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 4.049696564674378*${_u_distance} variable lattice_constant_converted equal 4.049696564674378*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 66.41996213140023*${_u_distance} variable xmax_converted equal 66.41996213140023*1 variable ymin_converted equal -66.4240118279649*${_u_distance} variable ymin_converted equal -66.4240118279649*1 variable ymax_converted equal 66.4240118279649*${_u_distance} variable ymax_converted equal 66.4240118279649*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049696564674378*${_u_distance} variable zmax_converted equal 4.049696564674378*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04969656467438 Lattice spacing in x,y,z = 4.0497 4.0497 4.0497 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 66.4199621314002 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.4199621314002 -66.4240118279649 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.4199621314002 -66.4240118279649 66.4240118279649 ${zmin_converted} ${zmax_converted} units box region whole block 0 66.4199621314002 -66.4240118279649 66.4240118279649 0 ${zmax_converted} units box region whole block 0 66.4199621314002 -66.4240118279649 66.4240118279649 0 4.04969656467438 units box create_box 2 whole Created orthogonal box = (0 -66.424 0) to (66.42 66.424 4.0497) 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 66.4240118279649 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -10 0 orient y 10 13 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 13 -10 0 orient y 10 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67903 5.67903 4.0497 create_atoms 1 region upper Created 1078 atoms create_atoms CPU = 0.000408888 secs group upper type 1 1078 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.380548760085527 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -66.4240118279649 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 10 0 orient y -10 13 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 13 10 0 orient y -10 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67903 5.67903 4.0497 create_atoms 2 region lower Created 1078 atoms create_atoms CPU = 0.000321865 secs group lower type 2 1078 atoms in group lower displace_atoms lower move -7.380548760085527 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_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*4.04969656467438 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02484828233719 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 18 35 2 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 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2128 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 18 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.638 | 5.638 | 5.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7118.1644 0 -7118.1644 2201.8925 453 0 -7155.5637 0 -7155.5637 -5097.531 Loop time of 4.42461 on 1 procs for 453 steps with 2128 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 = -7118.16438426 -7155.56367554 -7155.56367554 Force two-norm initial, final = 52.142 1.29601e-05 Force max component initial, final = 13.233 2.59419e-06 Final line search alpha, max atom move = 1 2.59419e-06 Iterations, force evaluations = 453 892 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3067 | 4.3067 | 4.3067 | 0.0 | 97.34 Neigh | 0.019477 | 0.019477 | 0.019477 | 0.0 | 0.44 Comm | 0.060076 | 0.060076 | 0.060076 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03833 | | | 0.87 Nlocal: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12417 ave 12417 max 12417 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: 250708 ave 250708 max 250708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250708 Ave neighs/atom = 117.814 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) = 5.638 | 5.638 | 5.638 Mbytes Step Temp E_pair E_mol TotEng Press Volume 453 0 -7155.5637 0 -7155.5637 -5097.531 35733.553 1092 0 -7155.8198 0 -7155.8198 -1009.1714 35556.772 Loop time of 6.73296 on 1 procs for 639 steps with 2128 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7155.56367554 -7155.8198256 -7155.8198256 Force two-norm initial, final = 142.004 0.00679222 Force max component initial, final = 105.773 0.00597311 Final line search alpha, max atom move = 0.140259 0.000837781 Iterations, force evaluations = 639 1276 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3599 | 6.3599 | 6.3599 | 0.0 | 94.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.080783 | 0.080783 | 0.080783 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2923 | | | 4.34 Nlocal: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12423 ave 12423 max 12423 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: 250968 ave 250968 max 250968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250968 Ave neighs/atom = 117.936 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 18 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 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) = 5.776 | 5.776 | 5.776 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7155.8198 0 -7155.8198 -1009.1714 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2128 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: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12424 ave 12424 max 12424 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: 258676 ave 258676 max 258676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258676 Ave neighs/atom = 121.558 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) = 5.776 | 5.776 | 5.776 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 -7155.8198 -7155.8198 66.307645 132.84802 4.0364876 -1009.1714 -1009.1714 -0.26869112 -3027.3325 0.086952169 2.5863842 760.60195 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2128 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: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12424 ave 12424 max 12424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129338 ave 129338 max 129338 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258676 ave 258676 max 258676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258676 Ave neighs/atom = 121.558 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_075.1372/numatoms.out 2128 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7155.8198255984-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7155.8198255984-2128*${isolated_atom_energy} variable adjusted_pe_metal equal -7155.8198255984-2128*0 print "${adjusted_pe_metal} eV" file output/dump_075.1372/energy.out -7155.8198255984 eV print "${mindist_metal} Angstroms" file output/dump_075.1372/mindistance.out 2.58638418682898 Angstroms write_dump all cfg output/dump_075.1372/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_075.1372/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11