forked from lijiext/lammps
183 lines
7.2 KiB
Plaintext
183 lines
7.2 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
:link(ld,Manual.html)
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
:line
|
|
|
|
compute saed command :h3
|
|
|
|
[Syntax:]
|
|
|
|
compute ID group-ID saed lambda type1 type2 ... typeN keyword value ... :pre
|
|
|
|
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
|
saed = style name of this compute command :l
|
|
lambda = wavelength of incident radiation (length units) :l
|
|
type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) :l
|
|
|
|
zero or more keyword/value pairs may be appended :l
|
|
keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l
|
|
{Kmax} value = Maximum distance explored from reciprocal space origin
|
|
(inverse length units)
|
|
{Zone} values = z1 z2 z3
|
|
z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
|
|
reciprocal space will be meshed up to {Kmax}
|
|
{dR_Ewald} value = Thickness of Ewald sphere slice intercepting
|
|
reciprocal space (inverse length units)
|
|
{c} values = c1 c2 c3
|
|
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
|
lattice nodes in the h, k, and l directions respectively
|
|
{manual} = flag to use manual spacing of reciprocal lattice points
|
|
based on the values of the {c} parameters
|
|
{echo} = flag to provide extra output for debugging purposes :pre
|
|
:ule
|
|
|
|
[Examples:]
|
|
|
|
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
|
|
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre
|
|
|
|
fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
|
|
fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
|
|
|
|
[Description:]
|
|
|
|
Define a computation that calculates electron diffraction intensity as
|
|
described in "(Coleman)"_#Coleman on a mesh of reciprocal lattice nodes
|
|
defined by the entire simulation domain (or manually) using simulated
|
|
radiation of wavelength lambda.
|
|
|
|
The electron diffraction intensity I at each reciprocal lattice point
|
|
is computed from the structure factor F using the equations:
|
|
|
|
:c,image(Eqs/compute_saed1.jpg)
|
|
:c,image(Eqs/compute_saed2.jpg)
|
|
|
|
Here, K is the location of the reciprocal lattice node, rj is the
|
|
position of each atom, fj are atomic scattering factors.
|
|
|
|
Diffraction intensities are calculated on a three-dimensional mesh of
|
|
reciprocal lattice nodes. The mesh spacing is defined either (a) by
|
|
the entire simulation domain or (b) manually using selected values as
|
|
shown in the 2D diagram below.
|
|
|
|
:c,image(JPG/saed_mesh_small.jpg,JPG/saed_mesh.jpg)
|
|
|
|
For a mesh defined by the simulation domain, a rectilinear grid is
|
|
constructed with spacing {c}*inv(A) along each reciprocal lattice
|
|
axis. Where A are the vectors corresponding to the edges of the
|
|
simulation cell. If one or two directions has non-periodic boundary
|
|
conditions, then the spacing in these directions is defined from the
|
|
average of the (inversed) box lengths with periodic boundary conditions.
|
|
Meshes defined by the simulation domain must contain at least one periodic
|
|
boundary.
|
|
|
|
If the {manual} flag is included, the mesh of reciprocal lattice nodes
|
|
will defined using the {c} values for the spacing along each reciprocal
|
|
lattice axis. Note that manual mapping of the reciprocal space mesh is
|
|
good for comparing diffraction results from multiple simulations; however
|
|
it can reduce the likelihood that Bragg reflections will be satisfied
|
|
unless small spacing parameters <0.05 Angstrom^(-1) are implemented.
|
|
Meshes with manual spacing do not require a periodic boundary.
