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 37.185205671437465*${_u_distance} variable xmax_converted equal 37.185205671437465*1 variable ymin_converted equal -74.37444464472013*${_u_distance} variable ymin_converted equal -74.37444464472013*1 variable ymax_converted equal 74.37444464472013*${_u_distance} variable ymax_converted equal 74.37444464472013*1 variable zmin_converted equal 0.0*${_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 37.1852056714375 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.1852056714375 -74.3744446447201 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.1852056714375 -74.3744446447201 74.3744446447201 ${zmin_converted} ${zmax_converted} units box region whole block 0 37.1852056714375 -74.3744446447201 74.3744446447201 0 ${zmax_converted} units box region whole block 0 37.1852056714375 -74.3744446447201 74.3744446447201 0 4.03330184519291 units box create_box 2 whole Created orthogonal box = (0 -74.3744 0) to (37.1852 74.3744 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 74.3744446447201 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 lattice fcc 4.03330184519291 orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.8122 4.8122 4.0333 create_atoms 1 region upper Created 681 atoms create_atoms CPU = 0.000237942 secs group upper type 1 681 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.148795005781799 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.3744446447201 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 lattice fcc 4.03330184519291 orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.8122 4.8122 4.0333 create_atoms 2 region lower Created 681 atoms create_atoms CPU = 0.000104904 secs group lower type 2 681 atoms in group lower displace_atoms lower move -4.148795005781799 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 9 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 kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 1351 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 = 9 35 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4522.2778 0 -4522.2778 2652.0375 647 0 -4542.4793 0 -4542.4793 -1097.3932 Loop time of 6.15199 on 1 procs for 647 steps with 1351 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4522.27779574 -4542.47928045 -4542.47928045 Force two-norm initial, final = 29.4351 2.06553e-05 Force max component initial, final = 7.40957 2.79277e-06 Final line search alpha, max atom move = 1 2.79277e-06 Iterations, force evaluations = 647 1276 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0386 | 6.0386 | 6.0386 | 0.0 | 98.16 Neigh | 0.010994 | 0.010994 | 0.010994 | 0.0 | 0.18 Comm | 0.064952 | 0.064952 | 0.064952 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03742 | | | 0.61 Nlocal: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9584 ave 9584 max 9584 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: 190408 ave 190408 max 190408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190408 Ave neighs/atom = 140.939 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press Volume 647 0 -4542.4793 0 -4542.4793 -1097.3932 22309.233 1647 0 -4542.4958 0 -4542.4958 177.86139 22272.896 Loop time of 10.2261 on 1 procs for 1000 steps with 1351 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 = -4542.47928045 -4542.49580604 -4542.49580604 Force two-norm initial, final = 28.3151 0.00854795 Force max component initial, final = 21.2061 0.00749781 Final line search alpha, max atom move = 1 0.00749781 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.794 | 9.794 | 9.794 | 0.0 | 95.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.097891 | 0.097891 | 0.097891 | 0.0 | 0.96 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3342 | | | 3.27 Nlocal: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9569 ave 9569 max 9569 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: 189666 ave 189666 max 189666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189666 Ave neighs/atom = 140.389 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 = 9 35 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) = 5.251 | 5.251 | 5.251 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4542.4958 0 -4542.4958 177.86139 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1351 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: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9584 ave 9584 max 9584 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: 189818 ave 189818 max 189818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189818 Ave neighs/atom = 140.502 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) = 5.251 | 5.251 | 5.251 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 -4542.4958 -4542.4958 37.161149 148.74889 4.0293392 177.86139 177.86139 -0.26083148 534.3838 -0.53881705 2.5424106 633.29155 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1351 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: 1351 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9584 ave 9584 max 9584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94909 ave 94909 max 94909 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 189818 ave 189818 max 189818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189818 Ave neighs/atom = 140.502 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.0576/numatoms.out 1351 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4542.4958060438-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4542.4958060438-1351*${isolated_atom_energy} variable adjusted_pe_metal equal -4542.4958060438-1351*0 print "${adjusted_pe_metal} eV" file output/dump_025.0576/energy.out -4542.4958060438 eV print "${mindist_metal} Angstroms" file output/dump_025.0576/mindistance.out 2.54241056280719 Angstroms write_dump all cfg output/dump_025.0576/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_025.0576/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:16