938 max 9938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115458 ave 115458 max 115458 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 230916 ave 230916 max 230916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230916 Ave neighs/atom = 172.454 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_008.7974/numatoms.out 1339 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4486.68164889797-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4486.68164889797-1339*${isolated_atom_energy} variable adjusted_pe_metal equal -4486.68164889797-1339*0 print "${adjusted_pe_metal} eV" file output/dump_008.7974/energy.out -4486.68164889797 eV print "${mindist_metal} Angstroms" file output/dump_008.7974/mindistance.out 2.63374474198111 Angstroms write_dump all cfg output/dump_008.7974/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_008.7974/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11