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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3329 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-11-06 16:15:26 +00:00
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54
doc/fix_imd.html
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@ -40,9 +40,15 @@ fix comm all imd 8888 trate 5 unwrap on fscale 10.0
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>This fix implements the "Interactive MD" (IMD) protocol which allows <P>This fix implements the "Interactive MD" (IMD) protocol which allows
to connect an IMD client, for example the VMD visualization program, to connect an IMD client, for example the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD visualization
to a running LAMMPS simulation and monitor the progress of the simulation program</A>, to a running LAMMPS simulation and monitor the progress
and interactively apply forces to selected atoms. of the simulation and interactively apply forces to selected atoms.
</P>
<P>The source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign. We thank them for providing a software
interface that allows codes like LAMMPS to hook to <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
</P> </P>
<P>Upon initialization of the fix, it will open a communication port <P>Upon initialization of the fix, it will open a communication port
on the node with MPI task 0 and wait for an incoming connection. on the node with MPI task 0 and wait for an incoming connection.
@ -97,39 +103,35 @@ PHANTOM allow you to feel the forces you are applying to your molecules,
as if they were real objects. See the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/imd/">VMD IMD Homepage</A> for as if they were real objects. See the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/imd/">VMD IMD Homepage</A> for
more details. more details.
</P> </P>
<P>If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B> <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P> </P>
<P>The fix does not write any information to restart files. <P>No information about this fix is written to <A HREF = "restart.html">binary restart
</P> files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant are relevant to this fix. No global scalar or vector or per-atom
to this fix. quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
</P> commands</A>. No parameter of this fix can be
<P>If IMD control messages are received, a line of text describing used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
the message and its effect will be printed to the screen, if This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
screen output is active.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>This source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign.
</P>
<P>This fix is part of the "user-imd" package. It is only enabled if <P>This fix is part of the "user-imd" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>When used in combination with VMD, a topology or coordinate file <P>When used in combination with VMD, a topology or coordinate file has
has to be loaded, which matches in number and ordering of atoms to be loaded, which matches (in number and ordering of atoms) the
the group the fix is applied to. The fix internally sorts atom group the fix is applied to. The fix internally sorts atom IDs by
IDs by ascending integer value; in VMD (and thus the IMD protocol) ascending integer value; in VMD (and thus the IMD protocol) those will
those will be assigned 0-based consecutive index numbers. be assigned 0-based consecutive index numbers.
</P> </P>
<P>When using multiple active IMD connections at the same time, <P>When using multiple active IMD connections at the same time,
each needs to use a different port number. each needs to use a different port number.
@ -138,6 +140,4 @@ each needs to use a different port number.
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none
</P> </P>
<HR>
</HTML> </HTML>

53
doc/fix_imd.txt
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@ -32,9 +32,15 @@ fix comm all imd 8888 trate 5 unwrap on fscale 10.0 :pre
[Description:] [Description:]
This fix implements the "Interactive MD" (IMD) protocol which allows This fix implements the "Interactive MD" (IMD) protocol which allows
to connect an IMD client, for example the VMD visualization program, to connect an IMD client, for example the "VMD visualization
to a running LAMMPS simulation and monitor the progress of the simulation program"_VMD, to a running LAMMPS simulation and monitor the progress
and interactively apply forces to selected atoms. of the simulation and interactively apply forces to selected atoms.
The source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign. We thank them for providing a software
interface that allows codes like LAMMPS to hook to "VMD"_VMD.
Upon initialization of the fix, it will open a communication port Upon initialization of the fix, it will open a communication port
on the node with MPI task 0 and wait for an incoming connection. on the node with MPI task 0 and wait for an incoming connection.
@ -89,39 +95,34 @@ PHANTOM allow you to feel the forces you are applying to your molecules,
as if they were real objects. See the "VMD IMD Homepage"_imdvmd for as if they were real objects. See the "VMD IMD Homepage"_imdvmd for
more details. more details.
If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)x
:link(imdvmd,http://www.ks.uiuc.edu/Research/vmd/imd/) :link(imdvmd,http://www.ks.uiuc.edu/Research/vmd/imd/)
[Restart, fix_modify, output, run start/stop, minimize info:] [Restart, fix_modify, output, run start/stop, minimize info:]
The fix does not write any information to restart files. No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
None of the "fix_modify"_fix_modify.html options are relevant are relevant to this fix. No global scalar or vector or per-atom
to this fix. quantities are stored by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
If IMD control messages are received, a line of text describing used with the {start/stop} keywords of the "run"_run.html command.
the message and its effect will be printed to the screen, if This fix is not invoked during "energy minimization"_minimize.html.
screen output is active.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] [Restrictions:]
This source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign.
This fix is part of the "user-imd" package. It is only enabled if This fix is part of the "user-imd" package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
When used in combination with VMD, a topology or coordinate file When used in combination with VMD, a topology or coordinate file has
has to be loaded, which matches in number and ordering of atoms to be loaded, which matches (in number and ordering of atoms) the
the group the fix is applied to. The fix internally sorts atom group the fix is applied to. The fix internally sorts atom IDs by
IDs by ascending integer value; in VMD (and thus the IMD protocol) ascending integer value; in VMD (and thus the IMD protocol) those will
those will be assigned 0-based consecutive index numbers. be assigned 0-based consecutive index numbers.
When using multiple active IMD connections at the same time, When using multiple active IMD connections at the same time,
each needs to use a different port number. each needs to use a different port number.
@ -129,5 +130,3 @@ each needs to use a different port number.
[Related commands:] none [Related commands:] none
[Default:] none [Default:] none
:line