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 4.049763545393944*${_u_distance} variable lattice_constant_converted equal 4.049763545393944*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 72.10398999522666*${_u_distance} variable xmax_converted equal 72.10398999522666*1 variable ymin_converted equal -72.10803975877205*${_u_distance} variable ymin_converted equal -72.10803975877205*1 variable ymax_converted equal 72.10803975877205*${_u_distance} variable ymax_converted equal 72.10803975877205*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049763545393944*${_u_distance} variable zmax_converted equal 4.049763545393944*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04976354539394 Lattice spacing in x,y,z = 4.04976 4.04976 4.04976 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 72.1039899952267 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 72.1039899952267 -72.1080397587721 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 72.1039899952267 -72.1080397587721 72.1080397587721 ${zmin_converted} ${zmax_converted} units box region whole block 0 72.1039899952267 -72.1080397587721 72.1080397587721 0 ${zmax_converted} units box region whole block 0 72.1039899952267 -72.1080397587721 72.1080397587721 0 4.04976354539394 units box create_box 2 whole Created orthogonal box = (0 -72.108 0) to (72.104 72.108 4.04976) 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 72.1080397587721 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -11 0 orient y 11 14 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 14 -11 0 orient y 11 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68643 5.68643 4.04976 create_atoms 1 region upper Created 1270 atoms create_atoms CPU = 0.000458956 secs group upper type 1 1270 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.012022216644183 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -72.1080397587721 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 11 0 orient y -11 14 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 14 11 0 orient y -11 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68643 5.68643 4.04976 create_atoms 2 region lower Created 1270 atoms create_atoms CPU = 0.000368118 secs group lower type 2 1270 atoms in group lower displace_atoms lower move -8.012022216644183 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_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*4.04976354539394 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02488177269697 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 17 34 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 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2514 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 17 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.42 | 10.42 | 10.42 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8301.907 0 -8301.907 1342.4826 106 0 -8329.6713 0 -8329.6713 -4301.6347 Loop time of 2.30497 on 1 procs for 106 steps with 2514 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -8301.90702259 -8329.67130414 -8329.67130414 Force two-norm initial, final = 28.8932 0.0339305 Force max component initial, final = 4.83401 0.00488843 Final line search alpha, max atom move = 7.62939e-06 3.72958e-08 Iterations, force evaluations = 106 236 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2633 | 2.2633 | 2.2633 | 0.0 | 98.19 Neigh | 0.01041 | 0.01041 | 0.01041 | 0.0 | 0.45 Comm | 0.019533 | 0.019533 | 0.019533 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01169 | | | 0.51 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14944 ave 14944 max 14944 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: 432324 ave 432324 max 432324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432324 Ave neighs/atom = 171.967 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) = 10.42 | 10.42 | 10.42 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -8329.6713 0 -8329.6713 -4301.6347 42111.688 112 0 -8329.8819 0 -8329.8819 -991.08778 41927.581 Loop time of 0.428448 on 1 procs for 6 steps with 2514 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -8329.67130414 -8329.88186453 -8329.88186453 Force two-norm initial, final = 132.554 0.183104 Force max component initial, final = 96.5307 0.131935 Final line search alpha, max atom move = 2.33729e-07 3.08369e-08 Iterations, force evaluations = 6 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41424 | 0.41424 | 0.41424 | 0.0 | 96.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032721 | 0.0032721 | 0.0032721 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01094 | | | 2.55 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14946 ave 14946 max 14946 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: 433708 ave 433708 max 433708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 433708 Ave neighs/atom = 172.517 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 17 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 9.929 | 9.929 | 9.929 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8329.8819 0 -8329.8819 -991.08778 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2514 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: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14946 ave 14946 max 14946 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: 434308 ave 434308 max 434308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434308 Ave neighs/atom = 172.756 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) = 9.929 | 9.929 | 9.929 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 -8329.8819 -8329.8819 72.031447 144.21608 4.0361192 -991.08778 -991.08778 3.7639284 -2982.0519 5.0246257 2.5279791 641.13449 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2514 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 | | 2.146e-06 | | |100.00 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14946 ave 14946 max 14946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 217154 ave 217154 max 217154 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 434308 ave 434308 max 434308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434308 Ave neighs/atom = 172.756 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_076.3145/numatoms.out 2514 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8329.88186453375-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8329.88186453375-2514*${isolated_atom_energy} variable adjusted_pe_metal equal -8329.88186453375-2514*0 print "${adjusted_pe_metal} eV" file output/dump_076.3145/energy.out -8329.88186453375 eV print "${mindist_metal} Angstroms" file output/dump_076.3145/mindistance.out 2.52797906636656 Angstroms write_dump all cfg output/dump_076.3145/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_076.3145/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02