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 34.83738327209045*${_u_distance} variable xmax_converted equal 34.83738327209045*1 variable ymin_converted equal -69.6788163077263*${_u_distance} variable ymin_converted equal -69.6788163077263*1 variable ymax_converted equal 69.6788163077263*${_u_distance} variable ymax_converted equal 69.6788163077263*1 variable zmin_converted equal 0.0*${_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 34.8373832720904 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.8373832720904 -69.6788163077263 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.8373832720904 -69.6788163077263 69.6788163077263 ${zmin_converted} ${zmax_converted} units box region whole block 0 34.8373832720904 -69.6788163077263 69.6788163077263 0 ${zmax_converted} units box region whole block 0 34.8373832720904 -69.6788163077263 69.6788163077263 0 4.04976354539394 units box create_box 2 whole Created orthogonal box = (0 -69.6788 0) to (34.8374 69.6788 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 69.6788163077263 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -5 0 orient y 5 7 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 7 -5 0 orient y 5 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.64931 5.64931 4.04976 create_atoms 1 region upper Created 594 atoms create_atoms CPU = 0.000225067 secs group upper type 1 594 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.871046370169182 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -69.6788163077263 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 5 0 orient y -5 7 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 7 5 0 orient y -5 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.64931 5.64931 4.04976 create_atoms 2 region lower Created 594 atoms create_atoms CPU = 0.00011301 secs group lower type 2 594 atoms in group lower displace_atoms lower move -3.871046370169182 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 9 33 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 18 atoms, new total = 1170 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 = 9 33 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) = 5.455 | 5.455 | 5.455 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3863.6364 0 -3863.6364 -66.405146 146 0 -3875.3638 0 -3875.3638 -6368.5664 Loop time of 1.41928 on 1 procs for 146 steps with 1170 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3863.63637669 -3875.36384225 -3875.36384225 Force two-norm initial, final = 15.2769 0.015303 Force max component initial, final = 5.34802 0.0028577 Final line search alpha, max atom move = 3.05176e-05 8.721e-08 Iterations, force evaluations = 146 298 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3827 | 1.3827 | 1.3827 | 0.0 | 97.43 Neigh | 0.012894 | 0.012894 | 0.012894 | 0.0 | 0.91 Comm | 0.015706 | 0.015706 | 0.015706 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00794 | | | 0.56 Nlocal: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9061 ave 9061 max 9061 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: 201332 ave 201332 max 201332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201332 Ave neighs/atom = 172.079 Neighbor list builds = 3 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) = 5.46 | 5.46 | 5.46 Mbytes Step Temp E_pair E_mol TotEng Press Volume 146 0 -3875.3638 0 -3875.3638 -6368.5664 19661.016 159 0 -3875.5888 0 -3875.5888 -1378.2563 19530.409 Loop time of 0.232906 on 1 procs for 13 steps with 1170 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3875.36384225 -3875.58876881 -3875.58876881 Force two-norm initial, final = 92.8248 0.0680468 Force max component initial, final = 68.2022 0.0233702 Final line search alpha, max atom move = 1.93107e-06 4.51296e-08 Iterations, force evaluations = 13 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22324 | 0.22324 | 0.22324 | 0.0 | 95.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023687 | 0.0023687 | 0.0023687 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007297 | | | 3.13 Nlocal: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9298 ave 9298 max 9298 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: 200860 ave 200860 max 200860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200860 Ave neighs/atom = 171.675 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 = 9 33 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) = 5.599 | 5.599 | 5.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3875.5888 0 -3875.5888 -1378.2563 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1170 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: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9345 ave 9345 max 9345 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: 201648 ave 201648 max 201648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201648 Ave neighs/atom = 172.349 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) = 5.599 | 5.599 | 5.599 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 -3875.5888 -3875.5888 34.791845 139.35763 4.0281266 -1378.2563 -1378.2563 1.5614212 -4138.2374 1.9069334 2.6031676 396.28167 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1170 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: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9345 ave 9345 max 9345 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100824 ave 100824 max 100824 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201648 ave 201648 max 201648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201648 Ave neighs/atom = 172.349 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_071.0754/numatoms.out 1170 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3875.58876880787-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3875.58876880787-1170*${isolated_atom_energy} variable adjusted_pe_metal equal -3875.58876880787-1170*0 print "${adjusted_pe_metal} eV" file output/dump_071.0754/energy.out -3875.58876880787 eV print "${mindist_metal} Angstroms" file output/dump_071.0754/mindistance.out 2.60316758907964 Angstroms write_dump all cfg output/dump_071.0754/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_071.0754/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01