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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4978 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-10-06 15:58:26 +00:00
parent af9d8dd1a0
commit 397f967521
4 changed files with 38 additions and 28 deletions
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4
doc/Section_errors.html
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@ -596,6 +596,10 @@ fix/deform are defined .
<DD>The frequency of writing dump dcd snapshots cannot be changed. <DD>The frequency of writing dump dcd snapshots cannot be changed.
<DT><I>Cannot change dump_modify every for dump xtc</I>
<DD>The frequency of writing dump xtc snapshots cannot be changed.
<DT><I>Cannot change timestep once fix srd is setup</I> <DT><I>Cannot change timestep once fix srd is setup</I>
<DD>This is because various SRD properties depend on the timestep <DD>This is because various SRD properties depend on the timestep

4
doc/Section_errors.txt
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@ -593,6 +593,10 @@ Self-explanatory. :dd
The frequency of writing dump dcd snapshots cannot be changed. :dd The frequency of writing dump dcd snapshots cannot be changed. :dd
{Cannot change dump_modify every for dump xtc} :dt
The frequency of writing dump xtc snapshots cannot be changed. :dd
{Cannot change timestep once fix srd is setup} :dt {Cannot change timestep once fix srd is setup} :dt
This is because various SRD properties depend on the timestep This is because various SRD properties depend on the timestep

29
doc/dump.html
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@ -200,21 +200,22 @@ files are binary and thus may not be portable to different machines.
The number of atoms per snapshot cannot change with the <I>dcd</I> style. The number of atoms per snapshot cannot change with the <I>dcd</I> style.
The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command
allows DCD coordinates to be written "unwrapped" by the image flags allows DCD coordinates to be written "unwrapped" by the image flags
for each atom. Unwrapped means that if the atom has passed thru a for each atom. Unwrapped means that if the atom has passed through
periodic boundary one or more times, the value is printed for what the a periodic boundary one or more times, the value is printed for what
coordinate would be if it had not been wrapped back into the periodic the coordinate would be if it had not been wrapped back into the
box. Note that these coordinates may thus be far outside the box size periodic box. Note that these coordinates may thus be far outside
stored with the snapshot. the box size stored with the snapshot.
</P> </P>
<P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used <P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described by the GROMACS molecular dynamics package, and described
<A HREF = "http://www.gromacs.org/documentation/reference_3.3/online/xtc.html">here</A>. <A HREF = "http://manual.gromacs.org/current/online/xtc.html">here</A>.
The precision used in XTC files can be adjusted via the The precision used in XTC files can be adjusted via the
<A HREF = "dump_modify.html">dump_modify</A> command. The default value of 1000 <A HREF = "dump_modify.html">dump_modify</A> command. The default value of 1000
means that coordinates are stored to 1/1000 nanometer accuracy. XTC means that coordinates are stored to 1/1000 nanometer accuracy. XTC
files are portable binary files written in the NFS XDR data format, so files are portable binary files written in the NFS XDR data format,
that any machine which supports XDR should be able to read them. The so that any machine which supports XDR should be able to read them.
<I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command allows The number of atoms per snapshot cannot change with the <I>xtc</I> style.
The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command allows
XTC coordinates to be written "unwrapped" by the image flags for each XTC coordinates to be written "unwrapped" by the image flags for each
atom. Unwrapped means that if the atom has passed thru a periodic atom. Unwrapped means that if the atom has passed thru a periodic
boundary one or more times, the value is printed for what the boundary one or more times, the value is printed for what the
@ -449,18 +450,18 @@ section of the documentation.
<P>The <I>xtc</I> style is part of the "xtc" package. It is only enabled if <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#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. This is because LAMMPS</A> section for more info. This is because
some machines may not support the lo-level XDR data format that XTC some machines may not support the low-level XDR data format that XTC
files are written with, which will result in a compile-time error when files are written with, which will result in a compile-time error when
a lo-level include file is not found. Putting this style in a package a low-level include file is not found. Putting this style in a package
makes it easy to exclude from a LAMMPS build for those machines. makes it easy to exclude from a LAMMPS build for those machines.
However, the XTC package also includes two compatibility header files However, the XTC package also includes two compatibility header files
and associated functions, which should be a suitable substitute on and associated functions, which should be a suitable substitute on
machines that do not have the appropriate native header files. This machines that do not have the appropriate native header files. This
option can be invoked at build time by adding -DLAMMPS_XDR to the option can be invoked at build time by adding -DLAMMPS_XDR to the
CCFLAGS variable in the appropriate lo-level Makefile, CCFLAGS variable in the appropriate low-level Makefile,
e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested
successfully on Cray XT3 and IBM BlueGene/L machines and should also successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L machines and
work on the Cray XT4, IBM BG/P, and Windows XP machines. should also work on IBM BG/P, and Windows XP/Vista/7 machines.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>

