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type offsets are only applied to numeric types

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This commit is contained in:
Axel Kohlmeyer
2022-09-04 22:12:59 -04:00
parent 53d82056ce
commit fc738ea239
3 changed files with 20 additions and 35 deletions
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7
doc/src/molecule.rst
View File

@ -89,6 +89,12 @@ molecule file. E.g. if *toff* = 2, and the file uses atom types
individual values will be ignored if the molecule template does not
use that attribute (e.g. no bonds).
.. note::
Offsets are **ignored** if the molecule file lines using type labels,
as the type labels will determine the actual types depending on the
current :doc:`labelmap <labelmap>` settings.
The *scale* keyword scales the size of the molecule. This can be
useful for modeling polydisperse granular rigid bodies. The scale
factor is applied to each of these properties in the molecule file, if
@ -183,6 +189,7 @@ type labels have been defined, either by the :doc:`labelmap
Type Labels, Angle Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
When using type labels, any values specified as *offset* are ignored.
If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections can also be used, if desired, to explicitly

6
doc/src/read_data.rst
View File

@ -164,6 +164,12 @@ other types already exist. All five offset values must be specified,
but individual values will be ignored if the data file does not use
that attribute (e.g. no bonds).
.. note::
Offsets are **ignored** for any data file lines using type labels, as
the type labels will determine the actual types depending on the
current :doc:`labelmap <labelmap>` settings.
The *shift* keyword can be used to specify an (Sx, Sy, Sz)
displacement applied to the coordinates of each atom. Sz must be 0.0
for a 2d simulation. This is a mechanism for adding structured

42
src/atom.cpp
View File

@ -1188,11 +1188,10 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
typestr = utils::utf8_subst(typestr);
if (id_offset) tag[nlocal-1] += id_offset;
if (mol_offset) molecule[nlocal-1] += mol_offset;
// clang-format on
switch (utils::is_type(typestr)) {
switch (utils::is_type(typestr)) {
case 0: { // numeric
int itype = utils::inumeric(FLERR, typestr, true, lmp);
int itype = utils::inumeric(FLERR, typestr, true, lmp) + type_offset;
if ((itype < 1) || (itype > ntypes))
error->one(FLERR, "Invalid atom type {} in {}: {}", itype, location,
utils::trim(buf));
@ -1200,7 +1199,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
if (labelflag) type[nlocal - 1] = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag)
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(buf));
@ -1209,13 +1207,11 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(buf));
break;
}
// clang-format off
if (type_offset) type[nlocal-1] += type_offset;
if (type[nlocal-1] <= 0 || type[nlocal-1] > ntypes)
error->one(FLERR,"Invalid atom type {} in {}", location, typestr);
}
@ -1300,30 +1296,24 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
atom2 += id_offset;
}
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp);
itype = utils::inumeric(FLERR, typestr, false, lmp) + type_offset;
if ((itype < 1) || (itype > nbondtypes))
error->all(FLERR, "Invalid bond type {} in {}: {}", itype, location, utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::BOND);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
itype += type_offset;
// clang-format off
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2))
@ -1399,30 +1389,24 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
atom3 += id_offset;
}
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp);
itype = utils::inumeric(FLERR, typestr, false, lmp) + type_offset;
if ((itype < 1) || (itype > nangletypes))
error->all(FLERR, "Invalid angle type {} in {}: {}", itype, location, utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::ANGLE);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
itype += type_offset;
// clang-format off
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||
@ -1514,31 +1498,25 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
atom4 += id_offset;
}
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp);
itype = utils::inumeric(FLERR, typestr, false, lmp) + type_offset;
if ((itype < 1) || (itype > ndihedraltypes))
error->all(FLERR, "Invalid dihedral type {} in {}: {}", itype, location,
utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::DIHEDRAL);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
itype += type_offset;
// clang-format off
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||
@ -1646,31 +1624,25 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
atom4 += id_offset;
}
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp);
itype = utils::inumeric(FLERR, typestr, false, lmp) + type_offset;
if ((itype < 1) || (itype > nimpropertypes))
error->all(FLERR, "Invalid improper type {} in {}: {}", itype, location,
utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::IMPROPER);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
itype += type_offset;
// clang-format off
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||