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Removed redundant element list from pair_coeff snap syntax

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This commit is contained in:
Aidan Thompson
2018-12-03 20:28:01 -07:00
parent 67041a5446
commit fa7e02ea71
19 changed files with 54 additions and 306 deletions
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32
doc/src/pair_snap.txt
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@ -16,7 +16,7 @@ pair_style snap :pre
[Examples:]
pair_style snap
pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
pair_coeff * * InP.snapcoeff InP.snapparam In In P P :pre
[Description:]
@ -48,14 +48,12 @@ not set in the pair_style or pair_coeff command; they are specified in
the SNAP potential files themselves.
Only a single pair_coeff command is used with the {snap} style which
specifies two SNAP files and the list SNAP element(s) to be
extracted.
The SNAP elements are mapped to LAMMPS atom types by specifying
N additional arguments after the 2nd filename in the pair_coeff
command, where N is the number of LAMMPS atom types:
specifies a SNAP coefficient file followed by a SNAP parameter file
and then N additional arguments specifying the mapping of SNAP
elements to LAMMPS atom types, where N is the number of
LAMMPS atom types:
SNAP element file
Elem1, Elem2, ...
SNAP coefficient file
SNAP parameter file
N element names = mapping of SNAP elements to atom types :ul
@ -63,13 +61,11 @@ As an example, if a LAMMPS indium phosphide simulation has 4 atoms
types, with the first two being indium and the 3rd and 4th being
phophorous, the pair_coeff command would look like this:
pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The two filenames are for the element and parameter files, respectively.
The 'In' and 'P' arguments (between the file names) are the two elements
which will be extracted from the element file. The
two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
The two filenames are for the coefficient and parameter files, respectively.
The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
3 and 4 to the SNAP 'P' element.
@ -79,10 +75,11 @@ This can be used when a {snap} potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
The name of the SNAP element file usually ends in the
The name of the SNAP coefficient file usually ends in the
".snapcoeff" extension. It may contain coefficients
for many SNAP elements.
Only those elements listed in the pair_coeff command are extracted.
for many SNAP elements. The only requirement is that it
contain at least those element names appearing in the
LAMMPS mapping list.
The name of the SNAP parameter file usually ends in the ".snapparam"
extension. It contains a small number
of parameters that define the overall form of the SNAP potential.
@ -110,8 +107,7 @@ It is convenient to keep these commands in a separate file that can
be inserted in any LAMMPS input script using the "include"_include.html
command.
The top of the SNAP element file can contain any number of blank and comment
lines (start with #), but follows a strict
The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict
format after that. The first non-blank non-comment
line must contain two integers: