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 4.049994595348835*${_u_distance} variable lattice_constant_converted equal 4.049994595348835*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 52.649929739534855*${_u_distance} variable xmax_converted equal 52.649929739534855*1 variable ymin_converted equal -52.6539797341302*${_u_distance} variable ymin_converted equal -52.6539797341302*1 variable ymax_converted equal 52.6539797341302*${_u_distance} variable ymax_converted equal 52.6539797341302*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049994595348835*${_u_distance} variable zmax_converted equal 4.049994595348835*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999459534883 Lattice spacing in x,y,z = 4.04999 4.04999 4.04999 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 52.6499297395349 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6499297395349 -52.6539797341302 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6499297395349 -52.6539797341302 52.6539797341302 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6499297395349 -52.6539797341302 52.6539797341302 0 ${zmax_converted} units box region whole block 0 52.6499297395349 -52.6539797341302 52.6539797341302 0 4.04999459534883 units box create_box 2 whole Created orthogonal box = (0 -52.654 0) to (52.6499 52.654 4.04999) 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 52.6539797341302 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -5 0 orient y 5 12 0 orient z 0 0 1 lattice fcc 4.04999459534883 orient x 12 -5 0 orient y 5 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29615 5.29615 4.04999 create_atoms 1 region upper Created 678 atoms create_atoms CPU = 0.000221968 secs group upper type 1 678 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.85 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -52.6539797341302 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 5 0 orient y -5 12 0 orient z 0 0 1 lattice fcc 4.04999459534883 orient x 12 5 0 orient y -5 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29615 5.29615 4.04999 create_atoms 2 region lower Created 678 atoms create_atoms CPU = 0.00011301 secs group lower type 2 678 atoms in group lower displace_atoms lower move -5.85 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style adp pair_coeff * * ./SM_667696763561_000-files/b'AlCu.adp' Al Al Reading potential file ./SM_667696763561_000-files/b'AlCu.adp' with DATE: 2011-06-20 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*4.04999459534883 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499729767441 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Deleted 24 atoms, new total = 1332 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual 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) = 7.396 | 7.396 | 7.396 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4443.1471 0 -4443.1471 -1942.8141 265 0 -4459.4993 0 -4459.4993 -6430.0067 Loop time of 2.76541 on 1 procs for 265 steps with 1332 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 = -4443.14707202 -4459.49927499 -4459.49927499 Force two-norm initial, final = 13.9668 2.41166e-05 Force max component initial, final = 2.89147 6.18186e-06 Final line search alpha, max atom move = 1 6.18186e-06 Iterations, force evaluations = 265 521 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7204 | 2.7204 | 2.7204 | 0.0 | 98.37 Neigh | 0.0047362 | 0.0047362 | 0.0047362 | 0.0 | 0.17 Comm | 0.025389 | 0.025389 | 0.025389 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01487 | | | 0.54 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8783 ave 8783 max 8783 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92470 ave 92470 max 92470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92470 Ave neighs/atom = 69.4219 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) = 7.396 | 7.396 | 7.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 265 0 -4459.4993 0 -4459.4993 -6430.0067 22455.02 1265 0 -4459.8204 0 -4459.8204 -813.22368 22292.594 Loop time of 10.4812 on 1 procs for 1000 steps with 1332 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 = -4459.49927499 -4459.82038344 -4459.82038351 Force two-norm initial, final = 124.575 0.0462613 Force max component initial, final = 91.3381 0.0385934 Final line search alpha, max atom move = 0.155104 0.00598599 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.093 | 10.093 | 10.093 | 0.0 | 96.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.086819 | 0.086819 | 0.086819 | 0.0 | 0.83 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3014 | | | 2.88 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8783 ave 8783 max 8783 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92488 ave 92488 max 92488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92488 Ave neighs/atom = 69.4354 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 -5.87828410947289e-10 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton 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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 7.027 | 7.027 | 7.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4459.8204 0 -4459.8204 -813.22368 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1332 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: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8788 ave 8788 max 8788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92506 ave 92506 max 92506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92506 Ave neighs/atom = 69.4489 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) = 7.027 | 7.027 | 7.027 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 -4459.8204 -4459.8204 52.484841 105.30796 4.0333463 -813.22368 -813.22368 1.7355309 -2444.1689 2.7623185 2.4896321 1070.9151 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1332 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: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8788 ave 8788 max 8788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92506 ave 92506 max 92506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 185012 ave 185012 max 185012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185012 Ave neighs/atom = 138.898 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_045.2397/numatoms.out 1332 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4459.82038350985-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4459.82038350985-1332*${isolated_atom_energy} variable adjusted_pe_metal equal -4459.82038350985-1332*-5.87828410947289e-10 print "${adjusted_pe_metal} eV" file output/dump_045.2397/energy.out -4459.82038272686 eV print "${mindist_metal} Angstroms" file output/dump_045.2397/mindistance.out 2.48963207326325 Angstroms write_dump all cfg output/dump_045.2397/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_045.2397/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:13