diff --git a/doc/compute_saed.html b/doc/compute_saed.html index 88a2fbb521..c99d3ae823 100644 --- a/doc/compute_saed.html +++ b/doc/compute_saed.html @@ -69,11 +69,11 @@ is computed from the structure factor F using the equations: 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 (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.

-
+

For a mesh defined by the simulation domain, a rectilinear grid is constructed with spacing c*inv(A) along each reciprocal lattice @@ -89,7 +89,7 @@ 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. +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 @@ -103,9 +103,9 @@ 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. +intestiety data and the intersection of a [010] zone axis in the below image.

-
+

The atomic scattering factors, fj, accounts for the reduction in diffraction intensity due to Compton scattering. Compute saed uses @@ -139,7 +139,7 @@ type. Valid chemical symbols for compute saed are: Tl: Pb: Bi: Po: At: Rn: Fr: Ra: Ac: Th: Pa: U: Np: Pu: Am: - Cm: Bk: Cf: + Cm: Bk: Cf:tb(c=5,s=:)

If the echo keyword is specified, compute saed will provide extra reporting information to the screen. @@ -160,11 +160,7 @@ options.

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 for more info. -

-

This command does not work for triclinic cells. +

The compute_saed command does not work for triclinic cells.

Related commands:

diff --git a/doc/compute_saed.txt b/doc/compute_saed.txt index 1a0ea4b331..1eef9de429 100644 --- a/doc/compute_saed.txt +++ b/doc/compute_saed.txt @@ -59,11 +59,11 @@ 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 (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/saed_mesh_small.jpg,saed_mesh.jpg) +: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 @@ -79,7 +79,7 @@ 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. +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 @@ -93,9 +93,9 @@ 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. +intestiety data and the intersection of a \[010\] zone axis in the below image. -:c,image(JPG/saed_ewald_intersect_small.jpg,saed_ewald_intersect.jpg) +: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 @@ -129,7 +129,7 @@ type. Valid chemical symbols for compute saed are: Tl: Pb: Bi: Po: At: Rn: Fr: Ra: Ac: Th: Pa: U: Np: Pu: Am: - Cm: Bk: Cf: + Cm: Bk: Cf:tb(c=5,s=:) If the {echo} keyword is specified, compute saed will provide extra @@ -151,11 +151,7 @@ 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_saed command does not work for triclinic cells. [Related commands:] diff --git a/doc/compute_xrd.html b/doc/compute_xrd.html index be78543107..e69612ac17 100644 --- a/doc/compute_xrd.html +++ b/doc/compute_xrd.html @@ -46,8 +46,8 @@ 
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
-
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
-fix 2 all ave/histo 1 1 1 10 100 250 c_2[1] mode vector weights c_2[2] file Deg2Theta.xrd 
+
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
+fix 2 all ave/histo/weights 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd 
 

 
 

@@ -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
 

 
Define a computation that calculates x-ray diffraction intensity as described
 in (Coleman) on a mesh of reciprocal lattice nodes defined 
-by the entire simulation domain (or manually) using simulated radiation
+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 
-is computed from the structure factor F using the equations:
+
The x-ray diffraction intensity, I, at each reciprocal lattice point, k, 
+is computed from the structure factor, F, using the equations:
 

 

 

@@ -73,14 +73,14 @@ is computed from the structure factor F using the equations:
 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 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.
 

-

+

 

 
For a mesh defined by the simulation domain, a rectilinear grid is
 constructed with spacing c*inv(A) along each reciprocal lattice
@@ -159,7 +159,7 @@ type. Valid chemical symbols for compute xrd are:
       Ac3+:      Th:    Th4+:      Pa:       U:
        U3+:     U4+:     U6+:      Np:    Np3+:
       Np4+:    Np6+:      Pu:    Pu3+:    Pu4+:
-      Pu6+:      Am:      Cm:      Bk:      Cf:
+      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.  
@@ -182,15 +182,11 @@ options.
 

 
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 for more info.
-

-
This command does not work for triclinic cells. 
+
The compute_xrd command does not work for triclinic cells. 
 

 
Related commands: 
 

-
fix ave/histo,
+
fix ave/histo,
 compute saed
 

 
Default: 
diff --git a/doc/compute_xrd.txt b/doc/compute_xrd.txt
index a67bed585d..49d5a5d2fe 100644
--- a/doc/compute_xrd.txt
+++ b/doc/compute_xrd.txt
@@ -37,8 +37,8 @@ keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l
 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 1 1 1 0.087 0.87 250 c_1\[1\] mode vector weights c_1\[2\] file Rad2Theta.xrd
-fix 2 all ave/histo 1 1 1 10 100 250 c_2\[1\] mode vector weights c_2\[2\] file Deg2Theta.xrd :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
+fix 2 all ave/histo/weights 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file Deg2Theta.xrd :pre
 
 :pre
 
@@ -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
 
 Define a computation that calculates x-ray 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
+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 
-is computed from the structure factor F using the equations:
+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)
@@ -61,14 +61,14 @@ 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 {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)
+:c,image(JPG/xrd_mesh_small.jpg,JPG/xrd_mesh.jpg)
 
 
 For a mesh defined by the simulation domain, a rectilinear grid is
@@ -148,8 +148,7 @@ type. Valid chemical symbols for compute xrd are:
       Ac3+:      Th:    Th4+:      Pa:       U:
        U3+:     U4+:     U6+:      Np:    Np3+:
       Np4+:    Np6+:      Pu:    Pu3+:    Pu4+:
-      Pu6+:      Am:      Cm:      Bk:      Cf:
-
+      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.  
@@ -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. 
 
 [Related commands:] 
 
-"fix ave/histo"_compute_ave_histo.html,
+"fix ave/histo"_fix_ave_histo.html,
 "compute saed"_compute_saed.html
 
 [Default:] 
diff --git a/doc/fix_ave_histo.html b/doc/fix_ave_histo.html
index 45eb55d515..96e16bd57b 100644
--- a/doc/fix_ave_histo.html
+++ b/doc/fix_ave_histo.html
@@ -76,7 +76,7 @@
 
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_XRD1 c_XRD2 
+fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2] 
 

 
Description:
 

diff --git a/doc/fix_ave_histo.txt b/doc/fix_ave_histo.txt
index cf256cdbff..c580987c93 100644
--- a/doc/fix_ave_histo.txt
+++ b/doc/fix_ave_histo.txt
@@ -60,7 +60,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
 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:]
 
diff --git a/doc/fix_saed_vtk.html b/doc/fix_saed_vtk.html
index 233444c6d7..25b281cb2c 100644
--- a/doc/fix_saed_vtk.html
+++ b/doc/fix_saed_vtk.html
@@ -17,7 +17,7 @@