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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8015 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-04-12 22:22:47 +00:00
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6
doc/Section_howto.html
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@ -820,7 +820,7 @@ are not valid for <B>c</B>. In this case, it is necessary
to first apply an inversion. This can be achieved
by interchanging two basis vectors or by changing the sign of one of them.
</P>
<P>For consistency, the same rotation/inversion appied to the basis vectors
<P>For consistency, the same rotation/inversion applied to the basis vectors
must also be applied to atom positions, velocities,
and any other vector quantities.
This can be conveniently achieved by first converting to
@ -1242,7 +1242,7 @@ discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
<TR><TD >c_ID[I][J] </TD><TD > one element of array
@ -1441,7 +1441,7 @@ data and scalar/vector/array data.
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>

14
doc/kspace_modify.html
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@ -28,7 +28,8 @@
rinv = PPPM G-ewald parameter
<I>slab</I> value = volfactor
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain
2d approximation compared with the volume of the simulation domain
<I>compute</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
@ -101,6 +102,15 @@ must prevent particle migration beyond the initial z-bounds, typically
by providing a wall-style fix. The methodology behind the <I>slab</I>
option is explained in the paper by <A HREF = "#Yeh">(Yeh)</A>.
</P>
<P>The <I>compute</I> keyword allows Kspace computations to be turned off,
even though a <A HREF = "kspace_style.html">kspace_style</A> is defined. This is
not useful for running a real simulation, but can be useful for
debugging purposes or for computing only partial forces that do not
include the Kspace contribution. You can also do this by simply not
defining a <A HREF = "kspace_style.html">kspace_style</A>, but a Kspace-compatible
<A HREF = "pair_style.html">pair_style</A> requires a kspace_style to be defined.
This keyword gives you that option.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
@ -110,7 +120,7 @@ option is explained in the paper by <A HREF = "#Yeh">(Yeh)</A>.
<P><B>Default:</B>
</P>
<P>The option defaults are mesh = 0 0 0, order = 5, force = -1.0, gewald
= 0.0, and slab = 1.0.
= 0.0, slab = 1.0, and compute = yes.
</P>
<HR>

14
doc/kspace_modify.txt
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@ -23,7 +23,8 @@ keyword = {mesh} or {order} or {gewald} or {slab} :l
rinv = PPPM G-ewald parameter
{slab} value = volfactor
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain :pre
2d approximation compared with the volume of the simulation domain
{compute} value = {yes} or {no} :pre
:ule
[Examples:]
@ -95,6 +96,15 @@ must prevent particle migration beyond the initial z-bounds, typically
by providing a wall-style fix. The methodology behind the {slab}
option is explained in the paper by "(Yeh)"_#Yeh.
The {compute} keyword allows Kspace computations to be turned off,
even though a "kspace_style"_kspace_style.html is defined. This is
not useful for running a real simulation, but can be useful for
debugging purposes or for computing only partial forces that do not
include the Kspace contribution. You can also do this by simply not
defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
"pair_style"_pair_style.html requires a kspace_style to be defined.
This keyword gives you that option.
[Restrictions:] none
[Related commands:]
@ -104,7 +114,7 @@ option is explained in the paper by "(Yeh)"_#Yeh.
[Default:]
The option defaults are mesh = 0 0 0, order = 5, force = -1.0, gewald
= 0.0, and slab = 1.0.
= 0.0, slab = 1.0, and compute = yes.
:line

16
doc/pair_modify.html
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@ -17,7 +17,7 @@
</PRE>
<UL><LI>one or more keyword/value pairs may be listed
<LI>keyword = <I>shift</I> or <I>mix</I> or <I>table</I> or <I>tabinner</I> or <I>tail</I>
<LI>keyword = <I>shift</I> or <I>mix</I> or <I>table</I> or <I>tabinner</I> or <I>tail</I> or <I>compute</I>
<PRE> <I>mix</I> value = <I>geometric</I> or <I>arithmetic</I> or <I>sixthpower</I>
<I>shift</I> value = <I>yes</I> or <I>no</I>
@ -25,7 +25,8 @@
2^N = # of values in table
<I>tabinner</I> value = cutoff
cutoff = inner cutoff at which to begin table (distance units)
<I>tail</I> value = <I>yes</I> or <I>no</I>
<I>tail</I> value = <I>yes</I> or <I>no</I>
<I>compute</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
@ -144,6 +145,15 @@ pair interactions beyond the cutoff, but the energy and pressure
reported by the simulation include an estimated contribution from
those interactions.
</UL>
<P>The <I>compute</I> keyword allows pairwise computations to be turned off,
even though a <A HREF = "pair_style.html">pair_style</A> is defined. This is not
useful for running a real simulation, but can be useful for debugging
purposes or for computing only partial forces that do not include the
pairwise contribution. You can also do this by simply not defining a
<A HREF = "pair_style.html">pair_style</A>, but a Kspace-compatible pair_style is
required if you also want to define a
<A HREF = "kspace_style.html">kspace_style</A>. This keyword gives you that option.
</P>
<P><B>Restrictions:</B> none
</P>
<P>You cannot use <I>shift</I> yes with <I>tail</I> yes, since those are
@ -157,7 +167,7 @@ conflicting options. You cannot use <I>tail</I> yes with 2d simulations.
<P><B>Default:</B>
</P>
<P>The option defaults are mix = geometric, shift = no, table = 12,
tabinner = sqrt(2.0), tail = no.
tabinner = sqrt(2.0), tail = no, and compute = yes.
</P>
<P>Note that some pair styles perform mixing, but only a certain style of
mixing. See the doc pages for individual pair styles for details.

16
doc/pair_modify.txt
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@ -13,14 +13,15 @@ pair_modify command :h3
pair_modify keyword value ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {shift} or {mix} or {table} or {tabinner} or {tail} :l
keyword = {shift} or {mix} or {table} or {tabinner} or {tail} or {compute} :l
{mix} value = {geometric} or {arithmetic} or {sixthpower}
{shift} value = {yes} or {no}
{table} value = N
2^N = # of values in table
{tabinner} value = cutoff
cutoff = inner cutoff at which to begin table (distance units)
{tail} value = {yes} or {no} :pre
{tail} value = {yes} or {no}
{compute} value = {yes} or {no} :pre
:ule
[Examples:]
@ -138,6 +139,15 @@ pair interactions beyond the cutoff, but the energy and pressure
reported by the simulation include an estimated contribution from
those interactions. :l,ule
The {compute} keyword allows pairwise computations to be turned off,
even though a "pair_style"_pair_style.html is defined. This is not
useful for running a real simulation, but can be useful for debugging
purposes or for computing only partial forces that do not include the
pairwise contribution. You can also do this by simply not defining a
"pair_style"_pair_style.html, but a Kspace-compatible pair_style is
required if you also want to define a
"kspace_style"_kspace_style.html. This keyword gives you that option.
[Restrictions:] none
You cannot use {shift} yes with {tail} yes, since those are
@ -151,7 +161,7 @@ conflicting options. You cannot use {tail} yes with 2d simulations.
[Default:]
The option defaults are mix = geometric, shift = no, table = 12,
tabinner = sqrt(2.0), tail = no.
tabinner = sqrt(2.0), tail = no, and compute = yes.
Note that some pair styles perform mixing, but only a certain style of
mixing. See the doc pages for individual pair styles for details.