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 4.05000014603138*${_u_distance} variable lattice_constant_converted equal 4.05000014603138*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 59.79753555007275*${_u_distance} variable xmax_converted equal 59.79753555007275*1 variable ymin_converted equal -59.80158555021878*${_u_distance} variable ymin_converted equal -59.80158555021878*1 variable ymax_converted equal 59.80158555021878*${_u_distance} variable ymax_converted equal 59.80158555021878*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.05000014603138*${_u_distance} variable zmax_converted equal 4.05000014603138*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000014603138 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 59.7975355500728 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7975355500728 -59.8015855502188 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7975355500728 -59.8015855502188 59.8015855502188 ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7975355500728 -59.8015855502188 59.8015855502188 0 ${zmax_converted} units box region whole block 0 59.7975355500728 -59.8015855502188 59.8015855502188 0 4.05000014603138 units box create_box 2 whole Created orthogonal box = (0 -59.8016 0) to (59.7975 59.8016 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 59.8015855502188 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48601 5.48601 4.05 create_atoms 1 region upper Created 874 atoms create_atoms CPU = 0.000248909 secs group upper type 1 874 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.64417037710503 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -59.8015855502188 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48601 5.48601 4.05 create_atoms 2 region lower Created 874 atoms create_atoms CPU = 0.000149012 secs group lower type 2 874 atoms in group lower displace_atoms lower move -6.64417037710503 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_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*4.05000014603138 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500007301569 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 15 29 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1722 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 15 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.577 | 5.577 | 5.577 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5752.4325 0 -5752.4325 -1879.8869 207 0 -5770.3001 0 -5770.3001 -5680.7176 Loop time of 2.76332 on 1 procs for 207 steps with 1722 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 = -5752.43249885 -5770.30009077 -5770.30009077 Force two-norm initial, final = 14.4311 2.94812e-05 Force max component initial, final = 3.3259 5.62363e-06 Final line search alpha, max atom move = 1 5.62363e-06 Iterations, force evaluations = 207 405 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7151 | 2.7151 | 2.7151 | 0.0 | 98.25 Neigh | 0.006804 | 0.006804 | 0.006804 | 0.0 | 0.25 Comm | 0.025279 | 0.025279 | 0.025279 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01615 | | | 0.58 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10868 ave 10868 max 10868 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: 242076 ave 242076 max 242076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242076 Ave neighs/atom = 140.578 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) = 5.577 | 5.577 | 5.577 Mbytes Step Temp E_pair E_mol TotEng Press Volume 207 0 -5770.3001 0 -5770.3001 -5680.7176 28965.499 1207 0 -5770.642 0 -5770.642 -568.7582 28775.362 Loop time of 13.0664 on 1 procs for 1000 steps with 1722 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 = -5770.30009077 -5770.64203783 -5770.64203783 Force two-norm initial, final = 146.726 0.011785 Force max component initial, final = 104.781 0.00956775 Final line search alpha, max atom move = 0.13705 0.00131126 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.559 | 12.559 | 12.559 | 0.0 | 96.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1115 | 0.1115 | 0.1115 | 0.0 | 0.85 Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3956 | | | 3.03 Nlocal: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10883 ave 10883 max 10883 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: 241256 ave 241256 max 241256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241256 Ave neighs/atom = 140.102 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 15 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 5.715 | 5.715 | 5.715 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5770.642 0 -5770.642 -568.7582 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1722 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: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10883 ave 10883 max 10883 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: 241720 ave 241720 max 241720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241720 Ave neighs/atom = 140.372 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) = 5.715 | 5.715 | 5.715 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 -5770.642 -5770.642 59.612248 119.60317 4.0359205 -568.7582 -568.7582 0.039518918 -1706.845 0.53086849 2.5768651 1193.8367 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1722 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: 1722 ave 1722 max 1722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10883 ave 10883 max 10883 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120860 ave 120860 max 120860 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 241720 ave 241720 max 241720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241720 Ave neighs/atom = 140.372 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.6015/numatoms.out 1722 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5770.64203783409-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5770.64203783409-1722*${isolated_atom_energy} variable adjusted_pe_metal equal -5770.64203783409-1722*0 print "${adjusted_pe_metal} eV" file output/dump_056.6015/energy.out -5770.64203783409 eV print "${mindist_metal} Angstroms" file output/dump_056.6015/mindistance.out 2.57686506711332 Angstroms write_dump all cfg output/dump_056.6015/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_056.6015/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15