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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13739 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
9ed741e904
commit
317744626c
|
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@ -69,11 +69,11 @@ is computed from the structure factor F using the equations:
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position of each atom, fj are atomic scattering factors.
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</P>
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<P>Diffraction intensities are calculated on a three-dimensional mesh of
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reciprocal lattice nodes. The mesh spacing is defined either (I) by
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the entire simulation domain or (II) manually using selected values as
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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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</P>
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<CENTER><A HREF = "saed_mesh.jpg"><IMG SRC = "JPG/saed_mesh_small.jpg"></A>
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<CENTER><A HREF = "JPG/saed_mesh.jpg"><IMG SRC = "JPG/saed_mesh_small.jpg"></A>
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</CENTER>
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<P>For a mesh defined by the simulation domain, a rectilinear grid is
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constructed with spacing <I>c</I>*inv(A) along each reciprocal lattice
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@ -89,7 +89,7 @@ will defined using the <I>c</I> 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 <B><0.05 Angstrom^(-1)</B> are implemented.
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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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</P>
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<P>The limits of the reciprocal lattice mesh are determined by the use of
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@ -103,9 +103,9 @@ 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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<I>dR_Ewald</I> thick surface of the Ewald sphere. See the example 3D
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intestiety data and the intersection of a <B>010</B> zone axis in the below image.
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intestiety data and the intersection of a [010] zone axis in the below image.
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</P>
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<CENTER><A HREF = "saed_ewald_intersect.jpg"><IMG SRC = "JPG/saed_ewald_intersect_small.jpg"></A>
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<CENTER><A HREF = "JPG/saed_ewald_intersect.jpg"><IMG SRC = "JPG/saed_ewald_intersect_small.jpg"></A>
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</CENTER>
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<P>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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@ -139,7 +139,7 @@ type. Valid chemical symbols for compute saed are:
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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:
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Cm: Bk: Cf:tb(c=5,s=:)
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</P>
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<P>If the <I>echo</I> keyword is specified, compute saed will provide extra
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reporting information to the screen.
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@ -160,11 +160,7 @@ options.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This command is part of the USER-DIFFRACTION package. It is only
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enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P>This command does not work for triclinic cells.
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<P>The compute_saed command does not work for triclinic cells.
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</P>
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<P><B>Related commands:</B>
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</P>
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@ -59,11 +59,11 @@ 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 (I) by
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the entire simulation domain or (II) manually using selected values as
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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,saed_mesh.jpg)
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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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@ -79,7 +79,7 @@ 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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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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@ -93,9 +93,9 @@ 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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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,saed_ewald_intersect.jpg)
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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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@ -129,7 +129,7 @@ type. Valid chemical symbols for compute saed are:
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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:
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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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@ -151,11 +151,7 @@ All array values calculated by this compute are "intensive".
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[Restrictions:]
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This command is part of the USER-DIFFRACTION package. It is only
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enabled if LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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This command does not work for triclinic cells.
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The compute_saed command does not work for triclinic cells.
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[Related commands:]
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@ -46,8 +46,8 @@
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<PRE>compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
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compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual
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</PRE>
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<PRE>fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1[1] mode vector weights c_1[2] file Rad2Theta.xrd
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fix 2 all ave/histo 1 1 1 10 100 250 c_2[1] mode vector weights c_2[2] file Deg2Theta.xrd
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<PRE>fix 1 all ave/histo/weights 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
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fix 2 all ave/histo/weights 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
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</PRE>
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<PRE>
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</PRE>
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@ -55,11 +55,11 @@ fix 2 all ave/histo 1 1 1 10 100 250 c_2[1] mode vector weights c_2[2] file Deg2
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</P>
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<P>Define a computation that calculates x-ray diffraction intensity as described
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in <A HREF = "#Coleman">(Coleman)</A> on a mesh of reciprocal lattice nodes defined
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by the entire simulation domain (or manually) using simulated radiation
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by the entire simulation domain (or manually) using a simulated radiation
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of wavelength lambda.
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</P>
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<P>The x-ray 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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<P>The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
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is computed from the structure factor, F, using the equations:
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</P>
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<CENTER><IMG SRC = "Eqs/compute_xrd1.jpg">
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</CENTER>
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@ -73,14 +73,14 @@ is computed from the structure factor F using the equations:
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position of each atom, fj are atomic scattering factors, LP is the
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Lorentz-polarization factor, and theta is the scattering angle of
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diffraction. The Lorentz-polarization factor can be turned off using
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the <I>LP</I> switch.
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the optional <I>LP</I> keyword.
