LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.039798453450203*${_u_distance} variable lattice_constant_converted equal 4.039798453450203*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 4.039798453450203*${_u_distance} variable xmax_converted equal 4.039798453450203*1 variable ymin_converted equal -40.40202433295548*${_u_distance} variable ymin_converted equal -40.40202433295548*1 variable ymax_converted equal 40.40202433295548*${_u_distance} variable ymax_converted equal 40.40202433295548*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.039798453450203*${_u_distance} variable zmax_converted equal 4.039798453450203*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0397984534502 Lattice spacing in x,y,z = 4.0398 4.0398 4.0398 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 4.0397984534502 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 4.0397984534502 -40.4020243329555 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 4.0397984534502 -40.4020243329555 40.4020243329555 ${zmin_converted} ${zmax_converted} units box region whole block 0 4.0397984534502 -40.4020243329555 40.4020243329555 0 ${zmax_converted} units box region whole block 0 4.0397984534502 -40.4020243329555 40.4020243329555 0 4.0397984534502 units box create_box 2 whole Created orthogonal box = (0 -40.402 0) to (4.0398 40.402 4.0398) 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 40.4020243329555 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.0398 4.0398 4.0398 create_atoms 1 region upper Created 42 atoms create_atoms CPU = 0.000159979 secs group upper type 1 42 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 0.45 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -40.4020243329555 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.0398 4.0398 4.0398 create_atoms 2 region lower Created 42 atoms create_atoms CPU = 2.59876e-05 secs group lower type 2 42 atoms in group lower displace_atoms lower move -0.45 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Al__MO_279544746097_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.0397984534502 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0198992267251 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 1 14 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 80 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 1 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -225.82301 0 -225.82301 9044.5278 136 0 -231.06728 0 -231.06728 -76.607368 Loop time of 0.484353 on 1 procs for 136 steps with 80 atoms 51.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -225.823009572 -231.067280038 -231.067280038 Force two-norm initial, final = 11.3754 5.16042e-06 Force max component initial, final = 3.71717 1.15659e-06 Final line search alpha, max atom move = 1 1.15659e-06 Iterations, force evaluations = 136 269 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47592 | 0.47592 | 0.47592 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0068879 | 0.0068879 | 0.0068879 | 0.0 | 1.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001547 | | | 0.32 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4561 ave 4561 max 4561 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: 34152 ave 34152 max 34152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34152 Ave neighs/atom = 426.9 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) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 136 0 -231.06728 0 -231.06728 -76.607368 1318.7198 383 0 -231.06728 0 -231.06728 -13.256103 1318.6107 Loop time of 0.972811 on 1 procs for 247 steps with 80 atoms 50.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -231.067280038 -231.067282326 -231.067282326 Force two-norm initial, final = 0.0782603 5.12532e-12 Force max component initial, final = 0.0553384 4.15507e-12 Final line search alpha, max atom move = 1 4.15507e-12 Iterations, force evaluations = 247 494 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86088 | 0.86088 | 0.86088 | 0.0 | 88.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.031599 | 0.031599 | 0.031599 | 0.0 | 3.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08034 | | | 8.26 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4229 ave 4229 max 4229 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: 34240 ave 34240 max 34240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34240 Ave neighs/atom = 428 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 1 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -231.06728 0 -231.06728 -13.256103 Loop time of 0 on 1 procs for 0 steps with 80 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 | | 0 | | | 0.00 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4229 ave 4229 max 4229 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: 34240 ave 34240 max 34240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34240 Ave neighs/atom = 428 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:52) Per MPI rank memory allocation (min/avg/max) = 4.598 | 4.598 | 4.598 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 -231.06728 -231.06728 4.0396314 80.804049 4.0396314 -13.256103 -13.256103 2.2489901e-09 -39.768309 -5.0484005e-09 2.8564508 3.0266227e-24 Loop time of 1.90735e-06 on 1 procs for 0 steps with 80 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 | | 1.907e-06 | | |100.00 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4229 ave 4229 max 4229 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17120 ave 17120 max 17120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34240 ave 34240 max 34240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34240 Ave neighs/atom = 428 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_000.0000/numatoms.out 80 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -231.067282326443-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -231.067282326443-80*${isolated_atom_energy} variable adjusted_pe_metal equal -231.067282326443-80*0 print "${adjusted_pe_metal} eV" file output/dump_000.0000/energy.out -231.067282326443 eV print "${mindist_metal} Angstroms" file output/dump_000.0000/mindistance.out 2.85645076047734 Angstroms write_dump all cfg output/dump_000.0000/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_000.0000/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01