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 4.03330184519291*${_u_distance} variable lattice_constant_converted equal 4.03330184519291*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 44.54927497144322*${_u_distance} variable xmax_converted equal 44.54927497144322*1 variable ymin_converted equal -44.55330827328841*${_u_distance} variable ymin_converted equal -44.55330827328841*1 variable ymax_converted equal 44.55330827328841*${_u_distance} variable ymax_converted equal 44.55330827328841*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.03330184519291*${_u_distance} variable zmax_converted equal 4.03330184519291*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03330184519291 Lattice spacing in x,y,z = 4.0333 4.0333 4.0333 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 44.5492749714432 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 44.5492749714432 -44.5533082732884 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 44.5492749714432 -44.5533082732884 44.5533082732884 ${zmin_converted} ${zmax_converted} units box region whole block 0 44.5492749714432 -44.5533082732884 44.5533082732884 0 ${zmax_converted} units box region whole block 0 44.5492749714432 -44.5533082732884 44.5533082732884 0 4.03330184519291 units box create_box 2 whole Created orthogonal box = (0 -44.5533 0) to (44.5493 44.5533 4.0333) 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 44.5533082732884 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -1 0 orient y 1 11 0 orient z 0 0 1 lattice fcc 4.03330184519291 orient x 11 -1 0 orient y 1 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.3819 4.3819 4.0333 create_atoms 1 region upper Created 489 atoms create_atoms CPU = 0.000244856 secs group upper type 1 489 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.970412457734268 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -44.5533082732884 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 1 0 orient y -1 11 0 orient z 0 0 1 lattice fcc 4.03330184519291 orient x 11 1 0 orient y -1 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.3819 4.3819 4.0333 create_atoms 2 region lower Created 489 atoms create_atoms CPU = 0.000102997 secs group lower type 2 489 atoms in group lower displace_atoms lower move -4.970412457734268 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_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*4.03330184519291 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01665092259646 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 17 atoms, new total = 961 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.002 | 5.002 | 5.002 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3215.1253 0 -3215.1253 338.01174 241 0 -3227.7457 0 -3227.7457 -6485.6196 Loop time of 1.76372 on 1 procs for 241 steps with 961 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 = -3215.1253455 -3227.74572217 -3227.74572217 Force two-norm initial, final = 21.1241 1.12823e-06 Force max component initial, final = 6.99264 2.08827e-07 Final line search alpha, max atom move = 1 2.08827e-07 Iterations, force evaluations = 241 479 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7309 | 1.7309 | 1.7309 | 0.0 | 98.14 Neigh | 0.003912 | 0.003912 | 0.003912 | 0.0 | 0.22 Comm | 0.018061 | 0.018061 | 0.018061 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01081 | | | 0.61 Nlocal: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6959 ave 6959 max 6959 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: 137514 ave 137514 max 137514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137514 Ave neighs/atom = 143.095 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) = 5.003 | 5.003 | 5.003 Mbytes Step Temp E_pair E_mol TotEng Press Volume 241 0 -3227.7457 0 -3227.7457 -6485.6196 16010.737 1241 0 -3227.934 0 -3227.934 -1586.0812 15909.827 Loop time of 7.78224 on 1 procs for 1000 steps with 961 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 = -3227.74572217 -3227.93397477 -3227.93397481 Force two-norm initial, final = 78.7618 0.0205772 Force max component initial, final = 63.2881 0.0180104 Final line search alpha, max atom move = 0.0523578 0.000942987 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.4573 | 7.4573 | 7.4573 | 0.0 | 95.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.072841 | 0.072841 | 0.072841 | 0.0 | 0.94 Output | 3.6001e-05 | 3.6001e-05 | 3.6001e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2521 | | | 3.24 Nlocal: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6954 ave 6954 max 6954 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: 137246 ave 137246 max 137246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137246 Ave neighs/atom = 142.816 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.141 | 5.141 | 5.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3227.934 0 -3227.934 -1586.0812 Loop time of 9.53674e-07 on 1 procs for 0 steps with 961 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: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6954 ave 6954 max 6954 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: 138332 ave 138332 max 138332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138332 Ave neighs/atom = 143.946 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) = 5.141 | 5.141 | 5.141 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 -3227.934 -3227.934 44.474337 89.106617 4.0146347 -1586.0812 -1586.0812 -1.8106637 -4756.9149 0.48190629 2.5594093 402.42072 Loop time of 9.53674e-07 on 1 procs for 0 steps with 961 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: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6954 ave 6954 max 6954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69166 ave 69166 max 69166 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138332 ave 138332 max 138332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138332 Ave neighs/atom = 143.946 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_010.3889/numatoms.out 961 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3227.93397481107-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3227.93397481107-961*${isolated_atom_energy} variable adjusted_pe_metal equal -3227.93397481107-961*0 print "${adjusted_pe_metal} eV" file output/dump_010.3889/energy.out -3227.93397481107 eV print "${mindist_metal} Angstroms" file output/dump_010.3889/mindistance.out 2.55940932253005 Angstroms write_dump all cfg output/dump_010.3889/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_010.3889/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09