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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13795 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp 2015-07-30 13:55:51 +00:00
parent f46b1657f8
commit 37fff687dc
11 changed files with 28 additions and 22 deletions
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8
doc/Section_python.html
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@ -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=""

6
doc/balance.html
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@ -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 &#8220;grid&#8221; 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=""

4
doc/compute_saed.html
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@ -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=""

5
doc/compute_temp_cs.html
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@ -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

7
doc/compute_temp_cs.txt
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@ -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

2
doc/compute_xrd.html
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@ -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=""

2
doc/create_atoms.html
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@ -341,7 +341,7 @@ variable v equal &quot;(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=""

4
doc/dump_image.html
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@ -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=""

6
doc/fix_balance.html
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@ -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 &#8220;grid&#8221; 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=""

4
doc/neb.html
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@ -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=""

2
doc/searchindex.js
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