''

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13795 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_python.html

@@ -860,7 +860,7 @@ variables that have to match the VMD installation on your system.</p>
 source code for individual scripts for comments about what they do.</p>
 <p>Here are screenshots of the vizplotgui_tool.py script in action for
 different visualization package options.  Click to see larger images:</p>
-<a data-lightbox="group-c530f122-6019-45af-8a35-e7cdc70ddb55"
+<a data-lightbox="group-default"
                    href="_images/screenshot_gl.jpg"
                    class=""
                    title=""
@@ -870,7 +870,7 @@ different visualization package options.  Click to see larger images:</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-f712591c-ea31-483b-86da-3905db788920"
+                    </a><a data-lightbox="group-default"
                    href="_images/screenshot_atomeye.jpg"
                    class=""
                    title=""
@@ -880,7 +880,7 @@ different visualization package options.  Click to see larger images:</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-4a2be907-5b47-4889-89de-f686acc6e915"
+                    </a><a data-lightbox="group-default"
                    href="_images/screenshot_pymol.jpg"
                    class=""
                    title=""
@@ -890,7 +890,7 @@ different visualization package options.  Click to see larger images:</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-e62d1b66-7f66-44c5-ba32-c4396e2529ed"
+                    </a><a data-lightbox="group-default"
                    href="_images/screenshot_vmd.jpg"
                    class=""
                    title=""

doc/balance.html

@@ -265,7 +265,7 @@ the processor that owns them.  The leftmost diagram is the default
 partitioning of the simulation box across processors (one sub-box for
 each of 16 processors); the middle diagram is after a “grid” method
 has been applied.</p>
-<a data-lightbox="group-1ea1982f-2af8-42b4-be30-2e7feb8e77f5"
+<a data-lightbox="group-default"
                    href="_images/balance_uniform.jpg"
                    class=""
                    title=""
@@ -275,7 +275,7 @@ has been applied.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-a4b3cf56-edc0-41c1-a22e-57acb6d303e2"
+                    </a><a data-lightbox="group-default"
                    href="_images/balance_nonuniform.jpg"
                    class=""
                    title=""
@@ -285,7 +285,7 @@ has been applied.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-c0259437-bded-4589-b518-4425480db921"
+                    </a><a data-lightbox="group-default"
                    href="_images/balance_rcb.jpg"
                    class=""
                    title=""

doc/compute_saed.html

@@ -182,7 +182,7 @@ position of each atom, fj are atomic scattering factors.</p>
 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.</p>
-<a data-lightbox="group-a30c5cda-68d7-4c1b-a26c-5316847c9103"
+<a data-lightbox="group-default"
                    href="_images/saed_mesh.jpg"
                    class=""
                    title=""
@@ -219,7 +219,7 @@ intersecting Ewald sphere.  Diffraction intensities will only be
 computed at the intersection of the reciprocal lattice mesh and a
 <em>dR_Ewald</em> thick surface of the Ewald sphere.  See the example 3D
 intestiety data and the intersection of a [010] zone axis in the below image.</p>
-<a data-lightbox="group-8fb8943f-067b-4621-ab85-ef00bd1882fd"
+<a data-lightbox="group-default"
                    href="_images/saed_ewald_intersect.jpg"
                    class=""
                    title=""

doc/compute_temp_cs.html

@@ -167,7 +167,10 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in the group, k = Boltzmann constant, and T = temperature.  Note that
 the velocity of each core or shell atom used in the KE calculation is
 the velocity of the center-of-mass (COM) of the core/shell pair the
-atom is part of.</p>
+atom is part of.  Note that atoms that are not core or shell particles
+are also included in the temperature calculation (if they are in the
+specified group-ID); they contribute to the total kinetic energy in
+the usual way.</p>
 <p>A kinetic energy tensor, stored as a 6-element vector, is also
 calculated by this compute for use in the computation of a pressure
 tensor.  The formula for the components of the tensor is the same as

doc/compute_temp_cs.txt

@@ -41,7 +41,7 @@ For this compute, core and shell particles are specified by two
 respective group IDs, which can be defined using the
 "group"_group.html command.  The number of atoms in the two groups
 must be the same and there should be one bond defined between a pair
-of atoms in the two groups.
+of atoms in the two groups.  
 
