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). +
+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.