|
|
|
|
The limits of the reciprocal lattice mesh are determined by the use of
|
|
the {Kmax}, {Zone}, and {dR_Ewald} parameters. The rectilinear mesh
|
|
created about the origin of reciprocal space is terminated at the
|
|
boundary of a sphere of radius {Kmax} centered at the origin. If
|
|
{Zone} parameters z1=z2=z3=0 are used, diffraction intensities are
|
|
computed throughout the entire spherical volume - note this can
|
|
greatly increase the cost of computation. Otherwise, {Zone}
|
|
parameters will denote the z1=h, z2=k, and z3=l (in a global since)
|
|
zone axis of an intersecting Ewald sphere. Diffraction intensities
|
|
will only be computed at the intersection of the reciprocal lattice
|
|
mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the
|
|
example 3D intestiety data and the intersection of a \[010\] zone axis
|
|
in the below image.
|
|
|
|
:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)
|
|
|
|
The atomic scattering factors, fj, accounts for the reduction in
|
|
diffraction intensity due to Compton scattering. Compute saed uses
|
|
analytical approximations of the atomic scattering factors that vary
|
|
for each atom type (type1 type2 ... typeN) and angle of diffraction.
|
|
The analytic approximation is computed using the formula
|
|
"(Brown)"_#Brown:
|
|
|
|
:c,image(Eqs/compute_saed3.jpg)
|
|
|
|
Coefficients parameterized by "(Fox)"_#Fox are assigned for each
|
|
atom type designating the chemical symbol and charge of each atom
|
|
type. Valid chemical symbols for compute saed are:
|
|
|
|
H: He: Li: Be: B:
|
|
C: N: O: F: Ne:
|
|
Na: Mg: Al: Si: P:
|
|
S: Cl: Ar: K: Ca:
|
|
Sc: Ti: V: Cr: Mn:
|
|
Fe: Co: Ni: Cu: Zn:
|
|
Ga: Ge: As: Se: Br:
|
|
Kr: Rb: Sr: Y: Zr:
|
|
Nb: Mo: Tc: Ru: Rh:
|
|
Pd: Ag: Cd: In: Sn:
|
|
Sb: Te: I: Xe: Cs:
|
|
Ba: La: Ce: Pr: Nd:
|
|
Pm: Sm: Eu: Gd: Tb:
|
|
Dy: Ho: Er: Tm: Yb:
|
|
Lu: Hf: Ta: W: Re:
|
|
Os: Ir: Pt: Au: Hg:
|
|
Tl: Pb: Bi: Po: At:
|
|
Rn: Fr: Ra: Ac: Th:
|
|
Pa: U: Np: Pu: Am:
|
|
Cm: Bk: Cf:tb(c=5,s=:)
|
|
|
|
|
|
If the {echo} keyword is specified, compute saed will provide extra
|
|
reporting information to the screen.
|
|
|
|
[Output info:]
|
|
|
|
This compute calculates a global vector. The length of the vector is
|
|
the number of reciprocal lattice nodes that are explored by the mesh.
|
|
The entries of the global vector are the computed diffraction
|
|
intensities as described above.
|
|
|
|
The vector can be accessed by any command that uses global values
|
|
from a compute as input. See "this
|
|
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
|
options.
|
|
|
|
All array values calculated by this compute are "intensive".
|
|
|
|
[Restrictions:]
|
|
|
|
This compute is part of the USER-DIFFRACTION package. It is only
|
|
enabled if LAMMPS was built with that package. See the "Making
|
|
LAMMPS"_Section_start.html#start_3 section for more info.
|
|
|
|
The compute_saed command does not work for triclinic cells.
|
|
|
|
[Related commands:]
|
|
|
|
"fix saed_vtk"_fix_saed_vtk.html, "compute xrd"_compute_xrd.html
|
|
|
|
[Default:]
|
|
|
|
The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
|
|
0.01.
|
|
|
|
:line
|
|
|
|
:link(Coleman)
|
|
[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020
|
|
(2013).
|
|
|
|
:link(Brown)
|
|
[(Brown)] Brown et al. International Tables for Crystallography
|
|
Volume C: Mathematical and Chemical Tables, 554-95 (2004).
|
|
|
|
:link(Fox)
|
|
[(Fox)] Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93
|
|
(1989).
|