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support typelabels for parsing xyz file with non-numeric types

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This commit is contained in:
Axel Kohlmeyer
2024-09-21 11:53:41 -04:00
parent 5290779554
commit 29fce19c19
1 changed files with 34 additions and 29 deletions
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63
src/reader_xyz.cpp
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@ -18,8 +18,10 @@
#include "reader_xyz.h"
#include "memory.h"
#include "atom.h"
#include "error.h"
#include "memory.h"
#include "tokenizer.h"
using namespace LAMMPS_NS;
@ -166,43 +168,46 @@ bigint ReaderXYZ::read_header(double /*box*/[3][3], int &boxinfo, int &/*triclin
void ReaderXYZ::read_atoms(int n, int nfield, double **fields)
{
int i,m,rv;
int i,m;
char *eof;
int mytype;
double myx, myy, myz;
for (i = 0; i < n; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of dump file");
try {
for (i = 0; i < n; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of dump file");
++nid;
rv = sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz);
if (rv != 3) error->one(FLERR,"Dump file is incorrectly formatted");
++nid;
// XXX: we could insert an element2type translation here
// XXX: for now we flag unrecognized types as type 0,
// XXX: which should trigger an error, if LAMMPS uses it.
mytype = std::stoi(line);
auto values = ValueTokenizer(line);
mytype = utils::expand_type_int(FLERR, values.next_string(), Atom::ATOM, lmp);
myx = values.next_double();
myy = values.next_double();
myz = values.next_double();
for (m = 0; m < nfield; m++) {
switch (fieldindex[m]) {
case X:
fields[i][m] = myx;
break;
case Y:
fields[i][m] = myy;
break;
case Z:
fields[i][m] = myz;
break;
case ID:
fields[i][m] = nid;
break;
case TYPE:
fields[i][m] = mytype;
break;
for (m = 0; m < nfield; m++) {
switch (fieldindex[m]) {
case X:
fields[i][m] = myx;
break;
case Y:
fields[i][m] = myy;
break;
case Z:
fields[i][m] = myz;
break;
case ID:
fields[i][m] = nid;
break;
case TYPE:
fields[i][m] = mytype;
break;
}
}
}
} catch (TokenizerException &e) {
error->one(FLERR, "Error reading xyz file: {}", e.what());
}
}