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relax a requirement

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relax requirement that all labels for all interactions must be defined
This commit is contained in:
jrgissing
2021-03-20 22:58:52 -04:00
parent ffa46ad951
commit e21c63192a
6 changed files with 98 additions and 60 deletions
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108
src/read_data.cpp
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@ -124,7 +124,8 @@ void ReadData::command(int narg, char **arg)
addflag = NONE;
coeffflag = 1;
id_offset = mol_offset = 0;
offsetflag = shiftflag = settypeflag = labelflag = 0;
offsetflag = shiftflag = settypeflag = 0;
tlabelflag = blabelflag = alabelflag = dlabelflag = ilabelflag = 0;
toffset = boffset = aoffset = doffset = ioffset = 0;
shift[0] = shift[1] = shift[2] = 0.0;
extra_atom_types = extra_bond_types = extra_angle_types =
@ -729,6 +730,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (atomflag == 1)
error->all(FLERR,"Must read Atom Type Labels before Atoms");
tlabelflag = 1;
typelabels(lmap->typelabel,ntypes,Atom::ATOM);
} else skip_lines(ntypes);
@ -737,6 +739,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (bondflag == 1)
error->all(FLERR,"Must read Bond Type Labels before Bonds");
blabelflag = 1;
typelabels(lmap->btypelabel,nbondtypes,Atom::BOND);
} else skip_lines(nbondtypes);
}
@ -746,6 +749,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (angleflag == 1)
error->all(FLERR,"Must read Angle Type Labels before Angles");
alabelflag = 1;
typelabels(lmap->atypelabel,nangletypes,Atom::ANGLE);
} else skip_lines(nangletypes);
}
@ -755,6 +759,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (dihedralflag == 1)
error->all(FLERR,"Must read Dihedral Type Labels before Dihedrals");
dlabelflag = 1;
typelabels(lmap->dtypelabel,ndihedraltypes,Atom::DIHEDRAL);
} else skip_lines(ndihedraltypes);
}
@ -764,6 +769,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (improperflag == 1)
error->all(FLERR,"Must read Improper Type Labels before Impropers");
ilabelflag = 1;
typelabels(lmap->itypelabel,nimpropertypes,Atom::IMPROPER);
} else skip_lines(nimpropertypes);
}
@ -1279,11 +1285,11 @@ void ReadData::atoms()
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (labelflag && !lmap->is_complete())
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,
shiftflag,shift,labelflag,lmap->lmap2lmap.atom);
shiftflag,shift,tlabelflag,lmap->lmap2lmap.atom);
nread += nchunk;
}
@ -1381,11 +1387,11 @@ void ReadData::bonds(int firstpass)
nchunk = MIN(nbonds-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (labelflag && !lmap->is_complete())
if (blabelflag && !lmap->is_complete(Atom::BOND))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_bonds(nchunk,buffer,count,id_offset,boffset,
labelflag,lmap->lmap2lmap.bond);
blabelflag,lmap->lmap2lmap.bond);
nread += nchunk;
}
@ -1459,11 +1465,11 @@ void ReadData::angles(int firstpass)
nchunk = MIN(nangles-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (labelflag && !lmap->is_complete())
if (alabelflag && !lmap->is_complete(Atom::ANGLE))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_angles(nchunk,buffer,count,id_offset,aoffset,
labelflag,lmap->lmap2lmap.angle);
alabelflag,lmap->lmap2lmap.angle);
nread += nchunk;
}
@ -1537,11 +1543,11 @@ void ReadData::dihedrals(int firstpass)
nchunk = MIN(ndihedrals-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (labelflag && !lmap->is_complete())
if (dlabelflag && !lmap->is_complete(Atom::DIHEDRAL))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset,
labelflag,lmap->lmap2lmap.dihedral);
dlabelflag,lmap->lmap2lmap.dihedral);
nread += nchunk;
}
@ -1615,11 +1621,11 @@ void ReadData::impropers(int firstpass)
nchunk = MIN(nimpropers-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (labelflag && !lmap->is_complete())
if (ilabelflag && !lmap->is_complete(Atom::IMPROPER))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
atom->data_impropers(nchunk,buffer,count,id_offset,ioffset,
labelflag,lmap->lmap2lmap.improper);
ilabelflag,lmap->lmap2lmap.improper);
nread += nchunk;
}
@ -1813,7 +1819,7 @@ void ReadData::mass()
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
if (labelflag && !lmap->is_complete())
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
@ -1821,7 +1827,7 @@ void ReadData::mass()
for (int i = 0; i < ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
atom->set_mass(FLERR,buf,toffset,labelflag,lmap->lmap2lmap.atom);
atom->set_mass(FLERR,buf,toffset,tlabelflag,lmap->lmap2lmap.atom);
buf = next + 1;
}
delete [] original;
@ -1837,11 +1843,16 @@ void ReadData::paircoeffs()
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
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 type label.");
char *original = buf;
for (int i = 0; i < ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,nullptr,1,2,toffset,lmap->lmap2lmap.atom);
parse_coeffs(buf,nullptr,1,2,toffset,tlabelflag,
lmap->lmap2lmap.atom);
if (narg == 0)
error->all(FLERR,"Unexpected empty line in PairCoeffs section");
force->pair->coeff(narg,arg);
@ -1863,12 +1874,17 @@ void ReadData::pairIJcoeffs()
int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf);
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 type label.");
