forked from lijiext/lammps
Merge pull request #1709 from lammps/units-example
New example/UNITS dir
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
0cf60d0c62
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@ -141,6 +141,7 @@ HEAT: compute thermal conductivity for LJ and water via fix ehex
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KAPPA: compute thermal conductivity via several methods
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MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
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SPIN: examples for features of the SPIN package
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UNITS: examples that run the same simulation in lj, real, metal units
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USER: examples for USER packages and USER-contributed commands
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VISCOSITY: compute viscosity via several methods :tb(s=:)
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@ -76,6 +76,7 @@ ellipse: ellipsoidal particles in spherical solvent, 2d system
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flow: Couette and Poiseuille flow in a 2d channel
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friction: frictional contact of spherical asperities between 2d surfaces
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gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
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gjf: use of fix langevin Gronbech-Jensen/Farago option
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granregion: use of fix wall/region/gran as boundary on granular particles
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hugoniostat: Hugoniostat shock dynamics
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hyper: global and local hyperdynamics of diffusion on Pt surface
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@ -163,6 +164,12 @@ The MC directory has an example script for using LAMMPS as an
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energy-evaluation engine in a iterative Monte Carlo energy-relaxation
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loop.
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The UNITS directory contains examples of input scripts modeling the
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same Lennard-Jones liquid model, written in 3 different unit systems:
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lj, real, and metal. So that you can see how to scale/unscale input
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and output values read/written by LAMMPS to verify you are performing
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the same simulation in different unit systems.
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The USER directory contains subdirectories of user-provided example
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scripts for ser packages. See the README files in those directories
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for more info. See the doc/Section_start.html file for more info
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@ -0,0 +1,54 @@
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This directory has 3 scripts which show how to run the same problem
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using the 3 most common units system used in LAMMPS: lj, real, and
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metal units. As stated on the units command doc page:
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"Any simulation you perform for one choice of units can be duplicated
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with any other unit setting LAMMPS supports. ... To perform the same
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simulation in a different set of units you must change all the
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unit-based input parameters in your input script and other input files
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(data file, potential files, etc) correctly to the new units. And you
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must correctly convert all output from the new units to the old units
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when comparing to the original results. That is often not simple to
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do."
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These examples are meant to illustrate how to do this for a simple
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Lennard-Jones liquid (argon). All of the scripts have a set of
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variables defined at the top which can be changed as command line
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arguments (e.g. -v cutoff 3.0). All 3 scripts give identical output,
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modulo round-offs due to the finite precision of the conversion
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factors used, either internally in LAMMPS or in the scripts. If there
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were run for a long time, the trajectories would diverge, but they
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would still give statistically identical results.
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The LJ script is the simplest; it is similar to the bench/in.lj
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script.
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The real and metal scripts each have a set of variables at the top
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which define scale factors for converting quantities like distance,
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energy, pressure from reduced LJ units to real or metal units. Once
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these are defined the rest of the input script is very similar to the
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LJ script. The approprate scale factor is applied to every input.
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Output quantities are printed in both the native real/metal units and
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unscaled back to LJ units. So that you can see the outputs are the
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same if you examine the log files. Comments about this comparison
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are at the bottom of the real and metal scripts.
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These 3 scripts are provided, because converting from lj reduced units
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to physical units (e.g. real or metal) or vice versa is the trickiest
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case. Converting input scripts between 2 sets of physical units
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(e.g. reak <--> metal) is much easier. But you can use the same ideas
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as in these scripts; just define a set of scale/unscale factors.
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See Allen & Tildesley's Computer Simulation of Liquids, Appendix B for
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a nice discussion of reduced units. It will explain the conversion
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formulas used in the real and metal scripts.
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Hopefully, if you study these scripts, you should be able to convert
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an input script of your own, written in one set of units, to an
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identical input script in an alternate set of units. Where
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"identical" means it runs the same simulation in a statistical sense.
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You can find the full set of scale factors LAMMPS uses internally for
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different unit systems it supports, at the top of the src/udpate.cpp
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file. A couple of those values are used in the real and metal
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scripts.
