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compute_rdf: direct type label support

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type label that is the same as the keyword ('cutoff') will break things. if syntax is otherwise 'correct', then will throw a syntax error. perhaps could run through typelabels to check first?
This commit is contained in:
Jacob Gissinger
2024-05-12 16:11:36 -04:00
parent c324afeaf1
commit f007be620a
2 changed files with 26 additions and 14 deletions
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22
doc/src/compute_rdf.rst
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@ -13,8 +13,8 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* rdf = style name of this compute command * rdf = style name of this compute command
* Nbin = number of RDF bins * Nbin = number of RDF bins
* itypeN = central atom type for Nth RDF histogram (see asterisk form below) * itypeN = central atom type for Nth RDF histogram (integer, type label, or asterisk form)
* jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) * jtypeN = distribution atom type for Nth RDF histogram (integer, type label, or asterisk form)
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *cutoff* * keyword = *cutoff*
@ -96,14 +96,16 @@ is computed for :math:`g(r)` between all atom types. If one or more pairs are
listed, then a separate histogram is generated for each listed, then a separate histogram is generated for each
*itype*,\ *jtype* pair. *itype*,\ *jtype* pair.
The *itypeN* and *jtypeN* settings can be specified in one of two The *itypeN* and *jtypeN* settings can be specified in one of three
ways. An explicit numeric value can be used, as in the fourth example ways. One or both of the types in the I,J pair can be a
above. Or a wild-card asterisk can be used to specify a range of atom :doc:`type label <Howto_type_labels>`. Or an explicit numeric value can be
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If used, as in the fourth example above. Or a wild-card asterisk can be used
:math:`N` is the number of atom types, then an asterisk with no numeric values to specify a range of atom types. This takes the form "\*" or "\*n" or
means all types from 1 to :math:`N`. A leading asterisk means all types from 1 "m\*" or "m\*n". If :math:`N` is the number of atom types, then an asterisk
to n (inclusive). A trailing asterisk means all types from m to :math:`N` with no numeric values means all types from 1 to :math:`N`. A leading
(inclusive). A middle asterisk means all types from m to n (inclusive). asterisk means all types from 1 to n (inclusive). A trailing asterisk
means all types from m to :math:`N` (inclusive). A middle asterisk means
all types from m to n (inclusive).
If both *itypeN* and *jtypeN* are single values, as in the fourth example If both *itypeN* and *jtypeN* are single values, as in the fourth example
above, this means that a :math:`g(r)` is computed where atoms of type *itypeN* above, this means that a :math:`g(r)` is computed where atoms of type *itypeN*

18
src/compute_rdf.cpp
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@ -102,10 +102,20 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
} else { } else {
iarg = 4; iarg = 4;
for (int ipair = 0; ipair < npairs; ipair++) { for (int ipair = 0; ipair < npairs; ipair++) {
utils::bounds(FLERR,arg[iarg],1,atom->ntypes,ilo[ipair],ihi[ipair],error); utils::bounds_typelabel(FLERR, arg[iarg], 1, atom->ntypes, ilo[ipair], ihi[ipair], error, lmp, Atom::ATOM);
utils::bounds(FLERR,arg[iarg+1],1,atom->ntypes,jlo[ipair],jhi[ipair],error); utils::bounds_typelabel(FLERR, arg[iarg+1], 1, atom->ntypes, jlo[ipair], jhi[ipair], error, lmp, Atom::ATOM);
if (ilo[ipair] > ihi[ipair] || jlo[ipair] > jhi[ipair])
error->all(FLERR,"Illegal compute rdf command"); // switch i,j if i > j, if wildcards were not used
if ( (ilo[ipair] == ihi[ipair]) &&
(jlo[ipair] == jhi[ipair]) &&
(ilo[ipair] > jlo[ipair]) ) {
jlo[ipair] = ihi[ipair];
ilo[ipair] = jhi[ipair];
ihi[ipair] = ilo[ipair];
jhi[ipair] = jlo[ipair];
}
iarg += 2; iarg += 2;
} }
} }