LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # script for mgpt t=0 eos with relaxed vacancy in bcc structure: # input for relaxed vacancy formation energy at constant pressure units electron atom_style atomic # Atomic volume for MGPT potential variable atomic_vol equal 121.863 # Derive effective lattice volume from atomic volume for 249-site cell variable lat_vol equal ${atomic_vol}*249/250 variable lat_vol equal 121.863*249/250 # Derive lattice constant from lattice volume variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0) variable lattice_constant equal (121.375548*2.0)^(1.0/3.0) # Create bcc lattice with 5x5x5 unit cells (250 atoms) lattice bcc ${lattice_constant} lattice bcc 6.23812011912273 Lattice spacing in x,y,z = 6.2381201 6.2381201 6.2381201 region box block 0 5 0 5 0 5 create_box 1 box Created orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 250 atoms using lattice units in orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601) create_atoms CPU = 0.000 seconds # Remove central atom from bcc lattice to create vacancy region vacancy sphere 2.5 2.5 2.5 0.1 units lattice delete_atoms region vacancy Deleted 1 atoms, new total = 249 # Define potential for use in simulation pair_style mgpt # Set parameters for potential: # parameter files atomic volume #pair_coeff * * parmin potin ${atomic_vol} pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol} pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.863 Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30 # Set neighbor list parameters neighbor 0.1 bin neigh_modify every 1 delay 0 check yes # Dump coordinates to file every 50 timesteps # dump id all atom 50 dump.vacmin-bcc # Output thermodynamical data every 10 timesteps thermo 10 # Set output quantities and output format thermo_style custom step vol temp pe etotal press ## Example: Output floating point number with 5 digits exponential notation. #thermo_modify format float %15.5e # minimize total energy min_style cg minimize 1.0e-10 1.0e-10 5000 10000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.171237 ghost atom cutoff = 13.171237 binsize = 6.5856184, bins = 5 5 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair mgpt, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) pair mgpt, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.88 | 4.88 | 4.88 Mbytes Step Volume Temp PotEng TotEng Press 0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09 10 30343.887 0 -74.002332 -74.002332 -1.107516e+09 20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09 30 30343.887 0 -74.005762 -74.005762 -1.143304e+09 40 30343.887 0 -74.006116 -74.006116 -1.149395e+09 50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09 60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09 70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09 80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09 90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09 100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09 110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09 120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09 130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09 139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09 Loop time of 2.58636 on 1 procs for 139 steps with 249 atoms 90.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -73.9945109564338 -74.0063705487283 -74.0063705557007 Force two-norm initial, final = 0.036622686 8.090814e-05 Force max component initial, final = 0.0073094815 8.0524205e-06 Final line search alpha, max atom move = 1 8.0524205e-06 Iterations, force evaluations = 139 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5671 | 2.5671 | 2.5671 | 0.0 | 99.26 Neigh | 0.015241 | 0.015241 | 0.015241 | 0.0 | 0.59 Comm | 0.001446 | 0.001446 | 0.001446 | 0.0 | 0.06 Output | 0.00038428 | 0.00038428 | 0.00038428 | 0.0 | 0.01 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002161 | | | 0.08 Nlocal: 249 ave 249 max 249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1479 ave 1479 max 1479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7936 ave 7936 max 7936 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15872 ave 15872 max 15872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15872 Ave neighs/atom = 63.742972 Neighbor list builds = 4 Dangerous builds = 0 # Convert energy to rydbergs and pressure to gpa variable natoms equal "count(all)" variable voltot equal "vol" variable atvol equal "v_voltot/v_natoms" variable etot equal "2.0*pe" variable etotry equal "v_etot/v_natoms" variable ptot equal "press" variable ptotgpa equal "v_ptot/1.0e+09" print "number of atoms = ${natoms}" number of atoms = 249 print "atomic volume (a.u.) = ${atvol}" atomic volume (a.u.) = 121.863 print "total energy (ry/atom) = ${etotry}" total energy (ry/atom) = -0.594428679162253 print "pressure (gpa) = ${ptotgpa}" pressure (gpa) = -1.15783109516516 print "${natoms} ${atvol} ${etot} ${ptotgpa}" 249 121.863 -148.012741111401 -1.15783109516516 print "${atvol} ${etotry} ${ptotgpa}" 121.863 -0.594428679162253 -1.15783109516516 Total wall time: 0:00:02