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@ -0,0 +1,43 @@
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# Ar in lj 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 = 1.0
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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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# script
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units lj
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atom_style atomic
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lattice fcc ${rhostar}
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region box block 0 $x 0 $y 0 $z
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create ${tinitial} 12345
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pair_style lj/cut ${cutoff}
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pair_coeff 1 1 1.0 1.0
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neighbor ${skin} 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 ${dt}
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thermo 10
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run 100
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@ -0,0 +1,98 @@
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# Ar in metal 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 8.617343e-5 # kB in eV/K
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variable avogadro index 6.02214129e23 # Avogadro's number
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# Ar properties in metal 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 eV
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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 eV
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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 ps
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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), mass (kg/atom), sigma (meter) to get t in seconds
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# pscale = scale factor on pressure, converts reduced pressure to bars
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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 bars
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variable eVtoJoule index 1.602e-19 # convert eV to Joules
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variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars
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variable tmpscale equal ${epskb}
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variable epsilonJ equal ${epsilon}*${eVtoJoule}
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variable massKgAtom equal ${mass}/1000.0/${avogadro}
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variable sigmaM equal ${sigma}/1.0e10
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variable sigmaMsq equal ${sigmaM}*${sigmaM}
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variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq})
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variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
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variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ}))
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# variables
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# alat = lattice constant in Angs (at reduced density rhostar)
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# temp = reduced temperature for output
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# epair,emol,etotal = reduced epair,emol,etotal energies for output
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# press = reduced pressure for output
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variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
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variable temp equal temp/${tmpscale}
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variable epair equal epair/${epsilon}
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variable emol equal emol/${epsilon}
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variable etotal equal etotal/${epsilon}
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variable press equal press/${pscale}
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# same script as in.ar.lj
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units metal
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atom_style atomic
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lattice fcc ${alat}
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region box block 0 $x 0 $y 0 $z
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create_box 1 box
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create_atoms 1 box
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mass 1 ${mass}
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velocity all create $(v_tinitial*v_epskb) 12345
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pair_style lj/cut $(v_cutoff*v_sigma)
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pair_coeff 1 1 ${epsilon} ${sigma}
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neighbor $(v_skin*v_sigma) 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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# columns 2,3,4 = temp,pe,press in metal 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 metal 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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run ${nsteps}
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@ -0,0 +1,98 @@
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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 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 epsJmole equal ${epsilon}*${KcaltoJoule}
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variable massKgmole equal ${mass}/1000.0
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variable sigmaM equal ${sigma}/1.0e10
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variable sigmaMsq equal ${sigmaM}*${sigmaM}
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variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
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variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
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variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
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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 temp equal temp/${tmpscale}
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variable epair equal epair/${epsilon}
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variable emol equal emol/${epsilon}
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variable etotal equal etotal/${epsilon}
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variable press equal press/${pscale}
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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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region box block 0 $x 0 $y 0 $z
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create_box 1 box
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create_atoms 1 box
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mass 1 ${mass}
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velocity all create $(v_tinitial*v_epskb) 12345
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pair_style lj/cut $(v_cutoff*v_sigma)
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pair_coeff 1 1 ${epsilon} ${sigma}
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neighbor $(v_skin*v_sigma) 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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# 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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run ${nsteps}
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@ -0,0 +1,109 @@
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LAMMPS (19 Sep 2019)
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# Ar in lj 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 = 1.0
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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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# script
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units lj
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atom_style atomic
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lattice fcc ${rhostar}
