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 55.08588204917512*${_u_distance} variable xmax_converted equal 55.08588204917512*1 variable ymin_converted equal -55.08993204377047*${_u_distance} variable ymin_converted equal -55.08993204377047*1 variable ymax_converted equal 55.08993204377047*${_u_distance} variable ymax_converted equal 55.08993204377047*1 variable zmin_converted equal 0.0*${_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 55.0858820491751 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 55.0858820491751 -55.0899320437705 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 55.0858820491751 -55.0899320437705 55.0899320437705 ${zmin_converted} ${zmax_converted} units box region whole block 0 55.0858820491751 -55.0899320437705 55.0899320437705 0 ${zmax_converted} units box region whole block 0 55.0858820491751 -55.0899320437705 55.0899320437705 0 4.04999459534883 units box create_box 2 whole Created orthogonal box = (0 -55.0899 0) to (55.0859 55.0899 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 55.0899320437705 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -4 0 orient y 4 13 0 orient z 0 0 1 lattice fcc 4.04999459534883 orient x 13 -4 0 orient y 4 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.06195 5.06195 4.04999 create_atoms 1 region upper Created 742 atoms create_atoms CPU = 0.000304937 secs group upper type 1 742 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.1206617289309495 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -55.0899320437705 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 4 0 orient y -4 13 0 orient z 0 0 1 lattice fcc 4.04999459534883 orient x 13 4 0 orient y -4 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.06195 5.06195 4.04999 create_atoms 2 region lower Created 742 atoms create_atoms CPU = 0.000179052 secs group lower type 2 742 atoms in group lower displace_atoms lower move -6.1206617289309495 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 14 27 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 = 1460 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 = 14 27 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) = 7.819 | 7.819 | 7.819 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4876.346 0 -4876.346 -1910.1764 329 0 -4889.929 0 -4889.929 -6396.7489 Loop time of 3.94352 on 1 procs for 329 steps with 1460 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4876.34603192 -4889.92898185 -4889.92898185 Force two-norm initial, final = 12.2836 5.82516e-06 Force max component initial, final = 2.72956 1.27764e-06 Final line search alpha, max atom move = 1 1.27764e-06 Iterations, force evaluations = 329 647 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8828 | 3.8828 | 3.8828 | 0.0 | 98.46 Neigh | 0.0050941 | 0.0050941 | 0.0050941 | 0.0 | 0.13 Comm | 0.034553 | 0.034553 | 0.034553 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02106 | | | 0.53 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9430 ave 9430 max 9430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101450 ave 101450 max 101450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101450 Ave neighs/atom = 69.4863 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) = 7.819 | 7.819 | 7.819 Mbytes Step Temp E_pair E_mol TotEng Press Volume 329 0 -4889.929 0 -4889.929 -6396.7489 24580.855 1329 0 -4890.2117 0 -4890.2117 -1404.05 24423.669 Loop time of 11.8482 on 1 procs for 1000 steps with 1460 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4889.92898185 -4890.21169389 -4890.2116939 Force two-norm initial, final = 121.222 0.0133 Force max component initial, final = 93.6261 0.0127412 Final line search alpha, max atom move = 0.96149 0.0122505 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.414 | 11.414 | 11.414 | 0.0 | 96.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.095608 | 0.095608 | 0.095608 | 0.0 | 0.81 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3389 | | | 2.86 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9450 ave 9450 max 9450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101460 ave 101460 max 101460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101460 Ave neighs/atom = 69.4932 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 = 14 27 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) = 7.451 | 7.451 | 7.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4890.2117 0 -4890.2117 -1404.05 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1460 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 | | 1.192e-06 | | |100.00 Nlocal: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9450 ave 9450 max 9450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101504 ave 101504 max 101504 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 = 101504 Ave neighs/atom = 69.5233 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) = 7.451 | 7.451 | 7.451 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 -4890.2117 -4890.2117 54.967851 110.17986 4.0327372 -1404.05 -1404.05 -0.83402372 -4211.2988 -0.01733562 2.5056419 1027.3135 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1460 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: 1460 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9450 ave 9450 max 9450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101504 ave 101504 max 101504 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203008 ave 203008 max 203008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203008 Ave neighs/atom = 139.047 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_034.2055/numatoms.out 1460 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4890.21169389932-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4890.21169389932-1460*${isolated_atom_energy} variable adjusted_pe_metal equal -4890.21169389932-1460*-5.87828410947289e-10 print "${adjusted_pe_metal} eV" file output/dump_034.2055/energy.out -4890.21169304109 eV print "${mindist_metal} Angstroms" file output/dump_034.2055/mindistance.out 2.50564190863414 Angstroms write_dump all cfg output/dump_034.2055/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_034.2055/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15