forked from lijiext/lammps
198 lines
8.5 KiB
Groff
198 lines
8.5 KiB
Groff
LAMMPS (19 Sep 2019)
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# Ar in real units
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# simulation params in reduced units
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# settable from command line
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# epsilon, sigma, mass set below
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variable x index 5
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variable y index 5
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variable z index 5
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variable rhostar index 0.8842
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variable dt index 0.005
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variable cutoff index 2.5
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variable skin index 0.3
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variable tinitial index 1.0
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variable nthermo index 10
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variable nsteps index 100
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# physical constants from update.cpp
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variable kb index 0.0019872067 # kB in Kcal/mole/K
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variable avogadro index 6.02214129e23 # Avogadro's number
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# Ar properties in real units
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variable epskb index 117.7 # LJ epsilon/kB in degrees K
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variable sigma index 3.504 # LJ sigma in Angstroms
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variable epsilon equal ${epskb}*${kb} # LJ epsilon in Kcal/mole
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variable epsilon equal 117.7*${kb}
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variable epsilon equal 117.7*0.0019872067
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variable mass index 39.95 # mass in g/mole
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# scale factors
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# sigma = scale factor on distance, converts reduced distance to Angs
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# epsilon = scale factor on energy, converts reduced energy to Kcal/mole
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# tmpscale = scale factor on temperature, converts reduced temp to degrees K
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# tscale = scale factor on time, converts reduced time to fs
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# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
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# use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds
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# pscale = scale factor on pressure, converts reduced pressure to atmospheres
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# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
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# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms
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variable KcaltoJoule index 4.1868e3 # convert Kcals to Joules
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variable NtMtoAtm equal 1.0/1.0135e5 # convert Nt/meter^2 to Atmospheres
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variable tmpscale equal ${epskb}
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variable tmpscale equal 117.7
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variable epsJmole equal ${epsilon}*${KcaltoJoule}
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variable epsJmole equal 0.23389422859*${KcaltoJoule}
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variable epsJmole equal 0.23389422859*4.1868e3
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variable massKgmole equal ${mass}/1000.0
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variable massKgmole equal 39.95/1000.0
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variable sigmaM equal ${sigma}/1.0e10
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variable sigmaM equal 3.504/1.0e10
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variable sigmaMsq equal ${sigmaM}*${sigmaM}
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variable sigmaMsq equal 3.504e-10*${sigmaM}
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variable sigmaMsq equal 3.504e-10*3.504e-10
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variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
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variable tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq})
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variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq})
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variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-19)
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variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
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variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
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variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
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variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
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variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
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variable pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro}))
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variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro}))
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variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro}))
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variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23))
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# variables
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# alat = lattice constant in Angs (at reduced density rhostar)
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# temp = reduced temperature for output
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# epair,emol,etotal = reduced epair,emol,etotal energies for output
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# press = reduced pressure for output
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variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
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variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
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variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
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variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
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variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
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variable temp equal temp/${tmpscale}
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variable temp equal temp/117.7
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variable epair equal epair/${epsilon}
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variable epair equal epair/0.23389422859
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variable emol equal emol/${epsilon}
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variable emol equal emol/0.23389422859
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variable etotal equal etotal/${epsilon}
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variable etotal equal etotal/0.23389422859
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variable press equal press/${pscale}
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variable press equal press/372.936366301003
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# same script as in.ar.lj
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units real
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atom_style atomic
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lattice fcc ${alat}
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lattice fcc 5.79518437579763
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Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
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region box block 0 $x 0 $y 0 $z
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region box block 0 5 0 $y 0 $z
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region box block 0 5 0 5 0 $z
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region box block 0 5 0 5 0 5
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create_box 1 box
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Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 500 atoms
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create_atoms CPU = 0.000664949 secs
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mass 1 ${mass}
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mass 1 39.95
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velocity all create $(v_tinitial*v_epskb) 12345
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velocity all create 117.70000000000000284 12345
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pair_style lj/cut $(v_cutoff*v_sigma)
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pair_style lj/cut 8.7599999999999997868
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pair_coeff 1 1 ${epsilon} ${sigma}
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pair_coeff 1 1 0.23389422859 ${sigma}
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pair_coeff 1 1 0.23389422859 3.504
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neighbor $(v_skin*v_sigma) bin
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neighbor 1.0511999999999999122 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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timestep $(v_dt*v_tscale)
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timestep 11.190297512378050371
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# columns 2,3,4 = temp,pe,press in real units
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# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
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# need to include real unit output to enable use of reduced variables
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thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press
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thermo_modify norm yes
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thermo ${nthermo}
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thermo 10
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run ${nsteps}
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run 100
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 9.8112
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ghost atom cutoff = 9.8112
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binsize = 4.9056, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
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Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press
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0 117.7 -1.6612661 -1909.5509 1 -7.1026383 0 -5.6056383 -5.1203128
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10 86.674156 -1.5707707 -1152.1077 0.73639895 -6.715731 0 -5.6133417 -3.0892877
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20 42.104452 -1.4412091 -141.16344 0.35772687 -6.1617986 0 -5.6262815 -0.37851883
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30 55.478223 -1.4819221 -410.58592 0.47135278 -6.3358644 0 -5.6302493 -1.1009544
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40 54.54231 -1.4793231 -409.58446 0.4634011 -6.3247524 0 -5.631041 -1.098269
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50 57.354168 -1.4876242 -457.34719 0.48729115 -6.3602431 0 -5.6307682 -1.2263411
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60 59.835295 -1.4949249 -512.38519 0.50837124 -6.391457 0 -5.6304252 -1.3739212
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70 60.005554 -1.4954174 -525.858 0.50981779 -6.3935625 0 -5.6303653 -1.4100475
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80 63.469566 -1.505493 -614.29111 0.53924865 -6.4366403 0 -5.6293851 -1.6471741
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90 65.064012 -1.5100983 -656.32951 0.55279535 -6.4563301 0 -5.6287955 -1.7598968
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100 64.63774 -1.5088033 -644.51211 0.54917366 -6.4507932 0 -5.6286803 -1.7282093
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Loop time of 0.0285767 on 4 procs for 100 steps with 500 atoms
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Performance: 3383.318 ns/day, 0.007 hours/ns, 3499.350 timesteps/s
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99.7% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.012398 | 0.014826 | 0.016774 | 1.6 | 51.88
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Neigh | 0.001797 | 0.0021547 | 0.0025899 | 0.6 | 7.54
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Comm | 0.0079622 | 0.010444 | 0.013427 | 2.3 | 36.55
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Output | 0.00042987 | 0.00047708 | 0.00059676 | 0.0 | 1.67
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Modify | 0.00028896 | 0.00038844 | 0.00049448 | 0.0 | 1.36
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Other | | 0.0002864 | | | 1.00
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Nlocal: 125 ave 133 max 117 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nghost: 1099 ave 1107 max 1091 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 4908.75 ave 5493 max 4644 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 19635
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Ave neighs/atom = 39.27
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Neighbor list builds = 5
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Dangerous builds not checked
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Total wall time: 0:00:00
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