char *original = buf;
for (i = 0; i < ntypes; i++)
for (j = i; j < ntypes; j++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,nullptr,0,2,toffset,lmap->lmap2lmap.atom);
parse_coeffs(buf,nullptr,0,2,toffset,tlabelflag,
lmap->lmap2lmap.atom);
if (narg == 0)
error->all(FLERR,"Unexpected empty line in PairCoeffs section");
force->pair->coeff(narg,arg);
@ -1889,11 +1905,15 @@ void ReadData::bondcoeffs()
int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf);
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 type label.");
char *original = buf;
for (int i = 0; i < nbondtypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,nullptr,0,1,boffset,lmap->lmap2lmap.bond);
parse_coeffs(buf,nullptr,0,1,boffset,blabelflag,lmap->lmap2lmap.bond);
if (narg == 0)
error->all(FLERR,"Unexpected empty line in BondCoeffs section");
force->bond->coeff(narg,arg);
@ -1914,13 +1934,20 @@ void ReadData::anglecoeffs(int which)
int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf);
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 type label.");
char *original = buf;
for (int i = 0; i < nangletypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,nullptr,0,1,aoffset,lmap->lmap2lmap.angle);
else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset,lmap->lmap2lmap.angle);
else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset,lmap->lmap2lmap.angle);
if (which == 0) parse_coeffs(buf,nullptr,0,1,aoffset,alabelflag,
lmap->lmap2lmap.angle);
else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset,alabelflag,
lmap->lmap2lmap.angle);
else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset,alabelflag,
lmap->lmap2lmap.angle);
if (narg == 0) error->all(FLERR,"Unexpected empty line in AngleCoeffs section");
force->angle->coeff(narg,arg);
buf = next + 1;
@ -1940,16 +1967,26 @@ void ReadData::dihedralcoeffs(int which)
int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf);
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 type label.");
char *original = buf;
for (int i = 0; i < ndihedraltypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,nullptr,0,1,doffset,lmap->lmap2lmap.dihedral);
else if (which == 1) parse_coeffs(buf,"mbt",0,1,doffset,lmap->lmap2lmap.dihedral);
else if (which == 2) parse_coeffs(buf,"ebt",0,1,doffset,lmap->lmap2lmap.dihedral);
else if (which == 3) parse_coeffs(buf,"at",0,1,doffset,lmap->lmap2lmap.dihedral);
else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset,lmap->lmap2lmap.dihedral);
else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset,lmap->lmap2lmap.dihedral);
if (which == 0) parse_coeffs(buf,nullptr,0,1,doffset,dlabelflag,
lmap->lmap2lmap.dihedral);
else if (which == 1) parse_coeffs(buf,"mbt",0,1,doffset,dlabelflag,
lmap->lmap2lmap.dihedral);
else if (which == 2) parse_coeffs(buf,"ebt",0,1,doffset,dlabelflag,
lmap->lmap2lmap.dihedral);
else if (which == 3) parse_coeffs(buf,"at",0,1,doffset,dlabelflag,
lmap->lmap2lmap.dihedral);
else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset,dlabelflag,
lmap->lmap2lmap.dihedral);
else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset,dlabelflag,
lmap->lmap2lmap.dihedral);
if (narg == 0)
error->all(FLERR,"Unexpected empty line in DihedralCoeffs section");
force->dihedral->coeff(narg,arg);
@ -1970,12 +2007,18 @@ void ReadData::impropercoeffs(int which)
int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf);
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 type label.");
char *original = buf;
for (int i = 0; i < nimpropertypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,nullptr,0,1,ioffset,lmap->lmap2lmap.improper);
else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset,lmap->lmap2lmap.improper);
if (which == 0) parse_coeffs(buf,nullptr,0,1,ioffset,ilabelflag,
lmap->lmap2lmap.improper);
else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset,ilabelflag,
lmap->lmap2lmap.improper);
if (narg == 0) error->all(FLERR,"Unexpected empty line in ImproperCoeffs section");
force->improper->coeff(narg,arg);
buf = next + 1;
@ -1991,7 +2034,6 @@ void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes, i
char *next;
char *buf = new char[myntypes*MAXLINE];
labelflag = 1;
if (!atom->labelmapflag) atom->add_label_map();
int eof = comm->read_lines_from_file(fp,myntypes,MAXLINE,buf);
@ -2181,12 +2223,8 @@ void ReadData::skip_lines(bigint n)
------------------------------------------------------------------------- */
void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag,
int noffset, int offset, int *ilabel)
int noffset, int offset, int labelmode, int *ilabel)
{
if (labelflag && !lmap->is_complete())
error->all(FLERR,"Label map is incomplete. "
"All types must be assigned a type label.");
settypeflag = 1;
char *ptr;
if ((ptr = strchr(line,'#'))) *ptr = '\0';
@ -2212,12 +2250,12 @@ void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag,
if (noffset) {
int value = utils::inumeric(FLERR,arg[0],false,lmp);
if (labelflag) value = ilabel[value-1];
if (labelmode) value = ilabel[value-1];
sprintf(argoffset1,"%d",value+offset);
arg[0] = argoffset1;
if (noffset == 2) {
value = utils::inumeric(FLERR,arg[1],false,lmp);
if (labelflag) value = ilabel[value-1];
if (labelmode) value = ilabel[value-1];
sprintf(argoffset2,"%d",value+offset);
arg[1] = argoffset2;
}