compute_xrd.txt
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compute_xrd.txt
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			"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 xrd command :h3

			[Syntax:]

			compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ... :pre

			ID, group-ID are documented in "compute"_compute.html command :ulb,l
			xrd = 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 = {2Theta} or {c} or {LP} or {manual} or {echo} :l
			{2Theta} values = Min2Theta Max2Theta
			Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
			(radians or degrees)
			{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
			{LP} value = switch to apply Lorentz-polarization factor
			0/1 = off/on
			{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 xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
			compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre

			fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd
			fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file Deg2Theta.xrd :pre

			[Description:]

			Define a computation that calculates x-ray diffraction intensity as described
			in "(Coleman)"_#xrd-Coleman on a mesh of reciprocal lattice nodes defined
			by the entire simulation domain (or manually) using a simulated radiation
			of wavelength lambda.

			The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
			is computed from the structure factor, F, using the equations:

			:c,image(Eqs/compute_xrd1.jpg)
			:c,image(Eqs/compute_xrd2.jpg)
			:c,image(Eqs/compute_xrd3.jpg)
			:c,image(Eqs/compute_xrd4.jpg)

			Here, K is the location of the reciprocal lattice node, rj is the
			position of each atom, fj are atomic scattering factors, LP is the
			Lorentz-polarization factor, and theta is the scattering angle of
			diffraction. The Lorentz-polarization factor can be turned off using
			the optional {LP} keyword.

			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/xrd_mesh_small.jpg,JPG/xrd_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 range of
			scattering angles explored. The {2Theta} parameters allows the user
			to reduce the scattering angle range to only the region of interest
			which reduces the cost of the computation.

			The atomic scattering factors, fj, accounts for the reduction in
			diffraction intensity due to Compton scattering. Compute xrd 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
			"(Colliex)"_#Colliex:

			:c,image(Eqs/compute_xrd5.jpg)

			Coefficients parameterized by "(Peng)"_#Peng are assigned for each
			atom type designating the chemical symbol and charge of each atom
			type. Valid chemical symbols for compute xrd are:

			H\| He1-\| He\| Li\| Li1+\|
			Be\| Be2+\| B\| C\| Cval\|
			N\| O\| O1-\| F\| F1-\|
			Ne\| Na\| Na1+\| Mg\| Mg2+\|
			Al\| Al3+\| Si\| Sival\| Si4+\|
			P\| S\| Cl\| Cl1-\| Ar\|
			K\| Ca\| Ca2+\| Sc\| Sc3+\|
			Ti\| Ti2+\| Ti3+\| Ti4+\| V\|
			V2+\| V3+\| V5+\| Cr\| Cr2+\|
			Cr3+\| Mn\| Mn2+\| Mn3+\| Mn4+\|
			Fe\| Fe2+\| Fe3+\| Co\| Co2+\|
			Co\| Ni\| Ni2+\| Ni3+\| Cu\|
			Cu1+\| Cu2+\| Zn\| Zn2+\| Ga\|
			Ga3+\| Ge\| Ge4+\| As\| Se\|
			Br\| Br1-\| Kr\| Rb\| Rb1+\|
			Sr\| Sr2+\| Y\| Y3+\| Zr\|
			Zr4+\| Nb\| Nb3+\| Nb5+\| Mo\|
			Mo3+\| Mo5+\| Mo6+\| Tc\| Ru\|
			Ru3+\| Ru4+\| Rh\| Rh3+\| Rh4+\|
			Pd\| Pd2+\| Pd4+\| Ag\| Ag1+\|
			Ag2+\| Cd\| Cd2+\| In\| In3+\|
			Sn\| Sn2+\| Sn4+\| Sb\| Sb3+\|
			Sb5+\| Te\| I\| I1-\| Xe\|
			Cs\| Cs1+\| Ba\| Ba2+\| La\|
			La3+\| Ce\| Ce3+\| Ce4+\| Pr\|
			Pr3+\| Pr4+\| Nd\| Nd3+\| Pm\|
			Pm3+\| Sm\| Sm3+\| Eu\| Eu2+\|
			Eu3+\| Gd\| Gd3+\| Tb\| Tb3+\|
			Dy\| Dy3+\| Ho\| Ho3+\| Er\|
			Er3+\| Tm\| Tm3+\| Yb\| Yb2+\|
			Yb3+\| Lu\| Lu3+\| Hf\| Hf4+\|
			Ta\| Ta5+\| W\| W6+\| Re\|
			Os\| Os4+\| Ir\| Ir3+\| Ir4+\|
			Pt\| Pt2+\| Pt4+\| Au\| Au1+\|
			Au3+\| Hg\| Hg1+\| Hg2+\| Tl\|
			Tl1+\| Tl3+\| Pb\| Pb2+\| Pb4+\|
			Bi\| Bi3+\| Bi5+\| Po\| At\|
			Rn\| Fr\| Ra\| Ra2+\| Ac\|
			Ac3+\| Th\| Th4+\| Pa\| U\|
			U3+\| U4+\| U6+\| Np\| Np3+\|
			Np4+\| Np6+\| Pu\| Pu3+\| Pu4+\|
			Pu6+\| Am\| Cm\| Bk\| Cf :tb(c=5,s=\|)

			If the {echo} keyword is specified, compute xrd will provide extra
			reporting information to the screen.

			[Output info:]

			This compute calculates a global array. The number of rows in the
			array is the number of reciprocal lattice nodes that are explored
			which by the mesh. The global array has 2 columns.

			The first column contains the diffraction angle in the units (radians
			or degrees) provided with the {2Theta} values. The second column contains
			the computed diffraction intensities as described above.

			The array 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_xrd command does not work for triclinic cells.

			[Related commands:]

			"fix ave/histo"_fix_ave_histo.html,
			"compute saed"_compute_saed.html

			[Default:]

			The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
			no manual flag, no echo flag.

			:line

			:link(xrd-Coleman)
			[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020
			(2013).

			:link(Colliex)
			[(Colliex)] Colliex et al. International Tables for Crystallography
			Volume C: Mathematical and Chemical Tables, 249-429 (2004).

			:link(Peng)
			[(Peng)] Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76
			(1996).

lammps/doc/src/compute_xrd.txtfd2ac15c2eadrunner

compute_xrd.txtView Options

lammps/doc/src/compute_xrd.txt
fd2ac15c2eadrunner

compute_xrd.txt
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