forked from lijiext/lammps
178 lines
7.0 KiB
Plaintext
178 lines
7.0 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute saed command :h3
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[Syntax:]
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compute ID group-ID saed lambda type1 type2 ... typeN keyword value ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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saed = style name of this compute command :l
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lambda = wavelength of incident radiation (length units) :l
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type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) :l
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zero or more keyword/value pairs may be appended :l
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keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l
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{Kmax} value = Maximum distance explored from reciprocal space origin
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(inverse length units)
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{Zone} values = z1 z2 z3
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z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
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reciprocal space will be meshed up to {Kmax}
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{dR_Ewald} value = Thickness of Ewald sphere slice intercepting
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reciprocal space (inverse length units)
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{c} values = c1 c2 c3
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c1,c2,c3 = parameters to adjust the spacing of the reciprocal
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lattice nodes in the h, k, and l directions respectively
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{manual} = flag to use manual spacing of reciprocal lattice points
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based on the values of the {c} parameters
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{echo} = flag to provide extra output for debugging purposes :pre
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:ule
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[Examples:]
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compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
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compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre
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fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
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fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
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[Description:]
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Define a computation that calculates electron diffraction intensity as
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described in "(Coleman)"_#Coleman on a mesh of reciprocal lattice nodes
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defined by the entire simulation domain (or manually) using simulated
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radiation of wavelength lambda.
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The electron diffraction intensity I at each reciprocal lattice point
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is computed from the structure factor F using the equations:
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:c,image(Eqs/compute_saed1.jpg)
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:c,image(Eqs/compute_saed2.jpg)
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Here, K is the location of the reciprocal lattice node, rj is the
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position of each atom, fj are atomic scattering factors.
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Diffraction intensities are calculated on a three-dimensional mesh of
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reciprocal lattice nodes. The mesh spacing is defined either (a) by
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the entire simulation domain or (b) manually using selected values as
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shown in the 2D diagram below.
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:c,image(JPG/saed_mesh_small.jpg,JPG/saed_mesh.jpg)
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For a mesh defined by the simulation domain, a rectilinear grid is
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constructed with spacing {c}*inv(A) along each reciprocal lattice
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axis. Where A are the vectors corresponding to the edges of the
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simulation cell. If one or two directions has non-periodic boundary
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conditions, then the spacing in these directions is defined from the
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average of the (inversed) box lengths with periodic boundary conditions.
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Meshes defined by the simulation domain must contain at least one periodic
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boundary.
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If the {manual} flag is included, the mesh of reciprocal lattice nodes
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will defined using the {c} values for the spacing along each reciprocal
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lattice axis. Note that manual mapping of the reciprocal space mesh is
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good for comparing diffraction results from multiple simulations; however
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it can reduce the likelihood that Bragg reflections will be satisfied
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unless small spacing parameters <0.05 Angstrom^(-1) are implemented.
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Meshes with manual spacing do not require a periodic boundary.
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The limits of the reciprocal lattice mesh are determined by the use of
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the {Kmax}, {Zone}, and {dR_Ewald} parameters. The rectilinear mesh
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created about the origin of reciprocal space is terminated at the
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boundary of a sphere of radius {Kmax} centered at the origin. If
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{Zone} parameters z1=z2=z3=0 are used, diffraction intensities are
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computed throughout the entire spherical volume - note this can greatly
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increase the cost of computation. Otherwise, {Zone} parameters will
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denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an
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intersecting Ewald sphere. Diffraction intensities will only be
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computed at the intersection of the reciprocal lattice mesh and a
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{dR_Ewald} thick surface of the Ewald sphere. See the example 3D
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intestiety data and the intersection of a \[010\] zone axis in the below image.
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:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)
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The atomic scattering factors, fj, accounts for the reduction in
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diffraction intensity due to Compton scattering. Compute saed uses
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analytical approximations of the atomic scattering factors that vary
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for each atom type (type1 type2 ... typeN) and angle of diffraction.
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The analytic approximation is computed using the formula
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"(Brown)"_#Brown:
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:c,image(Eqs/compute_saed3.jpg)
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Coefficients parameterized by "(Fox)"_#Fox are assigned for each
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atom type designating the chemical symbol and charge of each atom
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type. Valid chemical symbols for compute saed are:
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H: He: Li: Be: B:
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C: N: O: F: Ne:
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Na: Mg: Al: Si: P:
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S: Cl: Ar: K: Ca:
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Sc: Ti: V: Cr: Mn:
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Fe: Co: Ni: Cu: Zn:
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Ga: Ge: As: Se: Br:
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Kr: Rb: Sr: Y: Zr:
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Nb: Mo: Tc: Ru: Rh:
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Pd: Ag: Cd: In: Sn:
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Sb: Te: I: Xe: Cs:
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Ba: La: Ce: Pr: Nd:
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Pm: Sm: Eu: Gd: Tb:
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Dy: Ho: Er: Tm: Yb:
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Lu: Hf: Ta: W: Re:
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Os: Ir: Pt: Au: Hg:
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Tl: Pb: Bi: Po: At:
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Rn: Fr: Ra: Ac: Th:
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Pa: U: Np: Pu: Am:
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Cm: Bk: Cf:tb(c=5,s=:)
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If the {echo} keyword is specified, compute saed will provide extra
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reporting information to the screen.
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[Output info:]
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This compute calculates a global vector. The length of the vector is
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the number of reciprocal lattice nodes that are explored by the mesh.
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The entries of the global vector are the computed diffraction
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intensities as described above.
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The vector can be accessed by any command that uses global values
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from a compute as input. See "this
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section"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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All array values calculated by this compute are "intensive".
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[Restrictions:]
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The compute_saed command does not work for triclinic cells.
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[Related commands:]
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"fix saed_vtk"_fix_saed_vtk.html, "compute xrd"_compute_xrd.html
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[Default:]
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The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
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0.01.
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:line
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:link(Coleman)
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[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020
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(2013).
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:link(Brown)
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[(Brown)] Brown et al. International Tables for Crystallography
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Volume C: Mathematical and Chemical Tables, 554-95 (2004).
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:link(Fox)
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[(Fox)] Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93
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(1989).
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