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read_data: bond, etc. direct label support

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This commit is contained in:
Jacob Gissinger
2021-11-07 00:51:55 -04:00
parent 062b880661
commit 3fc47a9366
4 changed files with 80 additions and 37 deletions
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0
doc/src/Errors_messages.rst Executable file → Normal file
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45
doc/src/read_data.rst
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@ -587,7 +587,7 @@ label maps.
.. parsed-literal::
ID = number of angle (1-Nangles)
type = angle type (1-Nangletype)
type = angle type (1-Nangletype, or type label)
atom1,atom2,atom3 = IDs of 1st,2nd,3rd atom in angle
example:
@ -631,23 +631,24 @@ atom, bond, etc. types in terms of user-provided strings instead of
numbers. If a type label section exists for a given interaction
(atom, bond, angle, dihedral or improper), then all types must be
assigned a type label for that interaction. Type label sections must
come before any section that utilizes that type. The numeric types
listed in the *Atoms*, *Bonds*, etc. section are first converted into
their corresponding type label before being read into LAMMPS; type
labels cannot be directly substituted for numeric types used in data
files. Data files assign all types to the default label map; if the
type label does not already exist, the type label is created as a new
type and assigned to the default label map. The corresponding
interaction coefficients listed in the data file are associated to
this type. There must be enough space in the per-type data
arrays to create new types; see the *extra/atom/types* keyword for how
to reserve extra space for new types, e.g., when reading multiple data
files. Note that, in this case, the numeric-to-label mapping within a
data file does not necessary correspond to that of the simulation;
once the default label map is fully defined, the :doc:`write_data <write_data>`
command can be used to print out the default label map at a given
point in a simulation. See the :doc:`labelmap <labelmap>` command for
more discussion on how to use type label maps.
come before any section that utilizes that type. Type labels can be
directly substituted for numeric types listed in the *Atoms*, *Bonds*,
etc. sections of data files. If numeric types are used, each
interaction type is first converted into its corresponding type label
before being read into LAMMPS. Data files assign all types to the
default label map; if the type label does not already exist, the type
label is created as a new type and assigned to the default label map.
The corresponding interaction coefficients listed in the data file are
associated to this type. There must be enough space in the per-type
data arrays to create new types; see the *extra/atom/types* keyword
for how to reserve extra space for new types, e.g., when reading
multiple data files. Note that, in this case, the numeric-to-label
mapping within a data file does not necessary correspond to that of
the simulation; once the default label map is fully defined, the
:doc:`write_data <write_data>` command can be used to print out the
default label map at a given point in a simulation. See the
:doc:`labelmap <labelmap>` command for more discussion on how to use
type label maps.
----------
@ -720,7 +721,7 @@ of analysis.
The per-atom values have these meanings and units, listed alphabetically:
* atom-ID = integer ID of atom
* atom-type = type of atom (1-Ntype)
* atom-type = type of atom (1-Ntype, or type label)
* bodyflag = 1 for body particles, 0 for point particles
* bond_nt = bond NT factor for MESONT particles (?? units)
* buckling = buckling factor for MESONT particles (?? units)
@ -1044,7 +1045,7 @@ label maps.
.. parsed-literal::
ID = bond number (1-Nbonds)
type = bond type (1-Nbondtype)
type = bond type (1-Nbondtype, or type label)
atom1,atom2 = IDs of 1st,2nd atom in bond
* example:
@ -1108,7 +1109,7 @@ use type label maps.
.. parsed-literal::
ID = number of dihedral (1-Ndihedrals)
type = dihedral type (1-Ndihedraltype)
type = dihedral type (1-Ndihedraltype, or type label)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in dihedral
* example:
@ -1227,7 +1228,7 @@ use type label maps.
.. parsed-literal::
ID = number of improper (1-Nimpropers)
type = improper type (1-Nimpropertype)
type = improper type (1-Nimpropertype, or type label)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in improper
* example:

3
doc/src/write_data.rst
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@ -118,7 +118,8 @@ etc. types are written in the Atoms, Bonds, etc. sections. If the
value is specified as *numeric*, then numeric types are used. If the
value is specified as *labels*, then interaction types are written as
type labels using the default label map. When using type labels, the
default label map must be written to the data file.
default label map (i.e., Type Label sections) must be written to the
data file.
The *pair* keyword lets you specify in what format the pair
coefficient information is written into the data file. If the value

