forked from lijiext/lammps
Added elastic constant example at finite temperature
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14097 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps
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@ -42,12 +42,6 @@
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# that minimization is not required, you can set maxiter = 0.0 in
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# init.mod.
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#
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# There are two alternate versions of displace.mod provided.
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# They are displace_restart.mod and displace_reverse.mod.
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# The former resets the box using a restart file while
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# the latter reverses the deformation. Copy whichever
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# one you like best to displace.mod.
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#
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include init.mod
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include potential.mod
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@ -0,0 +1,18 @@
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# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985)
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# Stillinger-Weber parameters for various elements and mixtures
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units:
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# epsilon = eV; sigma = Angstroms
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# other quantities are unitless
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# format of a single entry (one or more lines):
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# element 1, element 2, element 3,
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# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
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# Here are the original parameters in metal units, for Silicon from:
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#
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# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
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#
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Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
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7.049556277 0.6022245584 4.0 0.0 0.0
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@ -0,0 +1,140 @@
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# NOTE: This script should not need to be
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# modified. See in.elastic for more info.
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#
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# Find which reference length to use
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if "${dir} == 1" then &
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"variable len0 equal ${lx0}"
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if "${dir} == 2" then &
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"variable len0 equal ${ly0}"
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if "${dir} == 3" then &
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"variable len0 equal ${lz0}"
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if "${dir} == 4" then &
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"variable len0 equal ${lz0}"
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if "${dir} == 5" then &
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"variable len0 equal ${lz0}"
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if "${dir} == 6" then &
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"variable len0 equal ${ly0}"
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# Reset box and simulation parameters
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clear
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box tilt large
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read_restart restart.equil
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include potential.mod
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# Negative deformation
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variable delta equal -${up}*${len0}
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variable deltaxy equal -${up}*xy
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variable deltaxz equal -${up}*xz
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variable deltayz equal -${up}*yz
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if "${dir} == 1" then &
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"change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box"
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if "${dir} == 2" then &
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"change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box"
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if "${dir} == 3" then &
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"change_box all z delta 0 ${delta} remap units box"
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if "${dir} == 4" then &
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"change_box all yz delta ${delta} remap units box"
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if "${dir} == 5" then &
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"change_box all xz delta ${delta} remap units box"
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if "${dir} == 6" then &
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"change_box all xy delta ${delta} remap units box"
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# Run MD
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run ${nequil}
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include potential.mod
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run ${nrun}
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# Obtain new stress tensor
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variable pxx1 equal f_avp[1]
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variable pyy1 equal f_avp[2]
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variable pzz1 equal f_avp[3]
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variable pxy1 equal f_avp[4]
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variable pxz1 equal f_avp[5]
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variable pyz1 equal f_avp[6]
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# Compute elastic constant from pressure tensor
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variable C1neg equal ${d1}
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variable C2neg equal ${d2}
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variable C3neg equal ${d3}
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variable C4neg equal ${d4}
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variable C5neg equal ${d5}
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variable C6neg equal ${d6}
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# Reset box and simulation parameters
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clear
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box tilt large
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read_restart restart.equil
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include potential.mod
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# Positive deformation
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variable delta equal ${up}*${len0}
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variable deltaxy equal ${up}*xy
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variable deltaxz equal ${up}*xz
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variable deltayz equal ${up}*yz
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if "${dir} == 1" then &
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"change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box"
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if "${dir} == 2" then &
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"change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box"
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if "${dir} == 3" then &
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"change_box all z delta 0 ${delta} remap units box"
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if "${dir} == 4" then &
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"change_box all yz delta ${delta} remap units box"
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if "${dir} == 5" then &
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"change_box all xz delta ${delta} remap units box"
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if "${dir} == 6" then &
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"change_box all xy delta ${delta} remap units box"
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# Run MD
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run ${nequil}
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include potential.mod
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run ${nrun}
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# Obtain new stress tensor
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variable tmp equal pe
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variable e1 equal ${tmp}
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variable tmp equal press
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variable p1 equal ${tmp}
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variable tmp equal pxx
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variable pxx1 equal ${tmp}
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variable tmp equal pyy
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variable pyy1 equal ${tmp}
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variable tmp equal pzz
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variable pzz1 equal ${tmp}
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variable tmp equal pxy
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variable pxy1 equal ${tmp}
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variable tmp equal pxz
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variable pxz1 equal ${tmp}
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variable tmp equal pyz
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variable pyz1 equal ${tmp}
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# Compute elastic constant from pressure tensor
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variable C1pos equal ${d1}
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variable C2pos equal ${d2}
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variable C3pos equal ${d3}
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variable C4pos equal ${d4}
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variable C5pos equal ${d5}
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variable C6pos equal ${d6}
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# Combine positive and negative
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variable C1${dir} equal 0.5*(${C1neg}+${C1pos})
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variable C2${dir} equal 0.5*(${C2neg}+${C2pos})
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variable C3${dir} equal 0.5*(${C3neg}+${C3pos})
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variable C4${dir} equal 0.5*(${C4neg}+${C4pos})
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variable C5${dir} equal 0.5*(${C5neg}+${C5pos})
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variable C6${dir} equal 0.5*(${C6neg}+${C6pos})
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# Delete dir to make sure it is not reused
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variable dir delete
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@ -0,0 +1,184 @@
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# Compute elastic constant tensor for a crystal at finite temperature
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#
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# Written by Aidan Thompson (Sandia, athomps@sandia.gov)
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#
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# This script uses the following three include files.
