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error messages

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This commit is contained in:
Jacob Gissinger
2021-12-07 23:32:14 -05:00
parent de635cc68d
commit 83a978d69b
8 changed files with 91 additions and 42 deletions
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24
doc/src/Errors_messages.rst
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@ -5446,6 +5446,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Mass command must set a type from 1-N where N is the number of atom
types.
*Invalid type label in variable formula*
Argument of a labelmap function must be a valid type label that has
been assigned to a numeric type.
*Invalid use of library file() function*
This function is called through the library interface. This
error should not occur. Contact the developers if it does.
@ -5578,9 +5582,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*LJ6 off not supported in pair_style buck/long/coul/long*
Self-explanatory.
*Label map is incomplete: all types must be assigned a unique type label*
For a given type-kind (atom types, bond types, etc.) to be written to
the data file, all associated types must be assigned a type label, and
each type label can be assigned to only one numeric type.
*Label wasn't found in input script*
Self-explanatory.
*Labelmap command before simulation box is defined*
The labelmap command cannot be used before a read_data,
read_restart, or create_box command.
*Lattice orient vectors are not orthogonal*
The three specified lattice orientation vectors must be mutually
orthogonal.
@ -7860,6 +7873,10 @@ keyword to allow for additional bonds to be formed
Number of local atoms times number of columns must fit in a 32-bit
integer for dump.
*Topology type exceeds system topology type*
The number of bond, angle, etc types exceeds the system setting. See
the create_box or read_data command for how to specify these values.
*Tree structure in joint connections*
Fix poems cannot (yet) work with coupled bodies whose joints connect
the bodies in a tree structure.
@ -7884,6 +7901,13 @@ keyword to allow for additional bonds to be formed
*Two groups cannot be the same in fix spring couple*
Self-explanatory.
*Type label already exists: type labels must be unique*
For a given type-kind (atom types, bond types, etc.), a given type
label can be assigned to only one numeric type.
*Type labels cannot start with a number*
Self-explanatory.
*Unable to initialize accelerator for use*
There was a problem initializing an accelerator for the gpu package

32
doc/src/Howto_type_labels.rst
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@ -19,10 +19,10 @@ of other commands below which can use label types in interesting ways.
A collection of type labels for all type-kinds (atom types, bond
types, etc.) is stored as a "label map" which is simply a list of
numeric types and associated type labels. Within a map, each type
label must be unique. It can be assigned to only one numeric type.
To read and write the default type labels to data files for a given
type-kind, all associated numeric types need have a type label
numeric types and associated type labels. Within a type-kind, each
type label must be unique. It can be assigned to only one numeric
type. To read and write the default type labels to data files for a
given type-kind, all associated numeric types need have a type label
assigned.
There can be multiple label maps defined. There is a default label
@ -45,19 +45,19 @@ a C-H bond with a type label "[C][H]".
There are two ways to define label maps. One is via the
:doc:`labelmap <labelmap>` command, which has an optional *mapID*
keyword to allow creation of type labels in either a default map or an
additional map with a mapID. The other is via the :doc:`read_data
keyword to allow creation of type labels in either the default map or
an additional map with a mapID. The other is via the :doc:`read_data
<read_data>` command. A data file can have sections such as Atom Type
Labels, Bond Type Labels, etc, which associate type labels with
numeric types. Only the default label map can be defined in this
manner.
If defined, the default label map can be written out to data files by
the :doc:`write_data <write_data>` command. They are also written to
and read from restart files, by the :doc:`write_restart <write_restart>`
and :doc:`read_restart <read_restart>` commands. Label maps with
mapIDs cannot be written to either data or restart files by these
commands.
the :doc:`write_data <write_data>` command. This map is also written
to and read from restart files, by the :doc:`write_restart
<write_restart>` and :doc:`read_restart <read_restart>` commands.
Label maps with mapIDs cannot be written to either data or restart
files by these commands.
----------
@ -135,12 +135,12 @@ using wildcards to further increase the portability of reaction
templates, as well as automatically inferring the types of newly
created bond, angle, etc. interactions.
LAMMPS label types will be used in a planned extension of OpenKIM to
LAMMPS type labels will be used in a planned extension of OpenKIM to
support bonded force fields (FFs) (such as CHARMM, AMBER, IFF, etc.).
Users will be able to use a bonded FF, packaged as an OpenKIM
Simulator Model (SM), using the `kim init` command. The SM will
include all required interaction parameters (pair, bond, angle,
dihedral, improper) defined in terms of the standard atom type labels
for that FF. Molecular configurations can then be defined within a
LAMMPS script or read in from a data file by defining the mapping from
standard LAMMPS integer atom type integers to the new label types.
dihedral, improper) defined in terms of the standard atom types for
that FF. Molecular configurations can then be specified within a
LAMMPS script or read in from a data file by using type labels that
match the atom types for that FF.

