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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12770 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2014-11-24 17:10:14 +00:00
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18
doc/Section_tools.html
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@ -55,6 +55,7 @@ own sub-directories with their own Makefiles.
<LI><A HREF = "#eff">eff</A>
<LI><A HREF = "#emacs">emacs</A>
<LI><A HREF = "#fep">fep</A>
<LI><A HREF = "#ipi">i-pi</A>
<LI><A HREF = "#ipp">ipp</A>
<LI><A HREF = "#kate">kate</A>
<LI><A HREF = "#arc">lmp2arc</A>
@ -250,6 +251,23 @@ Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
</P>
<HR>
<H4><A NAME = "ipi"></A>i-pi tool
</H4>
<P>The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
be used with the <A HREF = "fix_ipi.html">fix ipi</A> command to perform
path-integral molecular dynamics (PIMD).
</P>
<P>The i-PI package was created and is maintained by Michele Ceriotti,
michele.ceriotti at gmail.com, to interface to a variety of molecular
dynamics codes.
</P>
<P>See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
<A HREF = "fix_ipi.html">fix ipi</A> doc page for further details on running PIMD
calculations with LAMMPS.
</P>
<HR>
<H4><A NAME = "ipp"></A>ipp tool
</H4>
<P>The tools/ipp directory contains a Perl script ipp which can be used

18
doc/Section_tools.txt
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@ -51,6 +51,7 @@ own sub-directories with their own Makefiles.
"eff"_#eff
"emacs"_#emacs
"fep"_#fep
"i-pi"_#ipi
"ipp"_#ipp
"kate"_#kate
"lmp2arc"_#arc
@ -246,6 +247,23 @@ See README file in the tools/fep directory.
:line
i-pi tool :h4,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
be used with the "fix ipi"_fix_ipi.html command to perform
path-integral molecular dynamics (PIMD).
The i-PI package was created and is maintained by Michele Ceriotti,
michele.ceriotti at gmail.com, to interface to a variety of molecular
dynamics codes.
See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
"fix ipi"_fix_ipi.html doc page for further details on running PIMD
calculations with LAMMPS.
:line
ipp tool :h4,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used

36
doc/dump.html
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@ -25,7 +25,7 @@
<LI>group-ID = ID of the group of atoms to be dumped
<LI>style = <I>atom</I> or <I>atom/mpiio</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>xyz/mpiio</I> or <I>image</I> or <I>movie</I> or <I>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/mpiio</I>
<LI>style = <I>atom</I> or <I>atom/mpiio</I> or <I>cfg</I> or <I>cfg/mpiio</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>xyz/mpiio</I> or <I>image</I> or <I>movie</I> or <I>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/mpiio</I>
<LI>N = dump every this many timesteps
@ -36,6 +36,7 @@
<PRE> <I>atom</I> args = none
<I>atom/mpiio</I> args = none
<I>cfg</I> args = same as <I>custom</I> args, see below
<I>cfg/mpiio</I> args = same as <I>custom</I> args, see below
<I>dcd</I> args = none
<I>xtc</I> args = none
<I>xyz</I> args = none
@ -149,14 +150,14 @@ default. For the <I>dcd</I>, <I>xtc</I>, <I>xyz</I>, and <I>molfile</I> styles,
atom ID is on by default. See the <A HREF = "dump_modify.html">dump_modify</A> doc
page for details.
</P>
<P>As explained below, the <I>atom/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I>
styles are identical in command syntax and in the format of the dump
files they create, to the corresponding styles without "mpiio", except
the single dump file they produce is written in parallel via the
MPI-IO library. For the remainder of this doc page, you should thus
consider the <I>atom</I> and <I>atom/mpiio</I> styles (etc) to be
inter-changeable. The one exception is how the filename is specified
for the MPI-IO styles, as explained below.
<P>As explained below, the <I>atom/mpiio</I>, <I>cfg/mpiio</I>, <I>custom/mpiio</I>, and
<I>xyz/mpiio</I> styles are identical in command syntax and in the format
of the dump files they create, to the corresponding styles without
"mpiio", except the single dump file they produce is written in
parallel via the MPI-IO library. For the remainder of this doc page,
you should thus consider the <I>atom</I> and <I>atom/mpiio</I> styles (etc) to
be inter-changeable. The one exception is how the filename is
specified for the MPI-IO styles, as explained below.
</P>
<HR>
@ -367,10 +368,11 @@ when running on large numbers of processors.
<P>Note that using the "*" and "%" characters together can produce a
large number of small dump files!
</P>
<P>For the <I>atom/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I> styles, a single
dump file is written in parallel via the MPI-IO library, which is part
of the MPI standard for versions 2.0 and above. Using MPI-IO requires
two steps. First, build LAMMPS with its MPIIO package installed, e.g.
<P>For the <I>atom/mpiio</I>, <I>cfg/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I>
styles, a single dump file is written in parallel via the MPI-IO
library, which is part of the MPI standard for versions 2.0 and above.
Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
package installed, e.g.
</P>
<PRE>make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform
@ -585,10 +587,10 @@ per-atom quantities which could then be output into dump files.
-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
LAMMPS</A> section of the documentation.
</P>
<P>The <I>atom/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I> styles are part of
the MPIIO package. They are only enabled if LAMMPS was built with
that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
<P>The <I>atom/mpiio</I>, <I>cfg/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I> styles
are part of the MPIIO package. They are only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>The <I>xtc</I> style is part of the XTC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making

