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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4113 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2010-05-07 16:29:19 +00:00
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2
doc/Section_intro.html
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@ -319,7 +319,7 @@ debugging purposes. For high-quality visualization we recommend the
following packages: following packages:
</P> </P>
<UL><LI><A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> <UL><LI><A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>
<LI><A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> <LI><A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
<LI><A HREF = "http://pymol.sourceforge.net">PyMol</A> <LI><A HREF = "http://pymol.sourceforge.net">PyMol</A>
<LI><A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A> <LI><A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A>
<LI><A HREF = "http://www.openrasmol.org">RasMol</A> <LI><A HREF = "http://www.openrasmol.org">RasMol</A>

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doc/Section_intro.txt
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@ -315,7 +315,7 @@ debugging purposes. For high-quality visualization we recommend the
following packages: following packages:
"VMD"_http://www.ks.uiuc.edu/Research/vmd "VMD"_http://www.ks.uiuc.edu/Research/vmd
"AtomEye"_http://164.107.79.177/Archive/Graphics/A "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
"PyMol"_http://pymol.sourceforge.net "PyMol"_http://pymol.sourceforge.net
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html "Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"RasMol"_http://www.openrasmol.org :ul "RasMol"_http://www.openrasmol.org :ul

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doc/Section_tools.html
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@ -209,7 +209,7 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
post-processing LAMMPS output. The scripts include readers for log post-processing LAMMPS output. The scripts include readers for log
and dump files, a reader for EAM potential files, and a converter that and dump files, a reader for EAM potential files, and a converter that
reads LAMMPS dump files and produces CFG files that can be visualized reads LAMMPS dump files and produces CFG files that can be visualized
with the <A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> with the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
visualizer. visualizer.
</P> </P>
<P>See the README.pdf file for more information. <P>See the README.pdf file for more information.

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doc/Section_tools.txt
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@ -205,7 +205,7 @@ The matlab sub-directory contains several "MATLAB"_matlab scripts for
post-processing LAMMPS output. The scripts include readers for log post-processing LAMMPS output. The scripts include readers for log
and dump files, a reader for EAM potential files, and a converter that and dump files, a reader for EAM potential files, and a converter that
reads LAMMPS dump files and produces CFG files that can be visualized reads LAMMPS dump files and produces CFG files that can be visualized
with the "AtomEye"_http://164.107.79.177/Archive/Graphics/A with the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
visualizer. visualizer.
See the README.pdf file for more information. See the README.pdf file for more information.

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doc/pair_dpd.html
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@ -40,11 +40,11 @@ pair_coeff 1 1 1.0 1.0
</P> </P>
<P>Style <I>dpd/tstat</I> invokes a DPD thermostat on pairwise interactions, <P>Style <I>dpd/tstat</I> invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force which is equivalent to the non-conservative portion of the DPD force
field. This thermostat can be used in conjunction with any <A HREF = "doc/pair_style.html">pair field. This thermostat can be used in conjunction with any <A HREF = "pair_style.html">pair
style</A>, and in leiu of per-particle thermostats style</A>, and in leiu of per-particle thermostats like
like <A HREF = "fix_langevin.html">fix langevin</A> or ensemble thermostats like <A HREF = "fix_langevin.html">fix langevin</A> or ensemble thermostats like Nose
Nose Hoover as implemented by <A HREF = "fix_nvt.html">fix nvt</A>. To use Hoover as implemented by <A HREF = "fix_nh.html">fix nvt</A>. To use <I>dpd/stat</I>
<I>dpd/stat</I> with another pair style, use the <A HREF = "pair_hybrid.html">pair_style with another pair style, use the <A HREF = "pair_hybrid.html">pair_style
hybrid/overlay</A> command to compute both the desired hybrid/overlay</A> command to compute both the desired
pair interaction and the thermostat for each pair of particles. pair interaction and the thermostat for each pair of particles.
</P> </P>
@ -148,7 +148,7 @@ atoms.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_langevin.html">fix <P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_langevin.html">fix
langevin</A> langevin</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none

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doc/pair_dpd.txt
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@ -37,10 +37,10 @@ Style {dpd} computes a force field for dissipative particle dynamics
Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions, Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force which is equivalent to the non-conservative portion of the DPD force
field. This thermostat can be used in conjunction with any "pair field. This thermostat can be used in conjunction with any "pair
style"_doc/pair_style.html, and in leiu of per-particle thermostats style"_pair_style.html, and in leiu of per-particle thermostats like
like "fix langevin"_fix_langevin.html or ensemble thermostats like "fix langevin"_fix_langevin.html or ensemble thermostats like Nose
Nose Hoover as implemented by "fix nvt"_fix_nvt.html. To use Hoover as implemented by "fix nvt"_fix_nh.html. To use {dpd/stat}
{dpd/stat} with another pair style, use the "pair_style with another pair style, use the "pair_style
hybrid/overlay"_pair_hybrid.html command to compute both the desired hybrid/overlay"_pair_hybrid.html command to compute both the desired
pair interaction and the thermostat for each pair of particles. pair interaction and the thermostat for each pair of particles.
@ -144,7 +144,7 @@ atoms.
[Related commands:] [Related commands:]
"pair_coeff"_pair_coeff.html, "fix nvt"_fix_nvt.html, "fix "pair_coeff"_pair_coeff.html, "fix nvt"_fix_nh.html, "fix
langevin"_fix_langevin.html langevin"_fix_langevin.html
[Default:] none [Default:] none