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doc/dump.txt
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@ -190,21 +190,22 @@ files are binary and thus may not be portable to different machines.
The number of atoms per snapshot cannot change with the {dcd} style. The number of atoms per snapshot cannot change with the {dcd} style.
The {unwrap} option of the "dump_modify"_dump_modify.html command The {unwrap} option of the "dump_modify"_dump_modify.html command
allows DCD coordinates to be written "unwrapped" by the image flags allows DCD coordinates to be written "unwrapped" by the image flags
for each atom. Unwrapped means that if the atom has passed thru a for each atom. Unwrapped means that if the atom has passed through
periodic boundary one or more times, the value is printed for what the a periodic boundary one or more times, the value is printed for what
coordinate would be if it had not been wrapped back into the periodic the coordinate would be if it had not been wrapped back into the
box. Note that these coordinates may thus be far outside the box size periodic box. Note that these coordinates may thus be far outside
stored with the snapshot. the box size stored with the snapshot.
The {xtc} style writes XTC files, a compressed trajectory format used The {xtc} style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described by the GROMACS molecular dynamics package, and described
"here"_http://www.gromacs.org/documentation/reference_3.3/online/xtc.html. "here"_http://manual.gromacs.org/current/online/xtc.html.
The precision used in XTC files can be adjusted via the The precision used in XTC files can be adjusted via the
"dump_modify"_dump_modify.html command. The default value of 1000 "dump_modify"_dump_modify.html command. The default value of 1000
means that coordinates are stored to 1/1000 nanometer accuracy. XTC means that coordinates are stored to 1/1000 nanometer accuracy. XTC
files are portable binary files written in the NFS XDR data format, so files are portable binary files written in the NFS XDR data format,
that any machine which supports XDR should be able to read them. The so that any machine which supports XDR should be able to read them.
{unwrap} option of the "dump_modify"_dump_modify.html command allows The number of atoms per snapshot cannot change with the {xtc} style.
The {unwrap} option of the "dump_modify"_dump_modify.html command allows
XTC coordinates to be written "unwrapped" by the image flags for each XTC coordinates to be written "unwrapped" by the image flags for each
atom. Unwrapped means that if the atom has passed thru a periodic atom. Unwrapped means that if the atom has passed thru a periodic
boundary one or more times, the value is printed for what the boundary one or more times, the value is printed for what the
@ -439,18 +440,18 @@ section of the documentation.
The {xtc} style is part of the "xtc" package. It is only enabled if The {xtc} style is part of the "xtc" 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. This is because LAMMPS"_Section_start.html#2_3 section for more info. This is because
some machines may not support the lo-level XDR data format that XTC some machines may not support the low-level XDR data format that XTC
files are written with, which will result in a compile-time error when files are written with, which will result in a compile-time error when
a lo-level include file is not found. Putting this style in a package a low-level include file is not found. Putting this style in a package
makes it easy to exclude from a LAMMPS build for those machines. makes it easy to exclude from a LAMMPS build for those machines.
However, the XTC package also includes two compatibility header files However, the XTC package also includes two compatibility header files
and associated functions, which should be a suitable substitute on and associated functions, which should be a suitable substitute on
machines that do not have the appropriate native header files. This machines that do not have the appropriate native header files. This
option can be invoked at build time by adding -DLAMMPS_XDR to the option can be invoked at build time by adding -DLAMMPS_XDR to the
CCFLAGS variable in the appropriate lo-level Makefile, CCFLAGS variable in the appropriate low-level Makefile,
e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested
successfully on Cray XT3 and IBM BlueGene/L machines and should also successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L machines and
work on the Cray XT4, IBM BG/P, and Windows XP machines. should also work on IBM BG/P, and Windows XP/Vista/7 machines.
[Related commands:] [Related commands:]