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sjplimp 2008-01-17 18:29:47 +00:00
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6
doc/Section_start.html
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@ -190,7 +190,11 @@ files if you compile with -DGZIP. It requires that your Unix support
the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER,
and -DPACK_MEMCPY options can make for faster parallel FFTs (in the and -DPACK_MEMCPY options can make for faster parallel FFTs (in the
PPPM solver) on some platforms. The -DPACK_ARRAY setting is the PPPM solver) on some platforms. The -DPACK_ARRAY setting is the
default. default. If you compile with -DLAMMPS_XDR, the build will include XDR
compatability files for doing particle dumps in XTC format. This is
only necessary if your platform does have its own XDR files available.
See the Restrictions section of the <A HREF = "dump.html">dump</A> command for
details.
</P> </P>
<P>(8) The DEPFLAGS setting is how the C++ compiler creates a dependency <P>(8) The DEPFLAGS setting is how the C++ compiler creates a dependency
file for each source file. This speeds re-compilation when source file for each source file. This speeds re-compilation when source

6
doc/Section_start.txt
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@ -185,7 +185,11 @@ files if you compile with -DGZIP. It requires that your Unix support
the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER,
and -DPACK_MEMCPY options can make for faster parallel FFTs (in the and -DPACK_MEMCPY options can make for faster parallel FFTs (in the
PPPM solver) on some platforms. The -DPACK_ARRAY setting is the PPPM solver) on some platforms. The -DPACK_ARRAY setting is the
default. default. If you compile with -DLAMMPS_XDR, the build will include XDR
compatability files for doing particle dumps in XTC format. This is
only necessary if your platform does have its own XDR files available.
See the Restrictions section of the "dump"_dump.html command for
details.
(8) The DEPFLAGS setting is how the C++ compiler creates a dependency (8) The DEPFLAGS setting is how the C++ compiler creates a dependency
file for each source file. This speeds re-compilation when source file for each source file. This speeds re-compilation when source

44
doc/dump.html
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@ -30,8 +30,7 @@
<PRE> <I>atom</I> args = none <PRE> <I>atom</I> args = none
<I>bond</I> args = none <I>bond</I> args = none
<I>dcd</I> args = none <I>dcd</I> args = none
<I>xtc</I> args = precision (optional) <I>xtc</I> args = none
precision = power-of-10 value from 10 to 1000000 (default = 1000)
<I>xyz</I> args = none <I>xyz</I> args = none
<I>custom</I> args = list of atom attributes <I>custom</I> args = list of atom attributes
possible attributes = tag, mol, type, possible attributes = tag, mol, type,
@ -138,16 +137,31 @@ below.
<P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format <P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
files are binary and thus may not be portable to different machines. files are binary and thus may not be portable to different machines.
The dump group must be <I>all</I> for the <I>dcd</I> style. The dump group must be <I>all</I> for the <I>dcd</I> style. 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 for each atom. Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box. Note that these
coordinates may thus be far outside 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://www.gromacs.org/documentation/reference_3.3/online/xtc.html">here</A>.
The precision used in XTC files can be specified; for example, a value The precision used in XTC files can be adjusted via the
of 100 means that coordinates are stored to 1/100 nanometer accuracy. <A HREF = "dump_modify.html">dump_modify</A> command. The default value of 1000
XTC files are portable binary files written in the NFS XDR data means that coordinates are stored to 1/1000 nanometer accuracy. XTC
format, so that any machine which supports XDR should be able to read files are portable binary files written in the NFS XDR data format, so
them. The dump group must be <I>all</I> for the <I>xtc</I> style. that any machine which supports XDR should be able to read them. The
dump group must be <I>all</I> for 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 atom. Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box. Note that these
coordinates may thus be far outside the box size stored with the
snapshot.
</P> </P>
<P>The <I>xyz</I> style writes XYZ files, which is a simple text-based <P>The <I>xyz</I> style writes XYZ files, which is a simple text-based
coordinate format that many codes can read. coordinate format that many codes can read.
@ -310,12 +324,14 @@ some machines may not support the lo-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 lo-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.
</P> However, the XTC package also includes two compatibility header files
<P>Some pair potentials do not allow the calculation of per-atom energy and associated functions, which should be a suitable substitute on
and stress via the <I>epair</I>, <I>etotal</I>, <I>sxx</I>, etc keywords. One of machines that do not have the appropriate native header files. This
these are the granular pair potentials. However, for those option can be invoked at build time by adding -DLAMMPS_XDR to the
potentials, the <A HREF = "fix_gran_diag.html">fix gran/diag</A> command can be used CCFLAGS variable in the appropriate lo-level Makefile,
instead. e.g. src/MAKE/Makefile.foo. This compatability mode has been tested
successfully on Cray XT3 and IBM BlueGene/L machines and should also
work on the Cray XT4, IBM BG/P, and Windows XP machines.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>

44
doc/dump.txt
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@ -21,8 +21,7 @@ args = list of arguments for a particular style :l
{atom} args = none {atom} args = none
{bond} args = none {bond} args = none
{dcd} args = none {dcd} args = none
{xtc} args = precision (optional) {xtc} args = none
precision = power-of-10 value from 10 to 1000000 (default = 1000)
{xyz} args = none {xyz} args = none
{custom} args = list of atom attributes {custom} args = list of atom attributes
possible attributes = tag, mol, type, possible attributes = tag, mol, type,
@ -128,16 +127,31 @@ below.
The {dcd} style writes DCD files, a standard atomic trajectory format The {dcd} style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
files are binary and thus may not be portable to different machines. files are binary and thus may not be portable to different machines.
The dump group must be {all} for the {dcd} style. The dump group must be {all} for the {dcd} style. The {unwrap} option
of the "dump_modify"_dump_modify.html command allows DCD coordinates
to be written "unwrapped" by the image flags for each atom. Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box. Note that these
coordinates may thus be far outside 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://www.gromacs.org/documentation/reference_3.3/online/xtc.html.
The precision used in XTC files can be specified; for example, a value The precision used in XTC files can be adjusted via the
of 100 means that coordinates are stored to 1/100 nanometer accuracy. "dump_modify"_dump_modify.html command. The default value of 1000
XTC files are portable binary files written in the NFS XDR data means that coordinates are stored to 1/1000 nanometer accuracy. XTC
format, so that any machine which supports XDR should be able to read files are portable binary files written in the NFS XDR data format, so
them. The dump group must be {all} for the {xtc} style. that any machine which supports XDR should be able to read them. The
dump group must be {all} for 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 atom. Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box. Note that these
coordinates may thus be far outside the box size stored with the
snapshot.
The {xyz} style writes XYZ files, which is a simple text-based The {xyz} style writes XYZ files, which is a simple text-based
coordinate format that many codes can read. coordinate format that many codes can read.
@ -300,12 +314,14 @@ some machines may not support the lo-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 lo-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
Some pair potentials do not allow the calculation of per-atom energy and associated functions, which should be a suitable substitute on
and stress via the {epair}, {etotal}, {sxx}, etc keywords. One of machines that do not have the appropriate native header files. This
these are the granular pair potentials. However, for those option can be invoked at build time by adding -DLAMMPS_XDR to the
potentials, the "fix gran/diag"_fix_gran_diag.html command can be used CCFLAGS variable in the appropriate lo-level Makefile,
instead. e.g. src/MAKE/Makefile.foo. This compatability mode has been tested
successfully on Cray XT3 and IBM BlueGene/L machines and should also
work on the Cray XT4, IBM BG/P, and Windows XP machines.
[Related commands:] [Related commands:]

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doc/dump_modify.html
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@ -19,14 +19,16 @@
<LI>one or more keyword/value pairs may be appended <LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>format</I> or <I>scale</I> or <I>image</I> or <I>header</I> or <I>flush</I> or <I>region</I> or <I>thresh</I> <LI>keyword = <I>format</I> or <I>scale</I> or <I>image</I> or <I>flush</I> or <I>unwrap</I> or <I>every</I> or <I>precision</I> or <I>region</I> or <I>thresh</I>
<PRE> <I>format</I> arg = C-style format string for one line of output <PRE> <I>format</I> arg = C-style format string for one line of output
<I>scale</I> arg = <I>yes</I> or <I>no</I> <I>scale</I> arg = <I>yes</I> or <I>no</I>
<I>image</I> arg = <I>yes</I> or <I>no</I> <I>image</I> arg = <I>yes</I> or <I>no</I>
<I>flush</I> arg = <I>yes</I> or <I>no</I> <I>flush</I> arg = <I>yes</I> or <I>no</I>
<I>unwrap</I> arg = <I>yes</I> or <I>no</I>
<I>every</I> arg = N <I>every</I> arg = N
N = dump every this many timesteps N = dump every this many timesteps
<I>precision</I> arg = power-of-10 value from 10 to 1000000
<I>region</I> arg = region-ID or "none" <I>region</I> arg = region-ID or "none"
<I>thresh</I> args = attribute operation value <I>thresh</I> args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
@ -41,7 +43,8 @@
</P> </P>
<PRE>dump_modify 1 format "%d %d %20.15g %g %g" scale yes <PRE>dump_modify 1 format "%d %d %20.15g %g %g" scale yes
dump_modify myDump image yes scale no flush yes dump_modify myDump image yes scale no flush yes
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2 dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
dump_modify xtcdump precision 10000
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
@ -76,10 +79,23 @@ the output in that file is current (no buffering by the OS), even if
LAMMPS halts before the simulation completes. Flushes cannot be LAMMPS halts before the simulation completes. Flushes cannot be
performed with dump style <I>xtc</I>. performed with dump style <I>xtc</I>.
</P> </P>
<P>The <I>unwrap</I> option only applies to the dump <I>dcd</I> and <I>xtc</I> styles.
If set to <I>yes</I>, coordinates will be written "unwrapped" by the image
flags for each atom. Unwrapped means that if the atom has passed thru
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that these coordinates may thus be far outside the
box size stored with the snapshot.
</P>
<P>The <I>every</I> option changes the dump frequency originally specified by <P>The <I>every</I> option changes the dump frequency originally specified by
the <A HREF = "dump.html">dump</A> command to a new value which must be > 0. The the <A HREF = "dump.html">dump</A> command to a new value which must be > 0. The
dump frequency cannot be changed for the dump <I>dcd</I> style. dump frequency cannot be changed for the dump <I>dcd</I> style.
</P> </P>
<P>The <I>precision</I> option only applies to the dump <I>xtc</I> style. A
specified value of N means that coordinates are stored to 1/N
nanometer accuracy, e.g. for N = 1000, the coordinates are written to
1/1000 nanometer accuracy.
</P>
<P>The <I>region</I> keyword only applies to the dump <I>custom</I> style. If <P>The <I>region</I> keyword only applies to the dump <I>custom</I> style. If
specified, only atoms in the region will be written to the dump file. specified, only atoms in the region will be written to the dump file.
Only one region can be applied as a filter (the last one specified). Only one region can be applied as a filter (the last one specified).
@ -109,6 +125,8 @@ whose energy is above some threshhold.
</P> </P>
<P>The option defaults are format = %d and %g for each integer or <P>The option defaults are format = %d and %g for each integer or
floating point value, scale = yes, image = no, flush = yes (except for floating point value, scale = yes, image = no, flush = yes (except for
dump <I>xtc</I> style), region = none, and thresh = none. the dump <I>xtc</I> style), unwrap = no, every = whatever it was set to via
the <A HREF = "dump.html">dump</A> command, precision = 1000, region = none, and
thresh = none.
</P> </P>
</HTML> </HTML>

24
doc/dump_modify.txt
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@ -14,13 +14,15 @@ dump_modify dump-ID keyword values ... :pre
dump-ID = ID of dump to modify :ulb,l dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l one or more keyword/value pairs may be appended :l
keyword = {format} or {scale} or {image} or {header} or {flush} or {region} or {thresh} :l keyword = {format} or {scale} or {image} or {flush} or {unwrap} or {every} or {precision} or {region} or {thresh} :l
{format} arg = C-style format string for one line of output {format} arg = C-style format string for one line of output
{scale} arg = {yes} or {no} {scale} arg = {yes} or {no}
{image} arg = {yes} or {no} {image} arg = {yes} or {no}
{flush} arg = {yes} or {no} {flush} arg = {yes} or {no}
{unwrap} arg = {yes} or {no}
{every} arg = N {every} arg = N
N = dump every this many timesteps N = dump every this many timesteps
{precision} arg = power-of-10 value from 10 to 1000000
{region} arg = region-ID or "none" {region} arg = region-ID or "none"
{thresh} args = attribute operation value {thresh} args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
@ -34,7 +36,8 @@ keyword = {format} or {scale} or {image} or {header} or {flush} or {region} or {
dump_modify 1 format "%d %d %20.15g %g %g" scale yes dump_modify 1 format "%d %d %20.15g %g %g" scale yes
dump_modify myDump image yes scale no flush yes dump_modify myDump image yes scale no flush yes
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2 :pre dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
dump_modify xtcdump precision 10000 :pre
[Description:] [Description:]
@ -69,10 +72,23 @@ the output in that file is current (no buffering by the OS), even if
LAMMPS halts before the simulation completes. Flushes cannot be LAMMPS halts before the simulation completes. Flushes cannot be
performed with dump style {xtc}. performed with dump style {xtc}.
The {unwrap} option only applies to the dump {dcd} and {xtc} styles.
If set to {yes}, coordinates will be written "unwrapped" by the image
flags for each atom. Unwrapped means that if the atom has passed thru
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that these coordinates may thus be far outside the
box size stored with the snapshot.
The {every} option changes the dump frequency originally specified by The {every} option changes the dump frequency originally specified by
the "dump"_dump.html command to a new value which must be > 0. The the "dump"_dump.html command to a new value which must be > 0. The
dump frequency cannot be changed for the dump {dcd} style. dump frequency cannot be changed for the dump {dcd} style.
The {precision} option only applies to the dump {xtc} style. A
specified value of N means that coordinates are stored to 1/N
nanometer accuracy, e.g. for N = 1000, the coordinates are written to
1/1000 nanometer accuracy.
The {region} keyword only applies to the dump {custom} style. If The {region} keyword only applies to the dump {custom} style. If
specified, only atoms in the region will be written to the dump file. specified, only atoms in the region will be written to the dump file.
Only one region can be applied as a filter (the last one specified). Only one region can be applied as a filter (the last one specified).
@ -102,4 +118,6 @@ whose energy is above some threshhold.
The option defaults are format = %d and %g for each integer or The option defaults are format = %d and %g for each integer or
floating point value, scale = yes, image = no, flush = yes (except for floating point value, scale = yes, image = no, flush = yes (except for
dump {xtc} style), region = none, and thresh = none. the dump {xtc} style), unwrap = no, every = whatever it was set to via
the "dump"_dump.html command, precision = 1000, region = none, and
thresh = none.