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#
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# init.mod (must be modified for different crystal structures)
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# Define units, MD parameters, deformation parameters,
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# and initial configuration of the atoms and simulation cell.
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#
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#
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# potential.mod (must be modified for different pair styles)
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# Define pair style and other attributes
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# not stored in restart file
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#
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#
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# displace.mod (displace.mod should not need to be modified)
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# Perform positive and negative box displacements
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# in direction ${dir} and size ${up}.
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# It uses the resultant changes
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# in stress to compute one
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# row of the elastic stiffness tensor
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#
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# Inputs variables:
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# dir = the Voigt deformation component
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# (1,2,3,4,5,6)
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# Global constants:
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# up = the deformation magnitude (strain units)
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# cfac = conversion from LAMMPS pressure units to
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# output units for elastic constants
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#
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#
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# To run this on a different system, it should only be necessary to
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# modify the files init.mod and potential.mod. In order to calculate
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# the elastic constants correctly, care must be taken to specify
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# the correct units in init.mod (units, cfac and cunits). It is also
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# important to verify that the MD sampling of stress components
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# is generating accurate statistical averages.
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# One indication of this is that the elastic constants are insensitive
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# to the choice of the variable ${up} in init.mod. Another is to
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# check for finite size effects.
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#
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include init.mod
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# Compute initial state
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include potential.mod
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run ${nequil}
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include potential.mod
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run ${nrun}
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variable pxx0 equal f_avp[1]
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variable pyy0 equal f_avp[2]
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variable pzz0 equal f_avp[3]
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variable pxy0 equal f_avp[4]
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variable pxz0 equal f_avp[5]
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variable pyz0 equal f_avp[6]
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variable tmp equal lx
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variable lx0 equal ${tmp}
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variable tmp equal ly
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variable ly0 equal ${tmp}
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variable tmp equal lz
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variable lz0 equal ${tmp}
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# These formulas define the derivatives w.r.t. strain components
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# Constants uses $, variables use v_
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variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
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variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
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variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
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variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
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variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
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variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
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# Write restart
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write_restart restart.equil
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# uxx Perturbation
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variable dir equal 1
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include displace.mod
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# uyy Perturbation
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variable dir equal 2
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include displace.mod
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# uzz Perturbation
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variable dir equal 3
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include displace.mod
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# uyz Perturbation
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variable dir equal 4
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include displace.mod
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# uxz Perturbation
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variable dir equal 5
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include displace.mod
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# uxy Perturbation
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variable dir equal 6
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include displace.mod
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# Output final values
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variable C11all equal ${C11}
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variable C22all equal ${C22}
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variable C33all equal ${C33}
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variable C12all equal 0.5*(${C12}+${C21})
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variable C13all equal 0.5*(${C13}+${C31})
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variable C23all equal 0.5*(${C23}+${C32})
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variable C44all equal ${C44}
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variable C55all equal ${C55}
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variable C66all equal ${C66}
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variable C14all equal 0.5*(${C14}+${C41})
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variable C15all equal 0.5*(${C15}+${C51})
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variable C16all equal 0.5*(${C16}+${C61})
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variable C24all equal 0.5*(${C24}+${C42})
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variable C25all equal 0.5*(${C25}+${C52})
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variable C26all equal 0.5*(${C26}+${C62})
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variable C34all equal 0.5*(${C34}+${C43})
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variable C35all equal 0.5*(${C35}+${C53})
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variable C36all equal 0.5*(${C36}+${C63})
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variable C45all equal 0.5*(${C45}+${C54})
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variable C46all equal 0.5*(${C46}+${C64})
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variable C56all equal 0.5*(${C56}+${C65})
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variable C11cubic equal (${C11all}+${C22all}+${C33all})/3.0
