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Merge remote-tracking branch 'origin/master' into varargs-log-error-functions

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This commit is contained in:
Richard Berger
2021-04-28 18:13:31 -04:00
parent 6b04ebd617 ceb173135b
commit a9ff9312d6
28 changed files with 899 additions and 73 deletions
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47
src/read_data.cpp
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@ -41,24 +41,25 @@
using namespace LAMMPS_NS;
#define MAXLINE 256
#define LB_FACTOR 1.1
#define CHUNK 1024
#define DELTA 4 // must be 2 or larger
#define MAXBODY 32 // max # of lines in one body
static constexpr int MAXLINE = 256;
static constexpr double LB_FACTOR = 1.1;
static constexpr int CHUNK = 1024;
static constexpr int DELTA = 4; // must be 2 or larger
static constexpr int MAXBODY = 32; // max # of lines in one body
// customize for new sections
#define NSECTIONS 25 // change when add to header::section_keywords
// customize for new sections
// change when add to header::section_keywords
static constexpr int NSECTIONS = 25;
enum{NONE,APPEND,VALUE,MERGE};
// pair style suffixes to ignore
// when matching Pair Coeffs comment to currently-defined pair style
const char *suffixes[] = {"/cuda","/gpu","/opt","/omp","/kk",
"/coul/cut","/coul/long","/coul/msm",
"/coul/dsf","/coul/debye","/coul/charmm",
nullptr};
static const char *suffixes[] = {"/cuda","/gpu","/opt","/omp","/kk",
"/coul/cut","/coul/long","/coul/msm",
"/coul/dsf","/coul/debye","/coul/charmm",
nullptr};
/* ---------------------------------------------------------------------- */
@ -304,6 +305,12 @@ void ReadData::command(int narg, char **arg)
extra_dihedral_types || extra_improper_types))
error->all(FLERR,"Cannot use read_data extra with add flag");
// check if data file is available and readable
if (!utils::file_is_readable(arg[0]))
error->all(FLERR,fmt::format("Cannot open file {}: {}",
arg[0], utils::getsyserror()));
// first time system initialization
if (addflag == NONE) {
@ -950,7 +957,7 @@ void ReadData::header(int firstpass)
// skip 1st line of file
if (me == 0) {
char *eof = fgets(line,MAXLINE,fp);
char *eof = utils::fgets_trunc(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
}
@ -959,7 +966,7 @@ void ReadData::header(int firstpass)
// read a line and bcast length
if (me == 0) {
if (fgets(line,MAXLINE,fp) == nullptr) n = 0;
if (utils::fgets_trunc(line,MAXLINE,fp) == nullptr) n = 0;
else n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
@ -1662,7 +1669,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
m = 0;
while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
eof = fgets(&buffer[m],MAXLINE,fp);
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
rv = sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
if (rv != 3)
@ -1676,7 +1683,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
nword = 0;
while (nword < ninteger) {
eof = fgets(&buffer[m],MAXLINE,fp);
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
ncount = utils::trim_and_count_words(&buffer[m]);
if (ncount == 0)
@ -1690,7 +1697,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
nword = 0;
while (nword < ndouble) {
eof = fgets(&buffer[m],MAXLINE,fp);
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
ncount = utils::trim_and_count_words(&buffer[m]);
if (ncount == 0)
@ -1994,15 +2001,15 @@ void ReadData::parse_keyword(int first)
if (me == 0) {
if (!first) {
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
if (utils::fgets_trunc(line,MAXLINE,fp) == nullptr) eof = 1;
}
while (eof == 0 && done == 0) {
int blank = strspn(line," \t\n\r");
if ((blank == (int)strlen(line)) || (line[blank] == '#')) {
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
if (utils::fgets_trunc(line,MAXLINE,fp) == nullptr) eof = 1;
} else done = 1;
}
if (fgets(buffer,MAXLINE,fp) == nullptr) {
if (utils::fgets_trunc(buffer,MAXLINE,fp) == nullptr) {
eof = 1;
buffer[0] = '\0';
}
@ -2056,7 +2063,7 @@ void ReadData::skip_lines(bigint n)
if (me) return;
if (n <= 0) return;
char *eof = nullptr;
for (bigint i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
for (bigint i = 0; i < n; i++) eof = utils::fgets_trunc(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
}