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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9874 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-05-13 14:12:23 +00:00
parent 70feaba97d
commit 65ddcdb8e1
6 changed files with 24 additions and 24 deletions
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18
doc/fix_colvars.html
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@ -27,15 +27,15 @@
<I>output</I> arg = output filename prefix (default: out)
<I>seed</I> arg = seed for random number generator (default: 1966)
<I>unwrap</I> arg = <I>yes</I> or <I>no</I>
use unwrapped coordinates in collective variables (default: no)
use unwrapped coordinates in collective variables (default: yes)
<I>tstat</I> arg = fix id of a thermostat or NULL (default: NULL)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide unwrap yes
fix colvars all colvars.inp
<PRE>fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
fix abf all colvars colvars.inp tstat 1
</PRE>
<P><B>Description:</B>
</P>
@ -78,10 +78,10 @@ that will be used in the colvars module.
</P>
<P>The <I>unwrap</I> keyword controls whether wrapped or unwrapped coordinates
are passed to the colvars library for calculation of the collective
variables and the resulting forces. The default is <I>no</I>, i.e. to use the
current local coordinates that are wrapped back into the simulation cell
at each re-neighboring. Setting this to <I>yes</I> will use the image flags
to reconstruct the absolute atom positions.
variables and the resulting forces. The default is <I>yes</I>, i.e. to use
the image flags to reconstruct the absolute atom positions.
Setting this to <I>no</I> will use the current local coordinates that are
wrapped back into the simulation cell at each re-neighboring instead.
</P>
<P>The <I>tstat</I> keyword can be either NULL or the label of a thermostating
fix that thermostats all atoms in the fix colvars group. This will be
@ -120,8 +120,8 @@ really a deficit in practice.
</P>
<P><B>Default:</B>
</P>
<P>The default options are input = NULL, output = out, seed = 1966, and
tstat = NULL.
<P>The default options are input = NULL, output = out, seed = 1966, unwrap yes,
and tstat = NULL.
</P>
<HR>

18
doc/fix_colvars.txt
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@ -20,14 +20,14 @@ keyword = {input} or {output} or {seed} or {tstat} :l
{output} arg = output filename prefix (default: out)
{seed} arg = seed for random number generator (default: 1966)
{unwrap} arg = {yes} or {no}
use unwrapped coordinates in collective variables (default: no)
use unwrapped coordinates in collective variables (default: yes)
{tstat} arg = fix id of a thermostat or NULL (default: NULL) :pre
:ule
[Examples:]
fix colvars peptide peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide unwrap yes
fix colvars all colvars.inp :pre
fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
fix abf all colvars colvars.inp tstat 1 :pre
[Description:]
@ -70,10 +70,10 @@ that will be used in the colvars module.
The {unwrap} keyword controls whether wrapped or unwrapped coordinates
are passed to the colvars library for calculation of the collective
variables and the resulting forces. The default is {no}, i.e. to use the
current local coordinates that are wrapped back into the simulation cell
at each re-neighboring. Setting this to {yes} will use the image flags
to reconstruct the absolute atom positions.
variables and the resulting forces. The default is {yes}, i.e. to use
the image flags to reconstruct the absolute atom positions.
Setting this to {no} will use the current local coordinates that are
wrapped back into the simulation cell at each re-neighboring instead.
The {tstat} keyword can be either NULL or the label of a thermostating
fix that thermostats all atoms in the fix colvars group. This will be
@ -112,8 +112,8 @@ really a deficit in practice.
[Default:]
The default options are input = NULL, output = out, seed = 1966, and
tstat = NULL.
The default options are input = NULL, output = out, seed = 1966, unwrap yes,
and tstat = NULL.
:line

4
doc/pair_coeff.html
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@ -104,8 +104,8 @@ section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
<LI><A HREF = "pair_bop.html">pair_style bop</A> - BOP potential of Pettifor
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulombics
<LI><A HREF = "pair_born.html<A HREF = "pair_born.html">>pair_style born/coul/msm</A> - Born-Mayer-Huggins with long-range MSM Coulombics
<LI>pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_born.html">pair_style born/coul/msm</A> - Born-Mayer-Huggins with long-range MSM Coulombics
<LI><A HREF = "pair_born.html">pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_brownian.html">pair_style brownian</A> - Brownian potential for Fast Lubrication Dynamics
<LI><A HREF = "pair_brownian.html">pair_style brownian/poly</A> - Brownian potential for Fast Lubrication Dynamics with polydispersity
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential

2
doc/pair_coeff.txt
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@ -102,7 +102,7 @@ section of "this page"_Section_commands.html#cmd_5.
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
"pair_style born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics
pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
"pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
"pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
"pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
"pair_style buck"_pair_buck.html - Buckingham potential

4
doc/pair_style.html
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@ -106,8 +106,8 @@ section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
<LI><A HREF = "pair_bop.html">pair_style bop</A> - BOP potential of Pettifor
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulombics
<LI><A HREF = "pair_born.html<A HREF = "pair_born.html">>pair_style born/coul/msm</A> - Born-Mayer-Huggins with long-range MSM Coulombics
<LI>pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_born.html">pair_style born/coul/msm</A> - Born-Mayer-Huggins with long-range MSM Coulombics
<LI><A HREF = "pair_born.html">pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_brownian.html">pair_style brownian</A> - Brownian potential for Fast Lubrication Dynamics
<LI><A HREF = "pair_brownian.html">pair_style brownian/poly</A> - Brownian potential for Fast Lubrication Dynamics with polydispersity
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential

2
doc/pair_style.txt
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@ -104,7 +104,7 @@ section of "this page"_Section_commands.html#cmd_5.
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
"pair_style born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics
pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
"pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
"pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
"pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
"pair_style buck"_pair_buck.html - Buckingham potential