LAMMPS (19 Sep 2019) # Ar in real 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 0.0019872067 # kB in Kcal/mole/K variable avogadro index 6.02214129e23 # Avogadro's number # Ar properties in real 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 Kcal/mole variable epsilon equal 117.7*${kb} variable epsilon equal 117.7*0.0019872067 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 Kcal/mole # tmpscale = scale factor on temperature, converts reduced temp to degrees K # tscale = scale factor on time, converts reduced time to fs # formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs # use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds # pscale = scale factor on pressure, converts reduced pressure to atmospheres # 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 atms variable KcaltoJoule index 4.1868e3 # convert Kcals to Joules variable NtMtoAtm equal 1.0/1.0135e5 # convert Nt/meter^2 to Atmospheres variable tmpscale equal ${epskb} variable tmpscale equal 117.7 variable epsJmole equal ${epsilon}*${KcaltoJoule} variable epsJmole equal 0.23389422859*${KcaltoJoule} variable epsJmole equal 0.23389422859*4.1868e3 variable massKgmole equal ${mass}/1000.0 variable massKgmole equal 39.95/1000.0 variable sigmaM equal ${sigma}/1.0e10 variable sigmaM equal 3.504/1.0e10 variable sigmaMsq equal ${sigmaM}*${sigmaM} variable sigmaMsq equal 3.504e-10*${sigmaM} variable sigmaMsq equal 3.504e-10*3.504e-10 variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq}) variable tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq}) variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq}) variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-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}/(${epsJmole}/${avogadro})) variable pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro})) variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro})) variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro})) variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23)) # 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/0.23389422859 variable emol equal emol/${epsilon} variable emol equal emol/0.23389422859 variable etotal equal etotal/${epsilon} variable etotal equal etotal/0.23389422859 variable press equal press/${pscale} variable press equal press/372.936366301003 # same script as in.ar.lj units real 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 = 0.000664949 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 0.23389422859 ${sigma} pair_coeff 1 1 0.23389422859 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 11.190297512378050371 # columns 2,3,4 = temp,pe,press in real units # columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj # need to include real 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 -1.6612661 -1909.5509 1 -7.1026383 0 -5.6056383 -5.1203128 10 86.674156 -1.5707707 -1152.1077 0.73639895 -6.715731 0 -5.6133417 -3.0892877 20 42.104452 -1.4412091 -141.16344 0.35772687 -6.1617986 0 -5.6262815 -0.37851883 30 55.478223 -1.4819221 -410.58592 0.47135278 -6.3358644 0 -5.6302493 -1.1009544 40 54.54231 -1.4793231 -409.58446 0.4634011 -6.3247524 0 -5.631041 -1.098269 50 57.354168 -1.4876242 -457.34719 0.48729115 -6.3602431 0 -5.6307682 -1.2263411 60 59.835295 -1.4949249 -512.38519 0.50837124 -6.391457 0 -5.6304252 -1.3739212 70 60.005554 -1.4954174 -525.858 0.50981779 -6.3935625 0 -5.6303653 -1.4100475 80 63.469566 -1.505493 -614.29111 0.53924865 -6.4366403 0 -5.6293851 -1.6471741 90 65.064012 -1.5100983 -656.32951 0.55279535 -6.4563301 0 -5.6287955 -1.7598968 100 64.63774 -1.5088033 -644.51211 0.54917366 -6.4507932 0 -5.6286803 -1.7282093 Loop time of 0.0285767 on 4 procs for 100 steps with 500 atoms Performance: 3383.318 ns/day, 0.007 hours/ns, 3499.350 timesteps/s 99.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012398 | 0.014826 | 0.016774 | 1.6 | 51.88 Neigh | 0.001797 | 0.0021547 | 0.0025899 | 0.6 | 7.54 Comm | 0.0079622 | 0.010444 | 0.013427 | 2.3 | 36.55 Output | 0.00042987 | 0.00047708 | 0.00059676 | 0.0 | 1.67 Modify | 0.00028896 | 0.00038844 | 0.00049448 | 0.0 | 1.36 Other | | 0.0002864 | | | 1.00 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 5493 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