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doc/variable.html
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@ -76,11 +76,11 @@ which when evaluated produces a single numeric value which can be
output either directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix output either directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix
print</A>, and <A HREF = "run.html">run every</A> commands) or as part print</A>, and <A HREF = "run.html">run every</A> commands) or as part
of thermodynamic output (see the <A HREF = "thermo_style.html">thermo_style</A> of thermodynamic output (see the <A HREF = "thermo_style.html">thermo_style</A>
command), or used as input to an averaging fix (see the <A HREF = "fix_ave_time">fix command), or used as input to an averaging fix (see the <A HREF = "fix_ave_time.html">fix
ave/time</A> command). Variables of style <I>atom</I> store a ave/time</A> command). Variables of style <I>atom</I> store
formula which when evaluated produces one numeric value per atom which a formula which when evaluated produces one numeric value per atom
can be output to a dump file (see the <A HREF = "dump.html">dump custom</A> command) which can be output to a dump file (see the <A HREF = "dump.html">dump custom</A>
or used as input to an averaging fix (see the <A HREF = "fix_ave_spatial.html">fix command) or used as input to an averaging fix (see the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> and <A HREF = "fix_ave_atom.html">fix ave/atom</A> ave/spatial</A> and <A HREF = "fix_ave_atom.html">fix ave/atom</A>
commands). commands).
</P> </P>
@ -461,9 +461,9 @@ define the variable "v" as
this will assign the initial volume to the variable "v". That is not this will assign the initial volume to the variable "v". That is not
the case. Rather it assigns a formula which evaluates the volume the case. Rather it assigns a formula which evaluates the volume
(using the thermo_style keyword "vol") to the variable "v". If you (using the thermo_style keyword "vol") to the variable "v". If you
use the variable "v" in some other command like "fix ave/time" then use the variable "v" in some other command like <A HREF = "fix_ave_time.html">fix
the current volume of the box will be evaluated continuously during ave/time</A> then the current volume of the box will be
the run. evaluated continuously during the run.
</P> </P>
<P>If you want to store the initial volume of the system, you can do it <P>If you want to store the initial volume of the system, you can do it
this way: this way:

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doc/variable.txt
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@ -71,10 +71,10 @@ output either directly (see the "print"_print.html, "fix
print"_fix_print.html, and "run every"_run.html commands) or as part print"_fix_print.html, and "run every"_run.html commands) or as part
of thermodynamic output (see the "thermo_style"_thermo_style.html of thermodynamic output (see the "thermo_style"_thermo_style.html
command), or used as input to an averaging fix (see the "fix command), or used as input to an averaging fix (see the "fix
ave/time"_fix_ave_time command). Variables of style {atom} store a ave/time"_fix_ave_time.html command). Variables of style {atom} store
formula which when evaluated produces one numeric value per atom which a formula which when evaluated produces one numeric value per atom
can be output to a dump file (see the "dump custom"_dump.html command) which can be output to a dump file (see the "dump custom"_dump.html
or used as input to an averaging fix (see the "fix command) or used as input to an averaging fix (see the "fix
ave/spatial"_fix_ave_spatial.html and "fix ave/atom"_fix_ave_atom.html ave/spatial"_fix_ave_spatial.html and "fix ave/atom"_fix_ave_atom.html
commands). commands).
@ -450,9 +450,9 @@ before a run where the simulation box size changes. You might think
this will assign the initial volume to the variable "v". That is not this will assign the initial volume to the variable "v". That is not
the case. Rather it assigns a formula which evaluates the volume the case. Rather it assigns a formula which evaluates the volume
(using the thermo_style keyword "vol") to the variable "v". If you (using the thermo_style keyword "vol") to the variable "v". If you
use the variable "v" in some other command like "fix ave/time" then use the variable "v" in some other command like "fix
the current volume of the box will be evaluated continuously during ave/time"_fix_ave_time.html then the current volume of the box will be
the run. evaluated continuously during the run.
If you want to store the initial volume of the system, you can do it If you want to store the initial volume of the system, you can do it
this way: this way: