forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4794 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
cf897522fd
commit
1d3b37782f
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@ -108,22 +108,20 @@ on timesteps when neighbor lists are rebuilt, the coordinates of an
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atom written to a dump file may be slightly outside the simulation
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box.
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</P>
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<P>When LAMMPS is running on a single processor, if the <A HREF = "atom_modify.html">atom_modify
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sort</A> option is on, which it is by default, then
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atoms are re-ordered periodically during a simulation, due to spatial
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sorting, and hence the atom information written to dump files
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<P>IMPORTANT NOTE: Unless the <A HREF = "dump_modify.html">dump_modify sort</A> option
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is invoked, the lines of atom information written to dump files
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(typically one line per atom) will be in an indeterminate order for
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each snapshot.
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each snapshot. This is even true when running on a single processor,
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if the <A HREF = "atom_modify.html">atom_modify sort</A> option is on, which it is
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by default. In this case atoms are re-ordered periodically during a
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simulation, due to spatial sorting. It is also true when running in
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parallel, because data for a single snapshot is collected from
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multiple processors.
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</P>
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<P>When LAMMPS is running in parallel, this is also true, both due to
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sorting and because data for a single snapshot is collected from
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multiple processors. This is the case for the <I>atom</I>, <I>local</I>, and
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<I>custom</I> styles. It is also the case for the <I>xyz</I> style if the dump
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group is not <I>all</I>. It is not the case for the <I>dcd</I> and <I>xtc</I> styles
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which always write atoms in sorted order. So does the <I>xyz</I> style if
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the dump group is <I>all</I>. The <I>cfg</I> style supports the <I>sort</I> option
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of the <A HREF = "dump_modify.html">dump_modify</A> command which allows sorting to
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be turned on or off.
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<P>For the <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I> styles, sorting is off by
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default. For the <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> styles, sorting by atom ID
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is on by default. See the <A HREF = "dump_modify.html">dump_modify</A> doc page for
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details.
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</P>
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<HR>
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@ -199,14 +197,14 @@ atoms appropriately.
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<P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
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used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
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files are binary and thus may not be portable to different machines.
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The dump group must be <I>all</I> for the <I>dcd</I> style. The <I>unwrap</I> option
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of the <A HREF = "dump_modify.html">dump_modify</A> command allows DCD coordinates
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to be written "unwrapped" by the image flags for each atom. Unwrapped
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means that if the atom has passed thru a periodic boundary one or more
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times, the value is printed for what the coordinate would be if it had
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not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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The number of atoms per snapshot cannot change with the <I>dcd</I> style.
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The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command
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allows DCD coordinates to be written "unwrapped" by the image flags
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for each atom. Unwrapped means that if the atom has passed thru a
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periodic boundary one or more times, the value is printed for what the
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coordinate would be if it had not been wrapped back into the periodic
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box. Note that these coordinates may thus be far outside the box size
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stored with the snapshot.
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</P>
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<P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used
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by the GROMACS molecular dynamics package, and described
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@ -216,14 +214,13 @@ The precision used in XTC files can be adjusted via the
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means that coordinates are stored to 1/1000 nanometer accuracy. XTC
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files are portable binary files written in the NFS XDR data format, so
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that any machine which supports XDR should be able to read them. The
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dump group must be <I>all</I> for the <I>xtc</I> style. The <I>unwrap</I> option of
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the <A HREF = "dump_modify.html">dump_modify</A> command allows XTC coordinates to
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be written "unwrapped" by the image flags for each atom. Unwrapped
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means that if the atom has passed thru a periodic boundary one or more
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times, the value is printed for what the coordinate would be if it had
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not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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<I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command allows
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XTC coordinates to be written "unwrapped" by the image flags for each
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atom. Unwrapped means that if the atom has passed thru a periodic
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boundary one or more times, the value is printed for what the
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coordinate would be if it had not been wrapped back into the periodic
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box. Note that these coordinates may thus be far outside the box size
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stored with the snapshot.
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</P>
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<P>The <I>xyz</I> style writes XYZ files, which is a simple text-based
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coordinate format that many codes can read.
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57
doc/dump.txt
57
doc/dump.txt
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@ -98,22 +98,20 @@ on timesteps when neighbor lists are rebuilt, the coordinates of an
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atom written to a dump file may be slightly outside the simulation
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box.
