From 5e96663a664009b33fbf151d1ea905ff19c9dd6a Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 2 Sep 2010 23:27:22 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4670 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_tools.html | 24 +++++++++++++++++++++--- doc/Section_tools.txt | 24 +++++++++++++++++++++--- doc/dump.html | 26 ++++++++++++++++---------- doc/dump.txt | 26 ++++++++++++++++---------- 4 files changed, 74 insertions(+), 26 deletions(-) diff --git a/doc/Section_tools.html b/doc/Section_tools.html index f046597d24..6e1e3dec88 100644 --- a/doc/Section_tools.html +++ b/doc/Section_tools.html @@ -48,7 +48,8 @@ own sub-directories with their own Makefiles.
  • ch2lmp
  • chain
  • data2xmovie -
  • eam generate +
  • eam database +
  • eam generate
  • "eff_#eff
  • lmp2arc
  • lmp2cfg @@ -141,12 +142,29 @@ running the tool is

    -

    eam generate tool +

    eam database tool +

    +

    The tools/eam_database directory contains a Fortran program that will +generate EAM alloy setfl potential files for any combination of 16 +elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, +Zr. The files can then be used with the pair_style +eam/alloy command. +

    +

    The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, +and is based on his paper: +

    +

    X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, +144113 (2004). +

    +
    + +

    eam generate tool

    The tools/eam_generate directory contains several one-file C programs that convert an analytic formula into a tabulated embedded atom method (EAM) setfl potential file. The potentials they -produce are in the potentials directory. +produce are in the potentials directory, and can be used with the +pair_style eam/alloy command.

    The source files and potentials were provided by Gerolf Ziegenhain (gerolf at ziegenhain.com). diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index 238af10a5f..187eda98b2 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -44,7 +44,8 @@ own sub-directories with their own Makefiles. "ch2lmp"_#charmm "chain"_#chain "data2xmovie"_#data -"eam generate"_#eam +"eam database"_#eamdb +"eam generate"_#eamgn "eff_#eff "lmp2arc"_#arc "lmp2cfg"_#cfg @@ -137,12 +138,29 @@ See the top of the data2xmovie.c file for a discussion of the options. :line -eam generate tool :h4,link(eam) +eam database tool :h4,link(eamdb) + +The tools/eam_database directory contains a Fortran program that will +generate EAM alloy setfl potential files for any combination of 16 +elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, +Zr. The files can then be used with the "pair_style +eam/alloy"_pair_eam.html command. + +The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, +and is based on his paper: + +X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, +144113 (2004). + +:line + +eam generate tool :h4,link(eamgn) The tools/eam_generate directory contains several one-file C programs that convert an analytic formula into a tabulated "embedded atom method (EAM)"_pair_eam.html setfl potential file. The potentials they -produce are in the potentials directory. +produce are in the potentials directory, and can be used with the +"pair_style eam/alloy"_pair_eam.html command. The source files and potentials were provided by Gerolf Ziegenhain (gerolf at ziegenhain.com). diff --git a/doc/dump.html b/doc/dump.html index 21b20fbd83..dd05e52dde 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -108,16 +108,22 @@ on timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box.

    -

    When LAMMPS is running in parallel, the atom information written to -dump files (typically one line per atom) may be written in an -indeterminate order. This is because data for a single snapshot is -collected from multiple processors. This is always the case for the -atom, local, and custom styles. It is also the case for the -xyz style if the dump group is not all. It is not the case for -the dcd and xtc styles which always write atoms in sorted order. -So does the xyz style if the dump group is all. The cfg style -supports the sort option of the dump_modify -command which allows sorting to be turned on or off. +

    When LAMMPS is running on a single processor, if the atom_modify +sort option is on, which it is by default, then +atoms are re-ordered periodically during a simulation, due to spatial +sorting, and hence the atom information written to dump files +(typically one line per atom) will be in an indeterminate order for +each snapshot. +

    +

    When LAMMPS is running in parallel, this is also true, both due to +sorting and because data for a single snapshot is collected from +multiple processors. This is the case for the atom, local, and +custom styles. It is also the case for the xyz style if the dump +group is not all. It is not the case for the dcd and xtc styles +which always write atoms in sorted order. So does the xyz style if +the dump group is all. The cfg style supports the sort option +of the dump_modify command which allows sorting to +be turned on or off.

    diff --git a/doc/dump.txt b/doc/dump.txt index 99367655f5..edff15a51c 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -98,16 +98,22 @@ on timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. -When LAMMPS is running in parallel, the atom information written to -dump files (typically one line per atom) may be written in an -indeterminate order. This is because data for a single snapshot is -collected from multiple processors. This is always the case for the -{atom}, {local}, and {custom} styles. It is also the case for the -{xyz} style if the dump group is not {all}. It is not the case for -the {dcd} and {xtc} styles which always write atoms in sorted order. -So does the {xyz} style if the dump group is {all}. The {cfg} style -supports the {sort} option of the "dump_modify"_dump_modify.html -command which allows sorting to be turned on or off. +When LAMMPS is running on a single processor, if the "atom_modify +sort"_atom_modify.html option is on, which it is by default, then +atoms are re-ordered periodically during a simulation, due to spatial +sorting, and hence the atom information written to dump files +(typically one line per atom) will be in an indeterminate order for +each snapshot. + +When LAMMPS is running in parallel, this is also true, both due to +sorting and because data for a single snapshot is collected from +multiple processors. This is the case for the {atom}, {local}, and +{custom} styles. It is also the case for the {xyz} style if the dump +group is not {all}. It is not the case for the {dcd} and {xtc} styles +which always write atoms in sorted order. So does the {xyz} style if +the dump group is {all}. The {cfg} style supports the {sort} option +of the "dump_modify"_dump_modify.html command which allows sorting to +be turned on or off. :line