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 4.032082897424699*${_u_distance} variable lattice_constant_converted equal 4.032082897424699*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 31.49157414284002*${_u_distance} variable xmax_converted equal 31.49157414284002*1 variable ymin_converted equal -62.98718036857746*${_u_distance} variable ymin_converted equal -62.98718036857746*1 variable ymax_converted equal 62.98718036857746*${_u_distance} variable ymax_converted equal 62.98718036857746*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082897424699*${_u_distance} variable zmax_converted equal 4.032082897424699*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0320828974247 Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 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 31.49157414284 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 31.49157414284 -62.9871803685775 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 31.49157414284 -62.9871803685775 62.9871803685775 ${zmin_converted} ${zmax_converted} units box region whole block 0 31.49157414284 -62.9871803685775 62.9871803685775 0 ${zmax_converted} units box region whole block 0 31.49157414284 -62.9871803685775 62.9871803685775 0 4.0320828974247 units box create_box 2 whole Created orthogonal box = (0 -62.9872 0) to (31.4916 62.9872 4.03208) 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 62.9871803685775 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 -5 0 orient y 5 6 0 orient z 0 0 1 lattice fcc 4.0320828974247 orient x 6 -5 0 orient y 5 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67881 5.67881 4.03208 create_atoms 1 region upper Created 490 atoms create_atoms CPU = 0.000285149 secs group upper type 1 490 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.514612354157994 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -62.9871803685775 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 5 0 orient y -5 6 0 orient z 0 0 1 lattice fcc 4.0320828974247 orient x 6 5 0 orient y -5 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67881 5.67881 4.03208 create_atoms 2 region lower Created 490 atoms create_atoms CPU = 0.000149012 secs group lower type 2 490 atoms in group lower displace_atoms lower move -3.514612354157994 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002 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*4.0320828974247 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604144871235 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 9 34 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 962 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.996 | 4.996 | 4.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3214.766 0 -3214.766 -687.43807 249 0 -3223.4008 0 -3223.4008 -7419.6937 Loop time of 1.23896 on 1 procs for 249 steps with 962 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3214.7660211 -3223.40076884 -3223.40076884 Force two-norm initial, final = 11.9471 1.29276e-05 Force max component initial, final = 3.77288 2.46122e-06 Final line search alpha, max atom move = 1 2.46122e-06 Iterations, force evaluations = 249 489 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2078 | 1.2078 | 1.2078 | 0.0 | 97.49 Neigh | 0.0030968 | 0.0030968 | 0.0030968 | 0.0 | 0.25 Comm | 0.017592 | 0.017592 | 0.017592 | 0.0 | 1.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01045 | | | 0.84 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6759 ave 6759 max 6759 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: 104132 ave 104132 max 104132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104132 Ave neighs/atom = 108.245 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) = 4.996 | 4.996 | 4.996 Mbytes Step Temp E_pair E_mol TotEng Press Volume 249 0 -3223.4008 0 -3223.4008 -7419.6937 15995.801 1249 0 -3223.5588 0 -3223.5588 -2843.877 15903.991 Loop time of 5.34803 on 1 procs for 1000 steps with 962 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3223.40076884 -3223.55883168 -3223.55883171 Force two-norm initial, final = 74.8818 0.0124376 Force max component initial, final = 59.4913 0.006489 Final line search alpha, max atom move = 0.0581348 0.000377237 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0543 | 5.0543 | 5.0543 | 0.0 | 94.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.065287 | 0.065287 | 0.065287 | 0.0 | 1.22 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2284 | | | 4.27 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6274 ave 6274 max 6274 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: 103592 ave 103592 max 103592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103592 Ave neighs/atom = 107.684 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 5.129 | 5.129 | 5.129 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3223.5588 0 -3223.5588 -2843.877 Loop time of 9.53674e-07 on 1 procs for 0 steps with 962 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: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6320 ave 6320 max 6320 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: 109392 ave 109392 max 109392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109392 Ave neighs/atom = 113.713 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) = 5.129 | 5.129 | 5.129 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 -3223.5588 -3223.5588 31.372397 125.97436 4.0241694 -2843.877 -2843.877 0.4221467 -8532.7055 0.65242264 2.5876381 255.88791 Loop time of 1.90735e-06 on 1 procs for 0 steps with 962 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: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6320 ave 6320 max 6320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54696 ave 54696 max 54696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109392 ave 109392 max 109392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109392 Ave neighs/atom = 113.713 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_079.6111/numatoms.out 962 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3223.55883170992-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3223.55883170992-962*${isolated_atom_energy} variable adjusted_pe_metal equal -3223.55883170992-962*0 print "${adjusted_pe_metal} eV" file output/dump_079.6111/energy.out -3223.55883170992 eV print "${mindist_metal} Angstroms" file output/dump_079.6111/mindistance.out 2.58763811583924 Angstroms write_dump all cfg output/dump_079.6111/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_079.6111/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06