69
src/atom.cpp
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@ -53,6 +53,7 @@ using namespace MathConst;
#define DELTA 1
#define DELTA_PERATOM 64
#define EPSILON 1.0e-6
#define MAXLINE 256
/* ---------------------------------------------------------------------- */
@ -1198,9 +1199,9 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
if (id_offset) tag[nlocal-1] += id_offset;
if (mol_offset) molecule[nlocal-1] += mol_offset;
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Types section in molecule file");
if (!atom->labelmapflag) error->one(FLERR,"Invalid Atoms section in data file");
type[nlocal-1] = atom->find_label(typestr,Atom::ATOM);
if (type[nlocal-1] == -1) error->one(FLERR,"Invalid Types section in molecule file");
if (type[nlocal-1] == -1) error->one(FLERR,"Invalid Atoms section in data file");
} else {
type[nlocal-1] = utils::inumeric(FLERR,typestr.c_str(),true,lmp);
if (labelflag) type[nlocal-1] = ilabel[type[nlocal-1]-1];
@ -1275,20 +1276,30 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
int m,tmp,itype,rv;
tagint atom1,atom2;
char *next;
char typechar[MAXLINE];
std::string typestr;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2);
rv = sscanf(buf,"%d %s " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,typechar,&atom1,&atom2);
if (rv != 4)
error->one(FLERR,"Incorrect format of Bonds section in data file");
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
}
if (labelflag) itype = ilabel[itype-1];
typestr = typechar;
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Bonds section in data file");
itype = atom->find_label(typestr,Atom::BOND);
if (itype == -1) error->one(FLERR,"Invalid Bonds section in data file");
} else {
itype = utils::inumeric(FLERR,typechar,true,lmp);
if (labelflag) itype = ilabel[itype-1];
}
itype += type_offset;
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@ -1333,13 +1344,15 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
int m,tmp,itype,rv;
tagint atom1,atom2,atom3;
char *next;
char typechar[MAXLINE];
std::string typestr;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3);
rv = sscanf(buf,"%d %s " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,typechar,&atom1,&atom2,&atom3);
if (rv != 5)
error->one(FLERR,"Incorrect format of Angles section in data file");
if (id_offset) {
@ -1347,7 +1360,15 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
atom2 += id_offset;
atom3 += id_offset;
}
if (labelflag) itype = ilabel[itype-1];
typestr = typechar;
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Angles section in data file");
itype = atom->find_label(typestr,Atom::ANGLE);
if (itype == -1) error->one(FLERR,"Invalid Angles section in data file");
} else {
itype = utils::inumeric(FLERR,typechar,true,lmp);
if (labelflag) itype = ilabel[itype-1];
}
itype += type_offset;
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@ -1406,14 +1427,16 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
int m,tmp,itype,rv;
tagint atom1,atom2,atom3,atom4;
char *next;
char typechar[MAXLINE];
std::string typestr;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT
rv = sscanf(buf,"%d %s " TAGINT_FORMAT " " TAGINT_FORMAT
" " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
&tmp,typechar,&atom1,&atom2,&atom3,&atom4);
if (rv != 6)
error->one(FLERR,"Incorrect format of Dihedrals section in data file");
if (id_offset) {
@ -1422,7 +1445,15 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
atom3 += id_offset;
atom4 += id_offset;
}
if (labelflag) itype = ilabel[itype-1];
typestr = typechar;
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Dihedrals section in data file");
itype = atom->find_label(typestr,Atom::DIHEDRAL);
if (itype == -1) error->one(FLERR,"Invalid Dihedrals section in data file");
} else {
itype = utils::inumeric(FLERR,typechar,true,lmp);
if (labelflag) itype = ilabel[itype-1];
}
itype += type_offset;
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@ -1498,14 +1529,16 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
int m,tmp,itype,rv;
tagint atom1,atom2,atom3,atom4;
char *next;
char typechar[MAXLINE];
std::string typestr;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d "
rv = sscanf(buf,"%d %s "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
&tmp,typechar,&atom1,&atom2,&atom3,&atom4);
if (rv != 6)
error->one(FLERR,"Incorrect format of Impropers section in data file");
if (id_offset) {
@ -1514,7 +1547,15 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
atom3 += id_offset;
atom4 += id_offset;
}
if (labelflag) itype = ilabel[itype-1];
typestr = typechar;
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Impropers section in data file");
itype = atom->find_label(typestr,Atom::IMPROPER);
if (itype == -1) error->one(FLERR,"Invalid Impropers section in data file");
} else {
itype = utils::inumeric(FLERR,typechar,true,lmp);
if (labelflag) itype = ilabel[itype-1];
}
itype += type_offset;
if ((atom1 <= 0) || (atom1 > map_tag_max) ||