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modernize parsing of the Atoms section

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This commit is contained in:
Axel Kohlmeyer
2021-12-29 20:24:27 -05:00
parent c97483c46f
commit 64d6a2fd1f
3 changed files with 19 additions and 26 deletions
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29
src/atom.cpp
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@ -1058,6 +1058,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
double *coord;
char *next;
// use the first line to detect and validate the number of words/tokens per line
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::trim_and_count_words(buf);
@ -1066,8 +1067,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3)
error->all(FLERR,"Incorrect atom format in data file");
char **values = new char*[nwords];
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all data atoms will be owned even with round-off
@ -1138,21 +1137,16 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
for (m = 0; m < nwords; m++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
if (strlen(buf) == 0)
error->all(FLERR,"Incorrect atom format in data file");
values[m] = buf;
buf += strlen(buf)+1;
}
*next = '\0';
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
if (values.size() != nwords)
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
int imx = 0, imy = 0, imz = 0;
if (imageflag) {
imx = utils::inumeric(FLERR,values[iptr],false,lmp);
imy = utils::inumeric(FLERR,values[iptr+1],false,lmp);
imz = utils::inumeric(FLERR,values[iptr+2],false,lmp);
imx = utils::inumeric(FLERR,values[iptr].c_str(),false,lmp);
imy = utils::inumeric(FLERR,values[iptr+1].c_str(),false,lmp);
imz = utils::inumeric(FLERR,values[iptr+2].c_str(),false,lmp);
if ((domain->dimension == 2) && (imz != 0))
error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems");
if ((!domain->xperiodic) && (imx != 0)) { reset_image_flag[0] = true; imx = 0; }
@ -1163,9 +1157,9 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
(((imageint) (imy + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (imz + IMGMAX) & IMGMASK) << IMG2BITS);
xdata[0] = utils::numeric(FLERR,values[xptr],false,lmp);
xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp);
xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp);
xdata[0] = utils::numeric(FLERR,values[xptr].c_str(),false,lmp);
xdata[1] = utils::numeric(FLERR,values[xptr+1].c_str(),false,lmp);
xdata[2] = utils::numeric(FLERR,values[xptr+2].c_str(),false,lmp);
if (shiftflag) {
xdata[0] += shift[0];
xdata[1] += shift[1];
@ -1193,7 +1187,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------