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labels: introduce framework for multiple data files

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subsequent data files merge types with first

starting with support for selected atom types sections, will attach small example to PR
This commit is contained in:
Jacob Gissinger
2021-01-08 23:22:19 -05:00
parent d01b19923d
commit 03b697a6e0
7 changed files with 83 additions and 89 deletions
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68
src/read_data.cpp
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@ -124,7 +124,7 @@ void ReadData::command(int narg, char **arg)
addflag = NONE;
coeffflag = 1;
id_offset = mol_offset = 0;
offsetflag = shiftflag = 0;
offsetflag = shiftflag = labelflag = 0;
toffset = boffset = aoffset = doffset = ioffset = 0;
shift[0] = shift[1] = shift[2] = 0.0;
extra_atom_types = extra_bond_types = extra_angle_types =
@ -730,7 +730,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (atomflag == 1)
error->all(FLERR,"Must read Atom Type Labels before Atoms");
typelabels(lmap->typelabel,ntypes);
typelabels(lmap->typelabel,ntypes,lmap->ATOM);
} else skip_lines(ntypes);
} else if (strcmp(keyword,"Bond Type Labels") == 0) {
@ -738,7 +738,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (bondflag == 1)
error->all(FLERR,"Must read Bond Type Labels before Bonds");
typelabels(lmap->btypelabel,nbondtypes);
typelabels(lmap->btypelabel,nbondtypes,lmap->BOND);
} else skip_lines(nbondtypes);
}
@ -747,7 +747,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (angleflag == 1)
error->all(FLERR,"Must read Angle Type Labels before Angles");
typelabels(lmap->atypelabel,nangletypes);
typelabels(lmap->atypelabel,nangletypes,lmap->ANGLE);
} else skip_lines(nangletypes);
}
@ -756,7 +756,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (dihedralflag == 1)
error->all(FLERR,"Must read Dihedral Type Labels before Dihedrals");
typelabels(lmap->dtypelabel,ndihedraltypes);
typelabels(lmap->dtypelabel,ndihedraltypes,lmap->DIHEDRAL);
} else skip_lines(ndihedraltypes);
}
@ -765,7 +765,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (improperflag == 1)
error->all(FLERR,"Must read Improper Type Labels before Impropers");
typelabels(lmap->itypelabel,nimpropertypes);
typelabels(lmap->itypelabel,nimpropertypes,lmap->IMPROPER);
} else skip_lines(nimpropertypes);
}
@ -1280,7 +1280,8 @@ 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");
atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,shiftflag,shift);
atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,
shiftflag,shift,labelflag,lmap->lmap2lmap.atom);
nread += nchunk;
}
@ -1798,7 +1799,7 @@ void ReadData::mass()
for (int i = 0; i < ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
atom->set_mass(FLERR,buf,toffset);
atom->set_mass(FLERR,buf,toffset,labelflag,lmap->lmap2lmap.atom);
buf = next + 1;
}
delete [] original;
@ -1818,7 +1819,7 @@ void ReadData::paircoeffs()
for (int i = 0; i < ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,nullptr,1,2,toffset);
parse_coeffs(buf,nullptr,1,2,toffset,lmap->lmap2lmap.atom);
if (narg == 0)
error->all(FLERR,"Unexpected empty line in PairCoeffs section");
force->pair->coeff(narg,arg);
@ -1845,7 +1846,7 @@ void ReadData::pairIJcoeffs()
for (j = i; j < ntypes; j++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,nullptr,0,2,toffset);
parse_coeffs(buf,nullptr,0,2,toffset,lmap->lmap2lmap.atom);
if (narg == 0)
error->all(FLERR,"Unexpected empty line in PairCoeffs section");
force->pair->coeff(narg,arg);
@ -1870,7 +1871,7 @@ void ReadData::bondcoeffs()
for (int i = 0; i < nbondtypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,nullptr,0,1,boffset);
parse_coeffs(buf,nullptr,0,1,boffset,lmap->lmap2lmap.bond);
if (narg == 0)
error->all(FLERR,"Unexpected empty line in BondCoeffs section");
force->bond->coeff(narg,arg);
@ -1895,9 +1896,9 @@ void ReadData::anglecoeffs(int which)
for (int i = 0; i < nangletypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,nullptr,0,1,aoffset);
else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset);
else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset);
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 (narg == 0) error->all(FLERR,"Unexpected empty line in AngleCoeffs section");
force->angle->coeff(narg,arg);
buf = next + 1;
@ -1921,12 +1922,12 @@ void ReadData::dihedralcoeffs(int which)
for (int i = 0; i < ndihedraltypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,nullptr,0,1,doffset);
else if (which == 1) parse_coeffs(buf,"mbt",0,1,doffset);
else if (which == 2) parse_coeffs(buf,"ebt",0,1,doffset);
else if (which == 3) parse_coeffs(buf,"at",0,1,doffset);
else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset);
else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset);
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 (narg == 0)
error->all(FLERR,"Unexpected empty line in DihedralCoeffs section");
force->dihedral->coeff(narg,arg);
@ -1951,8 +1952,8 @@ void ReadData::impropercoeffs(int which)
for (int i = 0; i < nimpropertypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,nullptr,0,1,ioffset);
else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset);
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 (narg == 0) error->all(FLERR,"Unexpected empty line in ImproperCoeffs section");
force->improper->coeff(narg,arg);
buf = next + 1;
@ -1962,12 +1963,14 @@ void ReadData::impropercoeffs(int which)
/* ---------------------------------------------------------------------- */
void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes)
void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes, int mode)
{
int n;
char *next;
char *buf = new char[myntypes*MAXLINE];
labelflag = 1;
int eof = comm->read_lines_from_file(fp,myntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
@ -1981,14 +1984,12 @@ void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes)
}
delete [] typelabel;
// if first data file, assign this read_data label map to atom class
// else, determine mapping to let labels override numeric types
// merge this read_data label map to atom class
// determine mapping to let labels override numeric types
// valid operations for first or subsequent data files
if (addflag == NONE) {
atom->lmap->merge_lmap(lmap);
} else {
lmap->create_lmap2lmap(atom->lmap);
}
atom->lmap->merge_lmap(lmap,mode);
lmap->create_lmap2lmap(atom->lmap,mode);
}
/* ----------------------------------------------------------------------
@ -2151,10 +2152,11 @@ void ReadData::skip_lines(bigint n)
else add addstr before 2nd word
if dupflag, duplicate 1st word, so pair_coeff "2" becomes "2 2"
if noffset, add offset to first noffset args, which are atom/bond/etc types
if labelflag, use ilabel to find the correct remapping of numeric type
------------------------------------------------------------------------- */
void ReadData::parse_coeffs(char *line, const char *addstr,
int dupflag, int noffset, int offset)
void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag,
int noffset, int offset, int *ilabel)
{
char *ptr;
if ((ptr = strchr(line,'#'))) *ptr = '\0';
@ -2180,10 +2182,12 @@ void ReadData::parse_coeffs(char *line, const char *addstr,
if (noffset) {
int value = utils::inumeric(FLERR,arg[0],false,lmp);
if (labelflag) 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];
sprintf(argoffset2,"%d",value+offset);
arg[1] = argoffset2;
}