36
doc/dump.txt
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@ -17,13 +17,14 @@ dump ID group-ID style N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
style = {atom} or {atom/mpiio} or {cfg} or {dcd} or {xtc} or {xyz} or {xyz/mpiio} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/mpiio} :l
style = {atom} or {atom/mpiio} or {cfg} or {cfg/mpiio} or {dcd} or {xtc} or {xyz} or {xyz/mpiio} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/mpiio} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l
{atom} args = none
{atom/mpiio} args = none
{cfg} args = same as {custom} args, see below
{cfg/mpiio} args = same as {custom} args, see below
{dcd} args = none
{xtc} args = none
{xyz} args = none :pre
@ -135,14 +136,14 @@ default. For the {dcd}, {xtc}, {xyz}, and {molfile} styles, sorting by
atom ID is on by default. See the "dump_modify"_dump_modify.html doc
page for details.
As explained below, the {atom/mpiio}, {custom/mpiio}, and {xyz/mpiio}
styles are identical in command syntax and in the format of the dump
files they create, to the corresponding styles without "mpiio", except
the single dump file they produce is written in parallel via the
MPI-IO library. For the remainder of this doc page, you should thus
consider the {atom} and {atom/mpiio} styles (etc) to be
inter-changeable. The one exception is how the filename is specified
for the MPI-IO styles, as explained below.
As explained below, the {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and
{xyz/mpiio} styles are identical in command syntax and in the format
of the dump files they create, to the corresponding styles without
"mpiio", except the single dump file they produce is written in
parallel via the MPI-IO library. For the remainder of this doc page,
you should thus consider the {atom} and {atom/mpiio} styles (etc) to
be inter-changeable. The one exception is how the filename is
specified for the MPI-IO styles, as explained below.
:line
@ -353,10 +354,11 @@ when running on large numbers of processors.
Note that using the "*" and "%" characters together can produce a
large number of small dump files!
For the {atom/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles, a single
dump file is written in parallel via the MPI-IO library, which is part
of the MPI standard for versions 2.0 and above. Using MPI-IO requires
two steps. First, build LAMMPS with its MPIIO package installed, e.g.
For the {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio}
styles, a single dump file is written in parallel via the MPI-IO
library, which is part of the MPI standard for versions 2.0 and above.
Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
package installed, e.g.
make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre
@ -571,10 +573,10 @@ To write gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the "Making
LAMMPS"_Section_start.html#start_2 section of the documentation.
The {atom/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles are part of
the MPIIO package. They are only enabled if LAMMPS was built with
that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
The {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles
are part of the MPIIO package. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The {xtc} style is part of the XTC package. It is only enabled if
LAMMPS was built with that package. See the "Making