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 4.050000011920929*${_u_distance} variable lattice_constant_converted equal 4.050000011920929*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 77.37514158464737*${_u_distance} variable xmax_converted equal 77.37514158464737*1 variable ymin_converted equal -77.37919158465928*${_u_distance} variable ymin_converted equal -77.37919158465928*1 variable ymax_converted equal 77.37919158465928*${_u_distance} variable ymax_converted equal 77.37919158465928*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050000011920929*${_u_distance} variable zmax_converted equal 4.050000011920929*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000001192093 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 77.3751415846474 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.3751415846474 -77.3791915846593 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 77.3751415846474 -77.3791915846593 77.3791915846593 ${zmin_converted} ${zmax_converted} units box region whole block 0 77.3751415846474 -77.3791915846593 77.3791915846593 0 ${zmax_converted} units box region whole block 0 77.3751415846474 -77.3791915846593 77.3791915846593 0 4.05000001192093 units box create_box 2 whole Created orthogonal box = (0 -77.3792 0) to (77.3751 77.3792 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 77.3791915846593 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1 lattice fcc 4.05000001192093 orient x 14 -13 0 orient y 13 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72364 5.72364 4.05 create_atoms 1 region upper Created 1462 atoms create_atoms CPU = 0.000354052 secs group upper type 1 1462 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.59723792854426 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -77.3791915846593 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 13 0 orient y -13 14 0 orient z 0 0 1 lattice fcc 4.05000001192093 orient x 14 13 0 orient y -13 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72364 5.72364 4.05 create_atoms 2 region lower Created 1462 atoms create_atoms CPU = 0.000246048 secs group lower type 2 1462 atoms in group lower displace_atoms lower move -8.59723792854426 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_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*4.05000001192093 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500000596046 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 18 36 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 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2892 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 18 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9679.4338 0 -9679.4338 -1883.1646 214 0 -9705.1447 0 -9705.1447 -5630.7846 Loop time of 4.9085 on 1 procs for 214 steps with 2892 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9679.43384494 -9705.14465704 -9705.14465704 Force two-norm initial, final = 12.2924 2.7577e-05 Force max component initial, final = 2.0825 2.92671e-06 Final line search alpha, max atom move = 1 2.92671e-06 Iterations, force evaluations = 214 415 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8305 | 4.8305 | 4.8305 | 0.0 | 98.41 Neigh | 0.011981 | 0.011981 | 0.011981 | 0.0 | 0.24 Comm | 0.040535 | 0.040535 | 0.040535 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02546 | | | 0.52 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16898 ave 16898 max 16898 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: 500800 ave 500800 max 500800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 500800 Ave neighs/atom = 173.167 Neighbor list builds = 1 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) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press Volume 214 0 -9705.1447 0 -9705.1447 -5630.7846 48496.53 1214 0 -9705.4434 0 -9705.4434 -1942.0804 48267.006 Loop time of 24.3323 on 1 procs for 1000 steps with 2892 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 = -9705.14465704 -9705.4433783 -9705.44337847 Force two-norm initial, final = 177.977 0.0654983 Force max component initial, final = 126.638 0.0365186 Final line search alpha, max atom move = 0.0180082 0.000657634 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.523 | 23.523 | 23.523 | 0.0 | 96.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.17568 | 0.17568 | 0.17568 | 0.0 | 0.72 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.6336 | | | 2.60 Nlocal: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16900 ave 16900 max 16900 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: 502908 ave 502908 max 502908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502908 Ave neighs/atom = 173.896 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 -0.00607941459516994 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 18 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 10.4 | 10.4 | 10.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9705.4434 0 -9705.4434 -1942.0804 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2892 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: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16945 ave 16945 max 16945 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: 503588 ave 503588 max 503588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503588 Ave neighs/atom = 174.131 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) = 10.4 | 10.4 | 10.4 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 -9705.4434 -9705.4434 77.199122 154.75838 4.0400228 -1942.0804 -1942.0804 -0.78305421 -5824.2488 -1.2092147 2.5473398 298.55488 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2892 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: 2892 ave 2892 max 2892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16945 ave 16945 max 16945 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 251794 ave 251794 max 251794 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 503588 ave 503588 max 503588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503588 Ave neighs/atom = 174.131 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.7578/numatoms.out 2892 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9705.4433784708-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9705.4433784708-2892*${isolated_atom_energy} variable adjusted_pe_metal equal -9705.4433784708-2892*-0.00607941459516994 print "${adjusted_pe_metal} eV" file output/dump_085.7578/energy.out -9687.86171146157 eV print "${mindist_metal} Angstroms" file output/dump_085.7578/mindistance.out 2.54733980196022 Angstroms write_dump all cfg output/dump_085.7578/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_085.7578/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:29