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 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 14.602478652229673*${_u_distance} variable xmax_converted equal 14.602478652229673*1 variable ymin_converted equal -43.811485955575904*${_u_distance} variable ymin_converted equal -43.811485955575904*1 variable ymax_converted equal 43.811485955575904*${_u_distance} variable ymax_converted equal 43.811485955575904*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 14.6024786522297 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 14.6024786522297 -43.8114859555759 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 14.6024786522297 -43.8114859555759 43.8114859555759 ${zmin_converted} ${zmax_converted} units box region whole block 0 14.6024786522297 -43.8114859555759 43.8114859555759 0 ${zmax_converted} units box region whole block 0 14.6024786522297 -43.8114859555759 43.8114859555759 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -43.8115 0) to (14.6025 43.8115 4.05) 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 43.8114859555759 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 -2 0 orient y 2 3 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 3 -2 0 orient y 2 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.61634 5.61634 4.05 create_atoms 1 region upper Created 158 atoms create_atoms CPU = 0.000211954 secs group upper type 1 158 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.6224980739587953 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -43.8114859555759 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 2 0 orient y -2 3 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 3 2 0 orient y -2 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.61634 5.61634 4.05 create_atoms 2 region lower Created 158 atoms create_atoms CPU = 7.20024e-05 secs group lower type 2 158 atoms in group lower displace_atoms lower move -1.6224980739587953 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_811588957187_000-files/b'library-Al.meam' Al ./SM_811588957187_000-files/b'Al.meam' 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*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 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 10 atoms, new total = 306 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 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) = 10.61 | 10.61 | 10.61 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1016.7285 0 -1016.7285 2912.2991 259 0 -1022.6143 0 -1022.6143 -6291.7282 Loop time of 1.57009 on 1 procs for 259 steps with 306 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 = -1016.72849487 -1022.61425115 -1022.61425115 Force two-norm initial, final = 13.071 7.19118e-06 Force max component initial, final = 3.5538 1.05526e-06 Final line search alpha, max atom move = 1 1.05526e-06 Iterations, force evaluations = 259 514 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5552 | 1.5552 | 1.5552 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0080092 | 0.0080092 | 0.0080092 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006895 | | | 0.44 Nlocal: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2807 ave 2807 max 2807 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11786 ave 11786 max 11786 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23572 ave 23572 max 23572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23572 Ave neighs/atom = 77.0327 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) = 10.61 | 10.61 | 10.61 Mbytes Step Temp E_pair E_mol TotEng Press Volume 259 0 -1022.6143 0 -1022.6143 -6291.7282 5182.0245 1259 0 -1022.672 0 -1022.672 -1608.0884 5148.6653 Loop time of 7.06765 on 1 procs for 1000 steps with 306 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1022.61425115 -1022.67197163 -1022.67197163 Force two-norm initial, final = 24.6732 0.000449535 Force max component initial, final = 18.446 0.000422663 Final line search alpha, max atom move = 1 0.000422663 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9375 | 6.9375 | 6.9375 | 0.0 | 98.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.030276 | 0.030276 | 0.030276 | 0.0 | 0.43 Output | 1.3113e-05 | 1.3113e-05 | 1.3113e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09987 | | | 1.41 Nlocal: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2740 ave 2740 max 2740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11948 ave 11948 max 11948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23896 ave 23896 max 23896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23896 Ave neighs/atom = 78.0915 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 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) = 9.493 | 9.493 | 9.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1022.672 0 -1022.672 -1608.0884 Loop time of 9.53674e-07 on 1 procs for 0 steps with 306 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: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772 ave 2772 max 2772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12222 ave 12222 max 12222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24444 ave 24444 max 24444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24444 Ave neighs/atom = 79.8824 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) = 9.493 | 9.493 | 9.493 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 -1022.672 -1022.672 14.572262 87.622972 4.0322709 -1608.0884 -1608.0884 0.13125342 -4824.4373 0.040805332 2.5404078 229.9737 Loop time of 9.53674e-07 on 1 procs for 0 steps with 306 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: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772 ave 2772 max 2772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12222 ave 12222 max 12222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24444 ave 24444 max 24444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24444 Ave neighs/atom = 79.8824 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_067.3801/numatoms.out 306 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1022.67197162868-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1022.67197162868-306*${isolated_atom_energy} variable adjusted_pe_metal equal -1022.67197162868-306*0 print "${adjusted_pe_metal} eV" file output/dump_067.3801/energy.out -1022.67197162868 eV print "${mindist_metal} Angstroms" file output/dump_067.3801/mindistance.out 2.54040781922451 Angstroms write_dump all cfg output/dump_067.3801/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_067.3801/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:08