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detect and flag short reads with missing lines in utils::read_lines_from_file()

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This commit is contained in:
Axel Kohlmeyer
2023-06-22 10:48:07 -04:00
parent 558298ac04
commit ffda6596da
1 changed files with 38 additions and 29 deletions
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29
src/utils.cpp
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@ -272,6 +272,7 @@ int utils::read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, in
{ {
char *ptr = buffer; char *ptr = buffer;
*ptr = '\0'; *ptr = '\0';
int mylines = 0;
if (me == 0) { if (me == 0) {
if (fp) { if (fp) {
@ -282,13 +283,15 @@ int utils::read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, in
ptr += strlen(ptr); ptr += strlen(ptr);
// ensure buffer is null terminated. null char is start of next line. // ensure buffer is null terminated. null char is start of next line.
*ptr = '\0'; *ptr = '\0';
// count line
++mylines;
} }
} }
} }
int n = strlen(buffer); int n = strlen(buffer);
MPI_Bcast(&n, 1, MPI_INT, 0, comm); MPI_Bcast(&n, 1, MPI_INT, 0, comm);
if (n == 0) return 1; if ((n == 0) || (nlines != mylines)) return 1;
MPI_Bcast(buffer, n + 1, MPI_CHAR, 0, comm); MPI_Bcast(buffer, n + 1, MPI_CHAR, 0, comm);
return 0; return 0;
} }
@ -879,8 +882,8 @@ char *utils::expand_type(const char *file, int line, const std::string &str, int
caller decides what to do if arg is not a COMPUTE or FIX reference caller decides what to do if arg is not a COMPUTE or FIX reference
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
int utils::check_grid_reference(char *errstr, char *ref, int nevery, int utils::check_grid_reference(char *errstr, char *ref, int nevery, char *&id, int &igrid,
char *&id, int &igrid, int &idata, int &index, LAMMPS *lmp) int &idata, int &index, LAMMPS *lmp)
{ {
ArgInfo argi(ref, ArgInfo::COMPUTE | ArgInfo::FIX); ArgInfo argi(ref, ArgInfo::COMPUTE | ArgInfo::FIX);
index = argi.get_index1(); index = argi.get_index1();
@ -911,19 +914,24 @@ int utils::check_grid_reference(char *errstr, char *ref, int nevery,
int dim; int dim;
igrid = icompute->get_grid_by_name(gname, dim); igrid = icompute->get_grid_by_name(gname, dim);
if (igrid < 0) if (igrid < 0)
lmp->error->all(FLERR,"{} compute {} does not recognize grid name {}",errstr,idcompute,gname); lmp->error->all(FLERR, "{} compute {} does not recognize grid name {}", errstr, idcompute,
gname);
int ncol; int ncol;
idata = icompute->get_griddata_by_name(igrid, dname, ncol); idata = icompute->get_griddata_by_name(igrid, dname, ncol);
if (idata < 0) if (idata < 0)
lmp->error->all(FLERR,"{} compute {} does not recognize data name {}",errstr,idcompute,dname); lmp->error->all(FLERR, "{} compute {} does not recognize data name {}", errstr, idcompute,
dname);
if (argi.get_dim() == 0 && ncol) if (argi.get_dim() == 0 && ncol)
lmp->error->all(FLERR,"{} compute {} data {} is not per-grid vector",errstr,idcompute,dname); lmp->error->all(FLERR, "{} compute {} data {} is not per-grid vector", errstr, idcompute,
dname);
if (argi.get_dim() && ncol == 0) if (argi.get_dim() && ncol == 0)
lmp->error->all(FLERR,"{} compute {} data {} is not per-grid array",errstr,idcompute,dname); lmp->error->all(FLERR, "{} compute {} data {} is not per-grid array", errstr, idcompute,
dname);
if (argi.get_dim() && argi.get_index1() > ncol) if (argi.get_dim() && argi.get_index1() > ncol)
lmp->error->all(FLERR,"{} compute {} array {} is accessed out-of-range",errstr,idcompute,dname); lmp->error->all(FLERR, "{} compute {} array {} is accessed out-of-range", errstr, idcompute,
dname);
id = utils::strdup(idcompute); id = utils::strdup(idcompute);
return ArgInfo::COMPUTE; return ArgInfo::COMPUTE;
@ -1360,8 +1368,9 @@ bool utils::is_double(const std::string &str)
{ {
if (str.empty()) return false; if (str.empty()) return false;
return strmatch(str, "^[+-]?\\d+\\.?\\d*$") || strmatch(str, "^[+-]?\\d+\\.?\\d*[eE][+-]?\\d+$") || return strmatch(str, "^[+-]?\\d+\\.?\\d*$") ||
strmatch(str, "^[+-]?\\d*\\.?\\d+$") || strmatch(str, "^[+-]?\\d*\\.?\\d+[eE][+-]?\\d+$"); strmatch(str, "^[+-]?\\d+\\.?\\d*[eE][+-]?\\d+$") || strmatch(str, "^[+-]?\\d*\\.?\\d+$") ||
strmatch(str, "^[+-]?\\d*\\.?\\d+[eE][+-]?\\d+$");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------