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variable C12cubic equal (${C12all}+${C13all}+${C23all})/3.0
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variable C44cubic equal (${C44all}+${C55all}+${C66all})/3.0
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variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
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variable shearmodulus1 equal ${C44cubic}
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variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
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variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
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# For Stillinger-Weber silicon, the analytical results
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# are known to be (E. R. Cowley, 1988):
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# C11 = 151.4 GPa
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# C12 = 76.4 GPa
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# C44 = 56.4 GPa
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print "Elastic Constant C11all = ${C11all} ${cunits}"
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print "Elastic Constant C22all = ${C22all} ${cunits}"
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print "Elastic Constant C33all = ${C33all} ${cunits}"
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print "Elastic Constant C12all = ${C12all} ${cunits}"
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print "Elastic Constant C13all = ${C13all} ${cunits}"
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print "Elastic Constant C23all = ${C23all} ${cunits}"
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print "Elastic Constant C44all = ${C44all} ${cunits}"
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print "Elastic Constant C55all = ${C55all} ${cunits}"
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print "Elastic Constant C66all = ${C66all} ${cunits}"
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print "Elastic Constant C14all = ${C14all} ${cunits}"
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print "Elastic Constant C15all = ${C15all} ${cunits}"
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print "Elastic Constant C16all = ${C16all} ${cunits}"
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print "Elastic Constant C24all = ${C24all} ${cunits}"
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print "Elastic Constant C25all = ${C25all} ${cunits}"
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print "Elastic Constant C26all = ${C26all} ${cunits}"
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print "Elastic Constant C34all = ${C34all} ${cunits}"
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print "Elastic Constant C35all = ${C35all} ${cunits}"
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print "Elastic Constant C36all = ${C36all} ${cunits}"
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print "Elastic Constant C45all = ${C45all} ${cunits}"
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print "Elastic Constant C46all = ${C46all} ${cunits}"
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print "Elastic Constant C56all = ${C56all} ${cunits}"
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print "Bulk Modulus = ${bulkmodulus} ${cunits}"
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print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
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print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
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print "Poisson Ratio = ${poissonratio}"
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@ -0,0 +1,37 @@
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# NOTE: This script can be modified for different atomic structures,
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# units, etc. See in.elastic for more info.
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#
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# Define the finite deformation size. Try several values of this
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# variable to verify that results do not depend on it.
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variable up equal 1.0e-1
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# metal units, elastic constants in GPa
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units metal
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variable cfac equal 1.0e-4
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variable cunits string GPa
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# Define MD parameters
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variable nevery equal 10
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variable nrepeat equal 10
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variable nfreq equal ${nevery}*${nrepeat}
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variable nthermo equal ${nfreq}
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variable nequil equal 10*${nthermo}
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variable nrun equal 3*${nthermo}
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variable temp equal 2000.0
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variable timestep equal 0.001
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variable mass1 equal 28.06
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variable tdamp equal 0.01
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variable seed equal 123457
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# generate the box and atom positions using a diamond lattice
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variable a equal 5.431
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boundary p p p
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lattice diamond $a
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region box prism 0 3.0 0 3.0 0 3.0 0.0 0.0 0.0
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create_box 1 box
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create_atoms 1 box
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mass 1 ${mass1}
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# NOTE: This script can be modified for different pair styles
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# See in.elastic for more info.
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reset_timestep 0
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# Choose potential
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pair_style sw
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pair_coeff * * Si.sw Si
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# Setup neighbor style
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neighbor 1.0 nsq
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neigh_modify once no every 1 delay 0 check yes
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# Setup output
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fix avp all ave/time ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
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thermo ${nthermo}
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thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
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thermo_modify norm no
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# Setup MD
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timestep ${timestep}
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fix 4 all nve
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fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
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@ -144,9 +144,13 @@ either by itself or in tandem with another code or library. See the
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COUPLE/README file to get started.
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The ELASTIC directory has an example script for computing elastic
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constants, using a zero temperature Si example. See the
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constants at zero temperature, using an Si example. See the
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ELASTIC/in.elastic file for more info.
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The ELASTIC_T directory has an example script for computing elastic
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constants at finite temperature, using an Si example. See the
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ELASTIC_T/in.elastic file for more info.
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The KAPPA directory has example scripts for computing the thermal
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conductivity (kappa) of a LJ liquid using 4 different methods. See
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the KAPPA/README file for more info.
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