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avoid calling strtok() when reading per-atom data in data files

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This commit is contained in:
Axel Kohlmeyer
2021-03-13 19:12:43 -05:00
parent 9c13361a17
commit 3183c4bdb7
1 changed files with 49 additions and 22 deletions
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71
src/atom.cpp
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@ -1114,13 +1114,13 @@ 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');
values[0] = strtok(buf," \t\n\r\f");
if (values[0] == nullptr)
error->all(FLERR,"Incorrect atom format in data file");
for (m = 1; m < nwords; m++) {
values[m] = strtok(nullptr," \t\n\r\f");
if (values[m] == nullptr)
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;
}
int imx = 0, imy = 0, imz = 0;
@ -1217,9 +1217,12 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(nullptr," \t\n\r\f");
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
@ -1569,9 +1572,12 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(nullptr," \t\n\r\f");
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
@ -1611,8 +1617,10 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
// else skip values
for (int i = 0; i < n; i++) {
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f")) + id_offset;
else tagdata = ATOTAGINT(strtok(nullptr," \t\n\r\f")) + id_offset;
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
tagdata = utils::tnumeric(FLERR,buf,false,lmp) + id_offset;
buf += strlen(buf)+1;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
@ -1622,8 +1630,15 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
else
error->one(FLERR,"Duplicate atom ID in Bodies section of data file");
ninteger = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
ndouble = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ninteger = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ndouble = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
if ((m = map(tagdata)) >= 0) {
if (ninteger > maxint) {
@ -1637,17 +1652,29 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
dvalues = new double[maxdouble];
}
for (j = 0; j < ninteger; j++)
ivalues[j] = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
for (j = 0; j < ndouble; j++)
dvalues[j] = utils::numeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
for (j = 0; j < ninteger; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ivalues[j] = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
for (j = 0; j < ndouble; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
dvalues[j] = utils::numeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++)
strtok(nullptr," \t\n\r\f");
for (j = 0; j < nvalues; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
buf += strlen(buf)+1;
}
}
}