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@ -25,7 +25,7 @@
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<LI>group-ID = ID of the group of atoms to be dumped
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<LI>style = <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>image</I> or <I>molfile</I> or <I>local</I> or <I>custom</I>
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<LI>style = <I>atom</I> or <I>aotm\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>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/mpiio</I>
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<LI>N = dump every this many timesteps
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@ -34,11 +34,14 @@
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<LI>args = list of arguments for a particular style
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<PRE> <I>atom</I> args = none
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<I>atom/mpiio</I> args = none
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<I>cfg</I> args = same as <I>custom</I> args, see below
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<I>dcd</I> args = none
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<I>xtc</I> args = none
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<I>xyz</I> args = none
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</PRE>
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<PRE> <I>xyz/mpiio</I> args = none
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</PRE>
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<PRE> <I>image</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
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</PRE>
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<PRE> <I>molfile</I> args = discussed on <A HREF = "dump_molfile.html">dump molfile</A> doc page
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@ -52,6 +55,7 @@
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f_ID[N] = Nth column of local array calculated by a fix with ID
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</PRE>
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<PRE> <I>custom</I> args = list of atom attributes
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<I>custom/mpiio</I> args = list of atom attributes
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possible attributes = id, mol, type, element, mass,
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x, y, z, xs, ys, zs, xu, yu, zu,
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xsu, ysu, zsu, ix, iy, iz,
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@ -96,7 +100,9 @@
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<P><B>Examples:</B>
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</P>
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<PRE>dump myDump all atom 100 dump.atom
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dump myDump all atom/mpiio 100 dump.atom.mpiio
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dump 2 subgroup atom 50 dump.run.bin
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dump 2 subgroup atom 50 dump.run.mpiio.bin
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dump 4a all custom 100 dump.myforce.* id type x y vx fx
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dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
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dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
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@ -143,6 +149,15 @@ default. For the <I>dcd</I>, <I>xtc</I>, <I>xyz</I>, and <I>molfile</I> styles,
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atom ID is on by default. See the <A HREF = "dump_modify.html">dump_modify</A> doc
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page for details.
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</P>
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<P>As explained below, the <I>atom/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I>
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styles are identical in command syntax and in the format of the dump
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files they create, to the corresponding styles without "mpiio", except
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the single dump file they produce is written in parallel via the
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MPI-IO library. For the remainder of this doc page, you should thus
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consider the <I>atom</I> and <I>atom/mpiio</I> styles (etc) to be
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inter-changeable. The one exception is how the filename is specified
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for the MPI-IO styles, as explained below.
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</P>
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<HR>
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<P>The <I>style</I> keyword determines what atom quantities are written to the
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@ -352,6 +367,31 @@ when running on large numbers of processors.
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<P>Note that using the "*" and "%" characters together can produce a
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large number of small dump files!
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</P>
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<P>For the <I>atom/mpiio</I>, <I>custom/mpiio</I>, and <I>xyz/mpiio</I> styles, a single
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dump file is written in parallel via the MPI-IO library, which is part
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of the MPI standard for versions 2.0 and above. Using MPI-IO requires
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two steps. First, build LAMMPS with its MPIIO package installed, e.g.
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</P>
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<PRE>make yes-mpiio # installs the MPIIO package
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make g++ # build LAMMPS for your platform
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</PRE>
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<P>Second, use a dump filename which contains ".mpiio". Note that it
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does not have to end in ".mpiio", just contain those characters.
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Unlike MPI-IO restart files, which must be both written and read using
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MPI-IO, the dump files produced by these MPI-IO styles are identical
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in format to the files produced by their non-MPI-IO style
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counterparts. This means you can write a dump file using MPI-IO and
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use the <A HREF = "read_dump.html">read_dump</A> command or perform other
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post-processing, just as if the dump file was not written using
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MPI-IO.
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</P>
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<P>Note that MPI-IO dump files are one large file which all processors
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write to. You thus cannot use the "%" wildcard character described
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above in the filename since that specifies generation of multiple
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files. You can use the ".bin" suffix described below in an MPI-IO
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dump file; again this file will be written in parallel and have the
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same binary format as if it were written without MPI-IO.
