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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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67
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();
@ -889,80 +892,85 @@ int utils::check_grid_reference(char *errstr, char *ref, int nevery,
switch (argi.get_type()) { switch (argi.get_type()) {
case ArgInfo::UNKNOWN: { case ArgInfo::UNKNOWN: {
lmp->error->all(FLERR,"%s grid reference %s is invalid",errstr,ref); lmp->error->all(FLERR, "%s grid reference %s is invalid", errstr, ref);
} break; } break;
// compute value = c_ID // compute value = c_ID
case ArgInfo::COMPUTE: { case ArgInfo::COMPUTE: {
// split name = idcompute:gname:dname into 3 strings // split name = idcompute:gname:dname into 3 strings
auto words = parse_grid_id(FLERR,name,lmp->error); auto words = parse_grid_id(FLERR, name, lmp->error);
const auto &idcompute = words[0]; const auto &idcompute = words[0];
const auto &gname = words[1]; const auto &gname = words[1];
const auto &dname = words[2]; const auto &dname = words[2];
auto icompute = lmp->modify->get_compute_by_id(idcompute); auto icompute = lmp->modify->get_compute_by_id(idcompute);
if (!icompute) lmp->error->all(FLERR,"{} compute ID {} not found",errstr,idcompute); if (!icompute) lmp->error->all(FLERR, "{} compute ID {} not found", errstr, idcompute);
if (icompute->pergrid_flag == 0) if (icompute->pergrid_flag == 0)
lmp->error->all(FLERR,"{} compute {} does not compute per-grid info",errstr,idcompute); lmp->error->all(FLERR, "{} compute {} does not compute per-grid info", errstr, idcompute);
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;
} break; } break;
// fix value = f_ID // fix value = f_ID
case ArgInfo::FIX: { case ArgInfo::FIX: {
// split name = idfix:gname:dname into 3 strings // split name = idfix:gname:dname into 3 strings
auto words = parse_grid_id(FLERR,name,lmp->error); auto words = parse_grid_id(FLERR, name, lmp->error);
const auto &idfix = words[0]; const auto &idfix = words[0];
const auto &gname = words[1]; const auto &gname = words[1];
const auto &dname = words[2]; const auto &dname = words[2];
auto ifix = lmp->modify->get_fix_by_id(idfix); auto ifix = lmp->modify->get_fix_by_id(idfix);
if (!ifix) lmp->error->all(FLERR,"{} fix ID {} not found",errstr,idfix); if (!ifix) lmp->error->all(FLERR, "{} fix ID {} not found", errstr, idfix);
if (ifix->pergrid_flag == 0) if (ifix->pergrid_flag == 0)
lmp->error->all(FLERR,"{} fix {} does not compute per-grid info",errstr,idfix); lmp->error->all(FLERR, "{} fix {} does not compute per-grid info", errstr, idfix);
if (nevery % ifix->pergrid_freq) if (nevery % ifix->pergrid_freq)
lmp->error->all(FLERR,"{} fix {} not computed at compatible time",errstr,idfix); lmp->error->all(FLERR, "{} fix {} not computed at compatible time", errstr, idfix);
int dim; int dim;
igrid = ifix->get_grid_by_name(gname,dim); igrid = ifix->get_grid_by_name(gname, dim);
if (igrid < 0) if (igrid < 0)
lmp->error->all(FLERR,"{} fix {} does not recognize grid name {}",errstr,idfix,gname); lmp->error->all(FLERR, "{} fix {} does not recognize grid name {}", errstr, idfix, gname);
int ncol; int ncol;
idata = ifix->get_griddata_by_name(igrid,dname,ncol); idata = ifix->get_griddata_by_name(igrid, dname, ncol);
if (idata < 0) if (idata < 0)
lmp->error->all(FLERR,"{} fix {} does not recognize data name {}",errstr,idfix,dname); lmp->error->all(FLERR, "{} fix {} does not recognize data name {}", errstr, idfix, dname);
if (argi.get_dim() == 0 && ncol) if (argi.get_dim() == 0 && ncol)
lmp->error->all(FLERR,"{} fix {} data {} is not per-grid vector",errstr,idfix,dname); lmp->error->all(FLERR, "{} fix {} data {} is not per-grid vector", errstr, idfix, dname);
if (argi.get_dim() > 0 && ncol == 0) if (argi.get_dim() > 0 && ncol == 0)
lmp->error->all(FLERR,"{} fix {} data {} is not per-grid array",errstr,idfix,dname); lmp->error->all(FLERR, "{} fix {} data {} is not per-grid array", errstr, idfix, dname);
if (argi.get_dim() > 0 && argi.get_index1() > ncol) if (argi.get_dim() > 0 && argi.get_index1() > ncol)
lmp->error->all(FLERR,"{} fix {} array {} is accessed out-of-range",errstr,idfix,dname); lmp->error->all(FLERR, "{} fix {} array {} is accessed out-of-range", errstr, idfix, dname);
id = utils::strdup(idfix); id = utils::strdup(idfix);
return ArgInfo::FIX; return ArgInfo::FIX;
@ -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+$") ||
strmatch(str, "^[+-]?\\d*\\.?\\d+[eE][+-]?\\d+$");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------