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 71.65171873442425*${_u_distance} variable xmax_converted equal 71.65171873442425*1 variable ymin_converted equal -71.6557687290196*${_u_distance} variable ymin_converted equal -71.6557687290196*1 variable ymax_converted equal 71.6557687290196*${_u_distance} variable ymax_converted equal 71.6557687290196*1 variable zmin_converted equal 0.0*${_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 71.6517187344243 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 71.6517187344243 -71.6557687290196 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 71.6517187344243 -71.6557687290196 71.6557687290196 ${zmin_converted} ${zmax_converted} units box region whole block 0 71.6517187344243 -71.6557687290196 71.6557687290196 0 ${zmax_converted} units box region whole block 0 71.6517187344243 -71.6557687290196 71.6557687290196 0 4.04999459534883 units box create_box 2 whole Created orthogonal box = (0 -71.6558 0) to (71.6517 71.6558 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 71.6557687290196 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -12 0 orient y 12 13 0 orient z 0 0 1 lattice fcc 4.04999459534883 orient x 13 -12 0 orient y 12 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72298 5.72298 4.04999 create_atoms 1 region upper Created 1254 atoms create_atoms CPU = 0.00031805 secs group upper type 1 1254 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.96131270582936 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -71.6557687290196 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 12 0 orient y -12 13 0 orient z 0 0 1 lattice fcc 4.04999459534883 orient x 13 12 0 orient y -12 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72298 5.72298 4.04999 create_atoms 2 region lower Created 1254 atoms create_atoms CPU = 0.000216007 secs group lower type 2 1254 atoms in group lower displace_atoms lower move -7.96131270582936 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 18 35 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 32 atoms, new total = 2476 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 = 18 35 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) = 14.57 | 14.57 | 14.57 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8277.0782 0 -8277.0782 -1583.8278 289 0 -8305.6199 0 -8305.6199 -7381.8135 Loop time of 5.65338 on 1 procs for 289 steps with 2476 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 = -8277.07822349 -8305.61992152 -8305.61992152 Force two-norm initial, final = 14.8939 3.23148e-05 Force max component initial, final = 2.56172 3.66548e-06 Final line search alpha, max atom move = 1 3.66548e-06 Iterations, force evaluations = 289 562 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.572 | 5.572 | 5.572 | 0.0 | 98.56 Neigh | 0.004169 | 0.004169 | 0.004169 | 0.0 | 0.07 Comm | 0.047997 | 0.047997 | 0.047997 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02926 | | | 0.52 Nlocal: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14558 ave 14558 max 14558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 172950 ave 172950 max 172950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172950 Ave neighs/atom = 69.8506 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) = 14.58 | 14.58 | 14.58 Mbytes Step Temp E_pair E_mol TotEng Press Volume 289 0 -8305.6199 0 -8305.6199 -7381.8135 41587.442 1289 0 -8306.0568 0 -8306.0568 -2567.7024 41331.48 Loop time of 21.0162 on 1 procs for 1000 steps with 2476 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 = -8305.61992152 -8306.0568262 -8306.05682751 Force two-norm initial, final = 199.368 0.158463 Force max component initial, final = 145.01 0.135654 Final line search alpha, max atom move = 0.00397186 0.0005388 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.32 | 20.32 | 20.32 | 0.0 | 96.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15092 | 0.15092 | 0.15092 | 0.0 | 0.72 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5452 | | | 2.59 Nlocal: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14551 ave 14551 max 14551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173100 ave 173100 max 173100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173100 Ave neighs/atom = 69.9111 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 = 18 35 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) = 13.46 | 13.46 | 13.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8306.0568 0 -8306.0568 -2567.7024 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2476 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: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14571 ave 14571 max 14571 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173162 ave 173162 max 173162 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 = 173162 Ave neighs/atom = 69.9362 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) = 13.46 | 13.46 | 13.46 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 -8306.0568 -8306.0568 71.459082 143.31154 4.0359183 -2567.7024 -2567.7024 -5.2443713 -7700.7431 2.8802794 2.6176991 270.61489 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2476 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: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14571 ave 14571 max 14571 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173162 ave 173162 max 173162 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346324 ave 346324 max 346324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346324 Ave neighs/atom = 139.872 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.4188/numatoms.out 2476 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8306.05682750779-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8306.05682750779-2476*${isolated_atom_energy} variable adjusted_pe_metal equal -8306.05682750779-2476*-5.87828410947289e-10 print "${adjusted_pe_metal} eV" file output/dump_085.4188/energy.out -8306.05682605233 eV print "${mindist_metal} Angstroms" file output/dump_085.4188/mindistance.out 2.6176991193191 Angstroms write_dump all cfg output/dump_085.4188/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_085.4188/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:26