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</P>
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<P>If the filename ends with ".bin", the dump file (or files, if "*" or
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"%" is also used) is written in binary format. A binary dump file
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will be about the same size as a text version, but will typically
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@ -121,6 +121,15 @@ dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
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<P>Modify the parameters of a previously defined dump command. Not all
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parameters are relevant to all dump styles.
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</P>
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<P>As explained on the <A HREF = "dump.html">dump</A> doc page, the <I>atom/mpiio</I>,
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<I>custom/mpiio</I>, and <I>xyz/mpiio</I> dump styles are identical in command
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syntax and in the format of the dump files they create, to the
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corresponding styles without "mpiio", except the single dump file they
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produce is written in parallel via the MPI-IO library. Thus if a
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dump_modify option below is valid for the <I>atom</I> style, it is also
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valid for the <I>atom/mpiio</I> style, and similarly for the other styles
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which allow for use of MPI-IO.
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</P>
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<HR>
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<HR>
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@ -13,14 +13,15 @@
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>molecule ID file
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<PRE>molecule ID file1 file2 ...
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</PRE>
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<UL><LI>ID = user-assigned name for the molecule template
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<LI>file = name of file containing molecule description
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<LI>file1,file2,... = names of files containing molecule descriptions
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>molecule 1 mymol
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molecule 1 co2.txt h2o.txt
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molecule CO2 co2.txt
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</PRE>
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<P><B>Description:</B>
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@ -35,13 +36,21 @@ templates (or will in the future) include:
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<LI><A HREF = "fix_rigid.html">fix rigid/small</A>
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<LI><A HREF = "fix_shake.html">fix shake</A>
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<LI><A HREF = "fix_gcmc.html">fix gcmc</A> (not yet)
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<LI><A HREF = "create_atoms.html">create_atoms</A> (not yet)
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<LI><A HREF = "create_atoms.html">create_atoms</A>
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<LI><A HREF = "atom_style.html">atom_style template</A> (not yet)
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</UL>
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<P>The ID of a molecule template can only contain alphanumeric characters
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and underscores.
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</P>
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<P>The format of the molecule file is similar to the data file read by
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the <A HREF = "read_data.html">read_data</A> commands, and is as follows.
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<P>A single template can contain multiple molecules, listed one per file.
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Many of the commands listed above currently use only the first
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molecule in the template, and will issue a warning if the template
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contains multiple molecules. The <A HREF = "atom_style.html">atom_style
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template</A> command allows multiple-molecule templates
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to define a system with more than one templated molecule.
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</P>
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<P>The format of an individual molecule file is similar to the data file
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read by the <A HREF = "read_data.html">read_data</A> commands, and is as follows.
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</P>
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<P>A molecule file has a header and a body. The header appears first.
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The first line of the header is always skipped; it typically contains
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[Syntax:]
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molecule ID file :pre
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molecule ID file1 file2 ... :pre
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ID = user-assigned name for the molecule template
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file = name of file containing molecule description :ul
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file1,file2,... = names of files containing molecule descriptions :ul
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[Examples:]
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molecule 1 mymol
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molecule 1 co2.txt h2o.txt
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molecule CO2 co2.txt :pre
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[Description:]
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@ -32,13 +33,21 @@ templates (or will in the future) include:
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"fix rigid/small"_fix_rigid.html
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"fix shake"_fix_shake.html
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"fix gcmc"_fix_gcmc.html (not yet)
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"create_atoms"_create_atoms.html (not yet) :ul
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"create_atoms"_create_atoms.html
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"atom_style template"_atom_style.html (not yet) :ul
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The ID of a molecule template can only contain alphanumeric characters
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and underscores.
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The format of the molecule file is similar to the data file read by
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the "read_data"_read_data.html commands, and is as follows.
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A single template can contain multiple molecules, listed one per file.
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Many of the commands listed above currently use only the first
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molecule in the template, and will issue a warning if the template
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contains multiple molecules. The "atom_style
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template"_atom_style.html command allows multiple-molecule templates
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to define a system with more than one templated molecule.
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The format of an individual molecule file is similar to the data file
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read by the "read_data"_read_data.html commands, and is as follows.
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A molecule file has a header and a body. The header appears first.
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The first line of the header is always skipped; it typically contains
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