LAMMPS (19 Sep 2019) # Ar in metal units # simulation params in reduced units # settable from command line # epsilon, sigma, mass set below variable x index 5 variable y index 5 variable z index 5 variable rhostar index 0.8842 variable dt index 0.005 variable cutoff index 2.5 variable skin index 0.3 variable tinitial index 1.0 variable nthermo index 10 variable nsteps index 100 # physical constants from update.cpp variable kb index 8.617343e-5 # kB in eV/K variable avogadro index 6.02214129e23 # Avogadro's number # Ar properties in metal units variable epskb index 117.7 # LJ epsilon/kB in degrees K variable sigma index 3.504 # LJ sigma in Angstroms variable epsilon equal ${epskb}*${kb} # LJ epsilon in eV variable epsilon equal 117.7*${kb} variable epsilon equal 117.7*8.617343e-5 variable mass index 39.95 # mass in g/mole # scale factors # sigma = scale factor on distance, converts reduced distance to Angs # epsilon = scale factor on energy, converts reduced energy to eV # tmpscale = scale factor on temperature, converts reduced temp to degrees K # tscale = scale factor on time, converts reduced time to ps # formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs # use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds # pscale = scale factor on pressure, converts reduced pressure to bars # formula is P = P* / (sigma^3/epsilon), but need P in atmospheres # use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars variable eVtoJoule index 1.602e-19 # convert eV to Joules variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars variable tmpscale equal ${epskb} variable tmpscale equal 117.7 variable epsilonJ equal ${epsilon}*${eVtoJoule} variable epsilonJ equal 0.010142612711*${eVtoJoule} variable epsilonJ equal 0.010142612711*1.602e-19 variable massKgAtom equal ${mass}/1000.0/${avogadro} variable massKgAtom equal 39.95/1000.0/${avogadro} variable massKgAtom equal 39.95/1000.0/6.02214129e23 variable sigmaM equal ${sigma}/1.0e10 variable sigmaM equal 3.504/1.0e10 variable sigmaMsq equal ${sigmaM}*${sigmaM} variable sigmaMsq equal 3.504e-10*${sigmaM} variable sigmaMsq equal 3.504e-10*3.504e-10 variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq}) variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/${massKgAtom}/${sigmaMsq}) variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/${sigmaMsq}) variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/1.2278016e-19) variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM} variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM} variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM} variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10 variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ})) variable pscale equal 1e-05/(${sigmaM3}/(${epsilonJ})) variable pscale equal 1e-05/(4.3022168064e-29/(${epsilonJ})) variable pscale equal 1e-05/(4.3022168064e-29/(1.6248465563022e-21)) # variables # alat = lattice constant in Angs (at reduced density rhostar) # temp = reduced temperature for output # epair,emol,etotal = reduced epair,emol,etotal energies for output # press = reduced pressure for output variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0) variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0) variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0) variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0) variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0) variable temp equal temp/${tmpscale} variable temp equal temp/117.7 variable epair equal epair/${epsilon} variable epair equal epair/0.010142612711 variable emol equal emol/${epsilon} variable emol equal emol/0.010142612711 variable etotal equal etotal/${epsilon} variable etotal equal etotal/0.010142612711 variable press equal press/${pscale} variable press equal press/377.676586146256 # same script as in.ar.lj units metal atom_style atomic lattice fcc ${alat} lattice fcc 5.79518437579763 Lattice spacing in x,y,z = 5.79518 5.79518 5.79518 region box block 0 $x 0 $y 0 $z region box block 0 5 0 $y 0 $z region box block 0 5 0 5 0 $z region box block 0 5 0 5 0 5 create_box 1 box Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 500 atoms create_atoms CPU = 0.000674009 secs mass 1 ${mass} mass 1 39.95 velocity all create $(v_tinitial*v_epskb) 12345 velocity all create 117.70000000000000284 12345 pair_style lj/cut $(v_cutoff*v_sigma) pair_style lj/cut 8.7599999999999997868 pair_coeff 1 1 ${epsilon} ${sigma} pair_coeff 1 1 0.010142612711 ${sigma} pair_coeff 1 1 0.010142612711 3.504 neighbor $(v_skin*v_sigma) bin neighbor 1.0511999999999999122 bin neigh_modify delay 0 every 20 check no fix 1 all nve timestep $(v_dt*v_tscale) timestep 0.011194658410003900315 # columns 2,3,4 = temp,pe,press in metal units # columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj # need to include metal unit output to enable use of reduced variables thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press thermo_modify norm yes thermo ${nthermo} thermo 10 run ${nsteps} run 100 Neighbor list info ... update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.8112 ghost atom cutoff = 9.8112 binsize = 4.9056, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual 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) = 2.609 | 2.609 | 2.609 Mbytes Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press 0 117.7 -0.07203931 -1934.8523 1 -7.1026383 0 -5.6056383 -5.12304 10 86.648851 -0.06811179 -1166.7855 0.73618395 -6.7154088 0 -5.6133414 -3.0893774 20 42.107954 -0.062497536 -143.06615 0.35775662 -6.1618774 0 -5.6263157 -0.37880598 30 55.484504 -0.064263032 -416.20245 0.47140615 -6.3359445 0 -5.6302495 -1.1020075 40 54.538222 -0.064148334 -414.88071 0.46336637 -6.3246361 0 -5.6309766 -1.0985079 50 57.367693 -0.064511259 -463.67683 0.48740606 -6.3604182 0 -5.6307714 -1.2277087 60 59.828794 -0.064824938 -519.05997 0.50831601 -6.3913451 0 -5.630396 -1.3743504 70 60.014616 -0.064848979 -533.07604 0.50989478 -6.3937154 0 -5.6304029 -1.4114617 80 63.47861 -0.065285885 -622.71073 0.53932549 -6.4367917 0 -5.6294215 -1.6487936 90 65.060881 -0.065484011 -664.99883 0.55276874 -6.4563257 0 -5.6288309 -1.7607627 100 64.637033 -0.065427467 -653.00765 0.54916765 -6.4507508 0 -5.6286468 -1.7290128 Loop time of 0.0258265 on 4 procs for 100 steps with 500 atoms Performance: 3745.060 ns/day, 0.006 hours/ns, 3871.990 timesteps/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0090213 | 0.012419 | 0.015494 | 2.1 | 48.09 Neigh | 0.0013709 | 0.0018765 | 0.0022483 | 0.7 | 7.27 Comm | 0.0071132 | 0.010597 | 0.014538 | 2.6 | 41.03 Output | 0.00039983 | 0.00042897 | 0.00049567 | 0.0 | 1.66 Modify | 0.00024104 | 0.00028801 | 0.00031543 | 0.0 | 1.12 Other | | 0.0002173 | | | 0.84 Nlocal: 125 ave 133 max 117 min Histogram: 1 0 0 1 0 0 1 0 0 1 Nghost: 1099 ave 1107 max 1091 min Histogram: 1 0 0 1 0 0 1 0 0 1 Neighs: 4908.75 ave 5492 max 4644 min Histogram: 1 2 0 0 0 0 0 0 0 1 Total # of neighbors = 19635 Ave neighs/atom = 39.27 Neighbor list builds = 5 Dangerous builds not checked Total wall time: 0:00:00