mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4670 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
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@ -48,7 +48,8 @@ own sub-directories with their own Makefiles.
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<LI><A HREF = "#charmm">ch2lmp</A>
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<LI><A HREF = "#chain">chain</A>
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<LI><A HREF = "#data">data2xmovie</A>
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<LI><A HREF = "#eam">eam generate</A>
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<LI><A HREF = "#eamdb">eam database</A>
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<LI><A HREF = "#eamgn">eam generate</A>
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<LI>"eff_#eff
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<LI><A HREF = "#arc">lmp2arc</A>
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<LI><A HREF = "#cfg">lmp2cfg</A>
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@ -141,12 +142,29 @@ running the tool is
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</P>
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<HR>
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<H4><A NAME = "eam"></A>eam generate tool
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<H4><A NAME = "eamdb"></A>eam database tool
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</H4>
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<P>The tools/eam_database directory contains a Fortran program that will
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generate EAM alloy setfl potential files for any combination of 16
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elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
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Zr. The files can then be used with the <A HREF = "pair_eam.html">pair_style
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eam/alloy</A> command.
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</P>
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<P>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
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and is based on his paper:
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</P>
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<P>X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
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144113 (2004).
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</P>
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<HR>
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<H4><A NAME = "eamgn"></A>eam generate tool
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</H4>
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<P>The tools/eam_generate directory contains several one-file C programs
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that convert an analytic formula into a tabulated <A HREF = "pair_eam.html">embedded atom
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method (EAM)</A> setfl potential file. The potentials they
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produce are in the potentials directory.
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produce are in the potentials directory, and can be used with the
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<A HREF = "pair_eam.html">pair_style eam/alloy</A> command.
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</P>
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<P>The source files and potentials were provided by Gerolf Ziegenhain
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(gerolf at ziegenhain.com).
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@ -44,7 +44,8 @@ own sub-directories with their own Makefiles.
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"ch2lmp"_#charmm
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"chain"_#chain
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"data2xmovie"_#data
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"eam generate"_#eam
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"eam database"_#eamdb
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"eam generate"_#eamgn
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"eff_#eff
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"lmp2arc"_#arc
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"lmp2cfg"_#cfg
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@ -137,12 +138,29 @@ See the top of the data2xmovie.c file for a discussion of the options.
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:line
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eam generate tool :h4,link(eam)
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eam database tool :h4,link(eamdb)
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The tools/eam_database directory contains a Fortran program that will
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generate EAM alloy setfl potential files for any combination of 16
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elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
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Zr. The files can then be used with the "pair_style
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eam/alloy"_pair_eam.html command.
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The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
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and is based on his paper:
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X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
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144113 (2004).
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:line
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eam generate tool :h4,link(eamgn)
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The tools/eam_generate directory contains several one-file C programs
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that convert an analytic formula into a tabulated "embedded atom
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method (EAM)"_pair_eam.html setfl potential file. The potentials they
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produce are in the potentials directory.
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produce are in the potentials directory, and can be used with the
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"pair_style eam/alloy"_pair_eam.html command.
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The source files and potentials were provided by Gerolf Ziegenhain
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(gerolf at ziegenhain.com).
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@ -108,16 +108,22 @@ 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 in parallel, the atom information written to
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dump files (typically one line per atom) may be written in an
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indeterminate order. This is because data for a single snapshot is
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collected from multiple processors. This is always the case for the
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<I>atom</I>, <I>local</I>, and <I>custom</I> styles. It is also the case for the
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<I>xyz</I> style if the dump group is not <I>all</I>. It is not the case for
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the <I>dcd</I> and <I>xtc</I> styles which always write atoms in sorted order.
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So does the <I>xyz</I> style if the dump group is <I>all</I>. The <I>cfg</I> style
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supports the <I>sort</I> option of the <A HREF = "dump_modify.html">dump_modify</A>
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command which allows sorting to be turned on or off.
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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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(typically one line per atom) will be in an indeterminate order for
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each snapshot.
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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>
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<HR>
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26
doc/dump.txt
26
doc/dump.txt
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@ -98,16 +98,22 @@ 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 in parallel, the atom information written to
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dump files (typically one line per atom) may be written in an
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indeterminate order. This is because data for a single snapshot is
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collected from multiple processors. This is always the case for the
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{atom}, {local}, and {custom} styles. It is also the case for the
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{xyz} style if the dump group is not {all}. It is not the case for
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the {dcd} and {xtc} styles which always write atoms in sorted order.
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So does the {xyz} style if the dump group is {all}. The {cfg} style
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supports the {sort} option of the "dump_modify"_dump_modify.html
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command which allows sorting to be turned on or off.
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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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(typically one line per atom) will be in an indeterminate order for
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each snapshot.
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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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:line
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