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 4.051526293158533*${_u_distance} variable lattice_constant_converted equal 4.051526293158533*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 9.059488204130222*${_u_distance} variable xmax_converted equal 9.059488204130222*1 variable ymin_converted equal -45.30149254694427*${_u_distance} variable ymin_converted equal -45.30149254694427*1 variable ymax_converted equal 45.30149254694427*${_u_distance} variable ymax_converted equal 45.30149254694427*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.051526293158533*${_u_distance} variable zmax_converted equal 4.051526293158533*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05152629315853 Lattice spacing in x,y,z = 4.05153 4.05153 4.05153 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 9.05948820413022 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.05948820413022 -45.3014925469443 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.05948820413022 -45.3014925469443 45.3014925469443 ${zmin_converted} ${zmax_converted} units box region whole block 0 9.05948820413022 -45.3014925469443 45.3014925469443 0 ${zmax_converted} units box region whole block 0 9.05948820413022 -45.3014925469443 45.3014925469443 0 4.05152629315853 units box create_box 2 whole Created orthogonal box = (0 -45.3015 0) to (9.05949 45.3015 4.05153) 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 45.3014925469443 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.43569 5.43569 4.05153 create_atoms 1 region upper Created 102 atoms create_atoms CPU = 0.000210047 secs group upper type 1 102 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.0062305898749053 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.3014925469443 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.43569 5.43569 4.05153 create_atoms 2 region lower Created 102 atoms create_atoms CPU = 8.29697e-05 secs group lower type 2 102 atoms in group lower displace_atoms lower move -1.0062305898749053 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_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*4.05152629315853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02576314657927 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 3 23 2 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 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 196 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 3 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -649.40737 0 -649.40737 6303.8777 260 0 -655.34974 0 -655.34974 -7446.559 Loop time of 0.295005 on 1 procs for 260 steps with 196 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -649.407370125 -655.349737159 -655.349737159 Force two-norm initial, final = 23.5872 7.75176e-06 Force max component initial, final = 9.61294 1.3042e-06 Final line search alpha, max atom move = 1 1.3042e-06 Iterations, force evaluations = 260 513 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28347 | 0.28347 | 0.28347 | 0.0 | 96.09 Neigh | 0.0014353 | 0.0014353 | 0.0014353 | 0.0 | 0.49 Comm | 0.0073249 | 0.0073249 | 0.0073249 | 0.0 | 2.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002778 | | | 0.94 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2924 ave 2924 max 2924 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: 25768 ave 25768 max 25768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25768 Ave neighs/atom = 131.469 Neighbor list builds = 2 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) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press Volume 260 0 -655.34974 0 -655.34974 -7446.559 3325.5603 891 0 -655.39483 0 -655.39483 -1892.6341 3306.3305 Loop time of 0.855701 on 1 procs for 631 steps with 196 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -655.349737159 -655.394833544 -655.394833544 Force two-norm initial, final = 18.7197 2.1418e-05 Force max component initial, final = 15.8234 1.75212e-05 Final line search alpha, max atom move = 1 1.75212e-05 Iterations, force evaluations = 631 1257 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78068 | 0.78068 | 0.78068 | 0.0 | 91.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019014 | 0.019014 | 0.019014 | 0.0 | 2.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05601 | | | 6.55 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889 ave 2889 max 2889 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: 25792 ave 25792 max 25792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25792 Ave neighs/atom = 131.592 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 -9.23201098901316e-12 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 3 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 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) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -655.39483 0 -655.39483 -1892.6341 Loop time of 9.53674e-07 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889 ave 2889 max 2889 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: 25792 ave 25792 max 25792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25792 Ave neighs/atom = 131.592 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) = 4.554 | 4.554 | 4.554 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 -655.39483 -655.39483 9.056609 90.602985 4.0293792 -1892.6341 -1892.6341 -0.0021951627 -5677.9085 0.0084439618 2.6596056 199.04201 Loop time of 9.53674e-07 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889 ave 2889 max 2889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12896 ave 12896 max 12896 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25792 ave 25792 max 25792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25792 Ave neighs/atom = 131.592 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_053.1301/numatoms.out 196 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -655.394833543818-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -655.394833543818-196*${isolated_atom_energy} variable adjusted_pe_metal equal -655.394833543818-196*-9.23201098901316e-12 print "${adjusted_pe_metal} eV" file output/dump_053.1301/energy.out -655.394833542009 eV print "${mindist_metal} Angstroms" file output/dump_053.1301/mindistance.out 2.65960564805679 Angstroms write_dump all cfg output/dump_053.1301/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_053.1301/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01