5
src/input.h
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@ -329,6 +329,11 @@ E: KSpace style has not yet been set
Cannot use kspace_modify command until a kspace style is set.
E: Labelmap command before simulation box is defined
The labelmap command cannot be used before a read_data, read_restart,
or create_box command.
E: Mass command before simulation box is defined
The mass command cannot be used before a read_data, read_restart, or

2
src/label_map.cpp
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@ -107,7 +107,7 @@ void LabelMap::modify_lmap(int narg, char **arg)
if (isdigit(slabel[0]))
error->all(FLERR,"Type labels cannot start with a number");
if (search(slabel,(*labels_map)) != -1)
error->all(FLERR,"Type label already exists: types labels must be unique");
error->all(FLERR,"Type label already exists: type labels must be unique");
std::string &str = (*labels)[itype-1];
if (!str.empty()) (*labels_map).erase(str);
str = slabel;

9
src/label_map.h
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@ -79,4 +79,13 @@ E: Topology type exceeds system topology type
The number of bond, angle, etc types exceeds the system setting. See
the create_box or read_data command for how to specify these values.
E: Type label already exists: type labels must be unique
For a given type-kind (atom types, bond types, etc.), a given type
label can be assigned to only one numeric type.
E: Type labels cannot start with a number
Self-explanatory.
*/

48
src/read_data.cpp
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@ -1305,8 +1305,8 @@ void ReadData::atoms()
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,
shiftflag,shift,tlabelflag,lmap->lmap2lmap.atom);
nread += nchunk;
@ -1423,8 +1423,8 @@ void ReadData::bonds(int firstpass)
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (blabelflag && !lmap->is_complete(Atom::BOND))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
atom->data_bonds(nchunk,buffer,count,id_offset,boffset,
blabelflag,lmap->lmap2lmap.bond);
nread += nchunk;
@ -1501,8 +1501,8 @@ void ReadData::angles(int firstpass)
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (alabelflag && !lmap->is_complete(Atom::ANGLE))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
atom->data_angles(nchunk,buffer,count,id_offset,aoffset,
alabelflag,lmap->lmap2lmap.angle);
nread += nchunk;
@ -1579,8 +1579,8 @@ void ReadData::dihedrals(int firstpass)
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (dlabelflag && !lmap->is_complete(Atom::DIHEDRAL))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset,
dlabelflag,lmap->lmap2lmap.dihedral);
nread += nchunk;
@ -1657,8 +1657,8 @@ void ReadData::impropers(int firstpass)
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (ilabelflag && !lmap->is_complete(Atom::IMPROPER))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
atom->data_impropers(nchunk,buffer,count,id_offset,ioffset,
ilabelflag,lmap->lmap2lmap.improper);
nread += nchunk;
@ -1854,8 +1854,8 @@ void ReadData::mass()
int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
char *original = buf;
for (int i = 0; i < ntypes; i++) {
@ -1878,8 +1878,8 @@ void ReadData::paircoeffs()
if (eof) error->all(FLERR,"Unexpected end of data file");
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
char *original = buf;
for (int i = 0; i < ntypes; i++) {
@ -1908,8 +1908,8 @@ void ReadData::pairIJcoeffs()
if (eof) error->all(FLERR,"Unexpected end of data file");
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
char *original = buf;
for (i = 0; i < ntypes; i++)
@ -1938,8 +1938,8 @@ void ReadData::bondcoeffs()
if (eof) error->all(FLERR,"Unexpected end of data file");
if (blabelflag && !lmap->is_complete(Atom::BOND))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
char *original = buf;
for (int i = 0; i < nbondtypes; i++) {
@ -1967,8 +1967,8 @@ void ReadData::anglecoeffs(int which)
if (eof) error->all(FLERR,"Unexpected end of data file");
if (alabelflag && !lmap->is_complete(Atom::ANGLE))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
char *original = buf;
for (int i = 0; i < nangletypes; i++) {
@ -2000,8 +2000,8 @@ void ReadData::dihedralcoeffs(int which)
if (eof) error->all(FLERR,"Unexpected end of data file");
if (dlabelflag && !lmap->is_complete(Atom::DIHEDRAL))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
char *original = buf;
for (int i = 0; i < ndihedraltypes; i++) {
@ -2040,8 +2040,8 @@ void ReadData::impropercoeffs(int which)
if (eof) error->all(FLERR,"Unexpected end of data file");
if (ilabelflag && !lmap->is_complete(Atom::IMPROPER))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a unique type label.");
error->all(FLERR,"Label map is incomplete: "
"all types must be assigned a unique type label");
char *original = buf;
for (int i = 0; i < nimpropertypes; i++) {

6
src/read_data.h
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@ -367,6 +367,12 @@ E: Invalid data file section: EndBondTorsion Coeffs
Atom style does not allow dihedrals.
E: Label map is incomplete: all types must be assigned a unique type label
For a given type-kind (atom types, bond types, etc.) to be written to
the data file, all associated types must be assigned a type label, and
each type label can be assigned to only one numeric type.
E: Must define dihedral_style before EndBondTorsion Coeffs
Must use a dihedral_style command before reading a data file that

5
src/variable.h
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@ -223,6 +223,11 @@ E: All variables in next command must have same style
UNDOCUMENTED
E: Invalid type label in variable formula
Argument of a labelmap function must be a valid type label that has
been assigned to a numeric type.
E: Invalid variable style with next command
Variable styles {equal} and {world} cannot be used in a next