 The temperature is calculated by the formula KE = dim/2 N k T, where
 KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
@@ -49,7 +49,10 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
 in the group, k = Boltzmann constant, and T = temperature.  Note that
 the velocity of each core or shell atom used in the KE calculation is
 the velocity of the center-of-mass (COM) of the core/shell pair the
-atom is part of.
+atom is part of.  Note that atoms that are not core or shell particles
+are also included in the temperature calculation (if they are in the
+specified group-ID); they contribute to the total kinetic energy in
+the usual way.
 
 A kinetic energy tensor, stored as a 6-element vector, is also
 calculated by this compute for use in the computation of a pressure

doc/compute_xrd.html

@@ -185,7 +185,7 @@ the optional <em>LP</em> keyword.</p>
 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.</p>
-<a data-lightbox="group-1bc3f956-68f0-4615-8f93-ca954d919b33"
+<a data-lightbox="group-default"
                    href="_images/xrd_mesh.jpg"
                    class=""
                    title=""

doc/create_atoms.html

@@ -341,7 +341,7 @@ variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) +
 create_atoms 1 box var v set x xx set y yy
 </pre></div>
 </div>
-<a data-lightbox="group-f4ec1fe6-16bb-4d3a-9ef0-ecf4b57f6ec2"
+<a data-lightbox="group-default"
                    href="_images/sinusoid.jpg"
                    class=""
                    title=""

doc/dump_image.html

@@ -220,7 +220,7 @@ from an existing dump file, and using these dump commands in the rerun
 script to generate the images/movie.</p>
 <p>Here are two sample images, rendered as 1024x1024 JPEG files.  Click
 to see the full-size images:</p>
-<DIV ALIGN=center><a data-lightbox="group-24b43492-ff03-4c03-99b9-12f1dbf252d5"
+<DIV ALIGN=center><a data-lightbox="group-default"
                    href="_images/dump1.jpg"
                    class=""
                    title=""
@@ -230,7 +230,7 @@ to see the full-size images:</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-2540cc67-71aa-4053-b959-61451a4e4f0d"
+                    </a><a data-lightbox="group-default"
                    href="_images/dump2.jpg"
                    class=""
                    title=""

doc/fix_balance.html

@@ -237,7 +237,7 @@ that owns them.  The leftmost diagram is the default partitioning of
 the simulation box across processors (one sub-box for each of 16
 processors); the middle diagram is after a “grid” method has been
 applied.</p>
-<a data-lightbox="group-85269663-2cc5-4073-9d2b-e7fb01db4ec3"
+<a data-lightbox="group-default"
                    href="_images/balance_uniform.jpg"
                    class=""
                    title=""
@@ -247,7 +247,7 @@ applied.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-349a1bab-83d0-42b4-85c7-81050f4e3d61"
+                    </a><a data-lightbox="group-default"
                    href="_images/balance_nonuniform.jpg"
                    class=""
                    title=""
@@ -257,7 +257,7 @@ applied.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-c6a44ae9-1930-4d73-95ea-e4e0a56b953a"
+                    </a><a data-lightbox="group-default"
                    href="_images/balance_rcb.jpg"
                    class=""
                    title=""

doc/neb.html

@@ -479,7 +479,7 @@ barrier.</p>
 neb_combine.py script run on the dump files produced by the two
 example input scripts in examples/neb.  Click on them to see a larger
 image.</p>
-<a data-lightbox="group-5916a3a1-a368-4db3-a9ea-37c4eef93ee3"
+<a data-lightbox="group-default"
                    href="_images/hop1.jpg"
                    class=""
                    title=""
@@ -489,7 +489,7 @@ image.</p>
                     width="25%"
                     height="auto"
                     alt=""/>
-                    </a><a data-lightbox="group-ec426f39-1525-43c6-a3b4-d2aac49c6e80"
+                    </a><a data-lightbox="group-default"
                    href="_images/hop2.jpg"
                    class=""
                    title=""