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When LAMMPS is running on a single processor, if the "atom_modify
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sort"_atom_modify.html option is on, which it is by default, then
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atoms are re-ordered periodically during a simulation, due to spatial
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sorting, and hence the atom information written to dump files
|
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IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html option
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is invoked, the lines of atom information written to dump files
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(typically one line per atom) will be in an indeterminate order for
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each snapshot.
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each snapshot. This is even true when running on a single processor,
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if the "atom_modify sort"_atom_modify.html option is on, which it is
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by default. In this case atoms are re-ordered periodically during a
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simulation, due to spatial sorting. It is also true when running in
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parallel, because data for a single snapshot is collected from
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multiple processors.
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When LAMMPS is running in parallel, this is also true, both due to
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sorting and because data for a single snapshot is collected from
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multiple processors. This is the case for the {atom}, {local}, and
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{custom} styles. It is also the case for the {xyz} style if the dump
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group is not {all}. It is not the case for the {dcd} and {xtc} styles
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which always write atoms in sorted order. So does the {xyz} style if
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the dump group is {all}. The {cfg} style supports the {sort} option
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of the "dump_modify"_dump_modify.html command which allows sorting to
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be turned on or off.
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For the {atom}, {custom}, {cfg}, and {local} styles, sorting is off by
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default. For the {dcd}, {xtc}, and {xyz} styles, sorting by atom ID
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is on by default. See the "dump_modify"_dump_modify.html doc page for
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details.
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:line
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@ -189,14 +187,14 @@ atoms appropriately.
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The {dcd} style writes DCD files, a standard atomic trajectory format
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used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
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files are binary and thus may not be portable to different machines.
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The dump group must be {all} for the {dcd} style. The {unwrap} option
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of the "dump_modify"_dump_modify.html command allows DCD coordinates
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to be written "unwrapped" by the image flags for each atom. Unwrapped
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means that if the atom has passed thru a periodic boundary one or more
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times, the value is printed for what the coordinate would be if it had
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not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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The number of atoms per snapshot cannot change with the {dcd} style.
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The {unwrap} option of the "dump_modify"_dump_modify.html command
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allows DCD coordinates to be written "unwrapped" by the image flags
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for each atom. Unwrapped means that if the atom has passed thru a
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periodic boundary one or more times, the value is printed for what the
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coordinate would be if it had not been wrapped back into the periodic
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box. Note that these coordinates may thus be far outside the box size
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stored with the snapshot.
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The {xtc} style writes XTC files, a compressed trajectory format used
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by the GROMACS molecular dynamics package, and described
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@ -206,14 +204,13 @@ The precision used in XTC files can be adjusted via the
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means that coordinates are stored to 1/1000 nanometer accuracy. XTC
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files are portable binary files written in the NFS XDR data format, so
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that any machine which supports XDR should be able to read them. The
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dump group must be {all} for the {xtc} style. The {unwrap} option of
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the "dump_modify"_dump_modify.html command allows XTC coordinates to
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be written "unwrapped" by the image flags for each atom. Unwrapped
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means that if the atom has passed thru a periodic boundary one or more
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times, the value is printed for what the coordinate would be if it had
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not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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{unwrap} option of the "dump_modify"_dump_modify.html command allows
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XTC coordinates to be written "unwrapped" by the image flags for each
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atom. Unwrapped means that if the atom has passed thru a periodic
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boundary one or more times, the value is printed for what the
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coordinate would be if it had not been wrapped back into the periodic
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box. Note that these coordinates may thus be far outside the box size
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stored with the snapshot.
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The {xyz} style writes XYZ files, which is a simple text-based
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coordinate format that many codes can read.
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|
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@ -36,7 +36,10 @@
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<I>precision</I> arg = power-of-10 value from 10 to 1000000
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<I>region</I> arg = region-ID or "none"
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<I>scale</I> arg = <I>yes</I> or <I>no</I>
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<I>sort</I> arg = <I>yes</I> or <I>no</I>
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<I>sort</I> arg = <I>off</I> or 0 or N
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off = no sorting of per-atom lines within a snapshot
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0 = sort per-atom lines by atom ID
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N = sort per-atom lines by the Nth column
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<I>thresh</I> args = attribute operation value
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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operation = "<" or "<=" or ">" or ">=" or "==" or "!="
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@ -169,11 +172,21 @@ value of <I>yes</I> means atom coords are written in normalized units from
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value of <I>no</I> means they are written in absolute distance units
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(e.g. Angstroms or sigma).