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</P>
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<P>Diffraction intensities are calculated on a three-dimensional mesh of
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reciprocal lattice nodes. The mesh spacing is defined either (I)
|
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by the entire simulation domain or (II) manually using selected values as
|
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reciprocal lattice nodes. The mesh spacing is defined either (a)
|
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by 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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</P>
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<CENTER><A HREF = "xrd_mesh.jpg"><IMG SRC = "JPG/xrd_mesh_small.jpg"></A>
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<CENTER><A HREF = "JPG/xrd_mesh.jpg"><IMG SRC = "JPG/xrd_mesh_small.jpg"></A>
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</CENTER>
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<P>For a mesh defined by the simulation domain, a rectilinear grid is
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constructed with spacing <I>c</I>*inv(A) along each reciprocal lattice
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@ -159,7 +159,7 @@ type. Valid chemical symbols for compute xrd are:
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Ac3+: Th: Th4+: Pa: U:
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U3+: U4+: U6+: Np: Np3+:
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Np4+: Np6+: Pu: Pu3+: Pu4+:
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Pu6+: Am: Cm: Bk: Cf:
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Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:)
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</P>
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<P>If the <I>echo</I> keyword is specified, compute xrd will provide extra
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reporting information to the screen.
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@ -182,15 +182,11 @@ options.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This command is part of the USER-DIFFRACTION package. It is only
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enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P>This command does not work for triclinic cells.
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<P>The compute_xrd command does not work for triclinic cells.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_ave_histo.html">fix ave/histo</A>,
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<P><A HREF = "fix_ave_histo.html">fix ave/histo</A>,
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<A HREF = "compute_saed.html">compute saed</A>
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</P>
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<P><B>Default:</B>
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|
|
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@ -37,8 +37,8 @@ keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l
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compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
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compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre
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fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1\[1\] mode vector weights c_1\[2\] file Rad2Theta.xrd
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fix 2 all ave/histo 1 1 1 10 100 250 c_2\[1\] mode vector weights c_2\[2\] file Deg2Theta.xrd :pre
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fix 1 all ave/histo/weights 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd
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fix 2 all ave/histo/weights 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file Deg2Theta.xrd :pre
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:pre
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@ -46,11 +46,11 @@ fix 2 all ave/histo 1 1 1 10 100 250 c_2\[1\] mode vector weights c_2\[2\] file
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Define a computation that calculates x-ray diffraction intensity as described
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in "(Coleman)"_#Coleman on a mesh of reciprocal lattice nodes defined
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by the entire simulation domain (or manually) using simulated radiation
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by the entire simulation domain (or manually) using a simulated radiation
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of wavelength lambda.
|
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|
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The x-ray 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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The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
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is computed from the structure factor, F, using the equations:
|
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:c,image(Eqs/compute_xrd1.jpg)
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:c,image(Eqs/compute_xrd2.jpg)
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@ -61,14 +61,14 @@ 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, LP is the
|
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Lorentz-polarization factor, and theta is the scattering angle of
|
||||
diffraction. The Lorentz-polarization factor can be turned off using
|
||||
the {LP} switch.
|
||||
the optional {LP} keyword.
|
||||
|
||||
Diffraction intensities are calculated on a three-dimensional mesh of
|
||||
reciprocal lattice nodes. The mesh spacing is defined either (I)
|
||||
by the entire simulation domain or (II) manually using selected values as
|
||||
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,xrd_mesh.jpg)
|
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:c,image(JPG/xrd_mesh_small.jpg,JPG/xrd_mesh.jpg)
|
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|
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|
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For a mesh defined by the simulation domain, a rectilinear grid is
|
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|
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@ -148,8 +148,7 @@ type. Valid chemical symbols for compute xrd are:
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Ac3+: Th: Th4+: Pa: U:
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U3+: U4+: U6+: Np: Np3+:
|
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Np4+: Np6+: Pu: Pu3+: Pu4+:
|
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Pu6+: Am: Cm: Bk: Cf:
|
||||
|
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Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:)
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|
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If the {echo} keyword is specified, compute xrd will provide extra
|
||||
reporting information to the screen.
|
||||
|
|
@ -172,15 +171,11 @@ All array values calculated by this compute are "intensive".
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
This command 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.
|
||||
|
||||
This command does not work for triclinic cells.
|
||||
The compute_xrd command does not work for triclinic cells.