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lattice fcc 0.8842
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Lattice spacing in x,y,z = 1.65388 1.65388 1.65388
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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 (8.26938 8.26938 8.26938)
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1 by 1 by 1 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 = 0.000547171 secs
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mass 1 1.0
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velocity all create ${tinitial} 12345
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velocity all create 1.0 12345
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pair_style lj/cut ${cutoff}
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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neighbor ${skin} bin
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neighbor 0.3 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 ${dt}
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timestep 0.005
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thermo 10
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, 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) = 2.644 | 2.644 | 2.644 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 -7.1026383 0 -5.6056383 -5.1224757
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10 0.74213042 -6.7245488 0 -5.6135795 -3.1363153
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20 0.36167746 -6.1681704 0 -5.6267393 -0.40461854
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30 0.4684512 -6.3315744 0 -5.630303 -1.0390065
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40 0.46774191 -6.3308002 0 -5.6305906 -1.077533
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50 0.48323399 -6.3533122 0 -5.6299109 -1.1506287
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60 0.49569105 -6.3711644 0 -5.6291149 -1.2296104
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70 0.5208333 -6.4096336 0 -5.6299462 -1.4483636
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80 0.53708431 -6.4345933 0 -5.6305781 -1.5945708
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90 0.52618946 -6.4185937 0 -5.6308881 -1.5264055
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100 0.52862701 -6.4231724 0 -5.6318178 -1.5714077
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Loop time of 0.065218 on 1 procs for 100 steps with 500 atoms
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|
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Performance: 662394.104 tau/day, 1533.320 timesteps/s
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99.9% CPU use with 1 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 | 0.053584 | 0.053584 | 0.053584 | 0.0 | 82.16
|
||||
Neigh | 0.0075939 | 0.0075939 | 0.0075939 | 0.0 | 11.64
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Comm | 0.0022638 | 0.0022638 | 0.0022638 | 0.0 | 3.47
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Output | 0.00021172 | 0.00021172 | 0.00021172 | 0.0 | 0.32
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Modify | 0.0011077 | 0.0011077 | 0.0011077 | 0.0 | 1.70
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Other | | 0.0004568 | | | 0.70
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Nlocal: 500 ave 500 max 500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1946 ave 1946 max 1946 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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||||
Neighs: 19572 ave 19572 max 19572 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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||||
|
||||
Total # of neighbors = 19572
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Ave neighs/atom = 39.144
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||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
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||||
Total wall time: 0:00:00
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||||
|
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@ -0,0 +1,109 @@
|
|||
LAMMPS (19 Sep 2019)
|
||||
# Ar in lj units
|
||||
|
||||
# simulation params in reduced units
|
||||
# settable from command line
|
||||
# epsilon = sigma = mass = 1.0
|
||||
|
||||
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
|
||||
|
||||
# script
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rhostar}
|
||||
lattice fcc 0.8842
|
||||
Lattice spacing in x,y,z = 1.65388 1.65388 1.65388
|
||||
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 (8.26938 8.26938 8.26938)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
create_atoms CPU = 0.000570774 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create ${tinitial} 12345
|
||||
velocity all create 1.0 12345
|
||||
|
||||
pair_style lj/cut ${cutoff}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
timestep ${dt}
|
||||
timestep 0.005
|
||||
|
||||
thermo 10
|
||||
|
||||
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 = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, 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 E_pair E_mol TotEng Press
|
||||
0 1 -7.1026383 0 -5.6056383 -5.1224757
|
||||
10 0.73621446 -6.7154544 0 -5.6133413 -3.089257
|
||||
20 0.35775263 -6.1618707 0 -5.626315 -0.37875949
|
||||
30 0.47139877 -6.3359656 0 -5.6302816 -1.1018761
|
||||
40 0.46337135 -6.3247084 0 -5.6310415 -1.0985336
|
||||
50 0.48738877 -6.360393 0 -5.630772 -1.2274707
|
||||
60 0.50832261 -6.3913892 0 -5.6304302 -1.374293
|
||||
70 0.50988271 -6.3936997 0 -5.6304053 -1.4112286
|
||||
80 0.53931444 -6.4367444 0 -5.6293906 -1.6484686
|
||||
90 0.55277272 -6.4563334 0 -5.6288326 -1.760598
|
||||
100 0.54916776 -6.4507537 0 -5.6286495 -1.728837
|
||||
Loop time of 0.0237499 on 4 procs for 100 steps with 500 atoms
|
||||
|
||||
Performance: 1818955.951 tau/day, 4210.546 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0098808 | 0.011585 | 0.015043 | 1.9 | 48.78
|
||||
Neigh | 0.0015168 | 0.0017335 | 0.001997 | 0.4 | 7.30
|
||||
Comm | 0.005949 | 0.0097297 | 0.011739 | 2.3 | 40.97
|
||||
Output | 0.00019789 | 0.0002324 | 0.00032282 | 0.0 | 0.98
|
||||
Modify | 0.00021482 | 0.00025994 | 0.00031853 | 0.0 | 1.09
|
||||
Other | | 0.0002095 | | | 0.88
|
||||
|
||||
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: 4909 ave 5493 max 4644 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19636
|
||||
Ave neighs/atom = 39.272
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,197 @@
|
|||
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
|
||||
|
|
@ -0,0 +1,197 @@
|
|||
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
|
||||
|
|
@ -0,0 +1,197 @@
|
|||
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 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
create_atoms CPU = 0.000550985 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) = 2.644 | 2.644 | 2.644 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 87.369977 -1.5728967 -1169.6414 0.74231077 -6.7248204 0 -5.6135812 -3.1363029
|
||||
20 42.567295 -1.4427006 -150.87379 0.36165926 -6.1681752 0 -5.6267713 -0.40455638
|
||||
30 55.130978 -1.480902 -387.17817 0.46840253 -6.3315028 0 -5.6303042 -1.0381883
|
||||
40 55.054202 -1.4807485 -401.72653 0.46775023 -6.3308469 0 -5.6306248 -1.0771986
|
||||
50 56.873955 -1.4860029 -428.9126 0.48321117 -6.3533113 0 -5.6299442 -1.1500959
|
||||
60 58.33701 -1.490161 -458.23636 0.49564154 -6.3710892 0 -5.6291138 -1.2287253
|
||||
70 61.29671 -1.4991528 -539.72484 0.52078768 -6.4095331 0 -5.629914 -1.4472304
|
||||
80 63.214984 -1.504992 -594.34987 0.53708567 -6.4344983 0 -5.630481 -1.5937032
|
||||
90 61.936907 -1.5013008 -569.13985 0.5262269 -6.4187169 0 -5.6309552 -1.5261045
|
||||
100 62.20662 -1.5023046 -585.49121 0.52851844 -6.4230083 0 -5.6318162 -1.5699494
|
||||
Loop time of 0.047307 on 1 procs for 100 steps with 500 atoms
|
||||
|
||||
Performance: 2043.760 ns/day, 0.012 hours/ns, 2113.851 timesteps/s
|
||||
98.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.038646 | 0.038646 | 0.038646 | 0.0 | 81.69
|
||||
Neigh | 0.0056832 | 0.0056832 | 0.0056832 | 0.0 | 12.01
|
||||
Comm | 0.0015347 | 0.0015347 | 0.0015347 | 0.0 | 3.24
|
||||
Output | 0.0003581 | 0.0003581 | 0.0003581 | 0.0 | 0.76
|
||||
Modify | 0.00075364 | 0.00075364 | 0.00075364 | 0.0 | 1.59
|
||||
Other | | 0.0003314 | | | 0.70
|
||||
|
||||
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
|
||||
|
|
@ -0,0 +1,197 @@
|
|||
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
|
||||
Loading…
Reference in New Issue