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</P>
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<P>The <I>sort</I> keyword applies only to the dump <I>cfg</I> style. A sort value
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of <I>yes</I> means atoms will be written into the CFG file in sorted
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order, sorted by the atom ID. A value of <I>no</I> means a sort will not
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be performed and that atoms may be in an indeterminate order,
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depending on which processor owns which atoms.
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<P>The <I>sort</I> keyword determines whether lines of per-atom output in a
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snapshot are sorted or not. A sort value of <I>off</I> means they will
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typically be written in indeterminate order, either in serial or
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parallel. This is the case even in serial if the <A HREF = "atom_modify.html">atom_modify
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sort</A> option is turned on, which it is by default, to
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improve performance. A sort value of 0 means sort the output by atom
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ID. A sort value of N means sort the output by the value in the Nth
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column of per-atom info. The dump <I>local</I> style cannot be sorted by
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atom ID, since there are typically multiple lines of output per atom.
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Some dump styles, such as <I>dcd</I> and <I>xtc</I>, require sorting by atom
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ID to format the output file correctly.
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</P>
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<P>IMPORTANT NOTE: Unless it is required by the dump style, sorting dump
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file output requires extra overhead in terms of CPU and communication
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cost, as well as memory.
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</P>
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<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> and <I>cfg</I>
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styles. Multiple thresholds can be specified. Specifying "none"
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@ -215,7 +228,8 @@ box size stored with the snapshot.
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<LI>precision = 1000
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<LI>region = none
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<LI>scale = yes
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<LI>sort = no
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<LI>sort = off for dump styles <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I>
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<LI>sort = 0 for dump styles <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> meaning sort by atom ID
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<LI>thresh = none
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<LI>unwrap = no
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</UL>
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@ -30,7 +30,10 @@ keyword = {append} or {every} or {flush} or {format} or {image} or {label} or {p
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{precision} arg = power-of-10 value from 10 to 1000000
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{region} arg = region-ID or "none"
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{scale} arg = {yes} or {no}
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{sort} arg = {yes} or {no}
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{sort} arg = {off} or 0 or N
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off = no sorting of per-atom lines within a snapshot
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0 = sort per-atom lines by atom ID
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N = sort per-atom lines by the Nth column
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{thresh} args = attribute operation value
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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operation = "<" or "<=" or ">" or ">=" or "==" or "!="
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@ -162,11 +165,21 @@ value of {yes} means atom coords are written in normalized units from
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value of {no} means they are written in absolute distance units
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(e.g. Angstroms or sigma).
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The {sort} keyword applies only to the dump {cfg} style. A sort value
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of {yes} means atoms will be written into the CFG file in sorted
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order, sorted by the atom ID. A value of {no} means a sort will not
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be performed and that atoms may be in an indeterminate order,
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depending on which processor owns which atoms.
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The {sort} keyword determines whether lines of per-atom output in a
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snapshot are sorted or not. A sort value of {off} means they will
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typically be written in indeterminate order, either in serial or
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parallel. This is the case even in serial if the "atom_modify
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sort"_atom_modify.html option is turned on, which it is by default, to
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improve performance. A sort value of 0 means sort the output by atom
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ID. A sort value of N means sort the output by the value in the Nth
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column of per-atom info. The dump {local} style cannot be sorted by
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atom ID, since there are typically multiple lines of output per atom.
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Some dump styles, such as {dcd} and {xtc}, require sorting by atom
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ID to format the output file correctly.
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IMPORTANT NOTE: Unless it is required by the dump style, sorting dump
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file output requires extra overhead in terms of CPU and communication
|
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cost, as well as memory.
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The {thresh} keyword only applies to the dump {custom} and {cfg}
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styles. Multiple thresholds can be specified. Specifying "none"
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@ -208,6 +221,7 @@ label = ENTRIES
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precision = 1000
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region = none
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scale = yes
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sort = no
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sort = off for dump styles {atom}, {custom}, {cfg}, and {local}
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sort = 0 for dump styles {dcd}, {xtc}, and {xyz} meaning sort by atom ID
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thresh = none
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unwrap = no :ul
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