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 1 by 1 MPI processor grid create_atoms 1 box Created 500 atoms create_atoms CPU = 0.000549078 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) = 2.644 | 2.644 | 2.644 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 87.345225 -0.06820404 -1184.5618 0.74210047 -6.724504 0 -5.6135796 -3.1364449 20 42.569809 -0.062561408 -152.82812 0.36168062 -6.1681748 0 -5.6267389 -0.40465341 30 55.137637 -0.064219154 -392.49645 0.46845911 -6.3316185 0 -5.6303352 -1.0392396 40 55.053014 -0.064210828 -406.99941 0.46774014 -6.3307976 0 -5.6305906 -1.07764 50 56.87723 -0.064439241 -434.61958 0.483239 -6.3533177 0 -5.6299089 -1.1507718 60 58.344019 -0.064620383 -464.4684 0.4957011 -6.3711772 0 -5.6291126 -1.2298046 70 61.30301 -0.065010529 -547.09852 0.5208412 -6.4096433 0 -5.629944 -1.44859 80 63.214836 -0.065263563 -602.29599 0.53708442 -6.4345909 0 -5.6305755 -1.5947401 90 61.931826 -0.065101194 -576.5342 0.52618374 -6.4185823 0 -5.6308852 -1.5265288 100 62.221816 -0.065148028 -593.59878 0.52864755 -6.4231998 0 -5.6318144 -1.5717119 Loop time of 0.04864 on 1 procs for 100 steps with 500 atoms Performance: 1988.524 ns/day, 0.012 hours/ns, 2055.921 timesteps/s 99.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039802 | 0.039802 | 0.039802 | 0.0 | 81.83 Neigh | 0.0057771 | 0.0057771 | 0.0057771 | 0.0 | 11.88 Comm | 0.0015905 | 0.0015905 | 0.0015905 | 0.0 | 3.27 Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.69 Modify | 0.00077343 | 0.00077343 | 0.00077343 | 0.0 | 1.59 Other | | 0.0003595 | | | 0.74 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1946 ave 1946 max 1946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19572 ave 19572 max 19572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19572 Ave neighs/atom = 39.144 Neighbor list builds = 5 Dangerous builds not checked Total wall time: 0:00:00