|
||||
|
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[Related commands:]
|
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|
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"fix ave/histo"_compute_ave_histo.html,
|
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"fix ave/histo"_fix_ave_histo.html,
|
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"compute saed"_compute_saed.html
|
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|
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[Default:]
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|
|
|
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|
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@ -76,7 +76,7 @@
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<PRE>fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
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fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
|
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fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
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fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD<B>1</B> c_XRD<B>2</B>
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fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
|
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</PRE>
|
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<P><B>Description:</B>
|
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</P>
|
||||
|
|
|
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|
|
@ -60,7 +60,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
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fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
|
||||
fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[2\] c_thermo_press\[3\] title1 "My output values"
|
||||
fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
|
||||
fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2] :pre
|
||||
fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@
|
|||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
|
||||
<LI>ave/time/saed = style name of this fix command
|
||||
<LI>saed/vtk = style name of this fix command
|
||||
|
||||
<LI>Nevery = use input values every this many timesteps
|
||||
|
||||
|
|
@ -62,7 +62,7 @@ outside the <I>Kmax</I> range assigned in the compute saed. The ghost data is
|
|||
assigned a value of -1 and can be removed setting a minimum isovolume
|
||||
of 0 within the vizualiziton software. SAED images can be created by
|
||||
visualizing a spherical slice of the data that is centered at
|
||||
R_Ewald*<B>h k l</B>/norm(<B>h k l</B>), where R_Ewald=1/lambda.
|
||||
R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda.
|
||||
</P>
|
||||
<P>The group specified within this command is ignored. However, note that
|
||||
specified values may represent calculations performed by saed computes
|
||||
|
|
@ -102,16 +102,24 @@ diffraction intensity outputs.
|
|||
</P>
|
||||
<P>By default the header contains the following information (with example data):
|
||||
</P>
|
||||
<P># vtk DataFile Version 3.0 c_SAED
|
||||
<PRE># vtk DataFile Version 3.0 c_SAED
|
||||
Image data set
|
||||
ASCII
|
||||
DATASET STRUCTURED_POINTS
|
||||
DIMENSIONS 337 219 209
|
||||
ASPECT_RATIO 0.00507953 0.00785161 0.00821458
|
||||
ORIGIN -0.853361 -0.855826 -0.854316 \n POINT_DATA 15424827
|
||||
ORIGIN -0.853361 -0.855826 -0.854316
|
||||
POINT_DATA 15424827
|
||||
SCALARS intensity float
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||||
LOOKUP_TABLE default
|
||||
...data
|
||||
...data
|
||||
</PRE>
|
||||
<P>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
|
||||
where the mesh spacing is approximately 0.005, 0.007, and 0.008
|
||||
inv(length) units in the k1, k2, and k3 directions, respectively.
|
||||
The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that
|
||||
the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are
|
||||
sampled in total.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
@ -170,12 +178,8 @@ minimization</A>.
|
|||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This command is part of the USER-DIFFRACTION package. It is only
|
||||
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>The attributes for fix_saed_vtk must match the values assigned in the
|
||||
associated <A HREF = "compute_saed.txt">compute_saed</A> command.
|
||||
associated <A HREF = "compute_saed.html">compute_saed</A> command.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ fix saed/vtk command :h3
|
|||
fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
ave/time/saed = style name of this fix command :l
|
||||
saed/vtk = style name of this fix command :l
|
||||
Nevery = use input values every this many timesteps :l
|
||||
Nrepeat = # of times to use input values for calculating averages :l
|
||||
Nfreq = calculate averages every this many timesteps :l
|
||||
|
|
@ -54,7 +54,7 @@ outside the {Kmax} range assigned in the compute saed. The ghost data is
|
|||
assigned a value of -1 and can be removed setting a minimum isovolume
|
||||
of 0 within the vizualiziton software. SAED images can be created by
|
||||
visualizing a spherical slice of the data that is centered at
|
||||
R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda.
|
||||
R_Ewald*\[h k l\]/norm(\[h k l\]), where R_Ewald=1/lambda.
|
||||
|
||||
The group specified within this command is ignored. However, note that
|
||||
specified values may represent calculations performed by saed computes
|
||||
|
|
@ -100,10 +100,18 @@ ASCII
|
|||
DATASET STRUCTURED_POINTS
|
||||
DIMENSIONS 337 219 209
|
||||
ASPECT_RATIO 0.00507953 0.00785161 0.00821458
|
||||
ORIGIN -0.853361 -0.855826 -0.854316 \n POINT_DATA 15424827
|
||||
ORIGIN -0.853361 -0.855826 -0.854316
|
||||
POINT_DATA 15424827
|
||||
SCALARS intensity float
|
||||
LOOKUP_TABLE default
|
||||
...data
|
||||
...data :pre
|
||||
|
||||
In this example, kspace is sampled across a 337 x 219 x 209 point mesh
|
||||
where the mesh spacing is approximately 0.005, 0.007, and 0.008
|
||||
inv(length) units in the k1, k2, and k3 directions, respectively.
|
||||
The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that
|
||||
the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are
|
||||
sampled in total.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -162,12 +170,8 @@ minimization"_minimize.html.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
This command 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 attributes for fix_saed_vtk must match the values assigned in the
|
||||
associated "compute_saed"_compute_saed.txt command.
|
||||
associated "compute_saed"_compute_saed.html command.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue