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 4.024845376610756*${_u_distance} variable lattice_constant_converted equal 4.024845376610756*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 39.64012978845583*${_u_distance} variable xmax_converted equal 39.64012978845583*1 variable ymin_converted equal -79.28428442228827*${_u_distance} variable ymin_converted equal -79.28428442228827*1 variable ymax_converted equal 79.28428442228827*${_u_distance} variable ymax_converted equal 79.28428442228827*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.024845376610756*${_u_distance} variable zmax_converted equal 4.024845376610756*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.02484537661076 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 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 39.6401297884558 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.6401297884558 -79.2842844222883 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.6401297884558 -79.2842844222883 79.2842844222883 ${zmin_converted} ${zmax_converted} units box region whole block 0 39.6401297884558 -79.2842844222883 79.2842844222883 0 ${zmax_converted} units box region whole block 0 39.6401297884558 -79.2842844222883 79.2842844222883 0 4.02484537661076 units box create_box 2 whole Created orthogonal box = (0 -79.2843 0) to (39.6401 79.2843 4.02485) 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 79.2842844222883 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -4 0 orient y 4 9 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 9 -4 0 orient y 4 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.31259 5.31259 4.02485 create_atoms 1 region upper Created 778 atoms create_atoms CPU = 0.000336885 secs group upper type 1 778 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.431986010808247 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -79.2842844222883 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 4 0 orient y -4 9 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 9 4 0 orient y -4 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.31259 5.31259 4.02485 create_atoms 2 region lower Created 778 atoms create_atoms CPU = 0.000195026 secs group lower type 2 778 atoms in group lower displace_atoms lower move -4.431986010808247 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_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*4.02484537661076 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01242268830538 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 38 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1542 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 38 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.556 | 5.556 | 5.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4049.975 0 -4049.975 490.75943 428 0 -4069.7826 0 -4069.7826 -1138.2811 Loop time of 4.58801 on 1 procs for 428 steps with 1542 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 = -4049.97495226 -4069.78262169 -4069.78262169 Force two-norm initial, final = 19.8209 5.95651e-06 Force max component initial, final = 3.96734 6.40293e-07 Final line search alpha, max atom move = 1 6.40293e-07 Iterations, force evaluations = 428 850 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5045 | 4.5045 | 4.5045 | 0.0 | 98.18 Neigh | 0.0043371 | 0.0043371 | 0.0043371 | 0.0 | 0.09 Comm | 0.050264 | 0.050264 | 0.050264 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02887 | | | 0.63 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10553 ave 10553 max 10553 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: 215500 ave 215500 max 215500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215500 Ave neighs/atom = 139.754 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) = 5.556 | 5.556 | 5.556 Mbytes Step Temp E_pair E_mol TotEng Press Volume 428 0 -4069.7826 0 -4069.7826 -1138.2811 25298.885 1428 0 -4069.812 0 -4069.812 378.63896 25250.079 Loop time of 10.8216 on 1 procs for 1000 steps with 1542 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4069.78262169 -4069.81203404 -4069.81203405 Force two-norm initial, final = 38.3234 0.0046382 Force max component initial, final = 31.9735 0.00338621 Final line search alpha, max atom move = 0.130197 0.000440876 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.346 | 10.346 | 10.346 | 0.0 | 95.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10743 | 0.10743 | 0.10743 | 0.0 | 0.99 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3678 | | | 3.40 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10538 ave 10538 max 10538 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: 215432 ave 215432 max 215432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215432 Ave neighs/atom = 139.709 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 -0.0307342631051472 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 38 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.694 | 5.694 | 5.694 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4069.812 0 -4069.812 378.63896 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1542 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: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10538 ave 10538 max 10538 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: 215456 ave 215456 max 215456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215456 Ave neighs/atom = 139.725 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) = 5.694 | 5.694 | 5.694 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 -4069.812 -4069.812 39.62908 158.56857 4.0182009 378.63896 378.63896 -0.072821926 1136.2042 -0.21450844 2.5230989 745.70625 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1542 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: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10538 ave 10538 max 10538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107728 ave 107728 max 107728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 215456 ave 215456 max 215456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215456 Ave neighs/atom = 139.725 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_047.9250/numatoms.out 1542 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4069.81203404609-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4069.81203404609-1542*${isolated_atom_energy} variable adjusted_pe_metal equal -4069.81203404609-1542*-0.0307342631051472 print "${adjusted_pe_metal} eV" file output/dump_047.9250/energy.out -4022.41980033795 eV print "${mindist_metal} Angstroms" file output/dump_047.9250/mindistance.out 2.52309885432635 Angstroms write_dump all cfg output/dump_047.9250/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_047.9250/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15