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 4.0469995588064185*${_u_distance} variable lattice_constant_converted equal 4.0469995588064185*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 5.723321662981968*${_u_distance} variable xmax_converted equal 5.723321662981968*1 variable ymin_converted equal -45.790620303414556*${_u_distance} variable ymin_converted equal -45.790620303414556*1 variable ymax_converted equal 45.790620303414556*${_u_distance} variable ymax_converted equal 45.790620303414556*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.0469995588064185*${_u_distance} variable zmax_converted equal 4.0469995588064185*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04699955880642 Lattice spacing in x,y,z = 4.047 4.047 4.047 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 5.72332166298197 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 5.72332166298197 -45.7906203034146 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 5.72332166298197 -45.7906203034146 45.7906203034146 ${zmin_converted} ${zmax_converted} units box region whole block 0 5.72332166298197 -45.7906203034146 45.7906203034146 0 ${zmax_converted} units box region whole block 0 5.72332166298197 -45.7906203034146 45.7906203034146 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -45.7906 0) to (5.72332 45.7906 4.047) 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 45.7906203034146 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 -1 0 orient y 1 1 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 1 -1 0 orient y 1 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72332 5.72332 4.047 create_atoms 1 region upper Created 66 atoms create_atoms CPU = 0.000144005 secs group upper type 1 66 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 0.6363961030678927 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.7906203034146 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 1 0 orient y -1 1 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 1 1 0 orient y -1 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72332 5.72332 4.047 create_atoms 2 region lower Created 66 atoms create_atoms CPU = 3.38554e-05 secs group lower type 2 66 atoms in group lower displace_atoms lower move -0.6363961030678927 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_871795249052_000-files/b'library.NAlTi' N Al Ti ./SM_871795249052_000-files/b'meam.NAlTi' 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*4.04699955880642 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02349977940321 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 2 26 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 8 atoms, new total = 124 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 2 26 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -411.20433 0 -411.20433 -1792.6282 154 0 -415.56412 0 -415.56412 -22674.035 Loop time of 0.526126 on 1 procs for 154 steps with 124 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -411.204329141 -415.564119594 -415.564119594 Force two-norm initial, final = 3.20089 2.61926e-06 Force max component initial, final = 0.829453 4.99262e-07 Final line search alpha, max atom move = 1 4.99262e-07 Iterations, force evaluations = 154 301 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52187 | 0.52187 | 0.52187 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029147 | 0.0029147 | 0.0029147 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001339 | | | 0.25 Nlocal: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2095 ave 2095 max 2095 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5188 ave 5188 max 5188 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 10376 ave 10376 max 10376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10376 Ave neighs/atom = 83.6774 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) = 10.29 | 10.29 | 10.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 154 0 -415.56412 0 -415.56412 -22674.035 2121.2304 199 0 -415.82189 0 -415.82189 -6952.9338 2076.5521 Loop time of 0.139957 on 1 procs for 45 steps with 124 atoms 92.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -415.564119594 -415.821893913 -415.821893913 Force two-norm initial, final = 33.5289 2.85982e-06 Force max component initial, final = 25.0245 2.6638e-06 Final line search alpha, max atom move = 1 2.6638e-06 Iterations, force evaluations = 45 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13699 | 0.13699 | 0.13699 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077128 | 0.00077128 | 0.00077128 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0022 | | | 1.57 Nlocal: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2144 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5084 ave 5084 max 5084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 10168 ave 10168 max 10168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10168 Ave neighs/atom = 82 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 2 26 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 9.168 | 9.168 | 9.168 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -415.82189 0 -415.82189 -6952.9338 Loop time of 1.19209e-06 on 1 procs for 0 steps with 124 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: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2396 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5084 ave 5084 max 5084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 10168 ave 10168 max 10168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10168 Ave neighs/atom = 82 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) = 9.168 | 9.168 | 9.168 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 -415.82189 -415.82189 5.651735 91.581241 4.0119408 -6952.9338 -6952.9338 -0.0020295623 -20858.799 -0.00074971722 2.8258675 6.4622463e-13 Loop time of 9.53674e-07 on 1 procs for 0 steps with 124 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: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2396 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5084 ave 5084 max 5084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 10168 ave 10168 max 10168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10168 Ave neighs/atom = 82 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_090.0000/numatoms.out 124 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -415.821893912919-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -415.821893912919-124*${isolated_atom_energy} variable adjusted_pe_metal equal -415.821893912919-124*0 print "${adjusted_pe_metal} eV" file output/dump_090.0000/energy.out -415.821893912919 eV print "${mindist_metal} Angstroms" file output/dump_090.0000/mindistance.out 2.82586747622851 Angstroms write_dump all cfg output/dump_090.0000/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_090.0000/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:00